@article {pmid40749539,
year = {2025},
author = {Jiang, Y and Fu, B and Wu, WM and Zhou, C and Khan, A and Zhang, G and Salama, ES and Jeon, BH and Alreshidi, MA and Li, C and Han, H and Li, X},
title = {Soil microbes in the Tibetan Plateau degrade polyvinyl chloride and harbor novel dehalogenase SerB.},
journal = {Environment international},
volume = {202},
number = {},
pages = {109708},
doi = {10.1016/j.envint.2025.109708},
pmid = {40749539},
issn = {1873-6750},
abstract = {Polyvinyl chloride (PVC) stands as the third most widely produced synthetic polymer plastic. However, investigations into its microbial degradation significantly trail those of polyethylene (PE) and polystyrene (PS). Here, this study enriched a PVC-degrading consortium DC from the soil microbes of Tibet Plateau grasslands, confirming the formation of long-chain alkanes and the release of chloride ions via GC-MS and ion chromatography analysis. The response of DC to synthetic polymer PVC and natural polymer lignin revealed resistant polymer-response Burkholderia, opportunistic polymer-response Rhodococcus, and sensitive polymer-response Dyella. These PVC-degrading bacteria exist in 432 datasets of alpine meadows. Metaproteomic analysis highlighted distinct enzymatic profiles between PVC-DC and lignin-DC, with 298 proteins associated with PVC degradation compared to 123 proteins linked to lignin. Six key protein categories, including dehalogenase, peroxidase, monooxygenase, dioxygenase, esterase, and dehydrogenase, were involved in PVC degradation. An upregulated dehalogenase SerB from Rhodococcus, belonging to the clade of phosphoserine phosphatase, displayed proficiency in degrading chloroacetic acid and PVC films via hydrolytic dehalogenation. Furthermore, global metagenomic analysis from 38 datasets underscored the prevalence of dehalogenases and related enzymes in grasslands. This study elucidates the microbial responses and enzymatic pathways in PVC degradation, emphasizing the abundance of PVC-degrading enzymes in alpine ecosystems.},
}

@article {pmid40749451,
year = {2025},
author = {Taskan, B and Taskan, E and Lai, YS and Eustance, E and Mahmood, M and Luo, YH and Rittmann, BE},
title = {Polyhydroxybutyrate (PHB) production and methane uptake by methanotrophic bacteria in a membrane-based reactor.},
journal = {Chemosphere},
volume = {385},
number = {},
pages = {144590},
doi = {10.1016/j.chemosphere.2025.144590},
pmid = {40749451},
issn = {1879-1298},
abstract = {Methanotrophic bacteria use methane (CH4) as an electron donor and carbon source for growth and to produce a variety of valuable byproducts, including polyhydroxybutyrate (PHB), a feedstock for bioplastics. This study evaluated the effects of three independent parameters (nitrogen source, dissolved oxygen (DO) concentration, and CH4 availability) on biomass and PHB yield. The work employed a membrane-based approach to deliver CH4 and O2 gases independently for methanotrophic growth, a process referred to as Membrane Oxygenation and Methanotrophy (MOM). Performance metrics included bacterial yield, CH4 consumption rate, PHB content, and microbial community composition. Ammonium (NH4[+]) as an N-source with low DO concentration led to the highest biomass yield (up to 0.59 g produced biomass/g CH4) and PHB content (up to of 36% of dry weight). The MOM improved CH4 utilization efficiency up to 95.8% without gas circulation. Limiting CH4 availability during N-depletion promoted the PHB content of the methanotrophic bacteria. However, excess CH4 in the headspace (>70% CH4 not being utilized) for the limited DO condition inhibited biomass growth and PHB production. Shallow metagenomic analysis showed that the bacterial species in the MOM reactors mainly belonged to the genera Methylocytis (up to 87% relative abundance) and Hyphomicrobium (up to 70% relative abundance). Methylocystis, a Type II methanotroph known to produce PHB, became dominant during the conditions that led to the highest PHB content. The findings demonstrate the MOM operated with lower CH4 gas pressure and limited DO promoted CH4 utilization and conversion toward PHB production.},
}

@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},
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 {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 = {*Gastrointestinal Microbiome/genetics ; Humans ; *Phylogeny ; Porphyra/genetics/metabolism ; Asia, Eastern ; Genetic Variation ; Asian People ; East Asian People ; },
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.},
}

*Gastrointestinal Microbiome/genetics
Humans
*Phylogeny
Porphyra/genetics/metabolism
Asia, Eastern
Genetic Variation
Asian People
East Asian People

@article {pmid40748702,
year = {2025},
author = {Guzman-Cole, C and Huang, AD},
title = {nf-UnO-pipeline: A Nextflow metagenomic co-assembly pipeline for novel pathogen detection of mNGS outbreak sets.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf436},
pmid = {40748702},
issn = {1367-4811},
abstract = {MOTIVATION: nf-UnO is a pipeline implemented in Nextflow to identify novel pathogens from metagenomic shotgun sequencing of epidemiologically-related foodborne outbreak specimens. nf-UnO employs MIDAS2, metagenomic co-assembly, multiple binning programs, and read mapping to metagenomically-assembled genomes (MAGs) to detect potential etiological agents found in common across outbreak specimens.

AVAILABILITY: https://github.com/uel3/nf-UnO.},
}

@article {pmid40748669,
year = {2025},
author = {Cui, S and Ma, W and Peng, H and Ye, Y and Qing, Y and Wei, G and Wang, J and Zhang, X},
title = {Genome-wide mining reveals the genetic plasticity of antibiotic resistance/virulence factor genes in Enterobacter hormaechei subsp. xiangfangensis.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf196},
pmid = {40748669},
issn = {1365-2672},
abstract = {AIMS: This study aims to systematically characterize the genetic basis and intra-species differentiation of antibiotic resistance/virulence factor genes (ARGs/VFGs) in Enterobacter hormaechei subsp. xiangfangensis.

METHODS AND RESULTS: A high-quality metagenome-assembled genome of E. hormaechei subsp. xiangfangensis bin99 (97.22% completeness, 1.63% contamination) was acquired. Phylogenomic and average nucleotide identity (≥ 95%) analyses confirmed its taxonomic assignment. Pan-genomic analysis revealed an open configuration (Heap's exponent B = 0.34) with a large accessory genome (approximate 2 965 genes) and a stabilized core genome (1 139 genes). Critically, a strong positive correlation (r = 0.86, P < 2.2e-16) was observed between mobile genetic elements (MGEs) and accessory gene abundance, probably suggesting horizontal gene transfer (HGT) as a potential driver of genome diversity. Functional annotation highlighted distinct roles: core genes enriched in essential metabolism, while accessory/strain-specific genes were linked to adaptation. Screening identified significant inter-strain variation in ARGs (n = 31) and VFGs (n = 35). Bin99 itself harbored 19 ARGs (e.g. multidrug: soxS, ramA, oqxB) and 40 VFGs (e.g. flagella, T6SS). Importantly, MGE abundance showed a significant positive correlation with ARGs (r = 0.67, P < 2.2e-16) but a negative correlation with VFGs (r = -0.29, P < 3.7e-9), suggesting that ARGs were frequently linked to MGEs facilitating HGT-mediated spread, while VFGs might rely less on this route.

CONCLUSIONS: The findings provide genome-wide evidence for distinct genetic plasticity underlying ARG and VFG evolution in E. hormaechei subsp. xiangfangensis, highlighting implications for resistance and virulence dissemination.},
}

@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.},
}

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

@article {pmid40748267,
year = {2025},
author = {Taieb, F and Baidaliuk, A and Durand, A and Prot, M and Jidar, K and Hochedez, P and Consigny, PH and Itani, O and Simon-Loriere, E},
title = {Phylogenetic analysis of chikungunya virus in travellers returning from La Reunion Island.},
journal = {Journal of travel medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/jtm/taaf079},
pmid = {40748267},
issn = {1708-8305},
abstract = {Here, we present molecular detection and clinical metagenomic sequencing in 7 travellers returning from La Reunion and presenting with chikungunya. The viral load and the genomic signature of the novel lineage involved raise significant concerns for the risk of local circulation of the virus in more temperate regions such as Europe.},
}

@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 = {},
number = {},
pages = {e0071525},
doi = {10.1128/spectrum.00715-25},
pmid = {40748195},
issn = {2165-0497},
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 {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.},
}

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

@article {pmid40746758,
year = {2025},
author = {Wang, W and Yuan, L and Zhang, M and Zhao, Q and Pang, W and Sun, D and Jia, X and Tan, F and Niu, T and Tian, K and Li, X},
title = {Metagenomic Identification of a Novel Zoonotic Gemykibivirus in a Diarrheic Pig in China.},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {7560012},
pmid = {40746758},
issn = {1865-1682},
mesh = {Animals ; Swine ; China/epidemiology ; *Swine Diseases/virology/epidemiology ; *Diarrhea/veterinary/virology/epidemiology ; Phylogeny ; Metagenomics ; Genome, Viral ; *DNA Viruses/genetics/isolation & purification/classification ; *Viral Zoonoses/virology ; },
abstract = {Gemykibiviruses are circular, replication-associated protein (REP) encoding single-stranded DNA (ssDNA) viruses classified within the genus Gemykibivirus of the family Genomoviridae. In recent years, several gemykibiviruses have been detected in humans presenting with clinical symptoms, such as encephalitis, respiratory illness, sepsis, pericarditis, diarrhea, and multiple sclerosis. However, the presence of gemykibiviruses in other animal hosts, as well as the evolution of the Gemykibivirus genus, remains poorly understood. In this study, we identified a novel gemykibivirus from a diarrheic pig in China using metagenomic sequencing, which we designated as pGkV. The pGkV genome comprises 2200 nucleotides and encodes two key proteins as follows: the capsid-associated protein (CAP) and the REP. Phylogenetic analyses revealed that pGkV clusters within the zoonotic gemykibivirus (ZooGkV) clade, which includes nearly all gemykibivirus species recently identified in humans. Mutation and haplotype analyses revealed that pGkV is closely related to an avian gemykibivirus, while its CAP and REP proteins are identical to those of a human gemykibivirus, underscoring its potential zoonotic capability. Furthermore, recombination signals were detected among Zoo-GkVs, suggesting that recombination may contribute to the emergence of novel gemykibivirus strains. The identification of pGkV provides new insights into the evolution and cross-species transmission of gemykibiviruses.},
}

Animals
Swine
China/epidemiology
*Swine Diseases/virology/epidemiology
*Diarrhea/veterinary/virology/epidemiology
Phylogeny
Metagenomics
Genome, Viral
*DNA Viruses/genetics/isolation & purification/classification
*Viral Zoonoses/virology

@article {pmid40746313,
year = {2025},
author = {Wu, Y and Ouyang, J and Wang, L and Hu, J and Tang, H and Zheng, S and Xiong, Y and Gao, Y and Wu, Y and Xiong, R and Huang, Y and Xuan, R and Chen, Y and Chen, H},
title = {Breed-specific gut microbiota and enterotype divergence in Chinese indigenous ducks.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1602641},
pmid = {40746313},
issn = {1664-302X},
abstract = {The gut microbiota of domestic ducks plays an important role in digestion and absorption, immune regulation, and overall health. However, our knowledge about the gut microbial composition in ducks of various phylogeny is insufficient, especially if raised in the same farm environment. In this study, 260 fecal samples from 15 Chinese indigenous duck breeds living in a uniformed farm were collected and 16 S rRNA gene sequencing was performed. In addition, 202 blood samples from these ducks were used for whole-genome sequencing (WGS). The WGS results showed that the these domestic duck breeds exhibit breed-specific genetic characteristics. The gut microbiota of different native duck breeds exhibited great similarity at the phylum level with the most dominant phyla being Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes, while harboring distinct gut microbial communities at finer taxonomic levels. The host genetic-specific are associated with the microbial of these duck breeds. The prediction of metagenomic functions showed that the metabolism and function of the gut microbiomes among different duck breeds were more similar than that of their species composition. In addition, Principal coordinates analysis (PCoA) revealed that the gut microbiota of the 15 duck breeds could be divided into two distinct enterotype clusters based on Jensen-Shannon distance (JSD) dissimilarities, with representative breeds corresponding to layer ducks and dual-purpose ducks, respectively. There was no difference in richness index of the gut microbial composition and function between the two enterotypes, but the Shannon index values was significantly different. This study investigated the gut microbial structure and diversity among domestic duck populations with different genetic backgrounds, providing new insights into the relationship between host genetic variation and gut microbiota.},
}

@article {pmid40746232,
year = {2025},
author = {Ye, Y and Xiong, W and He, S and Xiang, Y and Xiao, J and Feng, W and Yang, Z and He, D and Wang, D},
title = {Niche Adaptation of Ammonia-Oxidizing Bacteria Nitrosomonas in Partial Nitrification System: Keystone Species and Unique Survival Strategies.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c04539},
pmid = {40746232},
issn = {1520-5851},
abstract = {Partial nitrification (PN) is of practical significance for achieving autotrophic nitrogen removal with impressive economic and environmental benefits. While most studies focused on the selective suppression of nitrite-oxidizing bacteria, maintaining stable ammonia oxidation as the primary source of nitrite remains equally critical but largely underexplored. Herein, we identified Nitrosomonas eutropha as the keystone species dominating ammonia oxidation in free ammonia treatment-based PN systems, comprising over 40% of the nitrifier community. Combined metagenomic and metaproteomic analyses revealed that N. eutropha orchestrated multiple cellular processes and reallocated intracellular resources to adapt to the PN niche. Specifically, enhanced primary metabolism and stress response systems within N. eutropha were observed, alongside significant upregulation of the protein synthesis machine, such as ribosomal proteins and translation factors. Notably, overexpression of the cell division protein FtsA was detected, which is known to disrupt Z-ring formation and inhibit cell division. These results suggest a protein synthesis-centered survival strategy, wherein N. eutropha maintained robust protein synthesis capacity while retarding propagation. This strategy differs fundamentally from conventional microbial stress responses, which typically involve the downregulation of protein synthesis to conserve resources. These findings provide multidimensional insights into the survival strategies of Nitrosomonas in PN systems, with practical implications for both understanding molecular responses to environmental stress and optimizing engineering strategies for autotrophic nitrogen removal.},
}

@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.},
}

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

@article {pmid40745049,
year = {2025},
author = {},
title = {Deep, long-read metagenome sequencing expands knowledge of prokaryotic phylogenetic diversity.},
journal = {Nature microbiology},
volume = {10},
number = {8},
pages = {1802-1803},
pmid = {40745049},
issn = {2058-5276},
}

@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.},
}

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

@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 = {},
number = {},
pages = {e0008425},
doi = {10.1128/spectrum.00084-25},
pmid = {40744840},
issn = {2165-0497},
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 {pmid40744236,
year = {2025},
author = {Zhang, S and Al-Gashgari, B and Medina, JS and Wang, C and Narayanasamy, S and Xiong, Y and Wang, K and Hong, PY},
title = {Extracellular DNA-associated dissemination of antimicrobial resistance in anaerobic versus aerobic membrane bioreactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133054},
doi = {10.1016/j.biortech.2025.133054},
pmid = {40744236},
issn = {1873-2976},
abstract = {Extracellular DNA (eDNA) in the environment can escalate antimicrobial resistance threats arising from natural transformation-based horizontal gene transfer (HGT). Reclaimed wastewater is a source of eDNA, particularly those associated with antibiotic resistance genes (ARGs), may vary depending on the wastewater treatment technology. Here, a comparison study was conducted in aerobic and anaerobic membrane bioreactors (AeMBR and AnMBR). A full-scale AeMBR and a pilot-scale AnMBR were analyzed through long-term sampling and time-series batch tests. Long-term sampling showed that AeMBR sludge increased eDNA content by 2.5 times compared to AnMBR sludge. Specifically, time-series batch tests showed eDNA levels in aerobic sludge followed a logistic growth model but not anaerobic sludge. The water matrix of AeMBR sludge increased natural transformation by 1.6-fold change compared to that of AnMBR sludge. This increase in natural transformation rates was mediated by reactive oxygen species (ROS) in the AeMBR sludge. Metagenomic analysis revealed that the AnMBR system maintained consistent extracellular ARG (eARG) ecological diversity from influent to effluent, whereas the AeMBR system significantly altered eARG diversity. This study provides vital insights into the behavior of eDNA arising from different wastewater treatment processes. Understanding these differences is crucial for optimizing treatment strategies to reduce the environmental impact of eDNA-associated dissemination of antibiotic resistance.},
}

@article {pmid40744195,
year = {2025},
author = {Deng, Z and Zhao, Y and Ren, Z and Hao, N and Sun, P and Zhao, W},
title = {Ecological distribution, dissemination potential, and health risks of antibiotic resistance genes and mobile genetic elements in soils across diverse land-use types in China.},
journal = {Environmental research},
volume = {285},
number = {Pt 2},
pages = {122459},
doi = {10.1016/j.envres.2025.122459},
pmid = {40744195},
issn = {1096-0953},
abstract = {Antibiotic resistance genes (ARGs) have emerged as critical environmental contaminants, while mobile genetic elements (MGEs) act as key vectors facilitating their horizontal transfer, collectively posing growing challenges to ecosystem and public health. This study presents a comprehensive metagenomic investigation of ARGs and MGEs across 180 soil samples from five major land use types in China: farmland, forest, grassland, urban planting, and bare land. Among 862 identified ARG subtypes, 28 were detected in over 95 % of samples, indicating the presence of ecologically dominant and widely disseminated resistance elements. By integrating taxonomic profiling, metagenomic assembly, and multiple statistical methods-including Kruskal-Wallis testing, redundancy analysis (RDA), PERMANOVA, and co-occurrence network analysis-we revealed distinct distributional patterns and ecological associations of ARGs and MGEs across land use gradients. Forest and agricultural soils exhibited higher ARG diversity and abundance, while urban and barren soils showed reduced resistome complexity. Network analysis identified key ARG-MGE co-occurrence modules and hub elements that may promote horizontal gene transfer, particularly under anthropogenic disturbance. Taxonomic annotation highlighted Actinomycetota and Pseudomonadota as dominant ARG hosts. A multi-indicator health risk framework incorporating environmental prevalence, gene mobility, and host pathogenicity classified 267 ARG subtypes as posing medium to high potential risks. These findings enhance our understanding of land use-mediated ARG dissemination and provide a scientific basis for targeted environmental monitoring and mitigation strategies.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.07.005},
pmid = {40744013},
issn = {1097-4172},
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 {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.},
}

*Soil Microbiology
*Archaeology
*Bacteria/genetics/classification/drug effects
*Caves/microbiology
RNA, Ribosomal, 16S/genetics
Humans
*Drug Resistance, Microbial/genetics
Microbiota/genetics
Turkey

@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 = {},
number = {},
pages = {},
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/ ; },
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 {pmid40742499,
year = {2025},
author = {Chen, W and Yuan, J and Liu, G and Cui, L and Tian, F and Zhang, Y},
title = {Metagenomic next-generation sequencing and chromosomal copy number variation analysis in cerebrospinal fluid for the detection of meningeal carcinomatosis.},
journal = {Journal of neuro-oncology},
volume = {},
number = {},
pages = {},
pmid = {40742499},
issn = {1573-7373},
support = {2020YFC2005403//National Key Research and Development Program of China/ ; },
abstract = {OBJECTIVE: To evaluate the diagnostic accuracy of copy number variations (CNVs) and metagenomic nextgeneration sequencing (mNGS) in identifying meningeal carcinomatosis (MC) within the cerebrospinal fluid (CSF).

METHODS: Patients diagnosed with MC at Xuanwu Hospital, Capital Medical University, from January 2022 to January 2024, were prospectively enrolled. The diagnosis was confirmed via CSF cytology or meningeal biopsy, and a control group of encephalitis patients was used for comparative analysis. We introduced Onco-mNGS, a novel diagnostic protocol integrating mNGS with CNVs analysis to concurrently identify malignancies and pathogens from CSF specimens.

RESULTS: The study cohort comprised 12 patients with MC, predominantly with lung cancer. Initial CSF CNVs analysis yielded a sensitivity of 83%, with all control samples testing negative for CNVs, thereby achieving 100% specificity.

CONCLUSIONS: CSF CNVs analysis, in combination with mNGS, presents a promising diagnostic modality for MC, offering high sensitivity and specificity and expanding the clinical utility of CSF mNGS in adjunctive diagnostics.},
}

@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 = {},
number = {},
pages = {e0098425},
doi = {10.1128/msystems.00984-25},
pmid = {40742180},
issn = {2379-5077},
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 = {},
number = {},
pages = {e0050225},
doi = {10.1128/msystems.00502-25},
pmid = {40742167},
issn = {2379-5077},
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 {pmid40742165,
year = {2025},
author = {Arakaki, W and Kinjo, T and Kami, W and Hashioka, H and Nabeya, D and Nagano, H and Yoshida, S and Tsuyuguchi, K and Matsumoto, Y and Nakamura, S and Fujita, J and Yamamoto, K},
title = {Evaluation of mlstverse system for accurate subspecies identification and drug resistance prediction in Mycobacterium abscessus species.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0064325},
doi = {10.1128/spectrum.00643-25},
pmid = {40742165},
issn = {2165-0497},
abstract = {UNLABELLED: Accurate subspecies identification and drug susceptibility testing (DST) are essential for appropriate clinical management, particularly in patients infected with Mycobacterium abscessus species (MABS). We developed a novel software, mlstverse, which uses multi-locus sequence typing to identify non-tuberculous mycobacteria (NTM) species, demonstrating rapid and accurate diagnostic performance. However, these studies included only a limited number of MABS samples. In this study, we focused on MABS and evaluated the diagnostic accuracy of the system for subspecies identification and drug resistance prediction for clarithromycin (CAM) and amikacin (AMK). A total of 56 clinical isolates, previously identified as MABS by conventional methods, were analyzed. The mlstverse identified two isolates as M. intracellulare and 54 isolates as MABS, with 28 identified as M. abscessus subsp. abscessus (MAB) and 26 as M. abscessus subsp. massiliense (MMA). All results obtained through mlstverse were fully consistent with the species/subspecies exhibiting the highest average nucleotide identity (ANI) values. In contrast to the identification by ANI values, the mlstverse system clearly distinguished between MABS subspecies, with the mean differences between the highest and second-highest MLST scores of 0.16 for MAB and 0.33 for MMA, respectively. The system predicted drug susceptibility to CAM and AMK with high concordance to phenotypic DST (CAM: 98.1%, AMK: 100%). These results suggest that mlstverse provides a reliable method for accurate subspecies identification and drug resistance prediction in MABS, supporting the potential of integrating portable next-generation sequencing technologies with real-time software analysis for improved diagnostic accuracy and treatment strategies in patients with NTM infections.

IMPORTANCE: Accurate subspecies identification and drug susceptibility testing (DST) are essential for appropriate clinical management of Mycobacterium abscessus species (MABS) infections. We previously developed mlstverse, a novel software utilizing multi-locus sequence typing to identify non-tuberculous mycobacteria (NTM species, demonstrating rapid and accurate diagnostic performance. However, these studies included only a limited number of MABS samples. In this study, we focused on MABS and evaluated the diagnostic accuracy of the system for subspecies identification and drug resistance prediction for clarithromycin (CAM) and amikacin (AMK). We showed that mlstverse can clearly distinguish MAB subspecies compared to ANI values and predicted drug susceptibility to CAM and AMK with high concordance to phenotypic DST. The mlstverse system provides a reliable method for accurate subspecies identification and drug resistance prediction in MABS, supporting the potential of integrating portable next-generation sequencing technologies with real-time software analysis for improved diagnostic accuracy and treatment strategies in patients with NTM infections.},
}

@article {pmid40742164,
year = {2025},
author = {Yang, R and Peng, C and Mo, Y and Kleindienst, S and Li, S and Wang, J and Kappler, A and Wang, Z and Lu, L},
title = {Electron acceptors modulate methane oxidation and active methanotrophic communities in anoxic urban wetland sediments.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0038625},
doi = {10.1128/aem.00386-25},
pmid = {40742164},
issn = {1098-5336},
abstract = {UNLABELLED: Urban wetlands, although often overlooked, are hotspots for CH4 cycling. However, the understanding of anaerobic CH4 oxidation and microbial responses to different electron acceptors in urban wetlands remains limited. Here, we employed DNA-stable isotope probing (SIP) and metagenomic techniques to identify the core CH4-oxidizing microbial groups in the presence of NO3[-], SO4[2-], or ferrihydrite (Fe(III)) in anoxic urban-lake sediments. The addition of NO3[-] to sediment microcosms promoted CH4 oxidation, whereas SO4[2-] and Fe(III) had minimal or inhibitory effects on CH4 oxidation rates in anoxic microcosms. The SIP-identified methanotrophs in response to the addition of CH4 comprised the Marine Benthic Group D (MBG-D), "Candidatus Methylomirabilis Sh765B-TzT-35 and Z114MB74," and the putatively aerobic methanotrophs Methylobacter and Methylocystis. The presence of NO3[-] further enriched Methylocaldum, Methylomonas, 'Ca. Methylomirabilis Sh765B-TzT-35 and Z114MB74', Methylococcaceae, and Methylospira. In contrast, SO4[2-] and Fe(III) amendments notably shifted the dominant methanotrophs through the significant labeling of Methylocystis. Furthermore, metagenomic analysis of [13]C-labeled DNA showed enrichment of genes for oxidation of CH4 and its intermediates, as well as the reduction of NO3[-], SO4[2-], Fe(III), and fermentation. These results underscore the activity of NO3[-]-dependent CH4-oxidizing microorganisms and highlight their potential metabolic versatility in highly anthropogenically influenced urban wetlands.

IMPORTANCE: Urban wetlands are critical ecosystems for CH4 cycling but are increasingly impacted by complex pollutants from urban development, such as nitrates, sulfates, and Fe(III) from industrial runoff, atmospheric deposition, and wastewater discharge. This study reveals how these pollutants act as electron acceptors, modulating microbial metabolic pathways and reshaping methanotrophic communities under anoxic conditions. By uncovering the microbial mechanisms driving CH₄ oxidation in urban wetland sediments, our findings provide a deeper understanding of how anthropogenic pollution alters biogeochemical cycles. These insights are crucial for developing targeted strategies to mitigate CH₄ emissions and improve greenhouse gas control in rapidly urbanizing regions.},
}

@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 {pmid40741762,
year = {2025},
author = {Acosta, N and Lee, J and Bautista, MA and Bhatnagar, S and Li, C and Waddell, BJ and Au, E and Pradhan, P and Clark, RG and Meddings, J and Achari, G and Pitout, JD and Conly, J and Frankowski, K and Hubert, CRJ and Parkins, MD},
title = {Metagenomic analysis after selective culture enrichment of hospital and community wastewater enhances antimicrobial resistance gene detection.},
journal = {mBio},
volume = {},
number = {},
pages = {e0167225},
doi = {10.1128/mbio.01672-25},
pmid = {40741762},
issn = {2150-7511},
abstract = {Antimicrobial resistance is an accelerating threat to global health. Wastewater-based surveillance (WBS) enables objective, inclusive, and comprehensive assessments of population-level antimicrobial resistance; however, it is limited in its ability to detect rare antibiotic resistance genes (ARG). We compared traditional high-depth metagenomic sequencing of raw wastewater with lower-depth sequencing following semi-selective culture enrichment for gram negatives for rare ARGs in wastewater from two tertiary-care hospitals and two nearby urban neighborhoods. In total, 26 antibiotic resistance gene types (1,225 subtypes) were identified, with beta-lactamase genes being the most prevalent. Resistomes differed between raw and culture-enriched wastewater metagenomes and clustered based on sample type (hospitals versus neighborhoods). Hospital wastewater had higher diversity and a greater abundance of ARGs relative to both raw and culture-enriched neighborhood wastewater metagenomes. Lower coverage sequencing following culture enrichment proved superior to deeper sequencing for identifying rare, clinically relevant targets, including carbapenemase genes. In particular, enrichment with meropenem proved the most sensitive to identifying clinically relevant genes and enabled significant cost savings. ARG WBS has enormous potential for augmenting hospital-based infection prevention and control and antimicrobial stewardship programs.IMPORTANCEAntimicrobial resistance (AMR) poses a considerable burden to healthcare systems and contributes to increased morbidity and mortality. This is expected to further increase with time. AMR surveillance programs are key to understanding and controlling this progressive threat. Wastewater-based surveillance (WBS) is an emerging tool that can be adapted to this end. This study explores the role of metagenomic analysis of WBS with/and without culture enrichment to detect rare antibiotic resistance genes (ARG) of clinically important pathogens across a range of scales. We were able to demonstrate that the resistome of hospitals significantly differs from communities having a greater abundance, and more heterogeneous ARGs. Culture enrichment, particularly with meropenem, improved the detection of clinically relevant ARGs even at lower sequencing depths. WBS is an important tool with the capacity to augment hospital-based infection control and antimicrobial stewardship programs, providing real-time, cost-effective information on the population within.},
}

@article {pmid40741758,
year = {2025},
author = {Yacoub, MN and Krumbeck, JA and Bogan, JE and Mason, AK},
title = {First metagenome-assembled genome of Cryptosporidium serpentis from Drymarchon couperi gastric lavage.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0034225},
doi = {10.1128/mra.00342-25},
pmid = {40741758},
issn = {2576-098X},
abstract = {Cryptosporidium serpentis is a protozoan parasite responsible for chronic clinical infections in reptiles, particularly snakes, leading to anorexia and lethargy. Here, we report the first metagenome-assembled genome of C. serpentis derived from a gastric lavage sample from the eastern indigo snake, Drymarchon couperi.},
}

@article {pmid40741743,
year = {2025},
author = {Lapidus, E and Uchimiya, M and Hay, A},
title = {Metagenome assembled genomes from hot sugarcane mill mud.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0041825},
doi = {10.1128/mra.00418-25},
pmid = {40741743},
issn = {2576-098X},
abstract = {The genomes of six bacteria from the phylum Bacillota were assembled from metagenomic DNA extracted from sugarcane mill mud obtained immediately after heat treatment. These metagenome-assembled genomes were 94.5%-99.8% complete, with <2% contamination, and ranged from 2.6 Mb to 6.5 Mb, encoded 2573-5724 predicted proteins, and had G + C contents from 37% to 46%.},
}

@article {pmid40741741,
year = {2025},
author = {Hernández, LHA and da Paz, TYB and da Silva, SP and da Silva, FS and Barros, BCVd and Casseb, LMN and Vasconcelos, PFdC and Cruz, ACR},
title = {Genome sequence of a novel Tetraparvovirus identified in a Rhinophylla pumilio bat from the Amazon region.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0059325},
doi = {10.1128/mra.00593-25},
pmid = {40741741},
issn = {2576-098X},
abstract = {A new Tetraparvovirus was identified in a pooled tissue sample of a Rhinophylla pumilio bat from Santa Bárbara, Pará State, Brazil. This is the second Tetraparvovirus described in bats and has higher nucleotide and amino acid identity with a Tetraparvovirus from opossum, also described in Brazil.},
}

@article {pmid40741085,
year = {2025},
author = {Nurmilah, S and Frediansyah, A and Cahyana, Y and Balia, RL and Andriana, BB and Utama, GL},
title = {Exploring microbial dynamics and metabolomic profiling of isoflavone transformation in black and yellow soybean tempe for sustainable functional foods.},
journal = {Food chemistry. Molecular sciences},
volume = {11},
number = {},
pages = {100279},
pmid = {40741085},
issn = {2666-5662},
abstract = {Tempe, a traditional Indonesian fermented food, is rich in bioactive isoflavones and peptides, offering significant health benefits. This study explores how fermentation methods and soybean varieties shape isoflavone profiles and microbial communities. Two fermentation approaches were compared: Raprima™ starter culture and a co-culture of Rhizopus oligosporus and R. stolonifer. Metabolomic analysis showed that co-culture fermentation significantly increased genistein levels and enhanced isoflavone bioavailability. Proteobacteria (78 %) and Firmicutes (18 %) dominated bacterial communities, with yellow soybeans containing more Enterobacteriaceae. Co-culture fermentation enriched Stenotrophomonas, while Raprima™ favored Acinetobacter. The fungal community, primarily Mucoromycota (92 %), exhibited significant correlations with isoflavone transformation. Co-culture fermentation improved microbial synergy and metabolic efficiency, boosting isoflavone aglycone production. While yellow soybeans had higher isoflavone content, black soybeans, with elevated genistein, present a promising alternative. These findings emphasize fermentation's role in enhancing tempe's functionality for sustainable, nutritionally rich food development.},
}

@article {pmid40741037,
year = {2025},
author = {Mentado-Sosa, E and Guerra-Solano, JM and Raffa, RB and Pagán, OR and Pisciotta, J},
title = {Microbiome Alteration Prevents Abstinence-Induced Nicotine Withdrawal in a Well-Established Planarian Model.},
journal = {Cureus},
volume = {17},
number = {7},
pages = {e89075},
pmid = {40741037},
issn = {2168-8184},
abstract = {The prevalence of substance use disorders (SUDs) is unequally distributed across socioeconomic strata. Although several genetic predispositions and psychosocial influences play integral roles, environmental factors are undoubtedly additional contributors. We propose that a potential common factor could be diet. More specifically, circumstances such as economic challenges could lead to limited food choices and poor-quality diets, and this could result in differences in microbiome composition compared to less SUD-susceptible populations having otherwise similar risk factors. The current study investigated the effect of altering the microbiome on drug withdrawal from nicotine using a standard planarian model. Planarians (Girardia dorotocephala) were treated with the broad-spectrum antibiotics ampicillin (a ß-lactam) and kanamycin (a non-ß-lactam), alone and in combination, and microbiomes were analyzed using culture techniques, microscopy, and metagenomic methods. Alphaproteobacteria such as Sphingomonadaceae were detected in the microbiome. Ampicillin or kanamycin reduced the microbiome diversity, notably reducing Sphingomonas and Pedobacter bacteria. One-week treatment with ampicillin and kanamycin did not affect planarian spontaneous locomotor activity. However, pretreatment with ampicillin, but not kanamycin or the combination, significantly attenuated abstinence-induced nicotine withdrawal-like behavior. These results suggest that alteration of the microbiome decreases nicotine withdrawal in this planarian species, and, more broadly, supports the idea that the microbiome might influence the susceptibility and/or maintenance of SUDs.},
}

@article {pmid40740937,
year = {2025},
author = {Zhang, L and Hu, L and Tan, L and Zhang, Z and Chen, M and Gan, W and Chen, L and Zou, Y and Wang, S and Pang, Y and Fan, Z and Liu, J},
title = {The dysbiosis of gut microbiota and dysregulation of metabolites in IgA nephropathy and membranous nephropathy.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1618947},
pmid = {40740937},
issn = {2296-858X},
abstract = {INTRODUCTION: Immunoglobulin A nephropathy (IgAN) and membranous nephropathy (MN) are among the most common forms of primary glomerular diseases, with a rising global incidence. Despite their clinical importance, the underlying pathogenesis of these diseases and the development of reliable non-invasive diagnostic tools remain inadequately understood. Accumulating evidence suggests that gut microbiota and its associated metabolites may play a crucial role in the development of kidney diseases via the gut-kidney axis. However, comprehensive studies integrating both microbiome and metabolomic data in IgAN and MN are still limited.

METHODS: In this study, we performed integrated metagenomic sequencing and untargeted metabolomic profiling to investigate alterations in gut microbial composition and systemic metabolic changes associated with IgAN and MN. Fecal samples were collected from 24 patients with IgAN, 20 patients with MN, and 17 healthy controls. Microbial diversity and composition were assessed using metagenomic analysis, while metabolic profiles were evaluated through untargeted LC -MS-based metabolomics. Multivariate statistical analyses and biomarker modeling were employed to identify discriminative features and evaluate diagnostic performance. Microbiota-metabolite correlation networks were constructed to explore potential mechanistic links.

RESULTS: Metagenomic analysis showed that both the IgAN and MN groups had significantly reduced α-diversity. Although β-diversity analysis did not reveal significant differences between the three groups, the IgAN and MN groups exhibited higher sample dispersion than the control group. Notably, both IgAN and MN patients showed a decrease in the abundance of certain specific microbial taxa. A total of 34 and 28 differentially abundant microbial species were identified in IgAN and MN, respectively, compared to healthy controls, with 16 taxa consistently downregulated in both disease groups. Notably, Streptococcus oralis was significantly enriched in the MN group, while [Clostridium] innocuum was markedly depleted. Metabolomic profiling identified 307 and 209 differentially abundant metabolites in IgAN and MN, respectively. Dipeptides (e.g., prolylleucine) were consistently upregulated, while the levels of certain short-chain fatty acids (SCFA) were reduced. Multivariate biomarker models demonstrated excellent diagnostic performance, achieving area under the curve (AUC) of 0.919 (IgAN vs. control), 0.897 (MN vs. control) and 0.912 (IgAN vs. MN), surpassing individual metabolite markers.

DISCUSSION: Our findings highlight significant alterations in gut microbial composition and systemic metabolite profiles in both IgAN and MN patients compared to healthy individuals. The consistent reduction in microbial diversity and SCFA-producing taxa, along with characteristic changes in metabolic signatures, supports the involvement of the gut-kidney axis in disease pathogenesis. The diagnostic models developed in this study provide promising non-invasive biomarkers for distinguishing IgAN and MN with high accuracy. These results contribute novel insights into the microbe-metabolite interplay in glomerular diseases and offer potential targets for future diagnostic and therapeutic strategies.},
}

@article {pmid40740339,
year = {2025},
author = {Shen, J and Hu, Y and Zhang, Y and Li, L and Deng, X and Chen, M and Li, L and Xie, P and Shao, M},
title = {Metagenomics-based analysis of microbial community structure and functional differences in fermented grains of Jiang-flavored baijiu from different production regions and policy recommendations for industrial development.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1619035},
pmid = {40740339},
issn = {1664-302X},
abstract = {INTRODUCTION: Recently, some regions that originally focused on strong-flavor baijiu production started producing Jiang-flavored baijiu, providing a new perspective for studying the dynamic changes in the microbial community during brewing.

METHODS: This study used second-round fermented grains of Jiang-flavored baijiu from three Guizhou production regions (Renhuai, Duyun, and Bijie). By applying metagenomics technology and various analytical and statistical methods, we analyzed the community structures of bacteria and fungi in fermented grains, their functional genes, and their correlations with environmental factors.

RESULTS: We identified 1063 bacterial genera and 411 fungal genera. Although the dominant microbial species were similar across regions, their relative abundances differed significantly. α-diversity analysis showed that grains from the Bijie region had higher species richness and evenness indices, indicating the significant impact of geographical location and the strong-flavor baijiu-brewing background on microbial structure and composition. Analysis of similarity and the Wilcoxon rank-sum test revealed significant differences in the microbial communities of different regions, and we identified genera with large differences in abundance, such as Desmospora and Kroppenstedtia among bacteria, and Pyrenophora and Blyttiomyces among fungi. Based on our Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis, the Duyun region had a significantly higher abundance of metabolism-related genes at the tertiary KEGG level. Redundancy analysis showed that six environmental factors (relative humidity, daily temperature difference, elevation, annual mean temperature, extreme cold temperature, and annual precipitation) exerted complex effects on microbial functional genes in fermented grains. Carbon metabolism, antibiotic biosynthesis, and elevation were positively correlated with microbial functional genes. Actinobacteria are crucial for carbon metabolism, followed by Proteobacteria and Chloroflexi.

DISCUSSION: This study elucidated the structural and functional characteristics of microbial communities in second-round fermented grains of Jiang-flavored baijiu under production area transitions and proposed policy recommendations to promote the differentiated development of the baijiu industry.},
}

@article {pmid40740338,
year = {2025},
author = {Mancabelli, L and Tarracchini, C and Longhi, G and Alessandri, G and Ventura, M and Turroni, F},
title = {Dissecting the molecular interactions between botanical extracts and the human gut microbiota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1610170},
pmid = {40740338},
issn = {1664-302X},
abstract = {Over millions of years, humans and their gut microbes have developed a symbiotic relationship that benefits both organisms. Many plants and herbs consumed as food by humans, such as aloe vera gel and dandelion root extracts, contain bioactive compounds with recognized therapeutic or preventive effects. However, the impact of these botanicals on the composition and functionality of the human gut microbiota is not yet understood. In this study, the molecular impact of these botanicals on reconstructed human gut microbiota was assessed by in-vitro bioreactor experiments followed by metagenomics and transcriptomic approaches, highlighting both taxonomic and functional changes in the human gut microbiome. Furthermore, cross-feeding activities established by common human gut microbial taxa like Bacteroides spp. when cultivated on these extracts were assessed. In conclusion, the results show that botanicals affect intestinal populations that are highly dependent on the microbial taxa present and that trophic interactions are established in few key gut members.},
}

@article {pmid40740321,
year = {2025},
author = {Wang, Y and Radosevich, M and Yang, L and Zhang, Y and Xie, N and Liang, X},
title = {The interplay of nitrogen sources and viral communities in the biodegradation of atrazine in agricultural soils.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1645559},
pmid = {40740321},
issn = {1664-302X},
abstract = {Atrazine is a widely used herbicide, and its degradation is primarily mediated by microbial activity. However, the interplay between nutrient availability and viral infections on microbial degradation of atrazine remains unexplored. Here, we investigated atrazine degradation under different nitrogen amendments (ammonium, nitrate, and urine) and the influence of soil viruses (intracellular and extracellular viruses). The results showed that atrazine degradation was greater with the addition of extracellular viruses without exogenous nitrogen sources. The added nitrogen sources (nitrate and urine) completely inhibited atrazine degradation. Ammonium impeded atrazine degradation, which was promoted with the addition of intracellular viruses. The metagenomic-based evidence revealed that nitrogen amendments significantly alter bacterial and viral community composition. Peduoviridae emerged as the predominant viral family, with its prevalence and temperate phage ratio strongly influenced by nitrogen availability, underscoring the role of nutrient dynamics in shaping virus-host interactions. The presence of viruses selectively enriched atrazine degradation genes and auxiliary metabolic genes (AMGs) associated with key microbial metabolic pathways, revealing potential mechanisms by which viral infections contribute to pollutant biodegradation. The findings highlight the complex interplay between viral predation, microbial adaptation, and nitrogen-driven shifts in microbial community structure and function, offering new perspectives on how viruses shape bioremediation processes in agroecosystems.},
}

@article {pmid40739825,
year = {2025},
author = {Xiang, T and Chi, J and Pan, J},
title = {Cooperative effect of N2H4 on anaerobic ammonium-oxidizing bacteria and heterotrophic bacteria and the underlying mechanism.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {92},
number = {2},
pages = {285-300},
pmid = {40739825},
issn = {0273-1223},
support = {Youth Project（No.JYTQN2023395）//Department of Education of Liaoning Province/ ; Natural Science Foundation - Doctoral Research Launch Project (No. 2024-BSLH-237)//Department of Education of Liaoning Province/ ; },
mesh = {*Ammonium Compounds/metabolism ; *Hydrazines/pharmacology/chemistry ; Nitrogen/metabolism ; Oxidation-Reduction ; *Bacteria/metabolism ; *Bacteria, Anaerobic/metabolism/drug effects ; Heterotrophic Processes ; Anaerobiosis ; Bioreactors/microbiology ; },
abstract = {Batch experiments investigated cooperative nitrogen removal between anaerobic ammonium-oxidizing bacteria (AnAOB) and heterotrophs under hydrazine (N2H4) and sodium acetate effects. A single addition of sodium acetate (optimal C/N = 2) or N2H4 (1 mg/L) achieved peak total nitrogen removal efficiency of 89.74 and 79.95%, respectively, showing initial enhancement followed by decline with increasing dosage. Combined additions exhibited a V-shaped efficiency trend, with the NH01_CN2 group (C/N = 2, N2H4 = 1 mg/L) achieving 76.76% removal efficiency. Appropriate carbon-to-nitrogen (C/N) ratios allowed hydrazine to promote synergistic interactions. These interactions improved the activity of critical nitrogen-converting genes. The enhanced genes included nitrite oxidoreductase (EC 1.7.99.-), nitrate reductase (EC 1.7.5.1), and cytochrome nitrate reductase (EC 1.9.6.1). Metagenomic analysis revealed that AnAOB primarily engaged in core metabolic pathways, while heterotrophs dominated nucleotide metabolism. Exogenous additives induced metabolic shifts in AnAOB toward versatile environmental adaptations. These findings elucidate the carbon-nitrogen coordination mechanisms governing AnAOB-heterotroph partnerships during nitrogen cycle optimization.},
}

*Ammonium Compounds/metabolism
*Hydrazines/pharmacology/chemistry
Nitrogen/metabolism
Oxidation-Reduction
*Bacteria/metabolism
*Bacteria, Anaerobic/metabolism/drug effects
Heterotrophic Processes
Anaerobiosis
Bioreactors/microbiology

@article {pmid40739820,
year = {2025},
author = {de Sousa, IB and Malvestiti, JA and Cavalcante, RP and Luchessi, AD and Tornisielo, VL and Dantas, RF},
title = {Biological activated carbon: E. coli and helminth eggs removal from urban wastewater and its impact on ecotoxicity.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {92},
number = {2},
pages = {205-219},
pmid = {40739820},
issn = {0273-1223},
support = {2022/00454-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2019/26210-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2022/04015-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 403211/2023-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 2022/16554-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
mesh = {*Wastewater/parasitology/microbiology ; *Escherichia coli/isolation & purification ; Animals ; *Helminths/isolation & purification ; *Waste Disposal, Fluid/methods ; *Charcoal/chemistry ; Ovum ; Filtration ; Biodegradation, Environmental ; Cities ; Water Purification/methods ; Biofilms ; Raphanus/drug effects/growth & development ; },
abstract = {The main objective of this study was to characterize metagenomically and evaluate the biofilter effectiveness for COD, total coliforms, Escherichia coli, and Helminth eggs removal from urban wastewater using different configurations. Several contact times of wastewater with the biofilm were tested, as well as physicochemical and biological parameters. The optimal treatment time for COD removal was 480 min for BAC1 and 360 min for BAC2, while for E. coli removal, it was 90 and 120 min by BAC1 and BAC2, respectively, and 200 min for Helminth eggs by both BACs. The metagenomic analysis revealed a diverse microbial community within the biofilms, which contributed to the biodegradation process. BAC1 exhibited greater microbiological diversity and better performance than BAC2. Key microbial species identified, such as Lysinibacillus sphaericus, Citrobacter freundii, and Saccharomyces sp. possess notable biodegradative and antimicrobial properties, further enhancing the filter's efficacy. The effluents treated by both BACs did not exhibit toxicity for germination and root elongation of radish seeds.},
}

*Wastewater/parasitology/microbiology
*Escherichia coli/isolation & purification
Animals
*Helminths/isolation & purification
*Waste Disposal, Fluid/methods
*Charcoal/chemistry
Ovum
Filtration
Biodegradation, Environmental
Cities
Water Purification/methods
Biofilms
Raphanus/drug effects/growth & development

@article {pmid40739342,
year = {2025},
author = {Ruffolo, JA and Nayfach, S and Gallagher, J and Bhatnagar, A and Beazer, J and Hussain, R and Russ, J and Yip, J and Hill, E and Pacesa, M and Meeske, AJ and Cameron, P and Madani, A},
title = {Design of highly functional genome editors by modelling CRISPR-Cas sequences.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40739342},
issn = {1476-4687},
abstract = {Gene editing has the potential to solve fundamental challenges in agriculture, biotechnology and human health. CRISPR-based gene editors derived from microorganisms, although powerful, often show notable functional tradeoffs when ported into non-native environments, such as human cells[1]. Artificial-intelligence-enabled design provides a powerful alternative with the potential to bypass evolutionary constraints and generate editors with optimal properties. Here, using large language models[2] trained on biological diversity at scale, we demonstrate successful precision editing of the human genome with a programmable gene editor designed with artificial intelligence. To achieve this goal, we curated a dataset of more than 1 million CRISPR operons through systematic mining of 26 terabases of assembled genomes and metagenomes. We demonstrate the capacity of our models by generating 4.8× the number of protein clusters across CRISPR-Cas families found in nature and tailoring single-guide RNA sequences for Cas9-like effector proteins. Several of the generated gene editors show comparable or improved activity and specificity relative to SpCas9, the prototypical gene editing effector, while being 400 mutations away in sequence. Finally, we demonstrate that an artificial-intelligence-generated gene editor, denoted as OpenCRISPR-1, exhibits compatibility with base editing. We release OpenCRISPR-1 to facilitate broad, ethical use across research and commercial applications.},
}

@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},
doi = {10.1186/s12866-025-04198-8},
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.},
}

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

@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},
doi = {10.1038/s41598-025-13788-5},
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.},
}

*Soil Microbiology
*Soil/chemistry
*Carbon/metabolism
Tibet
*Water/analysis
Carbon Cycle
Archaea/metabolism/genetics
Bacteria/metabolism/genetics
Fungi/metabolism/genetics
Microbiota

@article {pmid40739039,
year = {2025},
author = {Quijada, NM and Cobo-Díaz, JF and Valentino, V and Barcenilla, C and De Filippis, F and Cabrera-Rubio, R and Carlino, N and Pinto, F and Dzieciol, M and Calvete-Torre, I and Sabater, C and Rubino, F and Knobloch, S and Skirnisdottir, S and Ruiz, L and López, M and Prieto, M and Marteinsson, VT and Margolles, A and Segata, N and Cotter, PD and Wagner, M and Ercolini, D and Alvarez-Ordóñez, A},
title = {The food-associated resistome is shaped by processing and production environments.},
journal = {Nature microbiology},
volume = {10},
number = {8},
pages = {1854-1867},
doi = {10.1038/s41564-025-02059-8},
pmid = {40739039},
issn = {2058-5276},
mesh = {Anti-Bacterial Agents/pharmacology ; *Food Microbiology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Food Handling ; *Drug Resistance, Bacterial/genetics ; Animals ; Metagenome ; Vegetables/microbiology ; Humans ; Plasmids/genetics ; Meat/microbiology ; },
abstract = {Food production systems may act as transmission routes for antimicrobial-resistant (AMR) bacteria and AMR genes (AMRGs) to humans. However, the food resistome remains poorly characterized. Here 1,780 raw-material (milk, brine, fresh meat and so on), end-product (cheese, fish, meat products and vegetables) and surface (processing, cooling, smoking, ripening and packing rooms) samples from 113 food processing facilities were subjected to whole-metagenome sequencing. Assembly-free analyses demonstrated that >70% of all known AMRGs, including many predicted to confer resistance to critically important antibiotics, circulate throughout food production chains, with those conferring resistance to tetracyclines, β-lactams, aminoglycosides and macrolides being the most abundant overall. An assembly-based analysis highlighted that bacteria from the ESKAPEE group, together with Staphylococcus equorum and Acinetobacter johnsonii, were the main AMRG carriers. Further evaluation demonstrated that ~40% of the AMRGs were associated with mobile genetic elements, mainly plasmids. These findings will help guide the appropriate use of biocides and other antimicrobials in food production settings when designing efficient antimicrobial stewardship policies.},
}

Anti-Bacterial Agents/pharmacology
*Food Microbiology
*Bacteria/genetics/drug effects/classification/isolation & purification
*Food Handling
*Drug Resistance, Bacterial/genetics
Animals
Metagenome
Vegetables/microbiology
Humans
Plasmids/genetics
Meat/microbiology

@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 = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.5c00551},
pmid = {40738886},
issn = {1535-3907},
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 {pmid40738767,
year = {2025},
author = {Cauwenberghs, E and De Boeck, I and Delanghe, L and Van Rillaer, T and Demuyser, T and Spacova, I and Verhulst, S and Van Hoorenbeeck, K and Lebeer, S},
title = {Shallow metagenomic shotgun sequencing improves detection of pathogenic species in cystic fibrosis respiratory samples.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2025.07.011},
pmid = {40738767},
issn = {1873-5010},
abstract = {BACKGROUND: Chronic infection and inflammation of the lungs contribute significantly to disease progression in persons with cystic fibrosis (pwCF). Treatment regimens are largely based on isolating the putative causative pathogen(s) from respiratory samples using basic culturing methods. While this strategy has shown to be highly valuable in the management of CF, the approach is time-consuming and often misses detection of pathogenic microbes that are more difficult to culture, including Mycobacterium spp.

METHODS: In our proof-of-concept study, we evaluated shallow metagenomic shotgun sequencing to detect potential infection-causing pathogens at species level in sputum, oropharyngeal and salivary samples of pwCF (n = 13), and compared it to culture results from the clinic and standard 16S rRNA V4 amplicon sequencing.

RESULTS: Shallow shotgun sequencing improved the detection of pathogenic species in respiratory samples compared to culture methods. In particular, shallow shotgun sequencing could detect pathogenic species associated with CF, specifically Staphylococcus aureus, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, Haemophilus influenzae and Mycobacterium spp. in sputum, oropharyngeal and/or salivary samples. Notably, Mycobacterium spp. was not detected based on 16S rRNA amplicon sequencing. Moreover, our approach was able to distinguish S. aureus from S. epidermidis and H. influenzae from H. parainfluenzae. This is not possible with 16S amplicon sequencing, but highly valuable in a clinical setting.

CONCLUSIONS: The improved detection of CF pathogens and other critical microbiome members as well as insights into their relative abundance within the community, could provide more knowledge on patient's disease status leading to more personalized medicine and ultimately benefit patient care.},
}

@article {pmid40738407,
year = {2025},
author = {Wang, Y and Huang, Y and Peng, C and Yang, J and Hui, E and Zhou, J and He, Q and Wan, S and Chen, Y and Peng, M},
title = {Synergistic enhancement of acidogenic fermentation of waste activated sludge by combined nitrite and peracetic acid co-treatment: Insight into interfacial interaction, functional potential, oxidative stress and adaptive mechanisms.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122470},
doi = {10.1016/j.envres.2025.122470},
pmid = {40738407},
issn = {1096-0953},
abstract = {Compared to methane, volatile fatty acids (VFAs) offer superior economic benefits. Therefore, the extraction of VFAs from waste activated sludge (WAS) during anaerobic digestion (AD) has garnered significant attention. This study demonstrates that the NO2[-]-PAA combined treatment technology effectively promotes the accumulation of total volatile fatty acids (TVFAs) in the AD system, achieving a maximum VFAs accumulation of 1551.2 ± 6.6 mg COD/L and an acidification rate (ηa) of 47.8 ± 1.9%. Mechanistic study indicates that the reactive oxygen/nitrogen species (ROS/RNS, including CH3C(O)OO·, ·OH, ·O2[-], [1]O2 and NO·) induced by the combined treatment act synergistically to damage cell membranes, augment membrane permeability, disrupt protein structures, and stimulate lipid peroxidation. This significantly weakens the attraction between microorganisms in WAS, providing the first mechanistic explanation of how it overcomes the energy barrier of WAS dispersion under NO2[-]-PAA exposure (extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory). 16S rDNA and metagenomic analyses confirmed that NO2[-]-PAA combined treatment promoted the selective enrichment of hydrolytic-acidogenic bacteria, particularly Petrimonas (27.7%) and Macellibacteroides (17.0%). In addition, the increased abundance of VFAs biosynthesis-related genes and decreased abundance of methanogenic genes contribute to VFAs accumulation. Enhanced regulation of Quorum Sensing (QS) and Two-Component Systems (TCS) gene clusters improved microbial adaptation to NO2[-]-PAA stress. This study elucidated the synergistic effects of NO2[-]-PAA combined treatment on VFAs extraction from the perspectives of interface interactions, functional potential, oxidative stress, and adaptive mechanisms, and provided promising technical solutions for optimizing WAS carbon flux and efficient VFAs recovery.},
}

@article {pmid40738406,
year = {2025},
author = {Xiao, J and He, J and Shen, X and Lei, X and Zhang, H and Li, Y and Sun, C and Shao, Y},
title = {Characterization of the mulberry field antibiotic resistome and mobilome across China.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122471},
doi = {10.1016/j.envres.2025.122471},
pmid = {40738406},
issn = {1096-0953},
abstract = {Antibiotic resistance genes (ARGs) are emerging environmental contaminants that pose increasing risks to ecosystems and human health. However, the distribution and drivers of ARGs associated with woody plants remain underexplored. In this study, we leverage large-scale sampling and metagenomics to provide a comprehensive survey of ARGs in both mulberry (Morus) field soil and rhizosphere across China. Our findings revealed significant regional differences in ARG diversity and composition, exhibiting a distance-decay pattern. The most abundant ARG types identified were multidrug, novobiocin, and macrolide-lincosamide-streptogramin, with the dominant resistance mechanisms being efflux pumps, antibiotic target alteration, and enzymatic inactivation. Structural equation modelling further showed that ARG profiles were primarily influenced by mobile genetic elements (MGEs) and annual mean temperature, with high-risk ARGs increasing significantly. We also observed notable regional and compartmental differences in MGEs, with both richness and abundance being higher in the rhizosphere compared to bulk soil. Moreover, co-occurrence network analysis revealed that ARG-MGE associations in the rhizosphere were stronger and more complex, likely promoting ARG dissemination. Our results not only provide the first overview of ARG profiles in widely planted mulberry but also characterize the factors shaping the antibiotic resistome, paving the way for managing ARG risks in woody plants.},
}

@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},
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 {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 = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.07.005},
pmid = {40738105},
issn = {1934-6069},
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 {pmid40738085,
year = {2025},
author = {Li, J and Wang, D and Zhang, Q and He, X and Liu, P and Ye, L and Ren, H and Zhang, XX},
title = {Prevalence and functional impact of the interactions between lysogenic phages and hosts in activated sludge systems: Insights from large-scale metagenomics and experimental evidence.},
journal = {Water research},
volume = {286},
number = {},
pages = {124270},
doi = {10.1016/j.watres.2025.124270},
pmid = {40738085},
issn = {1879-2448},
abstract = {Bacteriophages are the most common biological entities in the activated sludge (AS) of wastewater treatment plants (WWTPs), playing an important role in maintaining or regulating the microbial community. However, the interactions between bacteria and lysogenic phages in AS systems remain poorly understood. In this study, we reconstructed metagenome-assembled genomes (MAGs) from 43 full-scale WWTPs across five countries and found that over 55 % of MAGs in AS were lysogenic, highlighting the widespread interactions between lysogenic phages and their hosts. Additionally, diverse novel prophages embedded in the lysogenic MAGs formed complex phage-host interactions, as revealed by the phage-host network, underscoring the intricate relationships between prophages and their microbial hosts. Through in-silico approaches and experimental validation, we confirmed the inducibility and activity of the prophages, showing that prophage induction significantly contributes to the lysis of microorganisms involved in the aerobic oxidation of organic matter, as well as nitrogen and phosphorus removal. This work represents a pioneering large-scale genome-centric metagenomic study, coupled with experimental validation, that uncovers the predominance of lysogenic phage-host interactions in AS systems. It advances our understanding of the pivotal role of prophages in shaping the AS microbiome, particularly in influencing the microbial processes responsible for pollutant degradation and nitrogen and phosphorus removal.},
}

@article {pmid40736902,
year = {2025},
author = {Gifford, H and Wilson, D and Rhodes, J and Farrer, RA},
title = {Seaside to Bedside: Assembly in Research for Emerging Human Fungal Pathogen Candida auris.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2955},
number = {},
pages = {263-291},
pmid = {40736902},
issn = {1940-6029},
mesh = {Humans ; *Candidiasis/microbiology/diagnosis ; *Candida auris/genetics/pathogenicity ; Animals ; Computational Biology/methods ; Host-Pathogen Interactions ; *Candida/genetics ; },
abstract = {Discovery science in Medical Mycology requires a range of tools, from optimized experimental models to near-patient clinical applications, with the common goal of reducing morbidity and mortality from fungal diseases. Assembly tools underpin bioinformatic discovery across this spectrum of research, setting the scene for genomic enquiry, and promising an unprecedented wave of breakthrough in mechanistic understanding of pathobiology that could unearth critical diagnostic and treatment advances. This chapter examines the investigation of Candida auris, an emerging human fungal pathogen, in the context of clinic detection and treatment of infection. In the laboratory, we cover the use of the Arabian Killifish (AK) as a non-model organism to understand transcriptional responses to both host and pathogen during infection.},
}

Humans
*Candidiasis/microbiology/diagnosis
*Candida auris/genetics/pathogenicity
Animals
Computational Biology/methods
Host-Pathogen Interactions
*Candida/genetics

@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.},
}

*Metagenomics/methods
*Environmental Monitoring/methods
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Computational Biology/methods
Gene Library

@article {pmid40736891,
year = {2025},
author = {Garg, S},
title = {Methods for Chromosome-Scale Haplotype Reconstruction.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2955},
number = {},
pages = {17-36},
doi = {10.1007/978-1-0716-4702-8_2},
pmid = {40736891},
issn = {1940-6029},
mesh = {*Haplotypes ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Computational Biology/methods ; *Chromosomes/genetics ; Sequence Analysis, DNA/methods ; Animals ; },
abstract = {Haplotypes are combinations of alleles inherited together on a chromosome. Traditional short-read sequencing methods can identify genotypes but often fail to capture detailed haplotype information, such as allele colocalization or parental origin. Third-generation sequencing technologies, including long-read and long-range methods, offer higher resolution, enabling more accurate haplotype reconstruction in diploid, polyploid, and metagenomic contexts. To achieve this, advanced computational strategies are needed to reconstruct haplotypes from sequencing data. This chapter explores the evolution of sequencing and computational approaches for integrating various sequencing methods to produce chromosome-scale haplotypes, while addressing the challenges and prospects for scaling haplotype analysis across species. Comprehensive haplotype analysis has great potential for enhancing our understanding of complex genetic variations and their roles in diseases.},
}

*Haplotypes
Humans
*High-Throughput Nucleotide Sequencing/methods
*Computational Biology/methods
*Chromosomes/genetics
Sequence Analysis, DNA/methods
Animals

@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},
doi = {10.1167/iovs.66.9.71},
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.},
}

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

@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 = {},
number = {},
pages = {},
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/ ; },
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 {pmid40735404,
year = {2025},
author = {Meng, D and Wang, P and Zhang, S and Chen, Z and Lai, C and Yi, X and Huang, X and Yu, H and Zhang, M and Gao, X},
title = {Exploring the Prevention of Lipid Deposition Caused by High-Fat Diet and Its Mechanism of Action of Rosa roxburghii Fermented Juice Based on Liver Metabolomics and Gut Microbiota.},
journal = {Food science & nutrition},
volume = {13},
number = {8},
pages = {e70449},
pmid = {40735404},
issn = {2048-7177},
abstract = {Hyperlipidemia has become a prevalent disease in the global epidemic, posing a threat to human health. This study aims to investigate the mechanism by which Rosa roxburghii fermented juice (RRFJ) can prevent lipid deposition induced by a high-fat diet in mice. The results showed that mice in the RRFJ intervention group had significantly reduced body weight as well as lower levels of serum and liver lipid indicators compared to the high-fat diet group. Metagenomic analysis revealed that the RRFJ intervention reversed the decrease in intestinal flora Alistipes and Colidextribacter genes in mice fed a high-fat diet. Liver metabolomics showed that the RRFJ prevented liver dyslipidemia by modulating the biosynthesis of phenylalanine, tyrosine, tryptophan, and phenylalanine metabolism. RRFJ is effective in preventing dyslipidemia through the 'gut-liver axis', which regulates the imbalance of intestinal flora and improves hepatic metabolic profiles. This provides a new intervention strategy for the prevention and treatment of hyperlipidemia.},
}

@article {pmid40733600,
year = {2025},
author = {Debat, H and Bejerman, N},
title = {An Update on RNA Virus Discovery: Current Challenges and Future Perspectives.},
journal = {Viruses},
volume = {17},
number = {7},
pages = {},
pmid = {40733600},
issn = {1999-4915},
mesh = {*RNA Viruses/genetics/isolation & purification/classification ; Humans ; Animals ; *RNA Virus Infections/virology/transmission/epidemiology ; Communicable Diseases, Emerging/virology ; Zoonoses/virology ; Public Health ; },
abstract = {The relentless emergence of RNA viruses poses a perpetual threat to global public health, necessitating continuous efforts in surveillance, discovery, and understanding of these pathogens. This review provides a comprehensive update on recent advancements in RNA virus discovery, highlighting breakthroughs in technology and methodologies that have significantly enhanced our ability to identify novel viruses across diverse host organisms. We explore the expanding landscape of viral diversity, emphasizing the discovery of previously unknown viral families and the role of zoonotic transmissions in shaping the viral ecosystem. Additionally, we discuss the potential implications of RNA virus discovery on disease emergence and pandemic preparedness. Despite remarkable progress, current challenges in sample collection, data interpretation, and the characterization of newly identified viruses persist. Our ability to anticipate and respond to emerging respiratory threats relies on virus discovery as a cornerstone for understanding RNA virus evolution. We address these challenges and propose future directions for research, emphasizing the integration of multi-omic approaches, advanced computational tools, and international collaboration to overcome barriers in the field. This comprehensive overview aims to guide researchers, policymakers, and public health professionals in navigating the intricate landscape of RNA virus discovery, fostering a proactive and collaborative approach to anticipate and mitigate emerging viral threats.},
}

*RNA Viruses/genetics/isolation & purification/classification
Humans
Animals
*RNA Virus Infections/virology/transmission/epidemiology
Communicable Diseases, Emerging/virology
Zoonoses/virology
Public Health

@article {pmid40733506,
year = {2025},
author = {Tóth, F and Pankovics, P and Urbán, P and Herczeg, R and Albert, E and Reuter, G and Boros, Á},
title = {Genomic Characterization and Molecular Epidemiology of Tusaviruses and Related Novel Protoparvoviruses (Family Parvoviridae) from Ruminant Species (Bovine, Ovine and Caprine) in Hungary.},
journal = {Viruses},
volume = {17},
number = {7},
pages = {},
pmid = {40733506},
issn = {1999-4915},
support = {PTE ÁOK-KA No:2025/09//University of Pécs Medical School/ ; },
mesh = {Animals ; Cattle ; Phylogeny ; Sheep/virology ; Goats/virology ; *Genome, Viral ; *Parvoviridae Infections/epidemiology/veterinary/virology ; Hungary/epidemiology ; Molecular Epidemiology ; *Sheep Diseases/virology/epidemiology ; Ruminants/virology ; *Cattle Diseases/virology/epidemiology ; Feces/virology ; Genomics ; *Parvoviridae/genetics/classification/isolation & purification ; *Goat Diseases/virology/epidemiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {Tusavirus 1 of species Protoparvovirus incertum 1 (family Parvoviridae) was first identified in humans and later in small ruminants (caprine and ovine). This study reports the full-length coding sequences (~4400-4600 nt) of three novel tusavirus-related protoparvoviruses from ovine ("misavirus", PV540792), for the first time bovine ("sisavirus", PV540793) and subsequently from caprine ("gisavirus" PV540850/51) fecal samples, using next-generation sequencing (NGS) and PCR techniques. Their NS1, VP1 and VP2 proteins shared 61-63% amino acid identities with each other and with tusaviruses, suggesting these three viruses belong to three novel species in the genus Protoparvovirus. Phylogenetic analyses placed them with tusaviruses on a separate main branch, implying a shared origin among these most likely ruminant protoparvoviruses. A small-scale epidemiological investigation on 318 ruminant enteric samples using novel generic NS1 primers found misavirus in 14/51 (27.5%) ovine and sisavirus in 19/203 (9.4%) bovine samples from multiple Hungarian farms. Tusavirus was present in 5/51 (9.8%) ovine and 15/62 (24.2%) caprine samples, all from one farm. The highest prevalences for all three viruses were found in animals aged 2-12 months, though sporadic cases were also found in other age groups. Partial NS and VP sequence-based phylogenetic trees showed virus-specific lineages for misa-, sisa-, gisa- and tusaviruses, with various strains forming sub-lineages. These findings suggest the presence of multiple genotypes and/or members of additional species, which was supported by a VP sequence-based hierarchical cluster analysis. The study's viruses were mostly phylogenetically separated by host; however, two bovine sisavirus strains with diverse phylogenetic localizations in the NS (belonging to bovine sisaviruses) and VP1 trees (distantly related to ovine misaviruses) could indicate previous (interspecies?) recombination events.},
}

Animals
Cattle
Phylogeny
Sheep/virology
Goats/virology
*Genome, Viral
*Parvoviridae Infections/epidemiology/veterinary/virology
Hungary/epidemiology
Molecular Epidemiology
*Sheep Diseases/virology/epidemiology
Ruminants/virology
*Cattle Diseases/virology/epidemiology
Feces/virology
Genomics
*Parvoviridae/genetics/classification/isolation & purification
*Goat Diseases/virology/epidemiology
High-Throughput Nucleotide Sequencing

@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.},
}

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

@article {pmid40732703,
year = {2025},
author = {Chen, Y and Fu, H and Zhu, Q and Ren, Y and Liu, J and Wu, Y and Xu, J},
title = {Clinical Features of Pulmonary Nocardiosis and Diagnostic Value of Metagenomic Next-Generation Sequencing: A Retrospective Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
pmid = {40732703},
issn = {2076-0817},
support = {76080151//the Pfizer Global Medical Grants/ ; },
mesh = {Humans ; *Nocardia Infections/diagnosis/microbiology/drug therapy ; Retrospective Studies ; Male ; Female ; Middle Aged ; *Nocardia/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; *Metagenomics/methods ; Adult ; Anti-Bacterial Agents/therapeutic use ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; Coinfection/microbiology/diagnosis ; },
abstract = {Pulmonary nocardiosis (PN) is a rare, opportunistic, and potentially life-threatening infection, especially in disseminated cases. This retrospective study aimed to characterize the clinical features of PN and assess the diagnostic utility of metagenomic next-generation sequencing (mNGS). We reviewed data from 19 patients diagnosed with PN between September 2019 and August 2022, including 3 with disseminated disease. Common symptoms included fever, cough, and sputum production, while chest imaging frequently revealed nodules, consolidations, exudates, cavities, and pleural effusions. The sensitivity of mNGS for detecting Nocardia was significantly higher than that of culture (100% vs. 36.84%, p < 0.001). mNGS successfully identified Nocardia species and co-infected pathogens. The most common species was Nocardia farcinica. Four PN cases were co-infected with Rhizomucor pusillus, Cryptococcus neoformans, Lichtheimia ramosa, and Aspergillus spp. Eighteen patients (94.7%) received trimethoprim-sulfamethoxazole (TMP-SMZ). Sixteen cases (84.2%) were improved or cured. Misdiagnosis is common due to the nonspecificity of clinical and imaging presentations of pulmonary nocardiosis. The timely combination of mNGS represents a promising approach to enhance the diagnosis of pulmonary nocardiosis and inform targeted antimicrobial therapy. TMP-SMZ is the first line of treatment.},
}

Humans
*Nocardia Infections/diagnosis/microbiology/drug therapy
Retrospective Studies
Male
Female
Middle Aged
*Nocardia/genetics/isolation & purification
*High-Throughput Nucleotide Sequencing/methods
Aged
*Metagenomics/methods
Adult
Anti-Bacterial Agents/therapeutic use
Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use
Coinfection/microbiology/diagnosis

@article {pmid40732219,
year = {2025},
author = {Hu, W and Zhou, X and Liu, Y and Zhang, Y and Wang, Y},
title = {Effects of Salinity Fluctuation on Antimicrobial Resistance and Virulence Factor Genes of Low and High Nucleic Acid-Content Bacteria in a Marine Environment.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071710},
pmid = {40732219},
issn = {2076-2607},
support = {252102320216//Henan Province Science and Technology Research Project/ ; },
abstract = {Salinity, as one of the critical environmental factors in marine ecosystems, has complex and wide-ranging biological effects. However, the effects of salinity fluctuation on antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the marine environment are not well understood. In this study, metagenomic sequencing analysis was used to reveal the response of ARGs and VFGs, hosted by low and high nucleic acid-content bacteria (HNA and LNA bacteria), to salinity, as it decreased from 26‱ to 16‱. The results showed that a total of 27 ARG types and 13 VFG types in HNA and LNA bacteria were found. Salinity changes had significant effects on the ARGs' and VFGs' composition and their hosts' composition. In the network topology relationship, the complexity of the network between the ARGs and their host as well as the VFGs and their host differed with the decrease in salinity. The abundance of most genera of HNA and LNA bacteria was significantly corrected with the abundance of ARGs and VFGs, respectively. Overall, this study demonstrates the effects of salinity on ARGs and VFGs hosted by HNA and LNA bacteria in the marine environment and suggests the importance of salinity in regulating HNA and LNA bacterial communities and functions.},
}

@article {pmid40732185,
year = {2025},
author = {Yaguchi, E and Komiyama, Y and Inami, S and Shibasaki, I and Shintani, T and Shiraishi, R and Hyodo, T and Shiba, H and Hamaguchi, S and Fukuda, H and Toyoda, S and Fukumoto, C and Izumi, S and Wakui, T and Kawamata, H},
title = {Oral Dysbiosis Is Associated with the Pathogenesis of Aortic Valve Diseases.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071677},
pmid = {40732185},
issn = {2076-2607},
abstract = {The involvement of oral bacteria in the pathogenesis of distant organs, such as the heart, lungs, brain, liver, and intestine, has been shown. We analyzed the distribution of bacterial species in the resected aortic valve by 16S rRNA metagenomic analysis and directly compared their gene sequences with those in the oral cavity. Thirty-two patients with aortic stenosis or aortic regurgitation who underwent aortic valve replacement were enrolled in this study. Antibody titer against periodontal pathogenic bacteria in the patient's serum was analyzed. The genetic background and distribution of bacterial species on subgingival plaque, the dorsal surface of the tongue, and the resected aortic valve were analyzed. Patients with aortic valve disease were shown to have more severe periodontal disease by the detection of antibodies against Socransky's red-complex bacteria of periodontitis. Bacterial DNA was detected in the aortic valves of 12 out of 32 patients. The genomic sequences of the V3-V4 region of the 16S rRNA in some bacteria isolated from the aortic valves of six patients who underwent metagenomic analysis were identical to those found in the oral cavity. The findings indicate that bacteria detected in the aortic valve may be introduced through oral dysbiosis, a condition characterized by an imbalance in the oral microbiota that increases the risk of periodontal disease and dental caries. Oral dysbiosis and the resulting potential bacteremia are associated with the pathogenesis of aortic valve diseases.},
}

@article {pmid40732173,
year = {2025},
author = {Harahap, AFP and Treinen, C and Zyl, LJV and Williams, WT and Conrad, J and Pfannstiel, J and Klaiber, I and Grether, J and Hiller, E and Vahidinasab, M and Perino, EHB and Lilge, L and Burger, A and Trindade, M and Hausmann, R},
title = {Glucoselipid Biosurfactant Biosynthesis Operon of Rouxiella badensis DSM 100043[T]: Screening, Identification, and Heterologous Expression in Escherichia coli.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071664},
pmid = {40732173},
issn = {2076-2607},
support = {01DG17018//German Federal Ministry of Education and Research/ ; UID105876//South African National Research Foundation/ ; 57552340//German Academic Exchange Service (DAAD)/ ; 317898569//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Rouxiella badensis DSM 100043[T] had been previously proven to produce a novel glucoselipid biosurfactant which has a very low critical micelle concentration (CMC) as well as very good stability against a wide range of pH, temperature, and salinity. In this study, we performed a function-based library screening from a R. badensis DSM 100043[T] genome library to identify responsible genes for biosynthesis of this glucoselipid. The identified open reading frames (ORFs) were cloned into several constructs in Escherichia coli for gene permutation analysis and the individual products were analyzed using high-performance thin-layer chromatography (HPTLC). Products of interest from positive expression strains were purified and analyzed by liquid chromatography/electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) and nuclear magnetic resonance (NMR) for further structure elucidation. Function-based screening of 5400 clones led to the identification of an operon containing three ORFs encoding acetyltransferase GlcA (ORF1), acyltransferase GlcB (ORF2), and phosphatase/HAD GlcC (ORF3). E. coli pCAT2, with all three ORFs, resulted in the production of identical R. badensis DSM 100043[T] glucosedilipid with Glu-C10:0-C12:1 as the main congener. ORF2-deletion strain E. coli pAFP1 primarily produced glucosemonolipids, with Glu-C10:0,3OH and Glu-C12:0 as the major congeners, predominantly esterified at the C-2 position of the glucose moiety. Furthermore, fed-batch bioreactor cultivation of E. coli pCAT2 using glucose as the carbon source yielded a maximum glucosedilipid titer of 2.34 g/L after 25 h of fermentation, which is 55-fold higher than that produced by batch cultivation of R. badensis DSM 100043[T] in the previous study.},
}

@article {pmid40732167,
year = {2025},
author = {He, W and Wang, X and Cao, Y and Liu, C and Qin, Z and Zuo, Y and Li, Y and Tang, F and Dai, J and Wang, S and Xue, F},
title = {Effects of Antibiotic Residues on Fecal Microbiota Composition and Antimicrobial Resistance Gene Profiles in Cattle from Northwestern China.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071658},
pmid = {40732167},
issn = {2076-2607},
support = {2023YFF0611501//National Key Research and Development Program of China/ ; },
abstract = {Grazing is a free-range farming model commonly practiced in low-external-input agricultural systems. The widespread use of veterinary antibiotics in livestock farming has led to significant environmental accumulation of antibiotic residues and antibiotic resistance genes (ARGs), posing global health risks. This study investigated the antibiotic residues, bacterial community, ARG profiles, and mobile genetic elements (MGEs) in cattle feces from three provinces in western China (Ningxia, Xinjiang, and Inner Mongolia) under grazing modes. The HPLC-MS detection showed that the concentration of tetracycline antibiotics was the highest in all three provinces. Correlation analysis revealed a significant negative correlation between antibiotic residues and the diversity and population abundance of intestinal microbiota. However, the abundance of ARGs was directly proportional to antibiotic residues. Then, the Sankey analysis revealed that the ARGs in the cattle fecal samples were concentrated in 15 human pathogenic bacteria (HPB) species, with 9 of these species harboring multiple drug resistance genes. Metagenomic sequencing revealed that carbapenemase-resistant genes (blaKPC and blaVIM) were also present in considerable abundance, accounting for about 10% of the total ARGs detected in three provinces. Notably, Klebsiella pneumoniae strains carrying blaCTX-M-55 were detected, which had a possibility of IncFII plasmids harboring transposons and IS19, indicating the risk of horizontal transfer of ARGs. This study significantly advances the understanding of the impact of antibiotic residues on the fecal microbiota composition and ARG profiles in grazing cattle from northwestern China. Furthermore, it provides critical insights for the development of rational antibiotic usage strategies and comprehensive public health risk assessments.},
}

@article {pmid40732166,
year = {2025},
author = {Deng, L and Xu, J and Xue, Q and Wei, Y and Wang, J},
title = {Healthy Ageing and Gut Microbiota: A Study on Longevity in Adults.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071657},
pmid = {40732166},
issn = {2076-2607},
support = {2020//National Project of Multidisciplinary Management of Major Diseases/ ; JKCJ202303//International Institute of Population Health, Peking University Health Science Center/ ; },
abstract = {Many studies have focused on ageing and gut microbiota, but the correlation between gut microbiota and physical function in older adults, especially those with longevity, remains obscure and deserves further exploration. In this study we investigated changes in the gut microbiota and the association between gut microbiota and physical function in adults with longevity. This is a prospective observational study. Fifty-one older adults aged ≥ 60 years (including 27 participants aged 90 years and above) were enrolled. Information on clinical data, physical function including intrinsic capacity by Integrated Care for Older People (ICOPE) tool, and dietary habits of participants was collected and analysed. Gut microbiota structure and functional pathways were analysed by Metagenomics. Intrinsic capacity (measured as ICOPE scores) of adults' longevity (aged 90-98, longe group) was significantly lower than older adults aged 60-89 years (CON group) (5.44 ± 2.15 vs. 6.71 ± 1.46, p = 0.017). Gut microbiota of the longe group is enriched in Akkermansia and Bifidobacterium, which may be beneficial to health. Gut microbiota was closely related to daily milk (including plain milk, flavoured milk with a content of cow's milk or reconstituted milk of ≥80%, or reconstituted milk or fermented milk with a content of cow's milk or milk powder of ≥80%) consumption, anxiety, and physical function including grip strength by the Short Physical Performance Battery (SPPB). Bacteroides plebeius and Bacteroides eggerthii were increased in long-living adults with better physical function. Escherichia coli was more abundant in frail young-old adults. Grip strength is positively correlated with the abundance of Roseburia hominis, Eubacterium rectale, Eubacterium eligens, and Roseburia intestinalis (p < 0.05). Pathways related to amino acid synthesis that include L-isoleucine, L-valine, and L-threonine were over-presented in long-living adults of better physical function. Adults with longevity showed comparable gut microbiota abundance to younger elderly individuals. The gut microbiota of long-living adults showed higher abundance of potentially beneficial bacteria, and the altered bacteria are closely associated with physical function. Changes in the gut microbiota may precede clinical indicators during the process of ageing. Gut microbiota may be a potential biomarker for longevity and healthy ageing. Nutrition and emotional state can be important influencing factors.},
}

@article {pmid40732140,
year = {2025},
author = {Madney, Y and Mahfouz, S and Bayoumi, A and Hassanain, O and Hassanain, O and Sayed, AA and Jalal, D and Lotfi, M and Tolba, M and Ziad, GA and Elanany, M and Hashem, M and Taha, G and Shalaby, L and Elhaddad, A},
title = {Carbapenem-Resistant Enterobacteriaceae (CRE) in Children with Cancer: The Impact of Rapid Diagnostics and Targeted Colonization Strategies on Improving Outcomes.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071627},
pmid = {40732140},
issn = {2076-2607},
support = {54699605//Pfizer Global Medical Grants/ ; },
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) pose an emerging threat, with a high mortality rate among children with cancer. This study aimed to evaluate the impact of routine rectal swab surveillance and rapid PCR-based detection of carbapenemase genes to facilitate the early initiation of appropriate treatment and assess its effects on outcomes. The study compared two groups of pediatric cancer patients with CRE bloodstream infections: a retrospective cohort of 254 patients from 2013 to 2017, and a prospective cohort of 186 patients from 2020 to 2022, following the implementation of these tools. A rapid diagnostic test in the prospective cohort resulted in the early initiation of proper antibiotics in 85% (165/186) of patients, compared to only 58% (147/254) in the retrospective group. This led to a decrease in the need for ICU admission related to sepsis from CRE and a significant reduction in the 30-day mortality rate (16% vs. 30%, p ≤ 0.01). Genotypic profiling revealed that class B carbapenemases were the most prevalent (69%), with the NDM type being identified in 67% of patients. OXA-48 and KPC enzymes were detected in 59% and 4% of patients, respectively. Multivariate analysis revealed that patients having Klebsiella pneumoniae, NDM genotype carbapenemases, presence of pneumonia, and septic shock requiring ICU admission were predictors of poor outcomes. Rapid diagnostics and targeted colonization lead to the appropriate use of targeted antibiotics, resulting in improved patient outcomes. Understanding carbapenemase-producing microorganisms and administering newer antibiotics may further reduce mortality and enhance treatment strategies for high-risk patients.},
}

@article {pmid40732132,
year = {2025},
author = {Thomas-White, K and Olmschenk, G and Lyttle, D and Markowitz, R and Navarro, P and McLean, K},
title = {Remote BV Management via Metagenomic Vaginal Microbiome Testing and Telemedicine.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071623},
pmid = {40732132},
issn = {2076-2607},
abstract = {Bacterial vaginosis (BV) affects 30% of women annually, but many face barriers to in-person care. Here we present real-world outcomes of remote BV diagnosis and management through self-collected vaginal microbiome (VMB) testing and telemedicine visits, focusing on symptom resolution, recurrence, and overall microbial shifts. Among the 1159 study participants, 75.5% experienced symptom resolution at four weeks when managed with our algorithm-guided treatment protocol. At a median follow-up of 4.4 months after the initial visit, 30.0% of patients experienced recurrent BV, which is lower than the typical recurrence rates seen in historical in-person cohorts. Across the entire cohort, metagenomic data demonstrated a significant increase in Lactobacillus abundance (mean of 32.9% to 48.4%, p < 0.0001) and a corresponding decrease in BV-associated taxa such as Gardnerella, Prevotella, and Fannyhessea. A PERMANOVA of pairwise Bray-Curtis distances showed significant separation between pre-and post-treatment samples (pseudo-F = 37.6, p < 0.0001), driven by an increase in Lactobacillus-dominated samples. Treatment adherence was high (a total of 78% reported perfect or near-perfect adherence), and adverse events were generally mild (in total, 22% reported vaginal irritation, and 13% reported abnormal discharge). These results demonstrate that Evvy's at-home metagenomic platform, paired with telemedicine and a smart treatment algorithm, delivers robust clinical and microbial outcomes. This work offers a novel approach to managing bacterial vaginosis, a challenging condition characterized by persistently high recurrence rates.},
}

@article {pmid40732125,
year = {2025},
author = {Feng, W and Gao, C and Cui, X and Yang, B and He, K and Huang, Q and Yang, X and Wen, K and Xie, J and Yang, Z and Zhu, L},
title = {Metagenome Analysis Reveals Changes in Gut Microbial Antibiotic Resistance Genes and Virulence Factors in Reintroduced Giant Pandas.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071616},
pmid = {40732125},
issn = {2076-2607},
support = {U21A20193//National Natural Science Foundation of China/ ; 32270546//National Natural Science Foundation of China/ ; },
abstract = {Antibiotic resistance has emerged as a critical global public health challenge. In this study, we employed metagenomic sequencing to analyze fecal samples from giant pandas (Ailuropoda melanoleuca) across three distinct stages-semi-wild, released, and wild populations-to investigate shifts in antibiotic resistance genes (ARGs) and virulence factors (VFs) during the reintroduction process. Our findings revealed significant variations in the composition of ARG and VF across different stages, with released and wild giant pandas exhibiting similar ARG and VF profiles. Further analyses identified that the increased abundance of ARGs and VFs in both released and wild individuals compared to semi-wild individuals was mainly from Pseudomonas. We hypothesized that the same geographic environment in which ARGs and VFs are transmitted between a host and the environment via mobile genetic elements (MGEs) may be responsible for the similar structure of ARGs and VFs in released and wild giant pandas. Additionally, diet may modulate the gut microbial community, thereby influencing the distributions of ARG and VF. This study elucidated the impact of geographic and dietary factors on ARGs and VFs dynamics in giant pandas, offering valuable insights for mitigating antibiotic resistance and virulence gene dissemination.},
}

@article {pmid40732124,
year = {2025},
author = {Tom, A and Yellapu, NK and Rahi, M and Saini, P},
title = {Metagenomic Analyses of Gut Bacteria of Two Sandfly Species from Western Ghats, India, Differing in Their Vector Competence for Leishmaniasis.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071615},
pmid = {40732124},
issn = {2076-2607},
abstract = {Phlebotomine sandflies are the primary vectors of Leishmania parasites, the causative agents of leishmaniasis. In India, Phlebotomus argentipes is the confirmed vector of Leishmania donovani. The sandfly gut microbiota plays a crucial role in Leishmania development and transmission, yet it remains largely understudied. This study used a metagenomic approach targeting the V3-V4 region of the 16S rRNA gene to compare the gut bacterial communities of P. argentipes and Sergentomyia babu prevalent in Kerala. A total of 18 distinct bacterial phyla were identified in P. argentipes, and 14 in S. babu, both dominated by Proteobacteria, Actinobacteria, and Firmicutes. A total of 315 genera were identified in P. argentipes, with a high relative abundance of Pseudomonas (6.3%), whereas S. babu harbored 327 genera, with Pseudomonas showing a higher relative abundance of 11%. Unique to P. argentipes, bacterial phyla such as Fusobacteria, Armatimonadetes, Elusimicrobia, Chlamydiae, and Crenarchaeota were identified, whereas Chlorobi was specific to S. babu. Additionally, 145 species were identified in P. argentipes, compared to 164 species in S. babu. These findings provide a comparative baseline of gut microbial diversity between vector and non-vector sandfly species, offering a foundation for future functional investigations into vector competence.},
}

@article {pmid40732102,
year = {2025},
author = {Liu, Y and Ren, J and Yu, B and Liu, S and Cao, X},
title = {Metagenomic and Metabolomic Perspectives on the Drought Tolerance of Broomcorn Millet (Panicum miliaceum L.).},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071593},
pmid = {40732102},
issn = {2076-2607},
support = {YDZJSX2022A044//the Central Guiding Local Science and Technology Development Funds/ ; CARS-06-14.5-A16//the earmarked fund for CARS/ ; 2025CYJSTX03-23//the earmarked fund for Modern Agro-Industry Technology Research System/ ; },
abstract = {Drought stress is an important abiotic stress factor restricting crop production. Broomcorn millet (Panicum miliaceum L.) has become an ideal material for analyzing the stress adaptation mechanisms of crops due to its strong stress resistance. However, the functional characteristics of its rhizosphere microorganisms in response to drought remain unclear. In this study, metagenomics and metabolomics techniques were employed to systematically analyze the compositional characteristics of the microbial community, functional properties, and changes in metabolites in the rhizosphere soil of broomcorn millet under drought stress. On this basis, an analysis was conducted in combination with the differences in functional pathways. The results showed that the drought treatment during the flowering stage significantly altered the species composition of the rhizosphere microorganisms of broomcorn millet. Among them, the relative abundances of beneficial microorganisms such as Nitrosospira, Coniochaeta, Diversispora, Gigaspora, Glomus, and Rhizophagus increased significantly. Drought stress significantly affects the metabolic pathways of rhizosphere microorganisms. The relative abundances of genes associated with prokaryotes, glycolysis/gluconeogenesis, and other metabolic process (e.g., ribosome biosynthesis, amino sugar and nucleotide sugar metabolism, and fructose and mannose metabolism) increased significantly. Additionally, the expression levels of functional genes involved in the phosphorus cycle were markedly upregulated. Drought stress also significantly alters the content of specific rhizosphere soil metabolites (e.g., trehalose, proline). Under drought conditions, broomcorn millet may stabilize the rhizosphere microbial community by inducing its restructuring and recruiting beneficial fungal groups. These community-level changes can enhance element cycling efficiency, optimize symbiotic interactions between broomcorn millet and rhizosphere microorganisms, and ultimately improve the crop's drought adaptability. Furthermore, the soil metabolome (e.g., trehalose and proline) functions as a pivotal interfacial mediator, orchestrating the interaction network between broomcorn millet and rhizosphere microorganisms, thereby enhancing plant stress tolerance. This study sheds new light on the functional traits of rhizosphere microbiota under drought stress and their mechanistic interactions with host plants.},
}

@article {pmid40732101,
year = {2025},
author = {Elbehiry, A and Marzouk, E and Abalkhail, A and Edrees, HM and Ellethy, AT and Almuzaini, AM and Ibrahem, M and Almujaidel, A and Alzaben, F and Alqrni, A and Abu-Okail, A},
title = {Microbial Food Safety and Antimicrobial Resistance in Foods: A Dual Threat to Public Health.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071592},
pmid = {40732101},
issn = {2076-2607},
abstract = {The intersection of microbial food safety and antimicrobial resistance (AMR) represents a mounting global threat with profound implications for public health, food safety, and sustainable development. This review explores the complex pathways through which foodborne pathogens-such as Salmonella spp., Escherichia coli (E. coli), Listeria monocytogenes (L. monocytogenes), and Campylobacter spp.-acquire and disseminate resistance within human, animal, and environmental ecosystems. Emphasizing a One Health framework, we examine the drivers of AMR across sectors, including the misuse of antibiotics in agriculture, aquaculture, and clinical settings, and assess the role of environmental reservoirs in sustaining and amplifying resistance genes. We further discuss the evolution of surveillance systems, regulatory policies, and antimicrobial stewardship programs (ASPs) designed to mitigate resistance across the food chain. Innovations in next-generation sequencing, metagenomics, and targeted therapeutics such as bacteriophage therapy, antimicrobial peptides (AMPs), and CRISPR-based interventions offer promising alternatives to conventional antibiotics. However, the translation of these advances into practice remains uneven, particularly in low- and middle-income countries (LMICs) facing significant barriers to diagnostic access, laboratory capacity, and equitable treatment availability. Our analysis underscores the urgent need for integrated, cross-sectoral action-anchored in science, policy, and education-to curb the global spread of AMR. Strengthening surveillance, investing in research, promoting responsible antimicrobial use, and fostering global collaboration are essential to preserving the efficacy of existing treatments and ensuring the microbiological safety of food systems worldwide.},
}

@article {pmid40732100,
year = {2025},
author = {Mourão, AV and Fernandes, D and de Sousa, T and Calouro, R and Saraiva, S and Igrejas, G and Poeta, P},
title = {Aquatic Resistome in Freshwater and Marine Environments: Interactions Between Commensal and Pathogenic in the Context of Aquaculture and One Health.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071591},
pmid = {40732100},
issn = {2076-2607},
support = {UI/00772//Fundacao para a Ciencia e a Tecnologia/ ; LA/P/0059/2020//Fundacao para a Ciencia e a Tecnologia/ ; },
abstract = {Aquatic resistomes are important reservoirs of antibiotic resistance genes (ARGs) and their precursors, which can proliferate and dissipate in pathogenic microorganisms that affect humans and animals, especially due to anthropogenic pressures such as the intensive use of antibiotics in aquaculture, often without effective regulation. This review addresses the mechanisms of horizontal gene transfer (HGT) in the dissemination of ARGs through mobile genetic elements (MGEs). In freshwater, genera such as Aeromonas, Pseudomonas and Microcystis stand out as vectors of ARGs. In the context of One Health, it is essential to implement sound public policies and strict regulations on the use of antibiotics in aquaculture, and the use of monitoring tools such as environmental DNA (eDNA) and metagenomics allows for the early detection of ARGs, contributing to the protection of human, animal and environmental health.},
}

@article {pmid40732084,
year = {2025},
author = {Ning, Z and Liang, J and Ti, J and Zhang, M and Cai, C},
title = {Enhanced Natural Attenuation of Gasoline Contaminants in Groundwater: Applications and Challenges of Nitrate-Stimulating Substances.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071575},
pmid = {40732084},
issn = {2076-2607},
support = {42330714//National Natural Science Foundation of China/ ; 242S4201Z//the S&T Program of Hebei/ ; 322074//Sinopec Science Department Project/ ; },
abstract = {Nitrate is a promising enhanced natural attenuation (ENA) material that enhances the microbial degradation of petroleum hydrocarbons by acting as an electron acceptor and nitrogen source. This study evaluated nitrate-containing materials (yeast extract, compound nitrogen fertilizer, and nitrate solutions) in microcosm experiments using gasoline-contaminated aquifer soils. Chemical analysis revealed that yeast extract achieved the highest degradation rate (34.33 mg/(kg·d)), reducing 600 mg/kg of petroleum hydrocarbons to undetectable levels within 18 days. Nitrate materials significantly increased nitrate-reducing activity and upregulated both aerobic/anaerobic hydrocarbon degradation genes, expanding microbial degradation potential. Metagenomic analysis identified Pseudomonas and Achromobacter as dominant genera across treatments, suggesting their critical roles in biodegradation. These findings demonstrate that nitrate-enhanced strategies effectively accelerate hydrocarbon attenuation under facultative anaerobic conditions, offering practical ENA solutions for petroleum-polluted sites.},
}

@article {pmid40732069,
year = {2025},
author = {Mushtaq, M and Ni, X and Khan, M and Zhao, X and Yang, H and Danzeng, B and Ali, S and Zafar, MH and Quan, G},
title = {Dietary Protein-Induced Changes in Archaeal Compositional Dynamics, Methanogenic Pathways, and Antimicrobial Resistance Profiles in Lactating Sheep.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071560},
pmid = {40732069},
issn = {2076-2607},
support = {CARS-39-08//The earmarked fund for the China Agriculture Research System/ ; 202403AP140017//Yunnan International Joint Laboratory of Conservation and Innovative Utilization of Sheep Germplasm Re sources/ ; },
abstract = {Dietary protein levels greatly influence gut microbial ecosystems; however, their effects on gut archaea and associated functions in ruminants require further elucidation. This study evaluated the impact of varying dietary protein levels on gut archaeal composition, antimicrobial resistance (AMR) genes, virulence factors, and functional capacities in sheep. Eighteen ewes (Yunnan semi-fine wool breed, uniparous, 2 years old, and averaging 50 ± 2 kg body weight) were randomly assigned to diets containing an 8.5 (low; H_1), 10.3 (medium; H_m), or 13.9% (high; H_h) crude protein level from the 35th day of pregnancy to the 90th day postpartum. The total duration of the experiment was approximately 202 days. A total of nine fecal samples (three from each group) were analyzed via 16S rRNA and metagenomics sequencing. Higher archaeal alpha diversity and richness were observed in the H_m and H_h groups compared to the H_l group (p < 0.05). A Beta diversity analysis revealed the archaeal community's distinct clustering mode based on protein levels. The methanogenic genera Methanobrevibacter and Methanocorpusculum were dominant across the three groups, and their abundance was influenced by protein intake. A functional prediction analysis indicated moderate changes in amino acid and carbohydrate metabolism, which are particularly associated with methane production, an important source of greenhouse gases. AMR genes (e.g., tetA (60), patA, vat, and Erm methyltransferase) and virulence factors (Bacillibactin, LPS) were significantly enriched when animals were fed high-protein diets. Our results demonstrated that dietary protein levels significantly influence gut archaeal composition, AMR gene enrichment, and related functional pathways. Medium-protein diets promoted greater archaeal diversity, whereas high-protein diets favored resistance gene proliferation and enhanced methanogenic activity. Optimizing dietary protein intake may enhance gut health, mitigate antimicrobial resistance risk, and reduce methane emissions, thereby supporting livestock sustainability and environmental protection.},
}

@article {pmid40732056,
year = {2025},
author = {Cayo, M and Solís-Cornejo, F and Santos, A and Zamorano, P and Valenzuela, B},
title = {The Abundance and Distribution of the acdS Gene in Microbial Communities from the Rhizosphere of Copiapoa solaris, a Native Cactus in the Arid Coastal Region of Antofagasta, Chile.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071547},
pmid = {40732056},
issn = {2076-2607},
support = {ANT22991//Fortaleciendo la Formación de Pregrado, Posgrado e Investigación con Estándares de Calidad, Ministerio de Educación/ ; },
abstract = {Copiapoa solaris is an endemic cactus species from the Antofagasta region, Chile, thriving in arid coastal ecosystems known as "fog oases," where the rising marine moisture is the primary water source. This study investigates the role of microbial communities associated with the rhizosphere of C. solaris in adapting to extreme environmental conditions, particularly focusing on the acdS gene, which encodes ACC deaminase-an enzyme that reduces ethylene production under stress. This research aims to elucidate the gene's contribution to the adaptation of C. solaris in these challenging environments. Samples were collected from three sites (El Cobre, Quebrada Botija, and Quebrada Izcuña) that differ in relative humidity, temperature, and topography. Environmental DNA was extracted, phylogenetic diversity was analyzed, and metagenomic annotation of the acdS gene was conducted. The acdS gene was detected in all samples, with the highest relative abundance at Quebrada Izcuña (0.05%), characterized by low relative humidity (<70%) and severe water stress. Phylogenetic analysis revealed conserved sequences across sites, while taxonomic and alpha diversity were similar among them. However, beta diversity indicated that Quebrada Izcuña was the least homogeneous, hosting distinct taxa potentially associated with stress mitigation. The acdS gene was detected on plasmids at El Cobre and Quebrada Izcuña, suggesting its potential mobility within the metagenome. The results of this study highlight the intricate relationships between microbial communities and the resilient cactus species C. solaris in extreme environments. The conservation and abundance of the acdS gene, particularly in low-humidity conditions, suggest its vital role in facilitating stress tolerance through microbial interactions. Understanding these dynamics is crucial for developing strategies to enhance plant resilience in arid ecosystems, with potential applications in sustainable agriculture and ecosystem management under changing climatic conditions.},
}

@article {pmid40732017,
year = {2025},
author = {Lianou, A and Tsantes, AG and Ioannou, P and Bikouli, ED and Batsiou, A and Kokkinou, A and Tsante, KA and Tsilidis, D and Lampridou, M and Iacovidou, N and Sokou, R},
title = {hMPV Outbreaks: Worldwide Implications of a Re-Emerging Respiratory Pathogen.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071508},
pmid = {40732017},
issn = {2076-2607},
abstract = {Human metapneumovirus (hMPV), a member of the Pneumoviridae subfamily, has emerged as a significant etiological agent of acute respiratory tract infections across diverse age groups, particularly affecting infants, the elderly, and immunocompromised individuals. Since its initial identification in 2001, hMPV has been recognized globally for its seasonal circulation pattern, predominantly in late winter and spring. hMPV is a leading etiological agent, accounting for approximately 5% to 10% of hospitalizations among pediatric patients with acute respiratory tract infections. hMPV infection can result in severe bronchiolitis and pneumonia, particularly in young children, with clinical manifestations often indistinguishable from those caused by human RSV. Primary hMPV infection typically occurs during early childhood; however, re-infections are frequent and may occur throughout an individual's lifetime. hMPV is an enveloped, negative-sense RNA virus transmitted through respiratory droplets and aerosols, with a 3-5-day incubation period. The host immune response is marked by elevated pro-inflammatory cytokines, which contribute to disease severity. Advances in molecular diagnostics, particularly reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and metagenomic next-generation sequencing (mNGS), have improved detection accuracy and efficiency. Despite these advancements, treatment remains largely supportive, as no specific antiviral therapy has yet been approved. Promising developments in vaccine research, including mRNA-based candidates, are currently undergoing clinical evaluation. This review synthesizes current knowledge on hMPV, highlighting its virological, epidemiological, and clinical characteristics, along with diagnostic advancements and emerging therapeutic strategies, while underscoring the critical role of continued research and sustained preventive measures-including vaccines, monoclonal antibodies, and non-pharmaceutical interventions-in mitigating the global burden of hMPV-related disease.},
}

@article {pmid40731996,
year = {2025},
author = {Asimakis, E and Galiatsatos, I and Apostolopoulou, G and Savvidou, EC and Balatsos, G and Karras, V and Evangelou, V and Dionyssopoulou, E and Augustinos, A and Papadopoulos, NT and Michaelakis, A and Stathopoulou, P and Tsiamis, G},
title = {The Symbiotic Bacterial Profile of Laboratory-Reared and Field-Caught Aedes albopictus Mosquitoes from Greece.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071486},
pmid = {40731996},
issn = {2076-2607},
support = {«moSquITo»: Innovative approaches for monitoring and management of the Asian tiger mosquito with emphasis on the Sterile Insect Technique (ΤΑΕΔΚ06173)//National Recovery and Resilience Plan, "Greece 2.0" & EU Funding - Next Generation EU/ ; },
abstract = {The Asian tiger mosquito Aedes albopictus is a highly invasive species capable of transmitting human pathogens. For population management, the sterile insect technique (SIT) is considered an effective and sustainable alternative to conventional methods, such as insecticides and reducing or eliminating breeding sites. The use of symbiotic bacteria to improve the application of SIT or design combined SIT/incompatible insect technique (IIT) approaches is currently considered. In this context, exploring the microbiota of local mosquito populations is crucial for identifying interesting components. This study employed 16S rRNA sequencing and microbiological methods to characterize the diversity of laboratory and wild Ae. albopictus in Greece. Differences were recorded between wild and lab-reared mosquitoes, with laboratory samples exhibiting higher diversity. Laboratory treatment, sex, and developmental stage also resulted in variations between communities. Populations reared in the same facility developed mostly similar bacterial profiles. Two geographically distant wild populations displayed similar bacterial profiles, characterized by seasonal changes in the relative abundance of Pantoea and Zymobacter. Wolbachia was dominant in most groups (63.7% relative abundance), especially in field-caught mosquitoes. It was identified with two strains, wAlbA (21.5%) and wAlbB (42.2%). Other frequent taxa included Elizabethkingia, Asaia, and Serratia. Blood feeding favored an increase in Serratia abundance. Various Enterobacter, Klebsiella, Aeromonas, and Acinetobacter strains were isolated from larval and adult mosquito extracts and could be further characterized as diet supplements. These findings suggest that the microbiota of local populations is highly variable due to multiple factors. However, they retain core elements shared across populations that may exhibit valuable nutritional or functional roles and could be exploited to improve SIT processes.},
}

@article {pmid40731980,
year = {2025},
author = {Karadedos, DM and Mantzios, T and Kiousi, DE and Tsifintaris, M and Giannenas, I and Sakkas, P and Papadopoulos, GA and Antonissen, G and Pappa, A and Galanis, A and Tsiouris, V},
title = {Metagenomic Insight into Cecal Microbiota Shifts in Broiler Chicks Following Eimeria spp. Vaccination.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071470},
pmid = {40731980},
issn = {2076-2607},
abstract = {Coccidiosis, caused by Eimeria spp., remains a major challenge in poultry production, significantly affecting poultry health and performance, leading to substantial economic losses. While its impact on gut health is well documented, the interplay of Eimeria spp. challenge and/or vaccination with the intestinal microbiota remain insufficiently understood. Therefore, the aim of this study was to investigate the effects of Eimeria spp. (E. acervulina, E. maxima, and E. tenella) challenge, alone or in combination with a commercially available vaccine, on broiler performance, intestinal gross lesions, and cecal microbiota structure and function in experimentally challenged broiler chicks. A total of 216 Ross 308[®] broilers were randomly divided into three groups, with six replicates per group, according to the following experimental design: (A) negative control, (B) Eimeria spp.-challenged birds on day 16, and (C) Eimeria spp.-vaccinated and -challenged birds. Performance parameters were recorded on a weekly basis, coccidiosis gross lesions in the intestine were evaluated on days 23 and 29, and microbiota samples were collected on day 23. Broilers in the challenged group exhibited significantly (p ≤ 0.05) increased coccidiosis gross lesions in the intestine at both sampling periods (7 and 19 days post-infection, dpi), whereas vaccination significantly (p ≤ 0.05) minimized the severity of lesions at both time points. The challenged-only group showed significantly (p ≤ 0.05) lower average daily weight gain (ADWG) during the finisher phase and the overall experimental period compared to the vaccinated group. Additionally, average daily feed intake (ADFI) during the post-challenge period (22-29 dpi) was significantly (p ≤ 0.05) reduced in both challenged groups. Alpha diversity decreased in the challenged (p = 0.016) and vaccinated-challenged (p = 0.016) groups compared to control, Accordingly, beta diversity was reduced in groups B and C compared to the control group. This reduction was accompanied by an increased relative abundance of Proteobacteria (18, 71% in Group B and 10, 87% in Group C) and potentially pathogenic genera (Escherichia spp. and Shigella spp. p < 0.05), along with a decline in short-chain fatty acid (SCFA)-producing bacteria (Oscillibacter spp. and Eisenbergiella spp.) in groups B and C, respectively, compared to the control. Predictive functional metagenomics indicated disruptions in amino acid metabolism, nucleotide degradation, and lipid metabolism, potentially affecting gut integrity and nutrient absorption. Additionally, in the vaccinated group, gross lesions in the intestine were reduced in severity and microbial diversity was partially preserved, resulting in a microbiota composition more similar to that of the control group. Overall, these findings support that Eimeria spp. infection alters gut microbiota and function in broiler chicks, underscoring the need for further research into alternative strategies, such as probiotics and phytobiotics, to support gut health and disease resilience in poultry.},
}

@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 = {},
doi = {10.3390/microorganisms13071468},
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 {pmid40731977,
year = {2025},
author = {Li, C and Cong, B and Zhang, W and Lu, T and Guo, N and Zhao, L and Zhang, Z and Liu, S},
title = {Comparative Metagenomics Reveals Microbial Diversity and Biogeochemical Drivers in Deep-Sea Sediments of the Marcus-Wake and Magellan Seamounts.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071467},
pmid = {40731977},
issn = {2076-2607},
support = {2023YFC2811402//the National Key Research and Development Program of China/ ; ZR2024QD224//the Shandong Provincial Natural Science Foundation/ ; SD0425017//the Global Deep-Sea Typical Habitat Discovery and Conservation Program/ ; SD0425020//the Global Deep-Sea Typical Habitat Discovery and Conservation Program/ ; },
abstract = {Seamounts are distributed globally across the oceans and are generally considered oases of biomass abundance as well as hotspots of species richness. Diverse microbial communities are essential for biogeochemical cycling, yet their functional partitioning among seamounts with geographic features remains poorly investigated. Through metagenomic sequencing and genome-resolved analysis, we revealed that Proteobacteria (33.18-40.35%) dominated the bacterial communities, while Thaumarchaeota (5.98-10.86%) were the predominant archaea. Metagenome-assembled genomes uncovered 117 medium-quality genomes, 81.91% of which lacked species-level annotation, highlighting uncultured diversity. In the Nazuna seamount, which is located in the Marcus-Wake seamount region, microbiomes exhibited heightened autotrophic potential via the 3-hydroxypropionate cycle and dissimilatory nitrate reduction, whereas in the Magellan seamounts regions, nitrification and organic nitrogen metabolism were prioritized. Sulfur oxidation genes dominated Nazuna seamount microbes, with 33 MAGs coupling denitrification to sulfur redox pathways. Metal resistance genes for tellurium, mercury, and copper were prevalent, alongside habitat-specific iron transport systems. Cross-feeding interactions mediated by manganese, reduced ferredoxin, and sulfur-metal integration suggested adaptive detoxification strategies. This study elucidates how deep-sea microbes partition metabolic roles and evolve metal resilience mechanisms across geographical niches. It also supports the view that microbial community structure and metabolic function across seamount regions are likely influenced by the geomorphological features of the seamounts.},
}

@article {pmid40731966,
year = {2025},
author = {Long, Y and Huang, J and Zheng, S and Bai, S and Liu, Z and Li, X and Gao, W and Ke, X and Tang, Y and Yang, L and Wang, H and Li, G},
title = {Disorders of Gut Microbiota and Plasma Metabolic Profiles May Be Associated with Lymph Node Tuberculosis.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071456},
pmid = {40731966},
issn = {2076-2607},
support = {25270G1032， G2022039//the Shenzhen Third People's Hospital Research Fund/ ; 2021YFA1300902//National Key R&D Program of china/ ; G03117K001//High Level Special Funds (Cell Homeostasis and Major Diseases)/ ; },
abstract = {The association of gut microbiota with lymph node tuberculosis (LNTB) remains unexplored. This study employed metagenomic sequencing and plasma metabolomics analyses to investigate the role of gut microbiota in LNTB patients. Significant alterations in gut microbial diversity were observed in LNTB patients, characterized by a notable reduction in bacterial taxa involved in short-chain fatty acid (SCFA) synthesis, including Ruminococcus, Faecalibacterium, Roseburia, and Blautia, compared to healthy individuals. KEGG pathway analysis further revealed that gut dysbiosis could negatively impact SCFA biosynthesis and metabolism. Plasma metabolomics demonstrated disruptions in metabolites associated with SCFA synthesis and inflammation pathways in the LNTB group. Integrated analysis indicated significant correlations between specific gut microbiota (Blautia, Butyricicoccus, Coprococcus, Ruminococcus, Bacteroides, Clostridium) and plasma metabolites, including α-benzylbutyric acid, acetic acid, and succinic acid. Our findings demonstrate that gut microbiota dysbiosis and related metabolic dysfunction significantly reduce SCFA production in LNTB patients, potentially identifying novel therapeutic targets for LNTB management.},
}

@article {pmid40731366,
year = {2025},
author = {Jiménez-González, A and Treitli, SC and Peña-Diaz, P and Janovská, A and Beneš, V and Žáček, P and Hampl, V},
title = {Comprehensive analysis of the microbial consortium in the culture of flagellate Monocercomonoides exilis.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {97},
doi = {10.1186/s40793-025-00758-7},
pmid = {40731366},
issn = {2524-6372},
support = {771592//H2020 European Research Council/ ; 771592//H2020 European Research Council/ ; 771592//H2020 European Research Council/ ; 771592//H2020 European Research Council/ ; 771592//H2020 European Research Council/ ; 771592//H2020 European Research Council/ ; 771592//H2020 European Research Council/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Centre for Research of Pathogenicity and Virulence of Parasites/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Centre for Research of Pathogenicity and Virulence of Parasites/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Centre for Research of Pathogenicity and Virulence of Parasites/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Centre for Research of Pathogenicity and Virulence of Parasites/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Centre for Research of Pathogenicity and Virulence of Parasites/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Centre for Research of Pathogenicity and Virulence of Parasites/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Centre for Research of Pathogenicity and Virulence of Parasites/ ; },
abstract = {Monocercomonoides exilis is a model species of the amitochondrial eukaryotic group Oxymonadida, which makes it a suitable organism for studying the consequences of mitochondrial loss. Although M. exilis has an endobiotic lifestyle, it can be cultured in vitro in polyxenic conditions alongside an uncharacterized prokaryotic community, while attempts to create axenic cultures have not been successful. In this study, we used metagenomic sequencing, transcriptomics, and metabolomics to characterize the microbial consortium that supports the growth of M. exilis. We assembled genomes for 24 bacterial species and identified at least 30 species in total. M. exilis accounted for less than 1.5% of the DNA reads, while bacterial species dominated the sequence data and shifted in abundance over time. Our metabolic reconstruction and differential gene expression analyses show that the bacterial community relies on organic carbon oxidation, fermentation, and hydrogen production, but does not engage in methanogenesis. We observed rapid depletion of amino acids, nucleotides, glyceraldehyde, lactate, fatty acids, and alcohols in the medium, indicating a reliance on external nutrient recycling. The nitrogen cycle in this community is incomplete, with limited nitrogen fixation and no ammonia oxidation. Despite detailed metabolic profiling, we did not find any direct biochemical connections between M. exilis and the prokaryotes. Several bacterial species produce siderophores to assist themselves and others in the community in acquiring iron. However, M. exilis does not appear to benefit directly from siderophore-mediated iron transport and lacks known iron uptake pathways. This indicates that M. exilis may rely indirectly on the iron metabolism of other bacteria through phagocytosis. Additionally, some bacteria synthesize polyamines like spermidine and phosphatidylcholine, which M. exilis may need but cannot produce on its own. As the culture ages, M. exilis shows changes in gene expression consistent with starvation responses, including the upregulation of carbohydrate storage pathways and processes related to exocytosis. These findings provide new insights into microbial interactions within xenic cultures and emphasize the complex nature of maintaining amitochondriate eukaryotes in vitro.},
}

@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.},
}

Bees/microbiology
Animals
*Microbiota/genetics
Metagenomics/methods
*Databases, Genetic
Metagenome

@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},
doi = {10.1186/s12866-025-04188-w},
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.},
}

*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

@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 = {T32GM135117/GM/NIGMS NIH HHS/United States ; R01GM126257/GM/NIGMS NIH HHS/United States ; R01GM126257/GM/NIGMS NIH HHS/United States ; P30ES000002/ES/NIEHS NIH HHS/United States ; R03DE027486/DE/NIDCR NIH HHS/United States ; R03DE027486/DE/NIDCR 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.},
}

*Microbiota/genetics
Metagenome
Algorithms
*Metagenomics/methods
Humans

@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},
doi = {10.4014/jmb.2502.02037},
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.},
}

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

@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 = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.07.002},
pmid = {40730159},
issn = {1934-6069},
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 {pmid40729914,
year = {2025},
author = {Shen, D and Gao, X and Hui, C and Long, Y and Shentu, J and Lu, L and Qi, S},
title = {Overlooked risk of antibiotic resistance genes in typical landfill plumes and their influencing factors.},
journal = {Ecotoxicology and environmental safety},
volume = {302},
number = {},
pages = {118765},
doi = {10.1016/j.ecoenv.2025.118765},
pmid = {40729914},
issn = {1090-2414},
abstract = {Landfills are one of the primary reservoirs of antibiotic resistance genes (ARGs). Previous studies always focus on the distribution of ARGs in landfill leachate, while the distribution of ARGs in groundwater around the landfill and the corresponding influencing factors are always overlooked. In this study, seven groundwater samples and one leachate sample were collected from a typical landfill in Yueqing, China. Sulfonamide was the most abundant antibiotic in groundwater with its concentration of 1.2-23.1 ng L[-1]. Metagenomic analysis revealed 13 major types and 88 subtypes of antibiotic resistance genes (ARGs) in the leachate and surrounding groundwater. Multidrug (23.2-51.4 %), sulfonamide (2.6-24.1 %), tetracycline (3.0-35.8 %), macrolides-lincosamide-streptogramin (MLS, 1.1-26.3 %) and aminoglycoside (0.9-13.1 %) resistance genes were the top five types in the detected ARGs, while the ARGs abundance in groundwater increased with landfill age. Heavy metals (Ni, Pb, Cr, Cd) were strongly correlated with certain ARG subtypes, while no significant correlations were observed between antibiotics and their corresponding ARGs due to their low concentrations. Through co-occurrence network analysis, it was found that ARGs were tightly correlated with mobile genetic elements (MGEs), while several types of virulence factors such as flmH, cylG and clbF were also tightly correlated with MGEs. Besides, ARGs were also correlated with some denitrification genes such as nirB and norC, showing that the denitrification process would enhance the dissemination of ARGs. This study provides important insights for assessing the risk of ARGs spreading through leachate leakage in groundwater and can help optimize the management strategy of landfill.},
}

@article {pmid40729529,
year = {2025},
author = {Dey, S and Gireesan, S and Solovou, T and Inniss, NL and Satchell, KJF},
title = {High-Throughput Pipeline for Protein Expression and Solubility Profiling Using Synthetically Generated Plasmids.},
journal = {Current protocols},
volume = {5},
number = {7},
pages = {e70188},
doi = {10.1002/cpz1.70188},
pmid = {40729529},
issn = {2691-1299},
mesh = {Solubility ; *Plasmids/genetics ; *High-Throughput Screening Assays/methods ; Cloning, Molecular/methods ; *Recombinant Proteins/genetics/chemistry/isolation & purification ; },
abstract = {High-throughput protein expression and purification can now take advantage of the copious expansion of genes from extensive genomics and metagenomic surveillance programs. This article outlines a pipeline that involves strategic selection of a large repertoire of protein targets for cloning by commercial synthetic services, followed by high-throughput transformation, expression, and solubility screening. This pipeline will be applicable to structural and functional genomics approaches, as well as any project that requires large-scale screening for production of soluble proteins in a time-efficient manner. The protocols involve transformation, protein expression and solubility determination in a high-throughput fashion in a 96-well plate format. Proteins screened in this pipeline are then able to be purified for any assay needed. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Target optimization Basic Protocol 2: High-throughput transformation Basic Protocol 3: High-throughput expression and solubility screening.},
}

Solubility
*Plasmids/genetics
*High-Throughput Screening Assays/methods
Cloning, Molecular/methods
*Recombinant Proteins/genetics/chemistry/isolation & purification

@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.},
}

*Manure/microbiology
Flow Cytometry
Metagenomics
*Poaceae/microbiology
Anaerobiosis
*Microbiota
Biofuels
Bacteria
Archaea
Animals

@article {pmid40728615,
year = {2025},
author = {Zou, J and Yuan, Q and Yang, Y},
title = {An Online Server for Geometry-Aware Protein Function Annotations Through Predicted Structure.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2947},
number = {},
pages = {191-208},
pmid = {40728615},
issn = {1940-6029},
mesh = {*Software ; *Molecular Sequence Annotation/methods ; *Proteins/chemistry/metabolism/genetics ; Databases, Protein ; Internet ; Binding Sites ; *Computational Biology/methods ; Ligands ; Protein Binding ; Protein Conformation ; },
abstract = {Understanding protein functions is critical for metagenomic research, disease mechanism elucidation, and rational drug discovery. Traditional biochemical methods to determine protein functions are often inefficient and costly, leading to a widening gap between the rapid accumulation of protein sequences and their functional annotations. To address this, we introduce GPSFun, a fast and accurate web server that provides comprehensive geometry-aware protein sequence function annotations, including protein-binding sites for multiple ligands, gene ontologies, subcellular locations, and protein solubility. GPSFun's web server can be accessed at https://bio-web1.nscc-gz.cn/app/GPSFun , offering users a result with a rich visualized interface. Additionally, GPSFun was adopted to annotate ligand-binding sites for over 568,000 proteins from Swiss-Prot, leading to a complementary database named GPSiteDB (https://bio-web1.nscc-gz.cn/database/GPSiteDB). In this chapter, we first overview the workflow and results of our method, and then, we provide a step-by-step instruction on the usage of GPSFun and GPSiteDB, along with the detailed interpretations of the corresponding results.},
}

*Software
*Molecular Sequence Annotation/methods
*Proteins/chemistry/metabolism/genetics
Databases, Protein
Internet
Binding Sites
*Computational Biology/methods
Ligands
Protein Binding
Protein Conformation

@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.},
}

Humans
*Gastrointestinal Microbiome
*Carcinoma, Non-Small-Cell Lung/therapy/microbiology/immunology
*Immunotherapy/methods
*Lung Neoplasms/therapy/microbiology/immunology
Immune Checkpoint Inhibitors/therapeutic use
Animals

@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 = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf154},
pmid = {40728316},
issn = {1751-7370},
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 {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 = {},
number = {},
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/ ; },
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 {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 = {},
number = {},
pages = {},
doi = {10.1039/d5fo01995h},
pmid = {40726156},
issn = {2042-650X},
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 {pmid40725792,
year = {2025},
author = {Issilbayeva, A and Kozhakhmetov, S and Jarmukhanov, Z and Vinogradova, E and Mukhanbetzhanov, N and Meiramova, A and Rib, Y and Ivanova-Razumova, T and Myrzakhmetova, G and Andossova, S and Zeinoldina, A and Kuantkhan, M and Ainabekova, B and Bekbossynova, M and Kushugulova, A},
title = {Metagenomic Characterization of Gut Microbiota in Individuals with Low Cardiovascular Risk.},
journal = {Journal of clinical medicine},
volume = {14},
number = {14},
pages = {},
pmid = {40725792},
issn = {2077-0383},
support = {АР23487014; BR21881970//The Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Background/Objectives: Cardiovascular diseases remain the leading cause of global mortality, with the gut microbiome emerging as a critical factor. This study aimed to characterize gut microbiome composition and metabolic pathways in individuals with low cardiovascular risk (LCR) compared to healthy controls to reveal insights into early disease shifts. Methods: We performed shotgun metagenomic sequencing on fecal samples from 25 LCR individuals and 25 matched healthy controls. Participants underwent a comprehensive cardiovascular evaluation. Taxonomic classification used MetaPhlAn 4, and functional profiling employed HUMAnN 3. Results: Despite similar alpha diversity, significant differences in bacterial community structure were observed between groups (PERMANOVA, p < 0.05). The LCR group showed enrichment of Faecalibacterium prausnitzii (p = 0.035), negatively correlating with atherogenic markers, including ApoB (r = -0.3, p = 0.025). Conversely, Fusicatenibacter saccharivorans positively correlated with ApoB (r = 0.4, p = 0.006). Metabolic pathway analysis revealed upregulation of nucleotide biosynthesis, glycolysis, and sugar degradation pathways in the LCR group, suggesting altered metabolic activity. Conclusions: We identified distinct gut microbiome signatures in LCR individuals that may represent early alterations associated with cardiovascular disease development. The opposing correlations between F. prausnitzii and F. saccharivorans with lipid parameters highlight their potential roles in cardiometabolic health. These findings suggest gut microbiome signatures may serve as indicators of early metabolic dysregulation preceding clinically significant cardiovascular disease.},
}

@article {pmid40725341,
year = {2025},
author = {López-Hernández, MG and Rincón-Rosales, R and Rincón-Molina, CI and Manzano-Gómez, LA and Gen-Jiménez, A and Maldonado-Gómez, JC and Rincón-Molina, FA},
title = {Diversity and Functional Potential of Gut Bacteria Associated with the Insect Arsenura armida (Lepidoptera: Saturniidae).},
journal = {Insects},
volume = {16},
number = {7},
pages = {},
pmid = {40725341},
issn = {2075-4450},
support = {19337.24-P and 19414.24-P//Tecnológico Nacional de México/ ; },
abstract = {Insects are often associated with diverse microorganisms that enhance their metabolism and nutrient assimilation. These microorganisms, residing in the insect's gut, play a crucial role in breaking down complex molecules into simpler compounds essential for the host's growth. This study investigates the diversity and functional potential of symbiotic bacteria in the gut of Arsenura armida (Lepidoptera: Saturniidae) larvae, an edible insect from southeastern Mexico, using culture-dependent and metagenomic approaches. Bacterial strains were isolated from different gut sections (foregut, midgut, and hindgut) and cultured on general-purpose media. Isolates were identified through 16S rRNA gene sequencing and genomic fingerprinting. Metagenomics revealed the bacterial community structure and diversity, along with their functional potential. A total of 96 bacterial strains were isolated, predominantly Gram-negative bacilli. Rapidly growing colonies exhibited enzymatic activity, cellulose degradation, and sugar production. Phylogenetic analysis identified eight genera, including Acinetobacter, Bacillus, Enterobacter, Pseudomonas, and others, with significant cellulose-degrading capabilities. Metagenomics confirmed Bacillota as the most abundant phylum. These complementary methods revealed abundant symbiotic bacteria with key metabolic roles in A. armida, offering promising biotechnological applications in enzymatic bioconversion and cellulose degradation.},
}

@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.},
}

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

@article {pmid40724243,
year = {2025},
author = {Geng, H and Xu, C and Ma, H and Dai, Y and Jiang, Z and Yang, M and Zhu, D},
title = {In Silico Discovery and Sensory Validation of Umami Peptides in Fermented Sausages: A Study Integrating Deep Learning and Molecular Modeling.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {14},
pages = {},
pmid = {40724243},
issn = {2304-8158},
abstract = {Deep learning has great potential in the field of functional peptide prediction. This study combines metagenomics and deep learning to efficiently discover potential umami peptides in fermented sausages. A candidate peptide library was generated using metagenomic data from fermented sausages, an integrated deep learning model was constructed for prediction, and SHAP (SHapley Additive exPlanations) interpretability analysis was performed to elucidate the key amino acid features and contributions of the model in predicting umami peptides, screening the top ten peptides with the highest predicted probability. Subsequently, molecular docking was performed to assess the binding stability of these peptides with the umami receptor T1R1/T1R3, selecting the three peptides DDSMAATGL, DGEEDASM, and DEEEVDI with the most stable binding for further study. Docking analysis revealed the important roles of the key receptor residues Glu301, Arg277, Lys328, and His71 in hydrogen bond formation. Molecular dynamics simulations validated the robust integrity of the peptide-receptor associations. Finally, sensory evaluation demonstrated that these three peptides possessed significant umami characteristics, with low umami thresholds (0.11, 0.37, and 0.44 mg/mL, respectively). This study, based on metagenomics and deep learning, provides a high-throughput strategy for the discovery and validation of functional peptides.},
}