@article {pmid40537881,
year = {2025},
author = {Linghu, Y and Hu, RS and Tang, XM and Li, RT and Li, WY and Wu, JH},
title = {Unveiling viral diversity and dynamics in mosquitoes through metagenomic analysis in Guizhou Province, China.},
journal = {Infectious diseases of poverty},
volume = {14},
number = {1},
pages = {51},
pmid = {40537881},
issn = {2049-9957},
support = {Qian Ke He Platform Talent-GCC [2022] 033-1//The Training Project for High-Level Innovative talents in Guizhou Province, China/ ; Qian Ke He Platform Talent-CXTD [2022] 004//The Science and Technology Innovation Talent team of Guizhou Province, China/ ; Project Contract Number: Xiao Bo He J Zi [2023] 44//The Scientific Research Foundation for Advanced Talents, Guizhou Medical University/ ; NO. 2024GCC16Z//The High-level Talent Research Start-up Project of Sichuan University of Arts and Science/ ; },
abstract = {BACKGROUND: Poverty, disease, and vector ecology intersect to present ongoing health threats, particularly in ecologically sensitive regions. Guizhou Province in China, with its complex karst topography and rich biodiversity, offers a unique environment to study mosquito-borne viral transmission. Despite over 5000 reported cases of Japanese encephalitis in the past two decades and the detection of Zika virus in 2016, the virological landscape of this region remains poorly understood. This study aims to characterize the mosquito-associated virome, assess viral diversity, and identify factors influencing transmission dynamics in Guizhou Province.

METHODS: Between 2021 and 2022, we conducted a 2-year mosquito surveillance across eight ecologically distinct regions in Guizhou Province. Adult mosquitoes were collected using a variety of methods, including BG Mosquitaire CO2 traps, mosquito-killing lamps, manual collection, human bait traps, and oviposition traps. To investigate the virome diversity and dynamics within mosquito populations, we performed metagenomic sequencing and bioinformatics analysis on pooled mosquito samples collected from geographically diverse sampling sites.

RESULTS: We collected more than 40,000 adult mosquitoes, primarily belonging to four genera: Aedes, Anopheles, Armigeres, and Culex. Dominant species included Aedes albopictus, Anopheles sinensis, Armigeres subalbatus, and Culex tritaeniorhynchus. Notably, we report the first provincial record of the Anopheles baileyi complex, expanding the known distribution of mosquito vector in this region. Viral metagenomic sequencing, coupled with bioinformatic analysis, identified 162 viral contigs, including 140 known and 22 previously uncharacterized viruses. We experimentally confirmed the genotypes of three medically important zoonotic viruses: Japanese encephalitis virus (JEV-GI), Getah virus (GETV-GIII) and Banna virus (BAV-A2). Comparative analysis of viral abundance across mosquito species revealed that Aedes albopictus populations in Guizhou harbor a distinct virome composition, diverging from those reported in other geographic regions.

CONCLUSIONS: This study presents the comprehensive characterization of the mosquito-associated virome in Guizhou Province, providing critical insights into viral diversity, vector competence, and transmission dynamics within karst ecosystems. The detection of multiple zoonotic viruses highlights the need for strengthened surveillance and targeted public health interventions in this region.},
}

@article {pmid40535544,
year = {2025},
author = {Wang, X and Cao, D and Chen, W and Sun, J and Hu, H},
title = {Metagenomics reveals unique gut mycobiome biomarkers in major depressive disorder - a non-invasive method.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1582522},
pmid = {40535544},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Depressive Disorder, Major/microbiology/diagnosis ; *Mycobiome ; Biomarkers/analysis ; Male ; Female ; Adult ; *Metagenomics/methods ; *Fungi/classification/genetics/isolation & purification ; Middle Aged ; Machine Learning ; Support Vector Machine ; Case-Control Studies ; Feces/microbiology ; },
abstract = {BACKGROUND: An increasing amount of evidence suggests a potential link between alterations in the intestinal microbiota and the onset of various psychiatric disorders, including depression. Nevertheless, the precise nature of the link between depression and the intestinal microbiota remains largely unknown. A significant proportion of previous research has concentrated on the study of gut bacterial communities, with relatively little attention paid to the link between gut mycobiome and depression.

METHODS: In this research, we analyzed the composition and differences of intestinal fungal communities between major depressive disorder (MDD) and healthy controls. Subsequently, we constructed a machine learning model using support vector machine-recursive feature elimination to search for potential fungal markers for MDD.

RESULTS: Our findings indicated that the composition and beta diversity of intestinal fungal communities were significantly changed in MDD compared to the healthy controls. A total of 22 specific fungal community markers were screened out by machine learning, and the predictive model had promising performance in the prediction of MDD (area under the curve, AUC = 1.000). Additionally, the intestinal fungal communities demonstrated satisfactory performance in the validation cohort, with an AUC of 0.884 (95% CI: 0.7871-0.9476) in the Russian validation cohort, which consisted of 36 patients with MDD and 36 healthy individuals. The AUC for the Wuhan validation cohort was 0.838 (95% CI: 0.7403-0.9102), which included 40 patients with MDD and 42 healthy individuals.

CONCLUSION: To summarize, our research revealed the characterization of intestinal fungal communities in MDD and developed a prediction model based on specific intestinal fungal communities. Although MDD has well-established diagnostic criteria, the strategy based on the model of gut fungal communities may offer predictive biomarkers for MDD.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Depressive Disorder, Major/microbiology/diagnosis
*Mycobiome
Biomarkers/analysis
Male
Female
Adult
*Metagenomics/methods
*Fungi/classification/genetics/isolation & purification
Middle Aged
Machine Learning
Support Vector Machine
Case-Control Studies
Feces/microbiology

@article {pmid40535541,
year = {2025},
author = {Kato-Kogoe, N and Tsuda, K and Kudo, A and Sakaguchi, S and Omori, M and Komori, E and Ohmichi, M and Hamada, W and Nakamura, S and Nakano, T and Tamaki, J and Ueno, T},
title = {Salivary microbiota and IgA responses are different in pre-diabetic individuals compared to normoglycemic controls.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1591285},
pmid = {40535541},
issn = {2235-2988},
mesh = {Humans ; *Saliva/microbiology/immunology ; Female ; Male ; *Immunoglobulin A/analysis/immunology ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Microbiota/immunology ; *Prediabetic State/immunology/microbiology ; Adult ; Bacteria/classification/genetics/isolation & purification ; Diabetes Mellitus, Type 2/immunology/microbiology ; Aged ; Metagenomics ; DNA, Bacterial/genetics/chemistry ; },
abstract = {INTRODUCTION: In recent years, changes in the oral microbiota of patients with type 2 diabetes mellitus (T2DM) have been increasingly recognized. The salivary microbiota may also be altered in pre-diabetes, which is the earliest stage of abnormal blood glucose regulation and a reversible stage preceding T2DM; however, its characteristics are poorly understood. Salivary immunoglobulin A (IgA) is a host defense factor central to the oral immune system and may play an important role in regulating the salivary microbiota. Given that alterations in immunoreactivity are observed in pre-diabetes, we hypothesized that the salivary IgA response may also be altered; however, limited knowledge exists regarding this. Therefore, in the present study, we aimed to evaluate the characteristics of salivary microbiota and IgA responses against salivary microbiota in individuals with pre-diabetes, comparing them to those in individuals with normoglycemia.

METHODS: Saliva samples were collected from 101 pre-diabetic individuals (PreDM group) and 101 age- and sex-matched normoglycemic controls (Normal group). Further, 16S rRNA metagenomic analysis was performed to compare bacterial microbiota composition. For each of the 19 saliva samples from the PreDM and Normal groups, IgA-enriched and IgA-nonenriched fractions were separated via magnetic-activated cell sorting, followed by 16S rRNA metagenomic analysis. The IgA index was calculated to evaluate the difference in the IgA response to each bacterium between the PreDM and Normal groups.

RESULTS: Bacterial species richness was significantly lower in the PreDM group than in the Normal group (observed operational taxonomic unit index, p = 0.042), and a difference between these groups was noted in the overall salivary microbiota structure (unweighted UniFrac distances, p = 0.009). Salivary IgA responses against several bacterial genera differed between the PreDM and Normal groups. Significantly higher IgA responses were noted against Haemophilus in the PreDM group, with lower responses against Capnocytophaga, Corynebacterium, and Streptococcus relative to those in the Normal group.

CONCLUSIONS: Salivary microbiota and IgA responses differ between pre-diabetic individuals and normoglycemic controls. The current findings advance our understanding of the interaction between oral bacteria and host immune responses in patients with a poor glycemic status.},
}

Humans
*Saliva/microbiology/immunology
Female
Male
*Immunoglobulin A/analysis/immunology
Middle Aged
RNA, Ribosomal, 16S/genetics
*Microbiota/immunology
*Prediabetic State/immunology/microbiology
Adult
Bacteria/classification/genetics/isolation & purification
Diabetes Mellitus, Type 2/immunology/microbiology
Aged
Metagenomics
DNA, Bacterial/genetics/chemistry

@article {pmid40533170,
year = {2025},
author = {Kumari Nawarathna, TNT and Fujii, N and Yamamoto, K and Kuroda, K and Narihiro, T and Ozaki, N and Ohashi, A and Kindaichi, T},
title = {Metagenomic Insights into Candidatus Scalindua in a Long-term Cultivated Marine Anammox Consortium: The Important Role of Tetrahydrofolate-mediated Carbon Fixation.},
journal = {Microbes and environments},
volume = {40},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME25007},
pmid = {40533170},
issn = {1347-4405},
mesh = {*Bacteria/metabolism/genetics/classification/isolation & purification ; *Carbon Cycle ; Metagenomics ; *Microbial Consortia/genetics ; *Ammonia/metabolism ; Folic Acid/metabolism/biosynthesis ; *Seawater/microbiology ; Metagenome ; Bioreactors/microbiology ; Metabolic Networks and Pathways ; Phylogeny ; Genome, Bacterial ; Wastewater/microbiology ; Carbon/metabolism ; },
abstract = {Marine anammox bacteria have been an exciting research area in recent years due to their high effectiveness in treating ammonia-containing saline wastewater. However, their direct implementation in the wastewater industry faces challenges due to slow growth, difficulty obtaining pure cultures, and their tendency to exist as part of an anammox consortium, interacting symbiotically with other bacteria. In the present study, 91 draft genome metagenome-assembled genomes (MAGs) from a long-term-operated reactor were recovered to clarify detailed symbiotic interactions within an anammox consortium. One marine anammox bacterial MAG, identified as Candidatus Scalindua, was successfully recovered and was abundant within the sampled microbial community. A comprehensive metabolic pathway ana-lysis revealed that Ca. Scalindua exhibited the complete anammox pathway and the Wood-Ljungdahl pathway for carbon fixation. The folate biosynthesis pathway in Ca. Scalindua was incomplete, lacking dihydrofolate reductase, a key enzyme for tetrahydrofolate (THF) production. The folate biopterin transporter, essential for transporting folate-related metabolites among coexisting bacteria, was identified exclusively in Ca. Scalindua. In addition, the impact of exogenously supplied THF on microbial activity and carbon uptake rates was investigated in batch experiments using [14]C-labeled bicarbonate. The results obtained revealed that 2‍ ‍mg L[-1] of exogenous THF resulted in a 43% increase in the carbon uptake rate, while anammox activity remained unaffected. The present results suggest that THF is a key intermediate for carbon fixation in Ca. Scalindua and may be essential for their growth.},
}

*Bacteria/metabolism/genetics/classification/isolation & purification
*Carbon Cycle
Metagenomics
*Microbial Consortia/genetics
*Ammonia/metabolism
Folic Acid/metabolism/biosynthesis
*Seawater/microbiology
Metagenome
Bioreactors/microbiology
Metabolic Networks and Pathways
Phylogeny
Genome, Bacterial
Wastewater/microbiology
Carbon/metabolism

@article {pmid40532696,
year = {2025},
author = {Er, YX and Lee, SC and Aneke, C and Conlan, S and Muslim, A and Deming, C and Che, Y and Yap, NJ and Tee, MZ and Abdull-Majid, N and Shahrizal, S and Leong, KF and Han, J and Shen, Z and Than, LTL and Park, M and Mohd Sayed, I and , and Seyedmousavi, A and Kong, HH and Loke, P and Segre, JA and Lim, YAL},
title = {Trichophyton concentricum fungal infections and skin microbiomes of Indigenous Peninsular Malaysians.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.05.034},
pmid = {40532696},
issn = {1097-4172},
abstract = {Recent outbreaks of multidrug-resistant fungi infecting human skin emphasize the importance of understanding fungal pathophysiology and spread. In efforts to address health concerns with various Indigenous Peninsular Malaysians (Orang Asli [OA]), tinea imbricata-a Trichophyton concentricum fungal skin infection-emerged as a particular concern. We investigated the etiology and transmission of tinea imbricata by culturing, testing antifungal sensitivities, and sequencing T. concentricum isolates in remote OA villages. Among regionally conserved isolates, we identified the emergence of terbinafine-resistant T. concentricum microbiologically and genomically. Investigating the skin microbiomes of 82 Indigenous OA, we found unique microbiota and lower relative abundances of bacterial commensals (Cutibacterium acnes, Staphylococcus epidermidis) among OA versus Malaysian and US urban populations, emphasizing how understudied populations provide unprecedented knowledge on host-microbiome co-evolution. These findings provide valuable insights into clinical, microbiological, and genomic features of chronic fungal skin infections, offering the potential to inform strategies to address drug resistance and effective therapy.},
}

@article {pmid40530822,
year = {2025},
author = {Wu, H and Sun, B and Li, J},
title = {Metagenomics research on PAH biodegradation in the lower reaches of the Shiwuli River in Chaohu, China.},
journal = {Environmental science. Processes & impacts},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5em00025d},
pmid = {40530822},
issn = {2050-7895},
abstract = {Metagenomics is a powerful tool for investigating functional microorganisms, molecular mechanisms and genes involved in the degradation of polycyclic aromatic hydrocarbons (PAHs) in situ complex environments. In this study, we selected three land use types in the lower reaches of the Shiwuli River in Chaohu and applied metagenomics technology. The results revealed that Rhodoplanes and Bradyrhizobium were the abundant PAH-degrading microorganisms across the three land use types. Based on the functional annotation and PAH degradation pathway, it was found that the in situ microbial communities of the three land use types shared common metabolic pathways for phenanthrene degradation. In addition, a unique metabolic pathway for PAH degradation was identified in the agricultural land. Only Patulibacter contributed to flnE (KO14604) in the agricultural land, which was involved in the metabolic pathway of fluorene degradation. Results of this study suggested that the in situ degradation of PAHs was not completed by a single genus, and it involved the synergy effects of different PAH-degrading microorganisms. There was no significant difference between the compositions and relative abundances of PAH-degrading microorganisms in the three land use types and those presented in the Kyoto Encyclopedia of Genes and Genomes Orthology (KO). However, the same microorganism contributed to different functional genes in different samples. Genes encoding protocatechuic acid 4,5-dioxygenase were widely distributed and relatively abundant. Therefore, this gene may serve as an indicator of PAH degradation potential. Among all the factors, the total organic carbon and nitrate nitrogen contents exhibited significant influences on the functional genes (KO) related to PAH degradation (p < 0.05).},
}

@article {pmid40528698,
year = {2025},
author = {Bonilla-Espadas, M and Lifante-Martínez, I and Camacho, M and Orgilés-Calpena, E and Arán-Aís, F and Bertazzo, M and Bonete, MJ},
title = {Chromium-Tanned Leather and Microbial Consortia: Identification of Taxa With Biodegradation Potential and Chromium Tolerance.},
journal = {Environmental microbiology reports},
volume = {17},
number = {3},
pages = {e70134},
pmid = {40528698},
issn = {1758-2229},
support = {IMDEEA/2021/11//European Union through the European Regional Development Fund within the Operational Programme of the Valencian Community 2014-2020/ ; UAIND21-02B//Universidad de Alicante/ ; },
mesh = {*Chromium/metabolism/toxicity ; *Microbial Consortia ; Biodegradation, Environmental ; Biofilms/growth & development ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Microscopy, Electron, Scanning ; Tanning ; },
abstract = {Chromium-tanned leather waste poses significant environmental challenges due to its resistance to degradation and heavy metal content. This study investigates the potential of naturally selected microbial consortia to initiate the degradation of chromium-tanned leather and identifies key bacterial genera capable of tolerating chromium and producing enzymes relevant to collagen breakdown. A novel multidisciplinary approach combining gravimetric assays, metagenomic sequencing, and scanning electron microscopy (SEM) was applied to characterise both microbial composition and degradation dynamics. Dominant genera such as Bacillus, Microbacterium, and Acinetobacter were associated with collagen degradation and metal tolerance, with Bacillus-rich communities showing the most pronounced mass loss (up to 3%). SEM analysis revealed the formation of robust biofilms and extensive matrix disruption, indicating enzymatic activity and structural breakdown of the leather. The formation of exopolysaccharide-rich biofilms was found to be critical for microbial adhesion and biodegradation efficacy. These findings provide initial insights into microbial mechanisms involved in the degradation of chromium-tanned leather and suggest potential applications for microbial consortia in future sustainable leather waste management strategies.},
}

*Chromium/metabolism/toxicity
*Microbial Consortia
Biodegradation, Environmental
Biofilms/growth & development
*Bacteria/metabolism/classification/genetics/isolation & purification
Microscopy, Electron, Scanning
Tanning

@article {pmid40528221,
year = {2025},
author = {Gao, L and Liao, H and Chen, Y and Ye, C and Huang, L and Xu, M and Du, J and Zhang, J and Huang, D and Cai, S and Dong, H},
title = {Airway microbiota associated D-phenylalanine promotes non-small cell lung cancer metastasis through epithelial mesenchymal transition.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {673},
pmid = {40528221},
issn = {1479-5876},
support = {82170032//National Natural Science Foundation of China/ ; 82470058//National Natural Science Foundation of China/ ; 82270024//National Natural Science Foundation of China/ ; YZ2022ZX04//President Foundation of The Fifth Affiliated Hospital, Southern Medical University/ ; 2023A1515110216//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023M731546//China Postdoctoral Science Foundation/ ; },
mesh = {*Epithelial-Mesenchymal Transition/drug effects ; Humans ; *Carcinoma, Non-Small-Cell Lung/pathology/microbiology ; *Lung Neoplasms/pathology/microbiology ; Animals ; Male ; Neoplasm Metastasis ; Female ; *Microbiota ; *Phenylalanine/metabolism/pharmacology/administration & dosage ; Middle Aged ; Bronchoalveolar Lavage Fluid/chemistry ; Cell Line, Tumor ; Mice ; Aged ; *Respiratory System/microbiology ; },
abstract = {BACKGROUND: Lung cancer is the leading cause of cancer-related death worldwide, and patients with distant metastasis have a poor prognosis. Various studies have reported that microbiota and metabolites significantly differ between healthy individuals and lung cancer patients. However, the effects of metabolites on tumor formation and metastasis are unclear. Therefore, our study aimed to determine the correlation between airway metabolites and microbiota, along with their respective roles in lung cancer metastasis.

METHODS: Bronchoalveolar lavage fluid (BALF) samples were collected from 30 non-small cell lung cancer (NSCLC) patients, including 11 patients without metastasis (M0) and 19 patients with metastasis (M1). Integrated pathogenic metagenomic and Liquid chromatography-mass spectrometry (LC‒MS) analyses were employed to explore differences between two groups. The omics data were analyzed and integrated via Spearman's correlation coefficient. Specific metabolites were subsequently used to intervene in lung cancer cells and animal models to assess their influence on tumor metastasis.

RESULTS: A total of 801 metabolites were identified in the BALF of all patients. Compared with those in the M0 group, 48 metabolites in the M1 group were significantly different. D-phenylalanine was notably upregulated in M1 and was positively related to Metamycoplasma salivarium. Intranasal administration of D-phenylalanine promoted tumor intrapulmonary metastasis and induced epithelial mesenchymal transition (EMT) process in NSCLC mouse models. Moreover, D-phenylalanine promotes the proliferation of non-small cell lung cancer cells and facilitates their migration and invasion via EMT.

CONCLUSION: The airway microbiota associated D-phenylalanine could promote lung cancer metastasis via EMT, which could be a new predictor for the diagnosis of tumor metastasis in NSCLC patients.},
}

*Epithelial-Mesenchymal Transition/drug effects
Humans
*Carcinoma, Non-Small-Cell Lung/pathology/microbiology
*Lung Neoplasms/pathology/microbiology
Animals
Male
Neoplasm Metastasis
Female
*Microbiota
*Phenylalanine/metabolism/pharmacology/administration & dosage
Middle Aged
Bronchoalveolar Lavage Fluid/chemistry
Cell Line, Tumor
Mice
Aged
*Respiratory System/microbiology

@article {pmid40528214,
year = {2025},
author = {Zhang, Y and Luo, J and Chen, K and Li, N and Luo, C and Di, S and Qin, J and Zhang, F and Chen, H and Dai, M},
title = {Cross-cohort analysis identifies shared gut microbial signatures and validates microbial risk scores for colorectal cancer.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {676},
pmid = {40528214},
issn = {1479-5876},
support = {2022-I2M-1-0031//Institute of Chinese Materia Medica, China Academy of Chinese Medical Science/ ; 82173606//National Natural Science Foundation of China/ ; 82273726//National Natural Science Foundation of China/ ; 20230484397//Beijing Nova Program of Science and Technology/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Risk Factors ; Risk Assessment ; Reproducibility of Results ; Male ; Female ; Middle Aged ; Metagenomics ; Case-Control Studies ; },
abstract = {BACKGROUND: Microbiome-wide association studies showed links between colorectal cancer (CRC) and gut microbiota. However, the clinical application of gut microbiota in CRC prevention has been hindered by the diversity of study populations and technical variations. We aimed to determine CRC-related gut microbial signatures based on cross-regional, cross-population, and cross-cohort metagenomic datasets, and elucidate its application value in CRC risk assessment.

METHODS: We used the MMUPHin tool to perform a meta-analysis of our own cohort and seven publicly available metagenomics datasets to identify gut microbial species associated with CRC across different cohorts, comprising of 570 CRC cases and 557 controls. Based on differential species sets, we constructed the microbial risk score (MRS) using α-diversity of the sub-community (MRSα), weighted/unweighted summation methods and machine learning algorithms. Cohort-to-cohort training and validation were performed to demonstrate the transferability.

RESULTS: We found that MRSα of core species was better validated and more interpretable than those constructed with summation methods or machine learning algorithms. Six species, including Parvimonas micra, Clostridium symbiosum, Peptostreptococcus stomatis, Bacteroides fragilis, Gemella morbillorum, and Fusobacterium nucleatum, were included in MRSα constructed by half or more of the cohorts. The AUC of MRSα, calculated based on the sub-community of six species, varied between 0.619 and 0.824 across the eight cohorts.

CONCLUSION: We identified six CRC-related species across regions, populations, and cohorts. The constructed MRSα could contribute to the risk prediction of CRC in different populations.},
}

Humans
*Colorectal Neoplasms/microbiology
*Gastrointestinal Microbiome/genetics
Cohort Studies
Risk Factors
Risk Assessment
Reproducibility of Results
Male
Female
Middle Aged
Metagenomics
Case-Control Studies

@article {pmid40523923,
year = {2025},
author = {Zhang, M and Liang, C and Li, B and Jiang, F and Song, P and Gu, H and Gao, H and Cai, Z and Zhang, T},
title = {Gut microbiome and diet contribute to ecological niche differentiation between argali (Ovis ammon hodgsoni) and blue sheep (Pseudois nayaur) on the Qinghai-Tibet Plateau.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {930},
pmid = {40523923},
issn = {2399-3642},
mesh = {Animals ; *Gastrointestinal Microbiome ; Tibet ; *Diet/veterinary ; Sheep/microbiology ; Ecosystem ; Herbivory ; },
abstract = {The gut microbiota plays a critical role in plant digestion, nutrient absorption, and ecological adaptation in herbivores. However, how gut microbiota and diet jointly influence ecological niche differentiation in sympatric species remains unclear. Here, we use metagenomic sequencing and plant trnL (UAA) fragment sequencing to examine the gut microbiota and dietary composition of sympatric Tibetan argali (Ovis ammon hodgsoni) and blue sheep (Pseudois nayaur) in the Kunlun Mountains of the Qinghai-Tibet Plateau. Despite inhabiting similar environments, the two species harbor distinct microbial compositions and functional profiles. Interestingly, higher dietary diversity does not correspond to higher microbial diversity. Tibetan argali, despite having a simpler diet, possesses a more diverse and flexible gut microbiome. In contrast, blue sheep show broader dietary preferences and stronger microbial metabolic adaptation to glycan biosynthesis and metabolism. These findings reveal significant associations between gut microbiota composition, function, and diet, supporting a microbial contribution to trophic niche differentiation. Our results highlight distinct microbial-dietary strategies in sympatric herbivores and underscore the role of the gut microbiome in ecological adaptation and species coexistence.},
}

Animals
*Gastrointestinal Microbiome
Tibet
*Diet/veterinary
Sheep/microbiology
Ecosystem
Herbivory

@article {pmid40520638,
year = {2025},
author = {Zakaria, D and Sandri, C and Modesto, M and Spiezio, C and Scarafile, D and Cedras, A and Borruso, L and Manghi, P and Trevisi, P and Segata, N and Mattarelli, P and Arita, M},
title = {Disentangling the gut microbiota of Aldabra giant tortoises of different ages and environments.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19566},
pmid = {40520638},
issn = {2167-8359},
mesh = {Animals ; *Turtles/microbiology ; *Gastrointestinal Microbiome/genetics ; Italy ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Age Factors ; Seychelles ; Environment ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: The gut microbiota plays a pivotal role in regulating the physiological functions of its host, including immunity, metabolism, and digestion. The impact of environment and age on microbiota can be assessed by observing long-lived animals across different age groups and environments. The Aldabra giant tortoise (Aldabrachelys gigantea) is an ideal species for this study due to its exceptionally long lifespan of over 100 years.

METHODS: Using 16S rRNA gene amplicon analysis, we analyzed 52 fecal samples from giant tortoises in Seychelles (Curieuse and Mahé islands) and in a zoological park in Italy, from very young individuals to those of >100 years old. We performed Alpha and Beta diversity analysis, relative abundance analysis, and complex upset plot analysis, comparing the results of tortoises from different environments and age groups.

RESULTS: The diversity and overall composition of the gut microbiota of tortoises were impacted mainly by geolocation rather than their age. The greater diversity of microbiota in wild tortoises was attributed to their food variance such as wild leaves and branches, compared to captive or domesticated conditions. Beta diversity analysis also revealed the contribution of both environment and age to the variation between samples, with environments accounting for a larger proportion of this contribution. Certain bacterial families, such as Spirochaetota and Fibrobacterota, were more prevalent in environments with higher fiber intake, reflecting dietary differences. Additionally, a range of host-independent environmental bacteria was found to be specific to individuals in Curieuse and not in other geolocations. On the other hand, there were no bacterial taxa specific to centenarians, whose microbial complexity was reduced compared to adult or elderly tortoises.

CONCLUSIONS: Our records showed that environment is the primary influence in the overall composition and diversity of the gut microbiota of Aldabra giant tortoises. As giant tortoises are amongst the longest-lived vertebrate animals, these findings can be utilized to monitor their health according to their ages, and enhance their conservation efforts.},
}

Animals
*Turtles/microbiology
*Gastrointestinal Microbiome/genetics
Italy
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Age Factors
Seychelles
Environment
Bacteria/genetics/classification

@article {pmid40520307,
year = {2025},
author = {Ye, S and Peng, S and Wang, X and Fan, J and Zhu, C and Huang, L and Huang, Y and Cheng, K and Ni, T and Qian, Y and Wu, X and Xu, Y},
title = {Microbial community structure and resistome dynamics on elevator buttons in response to surface disinfection practices.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1593114},
pmid = {40520307},
issn = {2296-2565},
mesh = {*Disinfection/methods ; *Disinfectants/pharmacology ; Humans ; COVID-19/prevention & control ; China ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; *Microbiota/drug effects ; SARS-CoV-2 ; },
abstract = {BACKGROUND: Disinfectants have been extensively used in public environments since the COVID-19 outbreak to help control the spread of the virus. This study aims to investigate whether disinfectant use influences the structure of bacterial communities and contributes to bacterial resistance to disinfectants and antibiotics.

METHODS: Using molecular biology techniques-including metagenomic sequencing and quantitative PCR (qPCR)-we analyzed the bacterial communities on elevator button surfaces from two tertiary hospitals, one infectious disease hospital, two quarantine hotels (designated for COVID-19 control), and five general hotels in Nanjing, Jiangsu Province, during the COVID-19 pandemic. We focused on detecting disinfectant resistance genes (DRGs), antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs).

RESULTS: Significant differences were observed in the bacterial community structures on elevator button surfaces across the four types of environments. Quarantine hotels, which implemented the most frequent disinfection protocols, exhibited distinct bacterial profiles at the phylum, genus, and species levels. Both α-diversity (within-sample diversity) and β-diversity (between-sample diversity) were lower and more distinct in quarantine hotels compared to the other environments. The abundance of DRGs, ARGs, and MGEs was also significantly higher on elevator button surfaces in quarantine hotels. Notably, antibiotic-resistant bacteria (ARBs), including Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa, were detected in all four settings.

CONCLUSION: The structure of bacterial communities on elevator button surfaces varies across different environments, likely influenced by the frequency of disinfectant use. Increased resistance gene abundance in quarantine hotels suggests that disinfection practices may contribute to the selection and spread of resistant bacteria. Enhanced monitoring of disinfection effectiveness and refinement of protocols in high-risk environments such as hospitals and hotels are essential to limit the spread of resistant pathogens.},
}

*Disinfection/methods
*Disinfectants/pharmacology
Humans
COVID-19/prevention & control
China
*Drug Resistance, Bacterial/genetics
*Bacteria/genetics/drug effects
*Microbiota/drug effects
SARS-CoV-2

@article {pmid40517085,
year = {2025},
author = {Schoenle, A and Francis, O and Archibald, JM and Burki, F and de Vries, J and Dumack, K and Eme, L and Florent, I and Hehenberger, E and Hoffmeyer, TT and Irisarri, I and Lara, E and Leger, MM and Lukeš, J and Massana, R and Mathur, V and Nitsche, F and Strassert, JFH and Worden, AZ and Yurchenko, V and Del Campo, J and Waldvogel, AM},
title = {Protist genomics: key to understanding eukaryotic evolution.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2025.05.004},
pmid = {40517085},
issn = {0168-9525},
abstract = {All eukaryotes other than animals, plants, and fungi are protists. Protists are highly diverse and found in nearly all environments, with key roles in planetary health and biogeochemical cycles. They represent the majority of eukaryotic diversity, making them essential for understanding eukaryotic evolution. However, these mainly unicellular, microscopic organisms are understudied and the generation of protist genomes lags far behind most multicellular lineages. Current genomic methods, which are primarily designed for animals and plants, are poorly suited for protists. Advancing protist genome research requires reevaluating plant- and animal-centric genomic standards. Future efforts must leverage emerging technologies and bioinformatics tools, ultimately enhancing our understanding of eukaryotic molecular and cell biology, ecology, and evolution.},
}

@article {pmid40515809,
year = {2025},
author = {Zhang, Z and Yang, Z and Lin, S and Jiang, S and Zhou, X and Li, J and Lu, W and Zhang, J},
title = {Probiotic-induced enrichment of Adlercreutzia equolifaciens increases gut microbiome wellness index and maps to lower host blood glucose levels.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2520407},
pmid = {40515809},
issn = {1949-0984},
mesh = {Humans ; *Probiotics/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Blood Glucose/analysis/metabolism ; Adult ; Middle Aged ; Metagenomics ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; Young Adult ; },
abstract = {The gut microbiome is essential for maintaining host health, influencing gut function and metabolic regulation. While probiotics are widely used to manage gut health, evidence of their specific effects in healthy individuals remains limited. Most studies focus on diseased populations, with little attention to early interventions in individuals without major diseases. In this study, we investigated the effects of probiotics on gut health in participants free from significant health conditions. Fifty-four participants were randomly assigned to receive either a placebo or composite probiotics for 60 d. Shotgun metagenomics revealed that individuals with lower baseline Gut Microbiome Wellness Index 2 (GMWI) exhibited more decisive responses to probiotic intervention, characterized by an increased abundance of beneficial commensal bacteria, including Adlercreutzia equolifaciens. Probiotic intake significantly improved the function of the gut microbiome, reducing antibiotic resistance genes and virulence factors while enhancing carbohydrate-active enzymes. Notably, A. equolifaciens promoted the production of palmitoyl serinol, a metabolite associated with improved GMWI and preventive benefits in blood glucose. In a population-based experiment, these findings were validated in a follow-up single-strain probiotic intervention with Lacticaseibacillus casei Zhang. Our study highlights the potential of probiotics as an early intervention strategy for maintaining gut health in individuals without significant health conditions.},
}

Humans
*Probiotics/administration & dosage/pharmacology
*Gastrointestinal Microbiome/drug effects
Male
Female
*Blood Glucose/analysis/metabolism
Adult
Middle Aged
Metagenomics
Feces/microbiology
Bacteria/classification/genetics/isolation & purification
Young Adult

@article {pmid40514168,
year = {2025},
author = {Ebrahimi, F and Maleki, H and Ebrahimi, M and Beiki, AH},
title = {A novel approach to finding the compositional differences and biomarkers in gut microbiota in type 2 diabetic patients via meta-analysis, data-mining, and multivariate analysis.},
journal = {Endocrinologia, diabetes y nutricion},
volume = {72},
number = {6},
pages = {501561},
doi = {10.1016/j.endien.2025.501561},
pmid = {40514168},
issn = {2530-0180},
mesh = {*Diabetes Mellitus, Type 2/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Data Mining ; Biomarkers/analysis ; Multivariate Analysis ; Male ; Middle Aged ; Female ; },
abstract = {Type 2 diabetes mellitus (T2DM)-one of the fastest globally spreading diseases-is a chronic metabolic disorder characterized by elevated blood glucose levels. It has been suggested that the composition of gut microbiota plays key roles in the prevalence of T2DM. In this study, a novel approach of large-scale data mining and multivariate analysis of the gut microbiome of T2DM patients and healthy controls was conducted to find the key compositional differences in their microbiota and potential biomarkers of the disease.

METHODS: First, suitable datasets were identified (9 in total with 946 samples), analyzed, and their operational taxonomic units (OTUs) were computed by identical parameters to increase accuracy. The following OTUs were merged and compared based on their health status, and compositional differences detected. For biomarker identification, the OTUs were subjected to 9 different attribute weighting models. Additionally, OTUs were independently analyzed by multivariate algorithms (LEfSe test) to verify the realized biomarkers.

RESULTS: Overall, 23 genera and 4 phyla were identified as possible biomarkers. At genus level, the decrease of Bacteroides, Methanobrevibacter, Paraprevotella, and [Eubacterium] hallii group in T2DM and the increase of Prevotella, Megamonas, Megasphaera, Ligilactobacillus, and Lachnoclostridium were selected as biomarkers; and at phylum level, the increase of Synergistota and the decrease of Euryarchaeota, Desulfobacterota (Thermodesulfobacteriota), and Ptescibacteria.

CONCLUSION: This is the first study ever conducted to find the microbial compositional differences and biomarkers in T2DM using data mining models applied on a widespread metagenome dataset and verified by multivariate analysis.},
}

*Diabetes Mellitus, Type 2/microbiology
Humans
*Gastrointestinal Microbiome
*Data Mining
Biomarkers/analysis
Multivariate Analysis
Male
Middle Aged
Female

@article {pmid40510676,
year = {2025},
author = {Bruins-van Sonsbeek, LGR and Verschuren, MCM and Kaal, S and Lindenburg, PW and Rodenburg, KCW and Clauss, M and Speksnijder, AGCL and Rutten, VPMG and Bonnet, BFJ and Wittink, F},
title = {Rhinoceromics: a multi-amplicon study with clinical markers to transferrin saturation levels in ex-situ black rhinoceros (Diceros bicornis michaeli).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1515939},
pmid = {40510676},
issn = {1664-302X},
abstract = {Iron overload disorder (IOD) is a common condition in ex-situ black rhinoceroses (Diceros bicornis), although it has not been reported in the wild. This study aimed to gain a deeper understanding of the relationship between 25-hydroxy vitamin D [25(OH)D], inflammatory markers, insulin levels, the gut microbiome, dietary components, and transferrin saturation (TS) in ex-situ black rhinoceroses. Blood and fecal samples from 11 black rhinoceroses at five different European zoological institutions were monitored over a 1-year period. Inflammatory markers such as interleukin 6 (IL-6), serum amyloid A (SAA), interferon γ (IFN-γ), and tumor necrosis factor α (TNF-α) were analyzed. Our study corroborates the findings of previous research, which demonstrated that insulin, inflammatory markers, and TS% are higher in ex-situ black rhinoceroses compared to published wild ranges. Our data show no correlations between insulin, 25(OH)D, TS%, inflammatory markers, or short-chain fatty acids (SFCAs). Serum 25(OH)D exhibited significantly higher levels in summer than in winter. Transferrin saturation was influenced by age, which is consistent with previous studies. The microbiome did not differ significantly among individuals, institutions, sex, or season, unlike the mycobiome, which exhibited significant differences across institutions. The impact of the mycobiome differences on the physiology of the animals could not be determined from this study.},
}

@article {pmid40508035,
year = {2025},
author = {Toto, F and Scanu, M and Gramegna, M and Putignani, L and Del Chierico, F},
title = {Impact of DNA Extraction and 16S rRNA Gene Amplification Strategy on Microbiota Profiling of Faecal Samples.},
journal = {International journal of molecular sciences},
volume = {26},
number = {11},
pages = {},
pmid = {40508035},
issn = {1422-0067},
support = {Current Research funds//Italian Ministry of Health/ ; n.a.//Technogenetics S.p.A./ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; Humans ; *DNA, Bacterial/genetics/isolation & purification ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; Bacteria/genetics/classification ; Metagenome ; },
abstract = {High-throughput 16S rRNA metagenomic sequencing has advanced our understanding of the gut microbiome, but its reliability depends on upstream processes such as DNA extraction and bacterial library preparation. In this study, we evaluated the impact of three different DNA extraction methods (a manual method with an ad hoc-designed pre-extraction phase (PE-QIA), and two automated magnetic bead-based methods (T180H and TAT132H)) and two bacterial library preparation protocols (home brew and VeriFi) on the 16S rRNA-based metagenomic profiling of faecal samples. T180H and TAT132H produced significantly higher DNA concentrations than PE-QIA, whereas TAT132H yielded DNA of lower purity compared to the others. In the taxonomic analysis, PE-QIA provided a balanced recovery of Gram-positive and Gram-negative bacteria, TAT132H was enriched in Gram-positive taxa, and T180H was enriched in Gram-negative taxa. An analysis of Microbial Community Standard (MOCK) samples showed that PE-QIA and T180H were more accurate than TAT132H. Finally, the VeriFi method yielded higher amplicon concentrations and sequence counts than the home brew protocol, despite the high level of chimeras. In conclusion, a robust performance in terms of DNA yield, purity, and taxonomic representation was obtained by PE-QIA and T180H. Furthermore, it was found that the impact of PCR-based steps on gut microbiota profiling can be minimized by an accurate bioinformatic pipeline.},
}

*RNA, Ribosomal, 16S/genetics
*Feces/microbiology
Humans
*DNA, Bacterial/genetics/isolation & purification
*Gastrointestinal Microbiome/genetics
Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
*Microbiota/genetics
Bacteria/genetics/classification
Metagenome

@article {pmid40507096,
year = {2025},
author = {Lutsiv, T and Fitzgerald, VK and Neil, ES and McGinley, JN and Hussan, H and Thompson, HJ},
title = {Cooked Bean (Phaseolus vulgaris L.) Consumption Alters Bile Acid Metabolism in a Mouse Model of Diet-Induced Metabolic Dysfunction: Proof-of-Concept Investigation.},
journal = {Nutrients},
volume = {17},
number = {11},
pages = {},
pmid = {40507096},
issn = {2072-6643},
support = {58-3060-8-031//USDA ARS/ ; 2020-05206//National Institute for Food and Agriculture:/ ; },
mesh = {Animals ; *Bile Acids and Salts/metabolism ; Mice, Inbred C57BL ; *Phaseolus ; Mice ; Male ; Liver/metabolism ; Disease Models, Animal ; Feces/chemistry ; Cecum/microbiology/metabolism ; Gastrointestinal Microbiome ; Cooking ; Obesity/metabolism ; Metabolomics ; *Diet ; *Metabolic Diseases/etiology/metabolism ; Diet, High-Fat/adverse effects ; },
abstract = {Background/Objectives: Metabolic dysregulation underlies a myriad of chronic diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD) and obesity, and bile acids emerge as an important mediator in their etiology. Weight control by improving diet quality is the standard of care in prevention and control of these metabolic diseases. Inclusion of pulses, such as common bean, is an affordable yet neglected approach to improving diet quality and metabolic outcomes. Thus, this study evaluated the possibility that common bean alters bile acid metabolism in a health-beneficial manner. Methods: Using biospecimens from several similarly designed studies, cecal content, feces, liver tissue, and plasma samples from C57BL/6 mice fed an obesogenic diet lacking (control) or containing cooked common bean were subjected to total bile acid analysis and untargeted metabolomics. RNA-seq, qPCR, and Western blot assays of liver tissue complemented the bile acid analyses. Microbial composition and predicted function in the cecal contents were evaluated using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Results: Bean-fed mice had increased cecal bile acid content and excreted more bile acids per gram of feces. Consistent with these effects, increased synthesis of bile acids in the liver was observed. Microbial composition and capacity to metabolize bile acids were markedly altered by bean, with greater prominence of secondary bile acid metabolites in bean-fed mice, i.e., microbial metabolites of chenodeoxycholate/lithocholate increased while metabolites of hyocholate were reduced. Conclusions: In rendering mice resistant to obesogenic diet-induced MASLD and obesity, cooked bean consumption sequesters bile acids, increasing their hepatic synthesis and enhancing their diversity through microbial metabolism. Bean-induced changes in bile acid metabolism have potential to improve dyslipidemia.},
}

Animals
*Bile Acids and Salts/metabolism
Mice, Inbred C57BL
*Phaseolus
Mice
Male
Liver/metabolism
Disease Models, Animal
Feces/chemistry
Cecum/microbiology/metabolism
Gastrointestinal Microbiome
Cooking
Obesity/metabolism
Metabolomics
*Diet
*Metabolic Diseases/etiology/metabolism
Diet, High-Fat/adverse effects

@article {pmid40507017,
year = {2025},
author = {Ying, J and Xu, X and Zhou, R and Chung, ACK and Ng, SK and Fan, X and Subramaniam, M and Wong, SH},
title = {The Gut Microbiota in Young Adults with High-Functioning Autism Spectrum Disorder and Its Performance as Diagnostic Biomarkers.},
journal = {Nutrients},
volume = {17},
number = {11},
pages = {},
pmid = {40507017},
issn = {2072-6643},
support = {Nil//NHG-LKCMedicine Clinician-Scientist Preparatory Programme Plus/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Autism Spectrum Disorder/microbiology/diagnosis ; Male ; Female ; Biomarkers ; Young Adult ; Adult ; Case-Control Studies ; Feces/microbiology ; Metagenomics ; Machine Learning ; ROC Curve ; Adolescent ; },
abstract = {Background/Objectives: Diagnosing ASD in adults presents unique challenges, and there are currently no specific biomarkers for this condition. Most existing studies on the gut microbiota in ASD are conducted in children; however, the composition of the gut microbiota in children differs significantly from that of adults. This study aimed to study the gut microbiota of young adults with high-functioning ASD. Methods: Using metagenomic sequencing, we evaluated the gut microbiota in 45 adults with high-functioning ASD and 45 matched healthy controls. Results: Adjusting for sociodemographic information, dietary habits, and clinical data, we observed a distinct microbiota profile of adults with ASD in comparison to controls, with the intensity of autistic traits strongly correlating to microbial diversity (correlation coefficient = -0.351, p-value < 0.001). Despite a similar dietary pattern, the ASD group exhibited more gastrointestinal symptoms than the healthy controls. An internally validated machine-learning predictive model that combines the Autism Spectrum Quotient questionnaire score of individuals with their microbial features could achieve an area under the receiver operating characteristic curve (AUC) of 0.955 in diagnosing ASD in adults. Conclusions: This study evaluates the gut microbiota in adult ASD and highlights its potential as a non-invasive biomarker to enhance the diagnosis of ASD in this population group.},
}

Humans
*Gastrointestinal Microbiome
*Autism Spectrum Disorder/microbiology/diagnosis
Male
Female
Biomarkers
Young Adult
Adult
Case-Control Studies
Feces/microbiology
Metagenomics
Machine Learning
ROC Curve
Adolescent

@article {pmid40506497,
year = {2025},
author = {Jung, DR and Choi, Y and Jeong, M and Singh, V and Jeon, SY and Seo, I and Park, NJ and Lee, YH and Park, JY and Han, HS and Shin, JH and Chong, GO},
title = {Metagenomic insight into the vaginal microbiome in women infected with HPV 16 and 18.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {105},
pmid = {40506497},
issn = {2055-5008},
mesh = {Female ; Humans ; *Vagina/microbiology/virology ; *Human papillomavirus 16/genetics/isolation & purification ; *Papillomavirus Infections/virology/microbiology ; *Microbiota/genetics ; Metagenomics ; *Human papillomavirus 18/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; Uterine Cervical Neoplasms/virology/microbiology ; Metagenome ; Adult ; Middle Aged ; },
abstract = {Human papillomavirus (HPV) 16 and 18 (HPV 16/18) account for over 70% of cervical cancer (CC) cases, yet their interaction with the vaginal microbiome (VM) remains unclear. This study explored the association between high-risk HPV types (HR-HPVs), VM composition and bacterial function using shotgun metagenomic sequencing. In early-stage cervical lesions, the HPV 16/18 group showed reduced Lactobacillus-dominant community state types compared to other HR-HPVs, while invasive CC exhibited increased pathogenic bacteria, including Streptococcus agalactiae, Fannyhessea vaginae, and Sneathia vaginalis. The VM associated with HPV 16/18 was enriched in immune response and inflammation pathways, whereas other HR-HPVs were linked to cellular metabolism and hormonal signaling. Notably, HPV 16/18 exhibited stronger bacterial-fungal correlations, indicating shifts in the microbial community. Furthermore, 137 metagenome-assembled genomes provided insights into unique microbial genomic signatures. Our study links VM differences with HPV 16/18 oncogenic potential across cervical lesion stages, urging further research for better diagnostics and treatments.},
}

Female
Humans
*Vagina/microbiology/virology
*Human papillomavirus 16/genetics/isolation & purification
*Papillomavirus Infections/virology/microbiology
*Microbiota/genetics
Metagenomics
*Human papillomavirus 18/genetics/isolation & purification
*Bacteria/classification/genetics/isolation & purification
Uterine Cervical Neoplasms/virology/microbiology
Metagenome
Adult
Middle Aged

@article {pmid40506443,
year = {2025},
author = {Bredon, M and Hausfater, P and Khalki, L and Tijani, Y and Cheikh, A and Brot, L and Creusot, L and Rolhion, N and Trottein, F and Lambeau, G and Georgin-Lavialle, S and Bleibtreu, A and Baudel, JL and Lefèvre, A and Emond, P and Tubach, F and Simon-Tillaux, N and Simon, T and Gorochov, G and Zaid, Y and Sokol, H},
title = {Gut microbiota alterations are linked to COVID-19 severity in North African and European populations.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {106},
pmid = {40506443},
issn = {2055-5008},
support = {ANR-23-CE15-0014-01, GUTSY//AAP générique 2022/ ; ANR-23-CE15-0014-01, GUTSY//AAP générique 2022/ ; PR-BLV-20220527//Balvi Filantropic Fund/ ; RPH20003DDP//DIM One Health 2020/ ; },
mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Bacteria/classification/genetics/isolation & purification ; *COVID-19/microbiology/pathology ; *Dysbiosis/microbiology ; Feces/microbiology ; France/epidemiology ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Morocco/epidemiology ; North African People ; Severity of Illness Index ; },
abstract = {Although COVID-19 primarily affects the respiratory system, many patients experience gastrointestinal symptoms, suggesting a role for the gut microbiota in disease pathogenesis. To explore this, we performed shotgun metagenomic sequencing on stool samples from 200 COVID-19 patients and 102 healthy controls in Morocco and France. Despite geographic differences in microbiota composition, patients with COVID-19 in both continents exhibited significant gut microbiota alterations, which were more pronounced in severe cases, with similar features compared with controls. Functional pathways, including L-Tryptophan biosynthesis, were disrupted, particularly in patients with severe disease. Machine learning models accurately predicted disease severity based on gut microbial profiles in the Moroccan cohort, though not in the French cohort. These results highlight consistent microbiota changes associated with COVID-19 and support a potential link between gut dysbiosis and disease severity.},
}

Adult
Aged
Female
Humans
Male
Middle Aged
Bacteria/classification/genetics/isolation & purification
*COVID-19/microbiology/pathology
*Dysbiosis/microbiology
Feces/microbiology
France/epidemiology
*Gastrointestinal Microbiome/genetics
Metagenomics
Morocco/epidemiology
North African People
Severity of Illness Index

@article {pmid40503898,
year = {2025},
author = {Han, H and Ji, M and Li, Y and Gong, X and Song, W and Zhou, J and Ma, K and Zhou, Y and Liu, X and Wang, M and Li, Y and Tu, Q},
title = {Tracing non-fungal eukaryotic diversity via shotgun metagenomes in the complex mudflat intertidal zones.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0041325},
doi = {10.1128/msystems.00413-25},
pmid = {40503898},
issn = {2379-5077},
abstract = {Eukaryotes, both micro- and macro-, constitute the dominant component of Earth's biosphere visible to the naked eye. Although relatively big in organismal size, tracing eukaryotic diversity in complex environments is not easy. For example, they may actively escape from sampling and be physically absent from the collected samples. In this study, we strived to recover non-fungal eukaryotic DNA sequences from typical shotgun metagenomes in the complex mudflat intertidal zones. Multiple recently developed approaches for identifying eukaryotic sequences from shotgun metagenomes were comparatively assessed. Considering the low overlap among different approaches, an integrative workflow was proposed. The integrative workflow was then used to recover the eukaryotic communities in complex intertidal sediments. The temporal dynamics of intertidal eukaryotic communities were investigated through a time-series sampling effort. Thirty-four non-fungal eukaryotic phyla were detected from 36 shotgun metagenomes. Clear temporal variation in relative abundance was observed for eukaryotic genera such as Timema and Navicula. Strong temporal turnover of intertidal eukaryotic communities was observed. By comparing to 18S rRNA gene amplicon sequencing, dramatically different community profiles were observed between these two approaches. However, the temporal patterns for intertidal eukaryotic communities recovered by both approaches were generally comparable. This study provides valuable technical insights into the recovery of non-fungal eukaryotic information from complex environments and demonstrates an alternative route for reusing the massive metagenomic data sets generated in the past and future.IMPORTANCEEukaryotes represent the dominant component visible to the naked eye and contribute to the primary biomass in the Earth's biosphere. Yet, tracing the eukaryotic diversity in complex environments remains difficult, as they can actively move around and escape from sampling. Here, using the intertidal sediments as an example, we strived to retrieve non-fungal eukaryotic sequences from typical shotgun metagenomes. Compared to 18S rRNA gene amplicon sequencing, the shotgun metagenome-based approach resolved dramatically different eukaryotic community profiles, though comparable ecological patterns could be observed. This study paves an alternative way for utilizing shotgun metagenomic data to recover non-fungal eukaryotic information in complex environments, demonstrating significant potential for environmental monitoring and biodiversity investigations.},
}

@article {pmid40500753,
year = {2025},
author = {Bograd, A and Oppenheimer-Shaanan, Y and Levy, A},
title = {Plasmids, prophages, and defense systems are depleted from plant microbiota genomes.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {163},
pmid = {40500753},
issn = {1474-760X},
support = {1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; },
mesh = {*Prophages/genetics ; *Plasmids/genetics ; *Plants/microbiology ; *Genome, Bacterial ; *Microbiota/genetics ; Metagenome ; *Bacteria/genetics/virology ; },
abstract = {Plant-associated bacteria significantly impact plant growth and health. Understanding how bacterial genomes adapt to plants can provide insights into their growth promotion and virulence functions. Here, we compare 38,912 bacterial genomes and 6073 metagenomes to explore the distribution of mobile genetic elements and defense systems in plant-associated bacteria. We reveal a consistent taxon-independent depletion of prophages, plasmids, and defense systems in plant-associated bacteria, particularly in the phyllosphere, compared to other ecosystems. The mobilome depletion suggests the presence of unique ecological constraints or molecular mechanisms exerted by plants to control the bacterial mobilomes independently of bacterial immunity.},
}

*Prophages/genetics
*Plasmids/genetics
*Plants/microbiology
*Genome, Bacterial
*Microbiota/genetics
Metagenome
*Bacteria/genetics/virology

@article {pmid40497237,
year = {2025},
author = {Feng, Y and Kuang, G and Pan, Y and Wang, J and Yang, W and Wu, WC and Pan, H and Wang, J and Han, X and Yang, L and Xin, GY and Shan, YT and Gou, QY and Liu, X and Guo, D and Liang, G and Holmes, EC and Gao, Z and Shi, M},
title = {Small mammals in a biodiversity hotspot harbor viruses of emergence risk.},
journal = {National science review},
volume = {12},
number = {6},
pages = {nwae463},
pmid = {40497237},
issn = {2053-714X},
abstract = {Metagenomic sequencing has transformed the understanding of viral diversity in wildlife and the potential threats these viruses pose to human health. Despite this progress, such sequencing studies often have lacked systematic and ecologically informed sampling, thereby likely missing many potential human pathogens and the drivers behind their ecology, evolution and emergence. We conducted an extensive search for viruses in the lungs, spleens and guts of 1688 mammals from 38 species across 428 sites in Yunnan Province, China-a hotspot for zoonoses emergence. We identified 162 mammalian viruses, including 102 new ones and 24 posing potential risks to humans due to their relationships with known human pathogens associated with serious diseases or their ability to cross major host species barriers. Our findings offer an in-depth view of virus organotropism, cross-host associations, host sharing patterns, and the ecological factors influencing viral evolution, all of which are critical for anticipating and mitigating future zoonotic outbreaks.},
}

@article {pmid40495477,
year = {2025},
author = {Hurst, C and Zobel, G and Young, W and Olson, T and Parkar, N and Bracegirdle, J and Hannaford, R and Anderson, RC and Dalziel, JE},
title = {Social Isolation Induces Sex-Specific Differences in Behavior and Gut Microbiota Composition in Stress-Sensitive Rats.},
journal = {Brain and behavior},
volume = {15},
number = {6},
pages = {e70621},
pmid = {40495477},
issn = {2162-3279},
support = {//Smarter Lives: New opportunities for dairy products across the lifespan/ ; C10X1706//Ministry of Business, Innovation and Employment/ ; },
mesh = {Animals ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Rats ; *Social Isolation/psychology ; *Stress, Psychological/microbiology/physiopathology ; *Behavior, Animal/physiology ; Rats, Inbred WKY ; Anxiety ; *Sex Characteristics ; Sex Factors ; Cecum/microbiology ; },
abstract = {BACKGROUND: Social isolation (SI) is an established rat model of chronic stress. We applied this to the stress-sensitive Wistar Kyoto (WKY) strain to explore brain-to-gut interactions associated with mood. Whether SI stress-induced behavioral changes are sex-specific or if they affect the microbiome in WKY is unknown. We hypothesized individually housed (IH) animals would be more anxious than pair-housed (PH), with sex differences. Male and female rats were either IH or PH from 70 to 112 days old and behavior was assessed in modified open field (OFTmod), elevated plus maze (EPM), and novel object recognition (NOR) tests. Cecal content DNA was analyzed by shotgun metagenome sequencing.

RESULTS: IH rats, particularly females, spent more time in the center of the OFTmod where the semi-novel feed was presented compared to PH group rats. There was a tendency for greater distance traveled, or potential hyperactivity, in IH female rats. Males stayed in the EPM closed arms more than females. No treatment difference occurred for recognition memory. SI altered cecal microbiome composition in females where housing was associated with seven differentially abundant taxa and 49 differentially abundant KEGG Level 3 ortholog/gene categories. Several relationships were noted between behavioral traits and relative abundance of microbiome taxa. There was a greater shift in female microbiome composition.

CONCLUSIONS: In summary, behavioral responses to the housing treatment were minimal. IH animals, particularly females, spent more time in the center of an OFT that contained food; this may have been an indication of depression, as opposed to anxiety. Housing status had a differential impact on the microbiome for females compared to males. The associations between cecal microbiota and activity in the modified OFT suggest that dietary interventions that influence the relative abundance of Bifidobacteria, Alistipes, and Muribaculaceae should be explored.},
}

Animals
Male
Female
*Gastrointestinal Microbiome/physiology
Rats
*Social Isolation/psychology
*Stress, Psychological/microbiology/physiopathology
*Behavior, Animal/physiology
Rats, Inbred WKY
Anxiety
*Sex Characteristics
Sex Factors
Cecum/microbiology

@article {pmid40494297,
year = {2025},
author = {Hibbett, D and Nagy, LG and Nilsson, RH},
title = {Fungal diversity, evolution, and classification.},
journal = {Current biology : CB},
volume = {35},
number = {11},
pages = {R463-R469},
doi = {10.1016/j.cub.2025.01.053},
pmid = {40494297},
issn = {1879-0445},
mesh = {*Fungi/classification/genetics ; Phylogeny ; *Biodiversity ; *Biological Evolution ; },
abstract = {Fungi include mushrooms, molds, lichens, yeasts, and zoosporic forms that occur as free-living or symbiotic organisms in every ecosystem on Earth. About 155,000 species of Fungi have been described, and possibly millions more remain to be named. Recent focus on aquatic habitats has illuminated major groups near the boundary between Fungi and protists. Fungal systematists have made remarkable progress toward resolving the major branches of the phylogeny, although some deep nodes have proven recalcitrant. Fungal taxonomists steadily describe about 3,000 new species per year, and fungal molecular ecologists routinely detect many thousands of unidentifiable 'dark fungi' through metagenomic analyses. To assemble the complete fungal tree of life, it will be necessary to connect the main branches of the phylogeny to information on all described species and integrate the vast and rapidly growing corpus of dark fungi.},
}

*Fungi/classification/genetics
Phylogeny
*Biodiversity
*Biological Evolution

@article {pmid40493399,
year = {2025},
author = {Han, S and Zhang, Q and Zhang, H and Ma, J},
title = {Eucommia ulmoides and its inhibitory effects on prevotella in piglet gut microbiome through metagenomic and metabolomic analysis.},
journal = {Animal biotechnology},
volume = {36},
number = {1},
pages = {2503753},
doi = {10.1080/10495398.2025.2503753},
pmid = {40493399},
issn = {1532-2378},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Prevotella/drug effects ; Swine/microbiology/growth & development ; *Eucommiaceae/chemistry ; Animal Feed/analysis ; Metagenomics ; Metabolomics ; Diet/veterinary ; Dietary Supplements ; Feces/microbiology ; },
abstract = {Eucommia ulmoides (EU) is a traditional medicinal plant widely cultivated across China. The combination of EU and feed significantly affects the growth performance, intestinal microbiota composition, and metabolic characteristics of weaned piglets. Forty Landrace x Yorkshire piglets were randomly assigned to four groups: a control group receiving a basal diet, three treatment groups receiving a basal diet supplemented with EU and EU with mix energy (EU+ME), and EU with high protein and energy (EU+HPE), respectively. Growth performance was monitored over a 25-day feeding period, and fecal samples were collected for subsequent metagenomic sequencing and metabolomic analysis. Piglets supplemented with EU, EU+ME, and EU+HPE exhibited significantly improved growth performance, compared to the control group. Metagenomic analysis revealed significant alterations in gut microbiota composition, with increased beneficial bacterial classes and suppression of Prevotella spp. Metabolomic profiling demonstrated distinct metabolic alterations among the treatment groups, with pathway impact analysis highlighting enhanced protein synthesis and energy metabolism. Furthermore, EU supplementation did not affect porcine epidemic diarrhea virus activity in vitro but reduced LPS-induced intestinal inflammation. These findings suggest that EU could be a promising natural additive for improving piglet health and growth, with potential implications for managing post-weaning challenges in swine production.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Prevotella/drug effects
Swine/microbiology/growth & development
*Eucommiaceae/chemistry
Animal Feed/analysis
Metagenomics
Metabolomics
Diet/veterinary
Dietary Supplements
Feces/microbiology

@article {pmid40491436,
year = {2025},
author = {Li, D and Zhang, DY and Chen, SJ and Lv, YT and Huang, SM and Chen, C and Zeng, F and Chen, RX and Zhang, XD and Xiong, JX and Chen, FD and Jiang, YH and Chen, Z and Mo, CY and Chen, JJ and Zhu, XL and Zhang, LJ and Bai, FH},
title = {Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1565887},
pmid = {40491436},
issn = {2235-2988},
mesh = {Humans ; *COVID-19/microbiology ; *Gastrointestinal Microbiome ; *Fungi/classification/genetics/isolation & purification ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Adult ; Middle Aged ; Feces/microbiology ; SARS-CoV-2 ; *Mycobiome ; Probiotics ; Metagenomics ; China ; },
abstract = {OBJECTIVE: COVID-19 has had a profound impact on public health globally. However, most studies have focused on patients with long COVID or those in the acute phase of infection, with limited research on the health of individuals who have recovered from mild COVID-19. This study investigates the long-term changes in bacterial and fungal communities in individuals recovering from mild COVID-19 and their clinical relevance.

METHODS: Healthy individuals from Hainan Province were enrolled before the COVID-19 outbreak, along with individuals recovering from COVID-19 at 3 months and 6 months post-recovery. Stool, blood samples, and metadata were collected. Metagenomic sequencing and Internal Transcribed Spacer (ITS) analysis characterized bacterial and fungal communities, while bacterial-fungal co-occurrence networks were constructed. A random forest model evaluated the predictive capacity of key taxa.

RESULTS: The gut microbiota of COVID-19 recoverees differed significantly from that of healthy individuals. At 3 months post-recovery, probiotics (e.g., Blautia massiliensis and Kluyveromyces spp.) were enriched, linked to improved metabolism, while at 6 months, partial recovery of probiotics (e.g., Acidaminococcus massiliensis and Asterotremella spp.) was observed alongside persistent pathogens (e.g., Streptococcus equinus and Gibberella spp.). Dynamic changes were observed, with Acidaminococcus massiliensis enriched at both baseline and 6 months but absent at 3 months. Co-occurrence network analysis revealed synergies between bacterial (Rothia spp.) and fungal (Coprinopsis spp.) taxa, suggesting their potential roles in gut restoration. The bacterial random forest model (10 taxa) outperformed the fungal model (8 taxa) in predicting recovery status (AUC = 0.99 vs. 0.80).

CONCLUSION: These findings highlight the significant long-term impacts of mild COVID-19 recovery on gut microbiota, with key taxa influencing metabolism and immune regulation, supporting microbiome-based strategies for recovery management.},
}

Humans
*COVID-19/microbiology
*Gastrointestinal Microbiome
*Fungi/classification/genetics/isolation & purification
Female
*Bacteria/classification/genetics/isolation & purification
Male
Adult
Middle Aged
Feces/microbiology
SARS-CoV-2
*Mycobiome
Probiotics
Metagenomics
China

@article {pmid40490984,
year = {2025},
author = {Vargas, BO and Carazzolle, MF and Galhardo, JP and José, J and de Souza, BC and Correia, JBL and Santos, JRD and Pereira, GAG and de de Mello, FDSB},
title = {Engineering Saccharomyces Cerevisiae With Novel Functional Xylose Isomerases From Rumen Microbiota for Enhanced Biofuel Production.},
journal = {Biotechnology journal},
volume = {20},
number = {6},
pages = {e70050},
pmid = {40490984},
issn = {1860-7314},
support = {//National Agency of Petroleum, Natural Gas and Biofuels/ ; JPG: 88887.479699/2020-0//National Council for the Improvement of Higher Education/ ; JRS: 142340/2020-0//National Council for the Improvement of Higher Education/ ; BCS: 2022/05001-4//Fundação de Amparo à Pesquisa no Estado de São Paulo/ ; },
mesh = {*Saccharomyces cerevisiae/genetics/metabolism/enzymology ; Animals ; *Rumen/microbiology ; *Biofuels ; Sheep ; Xylose/metabolism ; Cattle ; Camelus/microbiology ; *Metabolic Engineering/methods ; Ethanol/metabolism ; Fermentation ; Microbiota/genetics ; Aldose-Ketose Isomerases ; },
abstract = {Xylose metabolism in Saccharomyces cerevisiae remains a significant bottleneck due to the difficulty in identifying functional and efficient xylose isomerases (XI). In the present study, publicly available metagenomic and metatranscriptomic datasets of rumen microbiota from different herbivorous mammals were used to prospect novel XIs sequences. Seven putative XIs from moose, camel, cow, and sheep were cloned into a strain modified for xylose metabolism. Out of those, five XIs demonstrated activity and efficiently converted xylose into xylulose, resulting in ethanol as the final product. A XI from camel rumen microbiota exhibited a KM of 16.25 mM, indicating high substrate affinity. The strains expressing enzymes XI11 and XI12, obtained from sheep rumen microbiota, were able to deplete 40 g/L of xylose within 72 and 96 h, achieving theoretical ethanol yields of 90% and 88%, respectively. These results are comparable to those obtained with Orpinomyces sp. ukk1 XI, a benchmark enzyme previously reported as highly efficient in S. cerevisiae. This study also provides the first report on the successful expression of XIs mined from the ruminal microbiotas of sheep and camels in S. cerevisiae, expanding the perspectives for the optimization of fermentation processes and the production of lignocellulosic biofuels from xylose.},
}

*Saccharomyces cerevisiae/genetics/metabolism/enzymology
Animals
*Rumen/microbiology
*Biofuels
Sheep
Xylose/metabolism
Cattle
Camelus/microbiology
*Metabolic Engineering/methods
Ethanol/metabolism
Fermentation
Microbiota/genetics
Aldose-Ketose Isomerases

@article {pmid40489326,
year = {2025},
author = {Sun, Y and Guo, K and Tang, J and Zhao, J and Zhang, X and Yan, Y and Yuan, L and Zhang, Y and Qiu, C and Luo, J and Zhang, W and Fang, H and Chen, J},
title = {Changes of respiratory microbiota associated with prognosis in pulmonary infection patients with invasive mechanical ventilation-supported respiratory failure.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2514093},
pmid = {40489326},
issn = {1365-2060},
mesh = {Humans ; Male ; Female ; Retrospective Studies ; *Respiration, Artificial/methods/adverse effects ; Prognosis ; *Respiratory Insufficiency/therapy/microbiology/mortality ; Middle Aged ; Aged ; *Microbiota/genetics ; Intensive Care Units/statistics & numerical data ; High-Throughput Nucleotide Sequencing ; *Respiratory Tract Infections/microbiology/mortality ; Anti-Bacterial Agents/therapeutic use ; Risk Factors ; },
abstract = {BACKGROUND: Respiratory failure (RF) is an important cause of intensive care unit (ICU) admission and mortality due to respiratory diseases. This study aimed to evaluate the clinical performance of metagenomic next-generation sequencing (mNGS) testing in pathogen diagnosis, medication guidance and to explore dynamic changes in the respiratory microbiota associated with prognosis.

METHODS: This multicenter retrospective study enrolled ICU patients from five hospitals who underwent invasive mechanical ventilation (IMV) and had pathogenic microorganisms identified by both mNGS and conventional microbiological tests (CMT) from December 2021 to April 2024. Patients were classified into two groups based on discharge outcomes: survivors (n=122) and non-survivors (n=35).

RESULTS: Compared with the survivors, non-survivors had a significantly higher proportion of smokers, dyspnea, type I RF, blood urea nitrogen, and C-reactive protein (p < 0.05). All the above indicators were identified as independent risk factors for mortality, except for type I RF. mNGS showed a better performance for pathogen identification than CMT in both groups, and nearly 60% showed consistent results between the two methods. Among survivors, antibiotic adjustment was mainly based on mNGS results (35.25%), whereas non-survivors more frequently received adjustments based on mNGS and CMT results (34.29%). The richness and abundance of lung microorganisms in the non-survivors were significantly lower than those in the survivors (p < 0.05).

CONCLUSIONS: mNGS is a promising method for identifying pathogens in pulmonary infections in IMV-supported RF patients and for exploring changes in lung microbial composition to provide a reference for patient prognosis.},
}

Humans
Male
Female
Retrospective Studies
*Respiration, Artificial/methods/adverse effects
Prognosis
*Respiratory Insufficiency/therapy/microbiology/mortality
Middle Aged
Aged
*Microbiota/genetics
Intensive Care Units/statistics & numerical data
High-Throughput Nucleotide Sequencing
*Respiratory Tract Infections/microbiology/mortality
Anti-Bacterial Agents/therapeutic use
Risk Factors

@article {pmid40488306,
year = {2025},
author = {Yoshimura, E and Hamada, Y and Hatamoto, Y and Nakagata, T and Nanri, H and Nakayama, Y and Iwasaka, C and Hayashi, T and Suzuki, I and Ando, T and Ishikawa-Takata, K and Tanaka, S and Ono, R and Araki, M and Kawashima, H and Chen, YA and Park, J and Hosomi, K and Mizuguchi, K and Kunisawa, J and Miyachi, M},
title = {Effect of short-term dietary intervention on fecal serotonin, gut microbiome-derived tryptophanase, and energy absorption in a randomized crossover trial: an exploratory analysis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2514137},
pmid = {40488306},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/chemistry/microbiology ; Cross-Over Studies ; Male ; *Serotonin/analysis/metabolism ; Adult ; Female ; Young Adult ; *Tryptophanase/metabolism/analysis/genetics ; Energy Metabolism ; *Diet ; Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In this study, we investigated the effects of short-term energy loads on changes in gut microbiome-derived tryptophanase and fecal serotonin levels and their association with variations in energy absorption. This randomized crossover energy-load intervention study included 15 healthy participants subjected to three dietary conditions - overfeeding, control, and underfeeding - for eight days. The effects of the dietary conditions on energy absorption (digestible and metabolizable energy) were assessed using a bomb calorimeter. Fecal serotonin levels were assessed using LC-MS/MS, and the gut microbiota was analyzed using the 16S rRNA gene and metagenomic shotgun analysis. Significant differences were observed in digestible energy (p < 0.001), with higher values in the overfeeding than in the control (p = 0.032) conditions. Furthermore, significant differences were noted in metabolizable energy and gut transit time (p < 0.001), both of which were higher in the overfeeding than in the control (metabolizable energy: p = 0.001; gut transit time: p = 0.014) and underfeeding (metabolizable energy: p < 0.001; gut transit time: p = 0.004) conditions. Fecal serotonin levels differed significantly (p < 0.001), with significantly lower levels in the overfeeding than in the control (p = 0.005) and underfeeding (p < 0.001) conditions. Tryptophanase exhibited significant differences (p = 0.0019), with lower gene abundance in the overfeeding than in the underfeeding (p = 0.001) condition. Tryptophanase positively correlated with Bacteroides abundance under all conditions (correlation coefficient: 0.696-0.896). Intra-individual variability in fecal serotonin levels was significantly negatively associated with digestible energy (β = -0.077, p = 0.019). The findings suggest that short-term energy loads dynamically alter fecal serotonin, Bacteroides, and tryptophanase levels. Moreover, changes in fecal serotonin levels might be indirectly associated with energy absorption.},
}

Humans
*Gastrointestinal Microbiome
*Feces/chemistry/microbiology
Cross-Over Studies
Male
*Serotonin/analysis/metabolism
Adult
Female
Young Adult
*Tryptophanase/metabolism/analysis/genetics
Energy Metabolism
*Diet
Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics

@article {pmid40484531,
year = {2025},
author = {Hu, Q and Cheng, S and Qian, D and Wang, Y and Xie, G and Peng, Q},
title = {Identification of core microbial communities and their influence on flavor-oriented traditional fermented sour cucumbers.},
journal = {Food microbiology},
volume = {131},
number = {},
pages = {104810},
doi = {10.1016/j.fm.2025.104810},
pmid = {40484531},
issn = {1095-9998},
mesh = {Volatile Organic Compounds/metabolism/analysis ; Fermentation ; *Cucumis sativus/microbiology/chemistry ; *Fermented Foods/microbiology/analysis ; Taste ; *Bacteria/metabolism/classification/genetics/isolation & purification ; *Flavoring Agents/metabolism ; Humans ; *Microbial Consortia ; Food Microbiology ; *Microbiota ; },
abstract = {Sour cucumber is a traditional fermented vegetable with global popularity, yet its fermentation process often leads to inconsistencies in quality and flavor due to the reliance on natural fermentation. This study identifies 12 core volatile organic compounds (VOCs) contributing to its unique flavor and investigates the key microbial species involved in the fermentation process. Using a synthetic microbial consortium constructed from core microbial species, we successfully replicated the flavor profile of naturally fermented sour cucumbers while enhancing safety by reducing nitrite levels. This approach also reduced bitterness and astringency, while improving sourness and umami, providing a robust framework for standardized production of high-quality fermented vegetables. These findings offer practical solutions for improving flavor quality and ensuring the safety of fermented foods.},
}

Volatile Organic Compounds/metabolism/analysis
Fermentation
*Cucumis sativus/microbiology/chemistry
*Fermented Foods/microbiology/analysis
Taste
*Bacteria/metabolism/classification/genetics/isolation & purification
*Flavoring Agents/metabolism
Humans
*Microbial Consortia
Food Microbiology
*Microbiota

@article {pmid40483623,
year = {2025},
author = {Chi, Y and Luo, M and Ding, C},
title = {The role of microbiota in fish spoilage: biochemical mechanisms and innovative preservation strategies.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {7},
pages = {89},
pmid = {40483623},
issn = {1572-9699},
support = {202411049301XJ//National College Student Innovation and Entrepreneurship Training Program Funding Project/ ; },
mesh = {*Fishes/microbiology ; *Microbiota ; Animals ; *Food Preservation/methods ; *Food Microbiology ; *Seafood/microbiology ; *Bacteria/metabolism/classification/genetics ; },
abstract = {Fish spoilage is a microbially-mediated biochemical process resulting in quality deterioration, economic losses, and food safety risks. Studies have indicated that spoilage microbiota are phylogenetically diverse, with Gram-negative bacteria (Pseudomonas, Shewanella, Photobacterium) representing primary spoilage organisms, and Gram-positive bacteria (Lactobacillus, Brochothrix) causing spoilage only under specific conditions. Microorganisms cause spoilage through the utilization of three main metabolic processes: (i) proteolytic degradation of muscle proteins, (ii) lipolytic breakdown of triglycerides, and (iii) production of volatile bioactive organic compounds and biogenic amines. By combining high-throughput sequencing with metabolomics, researchers have been uncovering strain-specific metabolic networks and how they are influenced by environmental factors such as temperature, pH, and packaging. This review systematically examines: (1) patterns of taxonomic succession in spoilage microbiota, (2) enzymatic and biochemical pathways involved in spoilage, and (3) innovative preservation strategies targeting spoilage consortia. Emerging technologies, such as bacteriocin-mediated biopreservation, phage therapy, and modified atmosphere packaging, show considerable promise in inhibiting spoilage organisms while maintaining the sensory qualities of the fish. Microbiome-directed interventions combined with predictive modeling and precision storage systems also represent a novel approach to fish preservation. There is a critical need to integrate traditional microbiology with the use of multi-omic technologies for the development of sustainable, microbiota-based preservation strategies that address global seafood security challenges.},
}

*Fishes/microbiology
*Microbiota
Animals
*Food Preservation/methods
*Food Microbiology
*Seafood/microbiology
*Bacteria/metabolism/classification/genetics

@article {pmid40483486,
year = {2025},
author = {Bergholm, J and Tessema, TS and Blomström, AL and Berg, M},
title = {Metagenomic insights into the complex viral composition of the enteric RNA virome in healthy and diarrheic calves from Ethiopia.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {188},
pmid = {40483486},
issn = {1743-422X},
support = {2021-04343//Vetenskapsrådet/ ; 2021-04343//Vetenskapsrådet/ ; 2021-04343//Vetenskapsrådet/ ; 2021-04343//Vetenskapsrådet/ ; },
mesh = {Animals ; Cattle ; Ethiopia/epidemiology ; *Diarrhea/veterinary/virology ; *Virome ; Metagenomics ; *Cattle Diseases/virology ; Feces/virology ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; Genome, Viral ; RNA, Viral/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Viruses and the virome have received increased attention in the context of calf diarrhea and with the advancement of high-throughput sequencing the detection and discovery of viruses has been improved. Calf diarrhea, being the main contributor to calf morbidity and mortality, is a major issue within the livestock sector in Ethiopia. However, studies on viruses and the virome in calves is lacking in the country. Therefore, we utilized viral metagenomics to investigate the diversity of RNA viruses in healthy and diarrheic calves from central Ethiopia.

METHODS: Fecal material from 47 calves were collected, pooled, and sequenced using Illumina. Following sequencing, the virome composition and individual viral sequences were investigated using bioinformatic analysis.

RESULTS: The metagenomic analysis revealed the presence of several RNA viruses, including rotavirus and bovine coronavirus, known causative agents in calf diarrhea. In addition, several enteric RNA viruses that have not been detected in cattle in Ethiopia previously, such as norovirus, nebovirus, astrovirus, torovirus, kobuvirus, enterovirus, boosepivirus and hunnivirus were identified. Furthermore, a highly divergent viral sequence, which we gave the working name suluvirus, was found. Suluvirus showed a similar genome structure to viruses within the Picornaviridae family and phylogenetic analysis showed that it clusters with crohiviruses. However, due to its very divergent amino acid sequence, we propose that suluvirus represent either a new genus within the Picornaviridae or a new species within crohiviruses.

CONCLUSIONS: To our knowledge, this is the first characterization of the RNA virome in Ethiopian cattle and the study revealed multiple RNA viruses circulating in both diarrheic and healthy calves, as well as a putative novel virus, suluvirus. Our study highlights that viral metagenomics is a powerful tool in understanding the divergence of viruses and their possible association to calf diarrhea, enabling characterization of known viruses as well as discovery of novel viruses.},
}

Animals
Cattle
Ethiopia/epidemiology
*Diarrhea/veterinary/virology
*Virome
Metagenomics
*Cattle Diseases/virology
Feces/virology
*RNA Viruses/genetics/classification/isolation & purification
Phylogeny
Genome, Viral
RNA, Viral/genetics
High-Throughput Nucleotide Sequencing

@article {pmid40481853,
year = {2025},
author = {Chaverri, P and Escudero-Leyva, E and Mora-Rojas, D and Calvo-Obando, A and González, M and Escalante-Campos, E and Mesén-Porras, E and Wicki-Emmenegger, D and Rojas-Gätjens, D and Avey-Arroyo, J and Campos-Hernández, M and Castellón, E and Moreira-Soto, A and Drexler, JF and Chavarría, M},
title = {Differential Microbial Composition and Fiber Degradation in Two Sloth Species (Bradypus variegatus and Choloepus hoffmanni).},
journal = {Current microbiology},
volume = {82},
number = {7},
pages = {327},
pmid = {40481853},
issn = {1432-0991},
support = {VI 809-C3-102//Vicerrectoría de Investigación, Universidad de Costa Rica/ ; 57592642//Deutscher Akademischer Austauschdienst/ ; },
mesh = {Animals ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Gastrointestinal Microbiome ; Cellulose/metabolism ; *Dietary Fiber/metabolism ; *Fungi/classification/metabolism/genetics/isolation & purification ; Metagenomics ; },
abstract = {Sloths have the slowest digestion among mammals, requiring 5-20 times longer to digest food than other herbivores, which suggests differences in their gut microbiota, particularly in plant-fiber-degrading microorganisms. Bradypus variegatus has a lower metabolic rate and moves less than Choloepus hoffmanni. However, no comprehensive studies have compared the microbiota (e.g., fungi) of these species. We hypothesized that differences in digestion and metabolism between the two species would be reflected in their microbiota composition and functionality, which we characterized using metagenomics, metabarcoding, and cellulose degradation. Results revealed significant differences in microbiota composition and functionality. Both species are dominated by bacteria; fungi comprised only 0.06-0.5% of metagenomic reads. Neocallimastigomycota, an anaerobic fungus involved in fiber breakdown in other herbivores, was found in low abundance, especially in B. variegatus. Bacterial communities showed subtle differences: C. hoffmanni was dominated by Bacillota and Bacteroidota, while B. variegatus showed higher Actinomycetota. Expected herbivore bacterial taxa (e.g., Fibrobacter and Prevotella) were scarce. Functional analysis showed a low abundance of carbohydrate-active enzymes essential for polysaccharide breakdown. Cellulose degradation assays confirmed that sloths digest only ~ 3-30% of ingested plant material. This research sheds light on the potential multidirectional links between the gut microbiota, metabolism, and digestion.},
}

Animals
*Bacteria/classification/genetics/metabolism/isolation & purification
*Gastrointestinal Microbiome
Cellulose/metabolism
*Dietary Fiber/metabolism
*Fungi/classification/metabolism/genetics/isolation & purification
Metagenomics

@article {pmid40475999,
year = {2025},
author = {Hwang, D and Chong, E and Li, Y and Li, Y and Roh, K},
title = {Deciphering the gut microbiome's metabolic code: pathways to bone health and novel therapeutic avenues.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1553655},
pmid = {40475999},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bone and Bones/metabolism ; Animals ; Probiotics/therapeutic use ; *Bone Remodeling/physiology ; *Osteoporosis/metabolism/microbiology/therapy ; Prebiotics ; Fecal Microbiota Transplantation ; Bone Diseases/metabolism/microbiology/therapy ; },
abstract = {The gut microbiome plays an important role in the protection against various systemic diseases. Its metabolic products profoundly influence a wide range of pathophysiological events, including the regulation of bone health. This review discusses the recently established connections between the gut microbiome and bone metabolism, focusing on the impact of microbiome-derived metabolites such as SCFAs, Bile Acids, and tryptophan to the control of bone remodeling and immunoreactions. Recent advances in metagenomics and microbiome profiling have unveiled new exciting therapeutic opportunities, ranging from the use of probiotics, prebiotics, engineered microbes, and to fecal microbiota transplantation. Understanding of the interplay among diet, microbiota, and bone health provides new avenues for tailored interventions aimed at reducing disease risk in osteoporosis and other related disorders. By drawing knowledge from microbiology, metabolism, and bone biology, this review highlights the potential of microbiome-targeted therapies to transform skeletal health and the management of bone diseases.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Bone and Bones/metabolism
Animals
Probiotics/therapeutic use
*Bone Remodeling/physiology
*Osteoporosis/metabolism/microbiology/therapy
Prebiotics
Fecal Microbiota Transplantation
Bone Diseases/metabolism/microbiology/therapy

@article {pmid40475346,
year = {2025},
author = {Wang, Z and Wei, X and Piao, L and Zhang, X and Wang, H},
title = {Gut microbiota dysbiosis and metabolic shifts in pediatric norovirus infection: a metagenomic study in Northeast China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1600470},
pmid = {40475346},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; China/epidemiology ; *Caliciviridae Infections/microbiology/virology ; *Norovirus ; Metagenomics ; Feces/microbiology ; Male ; Female ; *Gastroenteritis/virology/microbiology ; Child, Preschool ; Child ; Infant ; Bacteria/classification/genetics/isolation & purification ; Longitudinal Studies ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Norovirus (NoV) is a leading cause of acute gastroenteritis in pediatric populations worldwide. However, the role of gut microbiota in NoV pathogenesis remains poorly understood.

METHODS: We conducted a longitudinal metagenomic analysis of fecal samples from 12 NoV-infected children and 13 age-matched healthy controls in Northeast China. Microbial composition and functional pathways were assessed using high-throughput shotgun sequencing and bioinformatic profiling.

RESULTS: NoV infection was associated with significant gut microbial dysbiosis, including increased alpha diversity and distinct taxonomic shifts. Notably, Bacteroides uniformis, Veillonella spp., and Carjivirus communis were enriched in infected individuals. Functional analysis revealed upregulation of metabolic pathways involved in carbohydrate and lipid processing. These microbial and functional alterations persisted over time and correlated with disease severity.

CONCLUSIONS: Our findings reveal novel associations between NoV infection and gut microbiota dysbiosis, particularly the enrichment of Bacteroides uniformis, which may influence host-pathogen interactions via metabolic or immune mechanisms. The identified microbial and metabolic signatures offer potential biomarkers for diagnosis and targets for microbiota-based therapeutic strategies in pediatric NoV infection.},
}

Humans
*Gastrointestinal Microbiome
*Dysbiosis/microbiology
China/epidemiology
*Caliciviridae Infections/microbiology/virology
*Norovirus
Metagenomics
Feces/microbiology
Male
Female
*Gastroenteritis/virology/microbiology
Child, Preschool
Child
Infant
Bacteria/classification/genetics/isolation & purification
Longitudinal Studies
High-Throughput Nucleotide Sequencing

@article {pmid40473843,
year = {2025},
author = {Wu, S and Wang, S and Wu, Z and Chen, M and Chen, X and Lei, D and Peng, C},
title = {Comparative analysis of the clinical characteristic and lung microbiota in adult and elderly patients with pulmonary tuberculosis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19777},
pmid = {40473843},
issn = {2045-2322},
support = {2023K146//Quzhou City science and technology plan project/ ; },
mesh = {Humans ; Middle Aged ; Male ; Female ; *Tuberculosis, Pulmonary/microbiology/diagnosis/diagnostic imaging ; Aged ; Adult ; *Lung/microbiology/diagnostic imaging ; *Microbiota/genetics ; Retrospective Studies ; Age Factors ; High-Throughput Nucleotide Sequencing ; Young Adult ; Aged, 80 and over ; },
abstract = {The proportion of elderly people infected with tuberculosis (TB) is increasing, and misdiagnosis and missed diagnosis are common. This study aimed to explore the diagnostic value of metagenomic next-generation sequencing (mNGS) for pulmonary TB (PTB) and to investigate age-related differences in lung microbial composition, clinical characteristics and imaging findings among PTB patients. We retrospectively recruited 162 suspected PTB patients, and finally 143 patients were used in this analysis. Patients were classified into two groups: adult (18 ≤ age < 60, n = 66) and elderly (Age ≥ 60, n = 77). Differences and associations in clinical characteristics, imaging findings, and lung microbiota were analyzed. Compared to adult patients, elderly patients had a higher prevalence of hypertension (31.17% vs. 9.09%, P = 0.0012), fever (20.78% vs. 4.55%, P = 0.0044) and chest tightness (24.68% vs. 10.61%, P = 0.0297), but a lower prevalence of chest pain (7.58% vs. 0%, P = 0.0139). For TB identification, mNGS had the highest positive rate (100%), followed by T-spot (74.75%), GeneXpert (37.80%) and acid-fast staining (AFS) (7.30%), and all the conventional methods showed slight higher positive rates in the elderly group compared to the adult group (P > 0.05). Bilateral lung infection was more common in elderly patients (79.22% vs. 60.61%, P = 0.0148), with infiltration (32.17%, 46/143), shadows (26.57%, 38/143), nodules (20.28%, 29/143), and bronchiectasis (20.28%, 29/143) being the most common imaging features. The diversity of the lung microbial communities was significantly lower in elderly patients compared to adults (P < 0.05). Clinical characteristics, imaging findings, and the top 20 most abundant species in lung microbiota showed significantly positive correlation. This study demonstrates that mNGS has excellent diagnostic value for PTB in both adult and elderly patients. Significant differences in clinical characteristics, imaging, and lung microbial composition were observed between the two groups. Understanding these differences may aid in the diagnosis and treatment of tuberculosis in elderly patients.},
}

Humans
Middle Aged
Male
Female
*Tuberculosis, Pulmonary/microbiology/diagnosis/diagnostic imaging
Aged
Adult
*Lung/microbiology/diagnostic imaging
*Microbiota/genetics
Retrospective Studies
Age Factors
High-Throughput Nucleotide Sequencing
Young Adult
Aged, 80 and over

@article {pmid40473141,
year = {2025},
author = {Luo, Y and Liao, H and Wu, L and Wu, M and Luo, Y and Yao, Y and Ji, W and Gao, L and Xia, X},
title = {Temperature adaptability drives functional diversity and horizontal gene transfer within microbial communities in Daqu solid-state fermentation.},
journal = {Bioresource technology},
volume = {433},
number = {},
pages = {132770},
doi = {10.1016/j.biortech.2025.132770},
pmid = {40473141},
issn = {1873-2976},
mesh = {*Fermentation ; *Gene Transfer, Horizontal/genetics ; *Microbiota/genetics ; *Temperature ; Volatile Organic Compounds ; Bacteria/genetics/metabolism ; Phylogeny ; *Wine/microbiology ; *Adaptation, Physiological ; },
abstract = {The spontaneous solid-state fermentation of high-temperature Daqu (HTD) is a temperature-dependent stacking bioprocessing for enriching microbiota and enzymes to guarantee efficient substrate utilization and fermentation. However, there is a lack of clarity regarding how temperature adaptability affects HTD microbial assembly, domestication direction, and metabolic profile. Here, the flavor substances, microbial assembly, metabolic network, and horizontal gene transfer (HGT) events of three HTDs from Renshu (RS), Jiushang (JS), and Maoyuan (MY) were analyzed. 125 volatile compounds were identified, tetramethylpyrazine, 3-methyl-butanoic acid, phenylethyl alcohol, and trimethylpyrazine were clarified as the typical flavor substances. Bacillus and Kroppenstedtia were the shared dominant bacterial genera. Paecilomyces, Aspergillus, Rasamsonia, and Lichtheimia were dominant fungal genera. Differences in flavor metabolism, microbial structure, and key enzyme metabolism are strongly correlated with sample distance. As proximity decreases, the microbial structural and functional metabolic traits tend to exhibit greater similarity. The frequency of HGT events was analyzed using MetaCHIP, 49, 9 and 69 groups of HGT events occurred in RS, JS, and MY, respectively. HGT events occurred most abundantly in Bacillaceae, and the microbial taxa with a closer phylogenetic relationship possessed the highest incidence of HGT. Specifically, the occurrence of HGT was mainly associated with high-temperature adaptability. It was also linked to characteristic flavor metabolism. Our results revealed the effects of temperature stress on microbial regulation of HTD and adaptive transfer of relevant genes in stacked fermented HTDs. This work provides important insights into HTD quality classification and regulation of solid-state fermentation quality and efficiency through microbial domestication.},
}

*Fermentation
*Gene Transfer, Horizontal/genetics
*Microbiota/genetics
*Temperature
Volatile Organic Compounds
Bacteria/genetics/metabolism
Phylogeny
*Wine/microbiology
*Adaptation, Physiological

@article {pmid40472396,
year = {2025},
author = {Zheng, F and Guo, X and Zhang, W and Wang, Y and Hu, E and Guo, X and Su, H and Deng, C},
title = {Insights into the functional characteristics of rhubarb (Rheum officinale Baill) treatment on experimental traumatic brain injury through network pharmacology with metagenomics.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {143},
number = {},
pages = {156853},
doi = {10.1016/j.phymed.2025.156853},
pmid = {40472396},
issn = {1618-095X},
mesh = {Animals ; *Rheum/chemistry ; Male ; *Brain Injuries, Traumatic/drug therapy ; Mice, Inbred C57BL ; Mice ; Metagenomics ; Network Pharmacology ; Gastrointestinal Microbiome/drug effects ; Apoptosis/drug effects ; *Plant Extracts/pharmacology ; Blood-Brain Barrier/drug effects ; Disease Models, Animal ; *Drugs, Chinese Herbal/pharmacology ; Neuroprotective Agents/pharmacology ; },
abstract = {BACKGROUND: Traumatic brain injury (TBI) imposes a heavy burden on society and families owing to its high morbidity and mortality. Rhubarb has been noticed in the Chinese herb for treating TBI. The pharmacological effects include anti-inflammation, anti-bacterial, and purgative. But little is known about its potential mechanism when treating TBI.

PURPOSE: In this study, we profiled the pharmacological and intestinal functional characteristics of rhubarb in post-TBI mice.

METHODS: Fifty adult male C57BL/6 mice were randomly allocated into five groups, including sham, controlled cortical impact (CCI), and rhubarb extract administered at low, medium, and high doses. The impaired neurobehavioral function was assessed using the modified neurological severity score (mNSS) and the wire hang test. hematoxylin-eosin (HE) and Nissl staining, terminal deoxynucleotidyl transferase-mediated dUTP-nick-end labeling (TUNEL) and immunoglobulin-γ (IgG) staining, immunostaining for GFAP, TNF-α and IL-1β were applied to detect the histological damage, neuronal apoptosis and blood-brain barrier (BBB) permeability, respectively. Subsequently, the network pharmacology approaches was used to identify putative therapeutic targets and the relevant pathway of rhubarb on TBI. In addition, metagenomics and targeted metabolomics revealed the alterations in composition and functions of gut flora and gut-derived serum short-chain fatty acids (SCFAs). Finally, we depleted the gut microbiota with an antibiotic cocktail (ampicillin, metronidazole, neomycin, vancomycin) to uncover the critical role of gut microbiota on rhubarb function.

RESULTS: Rhubarb reduced brain IgG leakage and neuronal apoptosis after TBI. The network pharmacology analysis identified seven genes as key potential therapeutic targets of rhubarb, and the genes were related to inflammation, oxidant and apoptosis. The enrichment analysis showed that three of the top signal pathways were involved in anti-inflammation, anti-apoptosis and anti-oxidant. The metagenomics analysis showed that rhubarb reshaped the structure and abundance of gut microbiota in TBI. The altered function of gut microbiota was enriched in the improvement of carbohydrate metabolism, gut-derived serum SCFAs and microbial resistance. Finally, gut microbiota depletion confirmed the effects of rhubarb on post-TBI IgG leakage and neuronal apoptosis were depended on gut microbiota.

CONCLUSIONS: Rhubarb may treat TBI by effects of targeting inflammatory factors and oxidant factors to inhibit neuronal apoptosis and protect the BBB. The therapeutic effects of rhubarb are partly mediated by altering gut microbiota. Our findings not only highlight a holistic and microbial potential of rhubarb's therapeutic functional actions but also elucidate previously unrecognized therapeutic development of novel targets and strategies for TBI therapies by rhubarb.},
}

Animals
*Rheum/chemistry
Male
*Brain Injuries, Traumatic/drug therapy
Mice, Inbred C57BL
Mice
Metagenomics
Network Pharmacology
Gastrointestinal Microbiome/drug effects
Apoptosis/drug effects
*Plant Extracts/pharmacology
Blood-Brain Barrier/drug effects
Disease Models, Animal
*Drugs, Chinese Herbal/pharmacology
Neuroprotective Agents/pharmacology

@article {pmid40468430,
year = {2025},
author = {Khoiri, AN and Costa, NR and Crusciol, CAC and Pariz, CM and Costa, C and Calonego, JC and de Castilhos, AM and de Souza, DM and de Lima Meirelles, PR and Cru, IV and Moretti, LG and Bossolani, JW and Kuramae, EE},
title = {Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize-palisade grass intercropping.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {60},
pmid = {40468430},
issn = {2524-6372},
support = {#2014/21772-4 and #2014/14935-4//São Paulo Research Foundation (FAPESP)/ ; #458225/2014-2//National Council for Scientific and Technological Development (CNPq)/ ; 1378/14//Fundação Agrisus/ ; },
abstract = {BACKGROUND: Intercropping systems enhance agricultural sustainability by promoting ecosystem multifunctionality (EMF). This study examined the impact of adding pigeon pea (M + PG + PP) into a maize-palisade grass (M + PG) intercropping system under a no-till system (NTS) on soil microbial communities and ecosystem services. After five consecutive growing seasons, bulk soil samples from a soybean-based crop-livestock system were analyzed using metagenomics.

RESULTS: The inclusion of pigeon pea significantly improved the EMF index, with higher plant productivity and slightly enhanced outcomes in soil health, lamb meat productivity, and climate protection. The M + PG + PP treatment enriched Bradyrhizobium spp., which were positively correlated with soil health, plant productivity, and EMF index. Functional analysis indicated that M + PG + PP treatment enhanced nitrogen metabolism, biofilm formation, and exopolysaccharide (EPS) biosynthesis, improving soil fertility and microbial activity. Similarly, functional analysis of microbial plant growth-promoting traits revealed that the M + PG + PP treatment promoted microbial functions related to nitrogen and iron acquisition, sulfur assimilation, and plant colonization, all essential for plant growth and nutrient cycling. In contrast, the M + PG treatment primarily enhanced pathways related to competitive exclusion and phytohormone production.

CONCLUSIONS: These findings highlight the importance of incorporating legumes such as pigeon pea into intercropping systems to optimize ecosystem services, enhance soil health, and promote long-term agricultural productivity and sustainability.},
}

@article {pmid40468269,
year = {2025},
author = {Li, B and Yang, Y and Xu, B and Song, P and Jiang, F and Gao, H and Cai, Z and Gu, H and Zhang, T},
title = {Comparative macrogenomics reveal plateau adaptation of gut microbiome in cervids.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {154},
pmid = {40468269},
issn = {1741-7007},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Deer/microbiology/genetics ; Phylogeny ; Metagenome ; Metagenomics ; *Adaptation, Physiological/genetics ; Energy Metabolism ; Biological Evolution ; },
abstract = {BACKGROUND: Diverse gut microbiota in animals significantly influences host physiology, ecological adaptation, and evolution. However, the specific functional roles of gut microbiota in facilitating host adaptation, as well as the coevolutionary dynamics between microbiota and their hosts, remain largely understudied.

RESULTS: A total of 41,847 metagenome-assembled genomes and 3193 high-quality species-level genome bins were generated, establishing a comprehensive gut microbiome catalog for cervids in this study. Phylogenetic analysis revealed a coevolutionary relationship between cervids and their gut microbiota. Comparative metagenomic analyses further indicated that the gut microbiota of plateau cervids have undergone genome-level adaptations related to energy metabolism. At the genus level, species-level genome bins from the genera Alistipes and Faecousia in plateau cervids exhibit enhanced energy metabolism capabilities. Structural variations analysis revealed that the insertion and duplications structural variations in the gut microbiota of plateau cervids were significantly enriched in energy metabolism pathways. In contrast, the deletions and contractions in structural variations were predominantly enriched with metabolic pathways involved in the biosynthesis of diverse biochemical molecules.

CONCLUSIONS: Our study provides a comprehensive gut microbiome catalog of the cervid gut microbiota, revealing the coevolutionary relationship between cervid gut microbiota and hosts. These findings highlight the adaptive genomic evolution of the gut microbiota in contributing to the plateau adaptability of cervids and offer new insights into the mechanisms by which the gut microbiota help hosts adapt to extreme environments.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Deer/microbiology/genetics
Phylogeny
Metagenome
Metagenomics
*Adaptation, Physiological/genetics
Energy Metabolism
Biological Evolution

@article {pmid40468214,
year = {2025},
author = {Yang, X and Chen, H and Wu, L and Guo, X and Xue, D},
title = {Diversity and correlation analysis of microbiomes and metabolites of Sphagnum palustre in various microhabitats.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {761},
pmid = {40468214},
issn = {1471-2229},
support = {2019QZKK0304//Second Tibetan Plateau Scientific Expedition/ ; QNTS202201//Youth Innovation Program of CIB/ ; 2022376//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 2021JDTD011//Youth Science and Technology Innovation Team Program of Sichuan Province of China/ ; },
mesh = {*Microbiota ; *Sphagnopsida/microbiology/metabolism ; Ecosystem ; Soil Microbiology ; Bacteria/genetics/metabolism ; },
abstract = {BACKGROUND: Sphagnum peat mosses are crucial contributors to global carbon sequestration and are a dominant presence in many northern peatland environments. These mosses host a wide variety of microorganisms, which reside within their tissues and on their surfaces. Despite this close association, the connection between these microorganisms and the production of metabolites across different parts of Sphagnum remains unclear.

RESULTS: This research explored the connection between microbial diversity and metabolite production in various microhabitats of Sphagnum palustre by employing metagenomic and metabolomic techniques. Our results indicate that the S. palustre microbiome composition is more strongly influenced by microhabitat than by geographic location. Microbiome diversity microbiomes related to S. palustre showed a steady decrease from soil to near soil, from X to CAP, and from belowground to aboveground habitats. In contrast, network complexity increased. Species abundance analysis indicated that Proteobacteria was the most prevalent bacterial phylum across CAP, S, Z, and X. Additionally, Ascomycota emerged as the predominant fungal phylum. There were significant differences in nitrogen fixation activity, methane oxidation activity, total nitrogen, and total carbon among different microhabitats. The FAPROTAX analysis revealed differences in the metabolic potential of the carbon (C) and nitrogen (N) cycles across the four microhabitats. LC-MS/MS technology was employed to quantitatively assess metabolites across various S. palustre microhabitats. A total of 3,822 metabolites and 353 differential metabolites were detected, predominantly including lipids, organic acids, and carboxylic acids. The majority of these differential metabolites were associated with metabolic pathways such as carotenoid biosynthesis, steroid biosynthesis, secondary bile acid biosynthesis, as well as the biosynthesis of neomycin, kanamycin, and gentamicin. Correlation analysis revealed both positive and negative relationships between microorganisms and differential metabolites. Methylocystis, which was significantly enriched in X and T, showed a strong positive correlation with differential metabolites in S vs T and Z vs X, but a negative correlation with those in X vs T (p < 0.05).

CONCLUSION: In summary, our study demonstrates that Sphagnum palustre microbiomes are primarily influenced by microhabitats rather than specific environmental conditions at different sites. We identified significant variations in microbial community diversity across various S. palustre microhabitats. Correlation analysis revealed links between microorganisms and differential metabolic processes. This comprehensive investigation of aboveground and belowground microbiomes and metabolites in S. palustre provides new insights into the distribution of microbial communities and metabolites across different microhabitats.},
}

*Microbiota
*Sphagnopsida/microbiology/metabolism
Ecosystem
Soil Microbiology
Bacteria/genetics/metabolism

@article {pmid40467587,
year = {2025},
author = {Xiong, S and Xie, B and Yin, N and Zhu, H and Gao, H and Xu, X and Xiao, K and Cai, X and Sun, G and Sun, X and Cui, Y and Van de Wiele, T and Zhu, Y},
title = {Prenatal exposure to trace elements impacts mother-infant gut microbiome, metabolome and resistome during the first year of life.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5186},
pmid = {40467587},
issn = {2041-1723},
support = {No. L232076//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Pregnancy ; Infant ; *Trace Elements/adverse effects ; *Metabolome/drug effects ; Feces/microbiology ; *Prenatal Exposure Delayed Effects/microbiology/metabolism ; Adult ; Male ; Metagenomics ; Hair/chemistry ; *Maternal Exposure/adverse effects ; Infant, Newborn ; Bacteria/genetics/classification/drug effects ; Copper ; },
abstract = {Infancy is a critical window for the colonization of gut microbiome. However, xenobiotic impacts on gut microbiome development in early life remain poorly understood. Here, we recruit 146 mother-infant pairs and collect stool samples at 3, 6, and 12 months after delivery for amplicon sequencing (N = 353), metagenomics (N = 65), and metabolomics (N = 198). Trace elements in maternal hair samples (N = 119) affect diversity and composition of the infant gut microbiome. Shannon diversity in 3 month-old infants is correlated positively with selenium and negatively with copper, and relative abundance of Bifidobacterium increases under high exposure to aluminum and manganese. During the first year of life, infants and their paired mothers have distinct microbial diversity and composition, and their bacterial community structures gradually approach. here are 56 differential metabolites between the first and second visit and 515 differential metabolites between the second and third visit. The typical profile of antibiotic resistance genes (ARGs) significantly differs between infants and their mothers. High levels of copper and arsenic exposure may induce the enrichment of ARGs in the infant gut. Our findings highlight the dynamics of the gut microbiome, metabolites, and ARG profiles of mother-infant pairs after delivery, associated with prenatal exposure to trace elements.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics
Female
Pregnancy
Infant
*Trace Elements/adverse effects
*Metabolome/drug effects
Feces/microbiology
*Prenatal Exposure Delayed Effects/microbiology/metabolism
Adult
Male
Metagenomics
Hair/chemistry
*Maternal Exposure/adverse effects
Infant, Newborn
Bacteria/genetics/classification/drug effects
Copper

@article {pmid40467244,
year = {2025},
author = {Li, S and Rao, C and Zang, X and Yang, Y and Yang, W and Huang, X and Li, J and Sun, J and Liu, Y and Ye, D},
title = {Characterization of aroma active compounds and microbial communities in spontaneously fermented Vitis quinquangularis wines.},
journal = {Food research international (Ottawa, Ont.)},
volume = {214},
number = {},
pages = {116676},
doi = {10.1016/j.foodres.2025.116676},
pmid = {40467244},
issn = {1873-7145},
mesh = {*Wine/analysis/microbiology ; *Fermentation ; *Vitis/microbiology/chemistry ; *Odorants/analysis ; *Volatile Organic Compounds/analysis ; Gas Chromatography-Mass Spectrometry ; *Microbiota ; *Food Microbiology ; },
abstract = {This study comprehensively investigated volatile compounds and microbial communities of spontaneously fermented Vitis quinquangularis wines from the Guangxi production regions. The aroma profiles of V. quinquangularis wines were analyzed by GC-O-MS, GC-QQQ-MS/MS, and quantitative descriptive analysis. The wines exhibit predominantly fruity and floral notes, with contributions from esters and (E)-β-damascenone. A distinctive and typical "green and earthy" aroma was observed, with contributions from C6 compounds and volatile phenols such as 1-hexanol, (E)-3-hexen-1-ol, hexanoic acid, 4-vinylguaiacol, eugenol, and isoeugenol. Metagenomics and culturomics analyses indicated that the dominant strains involved in the spontaneous fermentation process were Hanseniaspora opuntiae, Saccharomyces cerevisiae, Paenibacillus sp., Sphingomonas sp., and Bacillus sp. Additionally, microorganisms from sixteen generas, including Actinomycetospora and Ameyamaea, etc., along with six enzymes like EC 1.1.1.1 and EC 1.1.1.318, etc., were implicated in the production of the "green and earthy" aroma in V. quinquangularis wines.},
}

*Wine/analysis/microbiology
*Fermentation
*Vitis/microbiology/chemistry
*Odorants/analysis
*Volatile Organic Compounds/analysis
Gas Chromatography-Mass Spectrometry
*Microbiota
*Food Microbiology

@article {pmid40467108,
year = {2025},
author = {Ghensi, P and Heidrich, V and Bazzani, D and Asnicar, F and Armanini, F and Bertelle, A and Dell'Acqua, F and Dellasega, E and Waldner, R and Vicentini, D and Bolzan, M and Trevisiol, L and Tomasi, C and Pasolli, E and Segata, N},
title = {Shotgun Metagenomics Identifies in a Cross-Sectional Setting Improved Plaque Microbiome Biomarkers for Peri-Implant Diseases.},
journal = {Journal of clinical periodontology},
volume = {52},
number = {7},
pages = {999-1010},
pmid = {40467108},
issn = {1600-051X},
support = {//Italian Society of Periodontology and Implantology (SIdP)/ ; //Eklund Foundation/ ; //International Team for Implantology (ITI)/ ; //CLC Scientific S.r.l./ ; //PreBiomics S.r.l./ ; /ERC_/European Research Council/International ; },
mesh = {Humans ; *Peri-Implantitis/microbiology/diagnosis ; *Dental Plaque/microbiology ; *Metagenomics/methods ; Male ; Cross-Sectional Studies ; Female ; *Microbiota/genetics ; Middle Aged ; Biomarkers/analysis ; *Dental Implants/microbiology ; Aged ; Adult ; Machine Learning ; Mucositis/microbiology ; Stomatitis/microbiology ; },
abstract = {AIM: This observational study aimed to verify and improve the predictive value of plaque microbiome of patients with dental implant for peri-implant diseases.

MATERIALS AND METHODS: Patients were included in one of the following study groups according to the health status of their dental implants: (a) healthy, (b) affected by mucositis and (c) affected by peri-implantitis. From each patient, submucosal plaque microbiome samples were collected from the considered dental implant and from a contralateral healthy implant/tooth. After shotgun metagenomic sequencing, the plaque microbiome was profiled taxonomically and functionally with MetaPhlAn 4 and HUMAnN 3, respectively. Taxonomic and functional profiles were fed into machine-learning models, which were then evaluated with cross-validation to assess the extent to which the plaque microbiome could be used to pinpoint peri-implant diseases.

RESULTS: Shotgun metagenomics sequencing was performed for a total of 158 samples spanning 102 individuals. Four-hundred and forty-seven prokaryotic species were identified as part of the peri-implant microbiome, 34% of which were currently uncharacterized species. At the community level, the peri-implant microbiome differed according to the health status of the implant (p ≤ 0.006 for all pairwise comparisons) but this was site-specific, as healthy contralateral sites showed no discriminating microbiome features. Peri-implantitis microbiomes further showed lower inter-subject variability than healthy plaque microbiomes (p < 0.001), while mucositis-associated microbiomes were in the middle of the continuum between health and peri-implantitis. Each health condition was associated with a strong signature of taxonomic and functional microbiome biomarkers (log10 LDA score ≥ 2.5), 30% and 13% of which represented uncharacterized microbial functions and unknown species, respectively. Distinct Fusobacterium nucleatum clades were associated with implant status, highlighting the subspecies F. nucleatum's functional and phenotypic diversity. Machine-learning models trained on taxonomic or functional plaque microbiome profiles were highly accurate in differentiating clinical groups (AUC = 0.78-0.96) and highlighted the extent to which the peri-implant microbiome is associated with peri-implant clinical parameters (AUC = 0.79-0.87).

CONCLUSIONS: Plaque microbiome profiling with shotgun metagenomics revealed consistent associations between microbiome composition and peri-implant diseases. In addition to pointing to peri-implant-associated microbes, warranting further mechanistic studies, we showed high-resolution plaque microbiome evaluation via metagenomics as an effective tool. Its utility within protocols for clinical management of peri-implant diseases should be explored in the future.},
}

Humans
*Peri-Implantitis/microbiology/diagnosis
*Dental Plaque/microbiology
*Metagenomics/methods
Male
Cross-Sectional Studies
Female
*Microbiota/genetics
Middle Aged
Biomarkers/analysis
*Dental Implants/microbiology
Aged
Adult
Machine Learning
Mucositis/microbiology
Stomatitis/microbiology

@article {pmid40467000,
year = {2025},
author = {Potrykus, M and Kurpas, M and Gałęzowska, G and Gajewska, M},
title = {Linking chemical contamination to composition of bacterial communities in urban beach sands of a brackish sea under anthropogenic pressure.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {381},
number = {},
pages = {126596},
doi = {10.1016/j.envpol.2025.126596},
pmid = {40467000},
issn = {1873-6424},
abstract = {The water quality on recreational beaches is constantly monitored. However, given that beachgoers often spend more time in contact with the sand than the seawater, it is essential to also regularly assess beach sand quality. In this study, 34 beach sand samples were collected in seven locations along the south shore of the Baltic Sea (Europe) between 2022 and 2023. The samples were obtained from recreational beaches with significant anthropogenic pressure. Since the use of new chemicals is widespread, it is imperative to not only monitor known contaminants but also to actively search for the presence of new ones in the environment. In order to establish the connection between the bacterial biodiversity and their possible resilience in the contaminated marine environment, the bacterial abundances in the beach sand were compared based on 16S rDNA sequencing with chemical contamination examined with non-targeted GC-MS. One hundred forty-nine (149) distinct chemicals were detected, many of which are of human health concern. The presence of polycyclic aromatic hydrocarbons, plasticizers and benzothiazoles in the sand samples was observed, and these contaminants were found to be associated with alterations in the bacterial community structure, characterized by a decrease or increase in certain taxonomic groups. Notably, the bacterial communities exhibited specificity to each location and demonstrated stability throughout the seasons. Furthermore, the presence of DNA from 31 potential human pathogens was detected in the sand. These findings emphasize the necessity for regular monitoring of beach sand for the presence of toxic chemicals and pathogens to safeguard public health and the environment.},
}

@article {pmid40465720,
year = {2025},
author = {de Porto, AP and Dylla, NP and Stutz, M and Lin, H and Khalid, M and Mullowney, MW and Little, J and Rose, A and Moran, D and McMillin, M and Burgo, V and Smith, R and Woodson, C and Metcalfe, C and Ramaswamy, R and Lehmann, C and Odenwald, M and Bandealy, N and Zhao, J and Kim, M and Adler, E and Sundararajan, A and Sidebottom, A and Kress, JP and Wolfe, KS and Pamer, EG and Patel, BK},
title = {Fecal metabolite profiling identifies critically ill patients with increased 30-day mortality.},
journal = {Science advances},
volume = {11},
number = {23},
pages = {eadt1466},
pmid = {40465720},
issn = {2375-2548},
mesh = {Humans ; *Critical Illness/mortality ; *Feces/microbiology/chemistry ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Intensive Care Units ; *Metabolome ; Dysbiosis/mortality/microbiology ; Metabolomics/methods ; Prospective Studies ; },
abstract = {Critically ill patients admitted to the medical intensive care unit (MICU) have reduced intestinal microbiota diversity and altered microbiome-associated metabolite concentrations. Metabolites produced by the gut microbiota have been associated with survival of patients receiving complex medical treatments and thus might represent a treatable trait to improve clinical outcomes. We prospectively collected fecal specimens, defined microbiome compositions by shotgun metagenomic sequencing, and quantified microbiota-derived fecal metabolites by mass spectrometry from 196 critically ill patients admitted to the MICU for non-COVID-19 respiratory failure or shock to correlate microbiota features and metabolites with 30-day mortality. Microbiota compositions of the first fecal sample after MICU admission did not independently associate with 30-day mortality. We developed a metabolic dysbiosis score (MDS) that uses fecal concentrations of 13 microbiota-derived metabolites, which predicted 30-day mortality independent of known confounders. The MDS complements existing tools to identify patients at high risk of mortality by incorporating potentially modifiable, microbiome-related, independent contributors to host resilience.},
}

Humans
*Critical Illness/mortality
*Feces/microbiology/chemistry
Male
Female
Middle Aged
*Gastrointestinal Microbiome
Aged
Intensive Care Units
*Metabolome
Dysbiosis/mortality/microbiology
Metabolomics/methods
Prospective Studies

@article {pmid40465264,
year = {2025},
author = {Liu, M and Geng, J and Jin, S and Hu, P and Wang, X and Liu, X},
title = {Alterations of the Enteric Virome in Vogt-Koyanagi-Harada Disease.},
journal = {Investigative ophthalmology & visual science},
volume = {66},
number = {6},
pages = {15},
pmid = {40465264},
issn = {1552-5783},
mesh = {Humans ; *Uveomeningoencephalitic Syndrome/virology/microbiology ; Male ; Female ; *Virome/genetics ; Adult ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Middle Aged ; Bacteria/genetics ; Metagenomics ; Young Adult ; },
abstract = {PURPOSE: This study aims to explore the enteric virome characteristics of Vogt Koyanagi Harada (VKH) disease and its potential role in this disease.

METHODS: Shotgun metagenomic sequencing was used to detect the enteric virome and 16S rRNA to detect the bacteriome in new-onset, untreated patients with VKH (n = 25) and age- and sex-matched healthy controls without autoimmune diseases (n = 25).

RESULTS: Patients with VKH exhibited different enteric viral communities from healthy controls, characterized by decreased richness of core viral communities (present in > 80% of samples) and increased richness of common viral communities (present in 50%-80% of samples). Notably, within the core virus community, bacteriophage richness was markedly reduced, whereas eukaryotic virus richness significantly increased in patients with VKH. The case-control analysis identified 42 differentially abundant viruses, including a decrease in crAss-like phages, the eukaryotic virus Moumouvirus_moumou, and an enrichment of the Chlamydiamicrovirus_CPG1. Most of the differential phages predominantly targeted bacteria from the phyla Pseudomonadota and Firmicutes. The gut virome-bacteria community correlation analysis revealed a shift in the interactions between the core viruses and bacterial communities. Additionally, Wroclawvirus PA5oct (a Pseudomonas phage) correlated with leukotrichia, a clinically relevant symptom of VKH (P = 0.042). The impact of multiple Pseudomonas phages on the host folate biosynthesis was significantly enhanced in patients with VKH. Moreover, the protein (Earp361-372) encoded by VKH-enriched Pseudomonas was identified to share homology with the melanin antigen gp10044-59.

CONCLUSIONS: The gut virome of patients with VKH differs significantly from healthy controls, suggesting its disturbance may contribute to gut microbiome imbalance and VKH development.},
}

Humans
*Uveomeningoencephalitic Syndrome/virology/microbiology
Male
Female
*Virome/genetics
Adult
Case-Control Studies
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
Middle Aged
Bacteria/genetics
Metagenomics
Young Adult

@article {pmid40463374,
year = {2025},
author = {Gu, J and Ma, Y and Chang, Q and Chen, L},
title = {Influence of programmed death ligand 1 (PD-L1) knockout on gut microbiota in experimental autoimmune uveitis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1600673},
pmid = {40463374},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Uveitis/immunology/microbiology/genetics ; *B7-H1 Antigen/genetics/deficiency ; *Autoimmune Diseases/immunology/microbiology/genetics ; Mice, Knockout ; Mice ; Female ; Disease Models, Animal ; Mice, Inbred C57BL ; },
abstract = {PURPOSE: Programmed death ligand 1 (PD-L1) is a potential target for autoimmune disease therapies. The gut microbiota plays a critical role in autoimmunity, and may influence therapeutic outcomes of immune therapies in cancer. However, the relationship between PD-L1 and gut microbiota in autoimmune conditions remains unclear. This study aims to investigate the effect of PD-L1 knockout on gut microbiota in an experimental autoimmune uveitis (EAU) model.

METHODS: EAU was induced via immunization with interphotoreceptor retinoid-binding protein peptide 651-670 (IRBP651-670) in either wild type (WT) or PD-L1 knockout (KO) C57BL/6J female mice. Sham adjuvant was administered to WT or PD-L1 KO mice as healthy controls. The severity of EAU was evaluated through clinical evaluation and histopathological gradings. The characteristics of gut microbiota was analyzed using metagenomic sequencing.

RESULTS: Each group consisted of three biological replicates. The clinical and histopathological scores of EAU were significantly higher in KO_EAU mice than in WT_EAU mice. WT_EAU mice exhibited lower microbial richness than their healthy controls (WT mice), while PD-L1 KO in EAU mice (KO_EAU group) led to increased richness when compared to wild type EAU mice (WT_EAU group). EAU induced a reduction in the abundance of Akkermansia muciniphila A and an increased in CAG-485 sp002362485. PD-L1 knockout in EAU led to an increased abundance of families Bacteroidaceae, Lachnospiraceae and Ruminococcaceae. EAU was associated with declining microbial tryptophan metabolism and up-regulated functions related to lipid and carbohydrate metabolism; PD-L1 knockout in EAU further increased the metabolism of glycan and biosynthesis of 3-deoxy-α-D-manno-2-octulosonate (Kdo), a key component of bacterial lipopolysaccharide (LPS).

CONCLUSION: Both EAU and PD-L1 knockout modulate gut microbiota, affecting microbial composition - particularly Akkermansia, CAG-485, Bacteroidaceae, Lachnospiraceae and Ruminococcaceae - and microbial functions such as lipid, carbohydrate and glycan metabolism.},
}

Animals
*Gastrointestinal Microbiome/immunology
*Uveitis/immunology/microbiology/genetics
*B7-H1 Antigen/genetics/deficiency
*Autoimmune Diseases/immunology/microbiology/genetics
Mice, Knockout
Mice
Female
Disease Models, Animal
Mice, Inbred C57BL

@article {pmid40462511,
year = {2025},
author = {Qian, LM and Wang, SX and Zhou, W and Qin, ZX and Wang, YN and Zhao, Q and Xu, RH},
title = {Individualized metagenomic network model for colorectal cancer diagnosis: insights into viral regulation of gut microecology.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {3},
pages = {},
pmid = {40462511},
issn = {1477-4054},
support = {Y-HR2020QN-0474//Beijing Xisike Clinical Oncology Research Foundation/ ; 84000-31630002//Sun Yat-sen University clinical research 5010 program/ ; CIRP-SYSUCC-0004//Cancer Innovative Research Program of Sun Yat-sen University Cancer Center/ ; 2019-I2M-5-036//CAMS Innovation Fund for Medical Sciences (CIFMS)/ ; 82173128//National Natural Science Foundation of China/ ; 81930065//National Natural Science Foundation of China/ ; 82321003//National Natural Science Foundation of China/ ; },
mesh = {*Colorectal Neoplasms/diagnosis/virology/microbiology/genetics ; Humans ; *Gastrointestinal Microbiome ; *Metagenomics/methods ; *Metagenome ; Dysbiosis/virology ; },
abstract = {The role of gut microbiota, especially viruses, in colorectal cancer (CRC) pathogenesis remains unclear. This study investigated the interplay between gut microbiota and CRC development. We developed a viral/bacterial sequence analysis pipeline to reanalyze gut metagenomic datasets from eight CRC studies. A multisample co-occurrence network was constructed to delineate microbiota species interconnections. Our analysis confirmed dysbiosis in CRC patients and revealed enrichment of viral species, particularly those hosted by Lactococcus and Escherichia. These viruses were identified as central hubs in the multikingdom interaction network. We developed a network-based model using single sample networks (SSN) that distinguished CRC patients from controls with an area under the curve (AUC) of 0.93. Models combining relative abundance and SSN assessment achieved an AUC of 0.97, outperforming SSN-based models without viral data. This study highlights the crucial role of viruses in the gut microbiome network and their potential as targets for CRC prevention and intervention. Our approach offers a new perspective on noninvasive diagnostic criteria for CRC.},
}

*Colorectal Neoplasms/diagnosis/virology/microbiology/genetics
Humans
*Gastrointestinal Microbiome
*Metagenomics/methods
*Metagenome
Dysbiosis/virology

@article {pmid40462165,
year = {2025},
author = {Gao, H and Bai, H and Su, Y and Gao, Y and Fang, H and Li, D and Yu, Y and Lu, X and Xia, D and Mao, D and Luo, Y},
title = {Fecal microbiota transplantation from Helicobacter pylori carriers following bismuth quadruple therapy exacerbates alcohol-related liver disease in mice via LPS-induced activation of hepatic TLR4/NF-κB/NLRP3 signaling.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {627},
pmid = {40462165},
issn = {1479-5876},
support = {42377426//National Natural Science Foundation of China/ ; 42077382//National Natural Science Foundation of China/ ; 21JCYBJC01200//Tianjin Municipal Natural Science Foundation/ ; 2023220//Research Project on Integrated Traditional Chinese and Western Medicine of Tianjin Municipal Health Commission/ ; },
mesh = {Animals ; *Fecal Microbiota Transplantation/adverse effects ; *NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; *Helicobacter pylori/physiology/drug effects ; *Signal Transduction/drug effects ; Lipopolysaccharides/pharmacology ; *Bismuth/therapeutic use/pharmacology ; *Toll-Like Receptor 4/metabolism ; Gastrointestinal Microbiome/drug effects ; *NF-kappa B/metabolism ; *Liver/pathology/metabolism/drug effects ; *Liver Diseases, Alcoholic/microbiology/therapy/pathology ; Male ; Mice ; Mice, Inbred C57BL ; Helicobacter Infections/microbiology ; Disease Models, Animal ; Humans ; Dysbiosis ; },
abstract = {BACKGROUND: Helicobacter pylori infection is common in patients with alcohol-related liver disease (ALD), and bismuth quadruple therapy (BQT) is widely used for eradication. However, its impact on ALD remains unclear. This study aims to characterize BQT-induced gut microbiota alterations in asymptomatic H. pylori carriers and evaluate their effect on an ALD mouse model.

METHODS: Metagenomic sequencing was conducted to assess the gut microbiota composition of individuals before and after BQT. Fecal microbiota transplantation (FMT) from these donors was performed in an ALD mouse model. Gut microbiota in mice was analyzed by 16S rRNA sequencing. Liver and intestinal parameters were assessed using western blot, RT-qPCR, histopathology, ELISA, and flow cytometry.

RESULTS: BQT treatment significantly altered the gut microbiota in H. pylori carriers, increasing the abundance of opportunistic pathogens, including Klebsiella pneumoniae, Escherichia coli, Klebsiella quasipneumoniae, and Klebsiella variicola, while decreasing beneficial bacteria such as Bifidobacterium, Eubacterium, Bacteroides, Faecalibacterium, and Blautia. In ALD mice receiving FMT from post-BQT donors, exacerbated gut dysbiosis was observed, marked by an enrichment of Enterobacteriaceae and Escherichia-Shigella. These microbiota changes were associated with impairment of intestinal barrier integrity, as evidenced by reduced levels of mucins, tight junction proteins, and antimicrobial peptides, along with a decrease in Treg cells and an increase in Th17 and Th1 cells. Additionally, this dysbiosis led to elevated serum lipopolysaccharide (LPS) levels, which activated the hepatic NLRP3 inflammasome pathway and subsequently increased IL-18 and IL-1β levels. Furthermore, liver function and oxidative stress markers, including ALT, AST, MDA, GSSG/GSH ratio, and SOD, were significantly elevated, indicating severe liver dysfunction and increased oxidative stress. Finally, probiotic supplementation effectively mitigated the negative effects of BQT-induced gut microbiota remodeling on ALD in mice.

CONCLUSIONS: BQT markedly alters the gut microbiota in H. pylori carriers, promoting dysbiosis that exacerbates ALD in mice via LPS-mediated activation of hepatic inflammatory pathways. These findings highlight the need for careful consideration of BQT use in ALD patients.},
}

Animals
*Fecal Microbiota Transplantation/adverse effects
*NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
*Helicobacter pylori/physiology/drug effects
*Signal Transduction/drug effects
Lipopolysaccharides/pharmacology
*Bismuth/therapeutic use/pharmacology
*Toll-Like Receptor 4/metabolism
Gastrointestinal Microbiome/drug effects
*NF-kappa B/metabolism
*Liver/pathology/metabolism/drug effects
*Liver Diseases, Alcoholic/microbiology/therapy/pathology
Male
Mice
Mice, Inbred C57BL
Helicobacter Infections/microbiology
Disease Models, Animal
Humans
Dysbiosis

@article {pmid40462041,
year = {2025},
author = {Luo, Y and Wu, R and Wu, W and Zhao, D and Jiang, Y and Gu, H},
title = {Differences in pulmonary microbiota of severe community-acquired pneumonia with different pathogenic microorganisms in children.},
journal = {BMC pediatrics},
volume = {25},
number = {1},
pages = {449},
pmid = {40462041},
issn = {1471-2431},
support = {82200008//the Youth Program of National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Community-Acquired Infections/microbiology ; Male ; Female ; Child, Preschool ; Haemophilus influenzae/isolation & purification ; Infant ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota ; *Lung/microbiology ; Streptococcus pneumoniae/isolation & purification ; Mycoplasma pneumoniae/isolation & purification ; *Pneumonia, Bacterial/microbiology ; Child ; Severity of Illness Index ; Pneumonia, Mycoplasma/microbiology ; C-Reactive Protein/analysis ; Community-Acquired Pneumonia ; },
abstract = {BACKGROUND: Community-acquired pneumonia (CAP) is the leading cause of hospitalization and death in children under 5 years old. Recently, the number of children with severe CAP (SCAP) has increased significantly, and local or systemic complications may occur. However, changes in the pulmonary microbiota of SCAP with different pathogens and their relationship with the clinical features of SCAP remain unclear.

METHODS: This study collected bronchoalveolar lavage fluid (BALF) from 105 children with SCAP for metagenomics next generation sequencing (mNGS). According to the first pathogen of mNGS, the enrolled children were divided into the Streptococcus pneumoniae (SP), Mycoplasma pneumoniae (MP) and Haemophilus influenzae (HI) groups. We aimed to explore differences in clinical features and pulmonary microbiota of SCAP with different pathogens, and clarify the correlation between pulmonary microbiota and clinical features.

RESULTS: Fever days and the levels of C-reactive protein (CRP), procalcitonin (PCT), lactate dehydrogenase (LDH), D-dimer and heparin-binding protein (HBP) of children in MP group were significantly higher than those in HI group. The level of LDH of children in MP group was significantly higher than that in SP group. The abundance of MP was also positively correlated with fever days and the levels of PCT, LDH and D-dimer. The α diversity of SP group was significantly increased compared to MP group and HI group.

CONCLUSION: Compared to SP-infected and HI-infected children with SCAP, children with SCAP infected with MP tend to have a more intense inflammatory response. The α diversity was higher in the lower airways of children with SCAP and SP infections compared to MP-infected and HI-infected children with SCAP.},
}

Humans
*Community-Acquired Infections/microbiology
Male
Female
Child, Preschool
Haemophilus influenzae/isolation & purification
Infant
Bronchoalveolar Lavage Fluid/microbiology
*Microbiota
*Lung/microbiology
Streptococcus pneumoniae/isolation & purification
Mycoplasma pneumoniae/isolation & purification
*Pneumonia, Bacterial/microbiology
Child
Severity of Illness Index
Pneumonia, Mycoplasma/microbiology
C-Reactive Protein/analysis
Community-Acquired Pneumonia

@article {pmid40460542,
year = {2025},
author = {Smirnova, AV and Verbeke, TJ and Furgason, CC and Albakistani, EA and Nwosu, FC and Kim, JJ and Haupt, ES and Sheremet, A and Lee, ES and Trang, E and Richardson, E and Dacks, JB and Dunfield, PF},
title = {Microbial community development in an oil sands pit lake.},
journal = {The Science of the total environment},
volume = {987},
number = {},
pages = {179764},
doi = {10.1016/j.scitotenv.2025.179764},
pmid = {40460542},
issn = {1879-1026},
mesh = {*Lakes/microbiology ; *Microbiota ; *Oil and Gas Fields ; Mining ; *Environmental Monitoring ; RNA, Ribosomal, 16S/analysis ; *Water Microbiology ; Canada ; Bacteria ; },
abstract = {Surface mining and extraction of oil sands in Canada produces fluid tailings that contain several compounds of concern for the environment. One option for mine reclamation is the construction of Pit Lakes (PLs) to contain and remediate these tailings. Ultimately, PLs should support food webs typical of boreal lakes. From 2015 to 2021, we applied 16S/18S rRNA gene amplicon sequencing and metagenomics to monitor prokaryotic and eukaryotic microbes in the only full-scale PL of the oil sands industry (Base Mine Lake or BML), and compared it to two control environments: a freshwater reservoir unaffected by tailings, and active tailings ponds receiving regular industrial input. Microbial communities in BML were always intermediate to the two control environments based on alpha and beta diversity analyses. BML communities were highly variable with year, season, and water depth, and contained fewer core species than the freshwater reservoir. Several hydrocarbon degraders and sulfur cycling bacteria were identified as indicator species of tailings ponds, while several phototrophs were indicative of freshwater. However, all of these species were abundant in BML, suggesting that the PL supports food webs characteristic of each control environment. Over the 6-year study, the relative abundances of some common freshwater phytoplankton (Cryptomonas, Mychonastes, Trebouxiophyceae, Cyanobium) and heterotrophic bacteria (Sporichthyaceae, Ca. Fonsibacter, Ilumatobacteraceae, Microbacteriaceae, Ca. Planktophila) increased in BML. The results suggest that microbial communities and processes in BML represent an intermediate state between a tailings pond and a natural freshwater system, and did not stabilize within 10 years of its creation.},
}

*Lakes/microbiology
*Microbiota
*Oil and Gas Fields
Mining
*Environmental Monitoring
RNA, Ribosomal, 16S/analysis
*Water Microbiology
Canada
Bacteria

@article {pmid40460541,
year = {2025},
author = {Kang, MG and Kwak, MJ and Kang, A and Park, J and Lee, DJ and Mun, J and Kim, S and Mun, D and Lee, W and Choi, H and Seo, E and Choi, Y and Jeong, KC and Oh, S and Kim, J and Kim, Y},
title = {Metagenome-based microbial metabolic strategies to mitigate ruminal methane emissions using Komagataeibacter-based symbiotics.},
journal = {The Science of the total environment},
volume = {987},
number = {},
pages = {179793},
doi = {10.1016/j.scitotenv.2025.179793},
pmid = {40460541},
issn = {1879-1026},
mesh = {Animals ; *Methane/metabolism ; *Rumen/microbiology/metabolism ; *Metagenome ; Cattle ; Symbiosis ; Fermentation ; *Gastrointestinal Microbiome ; },
abstract = {Global warming increasingly threatens organisms in equatorial regions, where temperatures often exceed physiological limits. Rumen methanogens are a major biological source of anthropogenic methane, a potent greenhouse gas. Therefore, ruminal methane mitigation strategies that preserve animal productivity are urgently needed. Our In vitro analysis of Holstein steer rumen fluid-integrating gas production, volatile fatty acid (VFA) profiles, and metagenomic data-demonstrated that kombucha, a fermented beverage, effectively reduces methane emissions by modulating ruminal fermentation. Rumen fluid was incubated for 60 h under three treatments (control, 3-NOP, and kombucha). During the initial 30 h, kombucha reduced methane by 15.07 % compared to the control but was 17.54 % higher than 3-NOP. In the subsequent 30 h, kombucha achieved sustained reductions of 34.72 % versus the control and 26.28 % versus 3-NOP, highlighting its uniquely sustained methane-reducing effect. A metagenomics-guided screening and in vitro validation identified Komagataeibacter intermedius SLAM-NK6B as a key strain underlying the methane-reducing effect of kombucha. The genome of SLAM-NK6B encodes biosynthetic gene clusters for cellulose, malate, citrate, and methanobactin-metabolites that can modulate the rumen microbiota. SLAM-NK6B supplementation reduced methanogen abundance by 53.32 % and increased hydrogen pressure, shifting microbial metabolism. Excluding acetate, VFA production increased significantly, with propionate levels elevated by 15.39-43.81 %. Metagenomic data further indicated activation of alternative hydrogen sink pathways, including citrate-to-propionate and malate-to-propionate conversions. This study proposes a novel microbial metabolic strategy for methane mitigation, enabling both methane reduction and enhanced fermentation efficiency. Such metabolic guidance of the rumen microbiome offers a sustainable approach to low-emission ruminant production.},
}

Animals
*Methane/metabolism
*Rumen/microbiology/metabolism
*Metagenome
Cattle
Symbiosis
Fermentation
*Gastrointestinal Microbiome

@article {pmid40459709,
year = {2025},
author = {Quoc, NB and Nhu, LTT and Chau, NNB},
title = {Identification of diet resources of big-eyed bug Geocoris ochropterus (Fieber) (Hemiptera: Geocoridae) by multiplex PCR and shotgun metagenomic approaches.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {537},
pmid = {40459709},
issn = {1573-4978},
support = {E2022.02.1//Đại học Mở Thành phố Hồ Chí Minh/ ; },
mesh = {Animals ; *Metagenomics/methods ; Multiplex Polymerase Chain Reaction/methods ; *Hemiptera/genetics ; Diet ; Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; },
abstract = {BACKGROUND: Big-eyed bugs (Geocoris spp.) are important generalist predators in agricultural ecosystems, playing a crucial role in natural pest control.

METHODS: To better understand their dietary sources, we assessed the plant and animal food sources in the gut of Geocoris ochropterus using multiplex PCR and shotgun metagenomic analysis. The PCR assays targeted genetic markers from both animal (COI) and plant (matK and rbcL) DNA.

RESULTS: Results revealed the presence of both animal and plant-derived DNA in the gut samples, indicating that Geocoris ochropterus feeds on a mixed diet. Additionally, the results of shotgun metagenomic sequencing of the gut microbiota showed a predominance of Eukaryota, with over 80% of sequences belonging to this domain, while a diverse range of taxonomic groups were identified, including arthropods, plants, bacteria, and fungi. Arthropods particularly insects from the orders Lepidoptera, Hemiptera, Hymenoptera, Coleoptera, Phasmatodea and plants belonging to the orders Brassicales, Cucurbitales, and Poales constituted the most abundant dietary components. At the genus level, notable taxa included Maniola (family Nymphalidae), Carposina (Carposinidae), Helicoverpa (Noctuidae), and Solanum (Solanaceae). Species-level analysis confirmed the dominance of several insect species, including Maniola hyperanthus, Carposina sasakii, and Bombyx mori, alongside plant species such as Cucumis melo, Gossypium hirsutum, and Digitaria exilis.

CONCLUSIONS: These findings provide a comprehensive characterization of the diet of Geocoris ochropterus, highlighting its role as a generalist predator with a diverse diet consisting of both insect and plant food sources. This study contributes to the understanding of Geocoris ochropterus as a potential biocontrol agent in agricultural systems.},
}

Animals
*Metagenomics/methods
Multiplex Polymerase Chain Reaction/methods
*Hemiptera/genetics
Diet
Gastrointestinal Microbiome/genetics
Metagenome/genetics

@article {pmid40456950,
year = {2025},
author = {Kocharovskaya, Y and Delegan, Y and Sevostianov, S and Bogun, A and Demin, DV},
title = {Metagenomic Analysis of Pulp and Paper Wastes and Prospects for Their Self-purification.},
journal = {Current microbiology},
volume = {82},
number = {7},
pages = {320},
pmid = {40456950},
issn = {1432-0991},
mesh = {*Paper ; *Metagenomics ; Lignin/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Industrial Waste/analysis ; Biodegradation, Environmental ; *Microbiota ; High-Throughput Nucleotide Sequencing ; },
abstract = {Thousands of tons of waste accumulate, as a result of the activities of the pulp and paper industry, which is often stored in the form of dumps. However, intensifying the use of lignocellulose for more efficient bioremediation remains highly challenging. Therefore, the study of microbiomes with potentially desirable characteristics for the decomposition of pulp and paper wastes is currently an important task. In this study, a comprehensive assessment of the microbiota biodiversity of these dumps was carried out using high-throughput, high-resolution sequencing. In study 472 million high-quality clean reads assembled into 6,413,337 contigs with a total length of 4306 Mb, of which 3,633,174 open reading frames (ORFs) were identified. The core microbiome was composed of four phyla from Proteobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. Representatives of phylum Proteobacteria prevailed in samples. Annotation using the KEGG database in the Metabolism category resulted in 654,234 ORFs and 5138 ORFs encoding enzymes/proteins involved in degradation of lignocellulose which formed main pool of the wastes. By use of the created database, the search for lignocellulose degradation genes showed that genera Shewanella, Achromobacter, and Delftia covered significant part of the reads. The results indicate that the established microbiome of local landfills can be considered as an important source for improving lignocellulose bioremediation, provided that lignocellulosic fungi are sufficiently active. In whole, these new data can be used as a scientific basis to form an efficient eco-biotechnology for auto-remediation of pulp and paper industry waste.},
}

*Paper
*Metagenomics
Lignin/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
*Industrial Waste/analysis
Biodegradation, Environmental
*Microbiota
High-Throughput Nucleotide Sequencing

@article {pmid40456770,
year = {2025},
author = {Zhou, XQ and Chen, KH and Yu, RQ and Yang, M and Liu, Q and Hao, YY and Li, J and Liu, HW and Feng, J and Tan, W and Huang, Q and Gu, B and Liu, YR},
title = {Microbial potential to mitigate neurotoxic methylmercury accumulation in farmlands and rice.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5102},
pmid = {40456770},
issn = {2041-1723},
support = {42425701//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177022//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Methylmercury Compounds/metabolism/toxicity ; *Oryza/metabolism/microbiology ; *Soil Microbiology ; Biodegradation, Environmental ; Metagenomics ; *Soil Pollutants/metabolism/toxicity ; *Bacteria/metabolism/genetics/classification ; Soil/chemistry ; },
abstract = {Toxic methylmercury (CH3Hg[+]) is produced by microbial conversion of inorganic mercury in hypoxic environments such as rice paddy soils, and can accumulate in rice grains. Although microbial demethylation has been recognized as a crucial pathway for CH3Hg[+] degradation, the identities of microbes and pathways accountable for CH3Hg[+] degradation in soil remain elusive. Here, we combine [13]CH3Hg[+]-DNA stable-isotope probing experiments with shotgun metagenomics to explore microbial taxa and associated biochemical processes involved in CH3Hg[+] degradation in paddy and upland soils. We identify Pseudarthrobacter, Methylophilaceae (MM2), and Dechloromonas as the most significant taxa potentially engaged in the degradation of [13]CH3Hg[+] in paddy soil with high mercury contamination. We confirm that strains affiliated with two of those taxa (species Dechloromonas denitrificans and Methylovorus menthalis) can degrade CH3Hg[+] in pure culture assays. Metagenomic analysis further reveals that most of these candidate [13]CH3Hg[+] degraders carry genes associated with the Wood-Ljungdahl pathway, dicarboxylate-hydroxybutyrate cycle, methanogenesis, and denitrification, but apparently lack the merB and merA genes involved in CH3Hg[+] reductive demethylation. Finally, we estimate that microbial degradation of soil CH3Hg[+] contributes to 0.08-0.64 fold decreases in CH3Hg[+] accumulation in rice grains across China (hazard quotient (HQ) decrements of 0.62-13.75%). Thus, our results provide insights into microorganisms and pathways responsible for CH3Hg[+] degradation in soil, with potential implications for development of bioremediation strategies.},
}

*Methylmercury Compounds/metabolism/toxicity
*Oryza/metabolism/microbiology
*Soil Microbiology
Biodegradation, Environmental
Metagenomics
*Soil Pollutants/metabolism/toxicity
*Bacteria/metabolism/genetics/classification
Soil/chemistry

@article {pmid40454480,
year = {2025},
author = {Lynch, LE and Lahowetz, R and Maresso, C and Terwilliger, A and Pizzini, J and Melendez Hebib, V and Britton, RA and Maresso, AW and Preidis, GA},
title = {Present and future of microbiome-targeting therapeutics.},
journal = {The Journal of clinical investigation},
volume = {135},
number = {11},
pages = {},
pmid = {40454480},
issn = {1558-8238},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Probiotics/therapeutic use ; *Phage Therapy/trends/methods ; Bacteriophages ; Animals ; },
abstract = {A large body of evidence suggests that single- and multiple-strain probiotics and synbiotics could have roles in the management of specific gastrointestinal disorders. However, ongoing concerns regarding the quality and heterogeneity of the clinical data, safety in vulnerable populations, and the lack of regulation of products containing live microbes are barriers to widespread clinical use. Safety and regulatory issues must be addressed and new technologies considered. One alternative future strategy is the use of synthetic bacterial communities, defined as manually assembled consortia of two or more bacteria originally derived from the human gastrointestinal tract. Synthetic bacterial communities can model functional, ecological, and structural aspects of native communities within the gastrointestinal tract, occupying varying nutritional niches and providing the host with a stable, robust, and diverse gut microbiota that can prevent pathobiont colonization by way of colonization resistance. Alternatively, phage therapy is the use of lytic phage to treat bacterial infections. The rise of antimicrobial resistance has led to renewed interest in phage therapy, and the high specificity of phages for their hosts has spurred interest in using phage-based approaches to precisely modulate the microbiome. In this Review, we consider the present and future of microbiome-targeting therapies, with a special focus on early-life applications, such as prevention of necrotizing enterocolitis.},
}

Humans
*Gastrointestinal Microbiome
*Probiotics/therapeutic use
*Phage Therapy/trends/methods
Bacteriophages
Animals

@article {pmid40452057,
year = {2025},
author = {Francioli, D and Kampouris, ID and Kuhl-Nagel, T and Babin, D and Sommermann, L and Behr, JH and Chowdhury, SP and Zrenner, R and Moradtalab, N and Schloter, M and Geistlinger, J and Ludewig, U and Neumann, G and Smalla, K and Grosch, R},
title = {Microbial inoculants modulate the rhizosphere microbiome, alleviate plant stress responses, and enhance maize growth at field scale.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {148},
pmid = {40452057},
issn = {1474-760X},
support = {031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; },
mesh = {*Zea mays/microbiology/growth & development ; *Rhizosphere ; *Microbiota ; *Stress, Physiological ; Bacillus ; Plant Roots/microbiology ; Soil Microbiology ; *Agricultural Inoculants/physiology ; },
abstract = {BACKGROUND: Field inoculation of crops with beneficial microbes is a promising sustainable strategy to enhance plant fitness and nutrient acquisition. However, effectiveness can vary due to environmental factors, microbial competition, and methodological challenges, while their precise modes of action remain uncertain. This underscores the need for further research to optimize inoculation strategies for consistent agricultural benefits.

RESULTS: Using a comprehensive, multidisciplinary approach, we investigate the effects of a consortium of beneficial microbes (BMc) (Pseudomonas sp. RU47, Bacillus atrophaeus ABi03, Trichoderma harzianum OMG16) on maize (Zea mays cv. Benedictio) through an inoculation experiment conducted within a long-term field trial across intensive and extensive farming practices. Additionally, an unexpected early drought stress emerged as a climatic variable, offering further insight into the effectiveness of the microbial consortium. Our findings demonstrate that BMc root inoculation primarily enhanced plant growth and fitness, particularly by increasing iron uptake, which is crucial for drought adaptation. Inoculated maize plants show improved shoot growth and fitness compared to non-inoculated plants, regardless of farming practices. Specifically, BMc modulate plant hormonal balance, enhance the detoxification of reactive oxygen species, and increase root exudation of iron-chelating metabolites. Amplicon sequencing reveals shifts in rhizosphere bacterial and fungal communities mediated by the consortium. Metagenomic shotgun sequencing indicates enrichment of genes related to antimicrobial lipopeptides and siderophores.

CONCLUSIONS: Our findings highlight the multifaceted benefits of BMc inoculation on plant fitness, significantly influencing metabolism, stress responses, and the rhizosphere microbiome. These improvements are crucial for advancing sustainable agricultural practices by enhancing plant resilience and productivity.},
}

*Zea mays/microbiology/growth & development
*Rhizosphere
*Microbiota
*Stress, Physiological
Bacillus
Plant Roots/microbiology
Soil Microbiology
*Agricultural Inoculants/physiology

@article {pmid40451005,
year = {2025},
author = {Su, X and Liu, J and Chang, L and Hu, W and Fang, Y and Li, J and Huang, L and Shu, W and Dong, H},
title = {Viral insights into the acidification of sulfidic mine tailings.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138754},
doi = {10.1016/j.jhazmat.2025.138754},
pmid = {40451005},
issn = {1873-3336},
abstract = {The acidification of sulfidic mine tailings, driven primarily by sulfur- and iron-oxidizing microorganisms, can lead to severe environmental pollution and imperil human health. The role of viruses in this process and its underlying mechanisms yet remain poorly understood. In this study, we recovered 623 species-level viral genomes and 322 prokaryotic genomes from seven metagenomes of mine tailings with pH values ranging from 7.51 to 2.13. We observed that acidification drastically altered geochemical properties and degraded environmental quality, characterized by significant decreases in carbon/nitrogen ratio and heavy metal levels. The structure and function of viral communities were significantly correlated with pH and prokaryotic diversity, showing distinct dynamics across different acidification stages, similar to patterns observed in the prokaryotic community. Notably, potential sulfur-oxidizing prokaryotes increased in relative abundance as pH declined, while their virus-host abundance ratio exhibited a significant positive correlation with pH. Results indicated that viral "top-down" predation on sulfur-oxidizing prokaryotes was likely suppressed during acidification, providing a survival advantage to these organisms over iron-oxidizing counterparts. Moreover, viruses likely reprogrammed the sulfur and iron metabolism of prokaryotic hosts and enhanced their adaptability to environmental stressors through auxiliary metabolic genes. Additionally, a pH- and lifestyle-dependent evolutionary scenario for viruses revealed that frequent recombination and the accumulation of synonymous mutations in lytic viruses and chronic Inoviridae, likely increased their intrapopulation diversity and resilience. These findings provide new insights into the multifaceted roles of viruses in mine tailings acidification, deepening understanding of the underlying mechanisms and advancing potential strategies to mitigate associated environmental risks.},
}

@article {pmid40450783,
year = {2025},
author = {Rajput, V and Pramanik, R and Nannaware, K and Shah, P and Bhalerao, A and Jain, N and Shashidhara, LS and Kamble, S and Dastager, S and Dharne, M},
title = {Metagenomics based longitudinal monitoring of antibiotic resistome and microbiome in the inlets of wastewater treatment plants in an Indian megacity.},
journal = {The Science of the total environment},
volume = {986},
number = {},
pages = {179691},
doi = {10.1016/j.scitotenv.2025.179691},
pmid = {40450783},
issn = {1879-1026},
mesh = {India ; *Wastewater/microbiology ; *Microbiota ; Metagenomics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents ; *Environmental Monitoring ; Bacteria ; Waste Disposal, Fluid ; Cities ; },
abstract = {The growing threat of antimicrobial resistance (AMR) poses a significant global challenge, undermining advancements in healthcare, agriculture, and life expectancy. Despite its critical importance, data on population-level AMR trends, including seasonal and temporal variations, remain scarce. In this study, we conducted metagenomic analysis on 190 wastewater samples collected monthly from December 2022 to December 2023 in Pune, India, to assess the diversity, dynamics, and co-occurrence of AMR determinants. Using nanopore shotgun sequencing, we generated 87.86 Gbp of data, enabling the taxonomic classification of 157 bacterial phyla and 3291 genera. Proteobacteria dominated the microbial community, with notable seasonal shifts, including increased Streptococcus abundance correlating with SARS-CoV-2 viral surges in March 2023. We identified 637 distinct antimicrobial resistance genes (ARGs) associated with 29 antibiotic classes, with multidrug, macrolide-lincosamide-streptogramin, beta-lactams, and tetracyclines genes being the most prevalent, particularly within WHO priority pathogens such as Enterobacteriaceae and Pseudomonas. Temporal normalization of ARG abundance revealed significant seasonal variability, peaking during winter, potentially driven by increased antibiotic use for respiratory infections. The integration of viral load data with AMR trends highlighted complex interactions between viral outbreaks and AMR dissemination. This study demonstrates the potential of wastewater surveillance as an early warning system for AMR, providing valuable insights into environmental and community resistance dynamics. Our results underscore the importance of integrated AMR surveillance to inform public health strategies aimed at mitigating the global AMR threat.},
}

India
*Wastewater/microbiology
*Microbiota
Metagenomics
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents
*Environmental Monitoring
Bacteria
Waste Disposal, Fluid
Cities

@article {pmid40450182,
year = {2025},
author = {Wang, C and Dong, T and Rong, X and Yang, Y and Mou, J and Li, J and Ge, J and Mu, X and Jiang, J},
title = {Microbiome in prostate cancer: pathogenic mechanisms, multi-omics diagnostics, and synergistic therapies.},
journal = {Journal of cancer research and clinical oncology},
volume = {151},
number = {6},
pages = {178},
pmid = {40450182},
issn = {1432-1335},
support = {82172230//the National Natural Science Foundation of China/ ; 21ZGY29//the Changchun Scientific and Technological Development Program/ ; 3R218FM83430//Life Spring AKY Pharmaceuticals/ ; 20240205001YY//the Jilin Scientific and Technological Development Program/ ; 2017F014//the Jilin Health Service Capacity Improvement Program/ ; },
mesh = {Humans ; *Prostatic Neoplasms/microbiology/therapy/diagnosis/pathology ; Male ; *Microbiota ; Metagenomics/methods ; Multiomics ; },
abstract = {BACKGROUND: Prostate cancer (PCa) is a leading cause of cancer-related deaths in men, with the microbiome emerging as a significant factor in its development and progression. Understanding the microbiome's role could provide new insights into PCa pathogenesis and treatment.

OBJECTIVE: This review aims to explore the interactions between the microbiome and PCa, focusing on microbial imbalances and their effects on immune responses, inflammation, and hormone levels. It also discusses advanced research techniques and the potential for microbiome modulation in PCa management.

METHODS: The review synthesizes current literature on the microbiome's role in PCa, highlighting differences in microbial composition between cancerous and healthy prostate tissues. It examines techniques such as high-throughput sequencing and metagenomics and explores the mechanisms through which the microbiome influences PCa.

CONCLUSIONS: The review reveals substantial microbial differences in prostate tissues of PCa patients compared to healthy individuals, indicating a potential link between microbiome alterations and disease progression. It highlights the promise of microbiome-based strategies for diagnosis and treatment and underscores the need for further research into personalized, microbiome-centric approaches for PCa management.},
}

Humans
*Prostatic Neoplasms/microbiology/therapy/diagnosis/pathology
Male
*Microbiota
Metagenomics/methods
Multiomics

@article {pmid40449445,
year = {2025},
author = {Zheng, Z and Gustavsson, DJI and Zheng, D and Holmin, F and Falås, P and Wilén, BM and Modin, O and Persson, F},
title = {Genome-centric metagenomics reveals the effect of organic carbon source on one-stage partial denitrification-anammox in biofilm reactors.},
journal = {Journal of environmental management},
volume = {388},
number = {},
pages = {125972},
doi = {10.1016/j.jenvman.2025.125972},
pmid = {40449445},
issn = {1095-8630},
mesh = {*Denitrification ; *Bioreactors ; Biofilms ; Carbon/metabolism ; Nitrogen/metabolism ; Wastewater ; Metagenomics ; Microbiota ; Waste Disposal, Fluid ; },
abstract = {Nitrogen removal from wastewater with anammox saves energy and resources. Partial denitrification-anammox (PDA) is a promising process alternative for municipal wastewater treatment, given that the understanding about how to control the microbiome and its activity reach sufficient level. Here, two moving bed biofilm reactors were fed with either acetate or propionate to study the role of organic carbon type for microbiome composition and nitrogen turnover during development of PDA. With acetate, 87 % of the removed nitrogen was converted via anammox during stable operation at a rate of 0.52 g N/(m[2]·d). With propionate, the anammox contribution was considerably lower (41 %), as was the rate of nitrogen removal (0.27 g N/(m[2]·d)). The microbiome composition in the acetate- and propionate-fed reactors was however similar, with an enrichment of metagenome assembled genomes (MAGs) having genes for nitrate reduction (narG, napA). A large fraction of these MAGs had the potential to accumulate nitrite since they lacked genes for nitrite reduction (nirS, nirK, nrfA). Genes for acetate utilization were common among these MAGs, but the necessary genes for propionate conversion were rare, suggesting that the genetic make-up of the individual denitrifiers had major influence on the nitrogen turnover. One anammox MAG (Ca. Brocadia sapporoensis), harboring genes for organic carbon utilization, prevailed in the PDA reactors. Another three anammox MAGs (Ca. B. fulgida, Ca. B. pituitae and a potentially new species within Ca. Brocadia), lacking genes for organic carbon utilization, decreased in abundance in the reactors, indicating the importance of metabolic versatility for anammox bacteria in PDA.},
}

*Denitrification
*Bioreactors
Biofilms
Carbon/metabolism
Nitrogen/metabolism
Wastewater
Metagenomics
Microbiota
Waste Disposal, Fluid

@article {pmid40448221,
year = {2025},
author = {Fan, KC and Lin, CC and Chiu, YL and Koh, SH and Liu, YC and Chuang, YF},
title = {Compositional and functional gut microbiota alterations in mild cognitive impairment: links to Alzheimer's disease pathology.},
journal = {Alzheimer's research & therapy},
volume = {17},
number = {1},
pages = {122},
pmid = {40448221},
issn = {1758-9193},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Cognitive Dysfunction/microbiology/pathology/metabolism ; *Alzheimer Disease/microbiology/pathology/metabolism ; Male ; Female ; Aged ; Feces/microbiology ; Biomarkers ; Brain/pathology/metabolism ; Aged, 80 and over ; Dysbiosis ; tau Proteins ; Middle Aged ; },
abstract = {BACKGROUND: Emerging evidence highlights the bidirectional communication between the gut microbiota and the brain, suggesting a potential role for gut dysbiosis in Alzheimer's disease (AD) pathology and cognitive decline. Existing literature on gut microbiota lacks species-level insights. This study investigates gut microbiota alterations in mild cognitive impairment (MCI), focusing on their association with comprehensive AD biomarkers, including amyloid burden, tau pathology, neurodegeneration, and cognitive performance.

METHODS: We analyzed fecal samples from 119 individuals with MCI and 320 cognitively normal controls enrolled in the Taiwan Precision Medicine Initiative on Cognitive Impairment and Dementia cohort. Shotgun metagenomic sequencing was conducted with taxonomic profiling using MetaPhlAn4. Amyloid burden and plasma pTau181 were quantified via PET imaging and Simoa assays, respectively, while APOE genotyping was performed using TaqMan assays. Microbial diversity, differential abundance analysis, and correlation mapping with neuropsychological and neuroimaging measures were conducted to identify gut microbiota species signatures associated with MCI and AD biomarkers.

RESULTS: We identified 59 key microbial species linked to MCI and AD biomarkers. Notably, species within the same genera, such as Bacteroides and Ruminococcus, showed opposing effects, while Akkermansia muciniphila correlated with reduced amyloid burden, suggesting a protective role. Functional profiling revealed microbial pathways contributing to energy metabolism and neuroinflammation, mediating the relationship between gut microbes and brain health. Co-occurrence network analyses demonstrated complex microbial interactions, indicating that the collective influence of gut microbiota on neurodegeneration.

CONCLUSIONS: Our findings challenge genus-level microbiome analyses, revealing species-specific modulators of AD pathology. This study highlights gut microbial activity as a potential therapeutic target to mitigate cognitive decline and neurodegeneration.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Cognitive Dysfunction/microbiology/pathology/metabolism
*Alzheimer Disease/microbiology/pathology/metabolism
Male
Female
Aged
Feces/microbiology
Biomarkers
Brain/pathology/metabolism
Aged, 80 and over
Dysbiosis
tau Proteins
Middle Aged

@article {pmid40447596,
year = {2025},
author = {Wang, X and Jiang, Q and Tian, X and Chen, W and Mai, J and Lin, G and Huo, Y and Zheng, H and Yan, D and Wang, X and Li, T and Gao, Y and Mou, X and Zhao, W},
title = {Metagenomic analysis reveals the novel role of vaginal Lactobacillus iners in Chinese healthy pregnant women.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {92},
pmid = {40447596},
issn = {2055-5008},
mesh = {Adult ; Female ; Humans ; Pregnancy ; Young Adult ; Biofilms/growth & development ; China ; Gardnerella vaginalis/growth & development ; *Lactobacillus/genetics/isolation & purification/classification/physiology ; *Metagenomics/methods ; Microbiota ; Pregnant People ; *Vagina/microbiology ; Vaginosis, Bacterial/microbiology ; },
abstract = {This study investigated the relationship between vaginal microbiota and women's health conditions in 95 Chinese pregnant women in their third trimester. We conducted vaginal metagenomic analysis, examining species, functional pathways, and genes, and utilized correlation and LEfSe analyses to link microbiota to health conditions. Results revealed that healthy participants exhibited higher levels of Lactobacillus iners, with its abundance associated with tetrahydrofolate biosynthesis pathways. They also possessed more glycosyltransferase and ErmB antibiotic resistance genes compared to women with diagnosed conditions. Comparative genomics demonstrated that L. iners strains linked to bacterial vaginosis (BV) possessed more genes encoding biofilm-associated YhgE/Pip domain-containing proteins than healthy-associated strains. Notably, three BV-associated L. iners strains exhibited stronger biofilm formation abilities than four healthy-associated strains isolated in this study. Also, four out of seven L. iners strains inhibited the growth of Gardnerella vaginalis. Overall, L. iners may help maintain vaginal ecosystem stability in Chinese pregnant women.},
}

Adult
Female
Humans
Pregnancy
Young Adult
Biofilms/growth & development
China
Gardnerella vaginalis/growth & development
*Lactobacillus/genetics/isolation & purification/classification/physiology
*Metagenomics/methods
Microbiota
Pregnant People
*Vagina/microbiology
Vaginosis, Bacterial/microbiology

@article {pmid40447574,
year = {2025},
author = {Rodríguez Del Río, Á and Scheu, S and Rillig, MC},
title = {Soil microbial responses to multiple global change factors as assessed by metagenomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5058},
pmid = {40447574},
issn = {2041-1723},
mesh = {*Soil Microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/drug effects ; Metagenome ; Soil/chemistry ; Droughts ; Microbiota/genetics ; Salinity ; *Climate Change ; Global Warming ; },
abstract = {Anthropogenic activities impose multiple concurrent pressures on soils globally, but responses of soil microbes to multiple global change factors are poorly understood. Here, we apply 10 treatments (warming, drought, nitrogen deposition, salinity, heavy metal, microplastics, antibiotics, fungicides, herbicides and insecticides) individually and in combinations of 8 factors to soil samples, and monitor their bacterial and viral composition by metagenomic analysis. We recover 742 mostly unknown bacterial and 1865 viral Metagenome-Assembled Genomes (MAGs), and leverage them to describe microbial populations under different treatment conditions. The application of multiple factors selects for prokaryotic and viral communities different from any individual factor, favouring the proliferation of potentially pathogenic mycobacteria and novel phages, which apparently play a role in shaping prokaryote communities. We also build a 25 M gene catalog to show that multiple factors select for metabolically diverse, sessile and non-biofilm-forming bacteria with a high load of antibiotic resistance genes. Finally, we show that novel genes are relevant for understanding microbial response to global change. Our study indicates that multiple factors impose selective pressures on soil prokaryotes and viruses not observed at the individual factor level, and emphasizes the need of studying the effect of concurrent global change treatments.},
}

*Soil Microbiology
*Metagenomics/methods
*Bacteria/genetics/classification/drug effects
Metagenome
Soil/chemistry
Droughts
Microbiota/genetics
Salinity
*Climate Change
Global Warming

@article {pmid40445192,
year = {2025},
author = {Mullinax, SR and Darby, AM and Gupta, A and Chan, P and Smith, BR and Unckless, RL},
title = {A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {40445192},
issn = {2050-084X},
support = {CMADP COBRE P20-GM103638/NH/NIH HHS/United States ; R01 AI139154/AI/NIAID NIH HHS/United States ; AI139154/NH/NIH HHS/United States ; P20 GM103638/GM/NIGMS NIH HHS/United States ; 2330095//National Science Foundation/ ; },
mesh = {Animals ; *Alleles ; Female ; Male ; *Drosophila Proteins/genetics/immunology ; *Selection, Genetic ; Providencia/immunology ; *Drosophila/genetics/immunology/microbiology ; Gastrointestinal Microbiome ; *Drosophila melanogaster/genetics/immunology/microbiology ; *Antimicrobial Peptides/genetics/immunology ; },
abstract = {The innate immune system provides hosts with a crucial first line of defense against pathogens. While immune genes are often among the fastest evolving genes in the genome, in Drosophila, antimicrobial peptides (AMPs) are notable exceptions. Instead, AMPs may be under balancing selection, such that over evolutionary timescales, multiple alleles are maintained in populations. In this study, we focus on the Drosophila AMP Diptericin A, which has a segregating amino acid polymorphism associated with differential survival after infection with the Gram-negative bacteria Providencia rettgeri. Diptericin A also helps control opportunistic gut infections by common Drosophila gut microbes, especially those of Lactobacillus plantarum. In addition to genotypic effects on gut immunity, we also see strong sex-specific effects that are most prominent in flies without functional diptericin A. To further characterize differences in microbiomes between different diptericin genotypes, we used 16S metagenomics to look at the microbiome composition. We used both lab-reared and wild-caught flies for our sequencing and looked at overall composition as well as the differential abundance of individual bacterial families. Overall, we find flies that are homozygous for one allele of diptericin A are better equipped to survive a systemic infection from P. rettgeri, but in general have a shorter lifespans after being fed common gut commensals. Our results suggest a possible mechanism for the maintenance of genetic variation of diptericin A through the complex interactions of sex, systemic immunity, and the maintenance of the gut microbiome.},
}

Animals
*Alleles
Female
Male
*Drosophila Proteins/genetics/immunology
*Selection, Genetic
Providencia/immunology
*Drosophila/genetics/immunology/microbiology
Gastrointestinal Microbiome
*Drosophila melanogaster/genetics/immunology/microbiology
*Antimicrobial Peptides/genetics/immunology

@article {pmid40443669,
year = {2025},
author = {Zhang, C and Xu, Y and Zhang, M and Li, J and Sun, Z and Wang, Y and Lin, P},
title = {An exploratory study on the metagenomic and proteomic characterization of hypothyroidism in the first half of pregnancy and correlation with Th1/Th2 balance.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1500866},
pmid = {40443669},
issn = {1664-3224},
mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/immunology/microbiology/metabolism ; Adult ; Proteomics/methods ; *Th2 Cells/immunology/metabolism ; *Th1 Cells/immunology/metabolism ; Metagenomics/methods ; *Gastrointestinal Microbiome/immunology ; *Pregnancy Complications/immunology/metabolism/microbiology ; *Proteome ; Cytokines/metabolism ; },
abstract = {OBJECTIVE: To explore the gut microbiota and proteomic characteristics of hypothyroidism in the first half of pregnancy (referred to as hypothyroidism in the first half of pregnancy) and its association with Th (T helper cells, Th)1/Th2 balance using metagenomics combined with proteomics.

METHODS: Stool and blood samples were collected from 20 hypothyroid (hypothyroidism group) and normal pregnant women (normal group) in the first half of pregnancy. Flora and proteomic characteristics were analyzed using metagenomics sequencing and 4D-DIA proteomics. Th1 and Th2 cells were quantified, and cytokine levels were measured using cellular micro-bead arra. The enzyme-linked immunosorbent test (ELISA) was utilized to assess differential proteins.

RESULTS: (1) Metagenomic sequencing revealed distinct microbial profiles: The β-diversity of gut microbiota was diminished in the hypothyroidism group (p < 0.05). LEfSe analysis identified Phocaeicola vulgatus and Bacteroides fragilis enriched in the hypothyroidism group (p<0.05), and Kyoto Encyclopedia of Genes and Genomes(KEGG) analysis showed significant enrichment in pathways related to peptidoglycan biosynthesis and glycerol ester metabolism.(2) Proteomic analysis demonstrated downregulation of Diacylglycerol Kinase Kappa (DGKK) and P05109|S10A8(S10A8) proteins in the hypothyroidism group, with marked enrichment in the KEGG pathways for vascular smooth muscle contraction and phosphatidylinositol signaling. (3) ELISA validation confirmed that the proteins DGKK and S10A8 were downregulated in pregnant women in the hypothyroidism group.

CONCLUSION: Increased P. vulgatus and B. fragilis, decreased DGKK and S10A8 proteins, and a left shift in the Th1/Th2 balance in patients with hypothyroidism in the first half of pregnancy may be associated with the development of the disease.},
}

Humans
Female
Pregnancy
*Hypothyroidism/immunology/microbiology/metabolism
Adult
Proteomics/methods
*Th2 Cells/immunology/metabolism
*Th1 Cells/immunology/metabolism
Metagenomics/methods
*Gastrointestinal Microbiome/immunology
*Pregnancy Complications/immunology/metabolism/microbiology
*Proteome
Cytokines/metabolism

@article {pmid40442718,
year = {2025},
author = {Pivrncova, E and Bohm, J and Barton, V and Klanova, J and Borilova Linhartova, P},
title = {Viable bacterial communities in freshly pumped human milk and their changes during cold storage conditions.},
journal = {International breastfeeding journal},
volume = {20},
number = {1},
pages = {44},
pmid = {40442718},
issn = {1746-4358},
support = {LM2023069//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; 857560//Horizon 2020 Framework Programme/ ; },
mesh = {Humans ; *Milk, Human/microbiology ; Female ; *Bacteria/isolation & purification/genetics/classification ; *Food Storage/methods ; Adult ; RNA, Ribosomal, 16S ; *Microbiota ; Freezing ; Refrigeration ; Azides ; Propidium/analogs & derivatives ; },
abstract = {BACKGROUND: Human milk harbors diverse bacterial communities that contribute to infant health. Although pumping and storing milk is a common practice, the viable bacterial composition of pumped milk and the impact of storage practice on these bacteria remains under-explored. This metagenomic observational study aimed to characterize viable bacterial communities in freshly pumped human milk and its changes under different storage conditions.

METHODS: In 2023, twelve lactating mothers from the CELSPAC: TNG cohort (Czech Republic) provided freshly pumped milk samples. These samples were stored under various conditions (refrigeration for 24 h, 48 h, or freezing for six weeks) and treated with propidium monoazide (PMA) to selectively identify viable cells. The DNA extracted from individual samples was subsequently analyzed using 16S rRNA amplicon sequencing on the Illumina platform.

RESULTS: The genera Streptococcus, Staphylococcus, Diaphorobacter, Cutibacterium, and Corynebacterium were the most common viable bacteria in fresh human milk. The median sequencing depth and Shannon index of fresh human milk samples treated with PMA (+ PMA) were significantly lower than in untreated (-PMA) samples (p < 0.05 for all), which was true also for each time point. Also, significant changes in these parameters were observed between fresh human milk samples and their paired frozen samples (p < 0.05), while no differences were found between fresh human milk samples and those refrigerated for up to 48 h (p > 0.05). Of specific genera, only + PMA frozen human milk samples showed a significant decrease in the central log-ratio transformed relative abundances of the genera Diaphorobacter and Cutibacterium (p < 0.05) in comparison to + PMA fresh human milk samples.

CONCLUSIONS: The study demonstrated that the bacterial profiles significantly differed between human milk samples treated with PMA, which represent only viable bacteria, and those untreated. While storage at 4 °C for up to 48 h did not significantly alter the overall diversity and composition of viable bacteria in human milk, freezing notably affected both the viability and relative abundances of some bacterial genera.},
}

Humans
*Milk, Human/microbiology
Female
*Bacteria/isolation & purification/genetics/classification
*Food Storage/methods
Adult
RNA, Ribosomal, 16S
*Microbiota
Freezing
Refrigeration
Azides
Propidium/analogs & derivatives

@article {pmid40442154,
year = {2025},
author = {Seong, HJ and Park, YM and Kim, BS and Yoo, HJ and Kim, T and Yoon, SM and Kim, JH and Lee, SY and Lee, YK and Lee, DW and Nam, MH and Hong, SJ},
title = {Integrated multi-omics reveals different host crosstalk of atopic dermatitis-enriched Bifidobacterium longum Strains.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {91},
pmid = {40442154},
issn = {2055-5008},
mesh = {Humans ; *Dermatitis, Atopic/microbiology ; *Gastrointestinal Microbiome ; Infant ; *Bifidobacterium longum/genetics/isolation & purification/classification/metabolism ; Female ; Male ; Metabolomics ; Metagenomics/methods ; Feces/microbiology ; *Host Microbial Interactions ; Clostridium/genetics/isolation & purification ; Transcriptome ; Multiomics ; },
abstract = {The infant gut microbiome is essential for long-term health and is linked to atopic dermatitis (AD), although the underlying mechanisms are not fully understood. This study investigated gut microbiome-host interactions in 31 infants with AD and 29 healthy controls using multi-omics approaches, including metagenomic, host transcriptomic, and metabolomic analyses. Microbial diversity was significantly altered in AD, with Bifidobacterium longum and Clostridium innocuum associated with these changes. At the strain-level, only B. longum differed significantly between groups, with pangenome analyses identifying genetic variations potentially affecting amino acid and lipid metabolites. Notably, B. longum subclade I, which was more prevalent in healthy controls, correlated with host transcriptomic pathways involved in phosphatidylinositol 3-kinase-AKT signaling and neuroactive ligand-receptor pathways, as well as specific metabolites, including tetrahydrocortisol and ornithine. These findings highlight the role of B. longum strain-level variation in infants, offering new insights into microbiome-host interactions related to AD.},
}

Humans
*Dermatitis, Atopic/microbiology
*Gastrointestinal Microbiome
Infant
*Bifidobacterium longum/genetics/isolation & purification/classification/metabolism
Female
Male
Metabolomics
Metagenomics/methods
Feces/microbiology
*Host Microbial Interactions
Clostridium/genetics/isolation & purification
Transcriptome
Multiomics

@article {pmid40441146,
year = {2025},
author = {Yang, Y and Duan, Y and Lang, S and Fondevila, MF and Schöler, D and Harberts, A and Cabré, N and Chen, S and Shao, Y and Vervier, K and Miyamoto, Y and Zhang, X and Chu, H and Yang, L and Tan, C and Eckmann, L and Bosques-Padilla, F and Verna, EC and Abraldes, JG and Brown, RS and Vargas, V and Altamirano, J and Caballería, J and Shawcross, DL and Louvet, A and Lucey, MR and Mathurin, P and Garcia-Tsao, G and Bataller, R and Stärkel, P and Lawley, TD and Schnabl, B},
title = {Targeted inhibition of pathobiont virulence factor mitigates alcohol-associated liver disease.},
journal = {Cell host & microbe},
volume = {33},
number = {6},
pages = {957-972.e6},
pmid = {40441146},
issn = {1934-6069},
support = {I01 BX004594/BX/BLRD VA/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; R37 AA020703/AA/NIAAA NIH HHS/United States ; U01 AA021856/AA/NIAAA NIH HHS/United States ; },
mesh = {Humans ; Animals ; *Virulence Factors/genetics/antagonists & inhibitors/metabolism ; Mice ; *Escherichia coli/genetics/pathogenicity/drug effects/metabolism ; *Liver Diseases, Alcoholic/microbiology/drug therapy ; Gastrointestinal Microbiome ; Disease Models, Animal ; Feces/microbiology ; Kupffer Cells/metabolism/microbiology ; *Escherichia coli Proteins/genetics/metabolism/antagonists & inhibitors ; Male ; Female ; Liver/pathology/microbiology ; Germ-Free Life ; Ethanol ; Mice, Inbred C57BL ; Escherichia coli Infections/microbiology ; Bacterial Capsules/metabolism ; Hepatitis, Alcoholic/microbiology ; },
abstract = {Alcohol-associated liver disease poses a global health burden with high mortality. Imbalances in the gut microbiota are important for disease progression. Using metagenomic sequencing of fecal samples from a multicenter, international cohort of patients with alcohol-associated hepatitis, we found that the presence of virulence factor KpsM, encoded in the genome of Escherichia coli (E. coli), correlated with patient mortality. Functional studies using gnotobiotic mouse models and genetic manipulation of bacteria demonstrated that kpsM-positive E. coli exacerbate ethanol-induced liver disease. The kpsM gene mediates the translocation of capsular polysaccharides to the cell surface. This enables kpsM-positive E. coli to evade phagocytosis by the scavenger receptor Marco on Kupffer cells in the liver, leading to bacterial spread. Importantly, inhibiting kpsM-dependent capsules with the small molecule 2-(4-phenylphenyl)benzo[g]quinoline-4-carboxylic acid (C7) attenuated ethanol-induced liver disease in mice. We show that precision targeting of the virulence factor KpsM is a promising approach to improve outcomes of patients with alcohol-associated hepatitis.},
}

Humans
Animals
*Virulence Factors/genetics/antagonists & inhibitors/metabolism
Mice
*Escherichia coli/genetics/pathogenicity/drug effects/metabolism
*Liver Diseases, Alcoholic/microbiology/drug therapy
Gastrointestinal Microbiome
Disease Models, Animal
Feces/microbiology
Kupffer Cells/metabolism/microbiology
*Escherichia coli Proteins/genetics/metabolism/antagonists & inhibitors
Male
Female
Liver/pathology/microbiology
Germ-Free Life
Ethanol
Mice, Inbred C57BL
Escherichia coli Infections/microbiology
Bacterial Capsules/metabolism
Hepatitis, Alcoholic/microbiology

@article {pmid40440092,
year = {2025},
author = {Lawniczak, MKN and Kocot, KM and Astrin, JJ and Blaxter, M and Sotero-Caio, CG and Barker, KB and Childers, AK and Coddington, J and Davis, P and Howe, K and Johnson, WE and McKenna, DD and Wideman, JG and Pettersson, OV and Ras, V and Santos, BF and , },
title = {Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40440092},
issn = {2047-217X},
support = {//Science for Life Laboratory/ ; //Swedish Research Council/ ; 1846174//National Science Foundation/ ; 2138994//National Science Foundation/ ; 2321308//National Science Foundation/ ; 2001303//National Science Foundation/ ; 2110053//National Science Foundation/ ; 1937815//National Science Foundation/ ; DBI-2119963//National Science Foundation/ ; U24HG006941/HG/NHGRI NIH HHS/United States ; /NH/NIH HHS/United States ; //Agricultural Research Service/ ; },
mesh = {*Genome ; *Genomics/standards/methods ; *Metagenomics/standards/methods ; Earth, Planet ; *Specimen Handling/standards/methods ; },
abstract = {The Earth BioGenome Project has the extremely ambitious goal of generating, at scale, high-quality reference genomes across the entire Tree of Life. Currently in its first phase, the project is targeting family-level representatives and is progressing rapidly. Here we outline recommended standards and considerations in sample acquisition and processing for those involved in biodiverse reference genome creation. These standards and recommendations will evolve with advances in related processes. Additionally, we discuss the challenges raised by the ambitions for later phases of the project, highlighting topics related to sample collection and processing that require further development.},
}

*Genome
*Genomics/standards/methods
*Metagenomics/standards/methods
Earth, Planet
*Specimen Handling/standards/methods

@article {pmid40439232,
year = {2025},
author = {McGivern, BB and Ellenbogen, JB and Hoyt, DW and Bouranis, JA and Stemple, BP and Daly, RA and Bosman, SH and Sullivan, MB and Hagerman, AE and Chanton, JP and Tfaily, MM and Wrighton, KC},
title = {Polyphenol rewiring of the microbiome reduces methane emissions.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf108},
pmid = {40439232},
issn = {1751-7370},
mesh = {*Methane/metabolism ; *Microbiota/drug effects ; *Catechin/metabolism ; *Polyphenols/metabolism ; Hydrogen/metabolism ; *Bacteria/metabolism/genetics/classification ; Greenhouse Gases/metabolism ; Soil Microbiology ; },
abstract = {Methane mitigation is regarded as a critical strategy to combat the scale of global warming. Currently, ~40% of methane emissions originate from microbial sources, which is causing strategies to suppress methanogens-either through direct toxic effects or by diverting their substrates and energy-to gain traction. Problematically, current microbial methane mitigation knowledge lacks detailed microbiome-centered insights, limiting translation across conditions and ecosystems. Here we utilize genome-resolved metatranscriptomes and metabolomes to assess the impact of a proposed methane inhibitor, catechin, on greenhouse gas emissions for high-methane-emitting peatlands. In microcosms, catechin drastically reduced methane emissions by 72%-84% compared to controls. Longitudinal sampling allowed for reconstruction of a catechin degradation pathway involving Actinomycetota and Clostridium, which break down catechin into smaller phenolic compounds within the first 21 days, followed by degradation of phenolic compounds by Pseudomonas_E from Days 21 to 35. These genomes co-expressed hydrogen-uptake genes, suggesting hydrogenases may act as a hydrogen sink during catechin degradation and consequently reduce hydrogen availability to methanogens. In support of this idea, there was decreased gene expression by hydrogenotrophic and hydrogen-dependent methylotrophic methanogens under catechin treatment. There was also reduced gene expression from genomes inferred to be functioning syntrophically with hydrogen-utilizing methanogens. We propose that catechin metabolic redirection effectively starves hydrogen-utilizing methanogens, offering a potent avenue for curbing methane emissions across diverse environments including ruminants, landfills, and constructed or managed wetlands.},
}

*Methane/metabolism
*Microbiota/drug effects
*Catechin/metabolism
*Polyphenols/metabolism
Hydrogen/metabolism
*Bacteria/metabolism/genetics/classification
Greenhouse Gases/metabolism
Soil Microbiology

@article {pmid40438118,
year = {2025},
author = {Diallo, D and Sun, S and Somboro, AM and Baya, B and Koné, A and Diarra, B and Nantoumé, M and Koloma, I and Diakite, M and Holl, J and Maiga, AI and Seydi, M and Theron, G and Hou, L and Fodor, A and Maiga, M},
title = {Metabolic and immune consequences of antibiotic related microbiome alterations during first-line tuberculosis treatment in Bamako, Mali.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1561459},
pmid = {40438118},
issn = {1664-3224},
support = {D43 CA260658/CA/NCI NIH HHS/United States ; D43 TW010543/TW/FIC NIH HHS/United States ; R21 AI148033/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; Male ; Female ; Adult ; Mali ; *Dysbiosis/chemically induced/immunology ; Middle Aged ; *Tuberculosis/drug therapy/microbiology/immunology/metabolism ; Cytokines/blood ; Longitudinal Studies ; *Antitubercular Agents/therapeutic use/adverse effects ; Young Adult ; Metabolomics ; },
abstract = {BACKGROUND: Individuals with a history of tuberculosis (TB) treatment are at a higher risk of experiencing a recurrent episode of the disease. Previous cross-sectional studies identified a connection between dysbiosis (alterations) in the gut microbiota composition and the administration of first-line TB antibiotics. However, these studies have not successfully elucidated this dysbiosis's resulting metabolic and immune consequences.

METHODS: In a longitudinal assessment, we studied the antituberculosis drug-related changes in the gut microbiota's composition and the resulting functional consequences. Sputum for TB culture, peripheral blood for metabolomics and cytokines analysis, and stool for shotgun metagenomics were collected from TB participants at Month-0, Month-2, Month-6 of treatment, and 9 Months after treatment (Month-15). Healthy controls were sampled at Month-0 and Month-6.

FINDINGS: We found notable differences in gut microbiota between individuals with TB and healthy controls. While gut microbiota tended to resemble healthy controls at the end of TB treatment, significant differences for many taxa persisted up to Month-15. Concurrently, disturbances in plasma metabolites, including tryptophan, tricarboxylic acids, and cytokine levels were observed. Certain fatty acids associated with inflammation pathways negatively correlated with the abundance of several taxa.

CONCLUSION: We observed alterations in the gut microbiota composition and function during treatment and at Month-15. Numerous changes in bacterial taxa abundances and inflammation-linked metabolites did not reverse at Month-15. This study suggests potential influences of anti-TB drugs and the gut microbiome on the disease outcome, response to treatment, and resistance to future TB infections.},
}

Humans
*Gastrointestinal Microbiome/drug effects/immunology
Male
Female
Adult
Mali
*Dysbiosis/chemically induced/immunology
Middle Aged
*Tuberculosis/drug therapy/microbiology/immunology/metabolism
Cytokines/blood
Longitudinal Studies
*Antitubercular Agents/therapeutic use/adverse effects
Young Adult
Metabolomics

@article {pmid40437611,
year = {2025},
author = {Zhang, P and Tuo, X and Jiang, J and Zhang, Y and Zhao, J and Deng, C and Zhao, G and Cheng, Y and Song, L and Yang, Y and Guo, R and Zhang, H and Zhao, H and Ma, S and Li, L and Shi, H},
title = {Characteristics of the gut virome in patients with premalignant colorectal adenoma.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {597},
pmid = {40437611},
issn = {1479-5876},
support = {No.S2024-JC-QN-1554//Natural Science Basic Research Program of Shaanxi Province/ ; },
mesh = {Humans ; *Virome ; *Colorectal Neoplasms/virology/microbiology ; *Adenoma/virology/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Precancerous Conditions/virology/microbiology ; Case-Control Studies ; Aged ; Reproducibility of Results ; },
abstract = {BACKGROUND: The multi-kingdom gut microbiota (e.g., bacteriome, mycobiome, and virome) characteristics of colorectal cancer have been extensively studied, yet there is still an insufficient description of the microbiota features in its early-stage, colorectal adenoma, particularly in the gut virome aspect.

METHODS: Based on the Metagenomic Gut Virus catalogue (MGV) containing 54,118 non-redundant gut viral genomes, this study characterized the virome composition and diversity using publicly available metagenomic sequencing data from 419 individuals with premalignant colorectal adenoma and 552 healthy controls. Furthermore, we identified and assessed the reliability and classification performance of adenoma-associated microbial signatures through comparative analysis and the random forest model.

RESULTS: Our results revealed a notable shift in the gut virome structure of patients compared to healthy controls, characterized by a significant increase in viral families such as Microviridae, Podoviridae_crAss-like, and Quimbyviridae. At the viral operational taxonomic unit (vOTU) level, we identified 479 vOTU signatures showing significant differences in relative abundances between patients and controls, including some patient-enriched vOTUs tending to infect Bacteroidaceae and Lachnospiraceae. Correlation network analysis revealed specific bacterial species correlated with adenoma-associated viruses, suggesting frequent interactions between them. Moreover, random forest models trained on gut viral and bacterial signatures demonstrated area under the curve (AUC) scores of 0.68, 0.82, and 0.76 for classifying healthy individuals versus patients with tubular adenomas, patients with sessile serrated adenomas, and patients with both conditions, respectively. In three independent validation cohorts, the classification performance achieved AUC scores ranging from 0.61 to 0.65.

CONCLUSIONS: Our study provides insights into the gut virome in premalignant colorectal adenoma, highlighting its potential role in disease development and diagnosis. Further investigations are warranted to elucidate the underlying mechanisms of gut virus-bacteria interactions and validate diagnostic models in larger populations.},
}

Humans
*Virome
*Colorectal Neoplasms/virology/microbiology
*Adenoma/virology/microbiology
*Gastrointestinal Microbiome
Male
Female
Middle Aged
*Precancerous Conditions/virology/microbiology
Case-Control Studies
Aged
Reproducibility of Results

@article {pmid40436871,
year = {2025},
author = {Zeng, L and Yu, B and Zeng, P and Duoji, Z and Zuo, H and Lian, J and Yang, T and Dai, Y and Feng, Y and Yu, P and Yang, J and Yang, S and Dou, Q},
title = {Mediation effect and metabolic pathways of gut microbiota in the associations between lifestyles and dyslipidemia.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {90},
pmid = {40436871},
issn = {2055-5008},
support = {723B2017//National Natural Science Foundation of China/ ; XZ202201ZD0001G//Science and Technology Major Project of Tibetan Autonomous Region of China/ ; XZ202303ZY0007G//Science and Technology Plan Projects of Tibet Autonomous Region/ ; CQFYJB01005//Chongqing Maternal and Child Health Hospital/ ; 2023YFC3604702//National Key Research and Development Program of China/ ; 2023YFC3604701; 2020YFC2008005; 2018YFC2002405//National Key Research and Development Program of China/ ; 2023YFS0251//Key R&D Project of Sichuan Province/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dyslipidemias/microbiology/epidemiology ; Male ; Cross-Sectional Studies ; Female ; *Life Style ; Middle Aged ; Adult ; *Metabolic Networks and Pathways ; Feces/microbiology/chemistry ; China ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenome ; Metabolomics ; Triglycerides/blood ; Aged ; },
abstract = {Whether the role of gut microbial features lies in the pathways from lifestyles to dyslipidemia remains unclear. In this cross-sectional study, we conducted a metagenome-wide association analysis and fecal metabolomic profiling in 994 adults from the China Multi-Ethnic cohort. A total of 26 microbial species were identified as mediators between lifestyle factors and risk for dyslipidemia. Specifically, the abundance of [Ruminococcus] gnavus mediated the associations between lifestyles and risks for dyslipidemia, elevated low-density lipoprotein cholesterol, elevated total cholesterol, and elevated triglycerides. [Ruminococcus] gnavus, Alistipes shahii, and Lachnospira eligens were replicated to be associated with dyslipidemia in an external validation cohort. The potential metabolic pathways included arachidonic acid, bile acid, and aromatic amino-acid metabolism.},
}

Humans
*Gastrointestinal Microbiome
*Dyslipidemias/microbiology/epidemiology
Male
Cross-Sectional Studies
Female
*Life Style
Middle Aged
Adult
*Metabolic Networks and Pathways
Feces/microbiology/chemistry
China
*Bacteria/classification/genetics/metabolism/isolation & purification
Metagenome
Metabolomics
Triglycerides/blood
Aged

@article {pmid40436643,
year = {2025},
author = {Li, J and Wu, Y and Yang, Y and Chen, L and He, C and Zhou, S and Huang, S and Zhang, X and Wang, Y and Gui, Q and Lu, H and Zhang, Q and Yang, Y},
title = {Metagenomics reveals an increased proportion of an Escherichia coli-dominated enterotype in elderly Chinese people.},
journal = {Journal of Zhejiang University. Science. B},
volume = {26},
number = {5},
pages = {477-492},
pmid = {40436643},
issn = {1862-1783},
support = {82101665, 82271588, 82200665 and 82100795//the National Natural Science Foundation of China/ ; LY22H030009//the Zhejiang Provincial Natural Science Foundation of China/ ; 2023ZL480//the Zhejiang Provincial Science and Technology Program of Traditional Chinese Medicine/ ; 2023RC153//the Medical and Health Research Project of Zhejiang Province/ ; },
mesh = {Aged ; Aged, 80 and over ; Female ; Humans ; Male ; Middle Aged ; Bacteroides ; China ; Diabetes Mellitus, Type 2/microbiology ; *Escherichia coli/genetics/isolation & purification/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; East Asian People ; },
abstract = {Gut microbial communities are likely remodeled in tandem with accumulated physiological decline during aging, yet there is limited understanding of gut microbiome variation in advanced age. Here, we performed a metagenomics-based enterotype analysis in a geographically homogeneous cohort of 367 enrolled Chinese individuals between the ages of 60 and 94 years, with the goal of characterizing the gut microbiome of elderly individuals and identifying factors linked to enterotype variations. In addition to two adult-like enterotypes dominated by Bacteroides (ET-Bacteroides) and Prevotella (ET-Prevotella), we identified a novel enterotype dominated by Escherichia (ET-Escherichia), whose prevalence increased in advanced age. Our data demonstrated that age explained more of the variance in the gut microbiome than previously identified factors such as type 2 diabetes mellitus (T2DM) or diet. We characterized the distinct taxonomic and functional profiles of ET-Escherichia, and found the strongest cohesion and highest robustness of the microbial co-occurrence network in this enterotype, as well as the lowest species diversity. In addition, we carried out a series of correlation analyses and co-abundance network analyses, which showed that several factors were likely linked to the overabundance of Escherichia members, including advanced age, vegetable intake, and fruit intake. Overall, our data revealed an enterotype variation characterized by Escherichia enrichment in the elderly population. Considering the different age distribution of each enterotype, these findings provide new insights into the changes that occur in the gut microbiome with age and highlight the importance of microbiome-based stratification of elderly individuals.},
}

Aged
Aged, 80 and over
Female
Humans
Male
Middle Aged
Bacteroides
China
Diabetes Mellitus, Type 2/microbiology
*Escherichia coli/genetics/isolation & purification/classification
*Gastrointestinal Microbiome/genetics
*Metagenomics
East Asian People

@article {pmid40436373,
year = {2025},
author = {Vosough, M and Drees, F and Sieber, G and Stach, TL and Beisser, D and Probst, AJ and Boenigk, J and Schmidt, TC},
title = {Integrative Analysis of Nontargeted LC-HRMS and High-Throughput Metabarcoding Data for Aquatic Environmental Studies Using Combined Multivariate Statistical Approaches.},
journal = {Analytical chemistry},
volume = {97},
number = {22},
pages = {11563-11571},
pmid = {40436373},
issn = {1520-6882},
mesh = {Chromatography, Liquid ; Mass Spectrometry ; Multivariate Analysis ; Wastewater/chemistry/analysis ; RNA, Ribosomal, 16S/genetics ; *Water Pollutants, Chemical/analysis ; *High-Throughput Screening Assays ; *DNA Barcoding, Taxonomic ; },
abstract = {Significant progress in high-throughput analytical techniques has paved the way for novel approaches to integrating data sets from different compartments. This study leverages nontarget screening (NTS) via liquid chromatography-high-resolution mass spectrometry (LC-HRMS), a crucial technique for analyzing organic micropollutants and their transformation products, in combination with biological indicators. We propose a combined multivariate data processing framework that integrates LC-HRMS-based NTS data with other high-throughput data sets, exemplified here by 18S V9 rRNA and full-length 16S rRNA gene metabarcoding data sets. The power of data fusion is demonstrated by systematically evaluating the impact of treated wastewater (TWW) over time on an aquatic ecosystem through a controlled mesocosm experiment. Highly compressed NTS data were compiled through the implementation of the region of interest-multivariate curve resolution-alternating least-squares (MCR-ALS) method, known as ROIMCR. By integrating ANOVA-simultaneous component analysis with structural learning and integrative decomposition (SLIDE), the innovative SLIDE-ASCA approach enables the decomposition of global and partial common, as well as distinct variation sources arising from experimental factors and their possible interactions. SLIDE-ASCA results indicate that temporal variability explains a much larger portion of the variance (74.6%) than the treatment effect, with both contributing to global shared space variation (41%). Design structure benefits include enhanced interpretability, improved detection of key features, and a more accurate representation of complex interactions between chemical and biological data. This approach offers a greater understanding of the natural and wastewater-influenced temporal patterns for each data source, as well as reveals associations between chemical and biological markers in an exemplified perturbed aquatic ecosystem.},
}

Chromatography, Liquid
Mass Spectrometry
Multivariate Analysis
Wastewater/chemistry/analysis
RNA, Ribosomal, 16S/genetics
*Water Pollutants, Chemical/analysis
*High-Throughput Screening Assays
*DNA Barcoding, Taxonomic

@article {pmid40435563,
year = {2025},
author = {García-Pérez, P and Tomas, M and Giuberti, G and Capanoglu, E and Callegari, ML and Lucini, L and Patrone, V},
title = {Brassica microgreens shape gut microbiota and functional metabolite profiles in a species-related manner: A multi-omics approach following in vitro gastrointestinal digestion and large intestine fermentation.},
journal = {Microbiological research},
volume = {298},
number = {},
pages = {128226},
doi = {10.1016/j.micres.2025.128226},
pmid = {40435563},
issn = {1618-0623},
mesh = {*Gastrointestinal Microbiome/physiology ; *Brassica/metabolism/chemistry ; Fermentation ; Humans ; *Digestion ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Intestine, Large/microbiology/metabolism ; Metabolomics ; Metagenomics ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Polyphenols/metabolism ; Metabolome ; Isothiocyanates/metabolism ; Multiomics ; },
abstract = {Brassicaceae microgreens constitute a novel and promising source of bioactive compounds, such as polyphenols and glucosinolates. In this work, an integrative computational approach was performed to decipher the interaction between bioaccessible microgreen metabolites and human gut bacteria. To this end, in vitro gastrointestinal digestion and large intestine fermentation were performed on eight different microgreens, which were further subjected to a dual high-throughput approach that combined fecal metagenomics and untargeted metabolomics. Data reveal a significant correlation between Parabacteroides merdae and two isothiocyanates in arugula fermentates, suggesting a high bioaccessibility of these bioactive compounds. Meanwhile, two species of Roseburia were correlated with pseudooxynicotine, an anti-inflammatory catabolite of nicotine in Brassica oleracea fermentates (such as broccoli, Brussels sprouts, and red cabbage), coupled with an increase in short-chain fatty acid production. These findings confer evidence on the nutritional impact of microgreens consumption, revealing the most bioaccessible metabolites with associated health-promoting properties together with their participation in the shaping of gut microbial populations, possibly leading to prebiotic effects.},
}

*Gastrointestinal Microbiome/physiology
*Brassica/metabolism/chemistry
Fermentation
Humans
*Digestion
*Bacteria/classification/metabolism/genetics/isolation & purification
*Intestine, Large/microbiology/metabolism
Metabolomics
Metagenomics
Feces/microbiology
Fatty Acids, Volatile/metabolism
Polyphenols/metabolism
Metabolome
Isothiocyanates/metabolism
Multiomics

@article {pmid40434822,
year = {2025},
author = {Berelson, MFG and Heavens, D and Nicholson, P and Clark, MD and Leggett, RM},
title = {From air to insight: the evolution of airborne DNA sequencing technologies.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {5},
pages = {},
pmid = {40434822},
issn = {1465-2080},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Air Microbiology ; *Sequence Analysis, DNA/methods ; *DNA, Environmental/genetics/analysis/isolation & purification ; Humans ; Environmental Monitoring/methods ; Computational Biology/methods ; Biodiversity ; },
abstract = {Historically, the analysis of airborne biological organisms relied on microscopy and culture-based techniques. However, technological advances such as PCR and next-generation sequencing now provide researchers with the ability to gather vast amounts of data on airborne environmental DNA (eDNA). Studies typically involve capturing airborne biological material, followed by nucleic acid extraction, library preparation, sequencing and taxonomic identification to characterize the eDNA at a given location. These methods have diverse applications, including pathogen detection in agriculture and human health, air quality monitoring, bioterrorism detection and biodiversity monitoring. A variety of methods are used for airborne eDNA analysis, as no single pipeline meets all needs. This review outlines current methods for sampling, extraction, sequencing and bioinformatic analysis, highlighting how different approaches can influence the resulting data and their suitability for specific use cases. It also explores current applications of airborne eDNA sampling and identifies research gaps in the field.},
}

*High-Throughput Nucleotide Sequencing/methods
*Air Microbiology
*Sequence Analysis, DNA/methods
*DNA, Environmental/genetics/analysis/isolation & purification
Humans
Environmental Monitoring/methods
Computational Biology/methods
Biodiversity

@article {pmid40434093,
year = {2025},
author = {Koldaş, SS and Sezerman, OU and Timuçin, E},
title = {Exploring the role of microbiome in cystic fibrosis clinical outcomes through a mediation analysis.},
journal = {mSystems},
volume = {10},
number = {6},
pages = {e0019625},
pmid = {40434093},
issn = {2379-5077},
mesh = {*Cystic Fibrosis/microbiology/physiopathology ; Humans ; *Microbiota/genetics ; Sputum/microbiology ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Adult ; Lung/physiopathology/microbiology ; },
abstract = {UNLABELLED: Human microbiome plays a crucial role in host health and disease by mediating the impact of environmental factors on clinical outcomes. Mediation analysis is a valuable tool for dissecting these complex relationships. However, existing approaches are primarily designed for cross-sectional studies. Modern clinical research increasingly utilizes long follow-up periods, leading to complex data structures, particularly in metagenomic studies. To address this limitation, we introduce a novel mediation framework based on structural equation modeling that leverages linear mixed-effects models using penalized quasi-likelihood estimation with a debiased lasso. We applied this framework to a 16S rRNA sputum microbiome data set collected from patients with cystic fibrosis over 10 years to investigate the mediating role of the microbiome in the relationship between clinical states, disease aggressiveness phenotypes, and lung function. We identified richness as a key mediator of lung function. Specifically, Streptococcus was found to be significantly associated with mediating the decline in lung function on treatment compared to exacerbation, while Gemella was associated with the decline in lung function on recovery. This approach offers a powerful new tool for understanding the complex interplay between microbiome and clinical outcomes in longitudinal studies, facilitating targeted microbiome-based interventions.

IMPORTANCE: Understanding the mechanisms by which the microbiome influences clinical outcomes is paramount for realizing the full potential of microbiome-based medicine, including diagnostics and therapeutics. Identifying specific microbial mediators not only reveals potential targets for novel therapies and drug repurposing but also offers a more precise approach to patient stratification and personalized interventions. While traditional mediation analyses are ill-equipped to address the complexities of longitudinal metagenomic data, our framework directly addresses this gap, enabling robust investigation of these increasingly common study designs. By applying this framework to a decade-long cystic fibrosis study, we have begun to unravel the intricate relationships between the sputum microbiome and lung function decline across different clinical states, yielding insights that were previously unknown.},
}

*Cystic Fibrosis/microbiology/physiopathology
Humans
*Microbiota/genetics
Sputum/microbiology
Female
Male
RNA, Ribosomal, 16S/genetics
Adult
Lung/physiopathology/microbiology

@article {pmid40434078,
year = {2025},
author = {Weisse, L and Martin, L and Moumen, B and Héchard, Y and Delafont, V},
title = {Environmental diversity of Candidatus Babelota and their relationships with protists.},
journal = {mSystems},
volume = {10},
number = {6},
pages = {e0026125},
pmid = {40434078},
issn = {2379-5077},
support = {ANR-21-CE02-0001//Agence Nationale de la Recherche/ ; },
mesh = {*Bacteria/genetics/classification/isolation & purification ; Biodiversity ; Phylogeny ; *Eukaryota/genetics/classification ; High-Throughput Nucleotide Sequencing ; Metagenomics ; },
abstract = {Ca. Babelota is a phylum of strictly intracellular bacteria whose representatives are commonly detected in various environments through metagenomics, though their presence, ecology, and biology have never been addressed so far. As a group of strict intracellular, we hypothesize that their presence, occurrence, and abundance heavily depend on their hosts, which are known as heterotrophic protists, based on few described isolates. Here, we conducted a sampling campaign allowing to characterize protists and associated bacterial communities, using high-throughput sequencing. In parallel, a systematic enrichment of protists from samples was performed to attempt characterization and isolation of new Ca. Babelota within native hosts. We found that Ca. Babelota are among the most widespread phylum among the rare ones. Protist enrichments are allowed in certain cases to enrich as well for Ca. Babelota, which could be visualized in vivo infecting protist cells. Though cosmopolitan, Ca. Babelota diversity was highly site-specific. Cooccurrence analyses allowed to retrieve well-known as well as new putative associations involving numerous protists of various trophic regimes. The combination of approaches developed in this study enhances our understanding of Ca. Babelota ecology and biology, while paving the way for future isolation of new members of this elusive phylum, which could have huge impact on protists-and ecosystems-functioning.IMPORTANCEOur understanding of microbial diversity surrounding us and colonizing the environment has been dramatically impacted by the advent of DNA-based analyses. Such progress helped shine a new light on numerous lineages of yet-to-be-characterized microbes, whose ecology and biology are basically unknown. Among those uncharacterized clades is the Candidatus Babelota, a bacterial phylum for which parasitism seems to be an ancestral trait. All known Ca. Babelota thrive by infecting phagotrophic protist hosts, thereby impacting this basal link of the trophic chain. The Ca. Babelota constitutes a model that stands out, as phylum-wide conserved parasitism has only been described in one previous occurrence for Bacteria, with the Chlamydiota. Thus, exploring the intricate interplay between Ca. Babelota and their protist hosts will advance our knowledge of bacterial diversity, their ecology, and global impact on ecosystem functioning.},
}

*Bacteria/genetics/classification/isolation & purification
Biodiversity
Phylogeny
*Eukaryota/genetics/classification
High-Throughput Nucleotide Sequencing
Metagenomics

@article {pmid40433668,
year = {2025},
author = {von Ameln Lovison, O and Zempulski Volpato, FC and Weber, LG and Barth, AL and Simon Coitinho, A and Martins, AF},
title = {Unveiling the role of the upper respiratory tract microbiome in susceptibility and severity to COVID-19.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1531084},
pmid = {40433668},
issn = {2235-2988},
mesh = {Humans ; *COVID-19/microbiology/pathology/virology ; Cross-Sectional Studies ; Disease Susceptibility ; *Microbiota ; SARS-CoV-2 ; Female ; Male ; Severity of Illness Index ; Middle Aged ; *Respiratory System/microbiology ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Adult ; Biomarkers ; Aged ; },
abstract = {It is argued that commensal bacteria in the upper respiratory tract (URT) protect against pathogen colonization and infection, including respiratory viruses. Given that the microbiome can mediate immune modulation, a link between the URT microbiome (URTM) and COVID-19 susceptibility and severity is expected. This 16S metagenomics cross-sectional study assessed URTM composition, metabolic prediction, and association with laboratory biomarkers in non-COVID-19 pneumonia (NO-CoV), moderate (M-CoV), severe (S-CoV) COVID-19 patients, as well as COVID-19-negative, asymptomatic (NC) patients. The S-CoV group exhibited reduced URTM diversity, primarily due to a decreased abundance of eubiotic taxa. Some of these taxa (e.g., Haemophilus sp., Neisseria sp.) were also associated with inflammatory biomarkers. Multiple metabolic pathways (e.g., short-chain fatty acids, vitamin B12) linked to immune response, antiviral activity, and host susceptibility showed decreased abundance in S-CoV. These pathways could suggest potential alternatives for the therapeutic arsenal against COVID-19, providing reassurance about the progress in understanding and treating this disease.},
}

Humans
*COVID-19/microbiology/pathology/virology
Cross-Sectional Studies
Disease Susceptibility
*Microbiota
SARS-CoV-2
Female
Male
Severity of Illness Index
Middle Aged
*Respiratory System/microbiology
Metagenomics
Bacteria/classification/genetics/isolation & purification
Adult
Biomarkers
Aged

@article {pmid40431358,
year = {2025},
author = {Yue, Y and Yang, HJ and Li, C and Ryu, MS and Seo, JW and Jeong, DY and Park, S},
title = {Beneficial Effects of Traditional Fermented Soybean Sauce (Kanjang) on Memory Function, Body Water, and Glucose Metabolism: Roles of Gut Microbiota and Neuroinflammation.},
journal = {Nutrients},
volume = {17},
number = {10},
pages = {},
pmid = {40431358},
issn = {2072-6643},
support = {2023-3//functional research of fermented soybean food (safety monitoring)" under the Ministry of Agriculture, Food and Rural Affairs/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; Male ; Rats, Sprague-Dawley ; *Soy Foods/microbiology ; Rats ; *Memory/drug effects ; *Neuroinflammatory Diseases ; *Glucose/metabolism ; Scopolamine ; *Fermented Foods ; Water/metabolism ; Neuroprotective Agents/pharmacology ; *Glycine max ; Fermentation ; },
abstract = {Background: Traditional fermented soybean foods, acting as potential synbiotics, may help mitigate cognitive impairment associated with amnesia. This study investigated the neuroprotective effects of four kanjang (Korean fermented soy sauce) varieties and their underlying mechanisms. Methods: Male Sprague Dawley rats (n = 70) were divided into seven groups: normal control, scopolamine control, positive control (1 mg/kg bw/day of donepezil), and four scopolamine-treated groups receiving different kanjang varieties (0.5% in high-fat diet). Based on their Bacillus content, the kanjang samples were categorized as traditionally made kanjang (TMK) with high Bacillus (SS-HB), TMK with medium Bacillus (SS-MB), TMK with low Bacillus (SS-LB), and factory-made kanjang (SS-FM). Results: Scopolamine administration disrupted energy, glucose, and water metabolism and impaired memory function (p < 0.05). All kanjang treatments improved insulin sensitivity, reduced inflammation, enhanced glucose tolerance, and decreased visceral fat. SS-MB, SS-HB, and SS-FM increased skeletal muscle mass. They maintained body water homeostasis by suppressing the renin-angiotensin-aldosterone system. Kanjang treatments improved memory function, with SS-FM showing the least significant effects. The treatments reduced neuronal cell death in the hippocampal CA1 region, decreased acetylcholinesterase activity, and increased brain-derived neurotrophic factor mRNA expression. Gut microbiota analysis revealed that kanjang treatments increased Lactobacillaceae and decreased Lachnospiraceae, with SS-HB and SS-LB specifically elevating Ligilactobacillus. Metagenomic analysis demonstrated enhanced glycolysis/gluconeogenesis pathways and enhanced butanoate metabolism while reducing lipopolysaccharide biosynthesis and pro-inflammatory signaling. SS-MB and SS-LB increased intestinal goblet cell counts and the serum butyrate concentration. Conclusions: These findings suggest that kanjang consumption, particularly SS-HB and SS-LB varieties, can ameliorate memory impairment in this murine model through multiple mechanisms: metabolic improvements, enhanced neurotrophic signaling, gut microbiota modulation, and reduced neuroinflammation via gut-brain axis activation. Human clinical trials are warranted to determine if these promising neuroprotective effects translate to clinical applications.},
}

Animals
*Gastrointestinal Microbiome/drug effects/physiology
Male
Rats, Sprague-Dawley
*Soy Foods/microbiology
Rats
*Memory/drug effects
*Neuroinflammatory Diseases
*Glucose/metabolism
Scopolamine
*Fermented Foods
Water/metabolism
Neuroprotective Agents/pharmacology
*Glycine max
Fermentation

@article {pmid40431158,
year = {2025},
author = {Mirete, S and Sánchez-Costa, M and Díaz-Rullo, J and González de Figueras, C and Martínez-Rodríguez, P and González-Pastor, JE},
title = {Metagenome-Assembled Genomes (MAGs): Advances, Challenges, and Ecological Insights.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
pmid = {40431158},
issn = {2076-2607},
support = {PID2021-126114NB-C43//Spanish Ministry of Science and Innovation which also included European Regional Development Fund (FEDER)/ ; },
abstract = {Metagenome-assembled genomes (MAGs) have revolutionized microbial ecology by enabling the genome-resolved study of uncultured microorganisms directly from environmental samples. By leveraging high-throughput sequencing, advanced assembly algorithms, and genome binning techniques, researchers can reconstruct microbial genomes without the need for cultivation. These methodological advances have expanded the known microbial diversity, revealing novel taxa and metabolic pathways involved in key biogeochemical cycles, including carbon, nitrogen, and sulfur transformations. MAG-based studies have identified microbial lineages form Archaea and Bacteria responsible for methane oxidation, carbon sequestration in marine sediments, ammonia oxidation, and sulfur metabolism, highlighting their critical roles in ecosystem stability. From a sustainability perspective, MAGs provide essential insights for climate change mitigation, sustainable agriculture, and bioremediation. The ability to characterize microbial communities in diverse environments, including soil, aquatic ecosystems, and extreme habitats, enhances biodiversity conservation and supports the development of microbial-based environmental management strategies. Despite these advancements, challenges such as assembly biases, incomplete metabolic reconstructions, and taxonomic uncertainties persist. Continued improvements in sequencing technologies, hybrid assembly approaches, and multi-omics integration will further refine MAG-based analyses. As methodologies advance, MAGs will remain a cornerstone for understanding microbial contributions to global biogeochemical processes and developing sustainable interventions for environmental resilience.},
}

@article {pmid40431145,
year = {2025},
author = {Jiang, K and Ye, L and Cao, C and Che, G and Wang, Y and Hong, Y},
title = {Multi-Metagenome Analysis Unravels Community Collapse After Sampling and Hints the Cultivation Strategy of CPR Bacteria in Groundwater.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
pmid = {40431145},
issn = {2076-2607},
support = {32360005//National Natural Science Foundation of China/ ; 2022JBQN091//Fundamental Research Funds for the Inner Mongolia Normal University/ ; 2022JBTD010//Fundamental Research Funds for the Inner Mongolia Normal University/ ; },
abstract = {Groundwater harbors phylogenetically diverse Candidate Phyla Radiation (CPR) bacteria, representing an ideal ecosystem for studying this microbial dark matter. However, no CPR strains have been successfully isolated from groundwater, severely limiting further research. This study employed a multi-metagenome approach, integrating time-resolved sampling, antibiotic/nutrient interventions, and microbial correlation networks to unravel CPR ecological roles in groundwater and provide insights into their subsequent cultivation. Through 36 metagenomes from a groundwater system containing at least 68 CPR phyla, we revealed the time-sensitive collapse of CPR communities: total abundance plummeted from 7.9% to 0.15% within 48 h post-sampling, driven by competition with rapidly dividing non-CPR bacteria, such as members of Pseudomonadota. Ampicillin (100 mg/L) stabilized CPR communities by suppressing competitors, whereas low-nutrient conditions paradoxically reversed this effect. Long-term enrichment (14 months) recovered 63 CPR phyla (0.35% abundance), revealing their survival resilience despite nutrient deprivation. Correlation networks prioritized Actinomyces, a novel Acidimicrobiaceae genus, Aestuariivirga, Baekduia and Caedimonadaceae as potential CPR partners, providing actionable targets for co-culture trials. Here, we propose actionable recommendations spanning groundwater sampling, activation status, identification of CPR symbiotic partners, and optimization of culture conditions, which bypass traditional blind cultivation and are critical for future efforts to cultivate CPR bacterial strains from groundwater. Cultivating CPR bacteria will contribute to clarifying their diversity, ecological roles, evolutionary mechanisms, metabolic pathways, and genetic potential.},
}

@article {pmid40431076,
year = {2025},
author = {Mendybayeva, A and Makhambetov, A and Yanin, K and Taskuzhina, A and Khusnitdinova, M and Gritsenko, D},
title = {Metagenomic Analysis of Wild Apple (Malus sieversii) Trees from Natural Habitats of Kazakhstan.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
pmid = {40431076},
issn = {2223-7747},
support = {BR21882269//The Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Kazakhstan's rich biodiversity includes diverse apple populations, notably the wild apple tree (Malus sieversii) prized for traits like disease resistance and adaptability, potentially aiding breeding programs. Analyzing their microbiomes offers insights into bacterial diversity and how it influences apple tree development, making it a reliable method for understanding ecological interactions. In this research, 334 apple tree samples were collected from different mountain ranges in southeastern Kazakhstan. An analysis using nanopore-based 16S rRNA sequencing showed a distinct similarity in the microbiome compositions of samples from the Zhongar and Ile Alatau mountain ranges, with a predominance of Pseudomonadaceae, Enterobacteriaceae, and Microbacteriaceae. In contrast, samples from Ketmen ridge showed a higher prevalence of Enterobacteriaceae. Alongside the less represented Pseudomonadaceae family, in the Ketmen ridge region, bacteria of the Xanthomonadaceae, Alcaligenaceae, and Brucellaceae families were also present. Across all regions, beneficial plant-associated bacteria were identified, such as Pseudomonas veronii, Stenotrophomonas geniculata, and Kocuria rhizophila, potentially enhancing plant resilience. However, opportunistic phytopathogens were also detected, including Pseudomonas viridiflava and Serratia marcescens, particularly in the Ile Alatau region. These findings highlight the complex microbial interactions in M. sieversii, thus offering key insights into host-microbe relationships that can inform apple breeding and ecological preservation efforts.},
}

@article {pmid40429958,
year = {2025},
author = {San-Martin, MI and Chamizo-Ampudia, A and Sanchiz, Á and Ferrero, MÁ and Martínez-Blanco, H and Rodríguez-Aparicio, LB and Navasa, N},
title = {Microbiome Markers in Gastrointestinal Disorders: Inflammatory Bowel Disease, Colorectal Cancer, and Celiac Disease.},
journal = {International journal of molecular sciences},
volume = {26},
number = {10},
pages = {},
pmid = {40429958},
issn = {1422-0067},
mesh = {Humans ; *Celiac Disease/microbiology/metabolism ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Gastrointestinal Microbiome ; Biomarkers/metabolism ; *Colorectal Neoplasms/microbiology/metabolism ; Animals ; Metagenomics/methods ; },
abstract = {Intestinal microbiota and the host's immune system form a symbiotic alliance that sustains normal development and function in the human gut. Changes such as dietary habits among societies in developed countries have led to the development of unbalanced microbial populations in the gut, likely contributing to the dramatic increase in inflammatory diseases in the last few decades. Recent advances in DNA sequencing technologies have tremendously helped to characterize the microbiome associated with disease, both in identifying global alterations and discovering specific biomarkers that potentially contribute to disease pathogenesis, as evidenced by animal studies. Beyond bacterial alterations, non-bacterial components such as fungi, viruses, and microbial metabolites have been implicated in these diseases, influencing immune responses and gut homeostasis. Multi-omics approaches integrating metagenomics, metabolomics, and transcriptomics offer a more comprehensive understanding of the microbiome's role in disease pathogenesis, paving the way for innovative diagnostic and therapeutic strategies. Unraveling the metagenomic profiles associated with disease may facilitate earlier diagnosis and intervention, as well as the development of more personalized and effective therapeutic strategies. This review synthesizes recent and relevant microbiome research studies aimed at characterizing the microbial signatures associated with inflammatory bowel disease, colorectal cancer, and celiac disease.},
}

Humans
*Celiac Disease/microbiology/metabolism
*Inflammatory Bowel Diseases/microbiology/metabolism
*Gastrointestinal Microbiome
Biomarkers/metabolism
*Colorectal Neoplasms/microbiology/metabolism
Animals
Metagenomics/methods

@article {pmid40428846,
year = {2025},
author = {Torraco, A and Di Nicolantonio, S and Cardisciani, M and Ortu, E and Pietropaoli, D and Altamura, S and Del Pinto, R},
title = {Meta-Analysis of 16S rRNA Sequencing Reveals Altered Fecal but Not Vaginal Microbial Composition and Function in Women with Endometriosis.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {5},
pages = {},
pmid = {40428846},
issn = {1648-9144},
support = {SRA-882725/CCF/CCF/United States ; },
mesh = {Humans ; Female ; *Endometriosis/microbiology/physiopathology ; *Feces/microbiology ; *Vagina/microbiology ; *RNA, Ribosomal, 16S/analysis/genetics ; Dysbiosis/microbiology ; Adult ; Gastrointestinal Microbiome ; Metagenomics/methods ; },
abstract = {Background and Objectives: Dysbiosis of the oral-gut axis is related to several extraintestinal inflammatory diseases, including endometriosis. This study aims to assess the microbial landscape and pathogenic potential of distinct biological niches during endometriosis. Materials and Methods: A microbiome meta-analysis was conducted on 182 metagenomic sequences (79 of fecal and 103 of vaginal origin) from women with and without endometriosis. Fecal and vaginal microbial diversity, differential abundance, and functional analysis based on disease status were assessed. Random forest, gradient boosting, and generalized linear modeling were used to predict endometriosis based on differentially enriched bacteria. Results: Only intestinal microbes displayed distinctive taxonomic and functional characteristics in women with endometriosis compared to control women. Taxonomic differences were quantified using the microbial endometriosis index (MEI), which effectively distinguished between individuals with and without the disease. The observed functional enrichment pointed to proinflammatory pathways previously related to endometriosis development. Conclusions: Dysbiosis in the oral-gut microbial community appears to play a prevalent role in endometriosis. Our findings pave the ground for future studies exploring the potential mechanistic involvement of the oral-gut axis in disease pathogenesis.},
}

Humans
Female
*Endometriosis/microbiology/physiopathology
*Feces/microbiology
*Vagina/microbiology
*RNA, Ribosomal, 16S/analysis/genetics
Dysbiosis/microbiology
Adult
Gastrointestinal Microbiome
Metagenomics/methods

@article {pmid40428372,
year = {2025},
author = {Dimitrova, L and Ilieva, Y and Gouliamova, D and Kussovski, V and Hubenov, V and Georgiev, Y and Bratanova, T and Kaleva, M and Zaharieva, MM and Najdenski, H},
title = {Isolation, Enrichment and Analysis of Aerobic, Anaerobic, Pathogen-Free and Non-Resistant Cellulose-Degrading Microbial Populations from Methanogenic Bioreactor.},
journal = {Genes},
volume = {16},
number = {5},
pages = {},
pmid = {40428372},
issn = {2073-4425},
support = {КP-06-N71/8 from 08.12.2023//National Fund for Scientific Research, Republic of Bulgaria/ ; },
mesh = {*Cellulose/metabolism ; *Bioreactors/microbiology ; Anaerobiosis ; *Microbial Consortia/genetics ; Biodegradation, Environmental ; Bacteria/genetics/isolation & purification/metabolism ; Aerobiosis ; *Bacteria, Anaerobic/genetics/isolation & purification/metabolism ; Methane/metabolism ; Biofuels ; },
abstract = {Background: Nowadays, the microbial degradation of cellulose represents a new perspective for reducing cellulose waste from industry and households and at the same time obtaining energy sources. Methods: We isolated and enriched two aerobic (at 37 °C and 50 °C) and one anaerobic microbial consortium from an anaerobic bioreactor for biogas production by continuous subculturing on peptone cellulose solution (PCS) medium supplemented with 0.3% treated or untreated Whatman filter paper under static conditions. Samples were taken every 7 days until day 21 to determine the percentage of cellulose biodegradation. We determined the antimicrobial resistance of aerobic and anaerobic consortia and some single colonies by disc diffusion method, against 42 clinically applied antibiotics. PCR analyses were performed to search for the presence of eight genes for cellulolytic activity and nine genes for antibiotic resistance. By metagenomics analysis, the bacterial and fungal genus distributions in the studied populations were determined. Results: Aerobes cultured at 50 °C degraded cellulose to the greatest extent (47%), followed by anaerobes (24-38%) and aerobes (8%) cultured at 37 °C. The bacterial sequence analysis showed that the dominant phyla are Bacillota and Bacteroidetes and genera-Paraclostridium, Defluvitalea, Anaerobacillus, Acetivibrio, Lysinibacillus, Paenibacillus, Romboutsia, Terrisporobacter, Clostridium, Sporanaerobacter, Lentimicrobium, etc. in a different ratio depending on the cultivation conditions and the stage of the process. Some of these representatives are cellulolytic and hemicellulolytic microorganisms. We performed lyophilization and proved that it is suitable for long-term storage of the most active consortium, which degrades even after the 10th re-inoculation for a period of one year. We proved the presence of ssrA, ssrA BS and blaTEM genes. Conclusions: Our findings demonstrated the potential utility of the microbial consortium of anaerobes in the degradation of waste lignocellulose biomass.},
}

*Cellulose/metabolism
*Bioreactors/microbiology
Anaerobiosis
*Microbial Consortia/genetics
Biodegradation, Environmental
Bacteria/genetics/isolation & purification/metabolism
Aerobiosis
*Bacteria, Anaerobic/genetics/isolation & purification/metabolism
Methane/metabolism
Biofuels

@article {pmid40428326,
year = {2025},
author = {Sun, YF and Han, ZX and Yao, XK and Meng, J and Ren, WL and Wang, CK and Yuan, XX and Zeng, YQ and Wang, YF and Sun, ZW and Wang, JW},
title = {Effects of Different Stages of Training on the Intestinal Microbes of Yili Horses Analyzed Using Metagenomics.},
journal = {Genes},
volume = {16},
number = {5},
pages = {},
pmid = {40428326},
issn = {2073-4425},
mesh = {Animals ; Horses/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Feces/microbiology ; *Physical Conditioning, Animal ; *Bacteria/genetics/classification/isolation & purification ; },
abstract = {Objectives: The aim of this study was to investigate the effects of different stages of training on the intestinal microbial abundance of Yili horses. Methods: Ten Yili horses, all aged 2 years old and weighing 305 ± 20 kg, were selected and divided into a training group and an untrained group. The training group performed riding training 6 days a week, and the untrained group moved freely in the activity circle every day. Fecal samples were collected on days 30 and 60, and the intestinal microorganisms were detected and analyzed using metagenomics. Results: Compared with the 30-day untrained group, the relative abundances of Bacteroidetes were significantly increased in the 30-day training group (p < 0.01). Conversely, the abundances of Clostridiaceae, Clostridium, and Ruminococcus were significantly decreased (p < 0.01), whereas those of Prevotella, Bacteroideaceae, and Bacteroidetes were significantly increased (p < 0.05). Additionally, the relative abundances of Firmicutes and Actinomycetes were significantly decreased (p < 0.05). Compared with the 60-day untrained group, no significant differences in the phyla Bacteriaceae and Bacteriae of the 60-day training group (p > 0.05) were observed. In the linear discriminant analysis effect size analysis, seven significantly different bacteria were detected in the fecal flora of horses in the 30-day training group versus the untrained 30-day group, but only one significantly different bacterium was detected after 60 days. The Kyoto Encyclopedia of Genes and Genomes analysis showed that the differentially expressed genes were related to metabolism and the environmental information processing pathway, carbohydrate metabolism, and membrane transport pathways. Conclusions: Therefore, training seems to affect the diversity and composition of the gut microbiota of Yili horses, especially during the first 30 days of training.},
}

Animals
Horses/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Feces/microbiology
*Physical Conditioning, Animal
*Bacteria/genetics/classification/isolation & purification

@article {pmid40428305,
year = {2025},
author = {Guo, Q and Zhang, W and Xu, C and Li, X and Wang, B and Xiong, C and Duan, W and Luo, T and Wang, W and Zhou, J},
title = {Comparative Analysis of Gut Microbiome Community Structures in Different Populations of Asian Elephants in China and Their Correlation with Diet.},
journal = {Genes},
volume = {16},
number = {5},
pages = {},
pmid = {40428305},
issn = {2073-4425},
support = {202501AS070053//Key Project of Yunnan Basic Research Program/ ; },
mesh = {Animals ; *Elephants/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Diet ; China ; Metagenomics/methods ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: The interaction and co-evolution between the gut microbiome and the host play important roles in the host's physiology, nutrition, and health. Diet is considered an important driver of differences in the gut microbiota; however, research on the relationship between the gut microbiota and diet in Asian elephants remains limited.

METHODS: In this study, we explored the gut microbiota structure and its relationship with diet in different populations of Asian elephants through metagenomic sequencing, combined with previously published dietary data.

RESULTS: This study found that the dominant gut microbiota of Asian elephants includes the phyla Bacillota (29.85% in BP, 22.79% in RC, 21.89% in SM, 31.67% in ML, and 33.00% in NGH), Bacteroidota (25.25% in BP, 31.44% in RC, 16.44% in SM, 25.73% in ML, and 23.74% in NGH), and Spirochaetota (3.49% in BP, 6.18% in RC, 1.71% in SM, 2.69% in ML, and 3.52% in NGH), with significant differences in the gut microbiota among different populations. Correlation analysis between the gut microbiota and diet revealed that dietary diversity did not directly affect the alpha diversity of the gut microbiota. However, specific food types might play a key role in shaping the gut microbiota structure by regulating the abundance of certain microbiota.

CONCLUSIONS: This study reveals significant differences in the gut microbiota structure among different populations of Asian elephants and explores the impact of diet on the structure. The results provide foundational data for a deeper understanding of the gut microbiota structure of Asian elephants and offer important references for the scientific conservation and precise management strategies of this species.},
}

Animals
*Elephants/microbiology/genetics
*Gastrointestinal Microbiome/genetics
*Diet
China
Metagenomics/methods
Bacteria/genetics/classification

@article {pmid40427823,
year = {2025},
author = {Santos, AFB and Nunes, M and Filipa-Silva, A and Pimentel, V and Pingarilho, M and Abrantes, P and Miranda, MNS and Crespo, MTB and Abecasis, AB and Parreira, R and Seabra, SG},
title = {Wastewater Metavirome Diversity: Exploring Replicate Inconsistencies and Bioinformatic Tool Disparities.},
journal = {International journal of environmental research and public health},
volume = {22},
number = {5},
pages = {},
pmid = {40427823},
issn = {1660-4601},
support = {PTDC/CTA AMB/29586/2017//Fundação para a Ciência e Tecnologia, Portugal 568 through projects AgriWWAter/ ; 706, Internalproject IBETXplore 2017//VirusFreeWater/ ; GHTM- UID/04413/2020//Internal exploratory Project WasteWaterVir/ ; LA/P/0117/2020//LA-REAL/ ; },
mesh = {*Wastewater/virology ; *Computational Biology/methods ; *Virome ; Portugal ; *Metagenomics/methods ; *Viruses/classification/isolation & purification/genetics ; },
abstract = {This study investigates viral composition in wastewater through metagenomic analysis, evaluating the performance of four bioinformatic tools-Genome Detective, CZ.ID, INSaFLU-TELEVIR and Trimmomatic + Kraken2-on samples collected from four sites in each of two wastewater treatment plants (WWTPs) in Lisbon, Portugal in April 2019. From each site, we collected and processed separately three replicates and one pool of nucleic acids extracted from the replicates. A total of 32 samples were processed using sequence-independent single-primer amplification (SISPA) and sequenced on an Illumina MiSeq platform. Across the 128 sample-tool combinations, viral read counts varied widely, from 3 to 288,464. There was a lack of consistency between replicates and their pools in terms of viral abundance and diversity, revealing the heterogeneity of the wastewater matrix and the variability in sequencing effort. There was also a difference between software tools highlighting the impact of tool selection on community profiling. A positive correlation between crAssphage and human pathogens was found, supporting crAssphage as a proxy for public health surveillance. A custom Python pipeline automated viral identification report processing, taxonomic assignments and diversity calculations, streamlining analysis and ensuring reproducibility. These findings emphasize the importance of sequencing depth, software tool selection and standardized pipelines in advancing wastewater-based epidemiology.},
}

*Wastewater/virology
*Computational Biology/methods
*Virome
Portugal
*Metagenomics/methods
*Viruses/classification/isolation & purification/genetics

@article {pmid40427639,
year = {2025},
author = {DeSantis, AH and Buss, K and Coker, KM and Pasternak, BA and Chi, J and Patterson, JS and Gu, H and Jurutka, PW and Sandrin, TR},
title = {Multiomics-Based Profiling of the Fecal Microbiome Reveals Potential Disease-Specific Signatures in Pediatric IBD (PIBD).},
journal = {Biomolecules},
volume = {15},
number = {5},
pages = {},
pmid = {40427639},
issn = {2218-273X},
support = {GR39923//Phoenix Children's Hospital Foundation Leadership Grant/ ; },
mesh = {Humans ; Child ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Metagenomics/methods ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Metabolomics/methods ; Adolescent ; *Colitis, Ulcerative/microbiology/genetics/metabolism ; *Crohn Disease/microbiology/genetics/metabolism ; Biomarkers/metabolism ; Transcriptome ; Multiomics ; },
abstract = {Inflammatory bowel disease (IBD), which includes Crohn's Disease (CD) and Ulcerative Colitis (UC), is a chronic gastrointestinal (GI) disorder affecting 1 in 100 people in the United States. Pediatric IBD (PIBD) is estimated to impact 15 per 100,000 children in North America. Factors such as the gut microbiome (GM), genetic predisposition to the disease, and certain environmental factors are thought to be involved in pathogenesis. However, the pathophysiology of IBD is incompletely understood, and diagnostic biomarkers and effective treatments, particularly for PIBD, are limited. Recent work suggests that these factors may interact to influence disease development, and multiomic approaches have emerged as promising tools to elucidate the pathophysiology. We employed metagenomics, metabolomics- and metatranscriptomics-based approaches to examine the microbiome, its genetic potential, and its activity to identify factors associated with PIBD. Metagenomics-based analyses revealed pathways such as octane oxidation and glycolysis that were differentially expressed in UC patients. Additionally, metatranscriptomics-based analyses suggested enrichment of glycan degradation and two component systems in UC samples as well as protein processing in the endoplasmic reticulum, ribosome, and protein export in CD and UC samples. In addition, metabolomics-based approaches revealed patterns of differentially abundant metabolites between healthy and PIBD individuals. Interestingly, overall microbiome community composition (as measured by alpha and beta diversity indices) did not appear to be associated with PIBD. However, we observed a small number of differentially abundant taxa in UC versus healthy controls, including members of the Classes Gammaproteobacteria and Clostridia as well as members of the Family Rikenellaceae. Accordingly, when identifying potential biomarkers for PIBD, our results suggest that multiomics-based approaches afford enhanced potential to detect putative biomarkers for PIBD compared to microbiome community composition sequence data alone.},
}

Humans
Child
*Feces/microbiology
*Gastrointestinal Microbiome/genetics
Male
Female
Metagenomics/methods
*Inflammatory Bowel Diseases/microbiology/metabolism/genetics
Metabolomics/methods
Adolescent
*Colitis, Ulcerative/microbiology/genetics/metabolism
*Crohn Disease/microbiology/genetics/metabolism
Biomarkers/metabolism
Transcriptome
Multiomics

@article {pmid40426500,
year = {2025},
author = {Tóth, AG and Tóth, DL and Remport, L and Tóth, I and Németh, T and Dubecz, A and Patai, ÁV and Wagenhoffer, Z and Makrai, L and Solymosi, N},
title = {A One Health Approach Metagenomic Study on Antimicrobial Resistance Traits of Canine Saliva.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
pmid = {40426500},
issn = {2079-6382},
support = {SRF-001//University of Veterinary Medicine Budapest/ ; 874735 (VEO)//European Union's Horizon 2020/ ; 2024-2.1.2-EKÖP-2024-00018//Ministry of Culture and Innovation of Hungary/ ; },
abstract = {Background: According to the One Health concept, the physical proximity between pets and their owners facilitates the interspecies spread of bacteria including those that may harbor numerous antimicrobial resistance genes (ARGs). Methods: A shotgun sequencing metagenomic data-based bacteriome and resistome study of 1830 canine saliva samples was conducted considering the subsets of ARGs with higher public health risk, ESKAPE pathogen relatedness (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species), and survey results on the physical and behavioral characteristics of the participating dogs. Results: A total of 318 ARG types achieved sufficiently high detection rates. These ARGs can affect 31 antibiotic drug classes through various resistance mechanisms. ARGs against tetracyclines, cephalosporins, and, interestingly, peptides appeared in the highest number of samples. Other Critically Important Antimicrobials (CIAs, WHO), such as aminoglycosides, fluoroquinolones, or macrolides, were among the drug classes most frequently affected by ARGs of higher public health risk and ESKAPE pathogen-related ARGs of higher public health risk. Several characteristics, including coat color, sterilization status, size, activity, or aggressiveness, were associated with statistically significant differences in ARG occurrence rates (p < 0.0500). Conclusions: Although the oral microbiome of pet owners is unknown, the One Health and public health implications of the close human-pet bonds and the factors potentially underlying the increase in salivary ARG numbers should be considered, particularly in light of the presence of ARGs affecting critically important drugs for human medicine.},
}

@article {pmid40426336,
year = {2025},
author = {Wang, Y and Zhou, K and Zhang, Y and Li, C and Zhang, Y and Ren, X and Mi, C and Ma, L and Duan, Y and Liu, M and Ping, G and Tian, X and Song, Z},
title = {The Systemic Impact of Helicobacter pylori Infection on the Microbiome of Whole Digestive Tract Based on Mucosal, Gastric Juice, and Fecal Specimens.},
journal = {Helicobacter},
volume = {30},
number = {3},
pages = {e70047},
doi = {10.1111/hel.70047},
pmid = {40426336},
issn = {1523-5378},
support = {82170562//National Natural Science Foundation of China/ ; 7232199//Beijing Natural Science Foundation/ ; BYSYZD2023008//Key Clinical Projects of Peking University Third Hospital/ ; },
mesh = {Humans ; *Feces/microbiology ; Cross-Sectional Studies ; *Helicobacter Infections/microbiology ; Male ; Middle Aged ; Female ; *Gastric Juice/microbiology ; Adult ; *Helicobacter pylori/physiology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Bacteria/classification/genetics/isolation & purification ; Aged ; *Gastrointestinal Tract/microbiology ; Dysbiosis/microbiology ; Metagenomics ; },
abstract = {BACKGROUND: Recent studies have found that in addition to directly impacting the gastric microbiome, Helicobacter pylori (H. pylori) infection may cause intestinal microbial dysbiosis. However, most existing studies on the influence of H. pylori infection on the intestinal microbiome used fecal specimens with inconsistent conclusions. Only one limited study on 8 H. pylori-infected patients has previously assessed the impact of H. pylori infection on the microbiome of the entire gastrointestinal tract, finding no significant effect on the bacterial composition of the lower gastrointestinal tract.

METHODS: This single-center cross-sectional study collected mucosa of the esophagus, stomach, small intestine, and colon, as well as gastric juice and feces from 120 participants of the H. pylori-infected group (HIG) and 30 of the healthy control group (HCG). 16S rRNA sequencing was applied to analyze the bacterial composition and functional pathways, and metagenomics was adopted to assess the composition of viruses, eukaryotes, and archaea in the feces, as well as the antibiotic resistance gene (ARG) and virulence factors of bacteria (VF).

RESULTS: Compared with the HCG, the alpha and beta diversity of bacteria in the mucosa of the whole digestive tract and the gastric juice of the HIG showed significant changes, with increased microbial dysbiosis index and significantly different compositions at the phylum and genus levels. Functional pathway analysis revealed that the metabolic characteristics of the flora changed in the HIG, with site-specific differences. Fecal specimens demonstrated no significant differences in the above indicators between the two groups. In addition, feces-based metagenomic analysis revealed that only eukaryotes had higher diversity in the HIG, whereas viruses and archaea showed no significant changes; the Shannon index of ARG increased; and VF showed no significant change.

CONCLUSIONS: This study revealed that H. pylori infection significantly influenced the diversity, composition, and metabolic functional pathway of bacteria in different parts of the digestive tract and the gastric juice. Moreover, fecal microbial composition may not fully represent the mucosal microbial composition of the gastrointestinal tract.

TRIAL REGISTRATION: Chinese Clinical Trial Registry: ChiCTR2300073419.},
}

Humans
*Feces/microbiology
Cross-Sectional Studies
*Helicobacter Infections/microbiology
Male
Middle Aged
Female
*Gastric Juice/microbiology
Adult
*Helicobacter pylori/physiology
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
Bacteria/classification/genetics/isolation & purification
Aged
*Gastrointestinal Tract/microbiology
Dysbiosis/microbiology
Metagenomics