@article {pmid39900569,
year = {2025},
author = {Priest, T and Oldenburg, E and Popa, O and Dede, B and Metfies, K and von Appen, WJ and Torres-Valdés, S and Bienhold, C and Fuchs, BM and Amann, R and Boetius, A and Wietz, M},
title = {Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1326},
pmid = {39900569},
issn = {2041-1723},
mesh = {Arctic Regions ; *Seasons ; *Microbiota/genetics ; *Seawater/microbiology ; *Oceans and Seas ; Metagenomics/methods ; Bacteria/genetics/classification/metabolism ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; DNA Barcoding, Taxonomic ; Metagenome ; Phylogeny ; },
abstract = {Deciphering how microbial communities are shaped by environmental variability is fundamental for understanding the structure and function of ocean ecosystems. While seasonal environmental gradients have been shown to structure the taxonomic dynamics of microbiomes over time, little is known about their impact on functional dynamics and the coupling between taxonomy and function. Here, we demonstrate annually recurrent, seasonal structuring of taxonomic and functional dynamics in a pelagic Arctic Ocean microbiome by combining autonomous samplers and in situ sensors with long-read metagenomics and SSU ribosomal metabarcoding. Specifically, we identified five temporal microbiome modules whose succession within each annual cycle represents a transition across different ecological states. For instance, Cand. Nitrosopumilus, Syndiniales, and the machinery to oxidise ammonia and reduce nitrite are signatures of early polar night, while late summer is characterised by Amylibacter and sulfur compound metabolism. Leveraging metatranscriptomes from Tara Oceans, we also demonstrate the consistency in functional dynamics across the wider Arctic Ocean during similar temporal periods. Furthermore, the structuring of genetic diversity within functions over time indicates that environmental selection pressure acts heterogeneously on microbiomes across seasons. By integrating taxonomic, functional and environmental information, our study provides fundamental insights into how microbiomes are structured under pronounced seasonal changes in understudied, yet rapidly changing polar marine ecosystems.},
}

Arctic Regions
*Seasons
*Microbiota/genetics
*Seawater/microbiology
*Oceans and Seas
Metagenomics/methods
Bacteria/genetics/classification/metabolism
RNA, Ribosomal, 16S/genetics
Ecosystem
DNA Barcoding, Taxonomic
Metagenome
Phylogeny

@article {pmid39900484,
year = {2025},
author = {Van Etten, J and Stephens, TG and Bhattacharya, D},
title = {Genetic Transfer in Action: Uncovering DNA Flow in an Extremophilic Microbial Community.},
journal = {Environmental microbiology},
volume = {27},
number = {2},
pages = {e70048},
doi = {10.1111/1462-2920.70048},
pmid = {39900484},
issn = {1462-2920},
support = {//U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231/ ; 10.46936/10.25585/60000481//Joint Genome Institute/ ; NJ01180//National Institute of Food and Agriculture/ ; 80NSSC19K1542/NASA/NASA/United States ; NASA (80NSSC19K0462)/NASA/NASA/United States ; },
mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/classification ; Extremophiles/genetics ; Microbiota/genetics ; DNA, Bacterial/genetics ; Genome, Bacterial ; },
abstract = {Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. HGT has been investigated in many studies however, the focus has been on conspicuous protein-coding DNA transfers that often prove to be adaptive in recipient organisms and are therefore fixed longer-term in lineages. These results comprise a subclass of HGTs and do not represent exhaustive (coding and non-coding) DNA transfer and its impact on ecology. Uncovering exhaustive HGT can provide key insights into the connectivity of genomes in communities and how these transfers may occur. In this study, we use the term frequency-inverse document frequency (TF-IDF) technique, that has been used successfully to mine DNA transfers within real and simulated high-quality prokaryote genomes, to search for exhaustive HGTs within an extremophilic microbial community. We establish a pipeline for validating transfers identified using this approach. We find that most DNA transfers are within-domain and involve non-coding DNA. A relatively high proportion of the predicted protein-coding HGTs appear to encode transposase activity, restriction-modification system components, and biofilm formation functions. Our study demonstrates the utility of the TF-IDF approach for HGT detection and provides insights into the mechanisms of recent DNA transfer.},
}

*Gene Transfer, Horizontal
*Bacteria/genetics/classification
Extremophiles/genetics
Microbiota/genetics
DNA, Bacterial/genetics
Genome, Bacterial

@article {pmid39900940,
year = {2025},
author = {Prabhaharan, D and Go, YW and Kim, H and Kang, S and Sang, BI},
title = {Representative Metagenomes of Mesophilic Biogas Reactor Across South Korea.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {198},
pmid = {39900940},
issn = {2052-4463},
support = {MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; },
mesh = {Republic of Korea ; *Biofuels ; *Metagenome ; *Bioreactors ; Microbiota ; Anaerobiosis ; },
abstract = {Biogas production through the anaerobic digestion (AD) of organic waste plays a crucial role in promoting sustainability and closing the carbon cycle. Over the past decade, this has driven global research on biogas-producing microbiomes, leading to significant advances in our understanding of microbial diversity and metabolic pathways within AD plants. However, substantial knowledge gaps persist, particularly in understanding the specific microbial communities involved in biogas production in countries such as South Korea. The present dataset addresses one of these gaps by providing comprehensive information on the metagenomes of five full-scale mesophilic biogas reactors in South Korea. From 110 GB of raw DNA sequences, 401 metagenome-assembled genomes (MAGs) were created, which include 42,301 annotated genes. Of these, 187 MAGs (46.7%) were classified as high-quality based on Minimum Information about Metagenome-Assembled Genome (MIMAG) standards. The data presented here contribute to a broader understanding of biogas-specific microbial communities and offers a significant resource for future studies and advancements in sustainable biogas production.},
}

Republic of Korea
*Biofuels
*Metagenome
*Bioreactors
Microbiota
Anaerobiosis

@article {pmid39897560,
year = {2025},
author = {Zhang, P and Guo, R and Ma, S and Jiang, H and Yan, Q and Li, S and Wang, K and Deng, J and Zhang, Y and Zhang, Y and Wang, G and Chen, L and Li, L and Guo, X and Zhao, G and Yang, L and Wang, Y and Kang, J and Sha, S and Fan, S and Cheng, L and Meng, J and Yu, H and Chen, F and He, D and Wang, J and Liu, S and Shi, H},
title = {A metagenome-wide study of the gut virome in chronic kidney disease.},
journal = {Theranostics},
volume = {15},
number = {5},
pages = {1642-1661},
pmid = {39897560},
issn = {1838-7640},
mesh = {Humans ; *Renal Insufficiency, Chronic/virology ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; *Feces/virology/microbiology ; Middle Aged ; Male ; Female ; Aged ; Dysbiosis/virology/microbiology ; Adult ; Viruses/genetics/classification/isolation & purification ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Rationale: Chronic kidney disease (CKD) is a progressively debilitating condition leading to kidney dysfunction and severe complications. While dysbiosis of the gut bacteriome has been linked to CKD, the alteration in the gut viral community and its role in CKD remain poorly understood. Methods: Here, we characterize the gut virome in CKD using metagenome-wide analyses of faecal samples from 425 patients and 290 healthy individuals. Results: CKD is associated with a remarkable shift in the gut viral profile that occurs regardless of host properties, disease stage, and underlying diseases. We identify 4,649 differentially abundant viral operational taxonomic units (vOTUs) and reveal that some CKD-enriched viruses are closely related to gut bacterial taxa such as Bacteroides, [Ruminococcus], Erysipelatoclostridium, and Enterocloster spp. In contrast, CKD-depleted viruses include more crAss-like viruses and often target Faecalibacterium, Ruminococcus, and Prevotella species. Functional annotation of the vOTUs reveals numerous viral functional signatures associated with CKD, notably a marked reduction in nicotinamide adenine dinucleotide (NAD[+]) synthesis capacity within the CKD-associated virome. Furthermore, most CKD viral signatures are reproducible in the gut viromes of diabetic kidney disease and several other common diseases, highlighting the considerable universality of disease-associated viromes. Conclusions: This research provides comprehensive resources and novel insights into the CKD-associated gut virome, offering valuable guidance for future mechanistic and therapeutic investigations.},
}

Humans
*Renal Insufficiency, Chronic/virology
*Virome/genetics
*Gastrointestinal Microbiome/genetics
*Metagenome/genetics
*Feces/virology/microbiology
Middle Aged
Male
Female
Aged
Dysbiosis/virology/microbiology
Adult
Viruses/genetics/classification/isolation & purification
Bacteria/genetics/classification/isolation & purification

@article {pmid39895074,
year = {2025},
author = {Lee, KA and Ul-Haq, A and Seo, H and Jo, S and Kim, S and Song, HY and Kim, HS},
title = {Characteristics of skin microbiome associated with disease severity in systemic sclerosis.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {1},
pages = {e.2409018},
doi = {10.71150/jm.2409018},
pmid = {39895074},
issn = {1976-3794},
support = {//Korea Health Industry Development Institute/ ; HI21C1888//Ministry of Health and Welfare/ ; //National Research Foundation of Korea/ ; RS-2023-00219563//Ministry of Science and ICT/ ; //Soonchunhyang University Research Fund/ ; },
mesh = {Humans ; *Scleroderma, Systemic/microbiology ; *Skin/microbiology/pathology ; *Microbiota ; Female ; Middle Aged ; Male ; *RNA, Ribosomal, 16S/genetics ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Severity of Illness Index ; Aged ; Biomarkers ; Metagenomics ; },
abstract = {Systemic sclerosis (SSc) is a chronic autoimmune disorder characterised by skin fibrosis and internal organ involvement. Disruptions in the microbial communities on the skin may contribute to the onset of autoimmune diseases that affect the skin. However, current research on the skin microbiome in SSc is lacking. This study aimed to investigate skin microbiome associated with disease severity in SSc. Skin swabs were collected from the upper limbs of 46 healthy controls (HCs) and 36 patients with SSc. Metagenomic analysis based on the 16S rRNA gene was conducted and stratified by cutaneous subtype and modified Rodnan skin score (mRSS) severity. Significant differences in skin bacterial communities were observed between the HCs and patients with SSc, with further significant variations based on subtype and mRSS severity. The identified biomarkers were Bacteroides and Faecalibacterium for patients with diffuse cutaneous SSc with high mRSS (≥ 10) and Mycobacterium and Parabacteroides for those with low mRSS (< 10). Gardnerella, Abies, Lactobacillus, and Roseburia were the biomarkers in patients with limited cutaneous SSc (lcSS) and high mRSS, whereas Coprococcus predominated in patients with lcSS and low mRSS. Cutaneous subtype analysis identified Pediococcus as a biomarker in the HCs, whereas mRSS analysis revealed the presence of Pseudomonas in conjunction with Pediococcus. In conclusion, patients with SSc exhibit distinct skin microbiota compared with healthy controls. Bacterial composition varies by systemic sclerosis cutaneous subtype and skin thickness.},
}

Humans
*Scleroderma, Systemic/microbiology
*Skin/microbiology/pathology
*Microbiota
Female
Middle Aged
Male
*RNA, Ribosomal, 16S/genetics
Adult
*Bacteria/classification/genetics/isolation & purification
Severity of Illness Index
Aged
Biomarkers
Metagenomics

@article {pmid39868213,
year = {2025},
author = {Schechter, MS and Trigodet, F and Veseli, IA and Miller, SE and Klein, ML and Sever, M and Maignien, L and Delmont, TO and Light, SH and Eren, AM},
title = {Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39868213},
issn = {2692-8205},
support = {T32 GM007197/GM/NIGMS NIH HHS/United States ; },
abstract = {The increasing availability of microbial genomes is essential to gain insights into microbial ecology and evolution that can propel biotechnological and biomedical advances. Recent advances in genome recovery have significantly expanded the catalogue of microbial genomes from diverse habitats. However, the ability to explain how well a set of genomes account for the diversity in a given environment remains challenging for individual studies or biome-specific databases. Here we present EcoPhylo, a computational workflow to characterize the phylogeography of any gene family through integrated analyses of genomes and metagenomes, and our application of this approach to ribosomal proteins to quantify phylogeny-aware genome recovery rates across three biomes. Our findings show that genome recovery rates vary widely across taxa and biomes, and that single amplified genomes, metagenome-assembled genomes, and isolate genomes have non-uniform yet quantifiable representation of environmental microbes. EcoPhylo reveals highly resolved, reference-free, multi-domain phylogenies in conjunction with distribution patterns of individual clades across environments, providing a means to assess genome recovery in individual studies and benchmark biome-level genome collections.},
}

@article {pmid39856391,
year = {2025},
author = {Tisza, MJ and Lloyd, RE and Hoffman, K and Smith, DP and Rewers, M and Javornik Cregeen, SJ and Petrosino, JF},
title = {Longitudinal phage-bacteria dynamics in the early life gut microbiome.},
journal = {Nature microbiology},
volume = {10},
number = {2},
pages = {420-430},
pmid = {39856391},
issn = {2058-5276},
support = {U01 DK063821/DK/NIDDK NIH HHS/United States ; U01 DK63865//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; U01 DK63829//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; U01 DK63821//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Bacteriophages/genetics/physiology/classification ; Infant ; *Bacteria/virology/genetics/classification/isolation & purification ; Child, Preschool ; Longitudinal Studies ; Metagenome ; Diabetes Mellitus, Type 1/microbiology/virology ; Feces/microbiology ; Female ; Male ; Metagenomics ; Infant, Newborn ; },
abstract = {Microbial colonization of the human gut occurs soon after birth, proceeds through well-studied phases and is affected by lifestyle and other factors. Less is known about phage community dynamics during infant gut colonization due to small study sizes, an inability to leverage large databases and a lack of appropriate bioinformatics tools. Here we reanalysed whole microbial community shotgun sequencing data of 12,262 longitudinal samples from 887 children from four countries across four years of life as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We developed an extensive metagenome-assembled genome catalogue using the Marker-MAGu pipeline, which comprised 49,111 phage taxa from existing human microbiome datasets. This was used to identify phage marker genes and their integration into the MetaPhlAn 4 bacterial marker gene database enabled simultaneous assessment of phage and bacterial dynamics. We found that individual children are colonized by hundreds of different phages, which are more transitory than bacteria, accumulating a more diverse phage community over time. Type 1 diabetes correlated with a decreased rate of change in bacterial and viral communities in children aged one and two. The addition of phage data improved the ability of machine learning models to discriminate samples by country. Finally, although phage populations were specific to individuals, we observed trends of phage ecological succession that correlated well with putative host bacteria. This resource improves our understanding of phage-bacteria interactions in the developing early life microbiome.},
}

Humans
*Gastrointestinal Microbiome
*Bacteriophages/genetics/physiology/classification
Infant
*Bacteria/virology/genetics/classification/isolation & purification
Child, Preschool
Longitudinal Studies
Metagenome
Diabetes Mellitus, Type 1/microbiology/virology
Feces/microbiology
Female
Male
Metagenomics
Infant, Newborn

@article {pmid39833544,
year = {2025},
author = {Yan, X and Liu, Y and Hu, T and Huang, Z and Li, C and Guo, L and Liu, Y and Li, N and Zhang, H and Sun, Y and Yi, L and Wu, J and Feng, J and Zhang, F and Jiang, T and Tu, C and He, B},
title = {A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics.},
journal = {Nature microbiology},
volume = {10},
number = {2},
pages = {554-568},
pmid = {39833544},
issn = {2058-5276},
support = {32192423//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32022083//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32192424//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32371562//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Chiroptera/virology ; Animals ; China ; *Metagenome ; *Virome/genetics ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; RNA, Viral/genetics ; Humans ; Genetic Variation ; Genome, Viral/genetics ; Metagenomics/methods ; },
abstract = {Bats are natural hosts for many emerging viruses for which spillover to humans is a major risk, but the diversity and ecology of bat viruses is poorly understood. Here we generated 8,176 RNA viral metagenomes by metatranscriptomic sequencing of organ and swab samples from 4,143 bats representing 40 species across 52 locations in China. The resulting database, the BtCN-Virome, expands bat RNA virus diversity by over 3.4-fold. Some viruses in the BtCN-Virome are traced to mammals, birds, arthropods, mollusks and plants. Diet, infection dynamics and environmental parameters such as humidity and forest coverage shape virus distribution. Compared with those in the wild, bats dwelling in human settlements harboured more diverse viruses that also circulated in humans and domestic animals, including Nipah and Lloviu viruses not previously reported in China. The BtCN-Virome provides important insights into the genetic diversity, ecological drivers and circulation dynamics of bat viruses, highlighting the need for surveillance of bats near human settlements.},
}

*Chiroptera/virology
Animals
China
*Metagenome
*Virome/genetics
*RNA Viruses/genetics/classification/isolation & purification
Phylogeny
RNA, Viral/genetics
Humans
Genetic Variation
Genome, Viral/genetics
Metagenomics/methods

@article {pmid39777507,
year = {2025},
author = {Shelton, AN and Yu, FB and Grossman, AR and Bhaya, D},
title = {Abundant and active community members respond to diel cycles in hot spring phototrophic mats.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf001},
pmid = {39777507},
issn = {1751-7370},
support = {2125965//NSF/ ; 1921429//BBSRC-NSF/BIO/ ; //Office of Science of the U.S. Department of Energy/ ; },
mesh = {*Hot Springs/microbiology ; Metagenome ; Photosynthesis ; Phototrophic Processes ; Bacteria/genetics/classification/isolation & purification/metabolism ; Metagenomics ; Microbiota ; Transcriptome ; },
abstract = {Photosynthetic microbial mats in hot springs can provide insights into the diel behaviors of communities in extreme environments. In this habitat, photosynthesis dominates during the day, leading to super-oxic conditions, with a rapid transition to fermentation and anoxia at night. Multiple samples were collected from two springs over several years to generate metagenomic and metatranscriptomic datasets. Metagenome-assembled genomes comprised 71 taxa (in 19 different phyla), of which 12 core taxa were present at high abundance in both springs. The eight most active taxa identified by metatranscriptomics were an oxygenic cyanobacterium (Synechococcus sp.), five anoxygenic phototrophs from three different phyla, and two understudied heterotrophs from phylum Armatimonadota. In all eight taxa, a significant fraction of genes exhibited a diel expression pattern, although peak timing varied considerably. The two abundant heterotrophs exhibit starkly different peak timing of expression, which we propose is shaped by their metabolic and genomic potential to use carbon sources that become differentially available during the diel cycle. Network analysis revealed pathway expression patterns that had not previously been linked to diel cycles, including ribosome biogenesis and chaperones. This provides a framework for analyzing metabolically coupled communities and the dominant role of the diel cycle.},
}

*Hot Springs/microbiology
Metagenome
Photosynthesis
Phototrophic Processes
Bacteria/genetics/classification/isolation & purification/metabolism
Metagenomics
Microbiota
Transcriptome

@article {pmid39761633,
year = {2025},
author = {Lake, BB and McAdams, ZL and Ericsson, AC and Reinero, C and Gull, T and Lyons, BM},
title = {Feline urethral obstruction alters the urinary microbiota and comparison to oral, preputial, and rectal microbiotas.},
journal = {American journal of veterinary research},
volume = {86},
number = {2},
pages = {},
doi = {10.2460/ajvr.24.07.0213},
pmid = {39761633},
issn = {1943-5681},
mesh = {Animals ; Cats ; *Cat Diseases/microbiology/urine ; *Microbiota ; Male ; *Urethral Obstruction/veterinary/microbiology ; *Rectum/microbiology ; *RNA, Ribosomal, 16S/genetics ; Female ; Prospective Studies ; Mouth/microbiology ; Case-Control Studies ; },
abstract = {OBJECTIVE: To document differences in the microbiota of healthy cats versus cats with urethral obstruction (UO); compare the urinary microbiota with the oral, preputial, and rectal microbiota; and demonstrate that 16S rRNA gene sequencing will reveal rich and diverse urinary microbiota.

METHODS: 15 client-owned cats with UO and 15 age-matched healthy cats were included from July 2020 through April 2021. Exclusion criteria were evidence of urinary tract infection, urolithiasis, antimicrobial administration, urinary catheterization in the past 30 days, or a comorbidity. This study was a prospective, observational study. Both groups had a baseline CBC, chemistry panel, urinalysis, urine culture, and focal bladder ultrasound. Swabs of the cystocentesis site, buccal mucosa, rectum, prepuce, and urinary samples were collected, and 16S rRNA gene sequencing was used to compare the groups and sites.

RESULTS: Differences in the microbiota richness and diversity were found in the urine of cats with UO (n = 15) compared to healthy cats (15), along with differences in the preputial and oral samples, supporting the presence of a urinary dysbiosis in cats with UO.

CONCLUSIONS: Our preliminary data demonstrates a dramatic change in the urinary microbiota of cats with UO along with changes in microbiota in other sites compared to healthy cats.

CLINICAL RELEVANCE: A urinary dysbiosis in cats with UO has been minimally supported in prior studies using 16S rRNA gene sequencing. Although these are preliminary results, documenting this dysbiosis in cats with UO provides a potential avenue for novel therapeutics.},
}

Animals
Cats
*Cat Diseases/microbiology/urine
*Microbiota
Male
*Urethral Obstruction/veterinary/microbiology
*Rectum/microbiology
*RNA, Ribosomal, 16S/genetics
Female
Prospective Studies
Mouth/microbiology
Case-Control Studies

@article {pmid39693209,
year = {2025},
author = {Yamamoto, A and Kawashima, A and Uemura, T and Nakano, K and Matsushita, M and Ishizuya, Y and Jingushi, K and Hase, H and Katayama, K and Yamaguchi, R and Sassi, N and Motoyama, Y and Nojima, S and Mita, M and Kimura, T and Motooka, D and Horibe, Y and Okuda, Y and Oka, T and Yamamichi, G and Tomiyama, E and Koh, Y and Yamamoto, Y and Kato, T and Hatano, K and Uemura, M and Imoto, S and Wada, H and Morii, E and Tsujikawa, K and Nonomura, N},
title = {A novel mouse model of upper tract urothelial carcinoma highlights the impact of dietary intervention on gut microbiota and carcinogenesis prevention despite carcinogen exposure.},
journal = {International journal of cancer},
volume = {156},
number = {7},
pages = {1439-1456},
doi = {10.1002/ijc.35295},
pmid = {39693209},
issn = {1097-0215},
support = {19K09709//Japan Society for the Promotion of Science/ ; 21K20968//Japan Society for the Promotion of Science/ ; 22H03213//Japan Society for the Promotion of Science/ ; 22K09523//Japan Society for the Promotion of Science/ ; 22K18398//Japan Society for the Promotion of Science/ ; JP22ym0126809i0002//Japan Agency for Medical Research and Development/ ; JP23ama121054//Japan Agency for Medical Research and Development/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; Female ; *Disease Models, Animal ; Humans ; *Carcinogens/toxicity ; Male ; *Butylhydroxybutylnitrosamine ; Carcinogenesis ; Mice, Inbred BALB C ; Urinary Bladder Neoplasms/prevention & control/chemically induced/etiology/pathology ; Urologic Neoplasms/prevention & control/diet therapy/etiology/chemically induced/pathology ; Urothelium/pathology/metabolism/microbiology ; },
abstract = {Animal models of N-butyl-N-(4-hydroxy butyl) nitrosamine (BBN)-induced urothelial carcinoma (UC), particularly bladder cancer (BC), have long been established. However, the rare incidence of BBN-induced upper urinary tract UC (UTUC), which originates from the same urothelium as BC, remains elusive. The scarcity of animal models of UTUC has made it challenging to study the biology of UTUC. To address this problem, we tried to establish a novel mouse model of UTUC by treating multiple mice strains and sexes with BBN. The molecular consistency between the UTUC mouse model and human UTUC was confirmed using multi-omics analyses, including whole-exome, whole-transcriptome, and spatial transcriptome sequencing. 16S ribosomal RNA metagenome sequencing, metabolome analysis, and dietary interventions were employed to assess changes in the gut microbiome, metabolome, and carcinogenesis of UTUC. Of all treated mice, only female BALB/c mice developed UTUC over BC. Multi-omics analyses confirmed that the UTUC model reflected the molecular characteristics and heterogeneity of human UTUC with poor prognosis. Furthermore, the model exhibited increased Tnf-related inflammatory gene expression in the upper urinary tract and a low relative abundance of Parabacteroides distasonis in the gut. Dietary intervention, mainly without alanine, led to P. distasonis upregulation and successfully prevented UTUC, as well as suppressed Tnf-related inflammatory gene expression in the upper urinary tract despite the exposure to BBN. This is the first report to demonstrate a higher incidence of UTUC than BC in a non-engineered mouse model using BBN. Overall, this model could serve as a useful tool for comprehensively investigating UTUC in future studies.},
}

Animals
*Gastrointestinal Microbiome
Mice
Female
*Disease Models, Animal
Humans
*Carcinogens/toxicity
Male
*Butylhydroxybutylnitrosamine
Carcinogenesis
Mice, Inbred BALB C
Urinary Bladder Neoplasms/prevention & control/chemically induced/etiology/pathology
Urologic Neoplasms/prevention & control/diet therapy/etiology/chemically induced/pathology
Urothelium/pathology/metabolism/microbiology

@article {pmid39893166,
year = {2025},
author = {Bourquin, M and Peter, H and Michoud, G and Busi, SB and Kohler, TJ and Robison, AL and Styllas, M and Ezzat, L and Geers, AU and Huss, M and Fodelianakis, S and , and Battin, TJ},
title = {Predicting climate-change impacts on the global glacier-fed stream microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1264},
pmid = {39893166},
issn = {2041-1723},
mesh = {*Microbiota/genetics ; *Ice Cover/microbiology ; *Climate Change ; *Phylogeny ; *Bacteria/genetics/classification ; *Rivers/microbiology ; Metagenome ; Biodiversity ; Ecosystem ; },
abstract = {The shrinkage of glaciers and the vanishing of glacier-fed streams (GFSs) are emblematic of climate change. However, forecasts of how GFS microbiome structure and function will change under projected climate change scenarios are lacking. Combining 2,333 prokaryotic metagenome-assembled genomes with climatic, glaciological, and environmental data collected by the Vanishing Glaciers project from 164 GFSs draining Earth's major mountain ranges, we here predict the future of the GFS microbiome until the end of the century under various climate change scenarios. Our model framework is rooted in a space-for-time substitution design and leverages statistical learning approaches. We predict that declining environmental selection promotes primary production in GFSs, stimulating both bacterial biomass and biodiversity. Concomitantly, predictions suggest that the phylogenetic structure of the GFS microbiome will change and entire bacterial clades are at risk. Furthermore, genomic projections reveal that microbiome functions will shift, with intensified solar energy acquisition pathways, heterotrophy and algal-bacterial interactions. Altogether, we project a 'greener' future of the world's GFSs accompanied by a loss of clades that have adapted to environmental harshness, with consequences for ecosystem functioning.},
}

*Microbiota/genetics
*Ice Cover/microbiology
*Climate Change
*Phylogeny
*Bacteria/genetics/classification
*Rivers/microbiology
Metagenome
Biodiversity
Ecosystem

@article {pmid39893159,
year = {2025},
author = {Sampson, TR and Wallen, ZD and Won, WJ and Standaert, DG and Payami, H and Harms, AS},
title = {Alpha synuclein overexpression can drive microbiome dysbiosis in mice.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {4014},
pmid = {39893159},
issn = {2045-2322},
support = {ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-000375//Aligning Science Across Parkinson's/ ; },
mesh = {Animals ; *alpha-Synuclein/metabolism/genetics ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Mice ; *Mice, Transgenic ; *Parkinson Disease/microbiology/metabolism/genetics ; Disease Models, Animal ; Humans ; Aging ; Male ; },
abstract = {Growing evidence indicates that persons with Parkinson disease (PD), have a unique composition of indigenous gut microbes. Given the long prodromal or pre-diagnosed period, longitudinal studies of the human and rodent gut microbiome before symptomatic onset and for the duration of the disease are currently lacking. PD is partially characterized by the accumulation of the protein α-synuclein (α-syn) into insoluble aggregates, in both the central and enteric nervous systems. As such, several experimental rodent and non-human primate models of α-syn overexpression recapitulate some of the hallmark pathophysiologies of PD. These animal models provide an opportunity to assess how the gut microbiome changes with age under disease-relevant conditions. Here, we used a transgenic mouse strain, which overexpress wild-type human α-syn to test how the gut microbiome composition responds in this model of PD pathology during aging. Using shotgun metagenomics, we find significant, age and genotype-dependent bacterial taxa whose abundance becomes altered with age. We reveal that α-syn overexpression can drive alterations to the gut microbiome composition and suggest that it limits diversity through age. Taxa that were most affected by genotype-age interaction were Lactobacillus and Bifidobacteria. In a mouse model, we showed direct link between alpha synuclein geneotype (hallmark of PD), a dysbiotic and low-diversity gut microbiome, and dysbiotic levels of Bifidobacteria and Lactobacillus (most robust features of PD microbiome). Given emerging data on the potential contributions of the gut microbiome to PD pathologies, our data provide an experimental foundation to understand how the PD-associated microbiome may arise as a trigger or co-pathology to disease.},
}

Animals
*alpha-Synuclein/metabolism/genetics
*Dysbiosis/microbiology
*Gastrointestinal Microbiome
Mice
*Mice, Transgenic
*Parkinson Disease/microbiology/metabolism/genetics
Disease Models, Animal
Humans
Aging
Male

@article {pmid39793775,
year = {2025},
author = {Li, X and Ning, L and Zhao, H and Gu, C and Han, Y and Xu, W and Si, Y and Xu, Y and Wang, R and Ren, Q},
title = {Jiawei Ermiao Granules (JWEMGs) clear persistent HR-HPV infection though improving vaginal microecology.},
journal = {Journal of ethnopharmacology},
volume = {341},
number = {},
pages = {119342},
doi = {10.1016/j.jep.2025.119342},
pmid = {39793775},
issn = {1872-7573},
mesh = {Female ; Humans ; *Vagina/microbiology/drug effects/pathology ; *Papillomavirus Infections/drug therapy ; *Drugs, Chinese Herbal/pharmacology ; Adult ; Middle Aged ; Microbiota/drug effects ; Antiviral Agents/pharmacology ; Cytokines/metabolism ; Young Adult ; },
abstract = {Jiawei Ermiao Granules (JWEMGs), a traditional Chinese herbal formulation, has been widely used in China for the treatment of human papillomavirus (HPV) infections. However, the underlying mechanisms through which it exerts its antiviral effects remain poorly understood.

AIM OF THE STUDY: This study aimed to investigate the potential mechanisms by which JWEMGs modulate vaginal microecology and clear HPV infections, utilizing clinical trials, metagenomic sequencing, and in vitro models.

MATERIALS AND METHODS: Clinical indicators related to vaginal microecology, such as vaginal pH, cleanliness, Nugent score, Donders score, catalase, neuraminidase, and leukocyte esterase, were evaluated in 65 patients with high-risk HPV (HR-HPV) infection. The study examined the impact of two courses of oral JWEMGs on these clinical parameters. Additionally, metagenomic sequencing was performed on vaginal lavage samples from 33 patients to assess the alteration of the vaginal microbiome following JWEMGs treatment. Immunohistochemistry was used to detect ALPK1 expression in cervical exfoliated cells, and ELISA was employed to measure cytokine levels in vaginal lavage fluid. JWEMGs intervention was applied to HaCaT-HPV E6/E7 cells to evaluate its effects on restoring α-kinase 1 (ALPK1) expression and promoting the secretion of cytokines and chemokines.

RESULTS: Treatment with JWEMGs significantly improved several clinical indicators, including cleanliness, pH, Nugent score, Donders score, catalase, neuraminidase, and leukocyte esterase, in HR-HPV-infected patients. Furthermore, JWEMGs therapy led to an increased abundance of Lactobacillus species, especially Lactobacillus crispatus, and a marked reduction in Gardnerella species. JWEMGs treatment also significantly promoted ALPK1 expression in cervical exfoliated cells and augmented the secretion of key cytokines, including IL-6, IL-8, and TNF-α. In parallel, in vitro results showed that JWEMGs substantially enhanced IL-6, IL-8, TNF-α, CCL2, CCL5, and CCL7 secretion in HaCaT-HPV E6/E7 cells, which correlated with the activation of the ALPK1/NF-κB signaling pathway.

CONCLUSION: In conclusion, JWEMGs treatment effectively remodels the vaginal microbiota and bolsters mucosal immunity in the lower genital tract, thereby improving the vaginal microecology in HR-HPV-infected individuals. In vitro findings further demonstrated that JWEMGs promote cytokine and chemokine expression, activating the ALPK1/NF-κB pathway.},
}

Female
Humans
*Vagina/microbiology/drug effects/pathology
*Papillomavirus Infections/drug therapy
*Drugs, Chinese Herbal/pharmacology
Adult
Middle Aged
Microbiota/drug effects
Antiviral Agents/pharmacology
Cytokines/metabolism
Young Adult

@article {pmid39778648,
year = {2025},
author = {Bellanco, A and Requena, T and Martínez-Cuesta, MC},
title = {Polysorbate 80 and carboxymethylcellulose: A different impact on epithelial integrity when interacting with the microbiome.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {196},
number = {},
pages = {115236},
doi = {10.1016/j.fct.2025.115236},
pmid = {39778648},
issn = {1873-6351},
mesh = {*Polysorbates/pharmacology ; *Carboxymethylcellulose Sodium/chemistry ; *Gastrointestinal Microbiome/drug effects ; Humans ; Emulsifying Agents ; Bacteria/drug effects/classification/genetics/metabolism ; },
abstract = {The consumption of dietary emulsifiers, including polysorbate 80 (P80) and sodium carboxymethylcellulose (CMC), has raised safety concerns due to its interaction with the intestinal microbiome. This study demonstrated that increasing concentrations of P80 and CMC added to a dynamic four-stage gut microbiota model (BFBL gut simulator) altered the microbiome composition and impacted epithelial integrity in a dose-dependent manner. 16S rDNA amplicon-based metagenomics analysis revealed that these emulsifiers increased microbial groups with proinflammatory capacities while decreasing microbial taxa known to enhance barrier function. Increasing doses of P80 significantly decreased Bacteroides dorei and Akkermansia, taxa associated with anti-inflammatory potential, while increasing doses of CMC were linked to a higher abundance of Ruminococcus torques and Hungatella, which negatively impact barrier function. Both emulsifiers displayed a different impact on epithelial integrity when interacting with the microbiome. On one hand, supernatants from the BFBL simulator fed with P80 disrupted epithelial integrity to a lesser extent than the additive alone. On the other hand, both the microbiota and the supernatants from the BFBL simulator fed with CMC diminished the epithelial integrity, though the additive itself did not. These findings highlight the need to incorporate the gut microbiome in the risk assessment of these additives.},
}

*Polysorbates/pharmacology
*Carboxymethylcellulose Sodium/chemistry
*Gastrointestinal Microbiome/drug effects
Humans
Emulsifying Agents
Bacteria/drug effects/classification/genetics/metabolism

@article {pmid39701375,
year = {2025},
author = {Corbett, GA and Corcoran, S and Feehily, C and Soldati, B and Rafferty, A and MacIntyre, DA and Cotter, PD and McAuliffe, FM},
title = {Preterm-birth-prevention with Lactobacillus crispatus oral probiotics: Protocol for a double blinded randomised placebo-controlled trial (the PrePOP study).},
journal = {Contemporary clinical trials},
volume = {149},
number = {},
pages = {107776},
doi = {10.1016/j.cct.2024.107776},
pmid = {39701375},
issn = {1559-2030},
mesh = {Humans ; Female ; *Probiotics/administration & dosage/therapeutic use ; Double-Blind Method ; *Vagina/microbiology ; Pregnancy ; *Premature Birth/prevention & control/microbiology ; *Lactobacillus crispatus ; *Lactobacillus ; *Gastrointestinal Microbiome ; *Lacticaseibacillus rhamnosus ; Adult ; Administration, Oral ; Infant, Newborn ; },
abstract = {INTRODUCTION: Effective spontaneous preterm birth (sPTB) prevention is an urgent unmet clinical need. Vaginal depletion of Lactobacillus crispatus is linked to sPTB. This trial will investigate impact of an oral Lactobacillus spp. probiotic product containing an L. crispatus strain with other Lactobacilli spp., on the maternal vaginal and gut microbiome in pregnancies high-risk for sPTB.

METHODS: A double-blind, placebo-controlled, randomised trial will be performed at the National Maternity Hospital Dublin, Ireland. Inclusion criteria are women with history of sPTB or mid-trimester loss, cervical surgery (cone biopsy or two previous large-loop-excision-of-transformation-zone) or uterine anomaly. The intervention is oral supplementation for twelve weeks with probiotic or identical placebo. The probiotic will contains: ◦ 4 billion CFU Lactobacillus crispatus Lbv 88(2x10[9]CFU/Capsule) ◦ 4 billion CFU Lactobacillus rhamnosus Lbv 96(2x10[9]CFU/Capsule) ◦ 0.8 billion CFU Lactobacillus jensenii Lbv 116(0.4x10[9]CFU/Capsule) ◦ 1.2 billion CFU Lactobacillus gasseri Lbv 150(0.6x10[9]CFU/Capsule). Investigators and participants will be blinded to assignment.

RESULTS: The primary outcome is detectable L. crispatus in the vaginal microbiome after twelve weeks of treatment, measured using high-throughput DNA sequencing. A total of 126 women are required to detect a 25 % increase in detectable L. crispatus. Secondary outcomes include impact of intervention on the gut microbiome and metabolome, rate of sPTB and mid-trimester loss, neonatal outcomes and maternal morbidity.

CONCLUSIONS: This randomised trial will investigate ability of an oral probiotic containing L. crispatus to increase its abundance in the vaginal microbiome, both directly by horizontal transfer and indirectly via microbiome and metabolome of the gut.},
}

Humans
Female
*Probiotics/administration & dosage/therapeutic use
Double-Blind Method
*Vagina/microbiology
Pregnancy
*Premature Birth/prevention & control/microbiology
*Lactobacillus crispatus
*Lactobacillus
*Gastrointestinal Microbiome
*Lacticaseibacillus rhamnosus
Adult
Administration, Oral
Infant, Newborn

@article {pmid39891205,
year = {2025},
author = {Huang, D and Liao, J and Balcazar, JL and Ye, M and Wu, R and Wang, D and Alvarez, PJJ and Yu, P},
title = {Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {34},
pmid = {39891205},
issn = {2049-2618},
support = {42177113//National Natural Science Foundation of China/ ; 42277418//National Natural Science Foundation of China/ ; Y2022084//the Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; 2022YFC3704700//National Key Research and Development Program of China/ ; },
mesh = {*Chromium/pharmacology ; *Soil Microbiology ; *Stress, Physiological ; *Bacteria/genetics/classification/drug effects ; *Microbiota/drug effects ; Soil Pollutants ; Metagenomics/methods ; Viruses/genetics/drug effects/classification ; Soil/chemistry ; },
abstract = {BACKGROUND: The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress.

RESULTS: Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that antiviral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities.

CONCLUSIONS: Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation. Video Abstract.},
}

*Chromium/pharmacology
*Soil Microbiology
*Stress, Physiological
*Bacteria/genetics/classification/drug effects
*Microbiota/drug effects
Soil Pollutants
Metagenomics/methods
Viruses/genetics/drug effects/classification
Soil/chemistry

@article {pmid39890997,
year = {2025},
author = {Marter, P and Freese, HM and Ringel, V and Brinkmann, H and Pradella, S and Rohde, M and Jarek, M and Spröer, C and Wagner-Döbler, I and Overmann, J and Bunk, B and Petersen, J},
title = {Superior Resolution Profiling of the Coleofasciculus Microbiome by Amplicon Sequencing of the Complete 16S rRNA Gene and ITS Region.},
journal = {Environmental microbiology reports},
volume = {17},
number = {1},
pages = {e70066},
doi = {10.1111/1758-2229.70066},
pmid = {39890997},
issn = {1758-2229},
support = {34509606-TRR 51//Deutsche Forschungsgemeinschaft/ ; //Collaborative Research Center Roseobacter (TRR51)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Cyanobacteria/genetics/classification/isolation & purification ; Sequence Analysis, DNA ; Phylogeny ; DNA, Ribosomal Spacer/genetics ; DNA, Bacterial/genetics ; Bacteria/genetics/classification/isolation & purification ; Metagenomics ; },
abstract = {The filamentous cyanobacterium Coleofasciculus chthonoplastes is the key primary producer of marine microbial mats. We elucidated the microbiomes of 32 non-axenic Coleofasciculus isolates using PacBio-based amplicon sequencing of the complete 16S rRNA gene and the internally transcribed spacer (16S-ITS). The length of authentic amplicon sequence variants (ASVs) ranged from 1827 to 3044 nucleotides (median: 2267 nt). The results, which were complemented by metagenome analyses and cultivation approaches, revealed the presence of more than 70 associated heterotrophs in the culture of Coleofasciculus sp. WW12. The great bacterial diversity in the cyanosphere is dominated by Pseudomonadota (59%) and Bacteroidota (23%). Allelic ribosomal operon variants were detected in 18 Coleofasciculus strains and our analyses proposed the presence of at least four different species. A comparative analysis of cyanobacterial microbiomes documented complementary advantages of amplicon sequencing versus metagenomics with an individual strength of the 16S-ITS approach in terms of (i) ribosomal target sequence quality, (ii) contaminant detection and (iii) identification of rare bacteria. The characterisation of the Coleofasciculus microbiome showed that long-read amplicon sequencing of the 16S-ITS region is the method of choice for rapid profiling of non-axenic cyanobacteria. Its superior resolution allows a reliable differentiation of even very closely related strains.},
}

*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Cyanobacteria/genetics/classification/isolation & purification
Sequence Analysis, DNA
Phylogeny
DNA, Ribosomal Spacer/genetics
DNA, Bacterial/genetics
Bacteria/genetics/classification/isolation & purification
Metagenomics

@article {pmid39890137,
year = {2025},
author = {Kennedy, EC and Ross, FC and O'Shea, CA and Lavelle, A and Ross, P and Dempsey, E and Stanton, C and Hawkes, CP},
title = {Observational study protocol: the faecal microbiome in the acute stage of new-onset paediatric type 1 diabetes in an Irish cohort.},
journal = {BMJ open},
volume = {15},
number = {1},
pages = {e089206},
doi = {10.1136/bmjopen-2024-089206},
pmid = {39890137},
issn = {2044-6055},
mesh = {Humans ; *Diabetes Mellitus, Type 1/microbiology ; *Feces/microbiology ; Child ; *Gastrointestinal Microbiome ; Male ; Female ; Prospective Studies ; Ireland ; Child, Preschool ; Adolescent ; Metabolome ; },
abstract = {INTRODUCTION: Type 1 diabetes (T1D) is an autoimmune-mediated disorder caused by the destruction of pancreatic beta cells. Although there is an underlying genetic predisposition to developing T1D, the trigger is multifactorial and likely includes environmental factors. The intestinal microbiome has been identified as one such factor. Previous studies have illustrated differences in the microbiota of people with T1D compared with healthy controls. This study aims to describe the evolution of the microbiome and metabolome during the first year of clinical T1D, or stage 3 T1D diagnosis, and investigate whether there are differences in the microbiome and metabolome of children who present with and without diabetic ketoacidosis. The study will also explore possible associations between the microbiome, metabolome, glycaemic control and beta cell reserve.

METHODS AND ANALYSIS: This prospective cohort study will include children with newly diagnosed T1D and sibling controls (n=100, males and females) and their faecal microbiome will be characterised using shotgun metagenomic sequencing at multiple time points during the first year of diagnosis. We will develop a microbial culture biobank based on culturomic studies of stool samples from the healthy controls that will support future investigation. Metabolomic analysis will aim to identify additional biomarkers which may be involved in disease presentation and progression. Through this initial exploratory study, we aim to identify specific microbial biomarkers which may be used as future interventional targets throughout the various stages of T1D progression.

ETHICS AND DISSEMINATION: This study has been approved by the Clinical Research Ethics Committee of the Cork Teaching Hospitals. Study results will be available to patients with T1D and their families, carers, support networks and microbiome societies and other researchers.

TRIAL REGISTRATION NUMBER: The clinicaltrials.gov registration number for this trial is NCT06157736.},
}

Humans
*Diabetes Mellitus, Type 1/microbiology
*Feces/microbiology
Child
*Gastrointestinal Microbiome
Male
Female
Prospective Studies
Ireland
Child, Preschool
Adolescent
Metabolome

@article {pmid39793444,
year = {2025},
author = {Verheijden, RJ and van Eijs, MJM and Paganelli, FL and Viveen, MC and Rogers, MRC and Top, J and May, AM and van de Wijgert, JHHM and Suijkerbuijk, KPM and , },
title = {Gut microbiome and immune checkpoint inhibitor toxicity.},
journal = {European journal of cancer (Oxford, England : 1990)},
volume = {216},
number = {},
pages = {115221},
doi = {10.1016/j.ejca.2025.115221},
pmid = {39793444},
issn = {1879-0852},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Immune Checkpoint Inhibitors/adverse effects ; Male ; Female ; Middle Aged ; Aged ; Prospective Studies ; *Neoplasms/drug therapy/microbiology ; Dysbiosis/chemically induced/microbiology ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: Multiple studies have suggested that gut microbiome may influence immune checkpoint inhibitor (ICI) efficacy, but its association with immune-related adverse events (irAEs) is less well studied. In this prospective cohort study, we assessed whether gut microbiome composition at start, or changes during ICI, are associated with severe irAEs.

METHODS: Stool samples of cancer patients treated with anti-PD-1 ± anti-CTLA-4 were analyzed using 16S rRNA gene sequencing and metagenomic shotgun sequencing. Differences in alpha and beta diversity between patients with and without severe irAE were assessed, as well as differential relative abundance (RA) of taxa, MetaCyc pathways, and seven prespecified literature-based bacterial groups including pathobionts and Ruminococcaceae.

FINDINGS: We analyzed 497 samples of 195 patients before and soon after starting ICI, at severe irAE onset and after starting immunosuppression. Mean RA of the pathobionts group was significantly higher in patients who developed a severe irAE (8.2 %) compared to those who did not (4.8 %; odds ratio 1.40; 95 %CI 1.07-1.87) at baseline, and also early during ICI treatment and at severe irAE onset. A significantly stronger decrease in RA of Ruminococcaceae after starting ICI was observed in patients who developed a severe irAE compared to those who did not. RAs of Ruminococcaceae, the genus Ruminococcus, and the species R. bromii and R. callidus were significantly lower at severe irAE onset compared to other time points.

INTERPRETATION: Gut microbiome dysbiosis signaled by higher RA of pathobionts and decrease in RA of Ruminococcaceae may predispose to severe irAEs.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Immune Checkpoint Inhibitors/adverse effects
Male
Female
Middle Aged
Aged
Prospective Studies
*Neoplasms/drug therapy/microbiology
Dysbiosis/chemically induced/microbiology
Adult
Feces/microbiology

@article {pmid39628067,
year = {2025},
author = {Fujimoto, S and Hatano, K and Banno, E and Motooka, D and De Velasco, MA and Kura, Y and Toyoda, S and Hashimoto, M and Adomi, S and Minami, T and Yoshimura, K and Oka, T and Hata, J and Matsushita, M and Takao, T and Takada, S and Tsujimura, A and Kojima, Y and Obara, W and Nakamura, S and Uemura, H and Nonomura, N and Fujita, K},
title = {Comparative analysis of gut microbiota in hormone-sensitive and castration-resistant prostate cancer in Japanese men.},
journal = {Cancer science},
volume = {116},
number = {2},
pages = {462-469},
doi = {10.1111/cas.16408},
pmid = {39628067},
issn = {1349-7006},
support = {//Yakult Bio-Science Foundation/ ; //The Japanese Foundation for Prostate Research (JFPR)/ ; //The Japanese Urological Association/ ; },
mesh = {Male ; *Gastrointestinal Microbiome/genetics ; Animals ; Humans ; *Prostatic Neoplasms, Castration-Resistant/microbiology/genetics/pathology ; Mice ; Aged ; Japan ; *RNA, Ribosomal, 16S/genetics ; Mice, Transgenic ; Middle Aged ; Mice, Knockout ; Disease Progression ; Lactobacillus/genetics/isolation & purification ; Aged, 80 and over ; Disease Models, Animal ; East Asian People ; },
abstract = {Gut microbiota plays a crucial role in the development and progression of prostate cancer, with previous studies indicating that certain bacterial taxa are more abundant in castration-resistant prostate cancer (CRPC) compared to hormone-sensitive prostate cancer (HSPC). Notably, the composition of gut microbiota can vary significantly by geographic region, and Japanese individuals have a distinct microbial profile. However, research exploring these differences within Japanese populations remains limited. This study investigated the gut microbiota differences between Japanese men with HSPC and CRPC and further validated these findings using a transgenic mouse model. Rectal swab samples were collected from 140 Japanese men diagnosed with HSPC (n = 84) or CRPC (n = 56) between September 2020 and July 2022. Gut microbiota composition was analyzed using 16S rRNA gene sequencing. Additionally, Pten-KO mice, which model the progression from HSPC to CRPC, underwent similar microbiota analysis. Results revealed significant differences in gut microbiota composition between HSPC and CRPC patients. Specifically, the CRPC group showed a higher abundance of Firmicutes, including Gemella and Lactobacillus, compared to the HSPC group. These differences were mirrored in the mouse model, where CRPC mice also showed an increase in these bacteria. This study identifies distinct microbial differences between HSPC and CRPC in Japanese men, suggesting that Gemella and Lactobacillus may be associated with the progression to castration resistance in prostate cancer. These findings suggest that gut microbiota differences may be associated with prostate cancer progression. Further research is needed to explore the potential of targeting the microbiota as a therapeutic strategy.},
}

Male
*Gastrointestinal Microbiome/genetics
Animals
Humans
*Prostatic Neoplasms, Castration-Resistant/microbiology/genetics/pathology
Mice
Aged
Japan
*RNA, Ribosomal, 16S/genetics
Mice, Transgenic
Middle Aged
Mice, Knockout
Disease Progression
Lactobacillus/genetics/isolation & purification
Aged, 80 and over
Disease Models, Animal
East Asian People

@article {pmid39745433,
year = {2025},
author = {Grüterich, L and Woodhouse, JN and Mueller, P and Tiemann, A and Ruscheweyh, H-J and Sunagawa, S and Grossart, H-P and Streit, WR},
title = {Assessing environmental gradients in relation to dark CO2 fixation in estuarine wetland microbiomes.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {1},
pages = {e0217724},
doi = {10.1128/aem.02177-24},
pmid = {39745433},
issn = {1098-5336},
support = {407270017//Deutsche Forschungsgemeinschaft (DFG)/ ; 502681570//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {*Wetlands ; *Carbon Dioxide/metabolism ; *Microbiota ; *Estuaries ; *Carbon Cycle ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Soil Microbiology ; },
abstract = {UNLABELLED: The rising atmospheric concentration of CO2 is a major concern to society due to its global warming potential. In soils, CO2-fixing microorganisms are preventing some of the CO2 from entering the atmosphere. Yet, the controls of dark CO2 fixation are rarely studied in situ. Here, we examined the gene and transcript abundance of key genes involved in microbial CO2 fixation along major environmental gradients within estuarine wetlands. A combined multi-omics approach incorporating metabarcoding, deep metagenomic, and metatranscriptomic analyses confirmed that wetland microbiota harbor four out of seven known CO2 fixation pathways, namely, the Calvin cycle, reverse tricarboxylic acid cycle, Wood-Ljungdahl pathway, and reverse glycine pathway. These pathways are transcribed at high frequencies along several environmental gradients, albeit at different levels depending on the environmental niche. Notably, the transcription of the key genes for the reverse tricarboxylic acid cycle was associated with high nitrate concentration, while the transcription of key genes for the Wood-Ljungdahl pathway was favored by reducing, O2-poor conditions. The transcript abundance of the Calvin cycle was favored by niches high in organic matter. Taxonomic assignment of transcripts implied that dark CO2 fixation was mainly linked to a few bacterial phyla, namely, Desulfobacterota, Methylomirabilota, Nitrospirota, Chloroflexota, and Pseudomonadota.

IMPORTANCE: The increasing concentration of atmospheric CO2 has been identified as the primary driver of climate change and poses a major threat to human society. This work explores the mostly overlooked potential of light-independent CO2 fixation by soil microbes (a.k.a. dark CO2 fixation) in climate change mitigation efforts. Applying a combination of molecular microbial tools, our research provides new insights into the ecological niches where CO2-fixing pathways are most active. By identifying how environmental factors, like oxygen, salinity and organic matter availability, influence these pathways in an estuarine wetland environment, potential strategies for enhancing natural carbon sinks can be developed. The importance of our research is in advancing the understanding of microbial CO2 fixation and its potential role in the global climate system.},
}

*Wetlands
*Carbon Dioxide/metabolism
*Microbiota
*Estuaries
*Carbon Cycle
*Bacteria/genetics/classification/metabolism/isolation & purification
Soil Microbiology

@article {pmid39714193,
year = {2025},
author = {Midot, F and Goh, KM and Liew, KJ and Lau, SYL and Espenberg, M and Mander, Ü and Melling, L},
title = {Temporal dynamics of soil microbial C and N cycles with GHG fluxes in the transition from tropical peatland forest to oil palm plantation.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {1},
pages = {e0198624},
doi = {10.1128/aem.01986-24},
pmid = {39714193},
issn = {1098-5336},
support = {P015 790102009//The Twelfth Malaysian Plan through Ministry of Education, Innovation, and Talent Development of Sarawak/ ; FRGS/1/2023/STG02/UTM/02/1,Q.J130000.3854.22H63//Ministry of Higher Education of Malaysia through the Fundamental Research Grant Scheme and UTM Fundamental Research Grant/ ; No 101079192 (MLTOM23003R)//European Union Horizon program/ ; No 101096403 (MLTOM23415R)//EC | European Research Council (ERC)/ ; PRG-2302//Estonian Research Council/ ; },
mesh = {*Soil Microbiology ; *Greenhouse Gases/analysis ; *Forests ; Malaysia ; *Microbiota ; Methane/metabolism/analysis ; Nitrogen Cycle ; Carbon Cycle ; Soil/chemistry ; Nitrous Oxide/analysis/metabolism ; Nitrogen/analysis/metabolism ; Carbon/analysis/metabolism ; Wetlands ; Bacteria/classification/genetics/metabolism/isolation & purification ; Arecaceae ; Agriculture ; },
abstract = {Tropical peatlands significantly influence local and global carbon and nitrogen cycles, yet they face growing pressure from anthropogenic activities. Land use changes, such as peatland forests conversion to oil palm plantations, affect the soil microbiome and greenhouse gas (GHG) emissions. However, the temporal dynamics of microbial community changes and their role as GHG indicators are not well understood. This study examines the dynamics of peat chemistry, soil microbial communities, and GHG emissions from 2016 to 2020 in a logged-over secondary peat swamp forest in Sarawak, Malaysia, which transitioned to an oil palm plantation. This study focuses on changes in genetic composition governing plant litter degradation, methane (CH4), and nitrous oxide (N2O) fluxes. Soil CO2 emission increased (doubling from approximately 200 mg C m[-2] h[-1]), while CH4 emissions decreased (from 200 µg C m[-2] h[-1] to slightly negative) following land use changes. The N2O emissions in the oil palm plantation reached approximately 1,510 µg N m[-2] h[-1], significantly higher than previous land uses. The CH4 fluxes were driven by groundwater table, humification levels, and C:N ratio, with Methanomicrobia populations dominating methanogenesis and Methylocystis as the main CH4 oxidizer. The N2O fluxes correlated with groundwater table, total nitrogen, and C:N ratio with dominant nirK-type denitrifiers (13-fold nir to nosZ) and a minor role by nitrification (a threefold increase in amoA) in the plantation. Proteobacteria and Acidobacteria encoding incomplete denitrification genes potentially impact N2O emissions. These findings highlighted complex interactions between microbial communities and environmental factors influencing GHG fluxes in altered tropical peatland ecosystems.IMPORTANCETropical peatlands are carbon-rich environments that release significant amounts of greenhouse gases when drained or disturbed. This study assesses the impact of land use change on a secondary tropical peat swamp forest site converted into an oil palm plantation. The transformation lowered groundwater levels and changed soil properties. Consequently, the oil palm plantation site released higher carbon dioxide and nitrous oxide compared to previous land uses. As microbial communities play crucial roles in carbon and nitrogen cycles, this study identified environmental factors associated with microbial diversity, including genes and specific microbial groups related to nitrous oxide and methane emissions. Understanding the factors driving microbial composition shifts and greenhouse gas emissions in tropical peatlands provides baseline information to potentially mitigate environmental consequences of land use change, leading to a broader impact on climate change mitigation efforts and proper land management practices.},
}

*Soil Microbiology
*Greenhouse Gases/analysis
*Forests
Malaysia
*Microbiota
Methane/metabolism/analysis
Nitrogen Cycle
Carbon Cycle
Soil/chemistry
Nitrous Oxide/analysis/metabolism
Nitrogen/analysis/metabolism
Carbon/analysis/metabolism
Wetlands
Bacteria/classification/genetics/metabolism/isolation & purification
Arecaceae
Agriculture

@article {pmid39679708,
year = {2025},
author = {Liu, Z and Jiang, C and Yin, Z and Ibrahim, IA and Zhang, T and Wen, J and Zhou, L and Jiang, G and Li, L and Yang, Z and Huang, Y and Yang, Z and Gu, Y and Meng, D and Yin, H},
title = {Ecological features of microbial community linked to stochastic and deterministic assembly processes in acid mine drainage.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {1},
pages = {e0102824},
doi = {10.1128/aem.01028-24},
pmid = {39679708},
issn = {1098-5336},
support = {2023YFE0114500//MOST | National Key Research and Development Program of China (NKPs)/ ; 92351303//MOST | National Natural Science Foundation of China (NSFC)/ ; BX20230437//Postdoctoral Fellowship Program of CPSF/ ; },
mesh = {*Microbiota ; *Mining ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Phylogeny ; Stochastic Processes ; Metagenomics ; Acids/metabolism ; Metagenome ; },
abstract = {UNLABELLED: Ecological processes greatly shape microbial community assembly, but the driving factors remain unclear. Here, we compiled a metagenomic data set of microbial communities from global acid mine drainage (AMD) and explored the ecological features of microbial community linked to stochastic and deterministic processes from the perspective of species niche position, interaction patterns, gene functions, and viral infection. Our results showed that dispersal limitation (DL) (48.5%~93.5%) dominated the assembly of phylogenetic bin in AMD microbial community, followed by homogeneous selection (HoS) (3.1%~39.2%), heterogeneous selection (HeS) (1.4%~22.2%), and drift (DR) (0.2%~2.7%). The dominant process of dispersal limitation was significantly influenced by niche position in temperature (r = -0.518, P = 0.007) and dissolved oxygen (r = 0.471, P = 0.015). Network stability had a significantly negative correlation with the relative importance of dispersal limitation, while it had a positive correlation with selection processes, implying changes in network properties could be mediated by ecological processes. Furthermore, we found that ecological processes were mostly related to the gene functions of energy production and conversion (C), and amino acid transport and metabolism (E). Meanwhile, our results showed that the number of proviruses and viral genes involved in arsenic (As) resistance is negatively associated with the relative importance of ecological drift in phylogenetic bin assembly, implying viral infection might weaken ecological drift. Taken together, these results highlight that ecological processes are associated with ecological features at multiple levels, providing a novel insight into microbial community assembly in extremely acidic environments.

IMPORTANCE: Unraveling the forces driving community assemblage is a core issue in microbial ecology, but how ecological constraints impose stochasticity and determinism remains unknown. This study presents a comprehensive investigation to uncover the association of ecological processes with species niche position, interaction patterns, microbial metabolisms, and viral infections, which provides novel insights into community assembly in extreme environments.},
}

*Microbiota
*Mining
*Bacteria/genetics/classification/isolation & purification/metabolism
Phylogeny
Stochastic Processes
Metagenomics
Acids/metabolism
Metagenome

@article {pmid39665561,
year = {2025},
author = {Unzueta-Martínez, A and Girguis, PR},
title = {Taxonomic diversity and functional potential of microbial communities in oyster calcifying fluid.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {1},
pages = {e0109424},
doi = {10.1128/aem.01094-24},
pmid = {39665561},
issn = {1098-5336},
support = {2109473//National Science Foundation (NSF)/ ; 9208//Gordon and Betty Moore Foundation (GBMF)/ ; },
mesh = {Animals ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Archaea/classification/genetics/metabolism ; Metagenomics ; Calcification, Physiologic ; Ostreidae/microbiology ; Biomineralization ; Viruses/classification/genetics ; Biodiversity ; },
abstract = {UNLABELLED: Creating and maintaining an appropriate chemical environment is essential for biomineralization, the process by which organisms precipitate minerals to form their shells or skeletons, yet the mechanisms involved in maintaining calcifying fluid chemistry are not fully defined. In particular, the role of microorganisms in facilitating or hindering animal biomineralization is poorly understood. Here, we investigated the taxonomic diversity and functional potential of microbial communities inhabiting oyster calcifying fluid. We used shotgun metagenomics to survey calcifying fluid microbial communities from three different oyster harvesting sites. There was a striking consistency in taxonomic composition across the three collection sites. We also observed archaea and viruses that had not been previously identified in oyster calcifying fluid. Furthermore, we identified microbial energy-conserving metabolisms that could influence the host's calcification, including genes involved in sulfate reduction and denitrification that are thought to play pivotal roles in inorganic carbon chemistry and calcification in microbial biofilms. These findings provide new insights into the taxonomy and functional capacity of oyster calcifying fluid microbiomes, highlighting their potential contributions to shell biomineralization, and contribute to a deeper understanding of the interplay between microbial ecology and biogeochemistry that could potentially bolster oyster calcification.

IMPORTANCE: Previous research has underscored the influence of microbial metabolisms in carbonate deposition throughout the geological record. Despite the ecological importance of microbes to animals and inorganic carbon transformations, there have been limited studies characterizing the potential role of microbiomes in calcification by animals such as bivalves. Here, we use metagenomics to investigate the taxonomic diversity and functional potential of microbial communities in calcifying fluids from oysters collected at three different locations. We show a diverse microbial community that includes bacteria, archaea, and viruses, and we discuss their functional potential to influence calcifying fluid chemistry via reactions like sulfate reduction and denitrification. We also report the presence of carbonic anhydrase and urease, both of which are critical in microbial biofilm calcification. Our findings have broader implications in understanding what regulates calcifying fluid chemistry and consequentially the resilience of calcifying organisms to 21st century acidifying oceans.},
}

Animals
*Microbiota
*Bacteria/classification/genetics/metabolism/isolation & purification
*Archaea/classification/genetics/metabolism
Metagenomics
Calcification, Physiologic
Ostreidae/microbiology
Biomineralization
Viruses/classification/genetics
Biodiversity

@article {pmid39651865,
year = {2025},
author = {Howland, KE and Mouradian, JJ and Uzarski, DR and Henson, MW and Uzarski, DG and Learman, DR},
title = {Nutrient amendments enrich microbial hydrocarbon degradation metagenomic potential in freshwater coastal wetland microcosm experiments.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {1},
pages = {e0197224},
doi = {10.1128/aem.01972-24},
pmid = {39651865},
issn = {1098-5336},
mesh = {*Wetlands ; *Biodegradation, Environmental ; *Fresh Water/microbiology ; *Hydrocarbons/metabolism ; Bacteria/genetics/metabolism/classification ; Metagenomics ; Petroleum/metabolism ; Geologic Sediments/microbiology ; Nutrients/metabolism ; Microbiota ; Metagenome ; Benzene Derivatives/metabolism ; Volatile Organic Compounds/metabolism ; Toluene/metabolism ; Benzene/metabolism ; Water Pollutants, Chemical/metabolism ; },
abstract = {UNLABELLED: Biostimulating native microbes with fertilizers has proven to be a highly effective strategy to speed up biodegradation rates in microbial communities. This study investigates the genetic potential of microbes to degrade light synthetic crude oil in a freshwater coastal wetland. Experimental sediment microcosms were exposed to a variety of conditions (biological control, a light synthetic crude oil amendment, and light synthetic crude oil with nutrient amendment) and incubated for 30 days before volatile organic compounds (BTEX) were quantified and DNA was sequenced for metagenomic analysis. The resulting DNA sequences were binned into metagenome-assembled genomes (MAGs). Analyses of MAGs uncovered a 13-fold significant increase in the abundance of rate-limiting hydrocarbon degrading monooxygenases and dioxygenases, identified only in MAGs from the light synthetic crude oil with nutrient amendments. Further, complete degradation pathways for BTEX compounds were found only in MAGs resulting from the light synthetic crude with nutrient amendment. Moreover, volatile organic compounds (BTEX, cyclohexane, and naphthalene) analyses of microcosm sediments in the presence of nutrients documented that benzene was degraded below detection limits, toluene (98%) and ethylbenzene (67%) were predominantly reduced within 30 days. Results indicate that the genetic potential to degrade BTEX compounds in this freshwater wetland can be linked to the functional potential for bioremediation. BTEX compounds are typically more recalcitrant and tougher to degrade than alkanes. This study demonstrated that stimulating a microbial community with nutrients to enhance its ability to biodegrade hydrocarbons, even in a relatively nutrient-rich habitat like a freshwater wetland, is an effective remediation tactic.

IMPORTANCE: The impact of oil spills in a freshwater aquatic environment can pose dire social, economic, and ecological effects on the region. An oil spill in the Laurentian Great Lakes region has the potential to affect the drinking water of more than 30 million people. The light synthetic crude oil used in this experimental microcosm study is transported through an underground pipeline crossing the waterway between two Laurentian Great Lakes. This study collected metagenomic data (experiments in triplicate) and assessed the quantity of BTEX compounds, which connected microbial degradation function to gene potential. The resulting data documented the bioremediation capabilities of native microbes in a freshwater coastal wetland. This study also provided evidence for this region that bioremediation can be a viable remediation strategy instead of invasive physical methods.},
}

*Wetlands
*Biodegradation, Environmental
*Fresh Water/microbiology
*Hydrocarbons/metabolism
Bacteria/genetics/metabolism/classification
Metagenomics
Petroleum/metabolism
Geologic Sediments/microbiology
Nutrients/metabolism
Microbiota
Metagenome
Benzene Derivatives/metabolism
Volatile Organic Compounds/metabolism
Toluene/metabolism
Benzene/metabolism
Water Pollutants, Chemical/metabolism

@article {pmid39641605,
year = {2025},
author = {Bao, Z and Chen, B and Yu, K and Wei, Y and Liang, X and Yao, H and Liao, X and Xie, W and Yin, K},
title = {Microbiome dynamics and functional profiles in deep-sea wood-fall micro-ecosystem: insights into drive pattern of community assembly, biogeochemical processes, and lignocellulose degradation.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {1},
pages = {e0216524},
doi = {10.1128/aem.02165-24},
pmid = {39641605},
issn = {1098-5336},
support = {42090041, 42030502//MOST | National Natural Science Foundation of China (NSFC)/ ; 42306165//MOST | National Natural Science Foundation of China (NSFC)/ ; No. 2023JJB150027//| Natural Science Foundation of Guangxi Zhuang Autonomous Region (Guangxi Natural Science Foundation)/ ; No. 311022005//Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2021SP204, SML2023SP215, SML2023SP218, SML2023SP205//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; },
mesh = {*Lignin/metabolism ; *Wood/microbiology/metabolism ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Fungi/genetics/classification/metabolism ; *Seawater/microbiology ; China ; Ecosystem ; Geologic Sediments/microbiology ; },
abstract = {Wood-fall micro-ecosystems contribute to biogeochemical processes in the oligotrophic deep ocean. However, the community assembly processes and biogeochemical functions of microbiomes in wood fall remain unclear. This study investigated the diversity, community structure, assembly processes, and functional profiles of bacteria and fungi in a deep-sea wood fall from the South China Sea using physicochemical indices, amplicon sequencing, and metagenomics. The results showed that distinct wood-fall contact surfaces exhibit habitat heterogeneity. The bacterial community of all contact surfaces and the fungal community of seawater contact surface (SWCS) were affected by homogeneous selection. In SWCS and transition region (TR), bacterial communities were influenced by dispersal limitation, whereas fungal communities were affected by homogenizing dispersal. The Venn diagram visualization revealed that the shared fungal community between SWCS and TR was dominated by Aspergillaceae. Additionally, the bacterial community demonstrated a higher genetic potential for sulfur, nitrogen, and methane metabolism than fungi. The sediment contact surface enriched modules were associated with dissimilatory sulfate reduction and methanogenesis, whereas the modules related to nitrate reduction exhibited enrichment characteristics in TR. Moreover, fungi showed a stronger potential for lignocellulase production compared to bacteria, with Microascaceae and Nectriaceae identified as potential contributors to lignocellulose degradation. These results indicate that environmental filtering and organism exchange levels regulated the microbial community assembly of wood fall. The biogeochemical cycling of sulfur, nitrogen, and methane was mainly driven by the bacterial community. Nevertheless, the terrestrial fungi Microascaceae and Nectriaceae might degrade lignocellulose via the combined action of multiple lignocellulases.IMPORTANCEThe presence and activity of microbial communities may play a crucial role in the biogeochemical cycle of deep-sea wood-fall micro-ecosystems. Previous studies on wood falls have focused on the microbiome diversity, community composition, and environmental impact, while few have investigated wood-fall micro-ecosystems by distinguishing among distinct contact surfaces. Our study investigated the microbiome dynamics and functional profiles of bacteria and fungi among distinct wood-fall contact surfaces. We found that the microbiome community assembly was regulated by environmental filtering and organism exchange levels. Bacteria drive the biogeochemical cycling of sulfur, nitrogen, and methane in wood fall through diverse metabolic pathways, whereas fungi are crucial for lignocellulose degradation. Ultimately, this study provides new insights into the driving pattern of community assembly, biogeochemical processes, and lignocellulose degradation in the microbiomes of deep-sea wood-fall micro-ecosystems, enhancing our comprehension of the ecological impacts of organic falls on deep-sea oligotrophic environments.},
}

*Lignin/metabolism
*Wood/microbiology/metabolism
*Microbiota
*Bacteria/classification/genetics/metabolism/isolation & purification
*Fungi/genetics/classification/metabolism
*Seawater/microbiology
China
Ecosystem
Geologic Sediments/microbiology

@article {pmid37480259,
year = {2024},
author = {Ahmad, V and Jamal, A and Khan, MI and Alzahrani, FA and Albiheyri, R and Jamal, QMS},
title = {Cefoperazone targets D-alanyl-D-alanine carboxypeptidase (DAC) to control Morganella morganii-mediated infection: a subtractive genomic and molecular dynamics approach.},
journal = {Journal of biomolecular structure & dynamics},
volume = {42},
number = {13},
pages = {6799-6812},
doi = {10.1080/07391102.2023.2238088},
pmid = {37480259},
issn = {1538-0254},
mesh = {*Morganella morganii/drug effects/enzymology ; *Enterobacteriaceae Infections/drug therapy ; *Cefoperazone/pharmacology ; Humans ; *Serine-Type D-Ala-D-Ala Carboxypeptidase/chemistry/metabolism ; *Metagenome ; Gastrointestinal Microbiome ; Escherichia coli Proteins/chemistry/metabolism ; Penicillin-Binding Proteins/chemistry/metabolism ; Escherichia coli/enzymology ; *Molecular Dynamics Simulation ; Molecular Conformation ; },
abstract = {Morganella morganii is a Gram-negative bacterial pathogen that causes bacteremia, urinary tract infections, intra-abdominal infections, chorioamnionitis, neonatal sepsis, and newborn meningitis. To control this bacterial pathogen a total of 3565 putative proteins targets in Morganella morganii were screened using comparative subtractive analysis of biochemical pathways annotated by the KEGG that did not share any similarities with human proteins. One of the targets, D-alanyl-D-alanine carboxypeptidase DacB [Morganella] was observed to be implicated in the majority of cell wall synthesis pathways, leading to its selection as a novel pharmacological target. The drug that interacted optimally with the identified target was observed to be Cefoperazone (DB01329) with the estimated free energy of binding -8.9 Kcal/mol. During molecular dynamics simulations; it was observed that DB01328-2exb and DB01329-2exb complexes showed similar values as the control FMX-2exb complex near 0.2 nm with better stability. Furthermore, MMPBSA total free energy calculation showed better binding energy than the control complex for DB01329-2exb interaction i.e. -31.50 (±0.93) kcal/mol. Our presented research suggested that D-alanyl-D-alanine carboxypeptidase DacB could be a therapeutic target and cefoperazone could be a promising ligand to inhibit the D-alanyl-D-alanine carboxypeptidase DacB protein of Morganella morganii. To identify prospective therapeutic and vaccine targets in Morganella morganii, this is the first computational and subtractive genomics investigation of various metabolic pathways exploring other therapeutic targets of Morganella morganii. In vitro/in vivo experimental validation of the identified target D-alanyl-D-alanine carboxypeptidase and the design of its inhibitors is suggested to figure out the best dose, the drug's effectiveness, and its toxicity.Communicated by Ramaswamy H. Sarma.},
}

*Morganella morganii/drug effects/enzymology
*Enterobacteriaceae Infections/drug therapy
*Cefoperazone/pharmacology
Humans
*Serine-Type D-Ala-D-Ala Carboxypeptidase/chemistry/metabolism
*Metagenome
Gastrointestinal Microbiome
Escherichia coli Proteins/chemistry/metabolism
Penicillin-Binding Proteins/chemistry/metabolism
Escherichia coli/enzymology
*Molecular Dynamics Simulation
Molecular Conformation

@article {pmid39885140,
year = {2025},
author = {Shao, B and Xie, YG and Zhang, L and Ruan, Y and Liang, B and Zhang, R and Xu, X and Wang, W and Lin, Z and Pei, X and Wang, X and Zhao, L and Zhou, X and Wu, X and Xing, D and Wang, A and Lee, DJ and Ren, N and Canfield, DE and Hedlund, BP and Hua, ZS and Chen, C},
title = {Versatile nitrate-respiring heterotrophs are previously concealed contributors to sulfur cycle.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1202},
pmid = {39885140},
issn = {2041-1723},
support = {52076063//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52100035//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52400025//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52300155//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52321005//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32170014//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023DX04//State Key Laboratory of Urban Water Resource and Environment (SKLUWRE)/ ; 2024M754204//China Postdoctoral Science Foundation/ ; 2023M740917//China Postdoctoral Science Foundation/ ; },
mesh = {*Sulfur/metabolism ; *Nitrates/metabolism ; *Heterotrophic Processes ; *Denitrification ; *Oxidation-Reduction ; Bacteria/metabolism/genetics ; Geologic Sediments/microbiology ; Nitrous Oxide/metabolism ; Microbiota ; Sulfides/metabolism ; Metagenomics ; Greenhouse Gases/metabolism ; },
abstract = {Heterotrophic denitrifiers play crucial roles in global carbon and nitrogen cycling. However, their inability to oxidize sulfide renders them vulnerable to this toxic molecule, which inhibits the key enzymatic reaction responsible for reducing nitrous oxide (N2O), thereby raising greenhouse gas emissions. Here, we applied microcosm incubations, community-isotope-corrected DNA stable-isotope probing, and metagenomics to characterize a cohort of heterotrophic denitrifiers in estuarine sediments that thrive by coupling sulfur oxidation with denitrification through chemolithoheterotrophic metabolism. Remarkably, ecophysiology experiments from enrichments demonstrate that such heterotrophs expedite denitrification with sulfur acting as alternative electron sources and substantially curtail N2O emissions in both organic-rich and organic-limited environments. Their flexible, non-sulfur-dependent physiology may confer competitive advantages over conventional heterotrophic denitrifiers in detoxifying sulfide, adapting to organic matter fluctuations, and mitigating greenhouse gas emissions. Our study provides insights into the ecological role of heterotrophic denitrifiers in microbial communities with implications for sulfur cycling and climate change.},
}

*Sulfur/metabolism
*Nitrates/metabolism
*Heterotrophic Processes
*Denitrification
*Oxidation-Reduction
Bacteria/metabolism/genetics
Geologic Sediments/microbiology
Nitrous Oxide/metabolism
Microbiota
Sulfides/metabolism
Metagenomics
Greenhouse Gases/metabolism

@article {pmid39885121,
year = {2025},
author = {Nooij, S and Plomp, N and Sanders, IMJG and Schout, L and van der Meulen, AE and Terveer, EM and Norman, JM and Karcher, N and Larralde, MF and Vossen, RHAM and Kloet, SL and Faber, KN and Harmsen, HJM and Zeller, GF and Kuijper, EJ and Smits, WK and Ducarmon, QR},
title = {Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1182},
pmid = {39885121},
issn = {2041-1723},
mesh = {Humans ; *Crohn Disease/microbiology/genetics ; *Metagenomics/methods ; *Genome, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; Health Status ; Genome-Wide Association Study ; Clostridiales/genetics/isolation & purification ; Life Style ; Phylogeny ; Infant, Newborn ; Genomics ; Female ; Male ; Adult ; Virulence Factors/genetics ; },
abstract = {Ruminococcus gnavus is a gut bacterium found in > 90% of healthy individuals, but its increased abundance is also associated with chronic inflammatory diseases, particularly Crohn's disease. Nevertheless, its global distribution and intraspecies genomic variation remain understudied. By surveying 12,791 gut metagenomes, we recapitulated known associations with metabolic diseases and inflammatory bowel disease. We uncovered a higher prevalence and abundance of R. gnavus in Westernized populations and observed bacterial relative abundances up to 83% in newborns. Next, we built a resource of R. gnavus isolates (N = 45) from healthy individuals and Crohn's disease patients and generated complete R. gnavus genomes using PacBio circular consensus sequencing. Analysis of these genomes and publicly available high-quality draft genomes (N = 333 genomes) revealed multiple clades which separated Crohn's-derived isolates from healthy-derived isolates. Presumed R. gnavus virulence factors could not explain this separation. Bacterial genome-wide association study revealed that Crohn's-derived isolates were enriched in genes related to mobile elements and mucin foraging. Together, we present a large R. gnavus resource that will be available to the scientific community and provide novel biological insights into the global distribution and genomic variation of R. gnavus.},
}

Humans
*Crohn Disease/microbiology/genetics
*Metagenomics/methods
*Genome, Bacterial/genetics
*Gastrointestinal Microbiome/genetics
Metagenome/genetics
Health Status
Genome-Wide Association Study
Clostridiales/genetics/isolation & purification
Life Style
Phylogeny
Infant, Newborn
Genomics
Female
Male
Adult
Virulence Factors/genetics

@article {pmid39881417,
year = {2025},
author = {Ye, GC and Peng, H and Xiang, JC and Miao, LT and Liu, CZ and Wang, SG and Xia, QD},
title = {Comprehensive analysis of the interaction microbiome and prostate cancer: an initial exploration from multi-cohort metagenome and GWAS studies.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {130},
pmid = {39881417},
issn = {1479-5876},
mesh = {Humans ; Male ; *Prostatic Neoplasms/microbiology/genetics/pathology ; *Metagenome/genetics ; *Genome-Wide Association Study ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Neoplasm Metastasis ; Mendelian Randomization Analysis ; },
abstract = {INTRODUCTION: Prostate cancer is one of the most common cancers in the United States with a high mortality rate. In recent years, the traditional opinion about prostate microbiome was challenged. Although there still are some arguments, an escalating number of researchers are shifting their focus toward the microbiome within the prostate tumor environment.

METHODS: We mined the data of the microbiome extracted from the metagenome, and it offers a broader taxonomic coverage and accurate functional profiling. We used Kraken2, a mapping tool, to mine the gut microbiota of prostate cancer patients. A two-sample Mendelian Randomization was conducted to reflect the association between gut microbiome and cancer.

RESULTS: In the study, we found the consistency of the special intratumor microbiome of both non-metastatic tumors and metastatic tumors. And we dig the gut microbiome in patients with different treatments. We found that some microbiotas may be associated with prostate cancer progression and a special microbiome in metastatic prostate cancer may exist. The anti-androgen therapy can significantly change both the intratumor and gut microbiome.

CONCLUSION: With the progression and metastasis of prostate cancer, some intratumor microbiome changes. And anti-androgen influences both the intratumor and gut microbiome. Our discovery may help researchers further understand the progression, metastasis, and resistance of prostate cancer from the perspective of microbiome level.},
}

Humans
Male
*Prostatic Neoplasms/microbiology/genetics/pathology
*Metagenome/genetics
*Genome-Wide Association Study
*Gastrointestinal Microbiome/genetics
Cohort Studies
Neoplasm Metastasis
Mendelian Randomization Analysis

@article {pmid39881387,
year = {2025},
author = {Pangga, GM and Star-Shirko, B and Psifidi, A and Xia, D and Corcionivoschi, N and Kelly, C and Hughes, C and Lavery, U and Richmond, A and Ijaz, UZ and Gundogdu, O},
title = {Impact of commercial gut health interventions on caecal metagenome and broiler performance.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {30},
pmid = {39881387},
issn = {2049-2618},
support = {BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome ; *Cecum/microbiology ; *Metagenome ; *Probiotics/administration & dosage ; Prebiotics ; Bacteria/classification/genetics/isolation & purification ; Animal Feed/microbiology ; Vaccination/veterinary ; Dietary Supplements ; },
abstract = {BACKGROUND: Maintaining gut health is a persistent and unresolved challenge in the poultry industry. Given the critical role of gut health in chicken performance and welfare, there is a pressing need to identify effective gut health intervention (GHI) strategies to ensure optimal outcomes in poultry farming. In this study, across three broiler production cycles, we compared the metagenomes and performance of broilers provided with ionophores (as the control group) against birds subjected to five different GHI combinations involving vaccination, probiotics, prebiotics, essential oils, and reduction of ionophore use.

RESULTS: Using a binning strategy, 84 (≥ 75% completeness, ≤ 5% contamination) metagenome-assembled genomes (MAGs) from 118 caecal samples were recovered and annotated for their metabolic potential. The majority of these (n = 52, 61%) had a differential response across all cohorts and are associated with the performance parameter - European poultry efficiency factor (EPEF). The control group exhibited the highest EPEF, followed closely by the cohort where probiotics are used in conjunction with vaccination. The use of probiotics B, a commercial Bacillus strain-based formulation, was determined to contribute to the superior performance of birds. GHI supplementation generally affected the abundance of microbial enzymes relating to carbohydrate and protein digestion and metabolic pathways relating to energy, nucleotide synthesis, short-chain fatty acid synthesis, and drug-transport systems. These shifts are hypothesised to differentiate performance among groups and cycles, highlighting the beneficial role of several bacteria, including Rikenella microfusus and UBA7160 species.

CONCLUSIONS: All GHIs are shown to be effective methods for gut microbial modulation, with varying influences on MAG diversity, composition, and microbial functions. These metagenomic insights greatly enhance our understanding of microbiota-related metabolic pathways, enabling us to devise strategies against enteric pathogens related to poultry products and presenting new opportunities to improve overall poultry performance and health. Video Abstract.},
}

Animals
*Chickens/microbiology
*Gastrointestinal Microbiome
*Cecum/microbiology
*Metagenome
*Probiotics/administration & dosage
Prebiotics
Bacteria/classification/genetics/isolation & purification
Animal Feed/microbiology
Vaccination/veterinary
Dietary Supplements

@article {pmid39765196,
year = {2025},
author = {Caballero-Gómez, J and Ávalos, G and Matas-Méndez, P and Figueiredo, AM and Castro-Scholten, S and Jiménez-Martín, D and Köster, PC and Santín, M and Bailo, B and Cano-Terriza, D and Sarmento, P and Neves, N and Carrapato, C and González-Barrio, D and Mateo, M and García-Bocanegra, I and Dashti, A and Sánchez, S and Carmena, D},
title = {Dietary profiles of wild carnivores and Blastocystis occurrence: The case of the endangered Iberian lynx (Lynx pardinus) and systematic review.},
journal = {Research in veterinary science},
volume = {184},
number = {},
pages = {105518},
doi = {10.1016/j.rvsc.2024.105518},
pmid = {39765196},
issn = {1532-2661},
mesh = {Animals ; *Lynx/parasitology ; *Blastocystis/genetics/isolation & purification ; Portugal ; Spain ; *Feces/parasitology ; *Endangered Species ; *Animals, Wild/parasitology ; Diet/veterinary ; Blastocystis Infections/veterinary/epidemiology ; },
abstract = {Recent molecular and metagenomic studies have revealed that the obligate anaerobic protist Blastocystis is found more prevalently and with higher subtype diversities in herbivore species than in carnivore species. However, information on wild carnivore species is scarce. Here, we investigated the presence of Blastocystis by molecular methods in fecal DNA samples of free-ranging and captive Iberian lynxes from Spain (n = 243) and Portugal (n = 30). In addition, a systematic review was conducted to obtain information on the Blastocystis prevalence rates and subtype diversities reported in free-living and captive wild carnivores worldwide during the period 2000-2024. Blastocystis was not detected by PCR in any of the samples investigated. Analyses of the data gathered from our systematic review revealed that Blastocystis is uncommon either in free-living (2.1 %, 29/1377) or captive (8.5 %, 100/1175) wild carnivore species. Many of these findings seem to result from accidental acquisition via prey animals, scavenging, contaminated water/feed (free-ranging wild carnivores), or cross-species transmission among animals sharing enclosures (captive wild carnivores). Comparative metagenomic studies analyzing gut microbiota profiles of carnivores are needed to fully understand how microbial communities affect Blastocystis colonization.},
}

Animals
*Lynx/parasitology
*Blastocystis/genetics/isolation & purification
Portugal
Spain
*Feces/parasitology
*Endangered Species
*Animals, Wild/parasitology
Diet/veterinary
Blastocystis Infections/veterinary/epidemiology

@article {pmid38490247,
year = {2025},
author = {Ahmed, S and Mahapatra, S and Mishra, R and Murmu, KC and Padhan, P and Prasad, P and Misra, R},
title = {16s RNA-based metagenomics reveal previously unreported gut microbiota associated with reactive arthritis and undifferentiated peripheral spondyloarthritis.},
journal = {Rheumatology (Oxford, England)},
volume = {64},
number = {2},
pages = {870-879},
doi = {10.1093/rheumatology/keae165},
pmid = {38490247},
issn = {1462-0332},
support = {//APLAR/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Arthritis, Reactive/microbiology ; Female ; Male ; Adult ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Prohibitins ; *Spondylarthritis/microbiology ; Middle Aged ; Case-Control Studies ; Feces/microbiology ; Young Adult ; },
abstract = {OBJECTIVES: Reactive arthritis (ReA) provides a unique opportunity to comprehend how a mucosal infection leads to inflammatory arthritis at a distant site without the apparent invasion of the pathogen. Unfortunately, conventional stool cultures after ReA provide limited information, and there is a dearth of metagenomic studies in ReA. The objective of this study was to identify gut microbiota associated with the development of ReA.

METHODS: Patients with ReA or undifferentiated peripheral spondyloarthritis (UpSpA) were included if they presented within 4 weeks of the onset of the current episode of arthritis. Metagenomic DNA was extracted from the stools of these patients and of 36 age- and sex-similar controls. Sequencing and analysis were done using a standard 16S ribosomal pipeline.

RESULTS: Of 55 patients, there was no difference between the gut microbiota of postdiarrheal ReA (n = 20) and of upSpA (n = 35). Comparing the gut microbiota of patients vs healthy controls, the patients had significantly higher alpha and beta diversity measures. After stringency filters, Proteobacteria had high abundance while Firmicutes had lesser as compared with the controls. Six families were overexpressed in patients, while another five were overexpressed in controls. Sixteen genera and 18 species were significantly different between patients and controls. At the species level there was strong association of Staphylococcus aureus, Clostridium septicum Klebsiella pneumoniae, Escherichia coli, Empedobacter brevis, Roseburia hominis, Bacillus velezensis and Crassaminicella with ReA.

CONCLUSION: The microbiota of classical gut-associated ReA and upSpA is similar. Patients have higher diversities in their gut microbiota compared with healthy controls. Both known and previously unreported species associated with ReA/upSpA were identified.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Arthritis, Reactive/microbiology
Female
Male
Adult
*RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Prohibitins
*Spondylarthritis/microbiology
Middle Aged
Case-Control Studies
Feces/microbiology
Young Adult

@article {pmid39881163,
year = {2025},
author = {Dash, M and Thiyageshwari, S and Selvi, D and Johnson, HKV and Ariyan, M and Rajan, K and Anandham, R},
title = {Unveiling microbial diversity in slightly and moderately magnesium deficient acidic soils.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3696},
pmid = {39881163},
issn = {2045-2322},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Magnesium/metabolism/analysis ; *RNA, Ribosomal, 16S/genetics ; India ; Bacteria/genetics/classification/metabolism ; Metagenomics/methods ; Biodiversity ; Magnesium Deficiency/genetics ; Phosphorus/deficiency/metabolism ; Microbiota/genetics ; },
abstract = {Magnesium (Mg) an essential plant nutrient is widespread deficient in the acidic soils of Nilgiris of Tamil nadu, India. The vegetable yield and quality is especially affected due to deficiency of nutrients like Mg. This study investigates soil characteristics and bacterial diversity in the Nilgiris district of Tamil Nadu, India, with respect to Mg deficiency. The soil samples were collected from different vegetable growing regions of the Nilgiris to assess soil physiocochemical parameters, soil enzymes and soil Mg status. 16S rRNA gene-based metagenomic analysis used to investigate the functional potential and structural diversity of the bacterial communities in high Mg and low Mg deficiency soil. Results indicated mildly acidic soils with a sandy loam texture and high organic carbon content. While nitrogen (N), phosphorus (P), and potassium (K) levels were adequate, Mg deficiency was consistent. Soil enzymes such as dehydrogenase, acid phosphatase, urease and aryl sulfatase, varied across the soil samples. Additionally, 16S rRNA gene-based metagenomics analysis revealed the bacterial diversity and functional pathways in soils with high and low Mg deficiency. Low Mg levels were associated with increased bacterial richness, dominated by Proteobacteria, Gemmatimonadetes, Actinobacteria, Bacteroidetes, and Acidobacteria. Functional pathways related to carbon metabolism, amino acid biosynthesis, and various metabolic processes were more abundant in low Mg deficient soils. This research highlights the significant influence of Mg levels on bacterial diversity and functional potentials in acidic soils, providing insights into soil management strategies in Mg-deficient regions.},
}

*Soil Microbiology
*Soil/chemistry
*Magnesium/metabolism/analysis
*RNA, Ribosomal, 16S/genetics
India
Bacteria/genetics/classification/metabolism
Metagenomics/methods
Biodiversity
Magnesium Deficiency/genetics
Phosphorus/deficiency/metabolism
Microbiota/genetics

@article {pmid39876003,
year = {2025},
author = {Li, Q and Huo, J and Ni, G and Zhang, F and Zhang, S and Zhang, X and Wang, R and Jiao, J and Yu, Z and Pu, X and Yue, Y and Ungerfeld, EM and Zhang, X and Wu, J and Tan, Z and Greening, C and Wang, M},
title = {Reductive acetogenesis is a dominant process in the ruminant hindgut.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {28},
pmid = {39876003},
issn = {2049-2618},
mesh = {Animals ; *Rumen/microbiology ; *Goats/microbiology ; *Cecum/microbiology ; *Hydrogen/metabolism ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Gastrointestinal Microbiome ; *Fermentation ; *Acetates/metabolism ; *Fatty Acids, Volatile/metabolism ; Archaea/classification/metabolism/genetics ; Ruminants/microbiology ; Methane/metabolism ; },
abstract = {BACKGROUND: The microbes residing in ruminant gastrointestinal tracts play a crucial role in converting plant biomass to volatile fatty acids, which serve as the primary energy source for ruminants. This gastrointestinal tract comprises a foregut (rumen) and hindgut (cecum and colon), which differ in structures and functions, particularly with respect to feed digestion and fermentation. While the rumen microbiome has been extensively studied, the cecal microbiome remains much less investigated and understood, especially concerning the assembling microbial communities and overriding pathways of hydrogen metabolism.

RESULTS: To address this gap, we comparatively investigated the composition, capabilities, and activities of the rumen and the cecum microbiome using goats as an experimental ruminant model. In situ measurements showed significantly higher levels of dissolved hydrogen and acetate in the cecum than in the rumen. Increased dissolved hydrogen indicated distinct processes and reduced coupling between fermentative H2 production and utilization, whereas higher levels of acetate could be caused by slower VFA absorption through cecal papillae than through the rumen papillae. Microbial profiling indicated that the cecum harbors a greater abundance of mucin-degrading microbes and fermentative hydrogen producers, whereas the rumen contains a higher abundance of fibrolytic fermentative bacteria, hydrogenotrophic respiratory bacteria, and methanogenic archaea. Most strikingly, reductive acetogenic bacteria were 12-fold more abundant in the cecum. Genome-resolved metagenomic analysis unveiled that the cecum acetogens are both phylogenetically and functionally distinct from those found in the rumen. Further supporting these findings, two in vitro experiments demonstrated a marked difference in hydrogen metabolism pathways between the cecum and the rumen, with increased acetate production and reduced methanogenesis in the cecum. Moreover, comparative analysis across multiple ruminant species confirmed a strong enrichment of reductive acetogens in the hindguts, suggesting a conserved functional role.

CONCLUSIONS: These findings highlight an enrichment of acetogenesis in a key region of the gastrointestinal tract and reshape our understanding of ruminant hydrogen metabolism and how the H2 can be managed in accord to livestock methane mitigation efforts. Video Abstract.},
}

Animals
*Rumen/microbiology
*Goats/microbiology
*Cecum/microbiology
*Hydrogen/metabolism
*Bacteria/classification/metabolism/genetics/isolation & purification
*Gastrointestinal Microbiome
*Fermentation
*Acetates/metabolism
*Fatty Acids, Volatile/metabolism
Archaea/classification/metabolism/genetics
Ruminants/microbiology
Methane/metabolism

@article {pmid39742975,
year = {2025},
author = {Dougherty, PE and Pedersen, MS and Forero-Junco, LM and Carstens, AB and Raaijmakers, JM and Riber, L and Hansen, LH},
title = {Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks.},
journal = {Virus research},
volume = {352},
number = {},
pages = {199524},
doi = {10.1016/j.virusres.2024.199524},
pmid = {39742975},
issn = {1872-7492},
mesh = {*Triticum/microbiology/virology ; *Bacteriophages/genetics/classification/isolation & purification/physiology ; *Phylogeny ; *Genome, Viral ; DNA, Viral/genetics ; DNA Breaks, Single-Stranded ; Erwinia/virology/genetics ; Pseudomonas/virology/genetics ; Metagenome ; Microbiota ; Pseudomonas Phages/genetics/classification/isolation & purification ; Bacteria/virology/genetics/classification ; },
abstract = {The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequence eight novel phages targeting common phyllosphere Erwinia and Pseudomonas strains, including two jumbo phages. We characterize genomic, phylogenetic, and morphological traits from these phages and argue for establishing four novel viral genera. We also search the genomes for anti-defense systems and investigate DNA modifications using Nanopore sequencing. In Pseudomonas phage Rembedalsseter we find evidence of 13 motif-associated single-stranded DNA breaks. A bioinformatics search revealed that 60 related Pseudomonas phages are enriched in the same motif, suggesting these single-stranded nicks may be widely distributed in this family of phages. Finally, we also search the Sequence Read Archive for similar phages in public metagenomes. We find close hits to the Erwinia jumbo-phage Kaldavass in a wide variety of plant, food, and wastewater metagenomes including a near-perfect hit from a Spanish spinach sample, illustrating how interconnected geographically distant phages can be.},
}

*Triticum/microbiology/virology
*Bacteriophages/genetics/classification/isolation & purification/physiology
*Phylogeny
*Genome, Viral
DNA, Viral/genetics
DNA Breaks, Single-Stranded
Erwinia/virology/genetics
Pseudomonas/virology/genetics
Metagenome
Microbiota
Pseudomonas Phages/genetics/classification/isolation & purification
Bacteria/virology/genetics/classification

@article {pmid39875829,
year = {2025},
author = {Zhang, Z and Zong, X and Liu, Z and Dong, X and Bai, H and Fan, L and Li, T},
title = {Comprehensive analysis of vaginal microbiota in Chinese women with genital tuberculosis: implications for diagnosis and treatment.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {52},
pmid = {39875829},
issn = {1471-2180},
support = {2024-4-2119//Capital's Funds for Health Improvement and Research/ ; FCYY201916//Special Training Program for Young and Middle-aged Subject Backbone of Beijing Obstetrics and Gynecology Hospital, Capital Medical University/ ; YQRC201906//"Excellent young Talents" project of Beijing Obstetrics and Gynecology Hospital, Capital Medical University/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; Adult ; *Tuberculosis, Female Genital/microbiology/diagnosis ; *Microbiota ; China ; Middle Aged ; Young Adult ; Antitubercular Agents/therapeutic use ; Lactobacillus/isolation & purification/genetics ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; East Asian People ; },
abstract = {BACKGROUND: Tuberculosis remains an infectious disease of global concern, with potential impacts on respiratory and intestinal microbiota owing to prolonged broad-spectrum antibiotic therapy. Despite its potential to cause infertility, the vaginal microbiota of women with genital tuberculosis remains poorly understood. We comprehensively analyzed the vaginal microbiota in Chinese women with genital tuberculosis.

RESULTS: We recruited women with pelvic (n = 28), endometrial (n = 16), and pulmonary (n = 12) tuberculosis as the research group, and healthy women (n = 11) as the control group. Vaginal discharges were collected for metagenomic analysis of its microbiota. The alpha diversity of the vaginal microbiota in women with genital tuberculosis was slightly higher than that in healthy women, though the difference was not statistically significant (P = 0.23). Similarly, no significant differences in alpha diversity were observed between women with genital and pulmonary tuberculosis (P = 0.82) or between those with pelvic and endometrial tuberculosis (P = 0.82). Notably, the lowest alpha diversity was recorded six months to one year after initiating anti-tuberculosis treatment, with this decline being statistically significant (P = 0.023). The dominance of Lactobacillus iners in the vaginal microbiota was more common in women with genital tuberculosis than that of Lactobacillus crispatus. Furthermore, the abundance of short-chain fatty acid -producing anaerobes, such as Actinomycetes, Streptococcus, and Finegoldia, were significantly increased. Short-chain fatty acid precursor pathways, including the ko03010 ribosome pathway, ko00970 aminoacyl-tRNA synthesis, ko00230 purine metabolism, ko00240 pyrimidine metabolism, and ko00010 glycolysis gluconeogenesis pathway, were significantly upregulated in women with endometrial tuberculosis.

CONCLUSIONS: Extrapulmonary tuberculosis, particularly genital tuberculosis and its associated vaginal dysbiosis impacts female fecundity. Vaginal dysbiosis is more pronounced when M. tuberculosis invades the endometrium. Given the effect of antibiotics on vaginal flora, probiotic combined interventions could be used as a future research direction.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Humans
Female
*Vagina/microbiology
Adult
*Tuberculosis, Female Genital/microbiology/diagnosis
*Microbiota
China
Middle Aged
Young Adult
Antitubercular Agents/therapeutic use
Lactobacillus/isolation & purification/genetics
Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
East Asian People

@article {pmid39875095,
year = {2025},
author = {Moeller, AH},
title = {Partner fidelity, not geography, drives co-diversification of gut microbiota with hominids.},
journal = {Biology letters},
volume = {21},
number = {1},
pages = {20240454},
doi = {10.1098/rsbl.2024.0454},
pmid = {39875095},
issn = {1744-957X},
support = {/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Phylogeny ; Hominidae/microbiology ; Bacteria/classification/genetics/isolation & purification ; Genome, Bacterial ; Geography ; },
abstract = {Bacterial strains that inhabit the gastrointestinal tracts of hominids have diversified in parallel (co-diversified) with their host species. The extent to which co-diversification has been mediated by partner fidelity between strains and hosts or by geographical distance between hosts is not clear due to a lack of strain-level data from clades of hosts with unconfounded phylogenetic relationships and geographical distributions. Here, I tested these competing hypotheses through meta-analyses of 7121 gut bacterial genomes assembled from wild-living ape species and subspecies sampled throughout their ranges in equatorial Africa. Across the gut bacterial phylogeny, strain diversification was more strongly associated with host phylogeny than with geography. In total, approximately 14% of the branch length of the gut bacterial phylogeny showed significant evidence of co-diversification independent of geography, whereas only approximately 4% showed significant evidence of diversification associated with geography independent of host phylogeny. Geographically co-occurring heterospecific hosts (Pan and Gorilla) universally maintained distinct co-diversified bacterial strains. Strains whose diversification was associated with geography independent of host phylogeny included clades of Proteobacteria known to adopt free-living lifestyles (e.g. Escherichia). These results show that co-diversification of gut bacterial strains with hominids has been driven primarily by fidelity of strains to host lineages rather than geography.},
}

Animals
*Gastrointestinal Microbiome
*Phylogeny
Hominidae/microbiology
Bacteria/classification/genetics/isolation & purification
Genome, Bacterial
Geography

@article {pmid39874239,
year = {2025},
author = {Zhou, H and Balint, D and Shi, Q and Vartanian, T and Kriegel, MA and Brito, I},
title = {Lupus and inflammatory bowel disease share a common set of microbiome features distinct from other autoimmune disorders.},
journal = {Annals of the rheumatic diseases},
volume = {84},
number = {1},
pages = {93-105},
doi = {10.1136/ard-2024-225829},
pmid = {39874239},
issn = {1468-2060},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/immunology ; *Lupus Erythematosus, Systemic/microbiology/immunology ; *Gastrointestinal Microbiome/genetics ; *Autoimmune Diseases/microbiology/immunology ; Biomarkers ; Female ; Metagenomics/methods ; Metagenome ; Male ; Receptors, Glucocorticoid/genetics ; },
abstract = {OBJECTIVES: This study aims to elucidate the microbial signatures associated with autoimmune diseases, particularly systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), compared with colorectal cancer (CRC), to identify unique biomarkers and shared microbial mechanisms that could inform specific treatment protocols.

METHODS: We analysed metagenomic datasets from patient cohorts with six autoimmune conditions-SLE, IBD, multiple sclerosis, myasthenia gravis, Graves' disease and ankylosing spondylitis-contrasting these with CRC metagenomes to delineate disease-specific microbial profiles. The study focused on identifying predictive biomarkers from species profiles and functional genes, integrating protein-protein interaction analyses to explore effector-like proteins and their targets in key signalling pathways.

RESULTS: Distinct microbial signatures were identified across autoimmune disorders, with notable overlaps between SLE and IBD, suggesting shared microbial underpinnings. Significant predictive biomarkers highlighted the diverse microbial influences across these conditions. Protein-protein interaction analyses revealed interactions targeting glucocorticoid signalling, antigen presentation and interleukin-12 signalling pathways, offering insights into possible common disease mechanisms. Experimental validation confirmed interactions between the host protein glucocorticoid receptor (NR3C1) and specific gut bacteria-derived proteins, which may have therapeutic implications for inflammatory disorders like SLE and IBD.

CONCLUSIONS: Our findings underscore the gut microbiome's critical role in autoimmune diseases, offering insights into shared and distinct microbial signatures. The study highlights the potential importance of microbial biomarkers in understanding disease mechanisms and guiding treatment strategies, paving the way for novel therapeutic approaches based on microbial profiles.

TRIAL REGISTRATION NUMBER: NCT02394964.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/immunology
*Lupus Erythematosus, Systemic/microbiology/immunology
*Gastrointestinal Microbiome/genetics
*Autoimmune Diseases/microbiology/immunology
Biomarkers
Female
Metagenomics/methods
Metagenome
Male
Receptors, Glucocorticoid/genetics

@article {pmid39871406,
year = {2025},
author = {Noell, SE and Abbaszadeh, J and Richards, H and Labat Saint Vincent, M and Lee, CK and Herbold, CW and Stott, MB and Cary, SC and McDonald, IR},
title = {Antarctic Geothermal Soils Exhibit an Absence of Regional Habitat Generalist Microorganisms.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70032},
doi = {10.1111/1462-2920.70032},
pmid = {39871406},
issn = {1462-2920},
support = {18-UOW-028//Marsden Fund/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Archaea/classification/genetics ; *Bacteria/classification/isolation & purification/genetics ; *Ecosystem ; Microbiota ; Phylogeny ; Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Active geothermal systems are relatively rare in Antarctica and represent metaphorical islands ideal to study microbial dispersal. In this study, we tested the macro-ecological concept that high dispersal rates result in communities being dominated by either habitat generalists or specialists by investigating the microbial communities on four geographically separated geothermal sites on three Antarctic volcanoes (Mts. Erebus, Melbourne, and Rittman). We found that the microbial communities at higher temperature (max 65°C) sites (Tramway Ridge on Erebus and Rittmann) were unique from each other and were dominated by a variety of novel Archaea from class Nitrososphaeria, while lower temperature (max 50°C) sites (Western Crater on Erebus and Melbourne) had characteristically mesophilic communities (Planctomycetes, Acidobacteriota, etc.) that were highly similar. We found that 97% of the detected microbial taxa were regional habitat specialists, with no generalists, with community assembly driven by high dispersal rates and drift (25% and 30% of community assembly, respectively), not environmental selection. Our results indicate that for microbial communities experiencing high dispersal rates between isolated communities, habitat specialists may tend to out-compete habitat generalists.},
}

Antarctic Regions
*Soil Microbiology
*Archaea/classification/genetics
*Bacteria/classification/isolation & purification/genetics
*Ecosystem
Microbiota
Phylogeny
Hot Springs/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid39765072,
year = {2025},
author = {Khan, M and Nizamani, MM and Asif, M and Kamran, A and He, G and Li, X and Yang, S and Xie, X},
title = {Comprehensive approaches to heavy metal bioremediation: Integrating microbial insights and genetic innovations.},
journal = {Journal of environmental management},
volume = {374},
number = {},
pages = {123969},
doi = {10.1016/j.jenvman.2024.123969},
pmid = {39765072},
issn = {1095-8630},
mesh = {*Biodegradation, Environmental ; *Metals, Heavy/metabolism ; Microbiota ; Ecosystem ; Humans ; },
abstract = {The increasing contamination of ecosystems with heavy metals (HMs) due to industrial activities raises significant jeopardies to environmental health and human well-being. Addressing this issue, recent advances in the field of bioremediation have highlighted the potential of plant-associated microbiomes and genetically engineered organisms (GEOs) to mitigate HMs pollution. This review explores recent advancements in bioremediation strategies for HMs detoxification, with particular attention to omics technologies such as metagenomics, metabolomics, and metaproteomics in deepening the understanding of microbial interactions and their potential for neutralizing HMs. Additionally, Emerging strategies and technologies in GEOs and microorganism-aided nanotechnology have proven to be effective bioremediation tools, particularly for alleviating HM contamination. Despite the promising strategies developed in laboratory settings, several challenges impede their practical application, including ecological risks, regulatory limitations, and public concerns regarding the practice of genetically modified organisms. A comprehensive approach that involves interdisciplinary research is essential to enhance the efficacy and safety of bioremediation technologies. This approach should be coupled with robust regulatory frameworks and active public engagement to ensure environmental integrity and societal acceptance. This review underscores the importance of developing sustainable bioremediation strategies that align with ecological conservation goals and public health priorities.},
}

*Biodegradation, Environmental
*Metals, Heavy/metabolism
Microbiota
Ecosystem
Humans

@article {pmid39723822,
year = {2025},
author = {Beauchemin, ET and Hunter, C and Maurice, CF},
title = {Dextran sodium sulfate-induced colitis alters the proportion and composition of replicating gut bacteria.},
journal = {mSphere},
volume = {10},
number = {1},
pages = {e0082524},
doi = {10.1128/msphere.00825-24},
pmid = {39723822},
issn = {2379-5042},
support = {Frederick Banting and Charles Best Canada Graduate Scholarship-Master's//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; Ferrings Pharmaceuticals Fellowship//Faculty of Medicine, McGill University (McGill Faculty of Medicine)/ ; Doctoral Research grant//FRQ | Fonds de recherche du Québec - Nature et technologies (FRQNT)/ ; 950-230748 X-242502//Canada Research Chairs (Chaires de recherche du Canada)/ ; PJT-149098//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; Innovators award//Kenneth Rainin Foundation (KRF)/ ; Owens Catchpaugh IBD Graduate Research Award//McGill University Health Centre (MUHC)/ ; },
mesh = {Animals ; *Dextran Sulfate ; *Gastrointestinal Microbiome ; *Colitis/microbiology/chemically induced ; Mice ; *Disease Models, Animal ; *Bacteria/classification/isolation & purification/genetics/metabolism ; *Mice, Inbred C57BL ; Metagenomics ; Female ; Male ; Single-Cell Analysis ; },
abstract = {The bacteria living in the human gut are essential for host health. Though the composition and metabolism of these bacteria are well described in both healthy hosts and those with intestinal disease, less is known about the metabolic activity of the gut bacteria prior to, and during, disease development-especially regarding gut bacterial replication. Here, we use a recently developed single-cell technique alongside existing metagenomics-based tools to identify, track, and quantify replicating gut bacteria both ex vivo and in situ in the dextran sodium sulfate (DSS) mouse model of colitis. We show that the proportion of replicating gut bacteria decreases when mice have the highest levels of inflammation and returns to baseline levels as mice begin recovering. In addition, we report significant alterations in the composition of the replicating gut bacterial community ex vivo during colitis development. On the taxa level, we observe significant changes in the abundance of taxa such as the mucus-degrading Akkermansia and the poorly described Erysipelatoclostridium genus. We further demonstrate that many taxa exhibit variable replication rates in situ during colitis, including Akkermansia muciniphila. Lastly, we show that colitis development is positively correlated with increases in the presence and abundance of bacteria in situ which are predicted to be fast replicators. This could suggest that taxa with the potential to replicate quickly may have an advantage during intestinal inflammation. These data support the need for additional research using activity-based approaches to further characterize the gut bacterial response to intestinal inflammation and its consequences for both the host and the gut microbial community.IMPORTANCEIt is well known that the bacteria living inside the gut are important for human health. Indeed, the type of bacteria that are present and their metabolism are different in healthy people versus those with intestinal disease. However, less is known about how these gut bacteria are replicating, especially as someone begins to develop intestinal disease. This is particularly important as it is thought that metabolically active gut bacteria may be more relevant to health. Here, we begin to address this gap using several complementary approaches to characterize the replicating gut bacteria in a mouse model of intestinal inflammation. We reveal which gut bacteria are replicating, and how quickly, as mice develop and recover from inflammation. This work can serve as a model for future research to identify how actively growing gut bacteria may be impacting health, or why these particular bacteria tend to thrive during intestinal inflammation.},
}

Animals
*Dextran Sulfate
*Gastrointestinal Microbiome
*Colitis/microbiology/chemically induced
Mice
*Disease Models, Animal
*Bacteria/classification/isolation & purification/genetics/metabolism
*Mice, Inbred C57BL
Metagenomics
Female
Male
Single-Cell Analysis

@article {pmid39699190,
year = {2025},
author = {Prattico, C and Gonzalez, E and Dridi, L and Jazestani, S and Low, KE and Abbott, DW and Maurice, CF and Castagner, B},
title = {Identification of novel fructo-oligosaccharide bacterial consumers by pulse metatranscriptomics in a human stool sample.},
journal = {mSphere},
volume = {10},
number = {1},
pages = {e0066824},
doi = {10.1128/msphere.00668-24},
pmid = {39699190},
issn = {2379-5042},
support = {DO-16//UofA | Canadian Glycomics Network (GlycoNet)/ ; PJT-437944//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; },
mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Oligosaccharides/metabolism ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Prebiotics ; Gene Expression Profiling ; Metagenomics/methods ; Fermentation ; RNA, Ribosomal, 16S/genetics ; Transcriptome ; Dietary Fiber/metabolism ; },
abstract = {UNLABELLED: Dietary fibers influence the composition of the human gut microbiota and directly contribute to its downstream effects on host health. As more research supports the use of glycans as prebiotics for therapeutic applications, the need to identify the gut bacteria that metabolize glycans of interest increases. Fructo-oligosaccharide (FOS) is a common diet-derived glycan that is fermented by the gut microbiota and has been used as a prebiotic. Despite being well studied, we do not yet have a complete picture of all FOS-consuming gut bacterial taxa. To identify new bacterial consumers, we used a short exposure of microbial communities in a stool sample to FOS or galactomannan as the sole carbon source to induce glycan metabolism genes. We then performed metatranscriptomics, paired with whole metagenomic sequencing, and 16S amplicon sequencing. The short incubation was sufficient to cause induction of genes involved in carbohydrate metabolism, like carbohydrate-active enzymes (CAZymes), including glycoside hydrolase family 32 genes, which hydrolyze fructan polysaccharides like FOS and inulin. Interestingly, FOS metabolism transcripts were notably overexpressed in Blautia species not previously reported to be fructan consumers. We therefore validated the ability of different Blautia species to ferment fructans by monitoring their growth and fermentation in defined media. This pulse metatranscriptomics approach is a useful method to find novel consumers of prebiotics and increase our understanding of prebiotic metabolism by CAZymes in the gut microbiota.

IMPORTANCE: Complex carbohydrates are key contributors to the composition of the human gut microbiota and play an essential role in the microbiota's effects on host health. Understanding which bacteria consume complex carbohydrates, or glycans, provides a mechanistic link between dietary prebiotics and their beneficial health effects, an essential step for their therapeutic application. Here, we used a pulse metatranscriptomics pipeline to identify bacterial consumers based on glycan metabolism induction in a human stool sample. We identified novel consumers of fructo-oligosaccharide among Blautia species, expanding our understanding of this well-known glycan. Our approach can be applied to identify consumers of understudied glycans and expand our prebiotic repertoire. It can also be used to study prebiotic glycans directly in stool samples in distinct patient populations to help delineate the prebiotic mechanism.},
}

Humans
*Feces/microbiology
*Gastrointestinal Microbiome
*Oligosaccharides/metabolism
*Bacteria/genetics/classification/metabolism/isolation & purification
*Prebiotics
Gene Expression Profiling
Metagenomics/methods
Fermentation
RNA, Ribosomal, 16S/genetics
Transcriptome
Dietary Fiber/metabolism

@article {pmid39653637,
year = {2025},
author = {Lepcha, A and Kumar, R and Dindhoria, K and Bhargava, B and Pati, AM and Kumar, R},
title = {Metagenomic insights into the functional potential of non-sanitary landfill microbiomes in the Indian Himalayan region, highlighting key plastic degrading genes.},
journal = {Journal of hazardous materials},
volume = {484},
number = {},
pages = {136642},
doi = {10.1016/j.jhazmat.2024.136642},
pmid = {39653637},
issn = {1873-3336},
mesh = {India ; *Waste Disposal Facilities ; *Microbiota/genetics ; *Plastics ; *Metagenomics ; Biodegradation, Environmental ; Bacteria/genetics/metabolism/classification ; Metals, Heavy ; Soil Microbiology ; Soil Pollutants/metabolism ; Refuse Disposal ; },
abstract = {Solid waste management in the Indian Himalayan Region (IHR) is a growing challenge, intensified by increasing population and tourism, which strain non-sanitary landfills. This study investigates microbial diversity and functional capabilities within these landfills using a high-throughput shotgun metagenomic approach. Physicochemical analysis revealed that the Manali and Mandi landfill sites were under heavy metal contamination and thermal stress. Taxonomic annotation identified a dominance of bacterial phyla, including Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes, with genera like Pseudomonas and Bacillus prevalent. Squeezemeta analysis generated 9,216,983 open reading frames (ORFs) across the sampling sites, highlighting diverse metabolic potentials for heavy metal resistance and degrading organic, xenobiotics and plastic wastes. Hierarchical clustering and principal component analysis (PCA) identified distinct gene clusters in Manali and Mandi landfill sites, reflecting differences in pollution profiles. Functional redundancy of landfill microbiome was observed with notable xenobiotic and plastic degradation pathways. This is the first comprehensive metagenomic assessment of non-sanitary landfills in the IHR, providing valuable insights into the microbial roles in degrading persistent pollutants, plastic waste, and other contaminants in these stressed environments.},
}

India
*Waste Disposal Facilities
*Microbiota/genetics
*Plastics
*Metagenomics
Biodegradation, Environmental
Bacteria/genetics/metabolism/classification
Metals, Heavy
Soil Microbiology
Soil Pollutants/metabolism
Refuse Disposal

@article {pmid39642737,
year = {2025},
author = {Medriano, CA and Kim, S and Kim, LH and Bae, S},
title = {Chronic Exposure of Adult Zebrafish to Polyethylene and Polyester-based Microplastics: Metabolomic and Gut Microbiome Alterations Reflecting Dysbiosis and Resilience.},
journal = {Journal of hazardous materials},
volume = {484},
number = {},
pages = {136691},
doi = {10.1016/j.jhazmat.2024.136691},
pmid = {39642737},
issn = {1873-3336},
mesh = {Animals ; *Zebrafish ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/chemically induced ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; *Metabolomics ; *Polyesters ; *Polyethylene/toxicity ; },
abstract = {The study explored the ecotoxicological effects of chronic exposure to microplastic (MP) on adult zebrafish, focusing on environmentally relevant concentrations of polyethylene (PE) beads and polyester (PES). High-throughput untargeted metabolomics via UPLC-QToF-MS and 16S metagenomics for gut microbiota analysis were used to assess ecotoxicity in zebrafish exposed to varying concentrations of PE and PES. The VIP (Variable Importance in Projection) scores indicated PE exposure primarily impacted phospholipids, ceramides, and nucleotide-related compounds, while PES exposure led to alterations in lipid-related compounds, chitin, and amino acid derivatives. From MSEA (Metabolite Set Enrichment Analysis) and Mummichog analyses, PE and PES significantly disrupted key metabolomic pathways associated with inflammation, immune responses, and apoptosis, including leukotriene and arachidonic acid metabolism and the formation of putative anti-inflammatory metabolites from EPA. PE caused physical disruption and inflammation of the epithelial barrier, whereas PES affected gut microbiota interactions, impairing digestion and metabolism. Although alpha diversity within the gut microbiome remained stable, beta diversity analysis revealed significant shifts in microbial composition and structure, suggesting a disruption of functional balance and an increased susceptibility to pathogens. Chronic PE and PES exposures induced shifts in the gut microbial community and interaction network with potential increases in pathogenic bacteria and alteration in commensal bacteria, demonstrating the microbiome's resilience and adaptability to stressors of MPs exposure. High-throughput metabolomics and 16S metagenomics revealed potential chronic diseases associated with inflammation, immune system disorders, metabolic dysfunction, and gut dysbiosis, highlighting the complex relationship between gut microbiome resilience and metabolic disruption under MP-induced stress, with significant ecological implications.},
}

Animals
*Zebrafish
*Gastrointestinal Microbiome/drug effects
*Dysbiosis/chemically induced
*Microplastics/toxicity
*Water Pollutants, Chemical/toxicity
*Metabolomics
*Polyesters
*Polyethylene/toxicity

@article {pmid39571716,
year = {2025},
author = {González-Parra, JA and Barrera-Conde, M and Kossatz, E and Veza, E and de la Torre, R and Busquets-Garcia, A and Robledo, P and Pizarro, N},
title = {Microbiota and social behavior alterations in a mouse model of down syndrome: Modulation by a synbiotic treatment.},
journal = {Progress in neuro-psychopharmacology & biological psychiatry},
volume = {136},
number = {},
pages = {111200},
doi = {10.1016/j.pnpbp.2024.111200},
pmid = {39571716},
issn = {1878-4216},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; *Down Syndrome/genetics ; Mice ; *Synbiotics ; *Disease Models, Animal ; *Social Behavior ; Mice, Inbred C57BL ; Behavior, Animal/physiology ; Sex Characteristics ; },
abstract = {Sex differences in the composition and functionality of gut microbiota are an emerging field of interest in neurodevelopmental disorders, as they may help in understanding the phenotypic disparities between males and females. This study aimed to characterize sex-related specific alterations in gut microbiota composition in a mouse model of Down syndrome (Ts65Dn mice, TS mice) through the sequencing of the PCR-amplified 16S ribosomal DNA fraction. Moreover, it intended to examine whether the modulation of gut microbiota by the administration of a synbiotic (SYN) treatment would be beneficial for the behavioral alterations observed in male and female TS mice. Our results show that male, but not female, TS mice exhibit alterations in beta diversity compared to their wild-type (WT) littermates. Sex-dependent differences are also observed in the relative abundance of the classes Bacilli and Clostridia. Administering the SYN effectively counteracts hypersociability in females, and normalizes the overall abundance of Bacilli, specifically by increasing Lactobacillaceae. On the contrary, it rescues emotional recognition deficits in male TS mice and increases the relative abundance of the families Lactobacillaceae, Streptococcaceae and Atopobiaceae. In addition, a metagenome KEGG analysis of differentially enriched pathways shows relevant changes in the cofactor biosynthesis and the amino acid synthesis categories. Finally, following SYN treatment, both male and female TS mice exhibit a robust increase in propionic acid levels compared to WT littermates. These findings suggest sex-specific mechanisms that could link gut microbiota composition with behavior in TS mice, and underscore the potential of targeted gut microbiota interventions to modulate social abnormalities in neurodevelopmental disorders.},
}

Animals
*Gastrointestinal Microbiome/physiology
Male
Female
*Down Syndrome/genetics
Mice
*Synbiotics
*Disease Models, Animal
*Social Behavior
Mice, Inbred C57BL
Behavior, Animal/physiology
Sex Characteristics

@article {pmid38760649,
year = {2025},
author = {Kumar, A and Sharma, S and Dindhoria, K and Thakur, A and Kumar, R},
title = {Insight into physico-chemical properties and microbial community structure of biogas slurry from household biogas plants of sub-Himalaya for its implications in improved biogas production.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {28},
number = {1},
pages = {187-200},
pmid = {38760649},
issn = {1618-1905},
mesh = {*Biofuels ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *RNA, Ribosomal, 16S/genetics ; *Bioreactors/microbiology ; *Microbiota ; Phylogeny ; Anaerobiosis ; Manure/microbiology/analysis ; Carbon/analysis/metabolism ; Nitrogen/analysis ; Metagenomics ; Biodiversity ; },
abstract = {Numerous metagenomics studies, conducted in both full-scale anaerobic digesters and household biogas plants, have shed light on the composition and activity of microbial flora essential for optimizing the performance of biogas reactors, underscoring the significance of microbial community composition in biogas plant efficiency. Although the efficiency of household biogas plants in the sub-Himalayan region has been reported, there is no literature evidence on the microbial community structure of such household biogas plants in the sub-Himalayan region. The current study evaluated the physico-chemical properties and bacterial community structure from the slurry samples of household biogas plants prevalent in the sub-Himalayan region. The slurry samples were observed to be rich in nutrients; however, their carbon and nitrogen contents were higher than the recommended standard values of liquid-fermented organic manure. The species richness and diversity indices (Chao1, Shannon, and Simpson) of household biogas plants were quite similar to the advanced biogas reactors operating at mesophilic conditions. 16S rRNA gene amplicon sequencing reveals microbial diversity, showing a higher abundance of Firmicutes (70.9%) and Euryarchaeota (9.52%) in advanced biogas reactors compared to household biogas plants. Microbial analysis shows a lack of beneficial microbes for anaerobic digestion, which might be the reason for inefficient biogas production in household biogas plants of the sub-Himalayan region. The lack of efficient bacterial biomass may also be attributed to the digester design, feedstock, and ambient temperatures. This study emphasized the establishment of efficient microbial consortia for enhanced degradation rates that may increase the methane yield in biogas plants.},
}

*Biofuels
*Bacteria/classification/genetics/isolation & purification/metabolism
*RNA, Ribosomal, 16S/genetics
*Bioreactors/microbiology
*Microbiota
Phylogeny
Anaerobiosis
Manure/microbiology/analysis
Carbon/analysis/metabolism
Nitrogen/analysis
Metagenomics
Biodiversity

@article {pmid38758414,
year = {2025},
author = {Xiao, Z and Zhang, Y and Zhang, W and Zhang, A and Wang, G and Chen, C and Ullah, H and Ayaz, T and Li, S and Zhaxi, D and Yan, Q and Kang, J and Xu, X},
title = {Characterizations of gut bacteriome, mycobiome, and virome of healthy individuals living in sea-level and high-altitude areas.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {28},
number = {1},
pages = {173-186},
pmid = {38758414},
issn = {1618-1905},
support = {82370563//National Natural Science Foundation of China/ ; 31700697//National Natural Science Foundation of China/ ; QYXTZX-NQ2022-03//Characteristic Technology of Polysaccharides Research Programme of Naqu, Tibet/ ; },
mesh = {Humans ; *Altitude ; *Gastrointestinal Microbiome ; *Virome ; *Mycobiome ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/isolation & purification/genetics ; Adult ; Male ; Viruses/classification/isolation & purification/genetics ; Healthy Volunteers ; Female ; Feces/microbiology/virology ; Middle Aged ; Metagenome ; },
abstract = {BACKGROUND: The contribution of gut microbiota to human high-altitude adaptation remains inadequately understood.

METHODS: Here a comparative analysis of gut microbiota was conducted between healthy individuals living at sea level and high altitude using deep whole-metagenome shotgun sequencing, to investigate the adaptive mechanisms of gut microbiota in plateau inhabitants.

RESULTS: The results showed the gut bacteriomes in high-altitude individuals exhibited greater within-sample diversity and significant alterations in both bacterial compositional and functional profiles when compared to those of sea-level individuals, indicating the potential selection of unique bacteria associated with high-altitude environments. The strain-level investigation revealed enrichment of Collinsella aerofaciens and Akkermansia muciniphila in high-altitude populations. The characteristics of gut virome and gut mycobiome were also investigated. Compared to sea-level subjects, high-altitude subjects exhibited a greater diversity in their gut virome, with an increased number of viral operational taxonomic units (vOTUs) and unique annotated genes. Finally, correlation analyses revealed 819 significant correlations between 42 bacterial species and 375 vOTUs, while no significant correlations were observed between bacteria and fungi or between fungi and viruses.

CONCLUSION: The findings have significantly contributed to an enhanced comprehension of the mechanisms underlying the high-altitude geographic adaptation of the human gut microbiota.},
}

Humans
*Altitude
*Gastrointestinal Microbiome
*Virome
*Mycobiome
*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/isolation & purification/genetics
Adult
Male
Viruses/classification/isolation & purification/genetics
Healthy Volunteers
Female
Feces/microbiology/virology
Middle Aged
Metagenome

@article {pmid39867343,
year = {2024},
author = {Guimarães, LO and Ribeiro, GO and da Couto, R and Ramos, EDSF and Morais, VDS and Telles-de-Deus, J and Helfstein, VC and Dos Santos, JM and Deng, X and Delwart, E and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, É},
title = {Exploring mosquito virome dynamics within São Paulo Zoo: insights into mosquito-virus-environment interactions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1496126},
pmid = {39867343},
issn = {2235-2988},
mesh = {Animals ; Brazil ; *Virome ; *Mosquito Vectors/virology ; *Metagenomics ; Animals, Zoo/virology ; Arboviruses/genetics/classification/isolation & purification ; Culicidae/virology ; Aedes/virology ; Anopheles/virology ; Culex/virology ; Ecosystem ; },
abstract = {BACKGROUND: Mosquito-borne diseases have a significant public health threat worldwide, with arboviruses accounting for a high proportion of infectious diseases and mortality annually. Brazil, in particular, has been suffering outbreaks of diseases transmitted by mosquito viruses, notably those of the Aedes genus, such as dengue, Zika, and chikungunya. Against this background, the São Paulo Zoo is an intriguing ecological niche to explore the virome of mosquitoes, potentially shedding light on the dynamics of arbovirus transmission within a confined setting.

METHODS: In this study, we conducted a comprehensive metagenomic analysis of mosquitoes collected from diverse habitats within the zoo, focusing on the Aedes, Anopheles, and Culex genera. From 1,039 contigs of viral origin, we identified 229 viral species infecting mosquitoes, with the orders Picornavirales, Nodamuvirales and Sobelivirales being the most prevalent and abundant. The difference in virome composition was primarily driven by mosquito host species rather than specific collection sites or trap height.

RESULTS: Despite environmental disparities, the virome remained remarkably uniform across different areas of the zoo, emphasizing the strong association between mosquito species and their viral communities. Furthermore, we identified a core virome shared among mosquito species, highlighting potential cross-species transmission events and underscoring the need for targeted surveillance and control measures.

CONCLUSION: These results contribute to our understanding of the interplay between mosquitoes, the environment, and viruses, providing valuable insights for disease intervention strategies in mosquito-borne diseases.},
}

Animals
Brazil
*Virome
*Mosquito Vectors/virology
*Metagenomics
Animals, Zoo/virology
Arboviruses/genetics/classification/isolation & purification
Culicidae/virology
Aedes/virology
Anopheles/virology
Culex/virology
Ecosystem

@article {pmid39866568,
year = {2025},
author = {Pucci, N and Ujčič-Voortman, J and Verhoeff, AP and Mende, DR},
title = {Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18602},
pmid = {39866568},
issn = {2167-8359},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Milk, Human/microbiology/chemistry/metabolism ; Infant ; *Bifidobacterium/metabolism/genetics ; *Bifidobacterium longum/metabolism ; Female ; *Polysaccharides/metabolism ; Infant, Newborn ; Feces/microbiology ; Metagenome ; Breast Feeding ; Male ; },
abstract = {BACKGROUND: The initial colonization of the infant gut is a complex process that defines the foundation for a healthy microbiome development. Bifidobacterium longum is one of the first colonizers of newborns' gut, playing a crucial role in the healthy development of both the host and its microbiome. However, B. longum exhibits significant genomic diversity, with subspecies (e.g., Bifidobacterium longum subsp. infantis and subsp. longum) displaying distinct ecological and metabolic strategies including differential capabilities to break down human milk glycans (HMGs). To promote healthy infant microbiome development, a good understanding of the factors governing infant microbiome dynamics is required.

METHODOLOGY: We analyzed newly sequenced gut microbiome samples of mother-infant pairs from the Amsterdam Infant Microbiome Study (AIMS) and four publicly available datasets to identify important environmental and bifidobacterial features associated with the colonization success and succession outcomes of B. longum subspecies. Metagenome-assembled genomes (MAGs) were generated and assessed to identify characteristics of B. longum subspecies in relation to early-life gut colonization. We further implemented machine learning tools to identify significant features associated with B. longum subspecies abundance.

RESULTS: B. longum subsp. longum was the most abundant and prevalent gut Bifidobacterium at one month, being replaced by B. longum subsp. infantis at six months of age. By utilizing metagenome-assembled genomes (MAGs), we reveal significant differences between and within B. longum subspecies in their potential to break down HMGs. We further combined strain-tracking, meta-pangenomics and machine learning to understand these abundance dynamics and found an interplay of priority effects, milk-feeding type and HMG-utilization potential to govern them across the first six months of life. We find higher abundances of B. longum subsp. longum in the maternal gut microbiome, vertical transmission, breast milk and a broader range of HMG-utilizing genes to promote its abundance at one month of age. Eventually, we find B. longum subsp. longum to be replaced by B. longum subsp. infantis at six months of age due to a combination of nutritional intake, HMG-utilization potential and a diminishment of priority effects.

DISCUSSION: Our results establish a strain-level ecological framework explaining early-life abundance dynamics of B. longum subspecies. We highlight the role of priority effects, nutrition and significant variability in HMG-utilization potential in determining the predictable colonization and succession trajectories of B. longum subspecies, with potential implications for promoting infant health and well-being.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Milk, Human/microbiology/chemistry/metabolism
Infant
*Bifidobacterium/metabolism/genetics
*Bifidobacterium longum/metabolism
Female
*Polysaccharides/metabolism
Infant, Newborn
Feces/microbiology
Metagenome
Breast Feeding
Male

@article {pmid39814067,
year = {2024},
author = {Ji, J and Jung, S},
title = {PredCMB: predicting changes in microbial metabolites based on the gene-metabolite network analysis of shotgun metagenome data.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {1},
pages = {},
doi = {10.1093/bioinformatics/btaf020},
pmid = {39814067},
issn = {1367-4811},
support = {//National Research Foundation of Korea/ ; 2022R1A2C1007345//Korea government/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; Humans ; Metabolomics/methods ; Metabolic Networks and Pathways ; Microbiota/genetics ; Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Metabolome ; Stomach Neoplasms/metabolism/microbiology/genetics ; },
abstract = {MOTIVATION: Microbiota-derived metabolites significantly impact host biology, prompting extensive research on metabolic shifts linked to the microbiota. Recent studies have explored both direct metabolite analyses and computational tools for inferring metabolic functions from microbial shotgun metagenome data. However, no existing tool specifically focuses on predicting changes in individual metabolite levels, as opposed to metabolic pathway activities, based on shotgun metagenome data. Understanding these changes is crucial for directly estimating the metabolic potential associated with microbial genomic content.

RESULTS: We introduce Predicting Changes in Microbial metaBolites (PredCMB), a novel method designed to predict alterations in individual metabolites between conditions using shotgun metagenome data and enzymatic gene-metabolite networks. PredCMB evaluates differential enzymatic gene abundance between conditions and estimates its influence on metabolite changes. To validate this approach, we applied it to two publicly available datasets comprising paired shotgun metagenomics and metabolomics data from inflammatory bowel disease cohorts and the cohort of gastrectomy for gastric cancer. Benchmark evaluations revealed that PredCMB outperformed a previous method by demonstrating higher correlations between predicted metabolite changes and experimentally measured changes. Notably, it identified metabolite classes exhibiting major alterations between conditions. By enabling the prediction of metabolite changes directly from shotgun metagenome data, PredCMB provides deeper insights into microbial metabolic dynamics than existing methods focused on pathway activity evaluation. Its potential applications include refining target metabolite selection in microbial metabolomic studies and assessing the contributions of microbial metabolites to disease pathogenesis.

Freely available to non-commercial users at https://www.sysbiolab.org/predcmb.},
}

*Metagenome
*Metagenomics/methods
Humans
Metabolomics/methods
Metabolic Networks and Pathways
Microbiota/genetics
Inflammatory Bowel Diseases/microbiology/metabolism/genetics
Metabolome
Stomach Neoplasms/metabolism/microbiology/genetics

@article {pmid39556491,
year = {2025},
author = {Shete, O and Ghosh, TS},
title = {Normal Gut Microbiomes in Diverse Populations: Clinical Implications.},
journal = {Annual review of medicine},
volume = {76},
number = {1},
pages = {95-114},
doi = {10.1146/annurev-med-051223-031809},
pmid = {39556491},
issn = {1545-326X},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; },
abstract = {The human microbiome is a sensor and modulator of physiology and homeostasis. Remarkable tractability underpins the promise of therapeutic manipulation of the microbiome. However, the definition of a normal or healthy microbiome has been elusive. This is in part due to the underrepresentation of minority groups and major global regions in microbiome studies to date. We review studies of the microbiome in different populations and highlight a commonality among health-associated microbiome signatures along with major drivers of variation. We also provide an overview of microbiome-associated therapeutic interventions for some widespread, widely studied diseases. We discuss sources of bias and the challenges associated with defining population-specific microbiome reference bases. We propose a roadmap for defining normal microbiome references that can be used for population-customized microbiome therapeutics and diagnostics.},
}

Humans
*Gastrointestinal Microbiome/physiology

@article {pmid39865153,
year = {2025},
author = {Wu, Z and Jiang, M and Jia, M and Sang, J and Wang, Q and Xu, Y and Qi, L and Yang, W and Feng, L},
title = {The difference of oropharyngeal microbiome during acute respiratory viral infections in infants and children.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {127},
pmid = {39865153},
issn = {2399-3642},
support = {2022-I2M-CoV19-006//Chinese Academy of Medical Sciences (CAMS)/ ; },
mesh = {Humans ; *Respiratory Tract Infections/microbiology/virology ; Infant ; *Oropharynx/microbiology/virology ; *Microbiota ; Child, Preschool ; Male ; Female ; Child ; Acute Disease ; Virus Diseases/virology/microbiology/epidemiology ; },
abstract = {Acute respiratory infections (ARI) with multiple types of viruses are common in infants and children. This study was conducted to assess the difference of oropharyngeal microbiome during acute respiratory viral infection using whole-genome shotgun metagenomic sequencing. The overall taxonomic alpha diversity did not differ by the types of infected virus. The beta diversity differed by disease severity, disease-related symptoms, and types of infected virus. Nine species had significantly higher abundance in outpatients than in inpatients, with five of them in the genus Achromobacter. Three microbial community types were identified. The prevalence of community type (CT) 1 was higher among patients with influenza virus, enterovirus, and human adenvirus; CT2 was higher among patients with human metapneumovirus; and CT3 was higher among patients with respiratory syncytial virus and human adenvirus infections. Our results suggest that the oropharyngeal microbiome is associated with ARI disease severity, disease-related symptoms, and the types of infected virus.},
}

Humans
*Respiratory Tract Infections/microbiology/virology
Infant
*Oropharynx/microbiology/virology
*Microbiota
Child, Preschool
Male
Female
Child
Acute Disease
Virus Diseases/virology/microbiology/epidemiology

@article {pmid38385313,
year = {2025},
author = {Iqbal, S and Begum, F and Ullah, I and Jalal, N and Shaw, P},
title = {Peeling off the layers from microbial dark matter (MDM): recent advances, future challenges, and opportunities.},
journal = {Critical reviews in microbiology},
volume = {51},
number = {1},
pages = {1-21},
doi = {10.1080/1040841X.2024.2319669},
pmid = {38385313},
issn = {1549-7828},
mesh = {*Metagenomics ; *Bacteria/genetics/classification/metabolism ; Genomics ; Microbiota ; Metagenome ; },
abstract = {Microbes represent the most common organisms on Earth; however, less than 2% of microbial species in the environment can undergo cultivation for study under laboratory conditions, and the rest of the enigmatic, microbial world remains mysterious, constituting a kind of "microbial dark matter" (MDM). In the last two decades, remarkable progress has been made in culture-dependent and culture-independent techniques. More recently, studies of MDM have relied on culture-independent techniques to recover genetic material through either unicellular genomics or shotgun metagenomics to construct single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs), respectively, which provide information about evolution and metabolism. Despite the remarkable progress made in the past decades, the functional diversity of MDM still remains uncharacterized. This review comprehensively summarizes the recently developed culture-dependent and culture-independent techniques for characterizing MDM, discussing major challenges, opportunities, and potential applications. These activities contribute to expanding our knowledge of the microbial world and have implications for various fields including Biotechnology, Bioprospecting, Functional genomics, Medicine, Evolutionary and Planetary biology. Overall, this review aims to peel off the layers from MDM, shed light on recent advancements, identify future challenges, and illuminate the exciting opportunities that lie ahead in unraveling the secrets of this intriguing microbial realm.},
}

*Metagenomics
*Bacteria/genetics/classification/metabolism
Genomics
Microbiota
Metagenome

@article {pmid39861468,
year = {2025},
author = {Fricker, AD and Sejane, K and Desai, M and Snyder, MW and Duran, L and Mackelprang, R and Bode, L and Ross, MG and Flores, GE},
title = {A Pilot Study Exploring the Relationship Between Milk Composition and Microbial Capacity in Breastfed Infants.},
journal = {Nutrients},
volume = {17},
number = {2},
pages = {},
doi = {10.3390/nu17020338},
pmid = {39861468},
issn = {2072-6643},
support = {SC1GM136546/GM/NIGMS NIH HHS/United States ; R21HD104028/HD/NICHD NIH HHS/United States ; R01HD099813/HD/NICHD NIH HHS/United States ; },
mesh = {Humans ; *Milk, Human/chemistry/microbiology ; Pilot Projects ; Female ; *Gastrointestinal Microbiome ; Infant ; *Breast Feeding ; *Oligosaccharides/analysis ; Adult ; *Feces/microbiology/chemistry ; Cross-Sectional Studies ; Male ; Body Mass Index ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Overweight/microbiology ; Infant, Newborn ; Obesity/microbiology ; },
abstract = {BACKGROUND: Maternal obesity may contribute to childhood obesity in a myriad of ways, including through alterations of the infant gut microbiome. For example, maternal obesity may contribute both directly by introducing a dysbiotic microbiome to the infant and indirectly through the altered composition of human milk that fuels the infant gut microbiome. In particular, indigestible human milk oligosaccharides (HMOs) are known to shape the composition of the infant gut microbiome. The goal of this study was to characterize the HMO profiles of normal-weight and overweight mothers and to quantitatively link HMO concentrations to the taxonomic composition and functional potential of the infant gut microbiome.

METHODS: Normal-weight (BMI = 18.5-24.9; n = 9) and overweight/obese (OW/OB; BMI > 25; n = 11) breastfeeding mothers and their infants were enrolled in this single-center, cross-sectional pilot study. Human milk from the mothers and rectal stool swabs from the infants were collected 7-9 weeks postpartum. The HMO composition, microbiome composition, and microbial functions were assessed using HPLC, 16S rRNA gene sequencing, and metagenomic sequencing, respectively.

RESULTS: Neither the HMO profiles nor the infant microbiome composition varied according to maternal BMI status. Taxonomically, the gut microbiota of infants were dominated by typical gut lineages including Bifidobacterium. Significant correlations between individual HMOs and bacterial genera were identified, including for Prevotella, a genus of the Bacteroidota phylum that was positively correlated with the concentrations of lacto-N-neotetraose (LNnT) and lacto-N-hexaose (LNH). Using metagenomic assembled genomes, we were also able to identify the broad HMO-degradative capacity across the Bifidobacterium and Prevotella genera.

CONCLUSIONS: These results suggest that the maternal BMI status does not impact the HMO profiles of human milk. However, select HMOs were correlated with specific bacterial taxa, suggesting that the milk composition influences both the taxonomic composition and the functional capacity of the infant gut microbiome.},
}

Humans
*Milk, Human/chemistry/microbiology
Pilot Projects
Female
*Gastrointestinal Microbiome
Infant
*Breast Feeding
*Oligosaccharides/analysis
Adult
*Feces/microbiology/chemistry
Cross-Sectional Studies
Male
Body Mass Index
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification
Overweight/microbiology
Infant, Newborn
Obesity/microbiology

@article {pmid39860966,
year = {2024},
author = {Laryushina, Y and Samoilova-Bedych, N and Turgunova, L and Marchenko, A and Turgunov, Y and Kozhakhmetov, S and Suieubayev, M and Mukhanbetzhanov, N and Kabdulina, N},
title = {Interrelationships of the Intestinal Microbiome, Trimethylamine N-Oxide and Lipopolysaccharide-Binding Protein with Crohn's Disease Activity.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/pathogens14010005},
pmid = {39860966},
issn = {2076-0817},
support = {AP14871959//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {Humans ; *Methylamines/metabolism ; *Gastrointestinal Microbiome/physiology ; *Crohn Disease/microbiology/metabolism ; Female ; Male ; Adult ; *Acute-Phase Proteins/metabolism/analysis ; *Feces/microbiology/chemistry ; Middle Aged ; *Membrane Glycoproteins/metabolism ; Carrier Proteins/metabolism ; Young Adult ; Lipopolysaccharides/metabolism ; },
abstract = {UNLABELLED: Crohn's disease (CD) is a multifactorial inflammatory bowel disease whose pathogenetic mechanisms are a field of ongoing study. Changes in the intestinal microbiome in CD may influence metabolite production and reflect the disease's severity. We investigate the relationship between trimethylamine N-oxide (TMAO) and lipopolysaccharide-binding protein (LPS) levels and changes in the gut microbiome in patients with CD of various degrees of activity.

METHODS: In total, 29 CD patients and 15 healthy individuals were investigated for their levels of TMAO by HPLC-MS, and LPS protein by ELISA and metagenomic 16 s-sequencing of feces was performed.

RESULTS: We found significant differences in TMAO levels in patients in the remission/mild and moderate/severe groups compared to the control group (p = 0.02 and p = 0.014), changes in alpha diversity with the Shannon index (p = 0. 0151 and p = 0.0018) and in beta diversity (ANOSIM p = 0.009 and PERMANOVA p = 0.005) in both groups compared to controls. Strongly positive correlations in TMAO levels and mixed correlations of LPS with alpha diversity metrics were found, as well as significant correlations with microbiota species.

CONCLUSIONS: Changes in the level of metabolites may reflect specific disturbances in the composition of the intestinal microbiome at different degrees of severity of CD.},
}

Humans
*Methylamines/metabolism
*Gastrointestinal Microbiome/physiology
*Crohn Disease/microbiology/metabolism
Female
Male
Adult
*Acute-Phase Proteins/metabolism/analysis
*Feces/microbiology/chemistry
Middle Aged
*Membrane Glycoproteins/metabolism
Carrier Proteins/metabolism
Young Adult
Lipopolysaccharides/metabolism

@article {pmid39859429,
year = {2025},
author = {Vicente-Valor, J and Tesolato, S and Paz-Cabezas, M and Gómez-Garre, D and Ortega-Hernández, A and de la Serna, S and Domínguez-Serrano, I and Dziakova, J and Rivera, D and Jarabo, JR and Gómez-Martínez, AM and Hernando, F and Torres, A and Iniesta, P},
title = {Fecal Microbiota Strongly Correlates with Tissue Microbiota Composition in Colorectal Cancer but Not in Non-Small Cell Lung Cancer.},
journal = {International journal of molecular sciences},
volume = {26},
number = {2},
pages = {},
doi = {10.3390/ijms26020717},
pmid = {39859429},
issn = {1422-0067},
support = {PI19/00073//Carlos III Health Institute (Ministerio de Economía y Competitividad), Spain and co-funded by the European Union through the European Regional Development Fund (ERDF) 'A way to make Europe'/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/microbiology ; *Feces/microbiology ; *Colorectal Neoplasms/microbiology ; *Lung Neoplasms/microbiology ; Female ; Male ; Middle Aged ; Aged ; RNA, Ribosomal, 16S/genetics ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Adult ; },
abstract = {Microbiota could be of interest in the diagnosis of colorectal and non-small cell lung cancer (CRC and NSCLC). However, how the microbial components of tissues and feces reflect each other remains unknown. In this work, our main objective is to discover the degree of correlation between the composition of the tissue microbiota and that of the feces of patients affected by CRC and NSCLC. Specifically, we investigated tumor and non-tumor tissues from 38 recruited patients with CRC and 19 with NSCLC. DNA from samples was submitted for 16S rDNA metagenomic sequencing, followed by data analysis through the QIIME2 pipeline and further statistical processing with STATA IC16. Tumor and non-tumor tissue selected genera were highly correlated in both CRC and NSCLC (100% and 81.25%). Following this, we established tissue-feces correlations, using selected genera from a LEfSe analysis previously published. In CRC, we found a strong correlation between the taxa detected in feces and those from colorectal tissues. However, our data do not demonstrate this correlation in NSCLC. In conclusion, our findings strongly reinforce the utility of fecal microbiota as a non-invasive biomarker for CRC diagnosis, while highlighting critical distinctions for NSCLC. Furthermore, our data demonstrate that the microbiota components of tumor and non-tumor tissues are similar, with only minor differences being detected.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/microbiology
*Feces/microbiology
*Colorectal Neoplasms/microbiology
*Lung Neoplasms/microbiology
Female
Male
Middle Aged
Aged
RNA, Ribosomal, 16S/genetics
Microbiota/genetics
Gastrointestinal Microbiome/genetics
Metagenomics/methods
Adult

@article {pmid39856742,
year = {2025},
author = {Benitez, AJ and Tanes, C and Friedman, ES and Zackular, JP and Ford, E and Gerber, JS and DeRusso, PA and Kelly, A and Li, H and Elovitz, MA and Wu, GD and Zemel, B and Bittinger, K},
title = {Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {21},
pmid = {39856742},
issn = {2049-2618},
support = {KL2TR001879/TR/NCATS NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R35GM138369/GM/NIGMS NIH HHS/United States ; UL1TR001878//NIH National Center for Research Resources Clinical and Translational Science Program/ ; unrestricted donation//American Beverage Foundation for a Healthy America/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Infant ; *Feces/microbiology/chemistry ; Female ; *Bile Acids and Salts/metabolism ; Male ; Prospective Studies ; *Breast Feeding ; Longitudinal Studies ; Infant, Newborn ; Metagenomics ; Bacteria/classification/genetics/drug effects/isolation & purification ; Child, Preschool ; Black or African American ; Amoxicillin ; Bifidobacterium/drug effects/isolation & purification/genetics ; White ; },
abstract = {BACKGROUND: The evolving infant gut microbiome influences host immune development and later health outcomes. Early antibiotic exposure could impact microbiome development and contribute to poor outcomes. Here, we use a prospective longitudinal birth cohort of n = 323 healthy term African American children to determine the association between antibiotic exposure and the gut microbiome through shotgun metagenomics sequencing as well as bile acid profiles through liquid chromatography-mass spectrometry.

RESULTS: Stool samples were collected at ages 4, 12, and 24 months for antibiotic-exposed (n = 170) and unexposed (n = 153) participants. A short-term substudy (n = 39) collected stool samples at first exposure, and over 3 weeks following antibiotics initiation. Antibiotic exposure (predominantly amoxicillin) was associated with minimal microbiome differences, whereas all tested taxa were modified by breastfeeding. In the short-term substudy, we observed microbiome differences only in the first 2 weeks following antibiotics initiation, mainly a decrease in Bifidobacterium bifidum. The differences did not persist a month after antibiotic exposure. Four species were associated with infant age. Antibiotic exposure was not associated with an increase in antibiotic resistance gene abundance or with differences in microbiome-derived fecal bile acid composition.

CONCLUSIONS: Short-term and long-term gut microbiome perturbations by antibiotic exposure were detectable but substantially smaller than those associated with breastfeeding and infant age.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Anti-Bacterial Agents/adverse effects/pharmacology
Infant
*Feces/microbiology/chemistry
Female
*Bile Acids and Salts/metabolism
Male
Prospective Studies
*Breast Feeding
Longitudinal Studies
Infant, Newborn
Metagenomics
Bacteria/classification/genetics/drug effects/isolation & purification
Child, Preschool
Black or African American
Amoxicillin
Bifidobacterium/drug effects/isolation & purification/genetics
White

@article {pmid39856709,
year = {2025},
author = {Li, D and Chen, W and Luo, W and Zhang, H and Liu, Y and Shu, D and Wei, G},
title = {Seed microbiomes promote Astragalus mongholicus seed germination through pathogen suppression and cellulose degradation.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {23},
pmid = {39856709},
issn = {2049-2618},
support = {42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; },
mesh = {*Seeds/microbiology ; *Germination ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Cellulose/metabolism ; Astragalus Plant/microbiology ; Soil Microbiology ; Metagenome ; },
abstract = {BACKGROUND: Seed-associated microorganisms play crucial roles in maintaining plant health by providing nutrients and resistance to biotic and abiotic stresses. However, their functions in seed germination and disease resistance remain poorly understood. In this study, we investigated the microbial community assembly features and functional profiles of the spermosphere and endosphere microbiomes related to germinated and ungerminated seeds of Astragalus mongholicus by using amplicon and shotgun metagenome sequencing techniques. Additionally, we aimed to elucidate the relationship between beneficial microorganisms and seed germination through both in vitro and in vivo pot experiments.

RESULTS: Our findings revealed that germination significantly enhances the diversity of microbial communities associated with seeds. This increase in diversity is driven through environmental ecological niche differentiation, leading to the enrichment of potentially beneficial probiotic bacteria such as Pseudomonas and Pantoea. Conversely, Fusarium was consistently enriched in ungerminated seeds. The co-occurrence network patterns revealed that the microbial communities within germinated and ungerminated seeds presented distinct structures. Notably, germinated seeds exhibit more complex and interconnected networks, particularly for bacterial communities and their interactions with fungi. Metagenome analysis showed that germinated seed spermosphere soil had more functions related to pathogen inhibition and cellulose degradation. Through a combination of culture-dependent and germination experiments, we identified Fusarium solani as the pathogen. Consistent with the metagenome analysis, germination experiments further demonstrated that bacteria associated with pathogen inhibition and cellulose degradation could promote seed germination and vigor. Specifically, Paenibacillus sp. significantly enhanced A. mongholicus seed germination and plant growth.

CONCLUSIONS: Our study revealed the dynamics of seed-associated microorganisms during seed germination and confirmed their ecological role in promoting A. mongholicus seed germination by suppressing pathogens and degrading cellulose. This study offers a mechanistic understanding of how seed microorganisms facilitate successful seed germination, highlighting the potential for leveraging these microbial communities to increase plant health. Video Abstract.},
}

*Seeds/microbiology
*Germination
*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Cellulose/metabolism
Astragalus Plant/microbiology
Soil Microbiology
Metagenome

@article {pmid39856104,
year = {2025},
author = {Özcan, E and Yu, KB and Dinh, L and Lum, GR and Lau, K and Hsu, J and Arino, M and Paramo, J and Lopez-Romero, A and Hsiao, EY},
title = {Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {987},
pmid = {39856104},
issn = {2041-1723},
support = {R01NS115537//U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)/ ; },
mesh = {*Diet, Ketogenic ; Animals ; *Gastrointestinal Microbiome ; *Dietary Fiber/administration & dosage ; *Seizures/diet therapy/metabolism ; Mice ; Male ; Humans ; Mice, Inbred C57BL ; Disease Models, Animal ; Infant Formula ; Female ; },
abstract = {The gut microbiome modulates the anti-seizure effects of the ketogenic diet, but how specific dietary formulations differentially modify the gut microbiome in ways that impact seizure outcome is poorly understood. We find that medical ketogenic infant formulas vary in macronutrient ratio, fat source, and fiber content and differentially promote resistance to 6-Hz seizures in mice. Dietary fiber, rather than fat ratio or source, drives substantial metagenomic shifts in a model human infant microbial community. Addition of fiber to a fiber-deficient ketogenic formula restores seizure resistance, and supplementing protective formulas with excess fiber potentiates seizure resistance. By screening 13 fiber sources and types, we identify metagenomic responses in the model community that correspond with increased seizure resistance. Supplementing with seizure-protective fibers enriches microbial genes related to queuosine biosynthesis and preQ0 biosynthesis and decreases genes related to sucrose degradation and TCA cycle, which are also seen in seizure-protected mice that are fed fiber-containing ketogenic formulas. This study reveals that different formulations of ketogenic diets, and dietary fiber content in particular, differentially impact seizure outcome in mice, likely by modifying the gut microbiome. Understanding interactions between diet, microbiome, and host susceptibility to seizures could inform novel microbiome-guided approaches to treat refractory epilepsy.},
}

*Diet, Ketogenic
Animals
*Gastrointestinal Microbiome
*Dietary Fiber/administration & dosage
*Seizures/diet therapy/metabolism
Mice
Male
Humans
Mice, Inbred C57BL
Disease Models, Animal
Infant Formula
Female

@article {pmid39856097,
year = {2025},
author = {Pidgeon, R and Mitchell, S and Shamash, M and Suleiman, L and Dridi, L and Maurice, CF and Castagner, B},
title = {Diet-derived urolithin A is produced by a dehydroxylase encoded by human gut Enterocloster species.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {999},
pmid = {39856097},
issn = {2041-1723},
support = {PJT-437944//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; },
mesh = {Humans ; *Coumarins/metabolism ; *Gastrointestinal Microbiome ; *Operon/genetics ; Feces/microbiology ; Diet ; Bacterial Proteins/metabolism/genetics ; Proteomics ; },
abstract = {Urolithin A (uroA) is a polyphenol derived from the multi-step metabolism of dietary ellagitannins by the human gut microbiota. Once absorbed, uroA can trigger mitophagy and aryl hydrocarbon receptor signaling pathways, altering host immune function, mitochondrial health, and intestinal barrier integrity. Most individuals harbor a microbiota capable of uroA production; however, the mechanisms underlying the dehydroxylation of its catechol-containing precursor (uroC) are unknown. Here, we use a combination of untargeted bacterial transcriptomics, proteomics, and comparative genomics to uncover an inducible uroC dehydroxylase (ucd) operon in Enterocloster species. We show that the ucd operon encodes a predicted molybdopterin-dependent enzyme complex that dehydroxylates urolithins at a specific position (9-OH). By interrogating publicly available metagenomics datasets, we observed that uroC-metabolizing Enterocloster species and ucd operon genes are prevalent in human feces. In ex vivo experiments with human fecal samples, only samples actively transcribing ucd could produce uroA, possibly explaining differences in urolithin metabolism between individuals. Collectively, this work identifies Enterocloster species and the ucd operon as important contributors to uroA production and establishes a multi-omics framework to further our mechanistic understanding of polyphenol metabolism by the human gut microbiota.},
}

Humans
*Coumarins/metabolism
*Gastrointestinal Microbiome
*Operon/genetics
Feces/microbiology
Diet
Bacterial Proteins/metabolism/genetics
Proteomics

@article {pmid39856057,
year = {2025},
author = {Hu, H and Huang, Y and Yang, F and Ma, L and Zhang, J and Deng, X and Ma, N and Wang, K and Tao, Y and Lin, Q and Li, Y and Bai, X and Pan, H},
title = {Metagenome-assembled microbial genomes (n = 3,448) of the oral microbiomes of Tibetan and Duroc pigs.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {141},
pmid = {39856057},
issn = {2052-4463},
mesh = {Animals ; *Metagenome ; Swine/microbiology ; *Mouth/microbiology ; *Microbiota ; Genome, Microbial ; Metagenomics ; Tibet ; },
abstract = {Compared with leaner breeds, local Chinese pig breeds have distinct intestinal microbial, as determined by metagenomic techniques, and the interactions between oral microorganisms and their hosts are also gradually being clarified. However, the high host genome content means that few metagenome-based oral microbiomes have been reported. Here, we combined dilution-based metagenomic sequencing and binning approaches to extract the microbial genomes from the oral microbiomes of Tibetan and Duroc pigs. The host contamination rates were reduced to 13.64%, a quarter of the normal metagenomic level (65.25% on average). Medium-high-quality metagenome-assembled genomes (MAGs; n = 3,448) spanning nine phyla were retrieved and 70.79% were novel species. Of the nonredundant MAGs, only 13.37% were shared, revealing the strong disparities between Tibetan and Duroc pigs. The oral microbial diversity of the Duroc pig was greater than that of the Tibetan pig. We present the first large-scale dilute-based metagenomic data on the pig oral microbiome, which should facilitate further investigation of the functions of oral microorganisms in pigs.},
}

Animals
*Metagenome
Swine/microbiology
*Mouth/microbiology
*Microbiota
Genome, Microbial
Metagenomics
Tibet

@article {pmid39536492,
year = {2025},
author = {Chu, J and Ye, Y and Wu, YH},
title = {A glimpse of microbial potential in metal metabolism in the Clarion-Clipperton Fracture Zone in the eastern Pacific Ocean based on metagenomic analysis.},
journal = {Marine genomics},
volume = {79},
number = {},
pages = {101159},
doi = {10.1016/j.margen.2024.101159},
pmid = {39536492},
issn = {1876-7478},
mesh = {Pacific Ocean ; *Metagenome ; *Bacteria/genetics/metabolism/classification ; *Archaea/genetics/metabolism ; *Metagenomics ; Metals/metabolism ; Geologic Sediments/microbiology ; Microbiota ; },
abstract = {The polymetallic nodules distributed in the abyssal ocean floor are full of economic value, rich in manganese, iron, copper and rare-earth elements. Little is currently known about the diversity and the metabolic potential of microorganisms inhabiting the Clarion-Clipperton Fracture Zone (CCFZ) in eastern Pacific Ocean. In this study, the surface sediments (0-8 cm), which were divided into eight parts at 1 cm intervals were collected from the CCFZ. The microbial diversity and the metabolic potential of metal were examined by metagenomic sequencing and binning. The metal redox genes and metal transporter genes also showed a certain trend at different depths, the highest in the surface layer, about the same at 0-6 cm, and greater changes after >6 cm. 58 high- and medium metagenome-assembled genomes (MAGs) were recovered and assigned to 14 bacterial phyla and 1 archaeal phylum after dereplication. Alphaproteobacteria mainly carried out the oxidation of Fe/Mn and the reduction of Hg, Gammaproteobacteria mainly for the oxidation of Mn/Cu and the reduction of Cr/Hg and Methylomirabilota mainly for the oxidation of Mn and the reduction of As/Cr/Hg. Among the five Thermoproteota MAGs identified, only one had genes annotated for Mn oxidation, suggesting a limited but potentially significant role in this process at the bottom layer. By identifying the microbial diversity and the metabolic potential of metal in different depth, our study strengthens the understanding of metal metabolism in CCFZ and provides the foundation for further analyses of metal metabolism in such ecosystems.},
}

Pacific Ocean
*Metagenome
*Bacteria/genetics/metabolism/classification
*Archaea/genetics/metabolism
*Metagenomics
Metals/metabolism
Geologic Sediments/microbiology
Microbiota

@article {pmid39853798,
year = {2025},
author = {Lutz, KC and Neugent, ML and Bedi, T and De Nisco, NJ and Li, Q},
title = {A Generalized Bayesian Stochastic Block Model for Microbiome Community Detection.},
journal = {Statistics in medicine},
volume = {44},
number = {3-4},
pages = {e10291},
doi = {10.1002/sim.10291},
pmid = {39853798},
issn = {1097-0258},
support = {2113674//National Science Foundation/ ; 2210912//National Science Foundation/ ; AT-2030-20200401//Welch Foundation/ ; 1F32DK128975-01A1/NH/NIH HHS/United States ; 1R01DK131267-01/NH/NIH HHS/United States ; 1R01GM141519/NH/NIH HHS/United States ; },
mesh = {*Bayes Theorem ; Humans ; *Microbiota/genetics ; *Markov Chains ; Computer Simulation ; Female ; Monte Carlo Method ; Stochastic Processes ; Models, Statistical ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; },
abstract = {Advances in next-generation sequencing technology have enabled the high-throughput profiling of metagenomes and accelerated microbiome studies. Recently, there has been a rise in quantitative studies that aim to decipher the microbiome co-occurrence network and its underlying community structure based on metagenomic sequence data. Uncovering the complex microbiome community structure is essential to understanding the role of the microbiome in disease progression and susceptibility. Taxonomic abundance data generated from metagenomic sequencing technologies are high-dimensional and compositional, suffering from uneven sampling depth, over-dispersion, and zero-inflation. These characteristics often challenge the reliability of the current methods for microbiome community detection. To study the microbiome co-occurrence network and perform community detection, we propose a generalized Bayesian stochastic block model that is tailored for microbiome data analysis where the data are transformed using the recently developed modified centered-log ratio transformation. Our model also allows us to leverage taxonomic tree information using a Markov random field prior. The model parameters are jointly inferred by using Markov chain Monte Carlo sampling techniques. Our simulation study showed that the proposed approach performs better than competing methods even when taxonomic tree information is non-informative. We applied our approach to a real urinary microbiome dataset from postmenopausal women. To the best of our knowledge, this is the first time the urinary microbiome co-occurrence network structure in postmenopausal women has been studied. In summary, this statistical methodology provides a new tool for facilitating advanced microbiome studies.},
}

*Bayes Theorem
Humans
*Microbiota/genetics
*Markov Chains
Computer Simulation
Female
Monte Carlo Method
Stochastic Processes
Models, Statistical
Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
Metagenome

@article {pmid39853685,
year = {2025},
author = {Sun, Y and Gan, Z and Liu, S and Zhang, S and Zhong, W and Liu, J and Huang, X and He, W and Zhong, H and Cao, Q},
title = {Metagenomic and Transcriptomic Analysis Reveals Crosstalk Between Intratumor Mycobiome and Hosts in Early-Stage Nonsmoking Lung Adenocarcinoma Patients.},
journal = {Thoracic cancer},
volume = {16},
number = {2},
pages = {e15527},
doi = {10.1111/1759-7714.15527},
pmid = {39853685},
issn = {1759-7714},
support = {220904094208//Fifth Affiliated Hospital of Sun Yat-sen University Qingdong Cao's talent-attracting fund/ ; 3320104100430//Exploration and Practice of a Tri-Party Personalized Oncology Strategy Based on Precision Medicine in Patient-Doctor-Research Collaboration/ ; },
mesh = {Humans ; *Lung Neoplasms/microbiology/genetics/pathology ; *Adenocarcinoma of Lung/microbiology/genetics/pathology ; *Mycobiome ; Female ; *Metagenomics/methods ; Male ; Middle Aged ; Gene Expression Profiling ; Aged ; Transcriptome ; Prognosis ; Tumor Microenvironment ; Case-Control Studies ; },
abstract = {BACKGROUND: The mycobiome in the tumor microenvironment of non-smokers with early-stage lung adenocarcinoma (ES-LUAD) has been minimally investigated.

METHODS: In this study, we conducted ultra-deep metagenomic and transcriptomic sequencing on 128 samples collected from 46 nonsmoking ES-LUAD patients and 41 healthy controls (HC), aiming to characterize the tumor-resident mycobiome and its interactions with the host.

RESULTS: The results revealed that ES-LUAD patients exhibited fungal dysbiosis characterized by reduced species diversity and significant imbalances in specific fungal abundances. Concurrently, microbial functional analysis revealed significant alterations associated with genes such as ribosomal proteins and histones. We observed correlations between Yarrowia lipolytica, Saccharomyces paradoxus, and tumor-infiltrating immune cells (TIICs), and identified a strong association (|rho| > 0.7) between S. paradoxus and 14 transcription factors. A signature of three prognostic genes (GRIA1, CDO1, FHL1) closely associated with S. paradoxus was identified and they suggest that the interaction between the mycobiome and the host may contribute to prolonged overall survival (OS). Finally, a predictive model based on six fungi demonstrated decent classification performance in distinguishing ES-LUAD cases from HCs (AUC = 0.724).

CONCLUSIONS: Our study demonstrates that the interactions between the mycobiome and transcriptome within tumors may help elucidate the pathogenic mechanisms of ES-LUAD. Fungi, as a potential predictive tool, can be used as an additional resource for accurately detecting and discriminating individuals with ES-LUAD.},
}

Humans
*Lung Neoplasms/microbiology/genetics/pathology
*Adenocarcinoma of Lung/microbiology/genetics/pathology
*Mycobiome
Female
*Metagenomics/methods
Male
Middle Aged
Gene Expression Profiling
Aged
Transcriptome
Prognosis
Tumor Microenvironment
Case-Control Studies

@article {pmid39850835,
year = {2025},
author = {Zhang, Q and Zhen, M and Wang, X and Zhao, F and Dong, Y and Wang, X and Gao, S and Wang, J and Shi, W and Zhang, Y},
title = {Antibiotic exposure enriches streptococci carrying resistance genes in periodontitis plaque biofilms.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18835},
pmid = {39850835},
issn = {2167-8359},
mesh = {Humans ; *Biofilms/drug effects/growth & development ; *Periodontitis/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Streptococcus/drug effects/genetics ; Female ; Male ; Adult ; *Dental Plaque/microbiology ; *Amoxicillin/pharmacology/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Drug Resistance, Bacterial/genetics ; Microbiota/drug effects/genetics ; Tetracycline/pharmacology/therapeutic use ; Metronidazole/pharmacology/therapeutic use ; Clindamycin/pharmacology/therapeutic use ; },
abstract = {BACKGROUND: Periodontitis is not always satisfactorily treated with conventional scaling and root planing, and adjunctive use of antibiotics is required in clinical practice. Therefore, it is important for clinicians to understand the diversity and the antibiotic resistance of subgingival microbiota when exposed to different antibiotics.

MATERIALS AND METHODS: In this study, subgingival plaques were collected from 10 periodontitis patients and 11 periodontally healthy volunteers, and their microbiota response to selective pressure of four antibiotics (amoxicillin, metronidazole, clindamycin, and tetracycline) were evaluated through 16S rRNA gene amplicon and metagenomic sequencing analysis. Additionally, sensitive and resistant strains were isolated and cultured in vitro for resistance evaluation.

RESULTS: Cultivation of subgingival microbiota revealed the oral microbiota from periodontitis patients were more resistant to antibiotics than that of healthy. Significant differences were also observed for the microbial community between with and without antibiotics (especially amoxicillin and tetracycline) treated in periodontitis group.

CONCLUSION: Overall, after the two antibiotics (amoxicillin and tetracycline) exposed, the oral subgingival microbiota in periodontitis patients exhibited different diversity and composition. Streptococcus may account for oral biofilm-specific antibiotic resistance in periodontitis. This provides information for personalized treatment of periodontitis.},
}

Humans
*Biofilms/drug effects/growth & development
*Periodontitis/microbiology/drug therapy
*Anti-Bacterial Agents/pharmacology/therapeutic use
*Streptococcus/drug effects/genetics
Female
Male
Adult
*Dental Plaque/microbiology
*Amoxicillin/pharmacology/therapeutic use
RNA, Ribosomal, 16S/genetics
Middle Aged
Drug Resistance, Bacterial/genetics
Microbiota/drug effects/genetics
Tetracycline/pharmacology/therapeutic use
Metronidazole/pharmacology/therapeutic use
Clindamycin/pharmacology/therapeutic use

@article {pmid39849759,
year = {2025},
author = {Peng, Q and Huang, J and Li, S and Chen, Z and Zhu, Q and Yuan, H and Li, J and Massou, BB and Xie, G},
title = {Dynamics of microbial communities and metabolites during the fermentation of Ningxia goji berry wine: An integrated metagenomics and metabolomics approach.},
journal = {Food research international (Ottawa, Ont.)},
volume = {201},
number = {},
pages = {115609},
doi = {10.1016/j.foodres.2024.115609},
pmid = {39849759},
issn = {1873-7145},
mesh = {*Fermentation ; *Wine/analysis/microbiology ; *Metabolomics ; *Metagenomics ; *Microbiota ; Volatile Organic Compounds/analysis/metabolism ; Bacteria/metabolism/genetics/classification ; Fruit ; Taste ; Food Microbiology ; },
abstract = {Ningxia Goji Berry Wine (NGBW), a traditional Chinese fermented beverage, exhibits complex flavor quality changes during fermentation, the mechanisms of which remain insufficiently elucidated. This study aimed to elucidate the dynamic shifts in physicochemical properties, metabolites, and microbial communities throughout the controlled fermentation process of NGBW. Metabolomic analysis identified 8 key differential volatile metabolites (VOCs) and 406 differential non-volatile metabolites. The enrichment analysis of KEGG metabolic pathways revealed that, during the fermentation of NGBW, ten critical metabolic pathways-Purine metabolism, Glycine, Serine, and Threonine metabolism, Galactose metabolism, and the Citric Acid (TCA) Cycle-play essential roles. Amplicon sequencing indicated that 25 bacterial genera dominated the microbial ecosystem (relative abundance ≥ 0.1 %). Spearman correlation analysis revealed significant associations between 5 core microorganism and flavor compounds, and 25 core microbes with non-volatile metabolites, suggesting their pivotal roles in flavor formation. This study provides a theoretical basis for optimizing the fermentation process and enhancing the flavor quality of NGBW.},
}

*Fermentation
*Wine/analysis/microbiology
*Metabolomics
*Metagenomics
*Microbiota
Volatile Organic Compounds/analysis/metabolism
Bacteria/metabolism/genetics/classification
Fruit
Taste
Food Microbiology

@article {pmid39849445,
year = {2025},
author = {Xie, H and Chen, Z and Wu, G and Wei, P and Gong, T and Chen, S and Xu, Z},
title = {Application of metagenomic next-generation sequencing (mNGS) to describe the microbial characteristics of diabetic foot ulcers at a tertiary medical center in South China.},
journal = {BMC endocrine disorders},
volume = {25},
number = {1},
pages = {18},
pmid = {39849445},
issn = {1472-6823},
support = {[2021]76//the High-level Hospital and Clinical Specialty Discipline Construction Programme for Fujian Medical Development, China/ ; 2023J01692//Fujian Provincial Natural Science Foundation of China/ ; 2022J01243//Fujian Provincial Natural Science Foundation of China/ ; 2020Y9094//the Joint Funds for the innovation of science and Technology，Fujian province, China/ ; 2023Y9213//the Joint Funds for the innovation of science and Technology，Fujian province, China/ ; 2021Y9068//the Joint Funds for the innovation of science and Technology，Fujian province, China/ ; 82002034//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Diabetic Foot/microbiology/diagnosis ; China/epidemiology ; *High-Throughput Nucleotide Sequencing/methods ; *Tertiary Care Centers ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; Aged ; Microbiota/genetics ; Adult ; },
abstract = {BACKGROUND: Diabetic foot ulcers (DFUs) are characterized by dynamic wound microbiome, the timely and accurate identification of pathogens in the clinic is required to initiate precise and individualized treatment. Metagenomic next-generation sequencing (mNGS) has been a useful supplement to routine culture method for the etiological diagnosis of DFUs. In this study, we utilized a routine culture method and mNGS to analyze the same DFU wound samples and the results were compared.

METHODS: Forty samples from patients with DFUs at a tertiary medical center in South China were collected, the microorganisms were identified with mNGS and routine culture method simultaneously.

RESULTS: The results showed that the positive detection rate of microorganisms in DFUs with mNGS was much higher (95% vs. 60%). Thirteen strains of microorganisms were detected with routine culture method, and seventy-seven strains were detected with mNGS. Staphylococcus aureus was the most common microorganism detected with culture method, while Enterococcus faecalis was the most common microorganism detected with mNGS. The false negative rate of the culture method was 35%, that was, 14 samples with negative results with culture method were found to be positive with mNGS.

CONCLUSION: The mNGS method had a higher positive detection rate and identified a broader spectrum of microorganisms in DFUs, thus, mNGS provided a more comprehensive understanding of the microbiome of DFUs to facilitate the development of timely and optimal treatment.

TRIAL REGISTRATION: The study was conducted in accordance with the Declaration of Helsinki and approved by the Ethical Review Committee of the Fujian Medical University Union Hospital (approval number 2021KY054).},
}

Humans
*Diabetic Foot/microbiology/diagnosis
China/epidemiology
*High-Throughput Nucleotide Sequencing/methods
*Tertiary Care Centers
Male
Female
*Metagenomics/methods
Middle Aged
Aged
Microbiota/genetics
Adult

@article {pmid39693966,
year = {2025},
author = {Li, T and Wang, P and Zhi, Z and Guo, T and Zhou, J and Zhang, H and Cao, C and Cai, Y and Li, Y and Zhang, J},
title = {Free-caged rearing modes regulate chicken intestinal metabolism by influencing gut microbial homeostasis.},
journal = {Poultry science},
volume = {104},
number = {1},
pages = {104381},
pmid = {39693966},
issn = {1525-3171},
mesh = {Animals ; *Chickens ; *Gastrointestinal Microbiome/physiology ; *Homeostasis ; *Animal Husbandry/methods ; Cecum/microbiology/metabolism ; Housing, Animal ; Bacteria/classification/metabolism/genetics ; Male ; },
abstract = {Free-caged rearing modes, which prioritize animal welfare, are believed to enhance the quality of animal products. The impact of rearing modes on meat quality may play a key role in the superior quality of local chicken breeds. This study analyzed the cecal contents of free-range and caged black-bone chickens at different ages using metagenomic and metabolomic sequencing. We identified 32 metabolites and 367 microbial species significantly affected by the rearing mode. Linear discriminant analysis Effect Size (LefSe) highlighted five key microorganisms, Gemmiger formicilis, Bacteria unclassified, Bacteroides sp. ET225, Massilistercora timonensis, and Bacteroidales unclassified, that showed distinct abundance patterns across all age points. Among them, Bacteroides sp. ET225 and Massilistercora timonensis were positively associated with certain phospholipids and plant-derived metabolites, while negatively correlated with others like demissidine and acylcarnitine. Functional analysis revealed that rearing modes impact gut metabolites involved in gut metabolism as well as broader processes such as signal transduction, protein digestion, and autophagy. This study offers new insights into how rearing modes influence gut microbiota and metabolites, shedding light on the study of rearing mode-mediated muscle development and fat deposition.},
}

Animals
*Chickens
*Gastrointestinal Microbiome/physiology
*Homeostasis
*Animal Husbandry/methods
Cecum/microbiology/metabolism
Housing, Animal
Bacteria/classification/metabolism/genetics
Male

@article {pmid39849165,
year = {2025},
author = {Sandhu, S and Kumar, S and Singh, P and Singh, BP and Jurel, SK and Lal, N and Mohit, and Sharma, V and Rai, N and Chand, P},
title = {Metagenomic profiling of plaque microbiota in Indian subjects: identified hidden ecological tapestry.},
journal = {Current genetics},
volume = {71},
number = {1},
pages = {3},
pmid = {39849165},
issn = {1432-0983},
mesh = {Humans ; *Dental Plaque/microbiology ; *Metagenomics/methods ; Male ; *Microbiota/genetics ; Female ; India/epidemiology ; Adult ; *Metagenome ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; Young Adult ; Adolescent ; Bacteria/genetics/classification/isolation & purification ; Streptococcus/genetics/isolation & purification/classification ; },
abstract = {Dental plaque biofilms are the primary etiologic factor for various chronic oral infectious diseases. In recent years, dental plaque shows enormous potential to know about an individual microbiota. Various microbiome studies of oral cavity from different geographical locations reveals abundance of microbial species. Although, the representation of Indian population in this respect is limited, which make us curious to undergo this study. This study investigates the dental plaque microbiota of North Indian individuals based on their age, gender, and dietary patterns; specifically, food preference and availability of water source using 16 S rRNA metagenomics analysis. The findings from this study revealed that Streptococcus levels are high across genders, age groups, and water source, highlighting its role as a predominant dental caries associated species like Streptococcus mutans, Streptococcus pyogenes, Streptococcus sobrinus and Streptococcus oralis in the studied population groups. Additionally, the abundance of Actinomyces is observed higher in young individuals and females whereas Fusobacterium and Leptotrichia were high in elderly individuals. Moreover, non-vegetarians have higher abundance of Streptococcus and Fusobacterium, whereas vegetarians show higher abundance of Prevotella and Leptotrichia. The study also highlights the influence of water type on bacterial composition of dental plaque in the studied population i.e., individuals consuming underground water has high abundance of Streptococcus, whereas individuals consuming RO water exhibit elevated Prevotella and Leptotrichia. Insights emerged from the analysis illuminates the complex dynamics of microbiota in dental plaque among North Indians. This study also highlight that this variation of microbiome is influenced by age, gender, and dietary habits (vegetarian or non-vegetarian lifestyle). These results will fill a significant knowledge gap regarding the Indian dental plaque microbiome but also offer a foundation to conduct metagenome studies and potential therapeutic implications for future personalized oral health interventions.},
}

Humans
*Dental Plaque/microbiology
*Metagenomics/methods
Male
*Microbiota/genetics
Female
India/epidemiology
Adult
*Metagenome
*RNA, Ribosomal, 16S/genetics
Middle Aged
Young Adult
Adolescent
Bacteria/genetics/classification/isolation & purification
Streptococcus/genetics/isolation & purification/classification

@article {pmid39844180,
year = {2025},
author = {Chen, J and Pan, Q and Lu, L and Huang, X and Wang, S and Liu, X and Lun, J and Xu, X and Su, H and Guo, F and Yang, L and You, L and Xiao, H and Luo, W and Liu, HF and Pan, Q},
title = {Atg5 deficiency in basophils improves metabolism in lupus mice by regulating gut microbiota dysbiosis.},
journal = {Cell communication and signaling : CCS},
volume = {23},
number = {1},
pages = {40},
pmid = {39844180},
issn = {1478-811X},
support = {No. 82070757, 82270770//National Natural Science Foundation of China/ ; No. 82070757, 82270770//National Natural Science Foundation of China/ ; 2022B1212030003//Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Noncommunicable Diseases/ ; 2022B1212030003//Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Noncommunicable Diseases/ ; 2022B1212030003//Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Noncommunicable Diseases/ ; 2021A05067//Science and Technology Planning Project of Zhanjiang City/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Lupus Erythematosus, Systemic/metabolism ; *Basophils/metabolism ; *Dysbiosis ; Mice ; *Autophagy-Related Protein 5/genetics/metabolism ; Mice, Inbred MRL lpr ; Mice, Knockout ; Female ; Autophagy ; Mice, Inbred C57BL ; },
abstract = {Autophagic activation in immune cells, gut microbiota dysbiosis, and metabolic abnormalities have been reported separately as characteristics of systemic lupus erythematosus (SLE). Elucidating the crosstalk among the immune system, commensal microbiota, and metabolites is crucial to understanding the pathogenesis of autoimmune diseases. Emerging evidence shows that basophil activation plays a critical role in the pathogenesis of SLE; however, the underlying mechanisms remain largely unknown. Here, we investigated the effects of autophagic inhibition on the pathogenesis of basophils in SLE using Autophagy-related gene 5 (Atg5) knockout (Atg5[-/-]) as an autophagic inhibitor. Specifically, we knocked out basophilic Atg5 in vivo to investigate its impact on lupus metabolism. Furthermore, Atg5[-/-] basophils were transferred to basophil-depleted MRL/MpJ-Fas[lpr] (MRL/lpr) mice to study their effect on disease metabolism. Metagenomic and targeted metabolomic sequencing results indicated considerable reduction in the levels of plasma autoantibodies and inflammatory cytokines in the Atg5[-/-] basophil transfer group compared with that in the control group. Transplanting Atg5[-/-] basophils improved the gut microbiota balance in MRL/lpr mice, increasing the abundance of beneficial bacteria, such as Ligilactobacillus murinus and Faecalitalea rodentium, and reducing that of potentially pathogenic bacteria such as Phocaeicola salanitronis. The transplantation of Atg5-deficient basophils improved lupus symptoms by modulating lipid and amino acid metabolism. This improvement was linked to changes in the gut microbiota, particularly an increase in Ligilactobacillus murinus and Faecalitalea rodentium populations. These microbial shifts are believed to promote the production of beneficial metabolites, such as γ-linolenic acid and oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine, while reducing the levels of harmful metabolites such as arginine. These alterations in the metabolic profile contribute to the alleviation of lupus symptoms. Collectively, these findings reveal a novel role of basophil autophagy in SLE, highlighting its potential as a therapeutic target.},
}

Animals
*Gastrointestinal Microbiome
*Lupus Erythematosus, Systemic/metabolism
*Basophils/metabolism
*Dysbiosis
Mice
*Autophagy-Related Protein 5/genetics/metabolism
Mice, Inbred MRL lpr
Mice, Knockout
Female
Autophagy
Mice, Inbred C57BL

@article {pmid39843539,
year = {2025},
author = {Laczkó, L and Nagy, NA and Nagy, Á and Maroda, Á and Sály, P},
title = {An updated reference genome of Barbatula barbatula (Linnaeus, 1758).},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {137},
pmid = {39843539},
issn = {2052-4463},
support = {OTKA PD142602//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; },
mesh = {Animals ; *Genome ; *Microsatellite Repeats ; Cypriniformes/genetics ; },
abstract = {The stone loach Barbatula barbatula is a benthic fish species widely distributed throughout Europe, primarily inhabiting stony upper sections of stream networks. This study presents an updated genome assembly of B. barbatula, contributing to the species' available genomic resources for downstream applications such as conservation genetics. The draft assembly was 550 Mbp in size, with an N50 of 11.21 Mbp. We used the species' available chromosome scaffolds to finish the genome. The final assembly had a BUSCO score of 96.7%. We identified 23270 protein-coding genes, and the proteome exhibited high completeness with BUSCO (93.1%) and OMArk (90.81%). Despite using multiple approaches to reduce duplicate contigs, we observed a relatively high duplicate ratio of 6.1% (BUSCO) and 8.52% (OMArk) in the annotations. We aimed to find microsatellite loci present in both the species' publicly available genome and the new assembly to aid marker development for downstream analyses. This dataset serves as a reference for genomic analysis and is useful for developing markers to study the species' biodiversity and support conservation efforts.},
}

Animals
*Genome
*Microsatellite Repeats
Cypriniformes/genetics

@article {pmid39843522,
year = {2025},
author = {Bray, AS and Broberg, CA and Hudson, AW and Wu, W and Nagpal, RK and Islam, M and Valencia-Bacca, JD and Shahid, F and Hernandez, GE and Nutter, NA and Walker, KA and Bennett, EF and Young, TM and Barnes, AJ and Ornelles, DA and Miller, VL and Zafar, MA},
title = {Klebsiella pneumoniae employs a type VI secretion system to overcome microbiota-mediated colonization resistance.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {940},
pmid = {39843522},
issn = {2041-1723},
support = {AI178595//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI166642//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI173244//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {*Klebsiella pneumoniae/genetics/metabolism ; *Type VI Secretion Systems/genetics/metabolism ; Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Klebsiella Infections/microbiology ; Gene Expression Regulation, Bacterial ; Gastrointestinal Tract/microbiology ; Bacterial Proteins/metabolism/genetics ; DNA Transposable Elements/genetics ; Female ; Mice, Inbred C57BL ; },
abstract = {Microbial species must compete for space and nutrients to persist in the gastrointestinal (GI) tract, and our understanding of the complex pathobiont-microbiota interactions is far from complete. Klebsiella pneumoniae, a problematic, often drug-resistant nosocomial pathogen, can colonize the GI tract asymptomatically, serving as an infection reservoir. To provide insight on how K. pneumoniae interacts with the resident gut microbiome, we conduct a transposon mutagenesis screen using a murine model of GI colonization with an intact microbiota. Among the genes identified were those encoding a type VI secretion system (T6SS), which mediates contact-dependent killing of gram-negative bacteria. From several approaches, we demonstrate that the T6SS is critical for K. pneumoniae gut colonization. Metagenomics and in vitro killing assays reveal that K. pneumoniae reduces Betaproteobacteria species in a T6SS-dependent manner, thus identifying specific species targeted by K. pneumoniae. We further show that T6SS gene expression is controlled by several transcriptional regulators and that expression only occurs in vitro under conditions that mimic the gut environment. By enabling K. pneumoniae to thrive in the gut, the T6SS indirectly contributes to the pathogenic potential of this organism. These observations advance our molecular understanding of how K. pneumoniae successfully colonizes the GI tract.},
}

*Klebsiella pneumoniae/genetics/metabolism
*Type VI Secretion Systems/genetics/metabolism
Animals
*Gastrointestinal Microbiome/genetics
Mice
*Klebsiella Infections/microbiology
Gene Expression Regulation, Bacterial
Gastrointestinal Tract/microbiology
Bacterial Proteins/metabolism/genetics
DNA Transposable Elements/genetics
Female
Mice, Inbred C57BL

@article {pmid39843444,
year = {2025},
author = {Bechtold, EK and Ellenbogen, JB and Villa, JA and de Melo Ferreira, DK and Oliverio, AM and Kostka, JE and Rich, VI and Varner, RK and Bansal, S and Ward, EJ and Bohrer, G and Borton, MA and Wrighton, KC and Wilkins, MJ},
title = {Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {944},
pmid = {39843444},
issn = {2041-1723},
support = {EAR-2029686//National Science Foundation (NSF)/ ; PRFB-2109592//National Science Foundation (NSF)/ ; DEB-1754756//National Science Foundation (NSF)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; DE-SC000054//U.S. Department of Energy (DOE)/ ; DE-SC0007144//U.S. Department of Energy (DOE)/ ; DE-SC0012088//U.S. Department of Energy (DOE)/ ; DESC0023297//U.S. Department of Energy (DOE)/ ; DE-SC0023456//U.S. Department of Energy (DOE)/ ; DE-SC0023456//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC000054//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC000054//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; DE-SC0022191//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0021350//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0021350//U.S. Department of Energy (DOE)/ ; DESC000054//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; },
mesh = {*Methane/metabolism ; *Wetlands ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Fresh Water/microbiology ; Metagenome ; Bacteria/metabolism/genetics/classification ; Climate Change ; },
abstract = {Current estimates of wetland contributions to the global methane budget carry high uncertainty, particularly in accurately predicting emissions from high methane-emitting wetlands. Microorganisms drive methane cycling, but little is known about their conservation across wetlands. To address this, we integrate 16S rRNA amplicon datasets, metagenomes, metatranscriptomes, and annual methane flux data across 9 wetlands, creating the Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. This resource is used to link microbiome composition to function and methane emissions, focusing on methane-cycling microbes and the networks driving carbon decomposition. We identify eight methane-cycling genera shared across wetlands and show wetland-specific metabolic interactions in marshes, revealing low connections between methanogens and methanotrophs in high-emitting wetlands. Methanoregula emerged as a hub methanogen across networks and is a strong predictor of methane flux. In these wetlands it also displays the functional potential for methylotrophic methanogenesis, highlighting the importance of this pathway in these ecosystems. Collectively, our findings illuminate trends between microbial decomposition networks and methane flux while providing an extensive publicly available database to advance future wetland research.},
}

*Methane/metabolism
*Wetlands
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Fresh Water/microbiology
Metagenome
Bacteria/metabolism/genetics/classification
Climate Change

@article {pmid39809266,
year = {2025},
author = {Wang, D and Jiang, Y and Jiang, J and Pan, Y and Yang, Y and Fang, X and Liang, L and Li, H and Dong, Z and Fan, S and Ma, D and Zhang, XS and Li, H and He, Y and Li, N},
title = {Gut microbial GABA imbalance emerges as a metabolic signature in mild autism spectrum disorder linked to overrepresented Escherichia.},
journal = {Cell reports. Medicine},
volume = {6},
number = {1},
pages = {101919},
doi = {10.1016/j.xcrm.2024.101919},
pmid = {39809266},
issn = {2666-3791},
mesh = {*Gastrointestinal Microbiome/genetics ; *Autism Spectrum Disorder/metabolism/microbiology/genetics ; *gamma-Aminobutyric Acid/metabolism ; Humans ; Animals ; Female ; Male ; Mice ; Child ; Child, Preschool ; Metabolomics/methods ; RNA, Ribosomal, 16S/genetics ; Escherichia/metabolism/genetics ; Feces/microbiology ; Glutamic Acid/metabolism ; Mice, Inbred C57BL ; Escherichia coli/genetics/metabolism ; Metabolome ; },
abstract = {Gut microbiota (GM) alterations have been implicated in autism spectrum disorder (ASD), yet the specific functional architecture remains elusive. Here, employing multi-omics approaches, we investigate stool samples from two distinct cohorts comprising 203 children with mild ASD or typical development. In our screening cohort, regression-based analysis for metabolomic profiling identifies an elevated γ-aminobutyric acid (GABA) to glutamate (Glu) ratio as a metabolic signature of ASD, independent of age and gender. In the validating cohort, we affirm the GABA/Glu ratio as an ASD diagnostic indicator after adjusting for geography, age, gender, and specific food-consuming frequency. Integrated analysis of metabolomics, 16S rRNA sequencing, and metagenomics reveals a correlation between overrepresented Escherichia and disrupted GABA metabolism. Furthermore, we observe social behavioral impairments in weaning mice transplanted with E. coli, suggesting a potential link to ASD symptomatology. Collectively, these findings provide insights into potential diagnostic and therapeutic strategies aimed at evaluating and restoring gut microbial neurotransmitter homeostasis.},
}

*Gastrointestinal Microbiome/genetics
*Autism Spectrum Disorder/metabolism/microbiology/genetics
*gamma-Aminobutyric Acid/metabolism
Humans
Animals
Female
Male
Mice
Child
Child, Preschool
Metabolomics/methods
RNA, Ribosomal, 16S/genetics
Escherichia/metabolism/genetics
Feces/microbiology
Glutamic Acid/metabolism
Mice, Inbred C57BL
Escherichia coli/genetics/metabolism
Metabolome

@article {pmid39739308,
year = {2024},
author = {Chaabane, F and Pillonel, T and Bertelli, C},
title = {MeSS and assembly_finder: a toolkit for in silico metagenomic sample generation.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {1},
pages = {},
doi = {10.1093/bioinformatics/btae760},
pmid = {39739308},
issn = {1367-4811},
mesh = {*Metagenomics/methods ; *Software ; Microbiota/genetics ; Computational Biology/methods ; Humans ; Computer Simulation ; Metagenome ; Sequence Analysis, DNA/methods ; },
abstract = {SUMMARY: The intrinsic complexity of the microbiota combined with technical variability render shotgun metagenomics challenging to analyze for routine clinical or research applications. In silico data generation offers a controlled environment allowing for example to benchmark bioinformatics tools, to optimize study design, statistical power, or to validate targeted applications. Here, we propose assembly_finder and the Metagenomic Sequence Simulator (MeSS), two easy-to-use Bioconda packages, as part of a benchmarking toolkit to download genomes and simulate shotgun metagenomics samples, respectively. Outperforming existing tools in speed while requiring less memory, MeSS reproducibly generates accurate complex communities based on a list of taxonomic ranks and their abundance.

All code is released under MIT License and is available on https://github.com/metagenlab/MeSS and https://github.com/metagenlab/assembly_finder.},
}

*Metagenomics/methods
*Software
Microbiota/genetics
Computational Biology/methods
Humans
Computer Simulation
Metagenome
Sequence Analysis, DNA/methods

@article {pmid39523638,
year = {2024},
author = {Munjita, SM and Mubemba, B and Tembo, J and Bates, M and Munsaka, S},
title = {Rhipicephalus simus ticks: new hosts for phleboviruses.},
journal = {Parasitology},
volume = {151},
number = {9},
pages = {962-970},
doi = {10.1017/S0031182024001033},
pmid = {39523638},
issn = {1469-8161},
support = {RIA2016E-1609//European and Developing Countries Clinical Trials Partnership/ ; },
mesh = {*Rhipicephalus/microbiology/virology ; *Phlebovirus/classification/genetics ; Metagenome/genetics ; Genome, Viral/genetics ; Zambia ; Phylogeny ; Biodiversity ; Animals ; Disease Vectors ; },
abstract = {Ticks are widespread arthropods that transmit microorganisms of veterinary and medical significance to vertebrates, including humans. Rhipicephalus simus, an ixodid tick frequently infesting and feeding on humans, may play a crucial role in transmitting infectious agents across species. Despite the known association of many Rhipicephalus ticks with phleboviruses, information on R. simus is lacking. During a study in a riverine area in Lusaka Zambia, ten R. simus ticks were incidentally collected from the grass and bushes and subjected to metagenomic next generation sequencing (mNGS) in 2 pools of 5. Analysis detected a diverse microbial profile, including bacteria 82% (32/39), fungi 15.4% (6/39), and viruses 2.6% (1/39). Notably, viral sequence LSK-ZM-102022 exhibited similarity to tick phleboviruses, sharing 74.92% nucleotide identity in the RdRp gene and 72% in the NP gene with tick-borne phlebovirus (TBPV) from Greece and Romania, respectively. Its RNA-dependent RNA polymerase (RdRp) encoding region carried conserved RdRp and endonuclease domains characteristic of phenuiviridae viruses. Phylogenetic analysis positioned LSK-ZM-102022 in a distinct but lone lineage within tick phleboviruses basal to known species like brown dog tick phlebovirus and phlebovirus Antigone. Pair-wise genetic distance analysis revealed similar findings. This study emphasizes the urgency of further research on the ecology, transmission dynamics, and pathogenic potential of LSK-ZM-102022 and related TBPVs, crucial for local and global preparedness against emerging tick-borne diseases.},
}

*Rhipicephalus/microbiology/virology
*Phlebovirus/classification/genetics
Metagenome/genetics
Genome, Viral/genetics
Zambia
Phylogeny
Biodiversity
Animals
Disease Vectors

@article {pmid38709227,
year = {2025},
author = {Unzueta-Medina, JA and González-Chávez, SA and Salas-Leiva, JS and Silva-Sánchez, SE and Pacheco-Tena, C},
title = {Differential Composition and Structure of the Microbiota from Active and Inactive Stages of HLA-B27-associated Uveitis by Paired Fecal Metagenomes.},
journal = {Ocular immunology and inflammation},
volume = {33},
number = {1},
pages = {56-64},
doi = {10.1080/09273948.2024.2346818},
pmid = {38709227},
issn = {1744-5078},
mesh = {Humans ; *HLA-B27 Antigen/genetics/immunology ; Male ; *Feces/microbiology ; Prospective Studies ; Adult ; Female ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Uveitis, Anterior/microbiology/immunology ; Metagenome ; Bacteria/genetics/isolation & purification ; DNA, Bacterial/genetics ; Microbiota ; Acute Disease ; },
abstract = {PURPOSE: To compare the diversities and abundances of bacterial taxa in the microbiome of patients with HLA B27-positive acute anterior uveitis (AAU) in the active and inactive phases.

METHODS: An observational descriptive prospective and comparative study was conducted in ten HLA-B27-positive AAU patients (44.6 ± 13.4 years). The microbiome of the stool samples obtained in the active and inactive stages was analyzed by sequencing the V3 region of the 16S rRNA gene.

RESULTS: The differences in the bacteria profile between active and inactive stages in each individual were confirmed (p < 0.0001). Ten OTUs were found exclusively in the active phase of 90% of the individuals, suggesting a proinflammatory association. Blautia OUT_4 and Faecalibacterium OUT_2 abundances showed a direct relationship between abundance and severity of ocular inflammation. Two OTUs were exclusive of the inactive stage, suggesting an anti-inflammatory role.

CONCLUSION: The metagenomic profile of the fecal microbiota differs in the acute phase of the AAU compared to when the inflammation subsides, despite being the same individual and a short time-lapse. AAU is a fertile field for studying the connection between subtle rapid changes in microbiota and their systemic consequences.},
}

Humans
*HLA-B27 Antigen/genetics/immunology
Male
*Feces/microbiology
Prospective Studies
Adult
Female
*RNA, Ribosomal, 16S/genetics
Middle Aged
*Uveitis, Anterior/microbiology/immunology
Metagenome
Bacteria/genetics/isolation & purification
DNA, Bacterial/genetics
Microbiota
Acute Disease

@article {pmid39841201,
year = {2025},
author = {Geng, P and Zhao, N and Zhou, Y and Harris, RS and Ge, Y},
title = {Faecalibacterium prausnitzii regulates carbohydrate metabolic functions of the gut microbiome in C57BL/6 mice.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2455503},
doi = {10.1080/19490976.2025.2455503},
pmid = {39841201},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Mice, Inbred C57BL ; Mice ; *Carbohydrate Metabolism ; *Faecalibacterium prausnitzii/metabolism/genetics ; *Phylogeny ; *Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Probiotics/administration & dosage ; Male ; Metagenome ; },
abstract = {The probiotic impact of microbes on host metabolism and health depends on both host genetics and bacterial genomic variation. Faecalibacterium prausnitzii is the predominant human gut commensal emerging as a next-generation probiotic. Although this bacterium exhibits substantial intraspecies diversity, it is unclear whether genetically distinct F. prausnitzii strains might lead to functional differences in the gut microbiome. Here, we isolated and characterized a novel F. prausnitzii strain (UT1) that belongs to the most prevalent but underappreciated phylogenetic clade in the global human population. Genome analysis showed that this butyrate-producing isolate carries multiple putative mobile genetic elements, a clade-specific defense system, and a range of carbohydrate catabolic enzymes. Multiomic approaches were used to profile the impact of UT1 on the gut microbiome and associated metabolic activity of C57BL/6 mice at homeostasis. Both 16S rRNA and metagenomic sequencing demonstrated that oral administration of UT1 resulted in profound microbial compositional changes including a significant enrichment of Lactobacillus, Bifidobacterium, and Turicibacter. Functional profiling of the fecal metagenomes revealed a markedly higher abundance of carbohydrate-active enzymes (CAZymes) in UT1-gavaged mice. Accordingly, UT1-conditioned microbiota possessed the elevated capability of utilizing starch in vitro and exhibited a lower availability of microbiota-accessible carbohydrates in the gut. Further analysis uncovered a functional network wherein UT1 reduced the abundance of mucin-degrading CAZymes and microbes, which correlated with a concomitant reduction of fecal mucin glycans. Collectively, our results reveal a crucial role of UT1 in facilitating the carbohydrate metabolism of the gut microbiome and expand our understanding of the genetic and phenotypic diversity of F. prausnitzii.},
}

Animals
*Gastrointestinal Microbiome
*Mice, Inbred C57BL
Mice
*Carbohydrate Metabolism
*Faecalibacterium prausnitzii/metabolism/genetics
*Phylogeny
*Feces/microbiology
RNA, Ribosomal, 16S/genetics
Probiotics/administration & dosage
Male
Metagenome

@article {pmid39838431,
year = {2025},
author = {Sun, Q and Li, BR and Li, DH and Wang, XY and Wang, QY and Jiang, ZM and Ning, SB and Sun, T},
title = {WKB ameliorates DSS-induced colitis through inhibiting enteric glial cells activation and altering the intestinal microbiota.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {93},
pmid = {39838431},
issn = {1479-5876},
support = {No. 22YXQN034//Air Force Medical Center Youth Talent Program Project/ ; No. 2020-4-5123//Capital's Funds for Health Improvement and Research/ ; },
mesh = {Animals ; *Dextran Sulfate ; *Gastrointestinal Microbiome ; *Colitis/pathology/microbiology/chemically induced/complications ; *Mice, Inbred C57BL ; Male ; *Neuroglia/metabolism/pathology ; Cytokines/metabolism ; Colon/pathology/microbiology ; Permeability ; Body Weight ; Inflammation/pathology ; Intestinal Mucosa/pathology/microbiology/metabolism ; Mice ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic condition influenced by diet, which affects gut microbiota and immune functions. The rising prevalence of IBD, linked to Western diets in developing countries, highlights the need for dietary interventions. This study aimed to assess the impact of white kidney beans (WKB) on gut inflammation and microbiota changes, focusing on their effects on enteric glial cells (EGCs) and immune activity in colitis.

METHODS: Male C57BL/6 mice were divided into four groups: normal diet (ND), ND with 2.5% dextran sulfate sodium (DSS) for colitis induction, ND with 20% WKB, and WKB with 2.5% DSS. The dietary intervention lasted 17 weeks, with DSS given in the final week. Colonic inflammation was assessed by body weight, disease activity index, and histopathology. Epithelial barrier integrity was evaluated using immunofluorescence, transmission electron microscopy, and permeability assays. EGCs activity was analyzed via immunofluorescence and quantitative real-time PCR. Immune responses were measured using flow cytometry and cytokine profiling, while gut microbiota changes were examined through metagenomic sequencing.

RESULTS: WKB supplementation significantly alleviated DSS-induced colitis in mice, evidenced by reduced weight loss, disease activity, and improved colonic histology. This effect was linked to enhanced mucosal barrier integrity, seen through increased tight junction protein and Muc2 expression, accompanied by favorable ultrastructural changes. WKB modulated EGCs activity via TNF-like cytokine 1 A inhibition, resulting in reduced glial fibrillary acidic protein expression. Immunologically, it downregulated Th1 and Th17 pro-inflammatory cells, increased Treg cells, and altered cytokine profiles (reduced TNF-α, IFN-γ, IL-17; increased IL-10). Metagenomic analysis showed that WKB restored gut microbiota balance, particularly enhancing beneficial bacteria like Akkermansia. KEGG pathway analysis further indicated that WKB supplementation improved key metabolic pathways, notably those related to phenylalanine, tyrosine, and tryptophan biosynthesis, thereby countering DSS-induced metabolic disruptions.

CONCLUSIONS: WKB shows promise for treating IBD by enhancing mucosal barriers, inhibiting EGCs activity, balancing Th1/Th17/Treg cells, and restoring gut microbiota and metabolic homeostasis, thereby alleviating colitis symptoms.},
}

Animals
*Dextran Sulfate
*Gastrointestinal Microbiome
*Colitis/pathology/microbiology/chemically induced/complications
*Mice, Inbred C57BL
Male
*Neuroglia/metabolism/pathology
Cytokines/metabolism
Colon/pathology/microbiology
Permeability
Body Weight
Inflammation/pathology
Intestinal Mucosa/pathology/microbiology/metabolism
Mice

@article {pmid39838419,
year = {2025},
author = {Liu, X and Ding, H and Zhang, X and Ta, N and Zhao, J and Zhang, Q and Liu, H and Sun, M and Zhang, X},
title = {Dynamic changes in the gastrointestinal microbial communities of Gangba sheep and analysis of their functions in plant biomass degradation at high altitude.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {17},
pmid = {39838419},
issn = {2049-2618},
mesh = {Animals ; Sheep/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Altitude ; *Biomass ; Metagenome ; Animal Feed/microbiology ; Archaea/genetics/classification ; Gastrointestinal Tract/microbiology ; Plants/microbiology ; },
abstract = {BACKGROUND: While Gangba sheep being well known for their unique flavour and nutritional value, harsh environmental factors negatively affect their growth and development, leading to poor productivity. The gastrointestinal tract microbiota plays an important role in host nutrient absorption and metabolism. The identification of dynamic changes in the gastrointestinal microbial communities and their functions is an important step towards improving animal production performance and health.

RESULTS: A comprehensive multi-omics survey of the microbial communities of the Gangba sheep gastrointestinal tract was performed under three distinct feeding strategies: natural grazing, semi-grazing with supplementation, and barn feeding. The dynamic changes, cross-kingdom partnerships and functional potential profiles were analysed and the results revealed that the feeding strategies had a greater impact on the microbial communities than the site of the gastrointestinal tract. The different microbial associations among the groups were revealed by co-occurrence networks based on the amplicon sequence variants (ASVs). Moreover, a Gangba sheep gastrointestinal microbial genomic catalogue was constructed for the first time, including 1146 metagenome-assembled genomes (MAGs) with completeness > 50% and contamination < 10%, among which, 504 bacterial and 15 archaeal MAGs were of high quality with completeness > 80% and contamination < 10%. About 40% of the high-quality MAGs displaying enzyme activity were related to the microbial species that contribute to plant biomass degradation. Most of these enzymes were expressed in rumen metatranscriptome datasets, especially in Prevotella spp. and Ruminococcus spp., suggesting that gastrointestinal microbial communities in ruminants play major roles in the digestion of plant biomass to provide nutrition and energy for the host.

CONCLUSIONS: These findings suggest that feeding strategies are the primary cause of changes in the gastrointestinal microbiome. Diversification of livestock feed might be an effective strategy to maintain the diversity and ecological multifunctionality of microbial communities in the gastrointestinal tract. Additionally, the catalogue of microbial genomes and the encoded biomass-degrading enzymes identified here provide insights into the potential microbial functions of the gastrointestinal tract of Gangba sheep at high altitudes. This paves the way for microbial interventions to improve the growth performance, productivity and product quality of ruminant livestock. Video Abstract.},
}

Animals
Sheep/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification/metabolism
*Altitude
*Biomass
Metagenome
Animal Feed/microbiology
Archaea/genetics/classification
Gastrointestinal Tract/microbiology
Plants/microbiology

@article {pmid39838369,
year = {2025},
author = {Fan, J and Zeng, F and Zhong, H and Cai, J and Shen, W and Cheng, C and He, C and Liu, Y and Zhou, Y and Chen, S and Zhu, Y and Liu, T and Zheng, JS and Wang, L and Chen, YM and Ma, W and Zhou, D},
title = {Potential roles of cigarette smoking on gut microbiota profile among Chinese men.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {25},
pmid = {39838369},
issn = {1741-7015},
mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Cigarette Smoking/adverse effects ; Middle Aged ; Adult ; China ; RNA, Ribosomal, 16S/genetics ; Asian People ; Actinomyces ; Aged ; East Asian People ; },
abstract = {BACKGROUND: Cigarette smoking is posited as a potential factor in disrupting the balance of the human gut microbiota. However, existing studies with limited sample size have yielded inconclusive results.

METHODS: Here, we assessed the association between cigarette smoking and gut microbial profile among Chinese males from four independent studies (N total = 3308). Both 16S rRNA and shotgun metagenomic sequencing methods were employed, covering 206 genera and 237 species. Microbial diversity and abundance were compared among non-smokers, current smokers, and former smokers.

RESULTS: Actinomyces[g], Atopobium[g], Haemophilus[g], Turicibacter[g], and Lachnospira[g] were found to be associated with smoking status (current smokers vs. non-smokers). Metagenomic data provided a higher resolution at the species level, particularly for the Actinomyces[g] branch. Additionally, serum γ-glutamylcysteine (γ-Glu-Cys) was found to have a potential role in connecting smoking and Actinomyces[g]. Furthermore, we revealed putative mediation roles of the gut microbiome in the associations between smoking and common diseases including cholecystitis and type 2 diabetes.

CONCLUSIONS: We characterized the gut microbiota profile in male smokers and further revealed their potential involvement in mediating the impact of smoking on health outcomes. These findings advance our understanding of the intricate association between cigarette smoking and the gut microbiome.},
}

Humans
Male
*Gastrointestinal Microbiome
*Cigarette Smoking/adverse effects
Middle Aged
Adult
China
RNA, Ribosomal, 16S/genetics
Asian People
Actinomyces
Aged
East Asian People

@article {pmid39838275,
year = {2025},
author = {Nabisubi, P and Kanyerezi, S and Kebirungi, G and Sserwadda, I and Nsubuga, M and Kisitu, G and Nahirya, PN and Mulindwa, B and Akabwai, GP and Nantongo, S and Kekitiinwa, A and Kigozi, E and Luutu, NM and Katabazi, FA and Kalema, L and Katabalwa, A and Jjingo, D and Mboowa, G},
title = {Beyond the fever: shotgun metagenomic sequencing of stool unveils pathogenic players in HIV-infected children with non-malarial febrile illness.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {96},
pmid = {39838275},
issn = {1471-2334},
support = {TMA2020CDF-3159//European and Developing Countries Clinical Trials Partnership/ ; TMA2020CDF-3159//European and Developing Countries Clinical Trials Partnership/ ; TMA2020CDF-3159//European and Developing Countries Clinical Trials Partnership/ ; TMA2020CDF-3159//European and Developing Countries Clinical Trials Partnership/ ; TMA2020CDF-3159//European and Developing Countries Clinical Trials Partnership/ ; },
mesh = {Humans ; *Feces/microbiology/virology ; *Metagenomics ; Female ; *HIV Infections/complications/microbiology/virology ; Male ; Child, Preschool ; Child ; Fever/microbiology ; Uganda/epidemiology ; Infant ; Candida albicans/genetics/isolation & purification/classification/pathogenicity ; Giardia/genetics/isolation & purification/classification ; Bacteroides/genetics/isolation & purification/classification ; Gastrointestinal Microbiome/genetics ; },
abstract = {BACKGROUND: Non-malarial febrile illnesses (NMFI) pose significant challenges in HIV-infected children, often leading to severe complications and increased morbidity. While traditional diagnostic approaches focus on specific pathogens, shotgun metagenomic sequencing offers a comprehensive tool to explore the microbial landscape underlying NMFI in this vulnerable population ensuring effective management.

METHODS: In this study, we employed shotgun metagenomics to analyse stool samples from HIV-infected children at the Baylor Children's Clinic Uganda presenting with non-malarial febrile illness. Samples were collected and subjected to DNA extraction at the Molecular and Genomics Laboratory, Makerere University followed by shotgun metagenomics sequencing at the Chan Zuckerberg Biohub San Francisco. Bioinformatics analysis was conducted to identify and characterise the microbial composition and potential pathogenic taxa associated with NMFI using the CZID pipeline.

RESULTS: Our findings reveal a diverse array of microbial taxa in the stool samples of HIV-infected children with NMFI. Importantly, shotgun metagenomics revealed potentially pathogenic players including Trichomonas vaginalis, Candida albicans, Giardia, and Bacteroides in stool from this patient population. This sheds light on the complexities of microbial interactions that potentially underpin non-malarial febrile illness in this group. Taxonomic profiling identified recognised pathogens and comorbidities and revealed possible new correlations with NMFI, shedding light on the pathophysiology of fever in HIV-infected children.

CONCLUSION: Shotgun metagenomics is a valuable method for understanding the gut microbial landscape of NMFI in HIV-infected children, providing a comprehensive approach to pathogen identification and characterisation. By revealing potential pathogenic actors beyond the fever, this work demonstrates how metagenomic sequencing may improve our knowledge of infectious illnesses in vulnerable groups and inspire targeted therapies for better clinical care and outcomes.},
}

Humans
*Feces/microbiology/virology
*Metagenomics
Female
*HIV Infections/complications/microbiology/virology
Male
Child, Preschool
Child
Fever/microbiology
Uganda/epidemiology
Infant
Candida albicans/genetics/isolation & purification/classification/pathogenicity
Giardia/genetics/isolation & purification/classification
Bacteroides/genetics/isolation & purification/classification
Gastrointestinal Microbiome/genetics

@article {pmid39838107,
year = {2025},
author = {Teso-Pérez, C and López-Gazcón, A and Peralta-Sánchez, JM and Martínez-Bueno, M and Valdivia, E and Fárez-Vidal, ME and Martín-Platero, AM},
title = {Bacteriocin-Producing Enterococci Modulate Cheese Microbial Diversity.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {175},
pmid = {39838107},
issn = {1432-184X},
support = {PEJ2018-003019-A//Plan Estatal de Garantía Juvenil (Fondo Social Europeo, Gobierno de España/ ; Group BIO 309//PAIDI Program/ ; A-BIO-083-UGR18//Programa Operativo FEDER Andalucía 2014-2020/ ; },
mesh = {*Cheese/microbiology ; *Bacteriocins/metabolism/biosynthesis ; *Enterococcus/metabolism/genetics ; *Microbiota ; Biodiversity ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Milk/microbiology ; Animals ; },
abstract = {Cheese production involves various lactic acid bacteria (LAB) that break down lactose, milk proteins, and fats, producing key nutrients and influencing the cheese's flavor. They form communities that play a crucial role in determining the cheese's organoleptic properties. The composition of cheeses' microbial communities is shaped by physicochemical factors (e.g., temperature, pH, and salinity) and biological factors (i.e. microbial interactions). While starter cultures are introduced to control these communities, non-starter LAB represent a significant portion of the final microbial assemblage, but their interactions remain unclear. LAB often produce bacteriocins, antimicrobial peptides that antagonize other bacteria, but their role within LAB communities is not fully understood. This study aimed to assess the impact of bacteriocin production on LAB diversity in cheese, using Enterococcus as a model organism, a common bacteriocin producer. We analyzed enterocin production of enterococcal isolates by antimicrobial assays and microbial diversity differences in raw milk cheeses by two approaches: 16S RNA gene amplicon metagenomic sequencing for the whole microbial community and multi-locus sequence analysis (MLSA) for the enterococcal diversity. Our results revealed that LAB communities were dominated by lactococci, lactobacilli, and streptococci, with enterococci present in lower numbers. However, cheeses containing bacteriocin-producing enterococci exhibited higher microbial diversity. Interestingly, the highest diversity occurred at low levels of bacteriocin producers, but this effect was not observed within enterococcal populations. These findings suggest that bacteriocin production plays a key role in shaping LAB communities during cheese ripening, although further research is needed to understand its broader implications in other microbial ecosystems.},
}

*Cheese/microbiology
*Bacteriocins/metabolism/biosynthesis
*Enterococcus/metabolism/genetics
*Microbiota
Biodiversity
Food Microbiology
RNA, Ribosomal, 16S/genetics
Milk/microbiology
Animals

@article {pmid39772525,
year = {2025},
author = {Yum, SJ and Yu, SY and Kim, SM and Jeong, HG},
title = {Antibiotic Resistance Genes and Microbiota in Brassica oleracea var. acephala Cultivated in South Korea: Potential for Resistance Transmission.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {3},
pages = {2156-2166},
doi = {10.1021/acs.jafc.4c11161},
pmid = {39772525},
issn = {1520-5118},
mesh = {*Brassica/microbiology ; Republic of Korea ; *Microbiota/drug effects ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Antimicrobial resistance (AMR) poses a critical global public health challenge. This study investigates the microbiome of Brassica oleracea var. acephala (kale) to evaluate the role of food production systems, particularly plant-derived foods, in AMR dissemination. Using 16S rRNA gene sequencing and metagenomic shotgun sequencing, we analyzed microbial diversity and antimicrobial resistance genes (ARGs) in kale samples. Results showed significant regional differences in microbiota composition and ARG distribution, with traditional fertilizer use linked to higher ARG prevalence in coliform bacteria compared to farms using other fertilization methods. Additionally, we confirmed ARG transfer potential by Klebsiella pneumoniae within coliform populations. Storage conditions notably affected microbial dynamics, with higher temperatures promoting K. pneumoniae growth in washed samples. These findings revealed the importance of AMR research in plant-derived foods and highlight the need for improved agricultural practices to mitigate the risks associated with high ARG abundance in coliform bacteria.},
}

*Brassica/microbiology
Republic of Korea
*Microbiota/drug effects
*Bacteria/genetics/classification/drug effects/isolation & purification
*Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial/genetics
RNA, Ribosomal, 16S/genetics

@article {pmid39722326,
year = {2025},
author = {Liu, X and Chen, Y and Liu, Y and Hu, Y and Wang, K and Huang, L and Ke, X and Peng, L and Guo, Z},
title = {Protective effects and mechanisms of extracts of Gleditsia sinensis Lam. Thorn on DSS-induced colitis in mice.},
journal = {Journal of ethnopharmacology},
volume = {340},
number = {},
pages = {119244},
doi = {10.1016/j.jep.2024.119244},
pmid = {39722326},
issn = {1872-7573},
mesh = {Animals ; *Dextran Sulfate ; *Plant Extracts/pharmacology ; Mice ; Male ; *Gastrointestinal Microbiome/drug effects ; *Cytokines/metabolism ; *Mice, Inbred C57BL ; Colitis/chemically induced/drug therapy/pathology ; Disease Models, Animal ; Colon/drug effects/pathology/metabolism ; Anti-Inflammatory Agents/pharmacology ; Colitis, Ulcerative/chemically induced/drug therapy/pathology ; },
abstract = {Inflammatory Bowel Disease (IBD), encompassing Ulcerative Colitis (UC) and Crohn's Disease (CD), stems from a multifaceted interaction of hereditary, immunological, ecological, and microbial elements. Current treatments have limitations, necessitating new therapeutic approaches.

AIM OF THE STUDY: This study investigates the safeguarding impacts and fundamental processes of extracts of Gleditsia sinensis Lam. thorn (EGST) in a dextran sulfate sodium (DSS)-induced colitis model in mice.

MATERIALS AND METHODS: A total of 180g of dried EGST were prepared, and untargeted metabolomic profiling using high-resolution liquid chromatography electrospray ionization orbitrap mass spectrometry (HR-LC-ESI-Orbitrap-MS) identified 930 compounds. UC model mice were administered 3% DSS for 7 d, followed by EGST treatment. The analysis encompassed physiological and pathological evaluations, serum cytokine ELISA, gut microbiota (GM) metagenomic sequencing, GC-MS metabolomics, mRNA sequencing, and Western Blot.

RESULTS: EGST markedly mitigated colitis symptoms, evidenced by reduced weight loss, lower DAI scores, and less colon shortening. It also decreased levels of pro-inflammatory cytokines (TNF-α, IL-6, IL-1β) while boosting IL-10. Histological examination revealed diminished tissue damage, restoration of crypts, and reduced inflammation, with barrier integrity maintained via upregulation of occludin and ZO-1. Metagenomic sequencing demonstrated that EGST modulated the GM, enhancing the levels of Firmicutes and Bacteroidetes while reducing the levels of Proteobacteria and Verrucomicrobia. Metabolomic analysis indicated that EGST influenced critical pathways, including those involving D-amino acids, glutathione, cysteine, and methionine metabolism. Furthermore, mRNA sequencing identified 2625 differentially expressed genes (DEGs), comprising 1729 with increased and 896 with decreased expression, and highlighted EGST's impact on the PPARγ/AMPK/NF-κB pathway.

CONCLUSION: Overall, EGST mitigates DSS-induced colitis through modulation of GM, metabolic profiles, and gene expression, suggesting its promise as a naturally derived treatment for colitis.},
}

Animals
*Dextran Sulfate
*Plant Extracts/pharmacology
Mice
Male
*Gastrointestinal Microbiome/drug effects
*Cytokines/metabolism
*Mice, Inbred C57BL
Colitis/chemically induced/drug therapy/pathology
Disease Models, Animal
Colon/drug effects/pathology/metabolism
Anti-Inflammatory Agents/pharmacology
Colitis, Ulcerative/chemically induced/drug therapy/pathology

@article {pmid39675450,
year = {2025},
author = {Ye, X and Niu, X and Li, L and Lv, M and Zhang, D and Chen, D and Line, Y and Yang, Z},
title = {Insights into the impact of 6PPD-Q and 6PPD on nitrogen metabolism and microbial community in the anammox system.},
journal = {Environmental research},
volume = {266},
number = {},
pages = {120485},
doi = {10.1016/j.envres.2024.120485},
pmid = {39675450},
issn = {1096-0953},
mesh = {*Nitrogen/metabolism ; Water Pollutants, Chemical/metabolism ; Microbiota/drug effects ; Bacteria/metabolism/genetics ; Waste Disposal, Fluid/methods ; Wastewater/microbiology ; Bioreactors/microbiology ; Oxidation-Reduction ; Anaerobiosis ; },
abstract = {N-(1,3-Dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) is an antioxidant commonly used in tire manufacturing, and its release into the environment has significantly increased due to rapid urbanization. When subjected to ozonation, 6PPD converts into the harmful pollutant 6PPD quinone (6PPDQ). These substances enter wastewater treatment plants (WWTPs) via stormwater runoff and pipelines, posing significant risks to the functional microorganisms. Anammox, a strictly controlled and sensitive microbial nitrogen removal process, is especially susceptible to the effects of the pollutants. This study investigates the comprehensive impact of 6PPD-Q and 6PPD on anammox communities based on characterization analysis and metagenomics. At environmental concentrations, 6PPD-Q at 200 ng/L-1000 ng/L led to the disintegration of anammox granules. Extended exposure to both 6PPD-Q and 6PPD significantly reduces the population of anammox bacteria (AnAOB). By utilizing organic matter from dead cells and incoming carbonate as a carbon source, the system evolved into a nitrogen metabolism network primarily focused on denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This transformation was accompanied by a reshuffling of the microbial community and associated genes, resulting in an accumulation of NH4[+]-N. These findings underscore the toxicity of 6PPD-Q and 6PPD to anammox and stress the importance of incorporating 6PPD into regulatory and preventive strategies.},
}

*Nitrogen/metabolism
Water Pollutants, Chemical/metabolism
Microbiota/drug effects
Bacteria/metabolism/genetics
Waste Disposal, Fluid/methods
Wastewater/microbiology
Bioreactors/microbiology
Oxidation-Reduction
Anaerobiosis

@article {pmid39672497,
year = {2025},
author = {Zhou, L and Zhang, L and Dang, R and Han, G and Liu, J and Zhou, M and Xiao, L},
title = {Microbiota-induced asymmetry in coastal methane emission potential under experimental precipitation gradients.},
journal = {Environmental research},
volume = {266},
number = {},
pages = {120601},
doi = {10.1016/j.envres.2024.120601},
pmid = {39672497},
issn = {1096-0953},
mesh = {*Methane/metabolism ; *Microbiota ; China ; *Rain ; Wetlands ; Soil Microbiology ; Air Pollutants/analysis/toxicity ; },
abstract = {Climate models predict that the frequency and intensity of extreme precipitation events will increase globally. Despite carbon budget in coastal wetlands is known to be sensitive to precipitation variability, in where CH4 productions and potential mechanisms remain poorly understood. We investigated CH4 emission potential and its drivers after 7-year of field experiments with five precipitation gradients (-60%, -40%, ambient condition, +40%, +60%) in Yellow River Delta, China. The response of CH4 emission potential to precipitation gradients exhibited significant asymmetry, with the highest emission potential occurring under +40% precipitation. [13]C-isotope tracing experiment discovered the primary contribution of acetoclastic methanogenic pathway. +40% precipitation significantly improved the accumulation of aboveground biomass, soil organic carbon and total nitrogen. Microbial community abundance, but not composition, referring to metagenome-assembled genomes also actively responded to precipitation changes. For example, +40% precipitation increased the relative abundance of Methanosarcinia and Methanobacteria. Furthermore, CH4 emission potential was also promoted by higher microbial enzyme activity. Collectively, CH4 emission potential in response to 7-year experimental precipitations was regulated by microbiota-driven, showing obvious asymmetry.},
}

*Methane/metabolism
*Microbiota
China
*Rain
Wetlands
Soil Microbiology
Air Pollutants/analysis/toxicity