@article {pmid40268215,
year = {2025},
author = {Sun, X and Hu, P and Xiao, M and Zhang, S and Shi, J and Cai, D and Wang, D and Xu, L and Liu, L and Liu, Y},
title = {Synergy of Multi-Enzyme Pretreatment and Paraclostridium benzoelyticum Bioaugmentation: A Dual Strategy for Enhancing Methane Production in Dry Anaerobic Digestion of Kitchen Waste.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121671},
doi = {10.1016/j.envres.2025.121671},
pmid = {40268215},
issn = {1096-0953},
abstract = {Dry anaerobic digestion (DAD) of kitchen waste (KW) has low methane production due to the poor mass transfer and the low abundance of functional microorganisms. This study employed multi-enzyme pretreatment (PRE), bioaugmentation with Paraclostridium benzoelyticum (BIO), and their combination (COM) to enhance methane production. Interestingly, the COM group had the highest methane production, which was increased by 18.51%, 9.91% and 12.39% compared with the control, PRE and BIO groups, respectively, which indicated that there was a synergy between multi-enzyme pretreatment and bioaugmentation. Further analysis of microbial community and metagenome was conducted to reveal the synergistic mechanism. The results showed that in COM group, the enrichment of the Rikenellaceae, Methanobacteriaceae and Methanosaetaceae was the directly reason for enhancing methane production. Additionally, key metabolic functions including biosynthesis of cofactors, methane metabolism and oxidative phosphorylation also played a pivotal role in boosting methane production. Furthermore, the enhancement of the hydrogenotrophic methanogenesis pathway has been demonstrated to be a critical factor in the synergistic effects. It provided a reliable theoretical basis for the practical application of the multi-enzyme pretreatment combined with Paraclostridium benzoelyticum bioaugmentation for DAD.},
}

@article {pmid40268122,
year = {2025},
author = {Highmore, C and Cooper, K and Parker, J and Robinson, J and Castangia, R and Webb, JS},
title = {Real-time detection of Foodborne Pathogens and Biofilm in the food processing environment with Bactiscan, a macro-scale fluorescence device.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100511},
doi = {10.1016/j.jfp.2025.100511},
pmid = {40268122},
issn = {1944-9097},
abstract = {Food safety relies on rapid detection methods and rigorous sampling of the food processing environment, and is challenged by recurrent biofilm contamination and by sub-lethally injured bacteria that can evade detection. Bactiscan is investigated as an alternative detection approach, a macro-scale and reagentless device that detects microbial contamination through activating green fluorescence of glycoproteins in the bacterial cell wall. The detection capability of Bactiscan was tested on foodborne pathogens Escherichia coli, Listeria monocytogenes, Salmonella enterica, and Staphylococcus aureus. Detection by Bactiscan was assessed using 3 independent observers viewing bacterial samples dried on stainless steel, using 3 biological repeats and 5 technical repeats. Detection by Bactiscan was possible to 1.20*10[6] colony forming units (CFU), compared to 1.36*10[4] CFU by ATP swab testing, where Bactiscan detection limits were defined by the concentration at which 50% of the samples were observed under illumination of the device. Heat-killed and chlorine stressed E. coli and S. enterica caused a 2-log reduction in detection by ATP swab tests (p≤0.05), while detection by Bactiscan was unaffected (p≥0.05). Pathogen biofilms were detectable via Bactiscan with >80% accuracy at 4 days of growth; E. coli and L. monocytogenes biofilms were visible at 2 days of growth. In situ contamination studies determined that Bactiscan can detect microbial contamination on chicken, salmon, and yoghurt samples with stronger fluorescence than a competitor UV torch. The presence of one of the pathogens on the food samples was confirmed by metagenome sequencing, determining that S. aureus was present in 7 samples out of 9 with a relative abundance of >0.5%. These data demonstrate that Bactiscan can effectively detect bacteria present in the food processing environment and can complement existing technologies to improve food industry cleaning practices and infection prevention.},
}

@article {pmid40267797,
year = {2025},
author = {Sun, X and Sun, Y and Li, P and Gao, Y and Han, M and Zhang, P},
title = {Intensive oyster farming alters the microbial-regulated blue carbon storage in sediment.},
journal = {Marine pollution bulletin},
volume = {216},
number = {},
pages = {118016},
doi = {10.1016/j.marpolbul.2025.118016},
pmid = {40267797},
issn = {1879-3363},
abstract = {Intensive oyster farming enhances the organic matter coupling from water to sediment through biodeposition, potentially contributing to carbon storage. Microbes play a key role in regulating biogeochemical cycling in the coastal sediment. However, their specific contributions to carbon storage under oyster farming remain poorly understood. This study investigates microbial necromass and associated biogeochemical processes in sediments from an intensive oyster farm in Sanggou Bay, China, and compares these indicators with adjacent seagrass beds and bare zones. Additionally, carbon use efficiency (CUE) was employed to indicate microbial-regulated carbon cycling and storage in sediment. The results demonstrate that oyster farming promotes organic carbon accumulation in surface sediments but reduces its stability. Microbial necromass was identified as a critical driver of sedimentary organic carbon in oyster farm sediments, supported by enhanced nitrogen and sulfur cycling pathways. Notably, contrasting relationships between CUE and organic carbon were observed between the seagrass bed and the oyster farm. Functional metagenomic analysis further revealed distinct microbial metabolic pathways across habitats, highlighting the role of biodeposition in shaping microbial functions. These findings enhance our understanding of microbial contributions to blue carbon storage in aquaculture systems and provide new insights into coastal carbon storage beyond vegetated ecosystems.},
}

@article {pmid40267563,
year = {2025},
author = {Jian, Z and Wu, H and Yan, S and Li, T and Zhao, R and Zhao, J and Zi, X and Wang, K and Huang, Y and Gu, D and Zhao, S and Ge, C and Jia, J and Liu, L and Xu, Z and Dou, T},
title = {Species and functional composition of cecal microbiota and resistance gene diversity in different Yunnan native chicken breeds: A metagenomic analysis.},
journal = {Poultry science},
volume = {104},
number = {7},
pages = {105138},
doi = {10.1016/j.psj.2025.105138},
pmid = {40267563},
issn = {1525-3171},
abstract = {The gut microbiota of chickens not only modulates host immune function and production performance through nutrient metabolism but also serves as a reservoir for antibiotic resistance genes (ARGs), whose accumulation exacerbates bacterial resistance. This study integrated 108 cecal microbiome samples from six Yunnan native chicken breeds under free-range and caged farming systems, constructing a comprehensive catalog comprising 12,715 microbial genomes. We systematically revealed the dual mechanisms by which the gut microbiota regulates host phenotypes and ARG dissemination. Metagenomic analysis demonstrated that Alistipes, Prevotella, and Spirochaeta synergistically regulate body weight and immune indices through metabolic networks, which are linked to the significant enrichment of carbohydrate-active enzymes. GH23 and GT2 presented the greatest abundance, highlighting their pivotal role in dietary fiber metabolism. A total of 1327 ARGs were identified, spanning seven resistance mechanisms dominated by antibiotic efflux and target alteration. Alistipes_sp._CAG:831 presented the highest ARG abundance and diversity, with ARG levels strongly correlated with host bacterial abundance. Metagenomic-phenotype association networks further revealed that environmental stress drives disparities in ARG enrichment by altering the microbial community structure. This study elucidates the gut microbiota-host interaction network in Yunnan native chickens and provides critical insights into ARG transmission dynamics, offering a theoretical foundation for antibiotic resistance risk assessment and sustainable poultry farming strategies.},
}

@article {pmid40266944,
year = {2025},
author = {Herzog, F and Crissman, KR and Beckers, KF and Zhou, G and Liu, CC and Sones, JL},
title = {Lactobacillus Genus Complex Probiotic-Induced Changes on the Equine Clitoral Microbiome.},
journal = {Veterinary sciences},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/vetsci12030232},
pmid = {40266944},
issn = {2306-7381},
support = {2022//Louisiana State University Charles V. Cusimano/ ; },
abstract = {Dysbiosis of the lower reproductive tract (LRT) in mares may play a role in clinical diseases, including endometritis and placentitis. Metagenomic/metagenetic analysis of bacterial DNA can identify organisms that are not readily cultured and, thus, may go undetected. In this study, we tested the following hypotheses: (1) the clitoris of estrual mares harbors a unique resident microbiome, (2) topical Lactobacillus genus complex (LGC)-containing probiotic will alter the equine clitoral microbiome, and (3) early pregnancy rates following clitoral LGC application will not differ significantly from industry standards. Mares (n = 12) in estrus had sterile clitoral swabs collected (0) prior to daily topical LGC for 4 days. Second (12 h) and third clitoral swabs (48 h) were collected following final LGC application. During the next estrus, the mares were bred by artificial insemination. Genomic DNA was extracted and used for 16S rRNA sequencing via the Illumina Miseq platform. Abundance was evaluated via Friedman test with pairwise Dunn's post hoc comparisons. Statistical significance was set at p < 0.05. Compared to time 0, Desulfobacterota decreased and Corynebacterium spp. increased at 12 h and 48 h compared to 0, while Actinobacillus and Fusobacterium spp. increased in a time-dependent manner. Furthermore, Mobiluncus spp. and Christensenellacea_R-7_group decreased at 12 h and 48 h compared to 0. LGC changed the beta but not alpha diversity at both 12 h and 48 h. Mares with LGC application achieved an 85% pregnancy rate in the subsequent estrus. Future investigations are needed to understand the role of the LRT microbiome and probiotics in equine breeding.},
}

@article {pmid40266232,
year = {2025},
author = {Zhang, M and Shi, S and Feng, Y and Zhang, F and Xiao, Y and Li, X and Pan, X and Feng, Y and Liu, D and Guo, Y and Hu, Y},
title = {Synthetic microbial community improves chicken intestinal homeostasis and provokes anti-Salmonella immunity mediated by segmented filamentous bacteria.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf076},
pmid = {40266232},
issn = {1751-7370},
support = {2024TZXD026//Shandong Provincial Key Research and Development Program of China/ ; 2022YFA1304201//National Key Research and Development Program of China/ ; },
abstract = {Applying synthetic microbial communities to manipulate the gut microbiota is a promising manner for reshaping the chicken gut microbial community. However, it remains elusive the role of a designed microbial community in chicken physiological metabolism and immune responses. In this study, we constructed a ten-member synthetic microbial community (SynComBac10) that recapitulated the phylogenetic diversity and functional capability of adult chicken intestinal microbiota. We found that early life SynComBac10 exposure significantly enhanced chicken growth performance and facilitated the maturation of both the intestinal epithelial barrier function and the gut microbiota. Additionally, SynComBac10 promoted the pre-colonization and growth of segmented filamentous bacteria, which in turn induced Th17 cell-mediated immune responses, thereby conferring resistance to Salmonella infection. Through metagenomic sequencing, we assembled the genomes of two distinct species of segmented filamentous bacteria from the chicken gut microbiota, which displayed common metabolic deficiency with segmented filamentous bacteria of other host origins. In silico analyses indicated that the SynComBac10-stimulated early establishment of segmented filamentous bacteria in the chicken intestine was likely through SynComBac10-derived metabolite cross-feeding. Our study demonstrated the pivotal role of a designed microbial consortium in promoting chicken gut homeostasis and anti-infection immunity, providing a new avenue for engineering chicken gut microbiota.},
}

@article {pmid40265464,
year = {2025},
author = {Yan, X and Xie, F and Yang, S and Sun, Y and Lei, Y and Ren, Q and Si, H and Li, Z and Qiu, Q},
title = {Metagenomic Insights into the Rumen Microbiome in Solid and Liquid Fractions of Yaks and their Differences Compared to Other Ruminants.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.12984},
pmid = {40265464},
issn = {1749-4877},
support = {32225009//National Natural Science Foundation of China/ ; 32122083//National Natural Science Foundation of China/ ; 32402780//National Natural Science Foundation of China/ ; XDA26040301//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
abstract = {The rumen microbiome plays a critical role in nutrient metabolism and adaptation of the yak (Bos grunniens), an import livestock animal of the Qinghai-Tibet Plateau renowned for their superior plant fiber degradation capacity. However, the microbiome among the different ecological niches within yak's rumen remains unelucidated. Through shotgun sequencing of rumen solid and liquid fractions from five yaks, we identified significant differences in the microbial communities and their genetic functions between the solid and liquid fractions. Solid fractions exhibited dominance by Ruminococcus, Succiniclasticum, and Aspergillus, while Prevotella, Paludibacter, Parabacteroides, and Bacteroides prevailed in liquid fractions. Comparative CAZyme profiling revealed solid fractions were significantly enriched in cellulose/hemicellulose-targeting enzymes (GH5, GH11, and CBM63), implicating their specialization in breaking down the fibrous grasses. In contrast, liquid fractions showed higher abundances of starch-degrading enzymes (GH13, CBM48) and host-glycan utilizers (GH92), suggesting roles in soluble nutrient extraction and host-microbe interactions. Comparative analysis of 574 metagenome-assembled genomes suggested that Methanomethylophilaceae_UBA71 and nitrate-respiring Ruminococcaceae_Firm-04 preferentially colonized in the solids, whereas propionate-producing Quinella and animal glycan-degrading Bacteroides were more prevalent in the liquids. Moreover, compared to Hu sheep, yak's rumen microbiome showed significantly enhanced utilization of plant polysaccharide capacity. Comparative analysis across 10 ruminant species further highlighted host phylogeny as a key driver of rumen microbiome variation. These findings advance our understanding of niche differentiation and functional specialization within the unique yak rumen ecosystem.},
}

@article {pmid40265338,
year = {2025},
author = {Venkatraman, K and Lipp, NF and Budin, I},
title = {Origin and evolution of mitochondrial inner membrane composition.},
journal = {Journal of cell science},
volume = {138},
number = {9},
pages = {},
doi = {10.1242/jcs.263780},
pmid = {40265338},
issn = {1477-9137},
support = {GM142960/NH/NIH HHS/United States ; GBMF9734//Gordon and Betty Moore Foundation/ ; //University of California/ ; },
mesh = {*Mitochondrial Membranes/metabolism/chemistry ; *Mitochondria/metabolism/genetics ; Humans ; Animals ; Mitochondrial Proteins/metabolism ; *Evolution, Molecular ; },
abstract = {Unique membrane architectures and lipid building blocks underlie the metabolic and non-metabolic functions of mitochondria. During eukaryogenesis, mitochondria likely arose from an alphaproteobacterial symbiont of an Asgard archaea-related host cell. Subsequently, mitochondria evolved inner membrane folds known as cristae alongside a specialized lipid composition supported by metabolic and transport machinery. Advancements in phylogenetic methods and genomic and metagenomic data have suggested potential origins for cristae-shaping protein complexes, such as the mitochondrial contact site and cristae-organizing system (MICOS). MICOS protein homologs function in the formation of cristae-like intracytoplasmic membranes (ICMs) in diverse extant alphaproteobacteria. The machinery responsible for synthesizing key mitochondrial phospholipids - which cooperate with cristae-shaping proteins to establish inner membrane architecture - could have also evolved from a bacterial ancestor, but its origins have been less explored. In this Review, we examine the current understanding of mitochondrial membrane evolution, highlighting distinctions between prokaryotic and eukaryotic mitochondrial-specific proteins and lipids and their differing roles in shaping cristae and ICM architecture, and propose a model explaining the concurrent specialization of the mitochondrial lipidome and inner membrane structure in eukaryogenesis. We discuss how advancements across a range of disciplines are shedding light on how multiple membrane components co-evolved to support the central functions of eukaryotic mitochondria.},
}

*Mitochondrial Membranes/metabolism/chemistry
*Mitochondria/metabolism/genetics
Humans
Animals
Mitochondrial Proteins/metabolism
*Evolution, Molecular

@article {pmid40265160,
year = {2025},
author = {Fässler, D and Heinken, A and Hertel, J},
title = {Characterising functional redundancy in microbiome communities via relative entropy.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {1482-1497},
pmid = {40265160},
issn = {2001-0370},
abstract = {Functional redundancy has been hypothesised to be at the core of the well-evidenced relation between high ecological microbiome diversity and human health. Here, we conceptualise and operationalise functional redundancy on a single-trait level for functionally annotated microbial communities, utilising an information-theoretic approach based on relative entropy that also allows for the quantification of functional interdependency across species. Via constraint-based microbiome community modelling of a public faecal metagenomic dataset, we demonstrate that the strength of the relation between species diversity and functional redundancy is dependent on specific attributes of the function under consideration such as the rarity and the occurring functional interdependencies. Moreover, by integrating faecal metabolome data, we highlight that measures of functional redundancy have correlates in the host's metabolome. We further demonstrate that microbiomes sampled from colorectal cancer patients display higher levels of species-species functional interdependencies than those of healthy controls. By analysing microbiome community models from an inflammatory bowel disease (IBD) study, we show that although species diversity decreased in IBD subjects, functional redundancy increased for certain metabolites, notably hydrogen sulphide. This finding highlights their potential to provide valuable insights beyond species diversity. Here, we formalise the concept of functional redundancy in microbial communities and demonstrate its usefulness in real microbiome data, providing a foundation for a deeper understanding of how microbiome diversity shapes the functional capacities of a microbiome.},
}

@article {pmid40264979,
year = {2025},
author = {Zhong, Y and Chi, H and Wu, T and Fan, W and Su, H and Li, R and Jiang, W and Du, X and Ma, Z},
title = {Diversity of rhizosphere microbial communities in different rice varieties and their diverse adaptive responses to saline and alkaline stress.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1537846},
pmid = {40264979},
issn = {1664-302X},
abstract = {Rice rhizosphere microbiota plays a crucial role in crop yield and abiotic stress tolerance. However, little is known about how the composition and function of rhizosphere soil microbial communities respond to soil salinity, alkalinity, and rice variety in rice paddy ecosystems. In this study, we analyzed the composition and function of rhizosphere soil microbial communities associated with two rice varieties (Jida177 and Tongxi933) cultivated in soils with different levels of salinity-alkalinity in Northeast China using a metagenomics approach. Our results indicate that the rhizospheres of Jida177 and Tongxi933 rice varieties harbor distinct microbial communities, and these microbial communities are differentiated based on both soil salinity-alkalinity and rice varieties. Furthermore, the observed differences in rice yield and grain quality between the Jida177 and Tongxi933 rice varieties suggest that these changes may be attributed to alterations in the rhizosphere microbiome under varying salinity conditions. These findings may pave the way for more efficient soil management and deeper understanding of the potential effects of soil salinization on the rice rhizosphere system.},
}

@article {pmid40264936,
year = {2025},
author = {Hou, F and Qiao, Y and Qiao, Y and Shi, Y and Chen, M and Kong, M and Hu, X and Jiang, L and Liu, X},
title = {A retrospective analysis comparing metagenomic next-generation sequencing with conventional microbiology testing for the identification of pathogens in patients with severe infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1530486},
pmid = {40264936},
issn = {2235-2988},
abstract = {INTRODUCTION: The application value of metagenomic next-generation sequencing (mNGS) in detecting pathogenic bacteria was evaluated to promote the rational and accurate use of antibiotics. A total of 180 patients with severe infections were included in this study.

METHODS: Based on their different symptoms, bronchoalveolar lavage fluid (BALF) or blood samples were collected for conventional microbiological testing (CMT) and mNGS.

RESULTS: The results indicated that the etiological diagnosis rate of mNGS (78.89%) was significantly higher than that of CMT (20%) (p<0.001). Notably, mNGS exhibited greater sensitivity towards rare pathogens such as Chlamydia pneumoniae, Mycobacterium tuberculosis complex, and Legionella pneumophila, which were undetectable by CMT. Additionally, 64 cases underwent blood culture, BALF culture, and mNGS testing. Analysis revealed that the positive rate of blood culture (3.1%) was lower than that of BALF (25%), and the positive rate of CMT from both types was significantly lower than that of mNGS (89.1%) (p<0.001). In this study, 168 mNGS results were accepted, and 116 patients had their antibiotic therapy adjustment based on mNGS. Paired analysis indicated that white blood cell count (WBC), procalcitonin (PCT), C-reactive protein (CRP), and neutrophil (NEU) percentage provided valuable therapeutic guidance. The survival rate of patients was 55.36%, influenced by patient physical condition and age.

DISCUSSION: Our data indicated that mNGS had significant auxiliary value in the clinical diagnosis and treatment for critically ill patients, especially for those with negative CMT results and clinically undefined infections. mNGS could broaden the detection scope, especially for special pathogens, and improve the detection rate, providing powerful assistance for early clinical diagnosis and treatment.},
}

@article {pmid40263874,
year = {2025},
author = {Huang, X and Li, R and Xu, J and Kang, J and Chen, X and Han, B and Xue, Y},
title = {Integrated multi-omics uncover viruses, active fermenting microbes and their metabolic profiles in the Daqu microbiome.},
journal = {Food research international (Ottawa, Ont.)},
volume = {208},
number = {},
pages = {116061},
doi = {10.1016/j.foodres.2025.116061},
pmid = {40263874},
issn = {1873-7145},
mesh = {*Fermentation ; *Microbiota ; Fungi/metabolism/genetics ; *Bacteria/metabolism/genetics ; *Viruses/genetics/classification ; Metagenomics ; Food Microbiology ; *Fermented Foods/microbiology/virology ; Bacteriophages/genetics ; *Metabolome ; Multiomics ; },
abstract = {The coexistence and coevolution of viruses and fermenting microbes have a significant impact on the structure and function of microbial communities. Although the presence of viruses in Daqu, the fermentation starter for Chinese Baijiu, has been documented, their specific effects on the community composition and metabolic functions of low, medium, and high-temperature Daqu remain unclear. In this study, we employed multi-omics technology to explore the distribution of viruses and active bacteria and fungi in various Daqu and their potential metabolic roles. Viral metagenomic sequencing showed a predominance of Parvoviridae in High-Temperature Daqu (HTQ), while Genomoviridae were dominant in Medium-Temperature Daqu (MTQ) and Low- Temperature Daqu (LTQ). Phages belonging to the Siphoviridae, Podoviridae, Herelleviridae, and Myoviridae families showed significantly different abundances across three Daqu groups. Metatranscriptomic analysis showed that fungal communities were most active in LTQ, whereas bacterial communities were dominant in MTQ and HTQ. By employing the CRISPR-Cas spacer, a higher predicted number of phage-host linkages was identified in LTQ, particularly with hosts including Lactobacillus, Staphylococcus, Acinetobacter, Enterobacter, and Bacillus. Correlation analysis showed that bacteria like Acinetobacter, Lactobacillus, and Streptococcus exhibited the strongest associations with metabolites, particularly amino acids and organic acids. The potential phage-induced metabolic differences in the three Daqu groups were mainly linked to pathways involved in the metabolism of amino acids, sugars, and organic acids. Overall, our study elucidates the impact of viruses on shaping microbial composition and influencing metabolic functions in Daqu. These results improve our comprehension of viruses and microbes in Daqu microbial communities and provide valuable insights for enhancing quality control in Daqu production.},
}

*Fermentation
*Microbiota
Fungi/metabolism/genetics
*Bacteria/metabolism/genetics
*Viruses/genetics/classification
Metagenomics
Food Microbiology
*Fermented Foods/microbiology/virology
Bacteriophages/genetics
*Metabolome
Multiomics

@article {pmid40263747,
year = {2025},
author = {Liu, CG and Lin, MX and Xin, Y and Sun, M and Cui, J and Liu, D and Zang, D and Chen, J},
title = {Metagenomics and Non-Targeted Metabolomics Reveal the Role of Gut Microbiota and Its Metabolites in Brain Metastasis of Non-Small Cell Lung Cancer.},
journal = {Thoracic cancer},
volume = {16},
number = {8},
pages = {e70068},
doi = {10.1111/1759-7714.70068},
pmid = {40263747},
issn = {1759-7714},
support = {2022RQ091//Science and Technology Talent Innovation Support Plan of Dalian/ ; 82203056//National Natural Science Foundation of China/ ; 2022LCYJYB01//The "1+X" program for Clinical Competency enhancement-Clinical Research Incubation Project of the Second Hospital of Dalian Medical University/ ; 2023-BS-167//Natural Science Foundation of Liaoning Province/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/pathology/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Brain Neoplasms/secondary/metabolism ; *Lung Neoplasms/pathology/metabolism/microbiology ; *Metabolomics/methods ; Female ; Male ; *Metagenomics/methods ; Middle Aged ; Aged ; Prognosis ; },
abstract = {BACKGROUND: Brain metastasis is a common and severe complication in non-small cell lung cancer (NSCLC) patients, significantly affecting prognosis. However, the role of gut microbiota and its metabolites in NSCLC brain metastasis remains poorly understood. This study aims to explore the relationship between gut microbiota, metabolites, and the development of brain metastasis in NSCLC.

METHODS: We conducted an integrative analysis combining metagenomics and non-targeted metabolomics on baseline fecal samples from NSCLC patients with brain metastasis (n = 18) and those without distant metastasis (n = 12). Gut microbiota composition and metabolite profiles were detected and analyzed, and statistical methods, including machine learning models, were applied to identify differences and potential biomarkers.

RESULTS: Significant differences in gut microbiota composition were found between the two groups, with higher microbial diversity observed in patients with brain metastasis. Specific genera, such as Paenibacillus, Fournierella, and Adlercreutzia, were enriched in the brain metastasis group. Metabolomic analysis revealed altered levels of short-chain fatty acids and other metabolites associated with immune modulation and vascular permeability, including angiotensin (1-7). These changes were linked to the metastatic process and may influence brain metastasis development. Furthermore, machine learning models identified key biomarkers, such as Raoultibacter, Mobilibacterium, and N-acetyl-L-glutamic acid, which could serve as valuable indicators for brain metastasis.

CONCLUSIONS: Our findings suggest that gut microbiota dysbiosis and its metabolic products may contribute to the development of brain metastasis in NSCLC. The identification of microbiota-derived biomarkers holds potential for early detection and therapeutic intervention in NSCLC brain metastasis.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/pathology/metabolism/microbiology
*Gastrointestinal Microbiome
*Brain Neoplasms/secondary/metabolism
*Lung Neoplasms/pathology/metabolism/microbiology
*Metabolomics/methods
Female
Male
*Metagenomics/methods
Middle Aged
Aged
Prognosis

@article {pmid40263712,
year = {2025},
author = {Hör, J},
title = {Advancing RNA phage biology through meta-omics.},
journal = {Nucleic acids research},
volume = {53},
number = {8},
pages = {},
doi = {10.1093/nar/gkaf314},
pmid = {40263712},
issn = {1362-4962},
mesh = {*Bacteria/virology/genetics ; *RNA Phages/genetics/physiology/classification ; Genome, Viral ; *Metagenomics/methods ; *Genomics/methods ; Transcriptome ; Bacteriophages/genetics ; },
abstract = {Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in the 1960s, they have been used as important models to understand the principal processes of life, including translation and the genetic code. While RNA phages were generally thought of as rare oddities in nature, meta-omics methods are rapidly changing this simplistic view by studying diverse biomes with unprecedented resolution. Metatranscriptomics dramatically expanded the number of known RNA phages from tens to tens of thousands, revealed their widespread abundance, and discovered several new families of potential RNA phages with largely unknown hosts, biology, and environmental impact. At the same time, (meta)genomic analyses of bacterial hosts are discovering an arsenal of defense systems bacteria employ to protect themselves from predation, whose functions in immunity against RNA phages we are only beginning to understand. Here, I review how meta-omics approaches are advancing the field of RNA phage biology with a focus on the discovery of new RNA phages and how bacteria might fight them.},
}

*Bacteria/virology/genetics
*RNA Phages/genetics/physiology/classification
Genome, Viral
*Metagenomics/methods
*Genomics/methods
Transcriptome
Bacteriophages/genetics

@article {pmid40263502,
year = {2025},
author = {Canderan, J and Ye, Y},
title = {Identification of microbial species and proteins associated with colorectal cancer by reanalyzing CPTAC proteomic datasets.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13926},
pmid = {40263502},
issn = {2045-2322},
support = {R01AI143254//U.S. Department of Health & Human Services | NIH | Center for Information Technology (Center for Information Technology, National Institutes of Health)/ ; EF-202545//National Science Foundation (NSF)/ ; },
mesh = {*Colorectal Neoplasms/microbiology/metabolism ; Humans ; *Proteomics/methods ; *Bacterial Proteins/metabolism ; Aspergillus/metabolism ; },
abstract = {Microbiome research has revealed associations between microbial species and colorectal cancer (CRC). Most of the existing research relied on metagenomic data. We leveraged a tool that we recently developed for detecting human and microbial peptides from (meta)proteomics data to reanalyze Clinical Proteomic Tumor Analysis Consortium CRC proteomics datasets. Our analyses revealed potential microbial species and proteins that are associated with CRC, especially when analyzing multiplexed proteomics data consisting of cancerous and healthy tissue taken from the same individuals. Many of the identified proteins are associated with species with known links to CRC, such as the fungi Aspergillus kawachii, but many are unstudied or their specific roles unknown. Proteins from other microbial species, such as Paenibacillus cellulosilyticus, were also identified in the samples. We showed that Aspergillus kawachii and others are depleted overall in cancer samples, which is consistent with a previous genomic-based multi-cohort study. Our analysis also revealed that some proteins belonging to this species are more abundantly detected, while others in this and other species are not. Further, we showed that microbial identifications could be used to build predictive models for tumor detection, but caution needs to be taken when applying such models trained on one dataset to another due to the substantial impacts of different experimental techniques on peptide detection profiles.},
}

*Colorectal Neoplasms/microbiology/metabolism
Humans
*Proteomics/methods
*Bacterial Proteins/metabolism
Aspergillus/metabolism

@article {pmid40263397,
year = {2025},
author = {Li, C and Zhu, J and Wang, Y and Jiang, W and Lin, Y},
title = {Metagenomic NGS reveals determinants of polymicrobial spinal infection pathogenesis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13959},
pmid = {40263397},
issn = {2045-2322},
support = {20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; 20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; 20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; 20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; 20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; },
mesh = {Humans ; Male ; Female ; Middle Aged ; Retrospective Studies ; Aged ; Risk Factors ; *Coinfection/microbiology ; *Metagenomics/methods ; ROC Curve ; Adult ; *Spinal Diseases/microbiology ; },
abstract = {To explore the influencing factors of spinal mixed infection under mNGS-assisted detection. A retrospective analysis was conducted on the general clinical data of patients diagnosed with spinal infections at Guilin People's Hospital, covering the period from October 2022 to October 2024, to evaluate the effectiveness of different treatment modalities including conservative, pharmacological, and surgical interventions. In the end, a total of 45 cases were included, including 18 cases of mixed infection and 27 cases of single infection. The receiver operating characteristic (ROC) curve was utilized to evaluate the predictive efficacy of various indices for the occurrence of mixed infection in patients with spinal infections, with the curve's proximity to the top left corner indicating higher diagnostic accuracy. Multivariate Logistic regression was used to analyze the independent risk factors affecting the development of mixed infection in patients with spinal infection. No significant differences were found between the two groups regarding gender, smoking, alcohol consumption, hypertension, albumin levels, liver function, malignancy, or rheumatic immune disease history (P > 0.05). However, the mixed infection group had significantly higher proportions of patients aged > 60 years (78% (14/18) vs. 48% (13/27)), diabetes mellitus (44% (8/18) vs. 15% (4/27)), chronic kidney disease (17% (3/18) vs. 0.00 (0/27)), and previous spinal surgery (39% (7/18) vs. 11% (3/27)), along with lower BMI (20.70 ± 2.15 vs. 24.04 ± 3.76) and hemoglobin levels (105.17 ± 14.05 g/L vs. 117.48 ± 18.08 g/L). The results of the ROC curve analysis showed that the area under the curve for BMI and hemoglobin in predicting the occurrence of mixed infection in patients was 0.787 and 0.704, respectively, with optimal cutoff values of 21.12 kg/m[2] and 119 g/L. Multivariate logistic regression identified BMI < 21.12 kg/m[2], hemoglobin < 119 g/L, and diabetes as independent risk factors. Lower BMI, diabetes and hemoglobin are independent risk factors for spinal mixed infection. Increasing BMI, effectively controlling blood glucose and improving anemia are helpful to reduce the occurrence of spinal mixed infection.},
}

Humans
Male
Female
Middle Aged
Retrospective Studies
Aged
Risk Factors
*Coinfection/microbiology
*Metagenomics/methods
ROC Curve
Adult
*Spinal Diseases/microbiology

@article {pmid40263287,
year = {2025},
author = {Gao, D and Zhuang, Y and Liu, S and Ma, B and Xu, Y and Zhang, H and Nuermaimaiti, Y and Chen, T and Hou, G and Guo, W and You, J and Huang, Z and Xiao, J and Wang, W and Li, M and Li, S and Cao, Z},
title = {Multi-omics profiling of dairy cattle oxidative stress identifies hindgut-derived Phascolarctobacterium succinatutens exhibiting antioxidant activity.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {61},
pmid = {40263287},
issn = {2055-5008},
support = {2024BBF01006//Key Research and Development Program of Ningxia/ ; 2023YFD1300904//National Key Research and Development Program of China/ ; 2024-KFKT-026//National Center of Technology Innovation for Dairy/ ; PC2023B02002//Pinduoduo-China Agricultural University Research Fund/ ; },
mesh = {Animals ; Cattle ; *Oxidative Stress ; *Antioxidants/metabolism ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Female ; Mice ; Fatty Acids, Volatile/metabolism ; Metabolomics ; Metagenomics ; *Clostridiales/genetics/metabolism/isolation & purification ; Multiomics ; },
abstract = {An imbalance between oxidative and antioxidant processes in the host can lead to excessive oxidation, a condition known as oxidative stress (OS). Although changes in the hindgut microbiota have been frequently linked to OS, the specific microbial and metabolic underpinnings of this association remain unclear. In this study, we enrolled 81 postpartum Holstein cows and stratified them into high oxidative stress (HOS, n = 9) and low oxidative stress (LOS, n = 9) groups based on the oxidative stress index (OSi). Using a multi-omics approach, we performed 16S rRNA gene sequencing to evaluate microbial diversity, conducted metagenomic analysis to identify functional bacteria, and utilized untargeted metabolomics to profile serum metabolites. Our analyses revealed elevated levels of kynurenine, formyl-5-hydroxykynurenamine, and 5-hydroxyindole-3-acetic acid in LOS dairy cows. Additionally, the LOS cows had a higher abundance of short-chain fatty acids (SCFAs)-producing bacteria, including Bacteroidetes bacterium, Paludibacter propionicigenes, and Phascolarctobacterium succinatutens (P. succinatutens), which were negatively correlated with OSi. To explore the potential role of these bacteria in mitigating OS, we administered P. succinatutens (10[8] cfu/day for 14 days) to C57BL/6 J mice (n = 10). Oral administration of P. succinatutens significantly increased serum total antioxidant capacity, decreased total oxidants, and reduced OSi in mice. Moreover, this treatment promoted activation of the Nrf2-Keap1 antioxidant pathway, significantly enhancing the enzymatic activities of GSH-Px and SOD, as well as the concentrations of acetate and propionate in the colon. In conclusion, our findings suggest that systemic tryptophan metabolism and disordered SCFAs production are concurrent factors influenced by hindgut microbiota and associated with OS development. Modulating the hindgut microbiota, particularly by introducing specific SCFAs-producing bacteria, could be a promising strategy for combating OS.},
}

Animals
Cattle
*Oxidative Stress
*Antioxidants/metabolism
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Female
Mice
Fatty Acids, Volatile/metabolism
Metabolomics
Metagenomics
*Clostridiales/genetics/metabolism/isolation & purification
Multiomics

@article {pmid40263159,
year = {2025},
author = {Pandey, A and Israr, J and Pandey, J and Misra, S},
title = {Current Approaches and Implications in Discovery of Novel Bioactive Products from Microbial Sources.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {258},
pmid = {40263159},
issn = {1432-0991},
mesh = {*Biological Products/metabolism/pharmacology/isolation & purification/chemistry ; *Drug Discovery/methods ; *Bacteria/metabolism/genetics ; Multigene Family ; Biosynthetic Pathways/genetics ; Microbiota ; },
abstract = {Bioactive Natural Products (BNPs) are in high demand due to their disease-preventive capabilities and resistance to pathogens. However, our understanding of BNP-producing microbes is limited, because many microbial populations remain uncultivated. Various approaches have been employed to explore the potential of these hidden microbes for new bioactive therapeutic compounds. Nevertheless, the possibility of discovering BNPs from microbial communities is largely cryptic due to their unculturable nature and the absence of triggers to activate the dormant Biosynthetic Gene Clusters (BGCs). Metagenome sequencing, followed by mining and characterization, is an effective approach for discovering new therapeutic BNPs. The inactive state of BGCs can be activated through the combinatorial interaction of different microbial communities within a common niche, overcoming programmable co-evolutionary stress and producing new BNPs. The present review discusses and explores the potential of hidden, uncultivated microbes for discovering novel Bioactive Natural Products (BNPs). Moreover, it provides insights into optimizing microbial production systems and fostering sustainable drug discovery and development practices by integrating multidisciplinary strategies. This review also emphasizes the critical role of microbial sources in the ongoing search for new bioactive products that can meet the demands of modern healthcare and environmental sustainability.},
}

*Biological Products/metabolism/pharmacology/isolation & purification/chemistry
*Drug Discovery/methods
*Bacteria/metabolism/genetics
Multigene Family
Biosynthetic Pathways/genetics
Microbiota

@article {pmid40262434,
year = {2025},
author = {Lima, RAT and Garay, AV and Frederico, TD and de Oliveira, GM and Quirino, BF and Barbosa, JARG and Freitas, SM and Krüger, RH},
title = {Biochemical and structural characterization of a family-9 glycoside hydrolase bioprospected from the termite Syntermes wheeleri gut bacteria metagenome.},
journal = {Enzyme and microbial technology},
volume = {189},
number = {},
pages = {110654},
doi = {10.1016/j.enzmictec.2025.110654},
pmid = {40262434},
issn = {1879-0909},
abstract = {Glycosyl hydrolases (GH) are enzymes involved in the degradation of plant biomass. They are important for biorefineries that aim at the sustainable utilization of lignocellulosic residues to generate value-added products. The termite Syntermes wheeleri gut microbiota showed an abundance of bacteria from the phylum Firmicutes, a phylum with enzymes capable of breaking down cellulose and degrading lignin, facilitating the use of plant materials as a food source for termites. Using bioinformatics techniques, cellobiohydrolases were searched for in the gut metagenome of the termite Syntermes wheeleri, endemic to the Cerrado. After selecting sequences of the target enzymes, termite gut microbiome metatranscriptome data were used as the criteria to choose the GH9 enzyme sequence Exo8574. Here we present the biochemical and structural characterization of Exo8574, a GH9 enzyme that showed activity with the substrate p-nitrophenyl-D-cellobioside (pNPC), consistent with cellobiohydrolase activity. Bioinformatics tools were used to perform phylogeny studies of Exo8574 and to identify conserved families and domains. Exo8574 showed 48.8 % homology to a protein from a bacterium belonging to the phylum Firmicutes. The high-quality three-dimensional (3D) model of Exo8574 was obtained by protein structure prediction AlphaFold 2, a neural network-based method. After the heterologous expression of Exo8574 and its purification, biochemical experiments showed that the optimal activity of the enzyme was at a temperature of 55 ºC and pH 6.0, which was enhanced in the presence of metal ions, especially Fe[2 +]. The estimated kinetic parameters of Exo8574 using the synthetic substrate p-nithrophenyl-beta-D-cellobioside (pNPC) were: Vmax = 9.14 ± 0.2 x10[-5] μmol/min and Km = 248.27 ± 26.35 μmol/L. The thermostability test showed a 50 % loss of activity after 1 h incubation at 55 °C. The secondary structure contents of Exo8574 evaluated by Circular Dichroism were pH dependent, with greater structuring of protein in β-antiparallel and α-helices at pH 6.0. The similarity between the CD results and the Ramachandran plot of the 3D model suggests that a reliable model has been obtained. Altogether, the results of the biochemical and structural characterization showed that Exo8574 is capable of acting on p-nithrophenyl-beta-D-cellobioside (pNPC), a substrate that mimics bonds cleaved by cellobiohydrolases. These findings have significant implications for advancing in the field of biomass conversion while also contributing to efforts aimed at overcoming challenges in developing more efficient cellulase cocktails.},
}

@article {pmid40262432,
year = {2025},
author = {Wu, G and Zhang, H and Huang, T and Song, Y and Liu, X and Liu, X and Wang, X and Pei, T and Xu, G and Wang, Z},
title = {Hydraulic and thermal performance trigger the deterministic assembly of water microbiomes: From biogeographical homogenization to machine learning model.},
journal = {Water research},
volume = {282},
number = {},
pages = {123626},
doi = {10.1016/j.watres.2025.123626},
pmid = {40262432},
issn = {1879-2448},
abstract = {Water quality at the point of consumption has long been a health issue because of the potential for microbial ecology. However, research on water hydraulic performance remains in its infancy, and in particular, little is known about the effects of thermal performance during winter. This study explored the effects of stagnation and municipal heating on microbial communities in tap water, focusing on spatial and temporal variations in microbial community composition. The results revealed that stagnation significantly alters the microbial community, especially in heating areas, where the temperature exacerbates microbial growth. Furthermore, hydraulic and thermal performance drive deterministic assembly processes in microbial communities, as evidenced by the reductions in β-diversity, normalized stochasticity ratio (NST), and neutral community model (NCM) fit. Machine learning models revealed that stagnation time greater than 8 h results in increased community abundance because of longer exposure to organic matter and nutrients. The study finding illustrate the importance of environmental influences on microbial community dynamics, and provide valuable insights into the water microbial community, particularly in areas with prolonged stagnation.},
}

@article {pmid40261735,
year = {2025},
author = {Rogers, AB and Kale, V and Baldi, G and Alberdi, A and Gilbert, MTP and Gupta, D and Limborg, MT and Li, S and Payne, T and Petersen, B and Rasmussen, JA and Richardson, L and Finn, RD},
title = {HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
doi = {10.1093/database/baae112},
pmid = {40261735},
issn = {1758-0463},
mesh = {Animals ; *Chickens/microbiology ; *Microbiota ; *Salmon/microbiology ; *Databases, Genetic ; *Host Microbial Interactions ; Metadata ; *Gastrointestinal Microbiome ; },
abstract = {The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues. The HoloFood Data Portal is a web resource that simplifies access to the project datasets. For example, users can conveniently access multiomic datasets derived from the same individual or retrieve host phenotypic data with a linked gut microbiome sample. Project-specific metagenome-assembled genome and viral catalogues are also provided, linking to broader datasets in MGnify. The portal stores only data necessary to provide these relationships, with possible linking to the underlying repositories. The portal showcases a model approach for how future multiomics datasets can be made available. Database URL: https://www.holofooddata.org.},
}

Animals
*Chickens/microbiology
*Microbiota
*Salmon/microbiology
*Databases, Genetic
*Host Microbial Interactions
Metadata
*Gastrointestinal Microbiome

@article {pmid40261409,
year = {2025},
author = {Zhao, S and Guo, H and Wang, Z and Zhang, B and Chen, H and Klitzsch, N and Yue, L and Xia, D},
title = {Clay mineral content modulates biogenic gas production in coal: divergent microbial responses in low- and medium-rank coals revealed by multi-omics.},
journal = {Bioprocess and biosystems engineering},
volume = {},
number = {},
pages = {},
pmid = {40261409},
issn = {1615-7605},
support = {23ZX015//Key Scientific Research Project of Colleges and Universities in Henan Province/ ; 42172195//National Natural Science Foundation of China/ ; 42172199//National Natural Science Foundation of China/ ; AQ20240302//Double First-Class Initiative for Safety Discipline Construction Project/ ; 2024B03002//Xinjiang Key R & D Task Project/ ; },
abstract = {The influence of clay mineral content on biogenic gas production in coal seams remains insufficiently understood. This study systematically investigated the mechanisms by which clay minerals affect biogas production in low- and medium-rank coals by integrating simulated biogas production experiments with multidimensional analytical techniques, including infrared spectroscopy, X-ray diffraction, scanning electron microscopy, gas chromatography-mass spectrometry, fluorescence spectroscopy, and metagenomic analysis. The results demonstrated that in low-rank coal, increasing the clay content from 2.78 to 4.75 g per 20 g of coal reduced the biogas yield from 6.30 to 3.47 mL/g. Conversely, in medium-rank coal, increasing the clay content from 1.66 to 2.65 g per 20 g of coal enhanced the biogas yield from 3.45 to 5.28 mL/g. These contrasting outcomes are primarily attributed to the distinct mechanistic roles of clay minerals across coal ranks. In low-rank coal, the hydration-induced swelling of clay minerals intensified pore blockage, impeded gas diffusion, decreased the abundance of genes involved in propionate degradation, and suppressed microbial metabolic activity, ultimately limiting methane production. In contrast, in medium-rank coal, clay minerals facilitated the enrichment of key functional microbial taxa, such as Acetobacteroides and Methanoculleus, promoted the degradation of fatty acids, hydroxyls, and amines, and enhanced the activity of acidogenic and methanogenic pathways, thereby increasing methane yield. This study elucidates the microbial mechanisms underlying the regulatory role of clay minerals in biogas production, offering new theoretical insights into the origin of coalbed methane (CBM) and providing a scientific foundation for optimizing biogenic CBM recovery.},
}

@article {pmid40261207,
year = {2025},
author = {Liao, X and Li, Y and Wu, Y and Li, X and Shang, X},
title = {Deep Learning-Based Classification of CRISPR Loci Using Repeat Sequences.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00174},
pmid = {40261207},
issn = {2161-5063},
abstract = {With the widespread application of the CRISPR-Cas system in gene editing and related fields, along with the increasing availability of metagenomic data, the demand for detecting and classifying CRISPR-Cas systems in metagenomic data sets has grown significantly. Traditional classification methods for CRISPR-Cas systems primarily rely on identifying cas genes near CRISPR arrays. However, in cases where cas gene information is absent, such as in metagenomes or fragmented genome assemblies, traditional methods may fail. Here, we present a deep learning-based method, CRISPRclassify-CNN-Att, which classifies CRISPR loci solely based on repeat sequences. CRISPRclassify-CNN-Att utilizes convolutional neural networks (CNNs) and self-attention mechanisms to extract features from repeat sequences. It employs a stacking strategy to address the imbalance of samples across different subtypes and uses transfer learning to improve classification accuracy for subtypes with fewer samples. CRISPRclassify-CNN-Att demonstrates outstanding performance in classifying multiple subtypes, particularly those with larger sample sizes. Although CRISPR loci classification traditionally depends on cas genes, CRISPRclassify-CNN-Att offers a novel approach that serves as a significant complement to cas-based methods, enabling the classification of orphan or distant CRISPR loci. The proposed tool is freely accessible via https://github.com/Xingyu-Liao/CRISPRclassify-CNN-Att.},
}

@article {pmid40261064,
year = {2025},
author = {Žuštra, A and Leonard, VR and Holland, LA and Hu, JC and Mu, T and Holland, SC and Wu, LI and Begnel, ER and Ojee, E and Chohan, BH and Richardson, BA and Kinuthia, J and Wamalwa, D and Slyker, J and Lehman, DA and Gantt, S and Lim, ES},
title = {Longitudinal dynamics of the nasopharyngeal microbiome in response to SARS-CoV-2 Omicron variant and HIV infection in Kenyan women and their children.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0156824},
doi = {10.1128/msystems.01568-24},
pmid = {40261064},
issn = {2379-5077},
abstract = {UNLABELLED: The nasopharynx and its microbiota are implicated in respiratory health and disease. The interplay between viral infection and the nasopharyngeal microbiome is an area of increased interest. The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the coronavirus disease 2019 pandemic, on the nasopharyngeal microbiome among individuals living with HIV is not fully characterized. Here, we describe the nasopharyngeal microbiome before, during, and after SARS-CoV-2 infection in a longitudinal cohort of Kenyan women (21 living with HIV and 14 HIV-uninfected) and their children (18 HIV-exposed, uninfected and 7 HIV-unexposed, uninfected) between September 2021 and March 2022. We show using genomic epidemiology that mother and child dyads were infected with the same strain of the SARS-CoV-2 Omicron variant that spread rapidly across Kenya. We used metagenomic sequencing to characterize the nasopharyngeal microbiome of 20 women and children infected with SARS-CoV-2, six children negative for SARS-CoV-2 but experiencing respiratory symptoms, and 34 timepoint-matched SARS-CoV-2-negative mothers and children. Since individuals were sampled longitudinally before and after SARS-CoV-2 infection, we could characterize the short- (within a week of infection) and longer- (average of 38 days post-infection) term impact of SARS-CoV-2 infection on the nasopharyngeal microbiome. We found that mothers and children had significantly different microbiome composition and bacterial load (P-values < 0.0001). In both mothers and children, the nasopharyngeal microbiome did not differ before and after SARS-CoV-2 infection, regardless of HIV exposure status. Our results indicate that the nasopharyngeal microbiome is resilient to SARS-CoV-2 infection and was not significantly modified by HIV.

IMPORTANCE: The nasopharyngeal microbiome plays an important role in human health. The degree of impact that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has on the nasopharyngeal microbiome varies among studies and may be influenced by diverse SARS-CoV-2 variants and variations in the microbiome between individuals. Our results show that the nasopharyngeal microbiome was not altered substantially by SARS-CoV-2 infection nor by HIV infection in mothers or HIV exposure in children. Our findings highlight the resilience of the nasopharyngeal microbiome after SARS-CoV-2 infection. These findings advance our understanding of the nasopharyngeal microbiome and its interactions with viral infections.},
}

@article {pmid40261045,
year = {2025},
author = {Doing, G and Shanbhag, P and Bell, I and Cassidy, S and Motakis, E and Aiken, E and Oh, J and Adams, MD},
title = {TEAL-Seq: targeted expression analysis sequencing.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0098424},
doi = {10.1128/msphere.00984-24},
pmid = {40261045},
issn = {2379-5042},
abstract = {Metagenome sequencing enables the genetic characterization of complex microbial communities. However, determining the activity of isolates within a community presents several challenges, including the wide range of organismal and gene expression abundances, the presence of host RNA, and low microbial biomass at many sites. To address these limitations, we developed "targeted expression analysis sequencing" or TEAL-seq, enabling sensitive species-specific analyses of gene expression using highly multiplexed custom probe pools. For proof of concept, we targeted about 1,700 core and accessory genes of Staphylococcus aureus and S. epidermidis, two key species of the skin microbiome. Two targeting methods were applied to laboratory cultures and human nasal swab specimens. Both methods showed a high degree of specificity, with >90% reads on target, even in the presence of complex microbial or human background DNA/RNA. Targeting using molecular inversion probes demonstrated excellent correlation in inferred expression levels with bulk RNA-seq. Furthermore, we show that a linear pre-amplification step to increase the number of nucleic acids for analysis yielded consistent and predictable results when applied to complex samples and enabled profiling of expression from as little as 1 ng of total RNA. TEAL-seq is much less expensive than bulk metatranscriptomic profiling, enables detection across a greater dynamic range, and uses a strategy that is readily configurable for determining the transcriptional status of organisms in any microbial community.IMPORTANCEThe gene expression patterns of bacteria in microbial communities reflect their activity and interactions with other community members. Measuring gene expression in complex microbiome contexts is challenging, however, due to the large dynamic range of microbial abundances and transcript levels. Here we describe an approach to assessing gene expression for specific species of interest using highly multiplexed pools of targeting probes. We show that an isothermal amplification step enables the profiling of low biomass samples. TEAL-seq should be widely adaptable to the study of microbial activity in natural environments.},
}

@article {pmid40260991,
year = {2025},
author = {López-Gálvez, R and Orenes-Piñero, E and Rivera-Caravaca, JM and Pérez-Sanz, F and Ramos-Bratos, MP and Roca, MI and Mandaglio-Collados, D and López-García, C and Gil-Pérez, P and Esteve-Pastor, MA and Marín, F},
title = {Microbial Insights: The Role of Diet in Modulating Gut Microbiota and Metabolites After Acute Coronary Syndrome.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70046},
doi = {10.1002/mnfr.70046},
pmid = {40260991},
issn = {1613-4133},
support = {//Instituto de Salud Carlos III/ ; //Centro de investigación Biomédica en Red/ ; },
abstract = {Acute coronary syndrome (ACS) is a leading cause of global mortality, largely due to atherosclerosis influenced by lifestyle factors like diet. Gut microbiota impacts lipid metabolism, inflammation, and endothelial function, all vital in atherosclerosis. Dysbiosis increases intestinal permeability, causing inflammation and plaque instability, elevating cardiac event risk. This study investigates the impact of dietary improvements on gut microbiota and metabolite release in recent ACS patients versus healthy individuals. A cohort of 29 recent ACS patients receiving lipid-lowering therapy and dietary advice was analyzed alongside 56 healthy controls. Dietary habits, serum, and stool samples were collected at admission and after 3 months. Metagenomic analysis of stool and metabolomic analysis of serum were conducted. The results showed bacterial dysbiosis in ACS patients, characterized by a reduction in beneficial genera and an increase in potentially pro-inflammatory bacteria. After 3 months of dietary improvements, three metabolites with anti-inflammatory properties were significantly upregulated. The findings highlight the association between gut microbiota dysbiosis, fatty diets, and inflammation in ACS patients. The observed increase in anti-inflammatory metabolites following dietary changes underscore the following dietary interventions in modulating gut microbiota and improving cardiovascular and metabolic health.},
}

@article {pmid40260089,
year = {2025},
author = {Xu, P and Pan, C and Yuan, M and Zhu, Y and Wei, S and Lu, H and Zhang, W},
title = {Viral metagenomics reveals diverse viruses in the fecal samples of children with acute respiratory infection.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1564755},
pmid = {40260089},
issn = {1664-302X},
abstract = {INTRODUCTION: Changes in the gut microbiome have been associated with the development of acute respiratory infection (ARI). However, due to methodological limitations, our knowledge of the gut virome in patients with ARIs remains limited.

METHODS: In this study, fecal samples from children with ARI were investigated using viral metagenomics.

RESULTS: The fecal virome was analyzed, and several suspected disease-causing viruses were identified. The five viral families with the highest abundance of sequence reads were Podoviridae, Virgaviridae, Siphoviridae, Microviridae, and Myoviridae. Additionally, human adenovirus, human bocavirus, human astrovirus, norovirus, and human rhinovirus were detected. The genome sequences of these viruses were respectively described, and phylogenetic trees were constructed using the gene sequences of the viruses.

DISCUSSION: We characterized the composition of gut virome in children with acute respiratory infections. However, further research is required to elucidate the relationship between acute respiratory infection and gut viruses.},
}

@article {pmid40260085,
year = {2025},
author = {Perez, LJ and Perez-Restrepo, LS and Ciuoderis, K and Usuga, J and Moreno, I and Vargas, V and Arévalo-Arbelaez, AJ and Berg, MG and Cloherty, GA and Hernández-Ortiz, JP and Osorio, JE},
title = {Emergence, persistence, and positive selection of yellow fever virus in Colombia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1548556},
pmid = {40260085},
issn = {1664-302X},
abstract = {Yellow fever virus (YFV) is an arbovirus that causes acute febrile illness (AFI), in tropical areas of South America and Africa. Through a 2020-2023 AFI study in Leticia, Colombia, leveraging metagenomic next-generation sequencing (mNGS), we identified and isolated YFV (LET1450). Phylogenetic analysis showed this strain belongs to South American genotype II (SamII), linked to Peruvian and Bolivian sequences emerging around 1989. Phylodynamic analysis indicates these strains, with a unique genetic makeup, could have reduced vaccine susceptibility, and due to positive Darwinian selection have an enhanced adaptive capacity. Antigenic analysis identified additional immune-evasive traits and this strain's potential for wider Latin American spread. Phylogeographic reconstruction demonstrated the persistence of YFV in Colombia is not due to repeated external introductions, but results from continuous, cryptic internal circulation. This study highlights the crucial role of mNGS in monitoring emerging strains and underscores the need for genomic surveillance of YFV and other arboviral infections.},
}

@article {pmid40260047,
year = {2025},
author = {Guo, L and Wu, X and Cao, L},
title = {Clinical Characteristics of Miliary Pulmonary Tuberculosis in Pregnancy After In Vitro Fertilization-Embryo Transfer: A Retrospective Clinical Study.},
journal = {Health science reports},
volume = {8},
number = {4},
pages = {e70705},
pmid = {40260047},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Miliary pulmonary tuberculosis (MPTB) is rare in patients treated with In Vitro fertilization-embryo transfer (IVF-ET), and can be life-threatening to pregnant women and fetuses. We aimed to describe the clinical characteristics of MPTB after IVF-ET and pregnancy outcomes to provide reference for early diagnosis and treatment.

METHODS: Clinical data from patients who developed MPTB after IVF-ET from January 2018-December 2021 were retrospectively and statistically analyzed.

RESULTS: Ultimately, 21 patients (mean age: 29.81 ± 3.79 years) were included. Three patients had a history of pulmonary or extrapulmonary tuberculosis (TB), and were cured or showed no suggestive TB activity before pregnancy. Patients presented with atypical early symptoms, fever (39.16 ± 0.74°C), and vaginal bleeding, and lung imaging changes. Patients became febrile 78.90 ± 26.04 days after IVF-ET; the time from fever to diagnosis was 17.76 ± 9.05 days. Patients were admitted 96.05 ± 25.33 days after IVF-ET. Sputum Mycobacterium tuberculosis smear and culture, purified protein derivative, TB polymerase chain reaction, and other routine TB examinations had low positivity rates; the erythrocyte sedimentation rate was generally within normal limits. Chest imaging during pregnancy is limited, further increasing the diagnosis time. Two critically ill patients were diagnosed by metagenomic next-generation sequencing. Seven patients had TB meningitis or encephalitis. Pregnancy was terminated in all but three patients. All patients received anti-TB therapy; however, two patients died during hospitalization (mean hospitalization: 58.29 ± 33.40 days).

CONCLUSIONS: Comprehensive TB screening before IVF-ET is necessary for infertile patients. MPTB develops after IVF-ET with atypical symptoms and poor pregnancy outcomes. Clinicians should use multiple methods to confirm TB diagnoses early on, without delaying chest imaging.},
}

@article {pmid40259990,
year = {2025},
author = {Chen, Y and Liu, Y and Ji, M and Zhang, Z and Xing, T and Pan, H and Liu, K and Li, Y and Liu, P},
title = {Metabolic diversity and adaptation of carbon-fixing microorganisms in extreme glacial cryoconite.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf056},
pmid = {40259990},
issn = {2730-6151},
abstract = {Understanding the diversity and functionality of carbon-fixing microorganisms in glacial ecosystems is crucial for elucidating carbon cycling processes in extreme environments. This study investigates the composition, diversity, and metabolic potential of carbon-fixing microorganisms in Tibetan cryoconite. Through metagenomic sequencing, we identified 13 carbon-fixing metagenome-assembled genomes spanning ten known and three unclassified genera. Deoxyribonucleic acid -stable isotope probing experiments with [13]C-labeled sodium bicarbonate confirmed the metabolic activity of key genera, including Cyanobacteria (Microcoleus and Phormidesmis) and Proteobacteria (Rhizobacter and Rhodoferax). Our results reveal a diverse array of carbon fixation pathways, with the Calvin-Benson-Bassham cycle and 3-hydroxypropionate bicycle being the most prominent. In addition to photoautotrophic microorganisms, chemoautotrophic microorganisms also contribute to carbon fixation through mechanisms such as sulfur oxidation and atmospheric reducing gas utilization. The study highlights the adaptability of microbial communities to varying environmental conditions, including fluctuations in oxygen, light, and substrate availability. The findings underscore the complex interplay between carbon fixation pathways and environmental factors in cryoconite ecosystems. It also emphasizes the importance of exploring alternative carbon fixation pathways to gain a more comprehensive understanding of carbon cycling in these harsh and dynamic ecosystems.},
}

@article {pmid40259731,
year = {2025},
author = {Sun, YS and Zhao, L and Zheng, CL and Yan, XT and Li, Y and Gao, XL and Xue, TF and Zhang, YM and Li, ZP and Heller, R and Feng, CG and Xu, C and Wang, K and Qiu, Q},
title = {Convergent musk biosynthesis across host and microbiota in musk deer and muskrat.},
journal = {Zoological research},
volume = {46},
number = {3},
pages = {505-517},
doi = {10.24272/j.issn.2095-8137.2025.094},
pmid = {40259731},
issn = {2095-8137},
mesh = {Animals ; *Deer/microbiology/metabolism ; *Fatty Acids, Monounsaturated/metabolism ; *Microbiota ; Scent Glands/metabolism ; *Arvicolinae/microbiology/metabolism ; },
abstract = {Mammalian scent glands mediate species-specific chemical communication, yet the mechanistic basis for convergent musk production remain incompletely understood. Forest musk deer and muskrat have independently evolved specialized musk-secreting glands, representing a striking case of convergent evolution. Through an integrated multi-omics approach, this study identified cyclopentadecanone as a shared key metabolic precursor in musk from both forest musk deer and muskrat, although downstream metabolite profiles diverged between the two lineages. Single-cell RNA sequencing revealed that these specialized apocrine glands possessed unique secretory architecture and exhibited transcriptional profiles associated with periodic musk production, distinct from those in conventional apocrine glands. Convergent features were evident at the cellular level, where acinar, ductal, and basal epithelial subtypes showed parallel molecular signatures across both taxa. Notably, acinar cells in both species expressed common genes involved in fatty acid and glycerolipid metabolism (e.g., ACSBG1, HSD17B12, HACD2, and HADHA), suggesting a conserved molecular framework for musk precursor biosynthesis. Metagenomic analysis of musk samples further revealed parallel microbial community structures dominated by Corynebacterium and enriched in lipid metabolic pathways. These findings suggest multi-level convergence in musk biosynthesis, from molecular pathways to microbial communities, providing novel insights into mammalian chemical signaling and artificial musk production.},
}

Animals
*Deer/microbiology/metabolism
*Fatty Acids, Monounsaturated/metabolism
*Microbiota
Scent Glands/metabolism
*Arvicolinae/microbiology/metabolism

@article {pmid40259344,
year = {2025},
author = {Zhang, Q and Hutchison, ER and Pan, C and Warren, MF and Keller, MP and Attie, AD and Lusis, AJ and Rey, FE},
title = {Systems genetics uncovers associations among host amylase locus, gut microbiome, and metabolic traits in mice.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {101},
pmid = {40259344},
issn = {2049-2618},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Amylases/genetics/metabolism ; Genome-Wide Association Study ; Metagenomics/methods ; Male ; Bacteroidetes/genetics/classification/isolation & purification ; Mendelian Randomization Analysis ; Firmicutes/genetics/classification/isolation & purification ; Cecum/microbiology ; },
abstract = {BACKGROUND: Population studies have revealed associations between host genetic and gut microbiome in humans and mice. However, the molecular bases for how host genetic variation impacts the gut microbial community and bacterial metabolic niches remain largely unknown.

RESULTS: We leveraged 90 inbred hyperlipidemic mouse strains from the hybrid mouse diversity panel (HMDP), previously studied for a variety of cardio-metabolic traits. Metagenomic analysis of cecal DNA followed by genome-wide association analysis identified genomic loci that were associated with microbial enterotypes in the gut. Among these, we detected a genetic locus surrounding multiple amylase genes that were associated with abundances of Firmicutes (Lachnospiraceae family) and Bacteroidetes (Muribaculaceae family) taxa encoding distinct starch and sugar degrading capabilities. The genetic variants at the amylase gene locus were associated with distinct gut microbial communities (enterotypes) with different predicted metabolic capacities for carbohydrate degradation. Mendelian randomization analysis revealed host phenotypes, including liver fibrosis and plasma HDL-cholesterol levels, that were associated with gut microbiome enterotypes.

CONCLUSIONS: This work reveals novel relationships among host genetic variation, gut microbial enterotypes, and host metabolic traits and supports the notion that variation of host amylase may represent a key determinant of gut microbiome in mice. Video Abstract.},
}

Animals
Mice
*Gastrointestinal Microbiome/genetics
*Amylases/genetics/metabolism
Genome-Wide Association Study
Metagenomics/methods
Male
Bacteroidetes/genetics/classification/isolation & purification
Mendelian Randomization Analysis
Firmicutes/genetics/classification/isolation & purification
Cecum/microbiology

@article {pmid40258842,
year = {2025},
author = {Duru, IC and Lecomte, A and Laine, P and Shishido, TK and Suppula, J and Paulin, L and Scheperjans, F and Pereira, PAB and Auvinen, P},
title = {Comparison of phage and plasmid populations in the gut microbiota between Parkinson's disease patients and controls.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13723},
pmid = {40258842},
issn = {2045-2322},
support = {NNF22OC0080109//Novo Nordisk Foundation/ ; },
mesh = {Humans ; *Parkinson Disease/microbiology/virology ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics/isolation & purification ; Aged ; *Plasmids/genetics ; Male ; Female ; Middle Aged ; Feces/microbiology/virology ; Case-Control Studies ; Metagenomics/methods ; Machine Learning ; },
abstract = {The aging population worldwide is on the rise, leading to a higher number of Parkinson's disease (PD) cases each year. PD is presently the second most prevalent neurodegenerative disease, affecting an estimated 7-10 million individuals globally. This research aimed to identify mobile genetic elements in human fecal samples using a shotgun metagenomics approach. We identified over 44,000 plasmid contigs and compared plasmid populations between PD patients (n = 68) and controls (n = 68). Significant associations emerged between groups (control vs PD) based on plasmid alpha and beta diversity. Moreover, the gene populations present on plasmids displayed marked differences in alpha and beta diversity between PD patients and controls. We identified a considerable number of phage contigs that were differentially abundant in the two groups. We also developed a predictive machine learning model based on phage abundance data, achieving a mean Area Under the Curve (AUC) of 0.74 with a standard deviation of 0.105 and a mean F1 score of 0.68 with a standard deviation of 0.14 across cross-validation folds, indicating moderate discriminatory power. Additionally, when tested on external data, the model yielded an AUC of 0.74 and an F1 score of 0.8, further demonstrating the predictive potential of phage populations in Parkinson's disease. Further, we improved the continuity and identification of the protein coding regions of the phage contigs by implementing alternative genetic codes.},
}

Humans
*Parkinson Disease/microbiology/virology
*Gastrointestinal Microbiome/genetics
*Bacteriophages/genetics/isolation & purification
Aged
*Plasmids/genetics
Male
Female
Middle Aged
Feces/microbiology/virology
Case-Control Studies
Metagenomics/methods
Machine Learning

@article {pmid40258509,
year = {2025},
author = {Fang, C and Zhu, J and Xu, H and Qian, M and Jin, Y},
title = {Polystyrene microplastics and cypermethrin exposure interfered the complexity of antibiotic resistance genes and induced metabolic dysfunction in the gut of adult zebrafish.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {374},
number = {},
pages = {126288},
doi = {10.1016/j.envpol.2025.126288},
pmid = {40258509},
issn = {1873-6424},
abstract = {Environmental pollutants such as microplastics (MPs) and pesticides are becoming prevalent in aquatic ecosystems, posing risks to wildlife and human health. This study investigated the toxicological effects of polystyrene microplastics (PS-MPs) and cypermethrin (CYP) on adult female zebrafish (Danio rerio), focusing on intestinal microenvironment. Adsorption kinetics experimental results showed that PS-MPs can adsorb a certain amount of CYP on its surface, thereby forming a new type of composite pollutant. After exposure to red fluorescent PS-MPs for 4 days, it was found that the PS-MPs could enter the zebrafish and accumulate in the intestines. Five-month-old female zebrafish were exposed to PS-MPs, CYP, and a mixture of both for 21 days. After exposure, feces were collected and analyzed using metagenomic sequencing to determine microbial composition and functional changes. Metagenomic sequencing of naturally excreted feces showed that co-exposure synergistically reduced α-diversity and shifted community structure, with marked losses of beneficial Fusobacteriota, Firmicutes and Cetobacterium somerae and enrichment of pathogenic Preplasmiviricota. Functional annotation indicated that PS-MPs alone up-regulated glycoside hydrolases and glycosyl-transferases, whereas CYP and the co-exposure group suppressed a great number of the top 50 carbohydrate-active enzymes and decreased secondary metabolic pathways linked to amino-acid, lipid and carbohydrate metabolism pathways. Antibiotic-resistance gene (ARGs) profiling identified 57 ARG types (such as sul1, adeF, lnuC and mphA) after co-exposure. Finally, key genes related to amino acid metabolism, carbohydrate metabolism, and lipid metabolism in intestinal tissue were significantly altered. Collectively, our data demonstrated that PS-MPs and CYP exposure amplified gut dysbiosis, metabolic dysfunction and ARG complexity in zebrafish. Overall, the study highlighted the potential risks of combined environmental pollutants on intestinal microbiota, with implications for ecosystem health.},
}

@article {pmid40258462,
year = {2025},
author = {He, R and Li, X and Zhang, X},
title = {Methane enhancing nitrous oxide consumption in microaerobic sludge systems.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121658},
doi = {10.1016/j.envres.2025.121658},
pmid = {40258462},
issn = {1096-0953},
abstract = {Nitrous oxide (N2O) reduction is traditionally known to be active under extremely low oxygen concentrations and hypoxic conditions. Herein, microaerobic sludge systems (∼38.2 and ∼12.1 μM dissolved oxygen) were conducted to investigate the performance of simultaneous methane (CH4) oxidation and N2O consumption compared with hypoxic conditions. During the whole experiment, the average N2O consumption rate in the high dissolved oxygen sludge system with CH4 was 3.4-4.9 times that of the others. A positively linear correlation was observed between the CH4 oxidation rate and the N2O consumption rate in the sludge systems. Compared to the treatment without CH4, the N2O consumption rate was higher in the treatment with CH4, indicating that aerobic CH4 oxidation might be related with the N2O consumption in the systems. The N2O consumption in the microaerobic system was influenced by the O2, CH4 and NH4[+]-N concentrations and was regulated by the microbial species. Type I methane-oxidizing bacteria (MOB) including Methylococcus, Methylocaldum, Methylomagnum, Methylosarcina, Methylobacter and Methylogaea, type II MOB Methylocystis and NC10 phylum Candidatus Methylomirabilis were the main methanotrophs in the systems. Compared with type II MOB, type I MOB were more abundant in the system. Anaerolinea and Lautropia were the main denitrifying bacteria in the microaerobic system with CH4 and N2O. Clad I nosZ and clad II nosZ were both rich in the microaerobic system. These findings suggest that an appropriate oxygen concentration would be favorable for simultaneous mitigation of CH4 and N2O emission in the sludge systems.},
}

@article {pmid40257249,
year = {2025},
author = {Maggiori, C and John, Z and Bower, DM and Millan, M and Hahn, AS and McAdam, A and Johnson, SS},
title = {Draft genome sequence of a member of a putatively novel Rubrobacteraceae genus from lava tubes in Lava Beds National Monument.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0133524},
doi = {10.1128/mra.01335-24},
pmid = {40257249},
issn = {2576-098X},
abstract = {We report the draft genome sequence of a member of a potentially novel genus of Rubrobacteraceae isolated from Golden Dome Cave in Lava Beds National Monument. Members of this family are known to inhabit thermophilic environments. The metagenome-assembled genome presented here helps illuminate the genetic capacity of basaltic lava tube environments.},
}

@article {pmid40257199,
year = {2025},
author = {Wang, X and Wang, M and Zhang, W and Li, H and Tiedje, JM and Zhou, J and Topp, E and Luo, Y and Chen, Z},
title = {Treatment of antibiotic-manufacturing wastewater enriches for Aeromonas veronii, a zoonotic antibiotic-resistant emerging pathogen.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf077},
pmid = {40257199},
issn = {1751-7370},
abstract = {Antibiotic-manufacturing wastewater treatment plants primarily target chemical pollutants, but their processes may select for antibiotic-resistant pathogens and antibiotic resistance genes. Here, leveraging the combined strengths of deep metagenomic sequencing, 16S rRNA gene sequencing, qPCR, and bacterial culturing, we investigated bacterial communities and antibiotic resistomes across eleven treatment units in a full-scale antibiotic-manufacturing wastewater treatment plant processing wastewater from a β-lactam manufacturing facility. We demonstrated that both bacterial communities and antibiotic resistance gene compositions varied across the treatment units, but were associated. Certain antibiotic resistance gene persisted through treatment, either carried by identical bacterial species, or linked to mobile genetic elements in different species. Despite the satisfactory performance in chemical removal, the antibiotic-manufacturing wastewater treatment plant continuously enriched zoonotic antibiotic-resistant Aeromonas veronii (an emerging pathogen responsible for substantial economic losses in aquaculture and human health) from influent to effluent, probably due to prolonged β-lactam selection pressure and aquatic nature of A. veronii. This enrichment resulted in a significantly higher abundance of A. veronii in the antibiotic-manufacturing wastewater treatment plant compared to other aquatic samples worldwide. Furthermore, the closest evolutionary relative to the antibiotic-manufacturing wastewater treatment plant derived A. veronii was an isolate obtained from the stool of a local diarrhea patient. These findings highlighted a substantial public health risk posed by antibiotic-manufacturing wastewater treatment plants, underlining their potential role in enriching and disseminating zoonotic antibiotic-resistant pathogens. Beyond chemical monitoring, enhanced surveillance of antibiotic-resistant pathogens and antibiotic resistance genes is needed in antibiotic-manufacturing wastewater treatment plants to avoid creating environmental hotspots of antibiotic resistant pathogens from discharging wastewater effluents.},
}

@article {pmid40256453,
year = {2025},
author = {Shen, D and Ju, H and Wang, H and Wang, X and Li, G},
title = {The clinic application of mNGS and ENA-78 assays to identify intra-amniotic infection/inflammation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1510671},
pmid = {40256453},
issn = {2235-2988},
mesh = {Humans ; Female ; Pregnancy ; *Amniotic Fluid/microbiology/chemistry ; Adult ; *Chorioamnionitis/diagnosis ; *Inflammation/diagnosis ; *Pregnancy Complications, Infectious/diagnosis ; Biomarkers/analysis ; High-Throughput Nucleotide Sequencing ; Obstetric Labor, Premature/diagnosis ; Pregnancy Outcome ; Cerclage, Cervical ; Young Adult ; *Chemokine CXCL5/analysis ; },
abstract = {OBJECTIVE: The objective of this study is to explore whether metagenomic next-generation sequencing (mNGS) and Epithelial Neutrophil Activating Peptide-78 (ENA-78) assays in the amniotic fluid (AF) of patients with preterm labor (PTL) could be employed for diagnosing intra-amniotic infection/inflammation (IAI/I) and predict the outcomes of emergency cerclage in women with cervical insufficiency(CI).

METHODS: AF samples from 40 patients were subjected to PTL were subjected to mNGS and microbial culture to diagnose intra-amniotic infection known as microbial invasion of the amniotic cavity (MIAC); ELISA was used to analyze ENA-78 levels for prediction of intra-amniotic inflammation (IAI). Pregnancy outcomes were compared, the predictive performance of mNGS and ENA-78 were assessed to evaluate the efficacy of emergency cervical cerclage.

RESULTS: The diagnosis rate of MIAC was higher with mNGS (17.5%) compared to microbial culture (2.5%). AF ENA-78 levels were significantly higher in IAI patients than in non-IAI/I patients. ENA-78 demonstrated certain accuracy in identifying IAI, with sensitivity and specificity of 73.3% and 100%, respectively. Compared with non-IAI/I patients, patients with MIAC or IAI exhibited poor pregnancy outcomes after cervical cerclage.

CONCLUSIONS: mNGS and ENA-78 assays are valuable means for assessing the state of infection/inflammation in the amniotic cavity and predicting the outcomes of emergency cerclage.},
}

Humans
Female
Pregnancy
*Amniotic Fluid/microbiology/chemistry
Adult
*Chorioamnionitis/diagnosis
*Inflammation/diagnosis
*Pregnancy Complications, Infectious/diagnosis
Biomarkers/analysis
High-Throughput Nucleotide Sequencing
Obstetric Labor, Premature/diagnosis
Pregnancy Outcome
Cerclage, Cervical
Young Adult
*Chemokine CXCL5/analysis

@article {pmid40255248,
year = {2025},
author = {Favale, N and Costa, S and Summa, D and Sabbioni, S and Mamolini, E and Tamburini, E and Scapoli, C},
title = {Comparison of microbiome community structure and dynamics during anaerobic digestion of different renewable solid wastes.},
journal = {Current research in microbial sciences},
volume = {8},
number = {},
pages = {100383},
pmid = {40255248},
issn = {2666-5174},
abstract = {This study analysed the effect of the different lignocellulose composition of two crop substrates on the structure and dynamics of bacterial communities during anaerobic digestion (AD) processes for biogas production. To this end, cereal grains and grape pomace biomasses were analysed in parallel in an experimental AD bench-scale system to define and compare their metagenomic profiles for different experimental time intervals. The bacterial community structure and dynamics during the AD process were detected and characterised using high-resolution whole metagenomic shotgun analyses. Statistical evaluation identified 15 strains as specific to two substrates. Some strains, like Clostridium isatidis, Methanothermobacter wolfeii, and Methanobacter sp. MB1 in cereal grains, and Acetomicrobium hydrogeniformans and Acetomicrobium thermoterrenum in grape pomace, were never before detected in biogas reactors. The presence of bacteria such as Acetomicrobium sp. and Petrimonas mucosa, which degrade lipids and protein-rich substrates, along with Methanosarcina sp. and Peptococcaceae bacterium 1109, which tolerate high hydrogen pressures and ammonia concentrations, suggests a complex syntrophic community in lignin-cellulose-enriched substrates. This finding could help develop new strategies for the production of a tailor-made microbial consortium to be inoculated from the beginning of the digestion process of specific lignocellulosic biomass.},
}

@article {pmid40255076,
year = {2025},
author = {Buttler, L and Velázquez-Ramírez, DA and Tiede, A and Conradi, AM and Woltemate, S and Geffers, R and Bremer, B and Spielmann, V and Kahlhöfer, J and Kraft, ARM and Schlüter, D and Wedemeyer, H and Cornberg, M and Falk, C and Vital, M and Maasoumy, B},
title = {Distinct clusters of bacterial and fungal microbiota in end-stage liver cirrhosis correlate with antibiotic treatment, intestinal barrier impairment, and systemic inflammation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2487209},
doi = {10.1080/19490976.2025.2487209},
pmid = {40255076},
issn = {1949-0984},
mesh = {Humans ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/classification/genetics/isolation & purification/drug effects ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; Aged ; Dysbiosis/microbiology ; *Fungi/classification/isolation & purification/genetics ; *Inflammation/microbiology ; *Liver Cirrhosis/microbiology ; *Mycobiome ; Prospective Studies ; Metagenomics ; Intestinal Mucosa/microbiology ; *End Stage Liver Disease/microbiology/drug therapy ; Adult ; },
abstract = {Decompensated liver cirrhosis (dLC) is associated with intestinal dysbiosis, however, underlying reasons and clinical consequences remain largely unexplored. We investigated bacterial and fungal microbiota, their relation with gut barrier integrity, inflammation, and cirrhosis-specific complications in dLC-patients. Competing-risk analyses were performed to investigate clinical outcomes within 90 days. Samples were prospectively collected from 95 dLC-patients between 2017 and 2022. Quantitative metagenomic analyses clustered patients into three groups (G1-G3) showing distinct microbial patterns. G1 (n = 39) displayed lowest diversity and highest Enterococcus abundance, G2 (n = 24) was dominated by Bifidobacteria, G3 (n = 29) was most diverse and clustered most closely with healthy controls (HC). Of note, bacterial concentrations were significantly lower in cirrhosis compared with HC, especially for G1 that also showed the lowest capacity to produce short chain fatty acids and secondary bile acids. Consequently, fungal overgrowth, dominated by Candida spp. (51.63%), was observed in G1. Moreover, G1-patients most frequently received antibiotics (n = 33; 86.8%), had highest plasma-levels of Zonulin (p = 0.044) and a proinflammatory cytokine profile along with numerically higher incidences of subsequent infections (p = 0.09). In conclusion, distinct bacterial clusters were observed at qualitative and quantitative levels and correlated with fungal abundances. Antibiotic treatment significantly contributed to dysbiosis, which translated into intestinal barrier impairment and systemic inflammation.},
}

Humans
Male
Female
Middle Aged
*Gastrointestinal Microbiome/drug effects
*Bacteria/classification/genetics/isolation & purification/drug effects
*Anti-Bacterial Agents/therapeutic use/adverse effects
Aged
Dysbiosis/microbiology
*Fungi/classification/isolation & purification/genetics
*Inflammation/microbiology
*Liver Cirrhosis/microbiology
*Mycobiome
Prospective Studies
Metagenomics
Intestinal Mucosa/microbiology
*End Stage Liver Disease/microbiology/drug therapy
Adult

@article {pmid40254830,
year = {2025},
author = {Pham, CM and Rankin, TJ and Stinear, TP and Walsh, CJ and Ryan, FJ},
title = {TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf173},
pmid = {40254830},
issn = {1477-4054},
support = {GNT1194325//National Health and Medical Research Council of Australia/ ; },
mesh = {*Microbiota ; Humans ; *Software ; *Metagenomics/methods ; Diabetes Mellitus, Type 2/microbiology/genetics ; *Databases, Genetic ; *Computational Biology/methods ; Inflammatory Bowel Diseases/microbiology/genetics ; Metagenome ; },
abstract = {Microbial communities are essential regulators of ecosystem function, with their composition commonly assessed through DNA sequencing. Most current tools focus on detecting changes among individual taxa (e.g. species or genera), however in other omics fields, such as transcriptomics, enrichment analyses like gene set enrichment analysis are commonly used to uncover patterns not seen with individual features. Here, we introduce TaxSEA, a taxon set enrichment analysis tool available as an R package, a web portal (https://shiny.taxsea.app), and a Python package. TaxSEA integrates taxon sets from five public microbiota databases (BugSigDB, MiMeDB, GutMGene, mBodyMap, and GMRepoV2) while also allowing users to incorporate custom sets such as taxonomic groupings. In silico assessments show TaxSEA is accurate across a range of set sizes. When applied to differential abundance analysis output from inflammatory bowel disease and type 2 diabetes metagenomic data, TaxSEA can rapidly identify changes in functional groups corresponding to known associations. We also show that TaxSEA is robust to the choice of differential abundance analysis package. In summary, TaxSEA enables researchers to efficiently contextualize their findings within the broader microbiome literature, facilitating rapid interpretation, and advancing understanding of microbiome-host and environmental interactions.},
}

*Microbiota
Humans
*Software
*Metagenomics/methods
Diabetes Mellitus, Type 2/microbiology/genetics
*Databases, Genetic
*Computational Biology/methods
Inflammatory Bowel Diseases/microbiology/genetics
Metagenome

@article {pmid40254787,
year = {2025},
author = {Dame-Teixeira, N and Lynch, J and Yu, X and Cena, JA and Do, T},
title = {The Caries and Caries-Free Archaeome.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345251329343},
doi = {10.1177/00220345251329343},
pmid = {40254787},
issn = {1544-0591},
abstract = {The difficulty of establishing a relationship between archaea and oral diseases such as dental caries stems from the challenges of detecting, identifying, and isolating these microorganisms. This study aimed to detect archaea in publicly available datasets comprising caries and caries-free saliva and dental plaque by using a tailored bioinformatic pipeline for shotgun sequencing analysis. A systematic search was performed to identify studies using shotgun metagenomics or metatranscriptomics on samples obtained from individuals with dental caries. Two reviewers selected studies based on eligibility criteria. Sequencing and metadata from each study were retrieved from the SRA Bioproject. A count table was generated for each database by mapping reads against an archaea genome database, specifically tailored for this study, using stringent filtering parameters of greater than 97% similarity and 90% query coverage. Archaeal prevalence was determined using an arbitrary cutoff point (>500 reads). An effect size meta-analysis was performed to determine the overall prevalence. Phyloseq and DESeq2 packages were used to determine alpha and beta diversities, differential abundance in different taxonomic levels, and differential expression comparing caries and caries-free samples. Spearman correlation was performed with the bacteriome. The search yielded 154 titles, from which a collection of 7 datasets from 8 studies was obtained. Of 397 samples, N = 63 were positive for archaea using postfiltering, comprising a putative prevalence of 20% (confidence interval = 0%-40%) and identifying Euryarchaeota, Thermoplasmatota, and Nitrosphaeria. Methanogens were present in both the caries and caries-free groups (Methanobrevibacter spp., Methanosarcina, and Methanosphaera) and positively correlated with Stenotrophomonas, Streptococcus, Actinomyces, Abiotrophia, Gemella, and Corynebacterium. Several methanogenesis genes, including methyl-coenzyme M reductase, which catalyzes the final step of methane production in methanogens, were underexpressed in caries-active samples compared with caries-free samples. Saliva and dental plaque emerged as sites of low-abundance archaea, with methanogenesis genes underexpressed in caries-active samples.},
}

@article {pmid40254701,
year = {2025},
author = {Zaharuddin, AM and Muslim, A and Aazmi, S and Idorus, MY and Almabhouh, FA and Lim, SY and Loganathan, AL and Ayub, Q and Chong, CW and Khalil, KA and Ghani, NA and Lim, SM and Ramasamy, K},
title = {Probiotic Lactobacillus rhamnosus GG Alleviates Prehypertension and Restores Gut Health and Microbiota in NaCl-Induced Prehypertensive Rats.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40254701},
issn = {1867-1314},
abstract = {Probiotics could be used as adjuvant treatments in prehypertension management to restore gut microbiota dysbiosis caused by a high-salt diet. This study investigated the antihypertensive effects of the probiotic Lactobacillus rhamnosus strain GG (LGG) on high-salt diet-induced prehypertensive rats. Eighteen Sprague-Dawley rats were assigned equally into three groups: normotensive fed on a normal diet (ND), prehypertensive induced on a 4% NaCl high-salt diet (HSD), and prehypertensive induced on an HSD treated with LGG at 1 × 10[9] CFU daily for 8 weeks (LGG). Weekly changes in water, food, body weight, diastolic blood pressure (DBP), systolic blood pressure (SBP), and mean arterial pressure (MAP) were monitored. Serum levels of Na, K, Cl, ALB, Ca, and TP were measured at the end of treatment, along with morphological and histomorphometric changes in the small intestine. Stool samples collected before (W0) and 8 weeks after treatment (W8) were sequenced for bacterial 16S rDNA metagenomics. Probiotic LGG significantly reduces average DBP, SBP, and MAP while improving gut integrity through intact intestine morphology, higher villus heights, and a V/C ratio. At the genus level, the LGG group's gut microbiota composition is more similar to the HSD profile at W0 but shifts to the ND profile after treatment at W8. Thus, probiotic LGG lowers blood pressure indices, improves serum biochemistry profile, restores small intestinal integrity barrier, and modulates gut microbiota profile, indicating its potential as an adjuvant treatment for prehypertension and the significance of gut health in blood pressure regulation.},
}

@article {pmid40254251,
year = {2025},
author = {Chang, FM and Chen, YH and Hsu, PS and Wu, TH and Sung, IH and Wu, MC and Nai, YS},
title = {RNA metagenomics revealed insights into the viromes of honey bees (Apis mellifera) and Varroa mites (Varroa destructor) in Taiwan.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108341},
doi = {10.1016/j.jip.2025.108341},
pmid = {40254251},
issn = {1096-0805},
abstract = {The honey bee (Apis mellifera) is a vital pollinator for crops. However, they are infested by a worldwide spread ecto-parasite, Varroa mite (Varroa destructor). The Varroa mite is a vector of various western honey bee viruses. In this study, the prevalence of seven honey bee viruses (Deformed wing virus, Lake Sinai virus, Acute bee paralysis virus, Sacbrood virus, Kashmir bee virus, Black queen cell virus, Israeli acute paralysis virus), was screened with the honey bees, which were collected from fourteen apiaries from March 2023 to January 2024, and the Varroa mites, which were collected from two apiaries from July to October 2023 by using RT-PCR. Subsequently, metagenomic analyses were conducted on seven honey bee samples and two Varroa mite samples using next-generation sequencing with poly-A capture and rRNA depletion library construction methods. The results showed that 50% to 85.7% of honey bee viruses in each sample were detected by both methods, with up to three additional viruses identified when combining the two approaches. These findings underscore the importance of integrating both methods for comprehensive virome analysis. According to the virome analysis, 28 honey bee viruses were identified in honey bees and 11 in Varroa mites. Among these, 23 viruses were newly recorded in Taiwanese honey bee populations. Notably, three of the newly recorded viruses, Acute bee paralysis virus, Israeli acute paralysis virus, and Apis mellifera filamentous virus, are known to cause symptoms in honey bees, posing potential risks to their health. Six of these viruses were also detected in Varroa mites, highlighting their role in viral transmission. This study represents the first virome analysis of honey bees and Varroa mites in Taiwan, providing critical insights into honey bee health and establishing a foundation for future health assessment indices and mitigation strategies.},
}

@article {pmid40253770,
year = {2025},
author = {Zhu, Y and Tian, Q and Huang, Q and Wang, J},
title = {Bile-processed Rhizoma Coptidis alleviates type 2 diabetes mellitus through modulating the gut microbiota and short-chain fatty acid metabolism.},
journal = {International immunopharmacology},
volume = {156},
number = {},
pages = {114645},
doi = {10.1016/j.intimp.2025.114645},
pmid = {40253770},
issn = {1878-1705},
abstract = {BACKGROUND: Bile-Processed Rhizoma Coptidis (BPRC) is a processed products of Rhizoma Coptidis (RC) commonly used to treat type 2 diabetes mellitus (T2DM). However, the synergistic mechanism of its processing remains unknown. Current research indicates that the gut microbiota and its metabolites, such as short-chain fatty acids (SCFAs), are closely associated with the progression of T2DM.

PURPOSE: This study aims to investigate the effects of BPRC on the gut microbiota and its metabolite SCFAs in T2DM rats.

METHODS: T2DM rat model was induced by a high-fat diet (HFD) combined with streptozotocin (STZ), followed by a 4-week treatment with BPRC to observe its therapeutic effects. The impact of BPRC on the gut microbiota was studied through metagenomic sequencing. Quantitative analysis of SCFAs was conducted using GC-MS. Western blot and quantitative real-time PCR (qRT-PCR) were conducted to investigate the potential mechanisms of BPRC.

RESULTS: BPRC significantly improved insulin resistance in T2DM rats, downregulated levels of pancreatic cell apoptosis factors, and upregulated the abundance of Bacteroides uniformis, Bacteroides sp A1C1, Anaerostipes caccae, Alistipes finegoldii and Blautia sp.N6H1-15 in T2DM rats. Additionally, BPRC increased the levels of seven SCFAs in the intestines of T2DM rats. It activated intestinal TGR5, GPR41, GPR43, and GPR109a receptors, collectively upregulating GLP-1 protein expression, and exerted therapeutic effects on T2DM.

CONCLUSION: The results indicate that the synergistic mechanism of BPRC in treating T2DM is associated with modulating the gut microbiota, increasing SCFAs content in the intestines, and regulating intestinal GLP-1 production.},
}

@article {pmid40253436,
year = {2025},
author = {Huang, J and Zheng, X and Yu, T and Ali, M and Wiese, J and Hu, S and Huang, L and Huang, Y},
title = {Diverse lifestyles and adaptive evolution of uncultured UBA5794 actinobacteria, a sister order of "Candidatus actinomarinales".},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {39},
pmid = {40253436},
issn = {2524-6372},
support = {92351301, 32470005, 42376238, and 32393970//National Natural Science Foundation of China/ ; 91751000//Major Research Plan of the National Natural Science Foundation of China/ ; GML20240002//the PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; },
abstract = {Uncultured UBA5794 actinobacteria are frequently found in marine and inland water environments by using metagenomic approaches. However, knowledge about these actinobacteria is limited, hindering their isolation and cultivation, and they are always confused with "Candidatus Actinomarinales" based on 16S rRNA gene classification. Here, to conduct genomic characterization of them, we obtained three high-quality UBA5794 metagenome-assembled genomes (MAGs) from a hydrothermal sediment on the Carlsberg Ridge (CR) and retrieved 131 high-quality UBA5794 genomes from public datasets. Phylogenomic analysis confirms UBA5794 as an independent order within the class Acidimicrobiia. Genome-based metabolic predictions reveal that flexible metabolism and diversified energy acquisition, as well as heavy metal(loid) detoxification capacity, are crucial for the ability of UBA5794 to thrive in diverse environments. Moreover, there is separation between sponge-associated and free-living UBA5794 groups in phylogeny and functional potential, which can be attributed to the symbiotic nature of the sponge-associated group and the extensive horizontal gene transfer (HGT) events observed in these bacteria. Ancestral state reconstruction suggests that the UBA5794 clade may have originated from a free-living environment and then some members gradually migrated to the sponge host. Overall, our study sheds light on the ecological adaptation and evolutionary history of the ubiquitous but poorly understood UBA5794 actinobacteria.},
}

@article {pmid40253169,
year = {2025},
author = {Aryal, A and Nwachukwu, ID and Aryee, ANA},
title = {Examining the impact of crops and foods biofortified with micronutrients on the gut microbiome.},
journal = {Food research international (Ottawa, Ont.)},
volume = {209},
number = {},
pages = {116189},
doi = {10.1016/j.foodres.2025.116189},
pmid = {40253169},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/physiology ; *Micronutrients ; Humans ; *Crops, Agricultural ; *Biofortification ; *Food, Fortified ; Animals ; },
abstract = {Micronutrient deficiencies (MNDs) impact more than three billion individuals worldwide, particularly those in impoverished and marginalized communities, leading to adverse long-term health consequences. Biofortification, which focusses on enhancing the nutrient density of food crops, presents a promising strategy to address this challenge. Recent studies involving both model organisms and human subjects have demonstrated that, beyond remedying common dietary insufficiencies, micronutrients can modulate the composition and functionality of the gut microbiome. The microbiota, in turn, utilize these micronutrients, facilitating digestion, synthesizing essential nutrients, and modulating immune responses, thereby establishing a bidirectional relationship known as the micronutrient-microbiome axis. Numerous studies have also documented significant variations in these interactions, highlighting the complex dynamics of the micronutrient-microbiome relationship. The composition and interactions of the microbiota have been investigated using various methodologies, including 16S rRNA gene sequencing, RT-PCR, metagenomics, and metabolomics. This review explores recent advancements in understanding the reciprocal relationship between micronutrient levels and the gut microbiome, emphasizing key findings that provide critical insights for the development of targeted dietary strategies aimed at alleviating MNDs and improving overall health.},
}

*Gastrointestinal Microbiome/physiology
*Micronutrients
Humans
*Crops, Agricultural
*Biofortification
*Food, Fortified
Animals

@article {pmid40252922,
year = {2025},
author = {Charya, AV and Jang, MK and Kong, H and Park, W and Tian, X and Keller, M and Phipps, K and Sanders, A and Shah, P and Mathew, J and Aryal, S and Berry, GJ and Marboe, C and Orens, JB and Nathan, SD and Agbor-Enoh, S},
title = {Donor-derived cell-free DNA is associated with the degree of immunosuppression in lung transplantation.},
journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajt.2025.04.011},
pmid = {40252922},
issn = {1600-6143},
abstract = {Donor-derived cell-free DNA is increasingly used in clinical practice to monitor lung transplant patients for acute rejection. However, its association with conventional approaches to monitor immunosuppression remains unclear. This multicenter observational cohort study examines the association of donor-derived cell free DNA with surrogate measures of immunosuppression. Serial plasma samples were collected for quantification of donor-derived cell-free DNA and anellovirus abundance via shotgun and metagenomic sequencing. Adjudication committees reviewed clinical data to define acute cellular and antibody-mediated rejection. The association between ddcfDNA, anellovirus abundance, and serum tacrolimus trough concentrations over the study period and during episodes of acute rejection were examined via linear mixed effects modeling. Donor-derived cell-free DNA demonstrated a significant inverse association with tacrolimus troughs (p=0.027) and anellovirus abundance (p<0.001) over time. Acute rejection episodes were associated with significantly decreased anellovirus abundance (median, 0.042 vs. 0.708, p<0.001) and higher ddcfDNA levels (1.49% vs. 0.26%, p<0.001) compared to stable control timepoints. However, tacrolimus levels were similar between acute rejection and controls (10.1 ng/ml vs 10.3 ng/ml, p = 0.13). Our findings suggest donor-derived cell-free DNA correlates with measures of immunosuppression in lung transplant patients. Additional studies are needed to assess the utility of donor-derived cell-free DNA to assess immunosuppression adequacy.},
}

@article {pmid40252793,
year = {2025},
author = {Yang, R and Guo, S and Huo, L and Yang, G and Tian, S},
title = {Impact of Watershed-Scale Land Restoration on Soil Microbial Communities and Their Functions: Insights from Metagenomic Analysis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121609},
doi = {10.1016/j.envres.2025.121609},
pmid = {40252793},
issn = {1096-0953},
abstract = {Land restoration in the gully regions of China's Loess Plateau has significantly altered soil conditions and farming practices, yet its impact on soil microbes remains unclear. This study applied metagenomic sequencing and correlation analysis to examine microbial community shifts and key genes involved in carbon, nitrogen, and phosphorus cycling. Results show increased biodiversity and microbial activity, especially downstream, enhancing carbon metabolism and ecosystem resilience. Phosphorus activation improved, with related gene abundance rising by 27.45%-52.57%, facilitating phosphorus availability. Nitrogen cycling showed enhanced nitrification and nitrogen fixation, with reduced denitrification, promoting nitrogen retention. Soil organic carbon, total nitrogen, ammonium nitrogen, and available phosphorus (AP), particularly AP, strongly influenced microbial dynamics. These findings highlight the positive role of land restoration in improving soil health and nutrient cycling, supporting sustainable agriculture.},
}

@article {pmid40252750,
year = {2025},
author = {Yang, M and Peng, L and Mu, M and Yang, F and Li, Z and Han, B and Zhang, K},
title = {Significant effects of earthworm species on antibiotic resistome in livestock manure as revealed by metagenomic analysis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126277},
doi = {10.1016/j.envpol.2025.126277},
pmid = {40252750},
issn = {1873-6424},
abstract = {Animal-derived antibiotic resistance genes (ARGs) have emerged as a critical threat, while vermicomposting has been recognized as an effective strategy for reducing ARGs. However, the efficacy of different earthworm species in reducing ARGs remains poorly understood. In this study, 72 vermicompost and earthworm gut samples were collected from various earthworm farms to evaluate the impact of vermicomposting with different earthworm species on ARGs via metagenomic analysis. Approximately 28 ARG types were detected in gut and vermicompost samples. There were significant differences in ARGs among the four species of earthworm composting systems (p < 0.05), and each species possessed its dominant ARGs and microbes. Proteobacteria represented the predominant bacterial phylum within the gut microbiota of Pheretima guillelmi (46.89%) and Eisenia fetida (48.42%), whereas Euryarchaeota (36.71%) and Actinobacteria (39.42%) were the most abundant in Perionyx excavatus and Eudrilus eugeniae, respectively. The overall abundance of ARGs in vermicompost processed by Eisenia fetida (0.18 copies16S rRNA gene copies) was lower than that observed in other earthworm species (0.23-0.39 copies/16S rRNA gene copies), with gut microbial identified as a key determinant of variations in ARG reduction. These findings provide valuable insights into selecting suitable earthworm species to promote ARG degradation, thus contributing to the decrease in ARG dissemination risks in agricultural ecosystems.},
}

@article {pmid40252553,
year = {2025},
author = {Bariod, L and Fuentes, E and Millet, M and White, J and Jacquiod, S and Moreau, J and Monceau, K},
title = {Exposure to pesticides is correlated with gut microbiota alterations in a farmland raptor.},
journal = {Environment international},
volume = {199},
number = {},
pages = {109436},
doi = {10.1016/j.envint.2025.109436},
pmid = {40252553},
issn = {1873-6750},
abstract = {The gut microbiota is crucial for host health and can be impacted by various environmental disruptions, yet the effects of multiple pesticide exposures on farmland organisms' microbiomes remain largely unexplored. We assessed microbiota changes in a wild apex predator exposed to multiple pesticides in agricultural landscapes. Pesticides, including acetochlor and quinoxyfen, which are supposed to be banned, were significantly positively correlated with certain key bacteria from Actinobacteria, Alphaproteobacteria and Gammaproteobacteria classes. Our results light up the potential collateral effect of pesticides on gut bacterial assemblages through unknown mechanisms. These effects could result in dysbiosis and the promotion of potential pathogens and/or the selection of bacteria that might allow the organism to detoxify the organism. Although formal metagenomic analyses would be required soon, these microbial shifts underline the broader ecological consequences of pesticide exposure, emphasising the need for integrated biodiversity conservation and ecosystem management to protect environmental and public health.},
}

@article {pmid40252419,
year = {2025},
author = {Ciuchcinski, K and Kaczorowska, AK and Biernacka, D and Dorawa, S and Kaczorowski, T and Park, Y and Piekarski, K and Stanowski, M and Ishikawa, T and Stokke, R and Steen, IH and Dziewit, L},
title = {Computational pipeline for sustainable enzyme discovery through (re)use of metagenomic data.},
journal = {Journal of environmental management},
volume = {382},
number = {},
pages = {125381},
doi = {10.1016/j.jenvman.2025.125381},
pmid = {40252419},
issn = {1095-8630},
abstract = {Enzymes derived from extremophilic organisms, also known as extremozymes, offer sustainable and efficient solutions for industrial applications. Valued for their resilience and low environmental impact, extremozymes have found use as catalysts in various processes, ranging from dairy production to pharmaceutical manufacturing. However, discovery of novel extremozymes is often hindered by challenges such as culturing difficulties, underrepresentation of extreme environments in reference databases, and limitations of traditional sequence-based screening methods. In this work, we present a computational pipeline designed to discover novel enzymes from metagenomic data derived from extreme environments. This pipeline represents a versatile and sustainable approach that promotes reuse and recycling of existing datasets and minimises the need for additional environmental sampling. In its core, the algorithm integrates both traditional bioinformatic techniques and recent advances in structural prediction, enabling rapid and accurate identification of enzymes. However, due to its design, the algorithm relies heavily on existing databases, which can limit its effectiveness in situations where reference data is scarce or when encountering novel protein families. As a proof-of-concept, we applied the pipeline to metagenomic data from deep-sea hydrothermal vents, with a focus on β-galactosidases. The pipeline identified 11 potential candidate proteins, out of which 10 showed in vitro activity. One of the selected enzymes, βGal_UW07, showed strong potential for industrial applications. The enzyme exhibited optimal activity at 70 °C and was exceptionally resistant to high pH and the presence of metal ions and reducing agents. Overall, our results indicate that the pipeline is highly accurate and can play a key role in sustainable bioprospecting, leveraging existing metagenomic datasets and minimising in situ interventions in pristine regions.},
}

@article {pmid40252413,
year = {2025},
author = {Okamura, T and Hasegawa, Y and Ohno, Y and Saijo, Y and Nakanishi, N and Honda, A and Hamaguchi, M and Takano, H and Fukui, M},
title = {Oral exposure to nanoplastics and food allergy in mice fed a normal or high-fat diet.},
journal = {Chemosphere},
volume = {379},
number = {},
pages = {144401},
doi = {10.1016/j.chemosphere.2025.144401},
pmid = {40252413},
issn = {1879-1298},
abstract = {The global prevalence of food allergies, particularly IgE-mediated responses, is increasing at an alarming rate. This trend is likely driven by environmental factors such as nanoplastics (NPs) ingestion and the westernization of dietary and lifestyle habits. This study examines the impact of polystyrene nanoplastics (PS-NPs) on ovalbumin (OVA)-induced food allergies in mice subjected to either a normal diet (ND) or a high-fat diet (HFD). BALB/c mice were stratified into eight groups based on dietary regimen, NP exposure, and OVA sensitization. Food allergy was induced via OVA administration, and multiple physiological and immunological parameters were evaluated, including body weight, intestinal permeability, cytokine profiles, gut microbiota composition, and small intestinal gene expression. Mice in the HFD + OVA + NP group exhibited significant increases in intestinal permeability, diarrhea severity, and serum OVA-specific IgE levels compared to other groups. Flow cytometric analysis revealed an expansion of innate lymphoid cells (ILC2 and ILC1) within the lamina propria of the small intestine. Shotgun metagenomic sequencing demonstrated gut microbiota dysbiosis, characterized by a reduction in beneficial bacterial populations in the HFD + OVA + NP cohort. Weighted Gene Co-Expression Network Analysis (WGCNA) identified a negative correlation between NPs exposure or OVA sensitization and the expression of Slc1a1, Slc5a8, and Mep1a, while a positive correlation was observed with Aa467197 expression. These findings indicate that oral exposure to PS-NPs exacerbates OVA-induced food allergies, particularly in the context of an HFD, through mechanisms involving increased intestinal permeability, gut microbial dysbiosis, and gene expression modulation. This study highlights the potential health hazards posed by environmental microplastic contamination and its possible contribution to the escalating incidence of food allergies.},
}

@article {pmid40252307,
year = {2025},
author = {Qian, L and Jiang, J and Zhang, Y and Huang, X and Che, Z and Chen, G and Liu, S},
title = {Sublethal exposure to boscalid induced respiratory abnormalities and gut microbiota dysbiosis in adult zebrafish.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {283},
number = {},
pages = {107370},
doi = {10.1016/j.aquatox.2025.107370},
pmid = {40252307},
issn = {1879-1514},
abstract = {Boscalid (BO), one of the frequently detected fungicides of succinate dehydrogenase inhibitor in water environments, has unknown effects on the respiratory function and gut health of aquatic organisms. Therefore, zebrafish were exposed to BO solutions (0.01-1.0 mg/L) for 21 days to assess its effects on zebrafish respiration and intestinal microbiota in this study. The results showed that exposure to 0.1 and 1.0 mg/L BO for 21 days resulted in zebrafish exhibiting aggregation of gill filaments, reduction of mucous cells, and significantly decreased opercular movement, linked to a marked decline in the activity of respiratory chain complex II. 16S rRNA gene sequencing revealed significant changes in the intestinal microbiota composition of zebrafish exposed to 1.0 mg/L BO. Specifically, the relative abundance of beneficial bacteria (Cetobacterium) was markedly reduced, while pathogenic bacteria (such as Ralstonia, Legionella, Acinetobacter, Escherichia/Shigella) associated with energy metabolism and immune pathways in zebrafish showed a significant increase in relative abundance. Accordingly, metagenomic functional prediction analysis further revealed the potential impact of BO-induced gut microbiota changes on energy metabolism and immune pathways in zebrafish. Furthermore, histopathological analysis of intestinal tissues revealed that exposure to BO resulted in necrosis and shedding of epithelial cells, as well as a decrease in goblet cell count, which exacerbated adverse effects on intestinal health. In conclusion, sublethal exposure to BO affects the respiratory function and intestinal health of zebrafish. Therefore, the impact of BO in aquatic environments on fish health warrants attention.},
}

@article {pmid40252261,
year = {2025},
author = {Li, B and Liang, C and Xu, B and Song, P and Liu, D and Zhang, J and Gu, H and Jiang, F and Gao, H and Cai, Z and Zhang, T},
title = {Extreme winter environment dominates gut microbiota and metabolome of white-lipped deer.},
journal = {Microbiological research},
volume = {297},
number = {},
pages = {128182},
doi = {10.1016/j.micres.2025.128182},
pmid = {40252261},
issn = {1618-0623},
abstract = {Qinghai-Tibet Plateau (QTP) is marked by harsh environments that drive the evolution of unique nutrient metabolism mechanism in indigenous animal gut microbiotas. Yet, responses of these microbiotas to different extreme environments remain poorly understood. White-lipped deer (Przewalskium albirostris), a native endangered species in the QTP, serves as an ideal model to study how gut microbiotas adapt to season and human disturbances. Here, a multi-omics integrated analysis of 16S rRNA, metagenomics, and untargeted metabolomics was performed to investigate the composition, function, and metabolic characteristics of gut microbiota in White-lipped deer across different seasons and living environments. Our results revealed that extreme winter environment dominated the composition, function, and metabolism of gut microbiota in white-lipped deer. The white-lipped deer exhibited an enriched gut microbiota associated with producing short-chain fatty acids in winter, with core feature genera including norank_o_Rhodospirillales, Rikenellaceae_RC9_gut_group, and unclassified_c_Clostridia. However, potential pathogenic bacteria and few short-chain fatty acid producers, with core feature genera including norank_f_p-2534-18B5_gut_group, Cellulosilyticum, and Paeniclostridium, showed enrichment in captivity. Pathways associated with carbohydrate metabolism, amino acid metabolism, and immune regulation showed enrichment in winter group as an adaptation to the cold and food scarcity. Among these, Rikenellaceae_RC9_gut_group and unclassified_c_Clostridia contributed significantly to these metabolic pathways. The gut microbiota of white-lipped deer exhibited enrichment in pathways related to intestinal inflammation and enhanced immune regulation to alleviate the stress of captivity. Among these, norank_f_p-2534-18B5_gut_group contributed the most to these pathways. Butyric, valeric, and valproic acids were significantly more abundant in the winter group, while 3-hydroxybutyric and (S)-beta-aminoisobutyric acids were higher in the captive group. Furthermore, enriched metabolites and associated pathways in both groups further supported the inferences on metagenomic functions. This study confirms the key role of specific gut microbiota in adapting to high-altitude winters and anthropogenic disturbances, emphasizing its importance for environmental resilience in wild, high-altitude mammals.},
}

@article {pmid40251489,
year = {2025},
author = {Bini, F and Soffritti, I and D'Accolti, M and Mazziga, E and Caballero, JD and David, S and Argimon, S and Aanensen, DM and Volta, A and Bisi, M and Mazzacane, S and Caselli, E},
title = {Profiling the resistome and virulome of Bacillus strains used for probiotic-based sanitation: a multicenter WGS analysis.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {382},
pmid = {40251489},
issn = {1471-2164},
support = {INV-004891/GATES/Gates Foundation/United States ; },
mesh = {*Bacillus/genetics/isolation & purification/drug effects/classification/pathogenicity ; *Probiotics ; *Whole Genome Sequencing ; *Genome, Bacterial ; Polymorphism, Single Nucleotide ; *Sanitation ; Humans ; *Drug Resistance, Bacterial/genetics ; },
abstract = {BACKGROUND: Healthcare-associated infections (HAIs) caused by microbes that acquire antimicrobial resistance (AMR) represent an increasing threat to human health worldwide. The high use of chemical disinfectants aimed at reducing the presence of pathogens in the hospital environment can simultaneously favor the selection of resistant strains, potentially worsening AMR concerns. In the search for sustainable ways to control bioburden without affecting this aspect, probiotic-based sanitation (PBS) using Bacillus spp. was proposed to achieve stable reduction of pathogens, AMR, and associated HAIs. Although Bacillus probiotics are classified as nonpathogenic, comprehensive data about the potential genetic alterations of these probiotics following prolonged contact with surrounding pathogens are not yet available. This study aimed to assess in depth the genetic content of PBS-Bacillus isolates to evaluate any eventual variations that occurred during their usage.

RESULTS: WGS analysis was used for the precise identification of PBS-Bacillus species and detailed profiling of their SNPs, resistome, virulome, and mobilome. Analyses were conducted on both the original PBS detergent and 172 environmental isolates from eight hospitals sanitized with PBS over a 30-month period. The two species B. subtilis and B. velezensis were identified in both the original product and the hospital environment, and SNP analysis revealed the presence of two clusters in each species. No virulence/resistance genes or mobile conjugative plasmids were detected in either the original PBS-Bacillus strain or any of the analyzed environmental isolates, confirming their high genetic stability and their low/no tendency to be involved in horizontal gene transfer events.

CONCLUSIONS: The data obtained by metagenomic analysis revealed the absence of genetic sequences associated with PBS-Bacillus and the lack of alterations in all the environmental isolates analyzed, despite their continuous contact with surrounding pathogens. These results support the safety of the Bacillus species analyzed. Further metagenomic studies aimed at profiling the whole genomes of these and other species of Bacillus, possibly during longer periods and under stress conditions, would be of interest since they may provide further confirmation of their stability and safety.},
}

*Bacillus/genetics/isolation & purification/drug effects/classification/pathogenicity
*Probiotics
*Whole Genome Sequencing
*Genome, Bacterial
Polymorphism, Single Nucleotide
*Sanitation
Humans
*Drug Resistance, Bacterial/genetics

@article {pmid40251030,
year = {2025},
author = {Chen, J and Zhang, S and Wang, M and Kang, G and Lu, L and Chang, N and Wang, N and Xie, Z and Liu, Y and Zhang, H and Shen, W},
title = {Investigating the Impact of Landfill Age and Season on the Occurrence and Dissemination of Antibiotic Resistance Genes in Leachate and the Underlying Mechanisms Using Metagenomics.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf091},
pmid = {40251030},
issn = {1365-2672},
abstract = {AIMS: Antibiotic resistance genes (ARGs) pose a critical public health concern, with landfill leachate serving as a significant environmental reservoir. While ARG dynamics in leachate have been investigated in various contexts, their occurrence and influence factors in semi-arid regions remain poorly understood. This study investigated the occurrence and influence factors of ARG profiles, their potential hosts, and underlying mechanisms driving their proliferation.

METHODS AND RESULTS: Comprehensive metagenomic analysis of leachate samples collected from landfills of varying landfill ages (5, 10, and 20 years) in Hohhot, Inner Mongolia-a representative semi-arid region of northern China-across three seasons (autumn, spring, and summer). Metagenomic analysis revealed distinct patterns in core ARG abundances modulated by both landfill age and seasonal variations. Notably, landfill age predominantly influenced tetracycline- and glycopeptide- ARGs, while seasonal fluctuations primarily affected glycopeptide- and multidrug- ARGs. Taxonomic analysis identified Pseudomonas aeruginosa and Pseudomonas fluorescens as the predominant resistant pathogens, with elevated prevalence during spring and winter compared to summer. Network analysis and metabolic pathway reconstruction demonstrated that landfill age maybe impacted ARG dissemination through modulation of carbohydrate and nitrogen metabolic pathways. This novel finding suggests a previously unrecognized mechanism linking waste decomposition stages to ARG proliferation.

CONCLUSIONS: Our study provides the first systematic characterization of ARG dynamics in semi-arid landfill leachate, offering crucial insights for developing targeted strategies to mitigate ARG dissemination in these distinct ecological contexts. These findings establish a theoretical framework for understanding ARG transmission in semi-arid environments while providing empirical evidence to inform environmental management practices.},
}

@article {pmid40251011,
year = {2025},
author = {Dawson, SJT and Shibu, P and Garnett, S and Newberry, F and Brook, TC and Tijani, T and Kujawska, M and Hall, LJ and McCartney, AL and Negus, D and Hoyles, L},
title = {Weberviruses are gut-associated phages that infect Klebsiella spp.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf043},
pmid = {40251011},
issn = {1574-6941},
abstract = {Weberviruses are bacteriophages (phages) that can infect and lyse clinically relevant, multidrug-resistant (MDR) strains of Klebsiella. They are an attractive therapeutic option to tackle Klebsiella infections due to their high burst sizes, long shelf life and associated depolymerases. In this study we isolated and characterized seven new lytic phages and compared their genomes with those of their closest relatives. Gene-sharing network, ViPTree proteome and terL gene-sequence-based analyses incorporating all publicly available webervirus genomes [n=258 from isolates, n=65 from metagenome-assembled genome (MAG) datasets] confirmed the seven phages as members of the genus Webervirus and identified a novel genus (Defiantjazzvirus) within the family Drexlerviridae. Using our curated database of 265 isolated phage genomes and 65 MAGs (n=330 total), we found that weberviruses are distributed globally and primarily associated with samples originating from the gut: sewage (154/330, 47%), wastewater (83/330, 25%) and human faeces (66/330, 20%). We identified three distinct clusters of potential depolymerases encoded within the 330 genomes. Due to their global distribution, frequency of isolation and lytic activity against the MDR clinical Klebsiella strains used in this study, we conclude that weberviruses and their depolymerases show promise for development as therapeutic agents against Klebsiella spp.},
}

@article {pmid40250773,
year = {2025},
author = {Wu, X and Li, Y and Li, P and Lu, G and Wu, J and Wang, Z and Wen, Q and Cui, B and Wang, J and Zhang, F},
title = {Structural variations in ulcerative colitis-associated E. coli reduce fructose utilization and aggravate inflammation under high fructose diet.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.03.039},
pmid = {40250773},
issn = {1528-0012},
abstract = {BACKGROUND AND AIMS: Structural variations (SVs) have significant effects on the microbial phenotypes. The underlying mechanism of functional changes caused by gut microbial SVs in the development of ulcerative colitis (UC) need further investigation.

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

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

CONCLUSIONS: SV-caused difference in fructose utilization and proinflammatory properties in E. coli from UC patients influence the development of UC, emphasizing the importance of fine-scale metagenomic studies in disease.},
}

@article {pmid40250459,
year = {2025},
author = {Munroe, ES and Spicer, A and Castellvi-Font, A and Zalucky, A and Dianti, J and Graham Linck, E and Talisa, V and Urner, M and Angus, DC and Baedorf-Kassis, E and Blette, B and Bos, LD and Buell, KG and Casey, JD and Calfee, CS and Del Sorbo, L and Estenssoro, E and Ferguson, ND and Giblon, R and Granholm, A and Harhay, MO and Heath, A and Hodgson, C and Houle, T and Jiang, C and Kramer, L and Lawler, PR and Leligdowicz, A and Li, F and Liu, K and Maiga, A and Maslove, D and McArthur, C and McAuley, DF and Serpa Neto, A and Oosthuysen, C and Perner, A and Prescott, HC and Rochwerg, B and Sahetya, S and Samoilenko, M and Schnitzer, ME and Seitz, KP and Shah, F and Shankar-Hari, M and Sinha, P and Slutsky, AS and Qian, ET and Webb, SA and Young, PJ and Zampieri, FG and Zarychanski, R and Fan, E and Semler, MW and Churpek, M and Goligher, EC and , and , },
title = {Evidence-based personalised medicine in critical care: a framework for quantifying and applying individualised treatment effects in patients who are critically ill.},
journal = {The Lancet. Respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2213-2600(25)00054-2},
pmid = {40250459},
issn = {2213-2619},
abstract = {Clinicians aim to provide treatments that will result in the best outcome for each patient. Ideally, treatment decisions are based on evidence from randomised clinical trials. Randomised trials conventionally report an aggregated difference in outcomes between patients in each group, known as an average treatment effect. However, the actual effect of treatment on outcomes (treatment response) can vary considerably between individuals, and can differ substantially from the average treatment effect. This variation in response to treatment between patients-heterogeneity of treatment effect-is particularly important in critical care because common critical care syndromes (eg, sepsis and acute respiratory distress syndrome) are clinically and biologically heterogeneous. Statistical approaches have been developed to analyse heterogeneity of treatment effect and predict individualised treatment effects for each patient. In this Review, we outline a framework for deriving and validating individualised treatment effects and identify challenges to applying individualised treatment effect estimates to inform treatment decisions in clinical care.},
}

@article {pmid40250281,
year = {2025},
author = {Chen, Y and Hu, S and Hu, B and Li, Y and Chen, Z},
title = {Functional insights into microbial community dynamics and resilience in mycorrhizal associated constructed wetlands under pesticide stress.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138315},
doi = {10.1016/j.jhazmat.2025.138315},
pmid = {40250281},
issn = {1873-3336},
abstract = {Arbuscular mycorrhizal fungi (AMF) are critical mutualistic symbionts in most terrestrial ecosystems, where they facilitate nutrient acquisition, enhance plant resilience to environmental stressors, and shape the surrounding microbiome. However, its contributions (especially for microorganisms) to constructed wetlands (CWs) under pesticide stress remain poorly understood. This study investigated the effects of AMF on microbial community composition, diversity, metabolic pathways, and functional genes by metagenomics in CWs exposed to pesticides stress. Using comparative analyses of AMF-colonized and non-colonized CWs, we found that AMF enhanced overall microbial diversity, as evidenced by increases of 2.22 % (Chao1) and 2.83 % (observed species). Under fungicide stress, nitrogen-cycling microorganisms (e.g., Nitrososphaerota and Mucoromycota) increased in relative abundance, while carbon cycle-related microorganisms (e.g., Pseudomonadota and Bacteroidota) generally declined. AMF colonization improved microbial resilience, demonstrated by a 312 % rise in Rhizophagus abundance and significant increases in phosphorus-cycling microorganisms (e.g., Bradyrhizobium and Mesorhizobium). Functional gene analysis further revealed that AMF helped mitigate fungicide-induced reductions in genes related to nitrogen and carbon cycling, lowering the average decline rates to 4.02 % and 1.44 %, respectively, compared to higher rates in non-AMF treatments. In summary, these findings highlight the crucial role of AMF in enhancing pesticide stress resilience, maintaining microbial community stability, and improving the bioremediation capacity of CWs.},
}

@article {pmid40250270,
year = {2025},
author = {Yang, C and Xu, Y and Yu, T and Li, Y and Zeng, XC},
title = {Microbial reductive mobilization of As(V) in solid phase coupled with the oxidation of sulfur compounds: An overlooked biogeochemical reaction affecting the formation of arsenic-contaminated groundwater.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138234},
doi = {10.1016/j.jhazmat.2025.138234},
pmid = {40250270},
issn = {1873-3336},
abstract = {Dissimilatory As(V)-respiring prokaryotes (DARPs) are recognized as having a crucial role in the formation of arsenic-contaminated groundwater. DARPs use small-molecule organic acids as electron donor to directly reduce As(V) in solid phase to more mobile As(III). Therefore, DARPs are considered to be heterotrophic bacteria. However, these cannot explain why high concentrations of As(III) are produced in environments lacking soluble organic carbon. We thus propose that reduced sulfur compounds may also be utilized by DARPs and affect the DARPs-mediated arsenic mobilization. This study sought to confirm this hypothesis. Metagenomic investigations on the DARP population derived from As-contaminated soil indicated that approximately 84 % of DARP MAGs possess the enzymes potentially catalyzing the oxidation of S[2-], S[0], SO3[2-], or S2O3[2-]. Functional analysis of DARP population and a cultivable strain suggested that DARPs, in addition to small-molecule organic carbon, can effectively use sulfur compounds as electron donor to reduce As(V) to mobile As(III). Arsenic release experiments using DARP population and a cultivable DARP strain showed that DARPs indeed utilized sulfur compounds as the sole electron donors under autotrophic and anaerobic conditions to directly reduce adsorbed As(V) in the soils to mobile As(III). These findings provide new insights into the microbial mechanism responsible for the variation of As(III) concentrations in contaminated groundwater.},
}

@article {pmid40250268,
year = {2025},
author = {Yang, JH and Huang, DQ and Wu, GG and Han, NN and Fan, NS and Jin, RC},
title = {Quorum sensing-mediated microecological homeostasis in anammox consortia.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138285},
doi = {10.1016/j.jhazmat.2025.138285},
pmid = {40250268},
issn = {1873-3336},
abstract = {Quorum sensing (QS) mediated by signal molecules regulates bacterial communication and further affects the performance and microbial physiological characteristics of anaerobic ammonium oxidation (anammox) process. The potential application of low concentrations of typical exogenous signal molecules into maintaining the long-term homeostasis of anammox consortia were evaluated in this study. The results of 150-d continuous-flow experiment showed that 30 μg L[-1]N-hexanoyl-homoserine lactone (C6-HSL) and diffusible signaling factor (DSF) could maintain the stable nitrogen removal efficiency of anammox systems (90.3 ± 3.6 % and 90.2 ± 3.8 %). C6-HSL and DSF also significantly promoted the anammox activity and the production of extracellular polymeric substances (EPS). Microbial community analysis indicated that the relative abundance of Candidatus Kuenenia fluctuated and finally maintained at 27.0 % and 39.3 %, which was still significantly higher than that of initial phase. Meanwhile, the abundances of functional genes related to anammox process (hzsA, hdh and nirS) increased significantly. Metagenomic analysis revealed that the abundances of main functional genes involved in nitrogen metabolism, amino acid metabolism and QS were significantly upregulated. The interspecies interactions were also enhanced through QS-mediated intercellular communication, which was beneficial to microecological homeostasis in anammox systems. In contrast, DSF exhibited the more significant and longer-lasting promotion impact, while the effect of C6-HSL was rapid. These findings reveal the potential regulatory mechanism of exogenous signaling molecules on anammox consortia and drive the potential application of signaling molecules in the anammox process to treat real wastewater.},
}

@article {pmid40250228,
year = {2025},
author = {Wang, H and Yang, Q and Wang, S},
title = {Metagenomic insights into the impact of tillage practices on soil nutrient cycling and wheat yield.},
journal = {The Science of the total environment},
volume = {978},
number = {},
pages = {179427},
doi = {10.1016/j.scitotenv.2025.179427},
pmid = {40250228},
issn = {1879-1026},
abstract = {Decreasing tillage intensity (DT) are beneficial for soil health and crop yield; however, the relationship between microbial nutrient cycling function and crop yield remains poorly understood.The objective of this study was to investigate the impact of tillage practices of conventional tillage with rotary tillage (RT) and decreasing tillage intensity (DT) on the soil microbial community and the functions of carbon, nitrogen, and phosphorus cycles of wheat and examine the relationship between soil microbes and yield based on a four year field experiment. An increased maize yield of 9.3 % and 8.5 % in DT compared with that in RT in 2023 and 2024, respectively. Further analysis reveals that DT influences the availability of soil carbon, nitrogen, and phosphorus by altering microbial communities and their functions. Microbial function analysis indicates that DT leads to higher abundances of genes associated with glgP (starch degradation) and xynB (hemicellulose degradation), which play a crucial role in elevating POC levels (11.6 %-23.4 %). Additionally, DT shows increased abundances of genes related to organic nitrogen metabolism (glnA), nitrification (amoB), and nitrogen fixation (nifK), contributing to the rise in NO3[-]- N content (19.1 %-31.1 %). Furthermore, DT exhibits a high abundance of the organic phosphorus mineralization gene phnM, resulting in enhanced AP content (4.7 %-25.4 %). Moreover, among the microbial genera significantly influenced by DT, ten genera-Lysobacter, Luteimonas, Bradyrhizobium, Aromatoleum, Acidibacter, Variovorax, Polaromonas, Pseudorhodoplanes, Piscinibacter, and Ramlibacter-show increased abundance, positively impacting wheat yield. Our study offers a novel framework for comprehending the enhancement of wheat yield through the lens of microbial nutrient cycling functionality and mining of beneficial bacteria for wheat yield.},
}

@article {pmid40250042,
year = {2025},
author = {Menichini, D and Seta, F and Mastrolia, SA and Cetin, I and Carafa, A and Santagni, S and Foschi, C and Cerboneschi, M and Smeazzetto, S and Neri, I and Facchinetti, F},
title = {Probiotics in pregnancy and group B streptococcus colonization: A multicentric, randomized, placebo-controlled, double-blind study with a focus on vaginal microbioma.},
journal = {European journal of obstetrics, gynecology, and reproductive biology},
volume = {310},
number = {},
pages = {113976},
doi = {10.1016/j.ejogrb.2025.113976},
pmid = {40250042},
issn = {1872-7654},
abstract = {OBJECTIVE: To evaluate the feasibility and effects of the use of probiotics in pregnancy, starting in the third trimester, on rectovaginal colonization of group B streptococcus (GBS) in women at low obstetric risk.

METHODS: A multicentre, randomized, placebo-controlled, double-blind, parallel-group study was conducted in three tertiary hospitals in northern Italy and included low-risk pregnant women. The intervention consisted of oral administration of two capsules of probiotics or placebo from 30 weeks of pregnancy until 37 weeks of pregnancy. The primary outcome was GBS colonization, evaluated with rectovaginal swabs. In a subgroup, selected at random, changes in the vaginal microbiome after treatment administration were evaluated using 16S Metagenomic Sequencing Library Preparation sequencing and analysis.

RESULTS: In total, 267 pregnant women were randomized to receive probiotics (n = 133) or placebo (n = 134). The two groups were similar at baseline. After treatment, no differences were found in the rates of positive rectovaginal swabs (p = 0.24) and antibiotic administration (p = 0.27). Only one case of postpartum fever (>38 °C) was found in the placebo group. Labour and delivery outcomes and neonatal outcomes were similar in both groups. Analysis of the vaginal microbiota showed that the relative abundance of Lactobacillus spp. was not modified significantly by the probiotics, but the relative abundance of Gardnerella spp. decreased significantly (3.6 ± 7.9 vs 5.5 ± 10.2; p = 0.03). Interestingly, the relative abundance of Lactobacillus spp. reduced significantly in women who subsequently presented with partial rupture of membranes (46.9 ± 43.6 vs 77.7 ± 24.9; p = 0.02).

CONCLUSION: Although the clinical outcomes were unaffected, administration of probiotics led to favourable changes in vaginal microbiota. It remains to be established how this effect could be translated into clinical advantage.},
}

@article {pmid40249976,
year = {2025},
author = {Zhang, WG and Liang, S and Liao, Y and Ran, G and Ji, S and Gao, Y and Lei, Z},
title = {Insights into the impact of different phytoremediation strategies on antibiotic resistance genes at the metagenomic level in real scenarios.},
journal = {Ecotoxicology and environmental safety},
volume = {296},
number = {},
pages = {118211},
doi = {10.1016/j.ecoenv.2025.118211},
pmid = {40249976},
issn = {1090-2414},
abstract = {Engineered phytoremediation strategies provide cost effective options for eliminating antibiotics and antibiotic resistance genes (ARGs) from wastewater. However, there is a knowledge gap in understanding the impact of these phytoremediation strategies on the on the diversity and composition of ARGs as well as the key driving biotic and biological factors of ARGs at the metagenomic level in real scenarios. Through metagenomic sequencing, this study demonstrates that phytoremediation with Iris pseudacorus L., Myriophyllum verticillatum L., Eichhornia crassipes (Mart.) Solms and Oenanthe javanica (Bl. DC) significantly alters the pattern of antibiotic resistome. This study is the first to reveal, at the omics level, that phytoremediation enhances the diversity of ARGs (3.2 %∼11.6 % improvement), despite reducing their absolute abundances. Furthermore, this study highlights that plant varieties have a significant impact on the performance of phytoremediation in mitigating ARGs. The non-dominant bacterial taxa, specifically Verrucomicrobia, Planctomycetes, and Actinobacteria, play a crucial role in shaping the pattern of the antibiotic resistome during the wastewater treatment. The changes in the total organic carbon, total nitrogen and antibiotics robustly influence the environmental behaviors of antibiotic resistome and microbiome. In summary, this study gives insight into the impact of different phytoremediation strategies on mitigating ARGs at the omics level in real scenarios.},
}

@article {pmid40249811,
year = {2025},
author = {Huss, P and Kieft, K and Meger, A and Nishikawa, K and Anantharaman, K and Raman, S},
title = {Engineering bacteriophages through deep mining of metagenomic motifs.},
journal = {Science advances},
volume = {11},
number = {16},
pages = {eadt6432},
doi = {10.1126/sciadv.adt6432},
pmid = {40249811},
issn = {2375-2548},
mesh = {*Metagenomics/methods ; *Bacteriophage T7/genetics ; *Metagenome ; *Bacteriophages/genetics ; *Genetic Engineering ; },
abstract = {Bacteriophages can adapt to new hosts by altering sequence motifs through recombination or convergent evolution. Where these motifs exist and what fitness advantage they confer remains largely unknown. We report a new method, Metagenomic Sequence Informed Functional Scoring (Meta-SIFT), to find sequence motifs in metagenomic datasets to engineer phage activity. Meta-SIFT uses experimental deep mutational scanning data to create sequence profiles to mine metagenomes for functional motifs invisible to other searches. We experimentally tested ~17,000 Meta-SIFT-derived sequence motifs in the receptor binding protein of the T7 phage. The screen revealed thousands of T7 variants with novel host specificity with motifs sourced from distant families. Position, substitution, and location preferences dictated specificity across a panel of 20 hosts and conditions. To demonstrate therapeutic utility, we engineered active T7 variants against foodborne pathogen Escherichia coli O121. Meta-SIFT is a powerful tool to unlock the potential encoded in phage metagenomes to engineer bacteriophages.},
}

*Metagenomics/methods
*Bacteriophage T7/genetics
*Metagenome
*Bacteriophages/genetics
*Genetic Engineering

@article {pmid40249033,
year = {2025},
author = {Wei, Q and Chen, L and Yin, Y and Pai, M and Duan, H and Zeng, W and Hu, X and Xu, M and Li, S},
title = {Analysis of Blood Microbiome From People Living With HIV and Donors by 16S rRNA Metagenomic Sequencing.},
journal = {Journal of medical virology},
volume = {97},
number = {4},
pages = {e70341},
doi = {10.1002/jmv.70341},
pmid = {40249033},
issn = {1096-9071},
support = {//This work was supported by the Chinese Society of Blood Transfusion Weigao Research Fund Project (CSBT-MWG-2020-02) and the Chinese Academy of Medical Sciences Medical and Health Science and Technology Innovation Project (CAMS-2021-I2M-1-060)./ ; },
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *HIV Infections/microbiology/blood/drug therapy ; *Microbiota ; Metagenomics ; *Blood Donors ; *Bacteria/genetics/classification/isolation & purification ; Male ; Adult ; Female ; Middle Aged ; Sequence Analysis, DNA ; *Blood/microbiology ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; },
abstract = {Utilize 16S rRNA sequencing technology to characterize bacterial species susceptible to people living with HIV (PLWH) across different stages. This mapping aims to establish a foundational framework for preventing secondary HIV infections, prolonging patient survival, enhancing quality of life, and advancing the diagnosis, treatment, and research of bacterial co-infections. In this study, we classified the participants into three groups: The blood of donors living with HIV (DI group), AIDS patients who have received ART treatment (PI group), and healthy blood donors as the control group (DH group). Each group was divided into three parallel subgroups, with 30 samples pooled from each parallel group for plasma extraction. As initial processing steps, the nine parallel subgroups were subjected to nucleic acid extraction and PCR amplification targeting the 16SV34 region. The resulting amplified products were subsequently forwarded to a sequencing company. It can be seen from the Venn diagram that the DI groups showed significantly higher bacterial diversity than the PI group and the DH group. The PI group had lower bacterial relative abundance and diversity compared to the DI group, with a community structure more similar to the control group. The DI group is particularly susceptible to several significant pathogens, including Ralstonia, Pseudomonas, Acinetobacter, Methyloversatilis, and Vibrio. The study revealed a greater quantity and diversity of bacteria in the DI blood compared to the PI and DH groups. This observation may be attributed to PI group patients in this study being hospitalized and receiving treatment.},
}

Humans
*RNA, Ribosomal, 16S/genetics
*HIV Infections/microbiology/blood/drug therapy
*Microbiota
Metagenomics
*Blood Donors
*Bacteria/genetics/classification/isolation & purification
Male
Adult
Female
Middle Aged
Sequence Analysis, DNA
*Blood/microbiology
DNA, Bacterial/genetics/chemistry
DNA, Ribosomal/genetics/chemistry

@article {pmid40248366,
year = {2025},
author = {Lu, X and Lu, Q and Zhu, R and Sun, M and Chen, H and Ge, Z and Jiang, Y and Wang, Z and Zhang, L and Zhang, W and Dai, Z},
title = {Metagenomic analysis reveals the diversity of the vaginal virome and its association with vaginitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1582553},
pmid = {40248366},
issn = {2235-2988},
mesh = {Female ; Humans ; *Virome/genetics ; *Vagina/virology/microbiology ; *Metagenomics ; Phylogeny ; *Vaginitis/virology/microbiology ; Adult ; Microbiota ; Bacteriophages/genetics/classification ; *Viruses/classification/genetics/isolation & purification ; Middle Aged ; Biodiversity ; Young Adult ; Bacteria/classification/genetics ; },
abstract = {INTRODUCTION: The human vaginal virome is an essential yet understudied component of the vaginal microbiome. Its diversity and potential contributions to health and disease, particularly vaginitis, remain poorly understood.

METHODS: We conducted metagenomic sequencing on 24 pooled vaginal swab libraries collected from 267 women, including both healthy individuals and those diagnosed with vaginitis. Viral community composition, diversity indices (Shannon, Richness, and Pielou), and phylogenetic characteristics were analyzed. Virus-host associations were also investigated.

RESULTS: DNA viruses dominated the vaginal virome. Anelloviridae and Papillomaviridae were the most prevalent eukaryotic viruses, while Siphoviridae and Microviridae were the leading bacteriophages. Compared to healthy controls, the vaginitis group exhibited significantly reduced alpha diversity and greater beta diversity dispersion, indicating altered viral community structure. Anelloviruses, detected in both groups, showed extensive lineage diversity, frequent recombination, and pronounced phylogenetic divergence. HPV diversity and richness were significantly elevated in the vaginitis group, alongside an unbalanced distribution of viral lineages. Novel phage-bacterial associations were also identified, suggesting a potential role for bacteriophages in shaping the vaginal microbiome.

DISCUSSION: These findings provide new insights into the composition and structure of the vaginal virome and its potential association with vaginal dysbiosis. The distinct virome characteristics observed in women with vaginitis highlight the relevance of viral communities in reproductive health. Future studies incorporating individual-level sequencing and metatranscriptomics are warranted to explore intra-host viral dynamics, assess viral activity, and clarify the functional roles of vaginal viruses in host-microbiome interactions.},
}

Female
Humans
*Virome/genetics
*Vagina/virology/microbiology
*Metagenomics
Phylogeny
*Vaginitis/virology/microbiology
Adult
Microbiota
Bacteriophages/genetics/classification
*Viruses/classification/genetics/isolation & purification
Middle Aged
Biodiversity
Young Adult
Bacteria/classification/genetics

@article {pmid40247828,
year = {2025},
author = {Doorenspleet, K and Mailli, AA and van der Hoorn, BB and Beentjes, KK and De Backer, A and Derycke, S and Murk, AJ and Reiss, H and Nijland, R},
title = {Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19158},
pmid = {40247828},
issn = {2167-8359},
mesh = {*Biodiversity ; *Metagenomics/methods ; *DNA Barcoding, Taxonomic/methods ; North Sea ; Nanopores ; Belgium ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {DNA-based methods and developments of sequencing technologies are integral to macrobenthos biodiversity studies, and their implementation as standardized monitoring methods is approaching. Evaluating the efficacy and reliability of these technological developments is crucial for macrobenthos biodiversity assessments. In this study, we compared three DNA-based techniques for assessing the diversity of bulk macrobenthos samples from the Belgian North Sea. Specifically, we compared amplicon sequencing using Illumina MiSeq and portable real-time sequencing of Oxford Nanopore versus shotgun sequencing using Illumina NovaSeq sequencing. The 313 bp mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding fragment served as the target region for the metabarcoding analysis. Our results indicate that Oxford Nanopore and MiSeq metabarcoding had similar performances in terms of alpha and beta diversity, revealing highly similar location-specific community compositions. The NovaSeq metagenomics method also resulted in similar alpha diversity, but slightly different community compositions compared to the metabarcoding approach. Despite these differences, location-specific community compositions were maintained across all platforms. Notably, read counts from the NovaSeq metagenomic analysis showed the weakest correlation to size corrected morphological abundance and there were mismatches between morphological identification and all DNA based findings which are likely caused by a combination of factors such as primer efficiency and an incomplete reference database. Our findings underscore the critical importance of database completeness prior to implementing DNA-based techniques as standardized monitoring method, especially for metagenomics. Nevertheless, our findings emphasize that Oxford Nanopore metabarcoding proves to be a viable alternative to the conventional Illumina MiSeq metabarcoding platform for macrobenthos biodiversity monitoring.},
}

*Biodiversity
*Metagenomics/methods
*DNA Barcoding, Taxonomic/methods
North Sea
Nanopores
Belgium
High-Throughput Nucleotide Sequencing/methods

@article {pmid40247824,
year = {2025},
author = {Chen, P and Yu, Q and Wang, C and Montoya, L and West, PT and Xu, L and Varoquaux, N and Cole, B and Hixson, KK and Kim, YM and Liu, L and Zhang, B and Zhang, J and Li, B and Purdom, E and Vogel, J and Jansson, C and Hutmacher, RB and Dahlberg, JA and Coleman-Derr, D and Lemaux, PG and Taylor, JW and Gao, C},
title = {Holo-omics disentangle drought response and biotic interactions among plant, endophyte and pathogen.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70155},
pmid = {40247824},
issn = {1469-8137},
support = {32022002//National Natural Science Foundation of China/ ; 32101286//National Natural Science Foundation of China/ ; 32170129//National Natural Science Foundation of China/ ; 32322053//National Natural Science Foundation of China/ ; 2022YFC2303100//National Key Research and Development Program of China/ ; XDA28030401//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
abstract = {Holo-omics provide a novel opportunity to study the interactions among fungi from different functional guilds in host plants in field conditions. We address the entangled responses of plant pathogenic and endophytic fungi associated with sorghum when droughted through the assembly of the most abundant fungal, endophyte genome from rhizospheric metagenomic sequences followed by a comparison of its metatranscriptome with the host plant metabolome and transcriptome. The rise in relative abundance of endophytic Acremonium persicinum (operational taxonomic unit 5 (OTU5)) in drought co-occurs with a rise in fungal membrane dynamics and plant metabolites, led by ethanolamine, a key phospholipid membrane component. The negative association between endophytic A. persicinum (OTU5) and plant pathogenic fungi co-occurs with a rise in expression of the endophyte's biosynthetic gene clusters coding for secondary compounds. Endophytic A. persicinum (OTU5) and plant pathogenic fungi are negatively associated under preflowering drought but not under postflowering drought, likely a consequence of variation in fungal fitness responses to changes in the availability of water and niche space caused by plant maturation over the growing season. Our findings suggest that the dynamic biotic interactions among host, beneficial and harmful microbiota in a changing environment can be disentangled by a blending of field observation, laboratory validation, holo-omics and ecological modelling.},
}

@article {pmid40247698,
year = {2025},
author = {Zhao, J and Pachiadaki, M and Conrad, RE and Hatt, JK and Bristow, LA and Rodriguez-R, LM and Rossello-Mora, R and Stewart, FJ and Konstantinidis, KT},
title = {Promiscuous and genome-wide recombination underlies the sequence-discrete species of the SAR11 lineage in the deep ocean.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf072},
pmid = {40247698},
issn = {1751-7370},
abstract = {Surveys of microbial communities (metagenomics) or isolate genomes have revealed sequence-discrete species. That is, members of the same species show >95% Average Nucleotide Identity (ANI) of shared genes among themselves vs. <83% ANI to members of other species while genome pairs showing between 83-95% ANI are comparatively rare. In these surveys, aquatic bacteria of the ubiquitous SAR11 clade (Class Alphaproteobacteria) are an outlier and often do not exhibit discrete species boundaries, suggesting the potential for alternate modes of genetic differentiation. To explore evolution in SAR11, we analyzed high-quality, single-cell amplified genomes (SAGs) and companion metagenomes from an oxygen minimum zone (OMZ) in the Eastern Tropical Pacific Ocean, where the SAR11 make up ~20% of the total microbial community. Our results show that SAR11 do form several sequence-discrete species, but their ANI range of discreteness is shifted to lower identities between 86-91%, with intra-species ANI ranging between 91-100%. Measuring recent gene exchange among these genomes based on a recently developed methodology revealed higher frequency of homologous recombination within compared to between species that affects sequence evolution at least twice as much as diversifying point mutation across the genome. Recombination in SAR11 appears to be more promiscuous compared to other prokaryotic species, likely due to the deletion of universal genes involved in the mismatch repair, and has facilitated the spreading of adaptive mutations within the species (gene sweeps), further promoting the high intra-species diversity observed. Collectively, these results implicate rampant, genome-wide homologous recombination as the mechanism of cohesion for distinct SAR11 species.},
}

@article {pmid40247632,
year = {2025},
author = {Lee, JS and Kao, DJ and Worledge, CS and Villamaria, ZF and Wang, RX and Welch, NM and Kostelecky, RE and Colgan, SP},
title = {E. coli genetically modified for purine nucleobase release promotes butyrate generation and colonic wound healing during DSS insult.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2490211},
doi = {10.1080/19490976.2025.2490211},
pmid = {40247632},
issn = {1949-0984},
mesh = {Animals ; *Escherichia coli/genetics/metabolism ; *Wound Healing ; Gastrointestinal Microbiome ; Mice ; *Purines/metabolism ; *Colon/microbiology/metabolism/pathology ; *Butyrates/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; *Colitis/chemically induced/microbiology ; Intestinal Mucosa/metabolism/microbiology ; Male ; },
abstract = {The gut microbiota transforms energy stored as undigestible carbohydrates into a remarkable number of metabolites that fuel intestinal bacterial communities and the host tissue. Colonic epithelial cells at the microbiota-host interface depend upon such microbiota-derived metabolites (MDMs) to satisfy their energy requisite. Microbial dysbiosis eliciting MDM loss contributes to barrier dysfunction and mucosal disease. Recent work has identified a role for microbiota-sourced purines (MSPs), notably hypoxanthine, as an MDM salvaged by the colonic epithelium for nucleotide biogenesis and energy balance. Here, we investigated the role of MSPs in mice during disease-modeled colonic energetic stress using a strain of E. coli genetically modified for enhanced purine nucleobase release (E. coli Mutant). E. coli Mutant colonization protected against DSS-induced tissue damage and permeability while promoting proliferation for wound healing. Metabolite and metagenomic analyses suggested a colonic butyrate-purine nucleobase metabolic axis, wherein the E. coli Mutant provided purine substrate for Clostridia butyrate production and host purine salvage, altogether supplying the host substrate for efficient nucleotide biogenesis and energy balance.},
}

Animals
*Escherichia coli/genetics/metabolism
*Wound Healing
Gastrointestinal Microbiome
Mice
*Purines/metabolism
*Colon/microbiology/metabolism/pathology
*Butyrates/metabolism
Mice, Inbred C57BL
Disease Models, Animal
*Colitis/chemically induced/microbiology
Intestinal Mucosa/metabolism/microbiology
Male

@article {pmid40246700,
year = {2025},
author = {Iguchi, H and Watanabe, A},
title = {Honey flavors formed via yeast fermentation in honey from Japanese honeybees.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/bbb/zbaf057},
pmid = {40246700},
issn = {1347-6947},
abstract = {Honey is formed from floral nectar through bee-derived substances, dehydration, and chemical reactions during storage in beehives. While bacteria and fungi inhabit honey and beehives, their roles in honey maturation remain unclear. In this study, we characterized the fermentation process of honey from Apis cerana japonica (Japanese honeybee) with respect to its microbial and flavor compound profiles. Metagenomic analysis revealed that the fungi in Japanese honeybee honey are dominated by Zygosaccharomyces siamensis, with minor members of Talaromyces, Oidiodendron, Starmerella, and Priceomyces. Fermentation of diluted raw honey increased the population of Z. siamensis. Inoculating honey with Z. siamensis produced aromatic compounds, including isoamyl alcohol, hotrienol, 2-phenylethanol, and 2-phenylethyl acetate, as well as the organic acid succinate. These results indicate that fermentation by Z. siamensis can generate favorable flavor compounds, offering the potential for enhancing honey's sensory qualities and applications in the food industry.},
}

@article {pmid40246602,
year = {2025},
author = {Zeng, S and Wang, S and Mu, D},
title = {Metagenomics for IgA-coated gut microbiota: from taxonomy to function.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.04.001},
pmid = {40246602},
issn = {1878-4380},
abstract = {Immunoglobulin A (IgA) establishes intricate interactions with human gut microbiota, thereby forming IgA-coated microbiota. This forum first explores state-of-the-art metagenomic techniques for characterizing IgA-coated microbiota. Thereafter, metagenomic insights into its taxonomic diversity and microbial genomic functions that mediate IgA coating are provided. Finally, clinical implications for human health are highlighted.},
}

@article {pmid40246210,
year = {2025},
author = {Wani, AK and Qadir, F and Elboughdiri, N and Rahayu, F and Saefudin, and Pranowo, D and Martasari, C and Kosmiatin, M and Suhara, C and Sudaryono, T and Prayogo, Y and Yadav, KK and Muzammil, K and Eltayeb, LB and Alreshidi, MA and Singh, R},
title = {Metagenomics and plant-microbe symbioses: Microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108580},
doi = {10.1016/j.biotechadv.2025.108580},
pmid = {40246210},
issn = {1873-1899},
abstract = {Biogeochemical cycles are fundamental processes that regulate the flow of essential elements such as carbon, nitrogen, and phosphorus, sustaining ecosystem productivity and global biogeochemical equilibrium. These cycles are intricately influenced by plant-microbe symbioses, which facilitate nutrient acquisition, organic matter decomposition, and the transformation of soil nutrients. Through mutualistic interactions, plants and microbes co-regulate nutrient availability and promote ecosystem resilience, especially under environmental stress. Metagenomics has emerged as a transformative tool for deciphering the complex microbial communities and functional genes driving these cycles. By enabling the high-throughput sequencing and annotation of microbial genomes, metagenomics provides unparalleled insights into the taxonomic diversity, metabolic potential, and functional pathways underlying microbial contributions to biogeochemical processes. Unlike previous reviews, this work integrates recent advancements in metagenomics with complementary omics approaches to provide a comprehensive perspective on how plant-microbe interactions modulate biogeochemical cycles at molecular, genetic, and ecosystem levels. By highlighting novel microbial processes and potential biotechnological applications, this review aims to guide future research in leveraging plant-microbe symbioses for sustainable agriculture, ecosystem restoration, and climate change mitigation.},
}

@article {pmid40245994,
year = {2025},
author = {Yang, R and Liu, Z and Liu, Y and Yang, Z and Zhang, Y and Lei, J and Wang, J and Zhang, A and Li, Z},
title = {High-throughput community and metagenomic elucidate systematic performance variation and functional transition mechanisms during morphological evolution of aerobic sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132550},
doi = {10.1016/j.biortech.2025.132550},
pmid = {40245994},
issn = {1873-2976},
abstract = {In this study, high-throughput sequencing and metagenomics were used to investigate the microbial succession and functional gene dynamics during aerobic sludge granulation from activated sludge (AS) to aerobic granular sludge (AGS) to algal-bacterial granular sludge (ABGS). It was found that the settleability and pollutant removal efficiency of the sludge system increased with the sludge morphology evolution. Extracellular polymeric substances (EPS) analysis showed a rise in protein from 2.1 to 17.4 mg/gSS during stage of AGS and polysaccharides from 3.3 to 5.9 mg/gSS during stage of ABGS. Microbial community analysis revealed that the sludge evolution reduced species richness but enriched functional bacteria for nitrogen/phosphorus removal, while increasing the complexity of community structure and close interactions between species. Key genes involved in the tricarboxylic acid cycle, nitrogen/phosphorus and EPS metabolism were also upregulated. This study revealed the continuity mechanism and stage dependence of the functional transition during sludge morphology evolution.},
}

@article {pmid40245993,
year = {2025},
author = {Zhang, J and Zhang, B and Duan, F and Xuan, Z and Sun, T and Lu, L},
title = {Metagenomic exploration of novel β-galactosidases for glycosylation engineering.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132546},
doi = {10.1016/j.biortech.2025.132546},
pmid = {40245993},
issn = {1873-2976},
abstract = {β-Galactosidases are important enzymatic tools for glycosylation, but their properties vary greatly with the source. Here, ten putative β-galactosidase genes, designated as bga1 to bga10, encoding proteins Bga1 to Bga10, were mined from an environmental metagenomic dataset comprising 119,152 sequences. Five of the encoded enzyme proteins exhibited less than 80% sequence similarity to known enzymes, but displayed conserved catalytic sites in their predicted three-dimensional models. After heterologous expression and characterization, two recombinant enzymes showed specific hydrolysis activity toward o-nitrophenyl-β-d-galactopyranoside. One of them, Bga4R, exhibited remarkable activity at pH 7.4 and 50℃, with excellent alkaline stability. Notably, Bga4R tolerated a wide range of acceptors for transglycosylation. It catalyzed galactosyl transfer to various monosaccharides and sugar alcohols, and enabling the synthesis of diverse glycosylated derivatives. This study identifies a novel GH 1 β-galactosidase as a powerful tool for glycosylation engineering, with promising potential for synthesizing galactosides valuable to food and pharmaceutical industries.},
}

@article {pmid40245807,
year = {2025},
author = {Wang, J and Zhang, Y and Meng, Q and Hu, Z and Fu, J and Dang, C},
title = {New perspectives on bacterial chlorine resistance: Phages encoding chlorine resistance genes improve bacterial adaptation.},
journal = {Water research},
volume = {282},
number = {},
pages = {123607},
doi = {10.1016/j.watres.2025.123607},
pmid = {40245807},
issn = {1879-2448},
abstract = {Bacterial resistance to chlorine disinfectant reduces its effectiveness in killing pathogenic bacteria and poses a severe threat to environmental and health safety. The interaction between bacteria and phages is the most frequent biological activity in Earth's biosphere, but little is known about what role and mechanism phages play in the resistance of bacterial communities to chlorine disinfectants. Here, we investigated the changes in the abundance, activity and function of the bacterial-phage community under the effect of chlorine disinfectants in a 92-day running anaerobic-anoxic-oxic system, using metagenomics and metatranscriptomics sequencing. We found that transcriptional activities of both bacteria and phage are highly sensitive to chlorine disinfectants, although their relative abundance was not obviously altered. The increase in both phage diversity and the ratio of temperate to lytic phages' average activity indicated phages, especially temperate, could play a crucial role in the response to chlorine disinfectants. Interestingly, the phages that carry chlorine resistance genes (CRGs) were the drivers of the phage and microbial community when chlorine disinfectants were present, but they followed the dynamics of community in the absence of chlorine disinfectants. Based on the association bipartite network, we further found that phages directly mediated the horizontal transfer of CRGs among bacteria, facilitating the spread of CRGs in the bacterial community. Moreover, the 4 CRGs related to cell wall repair, redox balance regulation, and efflux pumps that were carried by the phages but lacking in the hosts suggest the potential compensatory effects of the phage for the chlorine resistance of their hosts. Our findings reveal the important role of phages in improving the resistance of bacterial communities to chlorine disinfectants, providing a new perspective on the co-evolution of phages and bacteria to adapt to environments.},
}

@article {pmid40245806,
year = {2025},
author = {Li, J and Zuo, X and Chen, Q and Lin, Y and Meng, F},
title = {Genome-resolved metagenomic analysis reveals a novel denitrifier with truncated nitrite reduction pathway from the genus SC-I-84.},
journal = {Water research},
volume = {282},
number = {},
pages = {123598},
doi = {10.1016/j.watres.2025.123598},
pmid = {40245806},
issn = {1879-2448},
abstract = {Understanding the genomic and ecological traits of partial denitrification (PD) bacteria is of high importance for developing wastewater treatment technologies. In this study, a PD-based bioreactor was operated, resulting in a mixed culture dominated by a potentially novel PD functional bacterium (SC-I-84). Progressively increased activity in both nitrate reduction and nitrite production were observed in the SC-I-84 enrichment system, whereas the nitrite reduction activity was always negligible. The phylogenetic analysis indicated that SC-I-84 was closely related to an uncultured beta-proteobacterium (99 %), whereas its denitrification functional genes (napA, napB, narV, and narY) exhibited evidence of co-evolution with chromosomal genes from the genus Cupriavidus, order Burkholderiales. In the genetic sketch of SC-I-84, only nitrate-reduction genes (nar and nap) were identified, whereas nitrite-reduction genes (nir) were absent. Notably, nitrate reduction genes were adjacent to carbon metabolism genes (sucB/C, mdh, idh) and a high abundance of tricarboxylic acid (TCA) cycling genes were found. This can promote the utilization efficiency of electron donors by nitrate reduction genes in SC-I-84, thus enhancing the denitrification activity. Furthermore, SC-I-84 positively cooperated with some bacteria that participate in nitrogen and carbon metabolism and other PD bacteria, but negatively interacted with full-denitrification bacteria. These results indicate that the enrichment of SC-I-84 restricted the growth of full-denitrification bacteria, aiding in the maintenance of a stable PD process. Taken together, the meta-genomic analysis of the novel PD functional bacterium is expected to enhance our understanding of PD processes and aid in the development of PD-based wastewater treatment processes.},
}

@article {pmid40245686,
year = {2025},
author = {Simó, C and Mamani-Huanca, M and Hernández-Hernández, O and Redondo-Río, Á and Muñoz, S and García-Cañas, V},
title = {Application of nanopore long-read sequencing and metabolomics in an in vitro dynamic intestinal digestion model: A genome-centric metatranscriptomic approach to investigating microbial TMA and SCFA metabolism.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {262},
number = {},
pages = {116896},
doi = {10.1016/j.jpba.2025.116896},
pmid = {40245686},
issn = {1873-264X},
abstract = {The gut microbiota plays a relevant role in human health by metabolizing dietary components into bioactive molecules, including short-chain fatty acids and trimethylamine. Understanding how dietary interventions modulate microbial metabolism is key to developing strategies for reducing harmful metabolites such as TMA, a precursor of the pro-atherogenic trimethylamine-N-oxide. In this study, we integrated a dynamic in vitro gastrointestinal model (simgi®) with nanopore sequencing technology and metabolomics to investigate the impact of red thyme extract on microbial trimethylamine metabolism from L-carnitine. Metabarcoding, metagenomic, and metatranscriptomic analyses were performed alongside targeted metabolite quantification. Our results showed that microbial trimethylamine production primarily occurred in the transverse and descending colon compartments, coinciding with increased transcriptional activity of taxa harboring gbu cluster, associated with trimethylamine production. The administration of red thyme extract transiently reduced L-carnitine utilization but had a limited effect on overall trimethylamine levels. In parallel, short-chain fatty acids analysis revealed a shift in microbial fermentation patterns, with Acidaminococcus emerging as a dominant butyrate producer. Carbohydrate-active enzyme profiling identified Bacteroides and Parabacteroides genera as key mucin utilizers under the simulation conditions. These findings highlight the metabolic plasticity of the gut microbiota in response to the presence of L-carnitine and reduced complex carbohydrates availability, and provide new insights into microbial functional responses to dietary interventions targeting trimethylamine metabolism. Additionally, this study represents the first integration of nanopore-based metagenomics and genome-centric metatranscriptomics with targeted metabolomics in a dynamic in vitro gastrointestinal model. This multi-omics approach enabled a detailed reconstruction of the microbial metabolic network involved in L-carnitine utilization and trimethylamine formation, offering a powerful tool for mechanistic studies of gut microbiota-diet interactions.},
}

@article {pmid40245533,
year = {2025},
author = {Zhao, J and Wang, Y and Zhang, D and Du, J and Gao, Y and Lu, MY and Guo, JY and Su, HT and Chen, XF and Wen, DH and Jia, SY and Xu, YC and Chen, J and Yang, QW},
title = {Uncovering the unseen: Metagenomic next-generation sequencing improves liver abscess diagnostics.},
journal = {Journal of infection and public health},
volume = {18},
number = {7},
pages = {102708},
doi = {10.1016/j.jiph.2025.102708},
pmid = {40245533},
issn = {1876-035X},
abstract = {BACKGROUND: This study retrospectively analyzed the metagenomic next-generation sequencing (mNGS) results and clinical data from patients with liver abscess (LA) to investigate the clinical value of mNGS in the diagnosis of LA.

METHODS: This retrospective observational study included patients with LA who were admitted to Peking Union Medical College Hospital (PUMCH) between April 2022 and July 2024. We comprehensively analyzed the final clinical etiological diagnosis, traditional pathogen detection through conventional microbiological testing (CMT), and mNGS results in terms of pathogen type and specimen turnaround time.

RESULTS: Among 60 patients with LA, 19 types of pathogens were identified. Using clinical etiological diagnosis as the standard, mNGS identified all pathogens, whereas CMT identified only 42.11 % of pathogens. The true-positivity rate of mNGS (86.67 %) was significantly higher than that of CMT (58.33 %; P < 0.001). The average specimen turnaround time for mNGS (57.66 h) was shorter than that for CMT (86.54 hours, P < 0.001).

CONCLUSIONS: Compared with existing CMT, mNGS offers higher true-positive rates, broader pathogen coverage, and shorter specimen turnaround time. These advantages contribute to more accurate clinical diagnosis and treatment.},
}

@article {pmid40245502,
year = {2025},
author = {Zhong, Y and Teo, JQ and Guo, S and Schlundt, J and Kwa, AL and Ong, RT},
title = {Characterization of mobile resistance elements in extended-spectrum β-lactamase producing gram-negative bacteria from aquatic environment.},
journal = {The Science of the total environment},
volume = {978},
number = {},
pages = {179353},
doi = {10.1016/j.scitotenv.2025.179353},
pmid = {40245502},
issn = {1879-1026},
abstract = {Extended-spectrum β-lactamase producing (ESBL) bacteria from aquatic environments can pose potential threats to public health due to their capability of spreading antimicrobial resistance (AMR) genes through mobile genetic elements (MGEs), such as plasmids, insertion sequences (ISs), transposons, and integrons. Currently, there is no policy for routine monitoring of AMR genes in aquatic environments and their roles in transmission are therefore unknown. Previous metagenomic and PCR-based culture-independent approaches are limited in recovering AMR resistant aquatic bacteria isolates and the data resolution generated are not able to provide detailed genetic comparison with known human pathogens particularly for determining genetic islands harbouring AMR genes. To address these gaps, we thus investigated the genetic profiles of ESBL-producing gram-negative aquatic bacteria found from water body sites within Singapore, examining the AMR genes carried and their associated MGEs. In total, 16 ESBL-producing gram-negative bacteria were identified, of which 8 were Escherichia coli, 3 Klebsiella pneumoniae, and 5 Aeromonas spp. Whole genome sequencing (WGS) analysis revealed the presence of 12 distinct classes of AMR genes, including 16 distinct variants of β-lactamase, of which blaCTX-M was the dominant beta-lactamase genotype in all 11 Enterobacterales. The AMR genetic islands in the aquatic bacteria were also found to share similar genetic structures similar to those of circulating ESBL bacteria causing human infections. These findings underscore the potential role of aquatic ESBL bacteria as AMR reservoirs for human pathogens, suggesting that aquatic bacteria may facilitate the hidden transmission of AMR mediated by MGEs through horizontal gene transfer across different sources and species, highlighting the importance of integrating environmental AMR monitoring into local surveillance strategies.},
}

@article {pmid40244604,
year = {2025},
author = {Koyanagi, Y and Sajiki, AF and Yuki, K and Ushida, H and Kawano, K and Fujita, K and Shimizu, H and Okuda, D and Kosaka, M and Yamada, K and Suzumura, A and Kachi, S and Kaneko, H and Komatsu, H and Usui, Y and Goto, H and Nishiguchi, KM},
title = {Application of Metagenomic Long-Read Sequencing for the Diagnosis of Herpetic Uveitis.},
journal = {Investigative ophthalmology & visual science},
volume = {66},
number = {4},
pages = {50},
doi = {10.1167/iovs.66.4.50},
pmid = {40244604},
issn = {1552-5783},
mesh = {Humans ; *Aqueous Humor/virology ; Female ; Male ; *Uveitis/diagnosis/virology ; Middle Aged ; *Metagenomics/methods ; *DNA, Viral/analysis/genetics ; *Eye Infections, Viral/diagnosis/virology ; Adult ; Sensitivity and Specificity ; Aged ; Multiplex Polymerase Chain Reaction ; *Herpesviridae/genetics/isolation & purification ; Young Adult ; },
abstract = {PURPOSE: To investigate the sensitivity and specificity of herpes virus detection by nanopore metagenomic analysis (NMA) compared with multiplex polymerase chain reaction (mPCR)-positive and -negative controls.

METHODS: This study included 43 patients with uveitis who had been screened for intraocular herpes virus infection using mPCR from aqueous humor samples. Aqueous humor samples stored after mPCR were subjected to whole-genome amplification, long-read sequencing, and analysis of the phylogenetic microorganism composition using a Flongle flow cell on the Oxford Nanopore MinION platform. For samples that tested positive with mPCR and negative with the Flongle flow cell, additional long-read sequencing was performed using a MinION flow cell, which enabled acquisition of more sequence data. The sensitivity and specificity of herpes virus detection by NMA were compared with the mPCR-positive and -negative controls.

RESULTS: NMA using a Flongle flow cell detected the pathogenic virus in 60.0% of those who tested positive by mPCR (12/20). Further analysis using the MinION flow cell successfully identified viral DNA fragments in three out of the eight initially undetected samples, yielding a collective sensitivity of 75.0% (15/20). All of the virus detected with the long-read sequencing were identical to those diagnosed by mPCR testing, and none of the samples that tested negative by mPCR revealed herpes viral DNA with the use of long-read sequencing.

CONCLUSIONS: For the detection of etiologic herpes virus DNA fragments, NMA revealed a reasonable sensitivity and high specificity. Our study highlights the potential of nanopore sequencing to facilitate further advances in uveitis diagnosis.},
}

Humans
*Aqueous Humor/virology
Female
Male
*Uveitis/diagnosis/virology
Middle Aged
*Metagenomics/methods
*DNA, Viral/analysis/genetics
*Eye Infections, Viral/diagnosis/virology
Adult
Sensitivity and Specificity
Aged
Multiplex Polymerase Chain Reaction
*Herpesviridae/genetics/isolation & purification
Young Adult

@article {pmid40244481,
year = {2025},
author = {Klangnurak, W and Hinthong, W and Aue-Umneoy, D and Yomla, R},
title = {Assessment of Bacterial Community and Other Microorganism Along the Lam Takhong Watercourse, Nakhon Ratchasima, Thailand.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {248},
pmid = {40244481},
issn = {1432-0991},
support = {grant number FRB650039/0240 project number 165430//Chulabhorn Royal Academy (Fundamental Fund: fiscal year 2022 by National Science Research and Innovation Fund (NSRF))/ ; contract number FF-65/008//Chulabhorn Royal Academy (Fundamental Fund: fiscal year 2022 by National Science Research and Innovation Fund (NSRF))/ ; },
mesh = {Thailand ; *Bacteria/classification/genetics/isolation & purification ; *Water Microbiology ; *Rivers/microbiology ; Metagenomics ; *Microbiota ; Water Quality ; Environmental Monitoring ; },
abstract = {Lam Takhong, a vital watercourse in Nakhon Ratchasima province, Thailand, supports agricultural, recreational, and urban activities. Originating in a national park, it flows through urban areas before discharging into a dam and running off via the sluice gate. While water quality monitoring is routine, microbial community data have never been reported. This study assesses the microorganism diversity and functional genes in Lam Takhong watercourse using a shotgun sequencing metagenomics approach. Water samples were collected from the upstream, midstream, and downstream sections. The midstream area exhibited the highest abundance of fecal coliform bacteria, plankton, and benthos, suggesting elevated pollution levels. Genes related to metabolism, particularly carbohydrate and amino acid pathways, were predominant. Proteobacteria was the most abundant phylum found in the water, with Limnohabitans as the dominant planktonic bacteria. Bacteria such as Staphylococcus, Mycobacterium, Escherichia, Pseudomonas, Enterococcus, Neisseria, Streptomyces, and Salmonella were detected, along with antibiotic resistance genes, raising public health concerns. These findings emphasize the need for microbial monitoring in the Lam Takhong to determine the potential water quality bioindicator and prevent potential disease spread through the water system.},
}

Thailand
*Bacteria/classification/genetics/isolation & purification
*Water Microbiology
*Rivers/microbiology
Metagenomics
*Microbiota
Water Quality
Environmental Monitoring

@article {pmid40244477,
year = {2025},
author = {Li, J and Zhang, Y and He, L},
title = {The role of urine microbiota in culture-negative patients with pyuria.},
journal = {World journal of urology},
volume = {43},
number = {1},
pages = {227},
pmid = {40244477},
issn = {1433-8726},
mesh = {Humans ; *Pyuria/microbiology/virology/urine ; Retrospective Studies ; Male ; Female ; *Microbiota ; Middle Aged ; *Urine/microbiology/virology ; Aged ; Adult ; },
abstract = {BACKGROUND: Pyuria is usually caused by bacteria and usually results in antibiotic prescriptions. However, traditional urine culture is time-consuming and has a high false negative possibility. Additionally, the role of urine viruses in pyuria is unclear. Metagenomics can enhance the precision and efficiency of diagnosis by directly sequencing the microbiota in urine. We aimed to determine the association of urine microbiota in patients with or without pyuria and culture negative.

METHODS: In this retrospective study, we screened urine samples from patients who received whole genome sequencing (WGS) and had a negative urine culture from October 2021 to May 2024. We compared differences in the top 10 detected genera of urine microbiota between the pyuria group and the non-pyuria group. Multivariable analysis was used for correlation analysis and performed to odds ratio (OR) and OR with 95% confidence interval (CI). The receiver operating characteristic (ROC) curve analyses tested the predictive ability of associated microbiota to pyuria.

RESULTS: We found 29 microbial genera including 2 viral genera. Escherichia [OR 11.688 (95%CI 2.190-62.362), p = 0.004], Gardnerella [OR 9.904 (95%CI 2.180-45.005), p = 0.003] or Polyomavirus [OR 5.205 (95%CI 1.295-20.919), p = 0.020] was associated with the independent risk factors of pyuria, while Lactobacillus was associated with a decreased risk of pyuria [OR 17.273 (95%CI 1.297-230.061), p = 0.031]. An integrated logistic regression model of Escherichia, Gardnerella, Polyomavirus, and Lactobacillus exhibited a predictive power for pyuria with the area under curve (AUC) of 0.8132 [95%CI (0.7098-0.9167), p < 0.001].

CONCLUSION: Urine microbiota is diverse. Escherichia, Gardnerella, or Polyomavirus are independently associated with pyuria, while Lactobacillus is a positive factor against pyuria.},
}

Humans
*Pyuria/microbiology/virology/urine
Retrospective Studies
Male
Female
*Microbiota
Middle Aged
*Urine/microbiology/virology
Aged
Adult

@article {pmid40244062,
year = {2025},
author = {Stevens, EJ and Li, JD and Hector, TE and Drew, GC and Hoang, K and Greenrod, STE and Paterson, S and King, KC},
title = {Within-host competition causes pathogen molecular evolution and perpetual microbiota dysbiosis.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf071},
pmid = {40244062},
issn = {1751-7370},
support = {COEVOPRO 802242//European Research Council Starting/ ; },
abstract = {Pathogens newly invading a host must compete with resident microbiota. This. within-host microbial warfare could lead to more severe disease outcomes or constrain the evolution of virulence. By passaging a widespread pathogen (Staphylococcus aureus) and a native microbiota community across populations of nematode hosts, we show that the pathogen displaced microbiota and reduced species richness, but maintained its virulence across generations. Conversely, pathogen populations and microbiota passaged in isolation caused more host harm relative to their respective no-host controls. For the evolved pathogens, this increase in virulence was partly mediated by enhanced biofilm formation and expression of the global virulence regulator agr. Whole genome sequencing revealed shifts in the mode of selection from directional (on pathogens evolving in isolation) to fluctuating (on pathogens evolving in host microbiota). This approach also revealed that competitive interactions with the microbiota drove early pathogen genomic diversification. Metagenome sequencing of the passaged microbiota shows that evolution in pathogen-infected hosts caused a significant reduction in community stability (dysbiosis), along with restrictions on the co-existence of some species based on nutrient competition. Our study reveals how microbial competition during novel infection could determine the patterns and processes of evolution with major consequences for host health.},
}

@article {pmid40243577,
year = {2025},
author = {Paradzik Simunovic, M and Degoricija, M and Korac-Prlic, J and Lesin, M and Stanic, R and Puljak, L and Olujic, I and Marin Lovric, J and Vucinovic, A and Ljubic, Z and Thissen, J and Reen Kok, C and Jaing, C and Bucan, K and Terzic, J},
title = {Potential Role of Malassezia restricta in Pterygium Development.},
journal = {International journal of molecular sciences},
volume = {26},
number = {7},
pages = {},
doi = {10.3390/ijms26072976},
pmid = {40243577},
issn = {1422-0067},
support = {IP-2020-02-8921//Croatian Science Foundation/ ; },
mesh = {Humans ; *Pterygium/microbiology/pathology/genetics ; *Malassezia/genetics/isolation & purification ; Male ; Female ; Middle Aged ; Conjunctiva/microbiology/pathology ; Microbiota ; Aged ; Gene Expression Profiling ; },
abstract = {Pterygium is a condition affecting the ocular surface, marked by a triangular-shaped growth of fibrotic tissue extending from the nasal conjunctiva toward the corneal center, potentially causing visual impairment. While ultraviolet (UV)light exposure is the primary risk factor for pterygium, its underlying cause remains unclear. In order to better understand the true genesis of pterygium development, we investigated pterygium tissue and compared it with healthy conjunctiva controls. Given the eye's direct environmental exposure, we analyzed the microbiota composition using metagenomic sequencing of pterygium tissue to identify microbes potentially associated with this condition. Metagenomic sequencing revealed a higher prevalence of the fungus Malassezia restricta in five pterygium samples, confirmed by in situ hybridization. The CHIT1 gene, which plays a role in antifungal defenses, displayed the highest expression in five pterygium tissue samples compared to healthy conjunctiva controls, suggesting the potential involvement of Malassezia restricta in pterygium development. Gene expression profiling of pterygium highlighted an IL-33 and IL-4 gene expression signature, along with an increased presence of M2 macrophages, emphasizing their role in promoting fibrosis-a hallmark feature of pterygium. The detection of Malassezia restricta in the pterygium samples and associated molecular changes provides novel insights into the ocular microbiome and raises the possibility of Malassezia's involvement in pterygium pathology.},
}

Humans
*Pterygium/microbiology/pathology/genetics
*Malassezia/genetics/isolation & purification
Male
Female
Middle Aged
Conjunctiva/microbiology/pathology
Microbiota
Aged
Gene Expression Profiling

@article {pmid40243351,
year = {2025},
author = {Li, Y and Liu, S and Han, P and Lei, J and Wang, H and Zhu, W and Dong, Z and Zhang, Y and Jiang, Z and Zheng, B and Rao, G and Yu, Z and Li, A},
title = {Performance and hypothetical clinical impact of an mNGS-based machine learning model for antimicrobial susceptibility prediction of five ESKAPEE bacteria.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0259224},
doi = {10.1128/spectrum.02592-24},
pmid = {40243351},
issn = {2165-0497},
abstract = {UNLABELLED: Antimicrobial resistance is an escalating global health crisis, underscoring the urgent need for timely and targeted therapies to ensure effective clinical treatment. We developed a machine learning model based on metagenomic next-generation sequencing (mNGS) for rapid antimicrobial susceptibility prediction (mNGS-based AST), which was tailored to five ESKAPEE bacteria: Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. However, the clinical utility remained unvalidated. Assuming that mNGS-based AST results were obtained during clinical management, we assessed its clinical utility using data from a previous observational cohort study of clinical mNGS applications. We collected the data from 114 patients infected with five ESKAPEE bacteria from 07/2021 to 03/2023 and incorporated the sequencing data into the model. We evaluated the performance and hypothetical impact of the method by comparing its results and therapy recommendations with those based on traditional culture-based AST. The primary outcome was the performance of mNGS-based AST (n = 113 strains). mNGS-based AST displayed an overall accuracy of 93.84% and shorter turnaround time (1.12 ± 0.33 days vs 2.81 ± 0.57 days for culture-based AST, t = -27.31, P < 0.05). The secondary outcomes included the proportion of patients who could benefit from mNGS-based AST. It could allow earlier and suitable antibacterial adjustments in 32.05% of culture-positive patients (25/78) and offer actionable antimicrobial susceptibility results in 16.67% of culture-negative cases (6/36). mNGS-based AST offers a promising approach for individualized antibacterial therapy.

IMPORTANCE: Metagenomic next-generation sequencing (mNGS)-based antimicrobial susceptibility prediction (AST) is a novel method for predicting the antimicrobial susceptibility of ESKAPEE bacteria using a machine learning approach and short-read sequencing data. Assuming that mNGS-based AST results were obtained during clinical management, it could significantly reduce turnaround time while maintaining a high level of accuracy, allowing for earlier therapeutic adjustments for patients. Furthermore, mNGS-based AST can be integrated with clinical mNGS to maximize the utility of short-read data without substantial cost increases. This study demonstrates the potential of mNGS-based AST for precise, individualized antibacterial selection and highlights its broader applicability in enhancing clinical antimicrobial use for various infections.},
}

@article {pmid40243342,
year = {2025},
author = {Gruninger, RJ and McCormack, ML and Chomistek, NC and Zaheer, R and McAllister, TA},
title = {Unraveling the microbial diversity of bovine liver abscesses: isolation, identification, and genomic characterization of the Bacteroides found in hepatic lesions.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0042325},
doi = {10.1128/spectrum.00423-25},
pmid = {40243342},
issn = {2165-0497},
abstract = {UNLABELLED: Liver abscesses in cattle reduce animal performance, increase the environmental footprint of beef production, and cause significant economic losses. The low pH of the rumen resulting from the consumption of high grain diets damages the rumen epithelium and facilitates the translocation of opportunistic pathogens from the gastrointestinal tract into the bloodstream where they can colonize the liver, causing infection. Recently, 16s rRNA sequencing has revealed that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides. Due to the inability to reliably classify amplicon sequences beyond the genus level, the identity of these microbes remains unknown. We have employed a combination of culture-independent and culture-based methods to isolate and identify the Bacteroides associated with liver abscesses in cattle. Shotgun metagenomic sequencing and assembly of metagenome-assembled genomes generated four high-quality genomes, two of which were putatively identified as Bacteroides. These microbes were subsequently isolated from the purulent material of liver abscesses. Whole-genome sequencing conclusively identified these isolates as Bacteroides pyogenes and a previously unknown species of Bacteroides, revealing distinct differences from Bacteroides typically found in the gut. Carbohydrate utilization assays revealed that both organisms metabolize glycogen and glycosaminoglycans found in the extracellular matrix of the liver but display differences in substrate specificity. These data not only identify Bacteroides found in bovine liver abscesses but also provide new insights into the potential role that these organisms may play in this production-limiting disease.

IMPORTANCE: Liver abscesses (LAs) are commonly found in cattle raised in feedlots and result from a bacterial infection of the liver. Not only are LAs a concern for animal health, but they also impact growth efficiency, animal welfare, and cost the North American beef industry upwards of $120 million per annum. Recently, it has been found that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides; however, to date, the biological relevance in LA pathogenesis and the identity of these bacteria are unknown. This research describes the isolation, identification, and genomic characterization of the Bacteroides found in bovine liver abscesses. These data provide a critical foundation for expanding our knowledge of the potential role Bacteroides play in liver abscess development and could contribute to the identification of novel targets for developing treatments to prevent this important production-limiting disease.},
}

@article {pmid40243306,
year = {2025},
author = {Wang, Z and Sun, Y and Wang, H and Yun, J and Du, W},
title = {Metagenome-assembled genome of a novel Pseudoalteromonas species from South Mid-Atlantic Ridge deep-sea water suggests potential for chitin degradation.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0018925},
doi = {10.1128/mra.00189-25},
pmid = {40243306},
issn = {2576-098X},
abstract = {We report a high-quality metagenome-assembled genome (MAG) of a novel Pseudoalteromonas species recovered from deep-sea water of the South Mid-Atlantic Ridge. This MAG encodes key chitinase-related genes, suggesting potential involvement in chitin degradation and organic matter remineralization in the deep sea.},
}

@article {pmid40242593,
year = {2025},
author = {Sun, S and He, R and Chen, S and Ren, J and Ma, X and Yang, J},
title = {Odontogenic brain abscess caused by Porphyromonas gingivalis and Streptococcus constellatus: a case report and review article.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2485197},
pmid = {40242593},
issn = {2000-2297},
abstract = {BACKGROUND: Odontogenic brain abscess is a rare, but potentially fatal, central nervous system infection, with insidious onset and unclear etiology.

METHODS: This case reports a 70-year-old male patient who developed an odontogenic brain abscess secondary to periodontal infection and underwent neurological surgery. Extract pus during surgery for the metagenomic next-generation sequencing (mNGS).

RESULTS: The mNGS of pus samples obtained from brain abscess aspiration identified the periodontal pathogens Porphyromonas gingivalis and Streptococcus constellatus. Consequently, he was referred to the department of stomatology for further examination and treatment.

CONCLUSIONS: Our study found that major periodontal pathogens including P. gingivalis and S. constellatus were essential in the development of odontogenic brain abscesses; thus, timely intervention and preventive measures are important for treatment.},
}

@article {pmid40242244,
year = {2025},
author = {Kang, Z and Zhang, R and Li, S and Wang, J and Huang, M and Li, W},
title = {Preliminary investigation of gut microbiota and associated metabolic pathways in the pathogenesis of primary central nervous system lymphoma.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1548146},
pmid = {40242244},
issn = {2234-943X},
abstract = {BACKGROUND: Primary central nervous system lymphoma (PCNSL) is a rare and highly aggressive form of non-Hodgkin lymphoma, primarily confined to the central nervous system. In recent years, growing evidence has indicated that dysbiosis of the gut microbiota is closely associated with the development of various malignancies. This study aims to systematically explore the potential role of gut microbiota and their metabolic pathways in the pathogenesis of PCNSL by integrating metagenomic and metabolomic approaches.

MATERIALS AND METHODS: A total of 33 PCNSL patients and 32 healthy controls were enrolled in this study, and fecal samples were collected from each participant. The fecal samples were analyzed using metagenomic and metabolomic techniques, followed by KEGG pathway enrichment analysis to investigate the biological pathways enriched by the differential gut microbiota and metabolites.

RESULTS: Significant differences were observed in the composition of gut microbiota and metabolites between PCNSL patients and healthy controls. In the gut microbiota of PCNSL patients, the abundance of the phylum Proteobacteria was markedly increased, while the Firmicutes/Bacteroidetes (F/B) ratio was significantly elevated. Metabolomic analysis revealed that the abundance of oleamide was significantly reduced in the PCNSL group, while the relative abundance of deoxycholic acid was significantly elevated. KEGG pathway analysis indicated that the differential gut microbiota and metabolites were primarily involved in key metabolic pathways such as nitrogen metabolism, phenylalanine metabolism, purine metabolism, and pyrimidine metabolism, with these pathways being more active in PCNSL patients.

CONCLUSION: This study is the first to systematically investigate the differences in gut microbiota and their metabolites between PCNSL patients and healthy individuals, highlighting the potential role of gut microbiota alterations in the pathogenesis of PCNSL.},
}

@article {pmid40241899,
year = {2025},
author = {Chen, L and Weng, W and Li, D and Xie, W and Lu, L and Li, S},
title = {Case Report: A clinically relevant isolation of Gardnerella leopoldii guided by morphological and molecular evidence from a urinary tract infection case.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1548067},
pmid = {40241899},
issn = {2296-858X},
abstract = {BACKGROUND: The genus Gardnerella is commonly found in the vaginal ecosystem and is considered a covert pathogen of the urinary tract. However, Gardnerella vaginalis had been the only recognized species of the genus Gardnerella for decades. Cases regarding the clinical relevance of Gardnerella leopoldii have rarely been reported, which is crucial for fully understanding the various species within the genus Gardnerella.

CASE PRESENTATION: A 72-year-old female patient was admitted to the hospital with gross hematuria and complaints of waist soreness. Physical examinations, including those of the head, chest, and abdomen, along with routine laboratory tests such as white blood cell (WBC) count and proportion, liver function, and renal function, yielded normal results. However, the patient also exhibited significantly elevated levels of serum C-reactive protein (CRP) and abnormal urinary test findings, which revealed positive results for occult blood and leukocyte esterase, and increased counts of erythrocyte and leukocyte. To further evaluate the urinary system, computerized tomography urography (CTU) was performed. The CTU results revealed multiple weakly enhanced foci in the right kidney and thickening of the right ureter, renal pelvis, calyces, and bladder walls. Based on the above findings, the initial diagnosis included hematuria, hydronephrosis, and urinary tract infection (UTI). To identify the causative pathogens, we employed a comprehensive approach that included microscopic morphology, Sanger sequencing, and metagenomic next-generation sequencing (mNGS). Finally, both Mycobacterium tuberculosis and G. leopoldii were identified as the co-infecting etiological agents responsible for the patient's urinary tract infection.

CONCLUSION: This case represents the first documented isolation of clinically relevant G. leopoldii, guided by morphological and molecular evidence from a clinical urine sample. It highlights the potential of mNGS as a promising tool for identifying previously unrecognized species and offers valuable insights to enhance the understanding of clinically relevant microorganisms.},
}

@article {pmid40241768,
year = {2025},
author = {Yao, XQ and Bao, H and La, NT and Jiang, GS and Zhai, PH and Liu, CB and Yu, L},
title = {Gut microbiota contribute to cold adaptation in mammals-primates and ungulates.},
journal = {iScience},
volume = {28},
number = {4},
pages = {112245},
pmid = {40241768},
issn = {2589-0042},
abstract = {Gut microbiota play an influential role in how animals adapt to extreme environments. Two phylogenetically distant mammals, Yunnan snub-nosed monkey and reindeer both adapted to frigid environments. Metagenomic analyses revealed they developed similar cold adaptation strategies in response to food scarcity (enhanced fiber degradation and nitrogen balance maintenance), energy shortages (increased short-chain fatty acid [SCFA] synthesis), and a constant body temperature sustainment (stimulation of non-shivering thermogenesis [NST]). Moreover, they evolved distinct adaptation strategies to cope with different cold ecosystems. Yunnan snub-nosed monkey adapt to high-altitude hypoxia environment through enhancing ability to synthesize lactate and metabolize purine, while reindeer adapt to extreme cold environment through increasing blood flow, strengthening urea cycling, and enriching fat storage associated bacteria. Notably, reindeer microbiota uniquely enriched cholesterol-degrading bacteria, potentially mitigating cardiovascular risks from lipid storage. Our study expands the knowledge of how gut microbiome promotes cold adaptation through shared and specialized mechanisms shaped by different phylogenetic and ecological contexts.},
}

@article {pmid40241748,
year = {2025},
author = {Liu, T and Kress, AM and Debelius, J and Zhao, N and Smirnova, E and Bandyopadhyay, S and Bonham, K and Comstock, SS and Gill, S and Gern, JE and Koinis-Mitchell, D and Klepac-Ceraj, V and Lee-Sarwar, K and Litonjua, AA and McKee, K and McCauley, K and O'Connor, TG and Rosas-Salazar, C and Scheible, K and Stanford, JB and Moore, B and Jacobson, LP and Mueller, NT and , },
title = {Maternal vaginal and fecal microbiota in later pregnancy contribute to child fecal microbiota development in the ECHO cohort.},
journal = {iScience},
volume = {28},
number = {4},
pages = {112211},
pmid = {40241748},
issn = {2589-0042},
abstract = {There is growing interest in the use of microbial-seeding interventions to mitigate the impacts of prenatal antibiotics, C-section, and lack of breastfeeding on mother-child microbe sharing. However, the relative importance of maternal vaginal vs. fecal microbiota in this process is unclear. Analyzing 16S rRNA sequences from five US birth cohorts, we found that maternal vaginal and fecal microbiota became more similar as pregnancy progressed, and both niches influenced the child's fecal microbiota. The relative contribution of maternal vaginal microbiota increased when vaginal sampling occurred later in gestation. As children aged from birth to 5 years, their fecal microbiota increasingly resembled their mother's fecal microbiota as compared to vaginal microbiota. Patterns of sharing appeared to differ by prenatal antibiotic use, birth mode (C-section vs. vaginal), and breastfeeding. Our findings enhance understanding of niche-specific mother-child microbe sharing and may inform microbial-seeding interventions. Metagenomic studies are needed to identify specific shared strains.},
}

@article {pmid40241728,
year = {2025},
author = {Xie, L and Wang, X and Wang, X and Liu, X},
title = {Changes in microbial community succession and volatile compounds during the natural fermentation of bangcai.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1581378},
pmid = {40241728},
issn = {1664-302X},
abstract = {INTRODUCTION: Fermented bangcai (Brassica juncea var. crassicaulis) is a traditional Chinese food with unique flavor. However, the formation mechanism of flavor compounds related to the fermentation process of bangcai has not been thoroughly studied.

METHODS: Gas chromatography-ion mobility spectrometry technology combined with metagenomics was used to analyze the characteristic volatile flavor compounds and microbial community structure of bangcai before and after fermentation in this study.

RESULTS: A total of 91 types of volatile organic compounds were detected in this study. The pungent odor brought by allyl isothiocyanate, 1-butene isothiocyanate, and other substances in the raw materials was removed through fermentation. This process led to the formation of flavor substances such as propyl acetate, ethyl acetate, and 2-methyl-3-furanthiol, which imparted bangcai with flavors of flower and fruit, roast meat, and fried coffee. In addition, our study found that after air drying, bangcai mainly contained γ-butyrolactone, nonanal and other flavor compounds, giving the bangcai products a richer floral and fruity flavor profile. Citrobacter, Lactobacillus, and Leuconostoc were the dominant bacteria in the fermentation process of bangcai. They were significantly related to the formation of differential flavor compounds such as γ-butyrolactone, ethyl 2-methylpropanoat, and benzaldehyde-D.

DISCUSSION: These results provide a theoretical basis for improving the flavor quality of fermented vegetable products.},
}

@article {pmid40241696,
year = {2025},
author = {Yang, Z and Xie, Y and Zhu, Y and Lei, M and Chen, X and Jin, W and Fu, C and Yu, L},
title = {Unraveling the flavor formation process of mellow and thick-type ripened Pu-erh tea through non-targeted metabolomics and metagenomics.},
journal = {Food chemistry: X},
volume = {27},
number = {},
pages = {102424},
pmid = {40241696},
issn = {2590-1575},
abstract = {Ripened Pu-erh tea (RPT) is renowned for its distinctive flavor and health benefits. However, its complex fermentation process poses challenges in ensuring consistency in production. This study investigated RPT flavor formation through sensory evaluation, multi-omics analysis, and multivariate statistical approaches. By day 24, the tea exhibited a reddish-brown infusion and a mellow, thick taste (MT_RPT), achieving the highest sensory score (94.0, P < 0.05). Sixteen flavor-related chemical components exhibited significant changes (P < 0.05). The contents of free amino acids, L-theanine, tea polyphenols, flavonoids, catechins, and thearubigins decreased. In contrast, the contents of total soluble sugars, caffeine, theobromine, epicatechin, and theabrownins (TBs) increased, reaching 74.1 mg/g, 65.38 mg/g, 3.13 mg/g, 3.33 mg/g, and 134.84 mg/g, respectively. Additionally, 33 nonvolatile metabolites (e.g., pelargonidin 3-O-glucoside, dihydroisorhamnetin, and puerarin) were significantly correlated with MT_RPT flavor (VIP > 1, |r| ≥ 0.8, P < 0.05) and influenced by key functional microbes, including Pantoea, Aspergillus, Brachybacterium, and Staphylococcus. By day 30, the infusion darkened, and sensory scores declined (81.4, P < 0.05), attributed to the dominance of Brevibacterium. This microbial shift reduced water-soluble pectin, free amino acids, and 11 metabolites while increasing TBs and theophylline (219.33 mg/g and 0.09 mg/g, respectively). Therefore, TBs were identified as a crucial indicator of optimal fermentation. Moreover, redundancy analysis indicated that the tea pile's central temperature, moisture content, and pH were essential fermentation parameters (P < 0.05). These findings deepen our understanding of MT_RPT flavor development mechanisms and provide valuable insights into precise fermentation control.},
}

@article {pmid40241220,
year = {2025},
author = {Yang, K and Li, G and Li, Q and Wang, W and Zhao, X and Shao, N and Qiu, H and Liu, J and Xu, L and Zhao, J},
title = {Distribution of gut microbiota across intestinal segments and their impact on human physiological and pathological processes.},
journal = {Cell & bioscience},
volume = {15},
number = {1},
pages = {47},
pmid = {40241220},
issn = {2045-3701},
support = {82272812//National Natural Science Foundation of China/ ; 82360018//National Natural Science Foundation of China/ ; },
abstract = {In recent years, advancements in metagenomics, metabolomics, and single-cell sequencing have enhanced our understanding of the intricate relationships between gut microbiota and their hosts. Gut microbiota colonize humans from birth, with their initial composition significantly influenced by the mode of delivery and feeding method. During the transition from infancy to early childhood, exposure to a diverse diet and the maturation of the immune system lead to the gradual stabilization of gut microbiota's composition and distribution. Numerous studies have demonstrated that gut microbiota can influence a wide range of physiological functions and pathological processes by interacting with various tissues and organs through the gut-organ axis. Different intestinal segments exhibit unique physical and chemical conditions, which leads to the formation of vertical gradients along the intestinal tract: aerobes and facultative aerobes mainly live in the small intestine and anaerobic bacteria mainly live in the large intestine, and horizontal gradients: mucosa-associated microbiota and lumen-associated microbiota. In this review, we systematically summarize the distribution characteristics of gut microbiota across six intestinal segments: duodenum, jejunum, ileum, cecum, colon, and rectum. We also draw a conclusion that gut microbiota distributed in different intestinal segments affect the progression of different diseases. We hope to elucidate the role of microbiota at specific anatomic sites within the gut in precisely regulating the processes of particular diseases, thereby providing a solid foundation for developing novel diagnostic and therapeutic strategies for related diseases.},
}

@article {pmid40240641,
year = {2025},
author = {Muñoz-Rivera, MP and Martínez-Morales, F and Guzmán-Morales, D and Rivera-Ramírez, A and Sánchez-Reyes, A and Trejo-Hernández, MR},
title = {Population dynamics of a bacterial consortium from a marine sediment of the Gulf of Mexico during biodegradation of the aromatic fraction of heavy crude oil.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40240641},
issn = {1618-1905},
abstract = {In the marine environment, uncontained crude oil is dispersed and degraded by abiotic or biotic processes; native bacterial populations gradually adapt to integrate interspecific and intraspecific metabolic networks for efficient and dynamic utilization of xenobiotic substrates as carbon source. Aromatic compounds accumulate in marine sediments and bacterial populations at these sites play a crucial role in the mobilization of those complex molecules into the global geochemical cycles. The aim of this work was to use native bacteria from a marine sediment sample in the Gulf of Mexico to enhance the biodegradation of the aromatic fraction from a heavy crude oil, as the sole carbon source, during a 200-day microcosm experiment. This process involved the gradual increase of the aromatic fraction into the culture to promote bacterial enrichment; the increase in viable cells correlated well with a biodegradation pattern of the aromatic fraction at some points. Bacterial biodiversity, as revealed by metagenomic and microbiological approaches, indicates that bacterial groups are present at all fraction concentrations, but with changes in abundance, richness and dominance. Population dynamics revealed the presence of bacteria that modify emulsification and surface tension reduction values, which could promote the incorporation of the highly hydrophobic polyaromatic compounds into the culture aqueous phase for their biodegradation by hydrocarbonoclastic bacteria present. On the other hand, the presence of non-hydrocarbonoclastic bacteria probably is sustained by cross-feeding events involving sugars, amino acids, short carbon compounds, lipids produced by the former bacteria by co-metabolism of complex aromatic substrates, which are transformed into diverse biomolecules for biofilm development to promote a bacterial population dynamics adapted to this environment.},
}