@article {pmid40933366,
year = {2025},
author = {Gutleben, J and Podell, S and Mizell, K and Sweeney, D and Neira, C and Levin, LA and Jensen, PR},
title = {Extremophile hotspots linked to containerized industrial waste dumping in a deep-sea basin.},
journal = {PNAS nexus},
volume = {4},
number = {9},
pages = {pgaf260},
doi = {10.1093/pnasnexus/pgaf260},
pmid = {40933366},
issn = {2752-6542},
abstract = {Decaying barrels on the seafloor linked to DDT contamination have raised concerns about the public health implications of decades old industrial waste dumped off the coast of Los Angeles. To explore their contents, we collected sediment cores perpendicular to five deep-sea barrels. The concentration of DDT and its breakdown products were highly elevated relative to control sites yet did not vary with distance from the barrels, suggesting that they were not associated with the contamination. Sediment cores collected through white halos surrounding three barrels were enriched in calcite and had elevated pH. The associated microbial communities were low diversity and dominated by alkalophilic bacteria with metagenome-assembled genomes adapted to high pH. A solid concretion sampled between a white halo and barrel was composed of brucite, a magnesium hydroxide mineral that forms at high pH. Based on these findings, we postulate that leakage of containerized alkaline waste triggered the formation of mineral concretions that are slowly dissolving and raising the pH of the surrounding sediment pore water. This selects for taxa adapted to extreme alkalinity and drives the precipitation of "anthropogenic" carbonates forming white halos, which serve as a visual identifier of barrels that contained alkaline waste. Remarkably, containerized alkaline waste discarded >50 years ago represents a persistent pollutant creating localized mineral formations and microbial communities that resemble those observed at some hydrothermal systems. These formations were observed at one-third of the visually identified barrels in the San Pedro Basin and have unforeseen, long-term consequences for benthic communities in the region.},
}

@article {pmid40931350,
year = {2025},
author = {Ye, G and Hong, H and Li, T and Li, J and Wu, JQ and Jiang, S and Meng, ZT and Yuan, HT and Xue, W and Li, AL and Zhou, T and Li, TT and Li, T},
title = {MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {276},
pmid = {40931350},
issn = {1474-760X},
support = {No. 32100421//China National Natural Science Foundation/ ; No. 82341098//China National Natural Science Foundation/ ; No. 82130052//China National Natural Science Foundation/ ; No. NSS2021CI05002//Nanhu Laboratory/ ; No. 2024ZYYDSA400333//The Central Government Guides Local Science and Technology Development Fund Projects/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Databases, Genetic ; *Microbiota ; },
abstract = {Metagenomic analyses of microbial communities have unveiled a substantial level of interspecies and intraspecies genetic diversity by reconstructing metagenome-assembled genomes (MAGs). The MAG database (MAGdb) boasts an impressive collection of 74 representative research papers, spanning clinical, environmental, and animal categories and comprising 13,702 paired-end run accessions of metagenomic sequencing and 99,672 high quality MAGs with manually curated metadata. MAGdb provides a user-friendly interface that users can browse, search, and download MAGs and their corresponding metadata information. It represents a valuable resource for researchers in discovering potential novel microbial lineages and understanding their ecological roles. MAGdb is publicly available at https://magdb.nanhulab.ac.cn/ .},
}

*Metagenome
*Metagenomics/methods
*Databases, Genetic
*Microbiota

@article {pmid40929115,
year = {2025},
author = {Gonzalez, FL and Kettenburg, G and Ranaivoson, HC and Andrianiaina, A and Andry, S and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Dussart, P and Héraud, JM and Brook, CE},
title = {Genomic characterization of novel bat kobuviruses in Madagascar: Implications for viral evolution and zoonotic risk.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331736},
pmid = {40929115},
issn = {1932-6203},
mesh = {*Chiroptera/virology ; Animals ; Madagascar ; Phylogeny ; *Zoonoses/virology ; *Genome, Viral ; *Evolution, Molecular ; *Viral Zoonoses/virology ; Humans ; Genomics ; High-Throughput Nucleotide Sequencing ; *Picornaviridae Infections/virology/veterinary/epidemiology ; },
abstract = {Kobuviruses (family Picornaviridae, genus Kobuvirus) are enteric viruses that infect a wide range of both human and animal hosts. Much of the evolutionary history of kobuviruses remains elusive, largely due to limited screening in wildlife. Bats have been implicated as major sources of virulent zoonoses, including coronaviruses, henipaviruses, lyssaviruses, and filoviruses, though much of the bat virome still remains uncharacterized. While most bat virus research has historically focused on immediately recognizable zoonotic clades (e.g., SARS-related coronaviruses), a handful of prior reports catalog kobuvirus carriage in bats and posit the role of bats as progenitors of downstream kobuvirus evolution. As part of a multi-year study, we carried out metagenomic Next Generation Sequencing (mNGS) on fecal samples obtained from endemic, wild-caught Madagascar fruit bats to characterize potentially zoonotic viruses circulating within these populations. The wild bats of Madagascar represent diverse Asian and African phylogeographic histories, presenting a unique opportunity for viruses from disparate origins to mix, posing a significant public health threat. Here, we report detection of kobuvirus RNA in Malagasy fruit bats (Eidolon dupreanum) and undertake phylogenetic characterization of Malagasy kobuvirus sequences, which nest within the Aichivirus A clade - a kobuvirus clade known to infect a wide range of hosts including humans, rodents, canids, felids, birds, and bats. Given the propensity of kobuviruses for recombination and cross-species transmission, further characterization of this clade is critical for accurate evaluation of future zoonotic threats.},
}

*Chiroptera/virology
Animals
Madagascar
Phylogeny
*Zoonoses/virology
*Genome, Viral
*Evolution, Molecular
*Viral Zoonoses/virology
Humans
Genomics
High-Throughput Nucleotide Sequencing
*Picornaviridae Infections/virology/veterinary/epidemiology

@article {pmid40765405,
year = {2025},
author = {Dai, G and Zhang, Y and Shen, C and Jiao, Y and Shen, W and Yu, F and Liu, R and Wang, D and Yuan, G and Jia, J},
title = {Luteolin Treats Obese Rats With Polycystic Ovary Syndrome by Improving Liver Lipid Metabolism and Regulating the Gut Microbiota.},
journal = {Phytotherapy research : PTR},
volume = {39},
number = {9},
pages = {4171-4180},
doi = {10.1002/ptr.70043},
pmid = {40765405},
issn = {1099-1573},
support = {JLY2021209//Clinical Medical Science and Technology Development Foundation of Jiangsu University/ ; BK20231251//Natural Science Foundation of Jiangsu Province/ ; JDY2022005//Key project for Medical Education Collaborative Innovation Fund of Jiangsu University/ ; BE2023757//Social Development Project of Jiangsu Province/ ; BRA2022008//the sixth phase 333 second level talent training project of Jiangsu Province (tackling bottleneck technology)/ ; jdfyRC2020010//Doctoral Research Initiation Fund/ ; BGYCA202207//Beigu Talent Cultivation Program of Affiliated Hospital of Jiangsu University/ ; SS202204-KFB05//open project of clinical medical research center of Gynecology and Traditional Chinese Medicine of Zhenjiang/ ; MS2024142//Science and Technology Development Program for Traditional Chinese Medicine of Jiangsu Province/ ; },
mesh = {Animals ; *Luteolin/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Female ; *Polycystic Ovary Syndrome/drug therapy/complications/metabolism ; *Obesity/drug therapy/complications ; *Lipid Metabolism/drug effects ; *Liver/metabolism/drug effects ; Rats ; Rats, Sprague-Dawley ; Body Weight/drug effects ; Disease Models, Animal ; },
abstract = {Polycystic ovary syndrome (PCOS) and obesity share a bidirectional relationship. While previous studies have indicated the anti-obesity effects of luteolin, its role in PCOS exacerbated by obesity remains unclear. This study aimed to investigate the ameliorative effects of luteolin on obese rats with PCOS and explore its underlying mechanisms. We established a rat model of PCOS with obesity and administered luteolin to evaluate its mitigating effects on the metabolic phenotype. Liver transcriptomics and fecal metagenomics were employed to analyze potential targets and alterations in the gut microbiota composition associated with luteolin's effects. Results showed that luteolin reduced body weight, improved estrous cycles, polycystic ovarian morphology, and glucose tolerance, and lowered serum levels of triglycerides (TG), total cholesterol (TC), and low-density lipoprotein cholesterol (LDL-c) in the model rats. Importantly, luteolin significantly alleviated hepatic steatosis and reversed the expression of 138 key differentially expressed genes (DEGs) in the liver, including UQCRC2, IRS2, NFIX, and ALDH6A1. In addition, luteolin significantly increased the alpha diversity of the gut microbiota and modulated its composition, specifically increasing the relative abundance of Bacteroidota and decreasing that of Firmicutes. Our findings suggest that luteolin exerts beneficial effects on PCOS with obesity, potentially mediated through the improvement of hepatic lipid metabolism and the restoration of gut microbiota homeostasis. Luteolin emerges as a promising therapeutic candidate for managing PCOS with obesity.},
}

Animals
*Luteolin/pharmacology
*Gastrointestinal Microbiome/drug effects
Female
*Polycystic Ovary Syndrome/drug therapy/complications/metabolism
*Obesity/drug therapy/complications
*Lipid Metabolism/drug effects
*Liver/metabolism/drug effects
Rats
Rats, Sprague-Dawley
Body Weight/drug effects
Disease Models, Animal

@article {pmid40689619,
year = {2025},
author = {Tambovtseva, RS and Arslan, LA and Grigoryeva, TA and Abdulkhakov, SR and Doludin, YV and Stoma, IO and Rizvanov, AA and Miftakhova, RR and Gabdoulkhakova, AG},
title = {Narrative review on bacteria-derived metabolites in the pathogenesis of ulcerative colitis.},
journal = {Clinical microbiology reviews},
volume = {38},
number = {3},
pages = {e0021024},
pmid = {40689619},
issn = {1098-6618},
support = {FZSM-2023-0011//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Colitis, Ulcerative/microbiology/pathology ; Humans ; *Gastrointestinal Microbiome ; *Bacteria/metabolism ; },
abstract = {SUMMARYThe pathogenesis of ulcerative colitis (UC) is heterogeneous; the causes are considered to be external factors such as stress, infections, antibiotics, and other medications, diet, and intrinsic factors such as genetic predisposition. The aim of this narrative review is to analyze data on intestinal flora and bacteria-derived metabolites in inflammatory bowel diseases and ulcerative colitis in particular. The main focus is on proteolytic, saccharolytic, mucin-degrading, and bile acid-metabolizing bacteria. What types of metabolites are beneficial for intestinal integrity and the patient's health? How can dietary preferences trigger disease and cause complications? What kind of changes in the microbiome promote the disease? We consider what targets/receptors metabolites act on and their physiological role. The knowledge accumulated over the past years on the gut metagenome, metabolome, and signaling mechanisms may allow, in the future, modulating the composition of the intestinal microbiome and suppressing the growth of pathogenic flora without the use of antibiotics, but due to pro- and prebiotics, products of bacterial metabolism, including quorum sensing molecules.},
}

*Colitis, Ulcerative/microbiology/pathology
Humans
*Gastrointestinal Microbiome
*Bacteria/metabolism

@article {pmid40927879,
year = {2025},
author = {Wang, X and Wang, J and Chen, J and Bezemer, TM and Song, Z and Wanek, W and Liu, G and Zhang, C},
title = {Environmental Stresses Constrain Soil Microbial Community Functions by Regulating Deterministic Assembly and Niche Width.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70096},
doi = {10.1111/mec.70096},
pmid = {40927879},
issn = {1365-294X},
support = {2023YFF1305103//National Key Research and Development Program of China/ ; 42130717//National Sciences Foundation of China/ ; 42177449//National Sciences Foundation of China/ ; 2024JC-JCQN-35//Shaanxi Provincial Science Fund for Distinguished Young Scholars/ ; },
abstract = {Increasing evidence indicates that the loss of soil microbial α-diversity triggered by environmental stress negatively impacts microbial functions; however, the effects of microbial α-diversity on community functions under environmental stress are poorly understood. Here, we investigated the changes in bacterial and fungal α- diversity along gradients of five natural stressors (temperature, precipitation, plant diversity, soil organic C and pH) across 45 grasslands in China and evaluated their connection with microbial functional traits. By quantifying the five environmental stresses into an integrated stress index, we found that the bacterial and fungal α-diversity declined under high environmental stress across three soil layers (0-20 cm, 20-40 cm and 40-60 cm). Metagenomic-based analyses showed that the diversity of functional genes decreased along the stress gradients. High stress enhanced the abundance of genes associated with broad functional categories (e.g., glycolysis/gluconeogenesis, TCA cycle, DNA replication/repair and cell growth/death) but reduced the abundance of genes linked to specialised functional categories (e.g., C, N, S and methane metabolism). Phylogenetic null models and niche analyses indicated that stochastic assembly processes predominated in high-diversity communities, in which bacterial and fungal taxa had a narrow ecological niche. However, in low-diversity communities, deterministic assembly processes were dominant, and taxa had wide niches, correlating with the reduction in gene abundance observed for broad and specialised functional categories. Given the essential role of the microbiome in regulating ecosystem functions, our findings suggest that low-diversity-induced deterministic community assembly processes and a wide niche under high environmental stress may regulate microbial functions. These findings emphasise the ecological mechanisms through which microbial biodiversity regulates terrestrial ecosystem functioning.},
}

@article {pmid40927726,
year = {2025},
author = {Eiman, L and Moazzam, K and Anjum, S and Kausar, H and Sharif, EAM and Ibrahim, WN},
title = {Gut dysbiosis in cancer immunotherapy: microbiota-mediated resistance and emerging treatments.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1575452},
pmid = {40927726},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology/therapy ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/therapy/immunology/microbiology ; *Immunotherapy/methods ; Animals ; *Drug Resistance, Neoplasm ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Tumor Microenvironment/immunology ; },
abstract = {Cancer is a multifaceted disease driven by a complex interplay of genetic predisposition, environmental factors and lifestyle habits. With the accelerating pace of cancer research, the gut microbiome has emerged as a critical modulator of human health and immunity. Disruption in the gut microbial populations and diversity, known as dysbiosis, has been linked with the development of chronic inflammation, oncogenesis, angiogenesis and metastasis. This review discusses the microbial species associated with various types of cancer and the pathways involved in their tumorigenic effect including mechanisms like inflammatory cytokine response, immune modulation, genotoxicity and modification of the tumor microenvironment. Diagnostic tools such as metagenomics, metabolomics, and the use of dysbiosis indexes help in the detection of gut bacterial imbalances, enabling early detection of cancer and potential intervention. Gut dysbiosis diminishes the efficacy of cancer treatments including immunotherapies, and creates immunotherapy resistance by altering drug metabolism and driving immunometabolic reprogramming, allowing tumor cells to evade immune attack. Immunometabolic reprogramming through gut microbiota modulation provides a new avenue to be explored that can restore anti-tumor immunity and reverse resistance to cancer treatments. This review also highlights the use of fecal microbiota transplantation and probiotics to mitigate chances of dysbiosis-related cancer progression. Through a comprehensive assessment of the role of gut microbiota in cancer, this review underscores the need for the use of gut microbial biomarkers for cancer detection and microbiome-targeting strategies to individualize cancer treatment.},
}

Humans
*Dysbiosis/immunology/therapy
*Gastrointestinal Microbiome/immunology
*Neoplasms/therapy/immunology/microbiology
*Immunotherapy/methods
Animals
*Drug Resistance, Neoplasm
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Tumor Microenvironment/immunology

@article {pmid40926344,
year = {2025},
author = {Sarango Flores, S and Cordovez, V and Oyserman, BO and Arias Giraldo, LM and Stopnisek, N and Raaijmakers, JM and van 't Hof, P},
title = {Microbiome-Mediated Resistance of Wild Tomato to the Invasive Insect Prodiplosis longifila.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70190},
doi = {10.1111/1758-2229.70190},
pmid = {40926344},
issn = {1758-2229},
support = {024.004.014/NWO_/Dutch Research Council/Netherlands ; CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Research Grant/ ; },
mesh = {*Solanum lycopersicum/microbiology/parasitology/immunology ; Animals ; *Microbiota ; *Soil Microbiology ; *Diptera/physiology ; Ecuador ; Plant Roots/microbiology/parasitology ; Introduced Species ; Bacteria/classification/genetics/isolation & purification ; Plant Leaves/parasitology ; },
abstract = {Plant roots are colonised by diverse communities of microorganisms that can affect plant growth and enhance plant resistance to (a) biotic stresses. We investigated the role of the indigenous soil microbiome in the resistance of tomato to the invasive sap-sucking insect Prodiplosis longifila (Diptera: Cecidomyiidae). Native and agricultural soils were sampled from the Andes in Southern Ecuador and tested, in greenhouse bioassays, for leaf tissue damage caused by P. longifila on domesticated Solanum lycopersicum cv. Moneymaker and wild tomato S. pimpinellifolium. We observed no significant differences in insect damage between domesticated and wild tomatoes grown in live native or agricultural soils. However, when grown in sterilised native and agricultural soils, wild tomato was more severely affected by the insect than the domesticated tomato. Microbiome analyses revealed that soil sterilisation impacted overall rhizobacterial diversity and abundance in wild tomato. Particularly, Actinoplanes abundance was reduced upon sterilisation, which significantly correlated with loss of insect resistance. Metagenome analyses and genome assembly of Micromonosporaceae (Actinoplanes family) suggested a putative association between motility, chemotaxis, membrane transport, chorismate, and lanthipeptide biosynthesis and insect resistance. This indicates that wild S. pimpinellifolium, in contrast to domesticated S. lycopersicum, relies on specific members of the root-associated microbiome for P. longifila protection.},
}

*Solanum lycopersicum/microbiology/parasitology/immunology
Animals
*Microbiota
*Soil Microbiology
*Diptera/physiology
Ecuador
Plant Roots/microbiology/parasitology
Introduced Species
Bacteria/classification/genetics/isolation & purification
Plant Leaves/parasitology

@article {pmid40924621,
year = {2025},
author = {Liu, L and Hu, L and Kuzyakov, Y and Rillig, MC and Duan, G and Wei, G and Chen, C},
title = {Microbial Physiological Adaptation to Biodegradable Microplastics Drives the Transformation and Reactivity of Dissolved Organic Matter in Soil.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c09633},
pmid = {40924621},
issn = {1520-5851},
abstract = {The turnover of dissolved organic matter (DOM) in soil regulated by biodegradable microplastics (MPs) has garnered much attention due to its profound impact on the storage and stability of soil organic matter. However, the transformation and reactivity of plant-derived and microbially derived DOM by microorganisms adapted to biodegradable MPs, and the involved microbial physiological processes, remain nearly unknown. Here, we added virgin and aged polylactic acid (PLA) and polyhydroxyalkanoate (PHA) to agricultural soils and incubated for 56 days. Using stable isotope techniques, reactomics, and metagenomics, we found that the addition of both virgin and aged PLA induced hydroxylation, demethylation, and dehydrogenation of lignin-derived DOM, resulting in a 3-fold increase in their oxidation degree. PLA activated the enzymatic pathway for lignin-derived DOM decomposition and downregulated genes involved in bacterial anabolism, such as those related to protein, amino sugar, and peptidoglycan biosynthesis. In contrast, PHA increased the content of microbially derived DOM compounds such as proteins and amino sugars by 2.1-fold relative to the control with peptide chain elongation. PHA resulted in the degradation of lignin-derived DOM into pyruvate and acetyl-CoA, accelerated bacterial ATP synthesis, the de novo biosynthesis of proteins and peptidoglycan, and cell renewal and death, thereby increasing PHA- and soil organic matter-derived microbial necromass carbon. Our study provides new insights into the impact of biodegradable MPs on soil DOM transformation and underscores the importance of the microbial physiological processes involved.},
}

@article {pmid40793781,
year = {2025},
author = {Cifuentes, SG and Graham, J and Trueba, G and Cárdenas, PA},
title = {Hi-C untangles the temporal dynamics of the children's gut resistome and mobilome, highlighting the role of transposable elements.},
journal = {mBio},
volume = {16},
number = {9},
pages = {e0113425},
doi = {10.1128/mbio.01134-25},
pmid = {40793781},
issn = {2150-7511},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *DNA Transposable Elements ; Feces/microbiology ; Ecuador ; Metagenomics ; Child ; Child, Preschool ; *Bacteria/genetics/drug effects/classification ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Female ; Gene Transfer, Horizontal ; Male ; Plasmids/genetics ; },
abstract = {Many metagenomic studies lack the ability to measure the temporal dynamics of the intestinal resistome (the collection of antibiotic resistance genes [ARGs]) and mobilome (the collection of all mobile genetic elements that enable their transfer) and link the genetic features to specific species in the gut. We applied Hi-C sequencing and shotgun metagenomics to study fecal matter from children (n = 15) living in semi-rural communities of Quito, Ecuador. We sampled at three different periods, with a 4- to 6-month interval between each sample collection. To understand the dynamics of ARGs from different genetic perspectives, we focused on identifying classes of mobile ARGs that are classified as high risk to human health. We selected those ARGs that appeared at least twice across sampling periods in the same child and focused the longitudinal analysis on the subset of children (n = 6) where these high-risk ARGs were consistently detected. The study demonstrated the temporal dynamics of these mobile ARGs from the taxonomic, plasmid, and transposable element perspectives, including insertion sequences and transposons. Our findings reveal that while plasmid composition fluctuates over time, transposons play a crucial role in the stability and dissemination of ARGs. Specifically, aph(3″)-Ib and aph(6)-Id genes were consistently mobilized by transposons across multiple multidrug-resistant Escherichia coli strains. These results highlight the importance of transposons in shaping the gut resistome and suggest that tracking regionally significant transposons could improve our understanding of ARG transmission in small geographic areas.IMPORTANCEAntibiotic resistance (ABR) is a growing global challenge, and particularly high-risk antibiotic resistance genes (ARGs) are a threat to public health. While plasmids are often considered the cornerstone of the spread of ARGs, our study emphasizes the critical role of transposons in the persistence and mobility of ARGs within the gut microbiota. By integrating Hi-C sequencing and shotgun metagenomics, we show that transposons mediate the transfer and persistence of ARGs across different Escherichia coli lineages, while plasmid composition changes over time. Recognizing the impact of transposons on resistome dynamics can help refine strategies to mitigate ABR transmission, particularly in regions where the impact of resistance is most significant, such as low- and middle-income countries. Our findings provide new insights into the mechanisms driving the persistence of ABR in the human gut, which are essential for developing more effective public health interventions and incorporating transposable elements into surveillance efforts.},
}

Humans
*Gastrointestinal Microbiome/genetics
*DNA Transposable Elements
Feces/microbiology
Ecuador
Metagenomics
Child
Child, Preschool
*Bacteria/genetics/drug effects/classification
*Drug Resistance, Bacterial
Anti-Bacterial Agents/pharmacology
Female
Gene Transfer, Horizontal
Male
Plasmids/genetics

@article {pmid40779866,
year = {2025},
author = {Lin, XQ and Li, ZL and Chen, XQ and Wang, L and Yu, L and Wang, AJ},
title = {Microbial synergistic metabolic mechanism of enhanced tetrabromobisphenol A removal by bio-electrochemical system coupled constructed wetland.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139382},
doi = {10.1016/j.jhazmat.2025.139382},
pmid = {40779866},
issn = {1873-3336},
mesh = {Biodegradation, Environmental ; *Bioreactors/microbiology/statistics & numerical data ; Desulfovibrio/metabolism ; Geobacter/metabolism ; Metagenome ; *Microbiota ; Nitrates/metabolism ; *Polybrominated Biphenyls/metabolism ; *Water Pollutants, Chemical/metabolism ; *Water Purification/methods/statistics & numerical data ; Wetlands ; Electrochemical Techniques ; },
abstract = {The widespread existence of tetrabromobisphenol A (TBBPA) in the aquatic environment requires efficient treatment technology. The feasibility and related molecular mechanisms for the simultaneous deep removal of nitrate and TBBPA in a bio-electrochemical system coupled with a constructed wetland (BES-CW) are unclear. This study fabricated the BES-CW to achieve simultaneously deep removal of nitrate and TBBPA. TBBPA majorly went through reductive debromination, hydrolytic debromination, ring-cleavage, and oxidation in the open and closed circuits of BES-CW. Electricity activated key genes encoded in oxidoreductase (pflA, pflX) and oxygenase (dmpB, pobA) from electroactive bacteria (Geobacter and Desulfovibrio), accelerating TBBPA metabolites' oxidation and mineralization. Nitrate enriched the Acinetobacter and stimulated genes encoded in hydrolytic dehalogenase, inducing TBBPA hydrolytic debromination and further mineralization. Electricity and nitrate synergistically enhance TBBPA degradation and mineralization, guiding the advanced treatment of emerging pollutants in the aquatic environment.},
}

Biodegradation, Environmental
*Bioreactors/microbiology/statistics & numerical data
Desulfovibrio/metabolism
Geobacter/metabolism
Metagenome
*Microbiota
Nitrates/metabolism
*Polybrominated Biphenyls/metabolism
*Water Pollutants, Chemical/metabolism
*Water Purification/methods/statistics & numerical data
Wetlands
Electrochemical Techniques

@article {pmid40671669,
year = {2025},
author = {Sánchez-Terrón, G and Martínez, R and Morcuende, D and Estévez, M},
title = {Deciphering the Physiological Responses to the Intake of Plant-Based Meat Analogues: On the Track of Microbiota and Biomarkers in Serum and Urine.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {36},
pages = {22698-22713},
doi = {10.1021/acs.jafc.5c02799},
pmid = {40671669},
issn = {1520-5118},
mesh = {Animals ; Rats, Wistar ; Rats ; *Gastrointestinal Microbiome ; Male ; *Biomarkers/urine/blood ; Bacteria/classification/isolation & purification/genetics/metabolism ; Triticum/metabolism ; *Meat/analysis ; Cattle ; Humans ; Urine/chemistry ; Glycine max/metabolism ; },
abstract = {Growing concerns about the alleged negative outcomes of the consumption of animal-based foods (ABF) lead a number of consumers to demand so-called plant-based meat analogues (PBMAs), which are designed to replicate the sensory and nutritional characteristics of genuine meat. This study aimed to characterize the physiological effects of long-term PBMA consumption by comparing their specific influence on both gut microbiota and fluids (i.e., plasma and urine) with those of conventional beef in a rodent model by using metagenomic and metabolomic tools. Twenty-one Wistar rats were divided into groups and consumed diets made with either wheat- and soy-based meat analogues or beef. The microbiota of PBMA-fed animals showed increased amounts of the harmful genus of gut bacteria, while their metabolomes reflected disturbances in the nitrogen-containing compound metabolism and the presence of potentially harmful metabolites. These results should raise concern and prompt further research into the long-term impact of consumption of PBMAs on health.},
}

Animals
Rats, Wistar
Rats
*Gastrointestinal Microbiome
Male
*Biomarkers/urine/blood
Bacteria/classification/isolation & purification/genetics/metabolism
Triticum/metabolism
*Meat/analysis
Cattle
Humans
Urine/chemistry
Glycine max/metabolism

@article {pmid40923121,
year = {2025},
author = {Li, Z and Zhao, K and Liu, H and Liu, J and Chen, X and Hu, W and Wen, E and Zhang, K and Chen, L},
title = {Construction of Predictive Machine Learning Model of Glioma-Associated Gut Microbiota.},
journal = {Brain and behavior},
volume = {15},
number = {9},
pages = {e70843},
doi = {10.1002/brb3.70843},
pmid = {40923121},
issn = {2162-3279},
support = {W2024SNKT13//the Research on Neurological Diseases and Nutritional Health at the Capacity Building and Continuing Education Center of the National Health Commission of China/ ; 82172680//the National Natural Science Foundation of China/ ; 82303586//the National Natural Science Foundation of China/ ; 82373220//the National Natural Science Foundation of China/ ; 82473264//the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Machine Learning ; *Gastrointestinal Microbiome/physiology/genetics ; *Glioma/microbiology/diagnosis ; *Brain Neoplasms/microbiology/diagnosis ; Male ; Female ; Middle Aged ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: The gut microbiota plays a crucial role in the development of glioma. With the evolution of artificial intelligence technology, applying AI to analyze the vast amount of data from the gut microbiome indicates the potential that artificial intelligence and computational biology hold in transforming medical diagnostics and personalized medicine.

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

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

CONCLUSIONS: This method's efficacy in discriminating between glioma cells and normal controls underscores the potential of machine learning models in leveraging large datasets for clinical insights.},
}

Humans
*Machine Learning
*Gastrointestinal Microbiome/physiology/genetics
*Glioma/microbiology/diagnosis
*Brain Neoplasms/microbiology/diagnosis
Male
Female
Middle Aged
Adult
Feces/microbiology

@article {pmid40922218,
year = {2025},
author = {Di Gianvito, P and Englezos, V and Ferrocino, I and Cocolin, L and Rantsiou, K},
title = {Survey of a grapevine microbiome through functional metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {219},
number = {},
pages = {117000},
doi = {10.1016/j.foodres.2025.117000},
pmid = {40922218},
issn = {1873-7145},
mesh = {*Vitis/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification ; Rhizosphere ; Fruit/microbiology ; Plant Leaves/microbiology ; },
abstract = {Microorganisms colonizing grapevines possess diverse functional capabilities that influence the health, growth, productivity and, consequently, wine quality. In this study, spatial and temporal dynamics of the microbiome of Vitis vinifera cv. Barbera grapevine were determined by shotgun sequencing. Bacterial and fungal populations and functions were monitored in samples of rhizosphere, leaves, and grapes, collected at different stages from fruit development to harvest in a conventionally managed vineyard. A compartmental specificity of diverse species was observed within both bacterial and fungal communities. A core microbiome was also identified. LEfSe analysis revealed significantly discriminant taxa associated with each plant compartment, but not according to the sampling time. KEGG genes associated with carbohydrate metabolism were the most abundant in all samples, followed by genes related to amino acid metabolism, respectively involved in carbon and nitrogen metabolic pathways. Interestingly, differences were observed in the functions of rhizosphere and phyllosphere communities with additional differences observed between functions of bacterial and fungal communities. Pathways involved in critical functions like nutrient acquisition, stress resistance, metabolic flexibility, and interaction with the grapevine, were detected within the microbiome. The findings of this study unravel ecological and functional characteristics of the Barbera microbiome. This fundamental understanding is a prerequisite for the development of tailored strategies to protect vineyards and promote sustainability in grapevine production.},
}

*Vitis/microbiology
*Metagenomics/methods
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
Fungi/genetics/classification/isolation & purification
Rhizosphere
Fruit/microbiology
Plant Leaves/microbiology

@article {pmid40922213,
year = {2025},
author = {Zhang, Z and Guo, Z and Cao, L and Hou, Q and Liu, Z and Zhong, J and Liu, N and Mei, X and Wang, Y},
title = {Dissecting the microbial, physicochemical, and flavor dynamics of core and peel layers in Houhuo Daqu: Insights into quality regulation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {219},
number = {},
pages = {116992},
doi = {10.1016/j.foodres.2025.116992},
pmid = {40922213},
issn = {1873-7145},
mesh = {*Taste ; *Fruit/microbiology/chemistry ; Odorants/analysis ; *Food Microbiology ; *Microbiota ; Bacteria/classification/genetics ; Humans ; Amino Acids/analysis ; Metagenomics ; },
abstract = {Houhuo Daqu (HHD) exhibits significant heterogeneity between its core and peel layers, yet their differences remain underexplored. This study integrates metagenomic sequencing and electronic sensory technologies to compare the physicochemical properties, microbial communities, and flavor profiles of HHD's core and peel. Results reveal distinct microbial communities and diversity between the layers. Both are dominated by bacteria (>90 % relative abundance). The core shows significantly higher relative abundance of Bacillus licheniformis, Bacillus haynesii, and Bacillus paralicheniformis, while the peel has elevated levels of Streptomyces sp. NHF165, Pantoea agglomerans, and Lactiplantibacillus plantarum. Bacillus licheniformis is linked to acetic acid biosynthesis. Flavor analysis indicates both layers are rich in pyrazines, contributing to HHD's distinctive aroma. Enzyme activities differed markedly between the core and peel. Structural equation modeling, regression, and ENVFIT analyses show that amino acid nitrogen directly influences enzymatic activity and indirectly affects it by shaping microbial community and diversity. Additionally, amino acid nitrogen significantly impacts HHD's taste and aroma, modulated by starch and ash content. These findings highlight amino acid nitrogen as a key factor for controlling HHD quality in future production.},
}

*Taste
*Fruit/microbiology/chemistry
Odorants/analysis
*Food Microbiology
*Microbiota
Bacteria/classification/genetics
Humans
Amino Acids/analysis
Metagenomics

@article {pmid40922105,
year = {2025},
author = {Petraro, S and Tarracchini, C and Mancabelli, L and Lugli, GA and Turroni, F and Ventura, M and Milani, C},
title = {Plastic-Microbial BioRemediation DB: A Curated Database for Multi-Omics Applications.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70178},
doi = {10.1111/1758-2229.70178},
pmid = {40922105},
issn = {1758-2229},
mesh = {Biodegradation, Environmental ; *Plastics/metabolism ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenomics ; Soil Microbiology ; Metagenome ; Genomics ; Multiomics ; },
abstract = {Plastic pollution is a major environmental challenge, with millions of tonnes produced annually and accumulating in ecosystems, causing long-term harm. Conventional disposal methods, such as landfilling and incineration, are often inadequate, emphasising the need for sustainable solutions like bioremediation. However, the bacterial biodiversity involved in plastic biodegradation remains poorly understood. To address this gap, we present the Plastic-Microbial BioRemediation (Plastic-MBR) database, a curated multi-omics resource that integrates publicly available genetic and enzymatic data related to putative plastic-degrading microorganisms. This database supports in silico analyses of metagenomic data from plastic-contaminated environments and comparative genomics, aiming to identify microbial taxa with potential plastic-degrading functions. We validated the functionality of the Plastic-MBR database by applying it to metagenomic datasets from plastic-contaminated soil and river water, successfully identifying numerous putative plastic-degrading genes across diverse microbial taxa. These results support the use of the Plastic-MBR database as a tool to identify candidate bacteria for future experimental validation, strain isolation, and functional studies, ultimately contributing to a deeper understanding of microbial potential in plastic bioremediation. While this study focuses on database development and computational validation, future studies will be essential to confirm and translate these genomic predictions into effective bioremediation strategies.},
}

Biodegradation, Environmental
*Plastics/metabolism
*Bacteria/metabolism/genetics/classification/isolation & purification
Metagenomics
Soil Microbiology
Metagenome
Genomics
Multiomics

@article {pmid40920777,
year = {2025},
author = {Nendl, A and Raju, SC and Braadland, PR and Nordborg, A and Bratseth, V and Broch, K and Jørgensen, SF and Aukrust, P and Kristiansen, K and Hov, JR and Trøseid, M and Awoyemi, A},
title = {Circulating metabolites in patients with chronic heart failure are not related to gut leakage or gut dysbiosis.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331692},
pmid = {40920777},
issn = {1932-6203},
mesh = {Humans ; *Dysbiosis/blood/microbiology/metabolism ; *Heart Failure/blood/microbiology/metabolism/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Aged ; Feces/microbiology ; Chronic Disease ; Case-Control Studies ; Metabolomics ; Metabolome ; },
abstract = {BACKGROUND: The gut microbiota produces numerous metabolites that can enter the circulation and exert effects outside the gut. Several studies have reported altered gut microbiota composition and circulating metabolites in patients with chronic heart failure (HF) compared to healthy controls. Limited data is available on the interplay between dysbiotic features of the gut microbiota and altered circulating metabolites in HF patients. We aimed to examine differences in circulating metabolites between people with and without chronic HF, and their association with gut microbiota dysbiosis and cardiac function.

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

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

CONCLUSIONS: Patients with chronic HF had distinct metabolomic and lipidomic profiles and energy metabolism differed significantly compared to healthy controls before adjusting for medication use. However, the alterations were not related to gut dysbiosis, gut leakage markers, cardiac function, or fiber intake.},
}

Humans
*Dysbiosis/blood/microbiology/metabolism
*Heart Failure/blood/microbiology/metabolism/physiopathology
Male
Female
*Gastrointestinal Microbiome
Middle Aged
Aged
Feces/microbiology
Chronic Disease
Case-Control Studies
Metabolomics
Metabolome

@article {pmid40795725,
year = {2025},
author = {Zhang, FL and Li, AY and Zhu, KX and Zhang, K and Tian, Z and Wang, T and Zhang, XH and Zang, J and Sun, XF and Shen, W and Li, L},
title = {Integrated multi-omics analysis uncovers Zearalenone-induced ovarian and intestinal inflammation is mediated by the tumor necrosis factor-α.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139476},
doi = {10.1016/j.jhazmat.2025.139476},
pmid = {40795725},
issn = {1873-3336},
mesh = {*Zearalenone/toxicity ; Animals ; Female ; *Tumor Necrosis Factor-alpha/genetics/metabolism ; *Inflammation/chemically induced/metabolism/genetics ; *Ovary/drug effects/pathology/metabolism ; Mice ; Gastrointestinal Microbiome/drug effects ; *Intestines/drug effects/pathology ; Mice, Knockout ; Mice, Inbred C57BL ; Dysbiosis/chemically induced ; Cell Line ; Multiomics ; },
abstract = {As a widely encountered foodborne mycotoxin, Zearalenone (ZEN) has the potential to accumulate along the food chain, posing threats to public health and safety. However, the precise mechanisms by which ZEN causes tissue damage remain incompletely understood. Here, we established in vivo (40 μg/kg) and in vitro (30 μM) models to elucidate the underlying processes of ZEN-induced damage to the ovary and intestine. Our results demonstrated that, following ZEN exposure, pro-inflammatory signaling factors, including NLR family pyrin domain containing 3 (NLRP3) and Interleukin 6 (IL6), were significantly elevated in both ovarian and intestines. Metagenomic analysis revealed dysbiosis of the gut microbiota, which was closely associated with tumor necrosis factor (TNF)-α signaling pathway. Transcriptomic results further indicated that inflammatory response are intricately linked to TNF signaling pathway. Additionally, the Tnf-α knockout mouse model showed a marked resistance to ZEN-induced ovarian and intestinal injuries. In vitro, RNA interference targeting TNF-α attenuated the inflammatory response in IPEC-J2 cells. Moreover, dysregulated expression of the hormone synthesis genes, including KISS-1 metastasis suppressor (Kiss1) and gonadotropin releasing hormone 1 (Gnrh1), was observed, suggesting that ZEN-induced microbial dysbiosis and ovary damage may be interconnected through hormonal disruption. In summary, our results emphasize the role of TNF-α in causing ovarian and intestinal damage after ZEN exposure.},
}

*Zearalenone/toxicity
Animals
Female
*Tumor Necrosis Factor-alpha/genetics/metabolism
*Inflammation/chemically induced/metabolism/genetics
*Ovary/drug effects/pathology/metabolism
Mice
Gastrointestinal Microbiome/drug effects
*Intestines/drug effects/pathology
Mice, Knockout
Mice, Inbred C57BL
Dysbiosis/chemically induced
Cell Line
Multiomics

@article {pmid40752173,
year = {2025},
author = {Li, WJ and Ghaly, TM and Tetu, SG and Huang, FY and Li, HZ and Li, H},
title = {Effects of agricultural inputs on soil virome-associated antibiotic resistance and virulence: A focus on manure, microplastic and pesticide.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139380},
doi = {10.1016/j.jhazmat.2025.139380},
pmid = {40752173},
issn = {1873-3336},
mesh = {*Manure ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Pesticides/toxicity ; *Soil Pollutants/toxicity ; *Microplastics/toxicity ; *Virome/drug effects ; Agriculture ; Virulence/genetics ; Virulence Factors/genetics ; Bacteria/genetics ; Soil/chemistry ; },
abstract = {Soil viruses are increasingly recognized as crucial mediators of horizontal gene transfer, yet their role in disseminating antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) under agricultural disturbances remains poorly understood. Here, we characterized the viromes and associated ARGs and VFGs in agricultural soils treated with low- and high-dose manures, microplastics, and pesticides. Using metagenomic sequencing coupled with advanced viral identification tools, we found that manure fertilization markedly altered viral community composition and increased viral diversity. Manure also enhanced the abundance of ARGs and VFGs in viromes by 2.0-9.8-fold and 2.0-8.1-fold, respectively, while microplastics and pesticides had limited impacts. Additionally, gene pathways related to human diseases and environmental adaptation were enriched in soil viromes treated with manures and high-dose pesticides. Virus-host prediction revealed that Actinomycetia dominated bacterial hosts of both ARG- and VFG-carrying viruses, with some VFG-carrying viruses linked to potential human pathogens, e.g., Escherichia albertii and Klebsiella pneumoniae. Co-occurrence network analysis indicated that these disturbances strengthened connections between bacteria, viruses, and ARGs (or VFGs). Our study provides a comprehensive profile of viromes and associated risks in agricultural soil under three disturbances, highlighting the role of viruses in spread of antibiotic resistance and pathogenic risks in agricultural soil.},
}

*Manure
*Soil Microbiology
*Drug Resistance, Microbial/genetics
*Pesticides/toxicity
*Soil Pollutants/toxicity
*Microplastics/toxicity
*Virome/drug effects
Agriculture
Virulence/genetics
Virulence Factors/genetics
Bacteria/genetics
Soil/chemistry

@article {pmid40749656,
year = {2025},
author = {Asghar, MU and Zhai, Y and Liu, T and Fan, P and Ain, NU and Zaidi, AH and Tariq, M and Mainar-Jaime, RC and Jeong, KC},
title = {A metagenomics-based approach to understanding the transmission of healthcare-associated antimicrobial resistance in Pakistan.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139384},
doi = {10.1016/j.jhazmat.2025.139384},
pmid = {40749656},
issn = {1873-3336},
mesh = {Pakistan ; *Metagenomics ; *Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Humans ; Bacteria/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Cross Infection/microbiology/transmission ; Microbiota ; },
abstract = {Hospital environments are critical yet underexamined reservoirs for hazardous antimicrobial resistance (AMR), particularly in lower-middle-income countries (LMICs) where resource constraints often hinder comprehensive surveillance. In this study, we employed 16S rRNA gene sequencing and shotgun metagenomics to characterize the microbiome, resistome, and potential transmission routes across five clinical environments within a hospital in Pakistan: the intensive care unit (ICU), surgical ward (SW), cardiac surgery ward (CSW), cardiac ward (CW), and operating theater (OT). Microbial community analysis revealed compositional similarities among the ICU, SW, and OT, with the ICU emerging as a primary source of microbial dissemination. Species-level profiling identified hospital-associated pathogens such as Acinetobacter baumannii, Klebsiella pneumoniae, and Enterobacter cloacae, and metagenome-assembled genome (MAG) analysis enabled the linkage of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) to specific bacterial hosts. ARGs and MGEs displayed setting-specific patterns, with the SW harboring the highest abundance of ARGs, particularly those conferring resistance to β-lactams and biocides. Insertion sequences were the most prevalent MGEs and were commonly linked to ARGs, indicating potential horizontal gene transfer. Co-occurrence network analysis identified Staphylococcus, Enterococcus, and Escherichia as central hub taxa within the microbial communities of the ICU, SW, and OT, indicating their critical roles in potential ARG transmission. These findings provide critical insights into the environmental transmission dynamics of AMR in LMIC healthcare settings and underscore the urgent need for metagenomics-informed infection control strategies.},
}

Pakistan
*Metagenomics
*Drug Resistance, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Humans
Bacteria/genetics/drug effects
*Anti-Bacterial Agents/pharmacology
*Cross Infection/microbiology/transmission
Microbiota

@article {pmid40712359,
year = {2025},
author = {Liu, Y and Li, S and Song, X and Bartlam, M and Wang, Y},
title = {Differential responses of bacterial and archaeal communities to biodegradable and non-biodegradable microplastics in river.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139327},
doi = {10.1016/j.jhazmat.2025.139327},
pmid = {40712359},
issn = {1873-3336},
mesh = {*Archaea/drug effects/genetics ; *Microplastics/toxicity ; *Bacteria/drug effects/genetics ; *Water Pollutants, Chemical/toxicity ; *Rivers/microbiology ; Biodegradation, Environmental ; Polyvinyl Chloride/toxicity ; Microbiota/drug effects ; Polyesters ; Drug Resistance, Microbial/genetics ; },
abstract = {Microplastics are widespread environmental pollutants that pose risks to ecosystems, yet their effects on bacterial and archaeal communities in aquatic ecosystems remain understudied. In this study, we performed a 14-day microcosm experiment combined with metagenomic sequencing to compare bacterial and archaeal responses to a biodegradable microplastic (polylactic acid, PLA) and a non-biodegradable microplastic (polyvinyl chloride, PVC). Microplastics selectively enriched distinct microbial assemblages, with Pseudomonadota and Euryarchaeota identified as the dominant bacterial and archaeal phyla, accounting for 67.83 % and 15.95 %, respectively. Archaeal community in surrounding water were more sensitive to colonization time than bacterial community. Compared to the surrounding water, the plastisphere displayed simpler and more loosely connected microbial networks. Notably, co-occurrence networks of both bacteria and archaea in the PVC plastisphere were predominantly shaped by symbiotic interactions. Both bacteria and archaea carried diverse antibiotic resistance genes (ARGs), but PLS-PM indicated that bacteria were the primary drivers of ARG dissemination (path coefficient = 0.952). While the PVC plastisphere showed higher ARG abundance than the PLA plastisphere, elevated intI1 expression in the PLA plastisphere suggests a potentially greater risk of ARG dissemination associated with PLA microplastics. These findings reveal the distinct effects of PLA and PVC microplastics on microbial communities and highlight the role of microplastics in ARG dissemination, emphasizing their ecological risks in aquatic ecosystems.},
}

*Archaea/drug effects/genetics
*Microplastics/toxicity
*Bacteria/drug effects/genetics
*Water Pollutants, Chemical/toxicity
*Rivers/microbiology
Biodegradation, Environmental
Polyvinyl Chloride/toxicity
Microbiota/drug effects
Polyesters
Drug Resistance, Microbial/genetics

@article {pmid40706155,
year = {2025},
author = {Wang, YC and He, LY and Wu, HY and Qiao, LK and Huang, Z and Bai, H and Gao, FZ and Shi, YJ and Zhao, JL and Liu, YS and Ying, GG},
title = {High-risk plasmid-borne resistance genes from swine farm environments infiltrate deep soil and interact with the human gut microbiome via horizontal transfer.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139281},
doi = {10.1016/j.jhazmat.2025.139281},
pmid = {40706155},
issn = {1873-3336},
mesh = {Animals ; *Gene Transfer, Horizontal ; Swine ; *Gastrointestinal Microbiome/genetics ; *Plasmids/genetics ; Humans ; Farms ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Swine farms serve as critical reservoirs of antibiotic resistance genes (ARGs), yet the frequency of horizontal gene transfer (HGT) remains poorly understood. In this study, we explored the gene exchange within the "swine farm-human-pig" network and assessed its risks. We identified 16,612 plasmid contigs from 107 field samples, revealing a significant presence of previously uncharacterized plasmid types. Notably, 52.88 % of acquired ARGs were located on plasmids, with 71.22 % containing at least one mobile genetic element (MGE). We quantified HGTs at the microbial community level among the human gut, pig gut, and swine farm environments. Among 4687 metagenome-assembled genomes (MAGs), 3008 were involved in 11,250 HGTs. HGT linkages were most frequently identified between microbial genomes from the swine farm and the human gut microbiome. ARGs were involved in 91 HGT events, with 645 events linked to MGEs and 16 related to virulence factors, suggesting potential cross-species transmission of clinical pathogens. The detection of 32 Rank I ARGs and the identification of increased resistome risks underscore the extensive dispersion of livestock-related contaminants into more distant environmental compartments. This study elucidates the complexities of gene exchange networks in swine farm environments, underscoring the urgent need for strategies to mitigate risks associated with the antibiotic resistome.},
}

Animals
*Gene Transfer, Horizontal
Swine
*Gastrointestinal Microbiome/genetics
*Plasmids/genetics
Humans
Farms
*Soil Microbiology
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics

@article {pmid40682875,
year = {2025},
author = {Beltrán de Heredia, I and Sbaffi, T and González-Gaya, B and Di Cesare, A and Sabatino, R and Alkorta, I and Ruiz-Romera, E},
title = {Comparative analysis of planktonic and sessile microbiomes and associated resistomes in a freshwater ecosystem impacted by municipal wastewater treatment plant discharge.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139250},
doi = {10.1016/j.jhazmat.2025.139250},
pmid = {40682875},
issn = {1873-3336},
mesh = {*Microbiota/drug effects ; *Wastewater ; Biofilms ; *Plankton/drug effects ; *Fresh Water/microbiology ; Rivers/microbiology ; Ecosystem ; Waste Disposal, Fluid ; Water Microbiology ; Bacteria/genetics/drug effects ; *Water Pollutants, Chemical ; },
abstract = {Wastewater treatment plants (WWTPs) disrupt freshwater ecosystems and are recognised as hotspots for antimicrobial resistance. This study assessed the effect of treated municipal wastewater discharge on both planktonic and sessile freshwater microbial communities. A monitoring network was established in a Spanish urban river basin during 2022 dry season, with sampling points upstream and downstream of a WWTP. Artificial glass-based substrates enabled biofilm colonisation, while river water and effluent samples were collected during biofilm harvesting. Chemical exposure was assessed by characterising nutrients and antimicrobial concentrations in water, while shotgun metagenomics revealed taxonomic composition and resistome pools in both matrices. River water exhibited greater genus richness and pathobiome diversity than biofilms. Wastewater discharge shaped microbial composition, leading to shifts in less dominant groups, with partial attenuation of this effect downstream. Resistome richness was higher in river water compared to biofilm, though the latter displayed greater total abundances and distinct resistance profiles suggesting their role as genetic reservoirs. While no consistent resistome trends were linked to sampling location, higher total resistance abundances occurred in river water at sites impacted by wastewaters. Background resistance levels found upstream likely persisted downstream due to pollutant-driven selection. Lower resistome richness in effluent water suggests downstream abundances may also result from microbiome shifts and environmental factors. Assembly-based analysis revealed resistance genetic contexts and indicators of gene dissemination.},
}

*Microbiota/drug effects
*Wastewater
Biofilms
*Plankton/drug effects
*Fresh Water/microbiology
Rivers/microbiology
Ecosystem
Waste Disposal, Fluid
Water Microbiology
Bacteria/genetics/drug effects
*Water Pollutants, Chemical

@article {pmid40645301,
year = {2025},
author = {Melamed, E and Rungratanawanich, W and Liangpunsakul, S and Maki, KA and McCullough, RL and Llorente, C},
title = {Alcohol, aging, and the gut microbiome: Intersections of immunity, barrier dysfunction, and disease.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {128},
number = {},
pages = {1-12},
doi = {10.1016/j.alcohol.2025.07.001},
pmid = {40645301},
issn = {1873-6823},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology/physiology ; *Aging/immunology ; *Alcohol Drinking/immunology/adverse effects ; Intestinal Mucosa/drug effects/immunology ; *Ethanol/adverse effects ; Animals ; Inflammation ; },
abstract = {Alcohol consumption exerts complex, dose- and context-dependent effects on human health, particularly by influencing the gut microbiome, intestinal barrier integrity, immune regulation, and aging processes. Genetic variation and advancing age are two major, and often interacting, factors that modify the risk of alcohol-related diseases. Among genetic factors, the prevalent aldehyde dehydrogenase 2 polymorphism (ALDH2∗2) compromises acetaldehyde clearance, driving toxic metabolite accumulation, oxidative stress, and increased intestinal permeability that disrupts gut microbial communities, even at low levels of alcohol consumption. Heavy and chronic alcohol use further disrupts gut microbial communities, erodes mucosal integrity, and drives systemic inflammation, contributing to alcohol-associated liver disease (ALD), neuroinflammation, and multi-organ injury. Aging independently worsens these effects by promoting chronic low-grade inflammation and impaired immune responses, heightening susceptibility to alcohol-induced pathology. In specific contexts, such as certain autoimmune diseases, low to moderate alcohol intake may exert immunomodulatory effects and influence the gut microbiome, potentially contributing to reduced inflammation and alterations in microbial composition. This review synthesizes current mechanistic insights into how alcohol, host genetics, the gut microbiome, immune regulatory pathways, and aging intersect to influence disease risk. As global populations age and the burden of alcohol-related health issues rises, there is an urgent need for integrated, systems-level approaches. Future research should prioritize precision-based, gut-targeted strategies aimed at restoring microbial balance, maintaining intestinal barrier integrity, and mitigating alcohol-related harm across the lifespan.},
}

Humans
*Gastrointestinal Microbiome/drug effects/immunology/physiology
*Aging/immunology
*Alcohol Drinking/immunology/adverse effects
Intestinal Mucosa/drug effects/immunology
*Ethanol/adverse effects
Animals
Inflammation

@article {pmid40643197,
year = {2025},
author = {Xu, T and Wu, X and Zhang, Y and Cai, Y and Zhang, X and Zeng, Q and Luo, J and Wei, J and Chen, T},
title = {L-Tryptophan Produced by Bifidobacterium pseudocatenulatum NCU-08 Delays Aging in SAMP8 Mice by Activating the Sirt1/P53/P21/Rb Signaling Pathway.},
journal = {Aging cell},
volume = {24},
number = {9},
pages = {e70166},
doi = {10.1111/acel.70166},
pmid = {40643197},
issn = {1474-9726},
support = {32201250//National Natural Science Foundation of China/ ; 2024YFA1307103//National Key R&D Program of China/ ; 2024SSY07061//Jiangxi Province Key Laboratory of bioengineering drugs/ ; 20242BAB25464//Jiangxi Provincial Natural Science Foundation/ ; },
mesh = {Animals ; Mice ; *Sirtuin 1/metabolism ; *Tryptophan/pharmacology/biosynthesis/metabolism ; *Signal Transduction/drug effects ; *Aging/drug effects ; *Bifidobacterium/metabolism ; *Tumor Suppressor Protein p53/metabolism ; Probiotics/pharmacology ; Male ; Gastrointestinal Microbiome ; Hippocampus ; },
abstract = {Gut microbiota delays aging by regulating the immune, metabolic, and neurological functions of the host. However, current research on novel probiotics with antiaging properties significantly lags, impacting their application in clinical treatments. In this study, metagenomics, culturomics, and probiotic property screening were used to identify Bifidobacterium pseudocatenulatum NCU-08 as a potential probiotic with anti-aging properties. In addition, B. pseudocatenulatum NCU-08 effectively improved the behavioral characteristics, significantly reduced the levels of the age-related protein β-galactosidase (β-gal) (BP: M = 0.81 vs. 1.13, p < 0.05), attenuated neuronal damage in the hippocampus, and improved the composition of the gut microbiota of senescence-accelerated mouse tendency-8 (SAMP8) mice. The targeted metabolomics suggested that L-tryptophan (L-Trp) may be a key substance for B. pseudocatenulatum NCU-08 to exert anti-aging effects (BP: M = 14878.6 ng/mL vs. 5464.99 ng/mL, p < 0.01). Mechanistically, using the aging model of SAMP8 mice and HT22 mouse hippocampal neuronal cells, it was found that B. pseudocatenulatum NCU-08 might enter the intestine to regulate L-Trp, and then transport it to the brain. In the brain, L-Trp was metabolized to NAD[+], which activated the Sirt1/P53/P21/Rb signaling pathway, thereby exerting antiaging effects. Interestingly, this antiaging effect was inhibited after the intervention of the Sirt1 inhibitor EX-527. This study is the first to confirm the antiaging properties of NCU-08 isolated from the fecal samples of seven centenarians in Jiangxi Province, providing data support for the future development of probiotic preparations with antiaging effects.},
}

Animals
Mice
*Sirtuin 1/metabolism
*Tryptophan/pharmacology/biosynthesis/metabolism
*Signal Transduction/drug effects
*Aging/drug effects
*Bifidobacterium/metabolism
*Tumor Suppressor Protein p53/metabolism
Probiotics/pharmacology
Male
Gastrointestinal Microbiome
Hippocampus

@article {pmid40461059,
year = {2025},
author = {Laiola, M and Koppe, L and Larabi, A and Thirion, F and Lange, C and Quinquis, B and David, A and Le Chatelier, E and Benoit, B and Sequino, G and Chanon, S and Vieille-Marchiset, A and Herpe, YE and Alvarez, JC and Glorieux, G and Krukowski, H and Huys, GR and Raes, J and Fouque, D and Massy, ZA and Ehrlich, SD and Stengel, B and Wagner, S and , },
title = {Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study.},
journal = {Gut},
volume = {74},
number = {10},
pages = {1624-1637},
doi = {10.1136/gutjnl-2024-334634},
pmid = {40461059},
issn = {1468-3288},
mesh = {*Renal Insufficiency, Chronic/microbiology ; *Gastrointestinal Microbiome/physiology ; Humans ; Disease Progression ; Male ; Female ; Middle Aged ; Animals ; Mice ; Fecal Microbiota Transplantation ; Longitudinal Studies ; *Uremic Toxins/metabolism/blood ; Aged ; Metagenomics ; Adult ; Diet ; },
abstract = {BACKGROUND: The gut microbiota has been linked to non-communicable diseases, including chronic kidney disease (CKD). However, the relationships between gut microbiome composition changes, uraemic toxins (UTs) accumulation, and diet on CKD severity and progression remain underexplored.

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

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

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

CONCLUSIONS: This study highlights the role of the microbiome and UTs in CKD, suggesting a potential therapeutic target to slow disease progression.},
}

*Renal Insufficiency, Chronic/microbiology
*Gastrointestinal Microbiome/physiology
Humans
Disease Progression
Male
Female
Middle Aged
Animals
Mice
Fecal Microbiota Transplantation
Longitudinal Studies
*Uremic Toxins/metabolism/blood
Aged
Metagenomics
Adult
Diet

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

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

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

CONCLUSION: These results underscore the value of integrating microbiome and resistome features to reveal potential protective mechanisms and improve risk prediction for AR outcomes in vulnerable patients.},
}

Humans
*Machine Learning
*Leukemia, Myeloid, Acute/drug therapy/microbiology/complications
*Anti-Bacterial Agents/therapeutic use/pharmacology
Gastrointestinal Microbiome/drug effects
Male
Female
Middle Aged
*Induction Chemotherapy/adverse effects
Bacteria/drug effects/genetics/classification
Aged
Adult
Feces/microbiology
Metagenomics
*Drug Resistance, Bacterial

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

RESULTS: To address these challenges, we developed DeepMobilome, a novel approach for accurately identifying target MGEs within the microbiome. DeepMobilome leverages a convolutional neural network trained on read alignment data derived from sequence alignment map (SAM) files, providing superior accuracy in detecting MGEs. Trained on 364 647 cases, DeepMobilome achieved a high validation accuracy of 0.99. DeepMobilome consistently outperformed existing methods in discerning the presence of target MGE sequences across diverse test sets. In single-genome test scenarios, DeepMobilome showed an F1-score of 0.935, compared to 0.755 and 0.670 for MGEfinder and ISMapper, respectively, demonstrating its substantial improvements in prediction accuracy. Extensive evaluations across simulated microbiomes further validated the robustness and reliability of DeepMobilome in practical applications. In real microbiome data, DeepMobilome successfully identified six ARG-carrying MGEs across diverse populations. By addressing the limitations of current methods, DeepMobilome offers a powerful tool for advancing our understanding of ARG dissemination and supports targeted interventions in combating antibiotic resistance.},
}

*Microbiota/genetics
*Interspersed Repetitive Sequences
Metagenome
Metagenomics/methods
Humans
Neural Networks, Computer
Sequence Analysis, DNA
Drug Resistance, Microbial/genetics
Computational Biology/methods
High-Throughput Nucleotide Sequencing

@article {pmid40780374,
year = {2025},
author = {Mao, Z and Liu, C and Ni, J and Huang, M and Qu, W and Chen, W and Shen, Y and Qin, T and Gao, M and Zheng, S and Chen, Y},
title = {Gut derived (S)-Equol mitigates influenza viral pneumonia by modulating macrophage polarization via Nrf2 mediated AKT/ERK/NF-κb signaling pathways.},
journal = {Free radical biology & medicine},
volume = {239},
number = {},
pages = {457-471},
doi = {10.1016/j.freeradbiomed.2025.08.004},
pmid = {40780374},
issn = {1873-4596},
mesh = {Animals ; *NF-E2-Related Factor 2/metabolism/genetics ; Mice ; NF-kappa B/metabolism/genetics ; Proto-Oncogene Proteins c-akt/metabolism/genetics ; *Gastrointestinal Microbiome/drug effects ; *Macrophages/drug effects/immunology/metabolism ; Signal Transduction/drug effects ; Humans ; *Pneumonia, Viral/drug therapy/pathology/metabolism/virology/immunology ; *Orthomyxoviridae Infections/drug therapy/virology/pathology ; *Influenza, Human/virology/drug therapy ; Male ; Influenza A virus/pathogenicity ; Disease Models, Animal ; Mice, Inbred C57BL ; Female ; },
abstract = {Respiratory virus including influenza A virus (IAV) infection induces alterations in gut microbiota structure and function, which in turn plays an essential role in the pathogenic process. Alterations in gut microbiota are usually accompanied with changes in metabolites. The specific relationship between dynamic changes in gut microbiota and serum metabolites in influenza remains unclear. In this study, we depicted dynamic changes in composition of gut microbiota by using metagenomic sequencing in an influenza mouse model. Through mass spectrometry based metabolomic, we identified (S)-Equol as a notable protective metabolite derived from intestinal flora. Serum (S)-Equol level decreased from the initial infection phase and increased gradually during the convalescence phase, which was positively associated with the changes in some Eggerthella and Bifidobacterium species. Antibiotic treatment reduced serum (S)-Equol level and exacerbated lung pathological damage. Oral administration of (S)-Equol relieved disease severity and controlled inflammatory infiltration. Mechanistically, (S)-Equol activated Nrf2 in macrophages, thereby inhibited AKT, ERK and NF-κB phosphorylation. The inhibition of these signaling pathways ultimately restrained pro-inflammatory cytokines release and repressed pro-inflammatory macrophage polarization. Moreover, serum (S)-Equol level was lower in influenza patients at progressed phase and was negatively correlated with serum levels of IL-6, IL-1β, and TNF-α. Collectively, our data highlighted gut derived (S)-Equol a promising postbiotic for alleviating influenza pneumonia.},
}

Animals
*NF-E2-Related Factor 2/metabolism/genetics
Mice
NF-kappa B/metabolism/genetics
Proto-Oncogene Proteins c-akt/metabolism/genetics
*Gastrointestinal Microbiome/drug effects
*Macrophages/drug effects/immunology/metabolism
Signal Transduction/drug effects
Humans
*Pneumonia, Viral/drug therapy/pathology/metabolism/virology/immunology
*Orthomyxoviridae Infections/drug therapy/virology/pathology
*Influenza, Human/virology/drug therapy
Male
Influenza A virus/pathogenicity
Disease Models, Animal
Mice, Inbred C57BL
Female

@article {pmid40773868,
year = {2025},
author = {Kim, SY and Woo, SY and Kim, HR and Kim, NY and Kim, HL and Chang, Y and Ryu, S and Kim, HN},
title = {Shotgun metagenomics reveals alteration of gut microbiota and metabolic pathways in adults with poor sleep quality.},
journal = {Psychoneuroendocrinology},
volume = {180},
number = {},
pages = {107565},
doi = {10.1016/j.psyneuen.2025.107565},
pmid = {40773868},
issn = {1873-3360},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Male ; Female ; Adult ; Middle Aged ; *Metabolic Networks and Pathways/genetics/physiology ; Feces/microbiology ; Metagenomics/methods ; *Sleep Quality ; *Sleep Wake Disorders/microbiology/metabolism ; Metagenome/genetics ; },
abstract = {INTRODUCTION: Emerging evidence suggests that the gut microbiome plays a role in sleep disturbance. This study explored the characteristics of the gut microbiome and the functional metabolic pathways related to sleep quality.

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

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

CONCLUSION: In summary, this study poses significant questions regarding the relationship between the gut microbiome and poor sleep quality.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
Male
Female
Adult
Middle Aged
*Metabolic Networks and Pathways/genetics/physiology
Feces/microbiology
Metagenomics/methods
*Sleep Quality
*Sleep Wake Disorders/microbiology/metabolism
Metagenome/genetics

@article {pmid40719338,
year = {2025},
author = {Louca, S and Mullin, CE},
title = {Effects of Vacuum-Heat-Assisted Sample Desiccation on Microbiome Surveys.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e70020},
pmid = {40719338},
issn = {1755-0998},
support = {2243038//US National Science Foundation/ ; },
mesh = {*Desiccation/methods ; Animals ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Specimen Handling/methods ; Vacuum ; Feces/microbiology ; Hot Temperature ; Metagenomics/methods ; Soil Microbiology ; },
abstract = {Sample preservation in the field and during transport can be a logistical challenge for microbiome surveys, particularly in remote areas. Sample desiccation eliminates the need for complicated cold chains and dangerous preservatives. However, the effects of desiccation on modern microbiome workflows such as gene-centric metagenomic profiling and metagenome-assembled genome (MAG) binning, remain poorly understood. In addition, most common desiccation tools such as lyophilisation cannot easily be deployed in the field. Here, we describe a proof-of-principle sample desiccator using vacuum and heat, specifically built for deployment in the field and exhibiting low power consumption and cost. We then test the effects of vacuum-heat-assisted sample desiccation followed by storage at room temperature, in comparison to conventional freezing, on multiple soil and animal faecal samples, via metagenomic and 16S rRNA amplicon sequencing. We consider multiple metrics related to the success of DNA extraction, sequencing, contig assembly, OTU clustering, gene annotation and MAG construction, as well as effects on inferred microbial community composition. We find that the impact of drying on considered success metrics was almost always either minor, non-significant or positive. For a subset of source materials we observed moderate but statistically significant differences in terms of inferred microbial taxonomic and genetic composition. We conclude that vacuum- and heat-assisted desiccation can be a useful, practical and cost-effective tool for microbiome field surveys, when a high consistency with frozen samples is not required.},
}

*Desiccation/methods
Animals
RNA, Ribosomal, 16S/genetics
*Microbiota
*Specimen Handling/methods
Vacuum
Feces/microbiology
Hot Temperature
Metagenomics/methods
Soil Microbiology

@article {pmid40671648,
year = {2025},
author = {Maiello, G and Lippert, MR and Neave, EF and Hanson, EA and Palumbi, SR and Mariani, S},
title = {Multi-Tool Marine Metabarcoding Bioassessment for Baselining and Monitoring Species and Communities in Kelp Habitats.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e70010},
pmid = {40671648},
issn = {1755-0998},
support = {//The Pew Charitable Trusts under the Lenfest Ocean Program/ ; //The Gordon and Betty Moore Foundation/ ; //Oceankind Labs/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Kelp ; Ecosystem ; California ; Animals ; *Biodiversity ; *Aquatic Organisms/classification/genetics ; *DNA, Environmental/genetics ; *Metagenomics/methods ; *Biota ; },
abstract = {The astonishing biological diversity found in Californian kelp forests requires efficient and robust monitoring tools to better understand ecological trends and mitigate against loss or disruption of ecosystem services due to human pressure and climate changes. With environmental DNA (eDNA) metabarcoding becoming a popular biodiversity assessment approach, we set out to evaluate a combination of powerful, rapid and sustainable eDNA solutions for characterising marine community composition in kelp-dominated habitats along the central California coast, in the newly proposed Chumash Heritage National Marine Sanctuary. We employed and compared the efficiency of several eDNA collection approaches, including 'traditional' surface water filtration, the collection of organisms encrusting cobble rocks and various deployments of an artificial passive sampler, the metaprobe (i.e., attached to divers, dangled from a boat and cast from the shore using a fishing rod). By combining the information from fish specific (Tele02 12S) and universal metazoan (COI) markers, we 'captured' 501 unique marine taxa, belonging to at least 36 phyla, over 400 of which were identified to genus/species level, and including 52 vertebrate species typical of Californian kelp forest ecosystems. Despite differences in the type of biodiversity returned by the tested sampling methods, the overall community structure of the surveyed area was highly spatially structured and strongly influenced by the biogeographic break around Point Conception (Humqaq). We discuss the benefits of integrating eDNA metabarcoding in existing monitoring programs and devising a reproducible approach to monitor faunal changes in kelp forest habitats and beyond.},
}

*DNA Barcoding, Taxonomic/methods
*Kelp
Ecosystem
California
Animals
*Biodiversity
*Aquatic Organisms/classification/genetics
*DNA, Environmental/genetics
*Metagenomics/methods
*Biota

@article {pmid40644733,
year = {2025},
author = {Zhou, Y and Wen, C and Zhang, Q and Gu, Z and Lian, L and Xue, K and Xu, T and Lin, Z and Wang, W and Zhu, H},
title = {Characteristics of oral microbiomics with soldiers in the army before and after high-intensity physical training.},
journal = {Archives of oral biology},
volume = {178},
number = {},
pages = {106347},
doi = {10.1016/j.archoralbio.2025.106347},
pmid = {40644733},
issn = {1879-1506},
mesh = {Humans ; *Military Personnel ; *Saliva/microbiology ; *Microbiota ; Male ; Adult ; Phylogeny ; *Mouth/microbiology ; Young Adult ; Bacteria/classification ; Metagenomics ; },
abstract = {OBJECTIVES: This paper aims to investigate the changes in soldiers' oral microbiome and metabolic levels after a month of high-intensity training.

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

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

CONCLUSIONS: This paper reveals the changes in the saliva microbiome of soldiers after one month of high-intensity training, in which the relative abundance of biomarkers of periodontal disease, caries, and other oral diseases represented by peptostreptococcus, prevotella oris, treponema, etc., are significantly reduced, suggesting that long-term high-intensity training may have a positive effect on oral health.},
}

Humans
*Military Personnel
*Saliva/microbiology
*Microbiota
Male
Adult
Phylogeny
*Mouth/microbiology
Young Adult
Bacteria/classification
Metagenomics

@article {pmid40577531,
year = {2025},
author = {Duxbury, SJN and Raguideau, S and Cremin, K and Richards, L and Medvecky, M and Rosko, J and Coates, M and Randall, K and Chen, J and Quince, C and Soyer, OS},
title = {Niche formation and metabolic interactions contribute to stable diversity in a spatially structured cyanobacterial community.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40577531},
issn = {1751-7370},
support = {GBMF9200//Gordon and Betty Moore Foundation/ ; 1394//UK NERC NEOF Pilot Genomics Competition/ ; MR/S037195/1//MRC Methodology Grant "Strain resolved metagenomics for medical microbiology"/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBX011089/1//Earlham Institute Strategic Programme Grant (Decoding Biodiversity)/ ; BBS/E/ER/230002C//Earlham Institute Strategic Programme Grant (Decoding Biodiversity)/ ; BB/CSP1720/1//Core Strategic Programme/ ; BBS/E/T/000PR9818//Core Strategic Programme/ ; BBS/E/T/000PR9817//Core Strategic Programme/ ; BB/CCG2220/1//Core Strategic Programme/ ; },
mesh = {*Cyanobacteria/metabolism/genetics/classification/growth & development ; *Biodiversity ; Metagenomics ; Gene Expression Profiling ; Oxygen/metabolism ; },
abstract = {Understanding how microbial communities maintain stable compositional diversity is a key question in microbial ecology. Studies from pairwise interactions and synthetic communities indicate that metabolic interactions and spatial organisation can influence diversity, but the relevance of these factors in more complex communities is unclear. Here we used a cyanobacterial enrichment community that consistently forms millimetre-scale granular structures, to investigate compositional diversity and its stability. Over a year of passaging in media without significant carbon source, we found stable co-existence of 17 species belonging to diverse bacterial phyla. Metagenomic analysis revealed polysaccharide breakdown genes and complementary vitamin biosynthesis pathways in these species. Supporting these findings, we show growth of several isolated species on cyanobacterial slime components and experimentally verify vitamin exchanges between two members of the community. Several species had genes for (an)oxygenic photosynthesis and sulfur cycling, the expression of which we verified via metatranscriptomics. Consistent with this, we found that the granular structures displayed oxygen gradients with anoxic interiors. Cyanobacteria and other bacteria were distributed on the periphery and insides of these structures, respectively. Perturbation of the community via glucose addition resulted in fold increases of the heterotrophs, whereas disturbing the community by continual shaking led to fold reductions in several heterotrophs, including anoxygenic phototrophs. In contrast, removal of vitamins supplementation did not consistently alter species coverages, due to predicted vitamin sharing amongst community members. Taken together, these findings indicate that spatial organisation, microenvironment niche formation and metabolic interactions contribute to community compositional diversity and stability.},
}

*Cyanobacteria/metabolism/genetics/classification/growth & development
*Biodiversity
Metagenomics
Gene Expression Profiling
Oxygen/metabolism

@article {pmid40499635,
year = {2025},
author = {Wen, C and Guan, J and Uea-Anuwong, T and Shang, J and Peng, C and Tang, X and Magouras, I and Sun, Y and Li, F},
title = {Dissecting the gut microbial communities and resistomes of wild rats from different ecological areas in Hong Kong.},
journal = {Environmental research},
volume = {283},
number = {},
pages = {122108},
doi = {10.1016/j.envres.2025.122108},
pmid = {40499635},
issn = {1096-0953},
mesh = {Animals ; Hong Kong ; Rats/microbiology ; *Gastrointestinal Microbiome ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Drug Resistance, Microbial/genetics ; },
abstract = {Antimicrobial resistance (AMR) is one of the top global public health issues shared across all One Health domains. Wild rats, as one of key intersections of the animal and environmental domains, are understudied reservoirs and spreaders for AMR. Our study employed the whole-metagenome shotgun sequencing to characterize the caecal microbiome of wild rats and examine the presence of antimicrobial resistance genes (ARGs) from different ecological areas in Hong Kong. We trapped 88 live rats, belonging to the species of Rattus norvegicus (n=57), R. tanezumi (n=24), and R. andamanensis (n=7), from city regions, livestock farms, and stables of horse-riding schools (referred to as "suburbs"). We identified 9672 ARGs belonging to 29 ARG types and 554 ARG subtypes. Among them, aminoglycosides, macrolide-lincosamide-streptogramin and chloramphenicol, known to be predominant in livestock gut resistome or manure compost were significantly more abundant in rats from livestock farms. Moreover, some ARGs with high-risk levels, including tetM, tetL, floR, mecR1 and lnuA, as well as plasmid-borne ARGs were significantly more abundant in rats from livestock farms than from city regions or suburbs. Furthermore, zoonotic antimicrobial-resistant bacteria (ARB) were detected, including but not limited to, prioritized antimicrobial-resistant Klebsiella pneumoniae, Proteus mirabilis, Escherichia coli, Enterococcus faecium, Acinetobacter baumannii, Campylobacter jejuni, and Staphylococcus aureus. Notably, resistant zoonotic bacteria of Streptococcus suis, Campylobacter coli, and Campylobacter jejuni were more abundant in wild rats from livestock farms. Our findings provides insights into the gut resistomes and zoonotic bacteria in wild rats in Hong Kong, highlighting the potential role of wild rats in the dissemination of ARGs and zoonotic pathogens, especially for those from agricultural settings.},
}

Animals
Hong Kong
Rats/microbiology
*Gastrointestinal Microbiome
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Bacteria/genetics
*Drug Resistance, Microbial/genetics

@article {pmid40459094,
year = {2025},
author = {Dahl, MB and Brachmann, S and Söllinger, A and Schnell, M and Ahlers, L and Wutkowska, M and Hoff, KJ and Nath, N and Groß, V and Wang, H and Weil, M and Piecha, M and Schaffer, M and Jensen, C and Kuss, AW and Gall, C and Wimmer, E and Pribasnig, T and Tveit, AT and Sigurdsson, BD and Schleper, C and Richter, A and Urich, T},
title = {Quantifying Soil Microbiome Abundance by Metatranscriptomics and Complementary Molecular Techniques-Cross-Validation and Perspectives.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e14130},
pmid = {40459094},
issn = {1755-0998},
support = {21-17322M//The Czech Science Foundation/ ; BO 5559/1-1//Deutsche Forschungsgemeinschaft/ ; INST 292/146-1 FUGB//Deutsche Forschungsgemeinschaft/ ; UR198/7-1//Deutsche Forschungsgemeinschaft/ ; 813114//HORIZON EUROPE European Innovation Council/ ; //Research Council of Norway/ ; },
mesh = {*Soil Microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Gene Expression Profiling/methods ; *Bacteria/genetics/classification ; Transcriptome ; Soil/chemistry ; },
abstract = {Linking meta-omics and biogeochemistry approaches in soils has remained challenging. This study evaluates the use of an internal RNA extraction standard and its potential for making quantitative estimates of a given microbial community size (biomass) in soil metatranscriptomics. We evaluate commonly used laboratory protocols for RNA processing, metatranscriptomic sequencing and quantitative reverse transcription polymerase chain reaction (qRT-PCR). Metatranscriptomic profiles from soil samples were generated using two library preparation protocols and prepared in triplicates. RNA extracted from pure cultures of Saccharolobus solfataricus was added to the samples as an internal nucleic acid extraction standard (NAEstd). RNA reads originating from NAEstd were identified with a 99.9% accuracy. A remarkable replication consistency between triplicates was seen (average Bray-Curtis dissimilarity 0.03 ± 0.02), in addition to a clear library preparation bias. Nevertheless, the between-sample pattern was not affected by library type. Estimates of 16S rRNA transcript abundance derived from qRT-PCR experiments, NAEstd and a previously published quantification method of metatranscriptomics (hereafter qMeTra) were compared with microbial biomass carbon (MBC) and nitrogen (MBN) extracts. The derived biomass estimates differed by orders of magnitude. While most estimates were significantly correlated with each other, no correlation was observed between NAEstd and MBC extracts. We discuss how simultaneous changes in community size and the soils nucleic acid retention strength might hamper accurate biomass estimation. Adding NAEstd has the potential to shed important light on nucleic acid retention in the substance matrix (e.g., soil) during extraction.},
}

*Soil Microbiology
*Microbiota
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Gene Expression Profiling/methods
*Bacteria/genetics/classification
Transcriptome
Soil/chemistry

@article {pmid40243260,
year = {2025},
author = {Bayer, PE and Bennett, A and Nester, G and Corrigan, S and Raes, EJ and Cooper, M and Ayad, ME and McVey, P and Kardailsky, A and Pearce, J and Fraser, MW and Goncalves, P and Burnell, S and Rauschert, S},
title = {A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e14107},
pmid = {40243260},
issn = {1755-0998},
support = {//Minderoo Foundation/ ; },
mesh = {Animals ; *Vertebrates/classification/genetics ; *Aquatic Organisms/classification/genetics ; *DNA Barcoding, Taxonomic/methods ; RNA, Ribosomal, 16S/genetics ; *DNA, Environmental/genetics ; Computational Biology/methods ; Australia ; *Metagenomics/methods ; Biodiversity ; RNA, Ribosomal/genetics ; },
abstract = {Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and a plethora of bioinformatic approaches are used for eDNA-based community composition analysis. Simulation studies and careful evaluation of taxonomic classifiers are essential to establish reliable benchmarks to improve the accuracy and reproducibility of eDNA-based findings. Here we present a comprehensive evaluation of nine taxonomic classifiers exploring three widely used mitochondrial markers (12S rDNA, 16S rDNA and COI) in Australian marine vertebrates. Curated reference databases and exclusion database tests were used to simulate diverse species compositions, including three positive control and two negative control datasets. Using these simulated datasets ranging from 36 to 302 marker genes, we were able to identify between 19% and 89% of marine vertebrate species using mitochondrial markers. We show that MMSeqs2 and Metabuli generally outperform BLAST with 10% and 11% higher F1 scores for 12S and 16S rDNA markers, respectively, and that Naive Bayes Classifiers such as Mothur outperform sequence-based classifiers except MMSeqs2 for COI markers by 11%. Database exclusion tests reveal that MMSeqs2 and BLAST are less susceptible to false positives compared to Kraken2 with default parameters. Based on these findings, we recommend that MMSeqs2 is used for taxonomic classification of marine vertebrates given its ability to improve species-level assignments while reducing the number of false positives. Our work contributes to the establishment of best practices in eDNA-based biodiversity analysis to ultimately increase the reliability of this monitoring tool in the context of marine vertebrate conservation.},
}

Animals
*Vertebrates/classification/genetics
*Aquatic Organisms/classification/genetics
*DNA Barcoding, Taxonomic/methods
RNA, Ribosomal, 16S/genetics
*DNA, Environmental/genetics
Computational Biology/methods
Australia
*Metagenomics/methods
Biodiversity
RNA, Ribosomal/genetics

@article {pmid40081359,
year = {2025},
author = {Ali, MJ},
title = {Metagenomic Profile of the Lacrimal Sac Microbial Communities in Congenital Nasolacrimal Duct Obstruction: The Lacriome Paper 7.},
journal = {Ophthalmic plastic and reconstructive surgery},
volume = {41},
number = {5},
pages = {584-588},
pmid = {40081359},
issn = {1537-2677},
mesh = {Humans ; Prospective Studies ; *Lacrimal Duct Obstruction/congenital/microbiology ; *Metagenomics/methods ; *Nasolacrimal Duct/microbiology ; Male ; Female ; *Bacteria/genetics/isolation & purification ; *Microbiota ; Dacryocystorhinostomy ; *Fungi/genetics/isolation & purification ; Child ; Child, Preschool ; *Metagenome ; Infant ; *Lacrimal Apparatus/microbiology ; },
abstract = {PURPOSE: To study the metagenomics of microbes isolated from the lacrimal sacs of patients with congenital nasolacrimal duct obstruction (CNLDO).

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

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

CONCLUSIONS: This is the first whole metagenome sequencing of the lacrimal sac contents from patients with CNLDO, which showed that the sacs harbored diverse microbial communities of bacteria, fungi, and viruses. Further work is needed to decipher the polymicrobial interactions and their relationship with CNLDO.},
}

Humans
Prospective Studies
*Lacrimal Duct Obstruction/congenital/microbiology
*Metagenomics/methods
*Nasolacrimal Duct/microbiology
Male
Female
*Bacteria/genetics/isolation & purification
*Microbiota
Dacryocystorhinostomy
*Fungi/genetics/isolation & purification
Child
Child, Preschool
*Metagenome
Infant
*Lacrimal Apparatus/microbiology

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

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

CONCLUSIONS: The dataset can be used to address fundamental questions about host-microbiota interactions and will be available to the research community under the EHI data usage conditions.},
}

Animals
*Metagenomics/methods
*Metagenome
*Microbiota/genetics
Earth, Planet
*Vertebrates/genetics/microbiology
Databases, Genetic

@article {pmid40749888,
year = {2025},
author = {Carella, F and Correggia, M and Cordone, A and Iacovino, O and Maresca, F and Villari, G and Roque, A and Vico, G},
title = {Bald disease in a natural population of the purple sea urchin Paracentrotus lividus of the Mediterranean Sea: From spines to tissues.},
journal = {Journal of invertebrate pathology},
volume = {213},
number = {},
pages = {108415},
doi = {10.1016/j.jip.2025.108415},
pmid = {40749888},
issn = {1096-0805},
mesh = {Animals ; *Paracentrotus/microbiology ; Mediterranean Sea ; Microbiota ; },
abstract = {Recently, unusual mortality outbreaks have been reported in the echinoderm populations over broad geographic regions. The present work used different diagnostic approaches to unravel the Bald Sea Urchin Disease (BSUD) causes in a natural population of Paracentrotus lividus from the Gulf of Naples sampled in 2021. Symptomatic individuals displayed the typical signs such as test discoloration and ulceration, loss of spines and pedicellariae and visceral hyperpigmentation. Scanning electron microscopy of diseased individuals (stage 2 and stage 3) revealed a bare exoskeleton with multiplying bacteria penetrating the damaged test, and histopathology revealed inflammatory lesions and phagocytosis only in stages 2 and 3, with Gram negative and positive bacteria at stage 3. Metagenomics revealed an increase in DNA virus and Proteobacteria during disease progression. Microbial community analyses failed to reveal a single putative pathogen associated with symptoms, but microbiome analysis showed higher diversity in asymptomatic individuals compared to the symptomatic. Different Vibrio spp. belonging to the Splendidus clade were also isolated, with V. crassostreae as the most represented in advanced stages of disease. We cannot confirm that the observed microorganisms were associated with tissue damage and their contribution to the disease outcome remains unclear as they could be just opportunistic in the lesions. This preliminary study on a wild population highlights the importance of morphological analysis (histopathology and SEM) coupled with microbiome and metagenome analyses in sea urchin disease investigations. Moreover, we suggest also performing transmission electron microscopy (TEM), experimental challenges and in situ hybridization methods (ISH) to provide morphological evidence of potential infective agents. Future studies should also include histopathology of the test.},
}

Animals
*Paracentrotus/microbiology
Mediterranean Sea
Microbiota

@article {pmid40909338,
year = {2025},
author = {Borgognone, A and Prats, A and Sharma, AA and Martinez-Zalacaín, I and Soriano-Mas, C and Brander, C and Clotet, B and Moltó, J and Mothe, B and Sekaly, RP and Paredes, R and Muñoz-Moreno, JA},
title = {Interactions between gut microbiota, plasma metabolome and brain function in the setting of a HIV cure trial.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1629901},
pmid = {40909338},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Metabolome ; *HIV Infections/drug therapy/complications/microbiology ; Male ; Female ; *Brain/physiopathology/physiology ; Adult ; Biomarkers/blood ; Middle Aged ; Feces/microbiology ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; HIV-1/drug effects ; },
abstract = {BACKGROUND: The intestinal microbiota composition has been linked to neurocognitive impairment in people with HIV (PWH). However, the potential interplay of microbial species and related metabolites, particularly in the context of an HIV cure strategy remains underexplored. The BCN02 trial evaluated the impact of romidepsin (RMD), used as a HIV-1 latency reversing agent and with reported beneficial neurological effects, combined with the MVA.HIVconsv vaccine on virus control during 32-weeks of monitored antiretroviral treatment interruption (MAP) in early-treated HIV-infected individuals. Here, we analyzed longitudinal gut microbiome, plasma metabolome and brain functioning data to identify potential associations and novel putative biomarkers of HIV-associated neurocognitive disorders (HAND).

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

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

CONCLUSIONS: While the direct effect of the intervention on the observed shifts cannot be conclusively determined in this study settings, these findings strengthen the link between gut bacteria, related metabolites, and neurocognitive function in PWH, and provide an analytical framework for future validation studies aimed at discovering predictive biomarkers for neurocognitive impairment in PWH.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Metabolome
*HIV Infections/drug therapy/complications/microbiology
Male
Female
*Brain/physiopathology/physiology
Adult
Biomarkers/blood
Middle Aged
Feces/microbiology
Metagenomics
Bacteria/classification/genetics/isolation & purification
HIV-1/drug effects

@article {pmid40908554,
year = {2025},
author = {Susilowati, A and Christita, M and Larekeng, SH and Lateef, AA and Ren, W and Azeez, AA and Simarmata, R and Khairina, Y and Khumairah, FH and Elfiati, D and Asiegbu, FO},
title = {Forest Type, Bark Wounding, and Tapping: Their Combined Influence on Bacteria Biota of Styrax Paralleloneurus in Natural and Community Forest.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70184},
doi = {10.1111/1758-2229.70184},
pmid = {40908554},
issn = {1758-2229},
support = {353365//Research Council of Finland/ ; 13/UN5.2.3.1/PPM/KP-WCU/2022//Universitas Sumatera Utara/ ; },
mesh = {*Forests ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Plant Bark/microbiology ; Biodiversity ; Indonesia ; Phylogeny ; *Trees/microbiology ; DNA, Bacterial/genetics ; *Biota ; },
abstract = {Styrax paralleloneurus is a resin-producing tree native to Sumatra, Indonesia. This study investigated the effects of tapping, bark wounding and forest type on bacterial biota in the stem of styrax in natural and community forests. Amplicon metagenomic sequencing of the 16S rRNA region was deployed to identify the bacterial communities associated with tapped and untapped trees across various environmental and experimental conditions. The results of the study showed that tapped trees had lower abundance and diversity of Pseudomonas compared to untapped trees, largely due to their increased exposure to external microbe communities and environmental elements. Serratia and Pantoea were more abundant in natural forest than community forest, while Bradyrhizobium lablabi was found abundantly in untapped trees. Additionally, the taxonomic analysis revealed distinct responses of bacterial genera to tapping and forest type, indicating that community forests could play a significant role in promoting biodiversity in forest ecosystems. This finding underscores the importance of community forests in biodiversity conservation. These insights can inform future conservation and management strategies to enhance biodiversity and underscore the need for sustainable forest management practices to maintain forest health and productivity.},
}

*Forests
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Plant Bark/microbiology
Biodiversity
Indonesia
Phylogeny
*Trees/microbiology
DNA, Bacterial/genetics
*Biota

@article {pmid40816430,
year = {2025},
author = {Kong, Z and Wang, H and Man, S and Yan, Q},
title = {Magnetite modulates bacterial cooperation during cathodic nitrogen removal in bioelectrochemical systems under trace dissolved oxygen.},
journal = {Bioresource technology},
volume = {437},
number = {},
pages = {133147},
doi = {10.1016/j.biortech.2025.133147},
pmid = {40816430},
issn = {1873-2976},
mesh = {*Bioelectric Energy Sources/microbiology ; *Denitrification/drug effects ; Electrodes ; *Ferrosoferric Oxide/pharmacology ; Oxygen ; *Water Purification/methods ; Metagenome ; Ammonium Compounds/metabolism ; *Microbiota ; },
abstract = {Nitrate and ammonium co-contamination poses a major challenge for sustainable nitrogen removal, especially under microoxic conditions. This study investigated the effect of magnetite on microbial nitrogen metabolism and nitrite accumulation in biocathodes of bioelectrochemical systems under 0.25 mg/L dissolved oxygen. Magnetite improved total nitrogen removal by 22.8 %, reduced peak nitrite levels by 22.6 %, and lowered residual ammonium by 49.2 %. Magnetite promoted interspecies cooperation, driving modular specialization in nitrite reduction while suppressing dissimilatory nitrate reduction to ammonium. Concurrently, it stimulated ammonia-oxidizing bacteria activity, accelerating ammonium conversion and mitigating nitrite accumulation through enhanced denitrification. A cooperative microbial pattern emerged, with dominant species such as Hanamia sp. and Moheibacter sp. carrying out nitrite reduction, while less abundant species performed single nitrogen metabolic processes. This study highlights the role of magnetite in integrating aerobic and anaerobic nitrogen pathways, offering a sustainable strategy for controlling complex nitrogen pollution.},
}

*Bioelectric Energy Sources/microbiology
*Denitrification/drug effects
Electrodes
*Ferrosoferric Oxide/pharmacology
Oxygen
*Water Purification/methods
Metagenome
Ammonium Compounds/metabolism
*Microbiota

@article {pmid40763378,
year = {2025},
author = {Mollick, SA},
title = {Genetic sex prediction from human gut shotgun metagenomic data: An ethical appraisal.},
journal = {Forensic science international},
volume = {376},
number = {},
pages = {112585},
doi = {10.1016/j.forsciint.2025.112585},
pmid = {40763378},
issn = {1872-6283},
mesh = {Humans ; Male ; Female ; *Metagenomics ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/genetics ; Machine Learning ; *Metagenome ; Sequence Analysis, DNA ; Chromosomes, Human, Y ; High-Throughput Nucleotide Sequencing ; Forensic Genetics ; },
abstract = {Human DNA inadvertently captured during gut shotgun metagenomic sequencing is typically treated as background contamination, yet it can reveal sensitive personal traits, raising ethical and forensic concerns. In this study, fecal metagenomes from 626 individuals were processed using four DNA extraction protocols and both paired and single-end sequencing, to evaluate the extent of identifiable human information. Host-derived reads exhibited uniform chromosomal coverage, enabling the accurate prediction of genetic sex based on the Y-to-X read-depth ratio. A machine learning model trained on this metric achieved over 92 % accuracy with the detection threshold (-β0/β1) = 0.34 across different protocols and sequencing configurations, demonstrating the method's robustness and general applicability. These findings highlight that even low levels of residual human DNA in microbiome datasets are sufficient to infer individual traits, such as sex, which can compromise participant anonymity. Given that such reads are often retained in public repositories, the risk of re-identification persists despite microbiome-focused study designs. This work serves as both a technical demonstration and an ethical imperative. Host-DNA masking should become standard before data sharing; ethics boards and data custodians must recognize the potential for unintentional disclosure; and informed consent procedures must reflect the realities of high-throughput sequencing. While the Y-to-X depth ratio offers a scalable quality control and forensic tool, its application must be balanced with rigorous privacy safeguards to uphold research integrity and participant trust.},
}

Humans
Male
Female
*Metagenomics
Feces/microbiology/chemistry
*Gastrointestinal Microbiome/genetics
Machine Learning
*Metagenome
Sequence Analysis, DNA
Chromosomes, Human, Y
High-Throughput Nucleotide Sequencing
Forensic Genetics

@article {pmid40738886,
year = {2025},
author = {Wang, S and Zhang, Z and Zhao, J and Yang, K and Zhang, W and Wang, Z and Liang, Z and Zhang, Y and Zhang, Y and Liu, J and Zhang, L},
title = {Metaproteomic Insights into Bioenergy Conversion Enzymes of Bathypelagic Microbial Communities in the South China Sea.},
journal = {Journal of proteome research},
volume = {24},
number = {9},
pages = {4780-4791},
doi = {10.1021/acs.jproteome.5c00551},
pmid = {40738886},
issn = {1535-3907},
mesh = {China ; *Proteomics/methods ; *Seawater/microbiology ; *Microbiota ; Energy Metabolism ; Metagenomics ; Metagenome ; Archaea/enzymology/genetics ; Oceans and Seas ; Bacteria/enzymology/genetics ; *Bacterial Proteins/metabolism/genetics ; Carbon Cycle ; },
abstract = {Marine microorganisms inhabiting the bathypelagic zone (1000-4000 m) exhibit distinctive environmental adaptability and serve as a valuable reservoir of bioenzymes. However, a limited understanding of deep-sea microbial community composition and metabolic activities hinders the broad application of their enzymatic potential. In this study, we employed a metaproteomic approach to investigate the protein profiles of microbial communities in the bathypelagic layers of the South China Sea (SCS), and we compared them with the corresponding metagenomic data. Our findings revealed a strong phylum-level correlation between metaproteomic and metagenomic datasets, along with a significant enrichment of proteins associated with inorganic ion metabolism and energy conversion. Deep-sea microbial communities are characterized by unique dominant taxa, such as Propionibacteriales, and exhibit diverse strategies for energy utilization. Notably, we identified several enzymes involved in energy conversion, including RuBisCO and carbon monoxide dehydrogenase in Proteobacteria and ammonia monooxygenase in Thaumarchaeota for carbon fixation. These enzymes catalyze reactions utilizing various inorganic substrates as energy sources. Additionally, the deep-sea environment significantly enhanced the expression of methane monooxygenase in methylotrophs, suggesting that such conditions may promote the development of methane-utilizing cell factories. This study not only deepens our understanding of energy conversion mechanisms in deep-sea microorganisms but also offers valuable enzymatic resources for the development of novel bioenergy technologies.},
}

China
*Proteomics/methods
*Seawater/microbiology
*Microbiota
Energy Metabolism
Metagenomics
Metagenome
Archaea/enzymology/genetics
Oceans and Seas
Bacteria/enzymology/genetics
*Bacterial Proteins/metabolism/genetics
Carbon Cycle

@article {pmid40738384,
year = {2025},
author = {Liang, T and Jiang, T and Liang, Z and Chen, Y and Chen, T and Dong, B and Xie, X and Gu, B and Wu, Q},
title = {Lactiplantibacillus plantarum strain 84-3-derived l-glutamine ameliorates glucose homeostasis via AMPK/PPARγ signaling pathway activation in type 2 diabetes.},
journal = {Metabolism: clinical and experimental},
volume = {172},
number = {},
pages = {156357},
doi = {10.1016/j.metabol.2025.156357},
pmid = {40738384},
issn = {1532-8600},
mesh = {*Glutamine/metabolism/pharmacology ; *Diabetes Mellitus, Type 2/metabolism ; Animals ; Rats ; Homeostasis/drug effects ; Signal Transduction/drug effects ; Humans ; Male ; *AMP-Activated Protein Kinases/metabolism ; Case-Control Studies ; *PPAR gamma/metabolism ; *Lactobacillus plantarum/metabolism ; *Glucose/metabolism ; Gastrointestinal Microbiome ; Probiotics ; Diabetes Mellitus, Experimental/metabolism ; Blood Glucose/metabolism ; Rats, Sprague-Dawley ; Middle Aged ; Adult ; Female ; },
abstract = {BACKGROUND: Gut microbiota and their metabolites play an essential role in type 2 diabetes (T2D). However, contributions of individual bacterial strains and their metabolites to T2D pathogenesis remain poorly understood. We investigated T2D regulation by Lactobacillus in various animal models to understand its therapeutic effects.

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

CONCLUSIONS: These findings revealed a novel therapeutic effect of L. plantarum in alleviating T2D-related glucose homeostasis by increasing circulating l-glutamine, which suggests viable preventive and therapeutic strategies for metabolic disorders.},
}

*Glutamine/metabolism/pharmacology
*Diabetes Mellitus, Type 2/metabolism
Animals
Rats
Homeostasis/drug effects
Signal Transduction/drug effects
Humans
Male
*AMP-Activated Protein Kinases/metabolism
Case-Control Studies
*PPAR gamma/metabolism
*Lactobacillus plantarum/metabolism
*Glucose/metabolism
Gastrointestinal Microbiome
Probiotics
Diabetes Mellitus, Experimental/metabolism
Blood Glucose/metabolism
Rats, Sprague-Dawley
Middle Aged
Adult
Female

@article {pmid40645526,
year = {2025},
author = {Xu, J and Zhang, Y and Wang, X and Xu, W and Chen, S and Pan, L and Gao, J},
title = {A P2X7 receptor antagonist alleviates PTSD-like behaviors in adolescent rats through gut microbiota modulation and hippocampal transcriptomic remodeling.},
journal = {Journal of affective disorders},
volume = {390},
number = {},
pages = {119859},
doi = {10.1016/j.jad.2025.119859},
pmid = {40645526},
issn = {1573-2517},
mesh = {Animals ; *Stress Disorders, Post-Traumatic/drug therapy/microbiology/genetics ; *Gastrointestinal Microbiome/drug effects ; *Hippocampus/drug effects/metabolism ; Rats ; Male ; *Transcriptome/drug effects ; *Purinergic P2X Receptor Antagonists/pharmacology ; Rats, Sprague-Dawley ; Disease Models, Animal ; Behavior, Animal/drug effects ; Receptors, Purinergic P2X7 ; *Rosaniline Dyes/pharmacology ; Dysbiosis/drug therapy ; },
abstract = {Post-traumatic stress disorder (PTSD) is a debilitating psychiatric disorder that frequently manifests during adolescence, a critical neurodevelopmental period. Although the P2X7 receptor is implicated in the pathophysiology of PTSD, its role in adolescent-onset PTSD, particularly concerning gut microbiota dysbiosis and hippocampal transcriptomic alterations, remains unclear. This study investigated the effects of the P2X7 receptor antagonist Brilliant Blue G (BBG) on PTSD-like behaviors, gut microbiota, and hippocampal transcriptomic profiles in adolescent rats subjected to single prolonged stress and electric foot shock (SPS&S). BBG treatment significantly ameliorated SPS&S-induced fear- and anxiety-like behaviors and spatial working memory deficits. Metagenomic analysis revealed that BBG partially reversed SPS&S-induced gut microbiota dysbiosis, significantly enriching key bacterial taxa (e.g., Bacteroidota) and modulating functional pathways related to immunity and metabolism. Hippocampal transcriptomic analysis demonstrated that BBG normalized a majority of SPS&S-induced differentially expressed genes; these corrected genes were significantly enriched in pathways for extracellular matrix organization, neural differentiation, and PI3K-Akt signaling pathway. Integrated multi-omics correlation analyses revealed significant correlations among key microbial abundances, hippocampal gene expression, and behavioral outcomes, supporting a gut-brain axis mechanism underlying the therapeutic effects of BBG. These findings position the P2X7 receptor as a promising therapeutic target for adolescent PTSD and highlight the crucial role of gut microbiota in modulating stress-related neuropathology via the gut-brain axis.},
}

Animals
*Stress Disorders, Post-Traumatic/drug therapy/microbiology/genetics
*Gastrointestinal Microbiome/drug effects
*Hippocampus/drug effects/metabolism
Rats
Male
*Transcriptome/drug effects
*Purinergic P2X Receptor Antagonists/pharmacology
Rats, Sprague-Dawley
Disease Models, Animal
Behavior, Animal/drug effects
Receptors, Purinergic P2X7
*Rosaniline Dyes/pharmacology
Dysbiosis/drug therapy

@article {pmid40908508,
year = {2025},
author = {Boden, L and Bludau, D and Sieber, G and Deep, A and Baikova, D and David, GM and Hadžiomerović, U and Stach, TL and Buchner, D and Boenigk, J},
title = {Varying Responses to Heat Stress and Salinization Between Benthic and Pelagic Riverine Microbial Communities.},
journal = {Environmental microbiology},
volume = {27},
number = {9},
pages = {e70173},
doi = {10.1111/1462-2920.70173},
pmid = {40908508},
issn = {1462-2920},
support = {CRC 1439/1//Deutsche Forschungsgemeinschaft/ ; //Open Access Publication Fund of the University of Duisburg-Essen/ ; },
abstract = {Microbial communities play a crucial role in the functioning of freshwater ecosystems but are continuously threatened by climate change and anthropogenic activities. Elevated temperatures and salinisation are particularly challenging for freshwater habitats, but little is known about how microbial communities respond to the simultaneous exposure to these stressors. Here, we use mesocosm experiments and amplicon sequencing data to investigate the responses of pelagic and benthic microbial communities to temperature and salinity increases, both individually and in combination. Our results highlight the varying responses of freshwater microbial communities, with sediment communities exhibiting greater stability in response to environmental changes compared to water column communities, and salinisation having a more pronounced impact on microeukaryotes compared to prokaryotes. Simultaneous exposure to elevated temperature and salinity reduced the impact of salinisation on prokaryotes, while microeukaryotes were similarly affected by the combined treatments and salinisation alone. These findings emphasise the complexity of microbial responses to single and multiple stressors, underscoring the need to consider both individual and interactive effects when predicting ecosystem responses to environmental changes.},
}

@article {pmid40904108,
year = {2025},
author = {Meaden, S and Westra, ER and Fineran, PC},
title = {Phage defence-system abundances vary across environments and increase with viral density.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {380},
number = {1934},
pages = {20240069},
pmid = {40904108},
issn = {1471-2970},
support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //James Cook Research Fellowship (RSNZ, Te Apārangi)/ ; //Philip Leverhulme/ ; //Bioprotection Aotearoa (Tertiary Education Commission, NZ)/ ; //UK Horizon Funding Guarantee/ ; },
mesh = {*Bacteriophages/physiology ; *Bacteria/virology/immunology ; *Microbiota ; *Metagenome ; *Virome ; },
abstract = {The defence systems bacteria use to protect themselves from their viruses are mechanistically and genetically diverse. Yet the ecological conditions that predict when defences are selected for remain unclear, as substantial variation in defence prevalence has been reported. Experimental work in simple communities suggests ecological factors can determine when specific defence systems are most beneficial, but applying these findings to complex communities has been challenging. Here, we use a comprehensive and environmentally balanced collection of metagenomes to survey the defence landscape across complex microbial communities. We also assess the association between the viral community and the prevalence of defence systems. We identify strong environmental effects in predicting overall defence abundance, with animal-host-associated environments and hot environments harbouring more defences overall. We also find a positive correlation between the density and diversity of viruses in the community and the abundance of defence systems. This study provides insights into the ecological factors that influence the composition and distribution of bacterial defence systems in complex microbial environments and outlines future directions for the study of defence-system ecology.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.},
}

*Bacteriophages/physiology
*Bacteria/virology/immunology
*Microbiota
*Metagenome
*Virome

@article {pmid40856172,
year = {2025},
author = {de-Dios, T and Bonucci, B and Barbieri, R and Kushniarevich, A and D'Atanasio, E and Dittmar, J and Cessford, C and Solnik, A and Robb, JE and Warinner, C and Oras, E and Scheib, CL},
title = {Bone Adhered Sediments as a Source of Target and Environmental DNA and Proteins.},
journal = {Molecular biology and evolution},
volume = {42},
number = {9},
pages = {},
pmid = {40856172},
issn = {1537-1719},
mesh = {Animals ; *Geologic Sediments/chemistry ; Humans ; *Bone and Bones/chemistry ; Rats ; *DNA, Ancient/analysis ; Archaeology ; Metagenomics ; Fossils ; Gastrointestinal Microbiome/genetics ; },
abstract = {In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, however, sediments are not always collected during excavation. In this study, we analyzed an overlooked but abundant resource in archaeological collections - sediments adhered to bone. We performed metagenomics and metaproteomics analysis on sediment from several human skeletal elements, originating from Neolithic to Medieval sites in England. We were able to reconstruct a partial human genome, the genetic profile of which matches that recovered from the original skeletal element. Additionally, aDNA sequences matching the genomes of endogenous gut microbiome bacteria were identified. We also found the presence of genetic sequences corresponding to animals and plants. In particular, we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medieval Rattus rattus. Our results demonstrate that material that is usually ignored or discarded, can be used to reveal information about the individual and the environmental conditions at the time of their death.},
}

Animals
*Geologic Sediments/chemistry
Humans
*Bone and Bones/chemistry
Rats
*DNA, Ancient/analysis
Archaeology
Metagenomics
Fossils
Gastrointestinal Microbiome/genetics

@article {pmid40848630,
year = {2025},
author = {Zhang, L and Zhang, Y and Huang, J and Zhou, R and Wu, C},
title = {Temperature-driven functional microbial interactions in soy sauce fermentation: Effects of Zygosaccharomyces rouxii and Wickerhamiella versatilis on flavor enrichment and biogenic amine reduction.},
journal = {International journal of food microbiology},
volume = {442},
number = {},
pages = {111399},
doi = {10.1016/j.ijfoodmicro.2025.111399},
pmid = {40848630},
issn = {1879-3460},
mesh = {Fermentation ; *Soy Foods/microbiology/analysis ; *Biogenic Amines/metabolism/analysis ; *Zygosaccharomyces/metabolism ; Temperature ; *Flavoring Agents/metabolism ; Food Microbiology ; Taste ; *Microbial Interactions ; Bacteria/metabolism/genetics/classification/isolation & purification ; Microbiota ; Amino Acids/metabolism ; Odorants/analysis ; Saccharomycetales ; },
abstract = {This study elucidates the temperature-dependent interactions between halotolerant yeasts and microbial communities during secondary fortified soy sauce fermentation (SFFSS) and their implications for flavor enhancement and safety. A dual-mode fermentation system compared natural temperature fermentation (NTF) and controlled temperature fermentation (CTF, 30 °C), each with and without co-inoculation of Zygosaccharomyces rouxii and Wickerhamiella versatilis (ZC). Multi-omics analyses integrating amplicon sequencing, metagenomics, and metabolomics revealed that CTF control elevated amino acid nitrogen and aroma compounds, while increasing biogenic amines (BA) by 47.88 %. In both NTF and CTF modes, the ZC pattern significantly reduced lactic acid while enhancing succinic acid, umami/sweet free amino acids, and key aroma compounds (e.g., 4-ethylguaiacol, 5-ethyl-4-hydroxy-2-methyl-3(2H)-furanone), alongside enriching functional bacteria (Staphylococcus, Weissella), stabilizing fungal communities, and suppressing Tetragenococcus and Ligilactobacillus pobuzihii. Mechanistically, ZC pattern promoted tricarboxylic acid cycle flux and amino acid metabolism, synergistically enhancing volatile phenolics, esters, and alcohols, and reduced BA by >87 % via dual modulation of decarboxylase inhibition and oxidase activation. Network analyses linked microbial composition shifts to targeted flavor metabolite synthesis, providing a mechanistic framework for microbial community engineering. These findings highlight yeast-mediated, temperature-driven modulation of microbiota-metabolite networks as a viable strategy for producing high-quality, safe soy sauce with optimized flavor complexity.},
}

Fermentation
*Soy Foods/microbiology/analysis
*Biogenic Amines/metabolism/analysis
*Zygosaccharomyces/metabolism
Temperature
*Flavoring Agents/metabolism
Food Microbiology
Taste
*Microbial Interactions
Bacteria/metabolism/genetics/classification/isolation & purification
Microbiota
Amino Acids/metabolism
Odorants/analysis
Saccharomycetales

@article {pmid40840192,
year = {2025},
author = {Yang, SB and Lu, ZM and Shen, HJ and Fu, JJ and Yang, Y and Zhang, XJ and Chai, LJ and Wang, ST and Zhang, SY and Shen, CH and Shi, JS and Xu, ZH},
title = {Unraveling Qu-aroma variation between inner and outer layers of medium-temperature Daqu: A multi-omics and sensory approach.},
journal = {International journal of food microbiology},
volume = {442},
number = {},
pages = {111392},
doi = {10.1016/j.ijfoodmicro.2025.111392},
pmid = {40840192},
issn = {1879-3460},
mesh = {*Volatile Organic Compounds/analysis/metabolism/chemistry ; Fermentation ; *Odorants/analysis ; Gas Chromatography-Mass Spectrometry ; Microbiota ; Bacteria/metabolism/genetics/classification/isolation & purification ; Humans ; Temperature ; Metagenomics ; Metabolic Networks and Pathways ; Edible Grain/microbiology/chemistry ; Taste ; Multiomics ; },
abstract = {Solid-state fermentation heterogeneity causes microenvironmental differences, shaping diverse microbial communities and metabolite compositions. Here, we aimed to investigate the variations in Qu-aroma between the inner (I-) and outer (O-) layers of medium-temperature Daqu (MT-Daqu) starter, and to analyze the differences in microbial communities as well as the associated metabolic pathways related to Qu-aroma volatile organic compounds (VOCs). Firstly, quantitative descriptive analysis revealed that the I-layer exhibited intensified rancid-roasted notes, whereas the O-layer showed stronger grain and woody notes. Secondly, a total of 225 VOCs were identified from 88 inner and outer layer samples using HS-SPME-GC-MS, among which 43 differential VOCs were confirmed between the layers (VIP > 1, P < 0.05, and Fold change ≥1.5 or ≤0.67). Thin film (TF)-SPME-GC-O/MS revealed 52 and 47 odors with corresponding VOCs in the I- and O-layers, respectively. Subsequently, cross-referencing metagenomic and metabolic databases revealed that 37 aroma-active VOCs were functionally linked to six metabolic modules within the MT-Daqu microbial metabolic network. Finally, integrated metagenomic and amplicon sequencing identified potential functional microorganisms associated with specific metabolic modules. Five genera, including Kroppenstedtia and Thermomyces, were identified as characteristic of the I-layer, while 22 genera, such as Lactobacillus and Saccharomycopsis, were characteristic of the O-layer. Notably, Kroppenstedtia, Thermomyces, Lactobacillus, Saccharomycopsis, and Weissella were ubiquitously associated with all six metabolic modules across both layers of MT-Daqu. This study delivers a perspective for clarifying the spatial heterogeneity of Qu-aroma and its microbial drivers.},
}

*Volatile Organic Compounds/analysis/metabolism/chemistry
Fermentation
*Odorants/analysis
Gas Chromatography-Mass Spectrometry
Microbiota
Bacteria/metabolism/genetics/classification/isolation & purification
Humans
Temperature
Metagenomics
Metabolic Networks and Pathways
Edible Grain/microbiology/chemistry
Taste
Multiomics

@article {pmid40780971,
year = {2025},
author = {Boulanger, N},
title = {Tick and host microbiotas: immunomodulators in tick-borne diseases?.},
journal = {Trends in parasitology},
volume = {41},
number = {9},
pages = {796-805},
doi = {10.1016/j.pt.2025.07.009},
pmid = {40780971},
issn = {1471-5007},
mesh = {Animals ; *Tick-Borne Diseases/microbiology/immunology/prevention & control ; *Microbiota/immunology ; *Ticks/microbiology/immunology ; Humans ; },
abstract = {Vector-borne diseases have a growing impact on human and animal health. Metagenomics has been largely used to characterize the microbiome and has highlighted the key role of the microbiota in modulating the vector competence of insects. Currently, an integrated approach combining vector control, vaccine prevention, and drug treatment is being developed to limit the transmission of insect-borne pathogens. This is more complex for tick-associated diseases, considering the biology of the tick and the possibility of modifications of its microbiota in vector control. Conversely, because the skin is an essential interface in tick-borne diseases, an in-depth study of the precise role of the tick and host microbiota during tick bite and pathogen inoculation opens up new prospects for controlling these diseases.},
}

Animals
*Tick-Borne Diseases/microbiology/immunology/prevention & control
*Microbiota/immunology
*Ticks/microbiology/immunology
Humans

@article {pmid40735808,
year = {2025},
author = {Maffei, VJ and Bertoni, AG and Wood, AC and Rotter, JI and Crago, O and Chen, YI and Petrosino, JF and Hoffman, KL and Goodarzi, MO and Jensen, ET},
title = {Menopause factors and alterations in gut microbiota and insulin homeostasis: A cross-sectional analysis of the microbiome and insulin longitudinal evaluation study (MILES).},
journal = {Diabetes, obesity & metabolism},
volume = {27},
number = {10},
pages = {5444-5454},
doi = {10.1111/dom.16578},
pmid = {40735808},
issn = {1463-1326},
support = {P30-DK063491/DK/NIDDK NIH HHS/United States ; R01-DK109588/DK/NIDDK NIH HHS/United States ; UL1-TR001420/TR/NCATS NIH HHS/United States ; UL1-TR001881/TR/NCATS NIH HHS/United States ; 58-3092-5-001//Agricultural Research Service/ ; P30-DK063491/DK/NIDDK NIH HHS/United States ; R01-DK109588/DK/NIDDK NIH HHS/United States ; UL1-TR001420/TR/NCATS NIH HHS/United States ; UL1-TR001881/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Female ; Middle Aged ; *Gastrointestinal Microbiome/physiology ; Longitudinal Studies ; Cross-Sectional Studies ; *Insulin Resistance/physiology ; *Menopause/physiology/metabolism ; Homeostasis/physiology ; *Insulin/metabolism/blood ; *Dysbiosis/microbiology/metabolism ; Adult ; Feces/microbiology ; Glucose Tolerance Test ; },
abstract = {AIM: To assess the risk for impaired insulin homeostasis as a function of menopause-related factors and gut microbiota dysbiosis in non-diabetic, post-menopausal women.

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

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

CONCLUSIONS: Menopause age and history of HRT are more strongly associated with insulin resistance than gynaecologic surgery before menopause. However, gynaecologic surgery is associated with shifts in gut microbial composition and plasma metabolite levels with a potential to contribute to future diabetes risk.},
}

Humans
Female
Middle Aged
*Gastrointestinal Microbiome/physiology
Longitudinal Studies
Cross-Sectional Studies
*Insulin Resistance/physiology
*Menopause/physiology/metabolism
Homeostasis/physiology
*Insulin/metabolism/blood
*Dysbiosis/microbiology/metabolism
Adult
Feces/microbiology
Glucose Tolerance Test

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

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

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

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

CONCLUSIONS: In healthy humans, diet impacts microbial metabolism and enzymatic activity but not the overall diversity of the gut microbiome. This emphasizes the relevance of dietary components in activating expression of specific bacterial genes and their impact on host metabolism. This trial was registered at clinicaltrials.gov as NCT00622661.},
}

Humans
*Gastrointestinal Microbiome
Male
Cross-Over Studies
Female
Adult
*Glycemic Load
*Diet
Feces/microbiology
*Bacteria/classification/genetics/metabolism
Young Adult
Middle Aged
RNA, Ribosomal, 16S/genetics

@article {pmid40600350,
year = {2025},
author = {Dike, CR and Duan, Q and Ahmed, F and Denson, LA and Haslam, D and Minar, P and Ollberding, NJ and Papachristou, GI and Setchell, KDR and Thompson, T and Vitale, DS and Zhao, X and Abu-El-Haija, M},
title = {Acute pancreatitis gut dysbiosis persists at 1-year follow-up and is associated with clinical outcomes.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {81},
number = {3},
pages = {690-698},
pmid = {40600350},
issn = {1536-4801},
support = {K23DK118190 (MAH)/DK/NIDDK NIH HHS/United States ; R03 DK131156 (MAH)/DK/NIDDK NIH HHS/United States ; P30DK078392/GF/NIH HHS/United States ; //Digestive Diseases Research Core Center in Cincinnati (LAD) and The Helmsley Charitable Trust (LAD, PM)/ ; K23DK118190/DK/NIDDK NIH HHS/United States ; R03 DK131156/DK/NIDDK NIH HHS/United States ; //Digestive Diseases Research Core Center in Cincinnati; The Helmsley Charitable Trust/ ; },
mesh = {Humans ; *Dysbiosis/microbiology/complications ; Male ; *Pancreatitis/microbiology/complications ; Female ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Prospective Studies ; Child ; Adolescent ; Feces/microbiology ; Acute Disease ; Child, Preschool ; Recurrence ; Case-Control Studies ; Young Adult ; },
abstract = {OBJECTIVES: Pediatric acute pancreatitis (AP) is associated with gut dysbiosis. We aimed to determine if dysbiosis persisted during follow-up and whether it is associated with clinical outcomes.

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

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

CONCLUSIONS: Gut dysbiosis persisted following AP in children at 3 and 12 months follow-up compared to HC. Microbiome signatures differed in the ARP cohort and those with multiple GI symptoms.},
}

Humans
*Dysbiosis/microbiology/complications
Male
*Pancreatitis/microbiology/complications
Female
Follow-Up Studies
*Gastrointestinal Microbiome
Prospective Studies
Child
Adolescent
Feces/microbiology
Acute Disease
Child, Preschool
Recurrence
Case-Control Studies
Young Adult

@article {pmid40901999,
year = {2025},
author = {Prabakaran, R and Bromberg, Y},
title = {Deciphering enzymatic potential in metagenomic reads through DNA language models.},
journal = {Nucleic acids research},
volume = {53},
number = {16},
pages = {},
doi = {10.1093/nar/gkaf836},
pmid = {40901999},
issn = {1362-4962},
support = {80NSSC18M0093//NASA Astrobiology Institute/ ; 2310114//National Science Foundation/ ; },
mesh = {*Metagenomics/methods ; Metagenome ; Molecular Sequence Annotation ; *Enzymes/genetics/metabolism ; Microbiota/genetics ; Software ; Sequence Analysis, DNA/methods ; },
abstract = {Microbial communities drive essential global processes, yet much of their functional potential remains unexplored. Metagenomics stands to elucidate this microbial "dark matter" by directly sequencing the microbial community DNA from environmental samples. However, the exploration of metagenomic sequences is mostly limited to establishing their similarity to curated reference sequences. A paradigm shift-language model (LM)-based methods-offers promising avenues for reference-free analysis of metagenomic reads. Here, we introduce two LMs, a pretrained foundation model REMME (Read EMbedder for Metagenomic Exploration), aimed at understanding the DNA context of metagenomic reads, and the fine-tuned REBEAN (Read Embedding-Based Enzyme ANnotator) for predicting the enzymatic potential encoded within the read-corresponding genes. By emphasizing function recognition over gene identification, REBEAN labels gene-encoded molecular functions of previously explored and new (orphan) sequences. Even though it was not trained to do so, REBEAN identifies the gene's function-relevant parts. It thus expands enzymatic annotation of unassembled metagenomic reads. Here, we present novel enzymes discovered using our models, highlighting model impact on our understanding of microbial communities.},
}

*Metagenomics/methods
Metagenome
Molecular Sequence Annotation
*Enzymes/genetics/metabolism
Microbiota/genetics
Software
Sequence Analysis, DNA/methods

@article {pmid40901884,
year = {2025},
author = {Robes, JMD and Liebergesell, TCE and Beals, DG and Yu, X and Brazelton, WJ and Puri, AW},
title = {Inverse stable isotope probing-metabolomics (InverSIP) identifies an iron acquisition system in a methane-oxidizing bacterial community.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {36},
pages = {e2507323122},
doi = {10.1073/pnas.2507323122},
pmid = {40901884},
issn = {1091-6490},
support = {R35 GM147018/GM/NIGMS NIH HHS/United States ; 2339190//National Science Foundation (NSF)/ ; LS-ECIAMEE-00006628//Simons Foundation (SF)/ ; T32 AI055434/AI/NIAID NIH HHS/United States ; },
mesh = {*Methane/metabolism ; *Iron/metabolism ; *Metabolomics/methods ; Oxidation-Reduction ; Isotope Labeling/methods ; *Microbiota ; *Bacteria/metabolism/genetics ; Siderophores/metabolism ; Multigene Family ; },
abstract = {Methane is a potent greenhouse gas and a target for near-term climate change mitigation. In many natural ecosystems, methane is sequestered by microbial communities, yet little is known about how constituents of methane-oxidizing communities interact with each other and their environment. This lack of mechanistic understanding is a common issue for many important microbial communities, but it is difficult to draw links between available sequencing information and the metabolites that govern community interactions. Here, we develop and apply a technique called inverse stable isotope probing-metabolomics (InverSIP) to bridge the gap between metagenomic and metabolomic information and functionally characterize interactions in a complex methane-oxidizing community. Using InverSIP, we link a highly transcribed biosynthetic gene cluster in the community with its secondary metabolite product: methylocystabactin, a triscatecholate siderophore not previously observed in nature. We find that production of methylocystabactin is widespread among methanotrophic alphaproteobacteria and that it can be used by another methanotroph in the community that does not produce this siderophore itself. Functional assays reveal that methylocystabactin supports methanotroph growth and the activity of the methane-oxidizing enzyme soluble methane monooxygenase under conditions where bioavailable iron is limited, establishing an important molecular link between methane-oxidation and the insoluble iron found in many natural environments. These findings contribute to a molecular-level understanding of these environmentally important bacterial communities and establish InverSIP as a broadly applicable genomics-guided strategy for characterizing metabolites in microbial ecosystems.},
}

*Methane/metabolism
*Iron/metabolism
*Metabolomics/methods
Oxidation-Reduction
Isotope Labeling/methods
*Microbiota
*Bacteria/metabolism/genetics
Siderophores/metabolism
Multigene Family

@article {pmid40901853,
year = {2025},
author = {Gómez-Palacio, A and Junca, H and Vivero-Gomez, RJ and Suaza, J and Moreno-Herrera, CX and Cadavid-Restrepo, G and Pieper, DH and Uribe, S},
title = {Metagenomic profiling of the insect-specific virome in non-urban mosquitoes (Culicidae: Culicinae) from Colombia's Northern inter-Andean valleys.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331552},
doi = {10.1371/journal.pone.0331552},
pmid = {40901853},
issn = {1932-6203},
mesh = {Animals ; Colombia ; *Virome/genetics ; *Culicidae/virology ; *Metagenomics/methods ; *Metagenome ; Phylogeny ; *Insect Viruses/genetics/classification ; },
abstract = {Hematophagous mosquitoes are major vectors of diverse pathogens and serve as bioindicators in tropical ecosystems, yet their virome in non-urban Neotropical regions remains poorly characterized. We analyzed the virome of 147 mosquitoes from two natural ecosystems in Colombia using a hybrid viral identification approach, combining high-confidence and less stringent methods. Most high-confidence viral contigs remained unclassified or unknown, as expected for metagenomic surveys in novel ecosystems. However, members for the Magrovirales and Ortervirales, and other six orders were detected at lower abundance. Using a complementary, less stringent approach, we identified 168 viral species from 68 genera and 22 families across four mosquito tribes (Aedini, Culicini, Orthopodomyiini, Sabethini), with dominance of Metaviridae, Retroviridae, Iridoviridae, and Poxviridae, though many sequences could not be taxonomically assigned. Insect-specific viruses predominated, while no medically relevant arboviruses were detected. Both methods consistently identified Trichoplusia ni TED virus, Cladosporium fulvum T-1 virus, Lymphocystis disease viruses, and Oryctes rhinoceros nudivirus among the most abundant and frequently detected taxa across samples. Alpha diversity indices revealed the highest virome diversity in Sabethini, followed by Orthopodmyiini, and substantially lower richness and diversity in Aedini and Culicini. These results provide a baseline for virome characterization in sylvatic mosquitoes from Colombia and highlight the need for further research on the ecological roles of the mosquito virome in pathogen transmission and microbiome evolution.},
}

Animals
Colombia
*Virome/genetics
*Culicidae/virology
*Metagenomics/methods
*Metagenome
Phylogeny
*Insect Viruses/genetics/classification

@article {pmid40901000,
year = {2025},
author = {Huang, F and Li, J and Liu, D and Li, Y and Tang, J},
title = {Neonatal microbiome dysbiosis decoded by mNGS: from mechanistic insights to precision interventions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1642072},
doi = {10.3389/fcimb.2025.1642072},
pmid = {40901000},
issn = {2235-2988},
mesh = {Humans ; Infant, Newborn ; *Dysbiosis/microbiology/diagnosis/therapy ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Infant, Newborn, Diseases/microbiology/diagnosis/therapy ; Precision Medicine/methods ; *Microbiota/genetics ; },
abstract = {The neonatal period is a critical stage for microbial colonization and immune system development, with dynamic changes in the microbiome closely linked to the pathogenesis of various diseases. Traditional microbiological testing methods have low sensitivity and time-consuming limitations compared to metagenomic next-generation sequencing (mNGS), which makes it difficult to meet the diagnostic and therapeutic needs of critically ill neonates. mNGS analyzes the total DNA in a sample without bias, allowing comprehensive identification of bacteria, viruses, fungi, and parasites, and resolution of functional genes, providing new avenues for precision diagnosis and treatment of diseases such as neonatal sepsis, necrotizing enterocolitis, neonatal pneumonia, neonatal meningitis, neonatal jaundice, and other diseases. However, challenges remain, including the need to optimize sample processing workflows and develop portable devices to enhance clinical conversion potential. In this review, we summarize the application, efficacy, and limitations of mNGS in neonatal diseases. This approach paves the way for novel avenues in mechanistic research, early diagnosis, and personalized therapy for these conditions.},
}

Humans
Infant, Newborn
*Dysbiosis/microbiology/diagnosis/therapy
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Infant, Newborn, Diseases/microbiology/diagnosis/therapy
Precision Medicine/methods
*Microbiota/genetics

@article {pmid40899487,
year = {2025},
author = {Gu, T and Zerry, Y and Zhang, B and Tan, J and Taft, DH},
title = {Influence of Resistant Starch-Added Meat Analogs on the Resistome of Fecal Fermentations Using Human Gut Microbiota.},
journal = {Journal of food science},
volume = {90},
number = {9},
pages = {e70430},
doi = {10.1111/1750-3841.70430},
pmid = {40899487},
issn = {1750-3841},
support = {//University of Florida/ ; //U.S. Department of Agriculture/ ; },
mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Fermentation ; *Starch/metabolism ; Bacteria/genetics/classification/isolation & purification/drug effects/metabolism ; *Meat/analysis ; Adult ; Male ; Female ; *Resistant Starch ; Drug Resistance, Bacterial/genetics ; Middle Aged ; Drug Resistance, Microbial ; Meat Substitutes ; },
abstract = {Meat analogs are emerging as a sustainable alternative to meat products, and novel meat analog products could potentially offer additional health benefits. Antimicrobial resistance (AMR) poses a serious threat to global human health. Dietary choices affect the composition of bacteria in the human gut microbiome and can influence the carriage of antimicrobial resistance genes (ARGs). Individuals with lower ARG carriage tend to consume more fiber, suggesting that novel fiber-rich meat analogs may help tackle the growing AMR crisis. We therefore hypothesized that adding resistant starch to meat analogs would reduce the number and abundance of ARGs in human gut microbial communities and tested this using in vitro fecal fermentation. Fecal samples were collected from three human donors. Meat analogs formulated from raw ingredients (pea, soy, and resistant starch)-including 100% pea, 90% pea and 10% resistant starch, 100% soy, and 90% soy and 10% resistant starch-served as the carbohydrate source for fecal fermentations. Whole metagenomic sequencing was performed on DNA from the fermentations. ANOVA showed significant differences in normalized ARG abundance by carbohydrate source (p = 0.021), though not in total ARG counts. Meat analogs with resistant starch resulted in a lower median normalized abundance of drug-resistant ARGs than meat analogs without resistant starch, but post-hoc testing could not determine which groups differed from each other due to limited sample size. Adding resistant starch to meat analogs is associated with reduced ARGs in human gut microbial communities, but more research is needed. PRACTICAL APPLICATIONS: Lowering the prevalence of antimicrobial resistance genes (ARGs) is an important public health goal, and emerging work suggests that diet may contribute to controlling the spread of ARGs. One association with diet and the resistome is a lower carriage of ARGs in individuals who consume more dietary fiber. This research therefore sought to pilot if adding resistant starch to meat analogs has the potential to reduce resistance gene carriage. The results found that adding resistant starch to plant-based meat products may help lower the abundance of antimicrobial resistance genes in the human gut microbiome. This provides the justification for larger scale studies and suggests that food manufacturers may be able to develop foods, including healthier meat alternatives, to assist in preserving the function of antibiotics for future generations.},
}

Humans
*Feces/microbiology
*Gastrointestinal Microbiome
Fermentation
*Starch/metabolism
Bacteria/genetics/classification/isolation & purification/drug effects/metabolism
*Meat/analysis
Adult
Male
Female
*Resistant Starch
Drug Resistance, Bacterial/genetics
Middle Aged
Drug Resistance, Microbial
Meat Substitutes

@article {pmid40895054,
year = {2025},
author = {Cárdenas-Hernández, V and Lemos-Lucumi, C and Toro-Perea, N},
title = {Uncovering tissue-specific endophytic microbiota composition and activity in Rhizophora mangle L.: a metagenomic and metatranscriptomic approach.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19728},
pmid = {40895054},
issn = {2167-8359},
mesh = {*Endophytes/genetics ; *Rhizophoraceae/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Plant Roots/microbiology ; Plant Leaves/microbiology ; Transcriptome ; Bacteria/genetics/classification ; Metagenome ; },
abstract = {The interaction of mangrove trees with endophytic microorganisms contributes to the successful establishment of these plants in the challenging intertidal environment. The red mangrove, Rhizophora mangle L. (Rhizophoraceae), is one of the dominant species in mangrove ecosystems and is characterized by the provision of several ecologically relevant services. In this work, we integrated metagenomics and metatranscriptomics to perform a robust characterization of the community of endophytic microorganisms associated with R. mangle leaf and root tissues. The microbiota were characterized at taxonomic and functional levels, and abundance and gene expression profiles were compared between these two plant tissues. We found that the endophyte community consisted mainly of bacteria and eukaryotes, which were the most active groups at the transcriptional level, while archaea and viral groups were identified in lower abundance and expression. In addition, the results show that the community of endophytic microorganisms changes depending on the tissue type, with root-associated microorganisms being the most abundant at the metagenome level and active at the metatranscriptome level. It was also found that R. mangle endophytes actively contribute to key functions for adaptation to an intertidal ecosystem with high human intervention, such as salinity tolerance and degradation of heavy metals and xenobiotic compounds. Thus, according to the functions found and contributed by the endophyte community of red mangrove leaf and root tissues, it can be concluded that these microbial communities are crucial for the survival of R. mangle in the extreme environment of mangrove forests. This study provides a solid basis for future research aimed at understanding the role of plant-endophyte interactions.},
}

*Endophytes/genetics
*Rhizophoraceae/microbiology
*Metagenomics/methods
*Microbiota/genetics
Plant Roots/microbiology
Plant Leaves/microbiology
Transcriptome
Bacteria/genetics/classification
Metagenome

@article {pmid40825855,
year = {2025},
author = {Gopaulchan, D and Moore, C and Ali, N and Sukha, D and Florez González, SL and Herrera Rocha, FE and Yang, N and Lim, M and Dew, TP and González Barrios, AF and Umaharan, P and Salt, DE and Castrillo, G},
title = {A defined microbial community reproduces attributes of fine flavour chocolate fermentation.},
journal = {Nature microbiology},
volume = {10},
number = {9},
pages = {2130-2152},
pmid = {40825855},
issn = {2058-5276},
support = {133788//Innovate UK/ ; },
mesh = {*Chocolate/microbiology/analysis ; *Fermentation ; *Cacao/microbiology/metabolism ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Microbiota ; Fungi/metabolism/genetics/classification/isolation & purification ; Colombia ; Hydrogen-Ion Concentration ; *Flavoring Agents/metabolism ; *Microbial Consortia ; Metagenomics ; Temperature ; Taste ; Food Microbiology ; },
abstract = {Cocoa (Theobroma cacao L.) bean fermentation is a spontaneous process involving interactions between abiotic and biotic factors that contribute to the final flavours of chocolate. Understanding these underlying interactions could enable desired flavour profiles to be reproduced under controlled conditions. Here, using bean fermentation samples from Colombian farms, we established that pH, temperature and microbiota composition, including both bacteria and fungi, influence key flavour attributes of premium chocolate. Genome-resolved metagenomics revealed that metabolic traits necessary for the development of the flavour profile of chocolate are redundantly present in the fermentation microbial community. Using a defined and metabolically competent microbial consortium, the feasibility of replicating fine flavour attributes of chocolate under controlled conditions was confirmed via omics, metabolic networks and a trained tasting panel. Our results provide the basis for the design of fermentation starters to robustly reproduce fine chocolate characteristics.},
}

*Chocolate/microbiology/analysis
*Fermentation
*Cacao/microbiology/metabolism
*Bacteria/metabolism/genetics/classification/isolation & purification
*Microbiota
Fungi/metabolism/genetics/classification/isolation & purification
Colombia
Hydrogen-Ion Concentration
*Flavoring Agents/metabolism
*Microbial Consortia
Metagenomics
Temperature
Taste
Food Microbiology

@article {pmid40787979,
year = {2025},
author = {Liu, Y and Zhao, X and Feng, X and Zhu, W and Feng, S and Ren, M and Tu, Y and Niu, G and Zhu, Y},
title = {Diversity and evolutionary analysis of viruses carried by mosquitoes in Shandong, China.},
journal = {Microbiology spectrum},
volume = {13},
number = {9},
pages = {e0101825},
pmid = {40787979},
issn = {2165-0497},
support = {KY202422//the Suqian Science and Technology Program/ ; },
mesh = {Animals ; China ; Phylogeny ; *Culicidae/virology/classification ; *Mosquito Vectors/virology ; *Arboviruses/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing ; Virome ; *Viruses/classification/genetics/isolation & purification ; Genetic Variation ; Biodiversity ; Evolution, Molecular ; Genome, Viral ; },
abstract = {UNLABELLED: Arboviruses represent a growing threat to global public health, as climate change is exacerbating the spread of these vectors and thereby increasing the transmission potential of arboviruses. As primary vectors, mosquitoes harbor remarkably diverse virus populations, broadly classified into mosquito-borne viruses and mosquito-specific viruses. Although metagenomic sequencing has revolutionized viral discovery, geographical variations in mosquito viromes remain poorly characterized. In this study, we conducted comprehensive viral surveillance on 5,051 mosquitoes representing six medically important species (grouped into 14 taxonomic units) collected from Shandong, China, in 2021. Using next-generation sequencing, we generated 3.7 billion clean reads and identified 10 distinct virus species spanning eight virus families. Phylogenetic analyses revealed substantial genomic diversity and complex evolutionary relationships, including two completely novel virus species and several incompletely characterized known viruses. Notably, Culex quinquefasciatus mosquitoes exhibited significantly greater viral diversity than other species, although we observed considerable overlap in viral communities across mosquito taxa, suggesting non-host-specific viral maintenance. The presence of two novel viruses in field populations was confirmed by RT-qPCR screening, wherein minimum infection rates of 0.16% and 0.38% were established. Our findings substantially expand the known diversity of mosquito-associated viruses in East Asia and provide critical baseline data for arbovirus surveillance programs. This work highlights the value of systematic virome characterization for predicting emerging arboviral threats and understanding virus-mosquito ecology in changing environments.

IMPORTANCE: Ten viruses, including two novel ones, were found in a study performed on mosquitoes in Shandong, China. It shows viral diversity and coexistence in different species, highlighting host impact on viral communities. The new viruses are prevalent locally, with infection rates of 0.38% and 0.16%. This work advances viral ecology understanding and has public health significance. This study sheds light on the circulation of the identified viruses in Shandong.},
}

Animals
China
Phylogeny
*Culicidae/virology/classification
*Mosquito Vectors/virology
*Arboviruses/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing
Virome
*Viruses/classification/genetics/isolation & purification
Genetic Variation
Biodiversity
Evolution, Molecular
Genome, Viral

@article {pmid40778433,
year = {2025},
author = {Li, W and Pan, S and Qian, J and Xia, Y and Han, G and Liu, J and Wang, Y and Peng, L and Huang, S and Chen, Y and Xie, Y and Xu, J and Zhang, W and Zhou, C},
title = {Comparisons of blood, upper respiratory tract and gut viromes from patients with lung cancer and healthy persons.},
journal = {International journal of cancer},
volume = {157},
number = {9},
pages = {1924-1938},
doi = {10.1002/ijc.70075},
pmid = {40778433},
issn = {1097-0215},
support = {TZKY20230204//Clinical Research Project of Taizhou Clinical Medical College, Nanjing Medical University/ ; TZKY20230305//Key Research Project of Taizhou Clinical Medical College, Nanjing Medical University/ ; 24142202800//Shanghai Science and Technology Innovation Action Plan/ ; 82341106//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Lung Neoplasms/virology/blood ; Male ; Female ; *Virome/genetics ; Middle Aged ; Aged ; Case-Control Studies ; Metagenomics/methods ; *Respiratory System/virology ; Adult ; *Viruses/genetics/classification/isolation & purification ; },
abstract = {Lung cancer is the leading cause of cancer-related mortality globally. Although some studies have proposed a potential association between viral infections and lung cancer pathogenesis, the evidence remains inconclusive. This study characterized the virome in blood, upper respiratory tract, and gut samples from 200 lung cancer patients and 75 healthy controls, with the goal of identifying potential microbial biomarkers for lung cancer, using viral metagenomics. Significant differences in viral diversity and composition were observed between cancer and healthy groups, with lower similarities in blood, respiratory, and gut viromes. Notably, LUSC and LUAD groups showed high similarity, with LUAD exhibiting the most diverse virome. In blood, Anelloviridae dominated in cancer patients, while Retroviridae was more abundant in specific subgroups. The upper respiratory tract virome in cancer patients was enriched with Siphoviridae and Myoviridae, contrasting with Retroviridae in healthy individuals. Gut viromes were dominated by Podoviridae and Virgaviridae in cancer patients, with Virgaviridae showing higher abundance compared to healthy controls. Alpha and beta diversity analyses indicated significant differences in blood and respiratory viromes but not in gut viromes. STAMP and LEfSe analyses identified Anelloviridae and Siphoviridae as potential biomarkers for lung cancer. Additionally, 242 anelloviruses with complete ORF1 were isolated, revealing high genetic diversity. These findings highlight distinct virome profiles in lung cancer patients, offering insights into potential diagnostic and therapeutic targets.},
}

Humans
*Lung Neoplasms/virology/blood
Male
Female
*Virome/genetics
Middle Aged
Aged
Case-Control Studies
Metagenomics/methods
*Respiratory System/virology
Adult
*Viruses/genetics/classification/isolation & purification

@article {pmid40759346,
year = {2025},
author = {Zhao, C and Song, Y and Chen, H and Li, Y and Lei, A and Wu, Q and Zhu, L and He, Q},
title = {Study on the selective regulation of microbial community structure in microbial fuel cells by magnetic field-coupled magnetic carbon dots.},
journal = {Bioresource technology},
volume = {437},
number = {},
pages = {133065},
doi = {10.1016/j.biortech.2025.133065},
pmid = {40759346},
issn = {1873-2976},
mesh = {*Bioelectric Energy Sources/microbiology ; *Carbon/chemistry ; *Magnetic Fields ; RNA, Ribosomal, 16S/genetics ; Electricity ; Bacteria/genetics/metabolism ; *Quantum Dots/chemistry ; *Microbiota ; },
abstract = {Microbial fuel cells (MFCs), as a green energy technology that simultaneously enables electricity generation and wastewater treatment, exhibit performance that is highly dependent on the structural distribution of the microbial community. In this study, we investigated the effect of magnetic field (MF)-coupled magnetic carbon dots (N-CD/Fe3O4) as a selective pressure on the structure of mixed microbial communities in an intermittent pulsating fluidized-bed bioelectrochemical reactor. Under a moderate magnetic field (15 mT), N-CD/Fe3O4 were effectively adsorbed onto microbial cells and subsequently aggregated, significantly enhancing electron transfer within the community. The maximum power density reached 38.43 mW/m[2], which is about 5.07 times that of the blank control group. 16S rRNA and metagenomic analyses showed that the MF (15 mT) group exhibited significant enrichment of typical electroactive bacteria (40.32 %), such as Geobacter, which directly contributed to improved power production performance. In contrast, under a stronger magnetic field (60 mT), the abundance of typical electroactive bacteria (17.94 %) decreased, while atypical electroactive (38 %) and metabolically complementary bacteria that facilitate syntrophic cooperation (42.85 %) showed adjusted abundances, forming a functionally more balanced microbial community with improved adaptability to real wastewater conditions. This study demonstrates that by tuning magnetic field intensity and coupling with magnetic carbon dots, the structure and function of microbial communities can be directionally regulated, providing an effective strategy for developing electroactive inocula with enhanced power generation and wastewater adaptability.},
}

*Bioelectric Energy Sources/microbiology
*Carbon/chemistry
*Magnetic Fields
RNA, Ribosomal, 16S/genetics
Electricity
Bacteria/genetics/metabolism
*Quantum Dots/chemistry
*Microbiota

@article {pmid40748195,
year = {2025},
author = {Bai, S and Wang, Z and Guo, Y and Xu, H and Li, J and Peng, X},
title = {Iron is an important influence of volcanic ash input on the evolution of deep-sea ecosystems.},
journal = {Microbiology spectrum},
volume = {13},
number = {9},
pages = {e0071525},
pmid = {40748195},
issn = {2165-0497},
mesh = {*Volcanic Eruptions/analysis ; *Iron/metabolism/analysis ; *Geologic Sediments/microbiology/chemistry ; *Seawater/microbiology/chemistry ; Bacteria/genetics/classification/metabolism/isolation & purification ; *Ecosystem ; Microbiota ; Metagenomics ; Metagenome ; },
abstract = {UNLABELLED: Volcanoes, originating from deep-seated magmatic activity, serve as crucial conduits connecting Earth's interior and surface. Volcanic eruptions, a primary manifestation of this connection, exert profound influence across Earth's surface systems. Volcanic ash, a significant product of these eruptions, has long been a focal point of Earth science research due to its far-reaching impacts. However, the challenges associated with deep-sea sampling and a relative lack of interdisciplinary collaboration have hindered our understanding of how volcanic ash deposition affects the abyssal environment. Here, leveraging a combined geological and microbiological approach, we investigated sediments within the Kermadec Trench impacted by rhyolitic volcanic ash. Our findings demonstrate that iron availability is the primary driver of microbial community structure in these ash-influenced deep-sea sediments. The mantel test analysis further revealed that four key categories of iron-related functional genes involved in iron acquisition (heme transport, iron transport, and siderophore transport) and iron storage significantly shape the resident microbial communities. Furthermore, metagenomic binning yielded numerous refined metagenome-assembled genomes (MAGs) from these deep-sea sediments, all of which harbored iron-related functional genes. Viral metagenomic analysis suggests that viruses in these sediments do not directly influence abyssal prokaryote-mediated iron cycling through the carriage of iron-related auxiliary genes. Instead, viral lysis of iron-cycling prokaryotes appears to be a key regulatory mechanism. These results provide critical new data and insights into microbial iron cycling in the deep sea under the influence of volcanic ash deposition.

IMPORTANCE: Volcanic eruptions emit vast amounts of ash, which eventually settle in the deep ocean. This study explores how the deposition of volcanic ash influences deep-sea microbial communities, primarily through iron enrichment. Our findings highlight the pivotal role of iron-related genes in shaping these communities, while viruses may play an indirect role in modulating iron cycling. These insights enhance our understanding of how volcanic activity affects deep-sea ecosystems and biogeochemical cycles. By elucidating the intricate link between volcanic ash, iron availability, and microbial dynamics, this research provides a novel perspective on how geological processes drive life in the deep ocean. Ultimately, this knowledge contributes to a deeper understanding of global nutrient cycles.},
}

*Volcanic Eruptions/analysis
*Iron/metabolism/analysis
*Geologic Sediments/microbiology/chemistry
*Seawater/microbiology/chemistry
Bacteria/genetics/classification/metabolism/isolation & purification
*Ecosystem
Microbiota
Metagenomics
Metagenome

@article {pmid40744840,
year = {2025},
author = {Zhan, J and Cheng, B and Guo, K and Tao, X and Cai, X and Li, Z and Tang, Z and Zhan, J and Wu, C},
title = {Absolute quantitative metagenomic analysis reveals unique gut bacteria underlying berberine and metformin's anti-metabolic disorders effects.},
journal = {Microbiology spectrum},
volume = {13},
number = {9},
pages = {e0008425},
pmid = {40744840},
issn = {2165-0497},
mesh = {*Berberine/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Metformin/pharmacology ; Animals ; Mice ; *Metagenomics/methods ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Metabolic Diseases/drug therapy/microbiology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Feces/microbiology ; },
abstract = {This study aimed to evaluate the potential functional bacteria in the efficacy of two drugs in ameliorating diet-induced metabolic disorder model using absolute and relative quantification methods and to evaluate the benefit of absolute quantification compared with relative quantification. The gut microbiota is implicated in the pathogenesis of various chronic diseases, including diet-induced metabolic disorder model. Berberine (BBR) and metformin (MET) are commonly used in the clinical management of metabolic disorder, yet their effects on gut microbiota regulation differ. This study employs both relative and absolute quantitative methods to assess the differential impacts of these drugs on the modulation of gut microbiota in metabolic disorder mice. Both BBR and MET effectively ameliorate the condition of metabolic disorder. While some relative quantitative sequencing results contradicted the absolute sequencing data, the latter was more consistent with the actual microbial community composition. Absolute quantitative sequencing provides a more accurate reflection of the drug's effects. Notably, both absolute and relative quantitative sequencing demonstrated an upregulation of Akkermansia.IMPORTANCEOur study underscores the importance of absolute quantitative analysis in accurately representing the true microbial counts in a sample and evaluating the modulatory effects of drugs on the microbiome, which plays a vital role in the study of the microbiome.},
}

*Berberine/pharmacology
*Gastrointestinal Microbiome/drug effects/genetics
*Metformin/pharmacology
Animals
Mice
*Metagenomics/methods
*Bacteria/genetics/classification/drug effects/isolation & purification
*Metabolic Diseases/drug therapy/microbiology
Male
Mice, Inbred C57BL
Disease Models, Animal
Feces/microbiology

@article {pmid40704918,
year = {2025},
author = {Pan, J and Tian, X and Wu, K and Ji, J and Dong, M and Sun, T and Lv, D and Yao, P and Lv, L and Yao, H},
title = {Gut microbiota-associated non-cholesterol sterol dysregulation modulates immune reconstitution during antiretroviral therapy in people living with HIV.},
journal = {Microbiology spectrum},
volume = {13},
number = {9},
pages = {e0140425},
pmid = {40704918},
issn = {2165-0497},
support = {2024YFC2309900//National Key Research and Development Program of China/ ; 2022R52029//Zhejiang Plan for the Special Support fort Top-notch Talents/ ; 2022ZFJH003//Fundamental Research Funds for the Central Universities/ ; SYS202202//Shandong Provincial Laboratory Project/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *HIV Infections/drug therapy/immunology/microbiology ; Male ; Leukocytes, Mononuclear/immunology ; Adult ; Female ; *Sterols/metabolism ; Middle Aged ; CD4-Positive T-Lymphocytes/immunology ; Dysbiosis/microbiology/immunology ; Phytosterols/metabolism ; },
abstract = {Non-cholesterol sterol metabolism plays a crucial role in immune regulation. However, the non-cholesterol sterol profiles, its association with gut dysbiosis, and its impact on the CD4[+] T cell recovery in people living with HIV (PLWH) are yet to be elucidated. In this study, we recruited 37 PLWH and 50 healthy controls to characterize non-cholesterol sterol profiles and gut microbiota composition using targeted liquid chromatography-mass spectrometry and metagenomic analysis. Correlations between sterol profiles and immune cell subsets were assessed. In vitro peripheral blood mononuclear cell (PBMC) model was used to validate key findings. We identified a distinct dysregulation of non-cholesterol sterol metabolism in PLWH, characterized by elevated levels of cholesterol precursors and metabolites and depleted levels of plant sterols, which were linked to gut dysbiosis. Our study results highlighted Oscillibacter spp. as the key regulator of sterol metabolism. Specifically, plant sterols (e.g., brassicasterol and campesterol) were found to be associated with impaired CD4[+] T cell recovery during antiretroviral therapy (ART). These findings were validated using ex vivo PBMC models, which revealed that brassicasterol stimulates T cell abnormal activation and pro-inflammatory cytokine release, whereas lathosterol dampens immune activation and inflammation. In summary, our study highlights the interplay between gut dysbiosis and sterol dysregulation in PLWH, demonstrating that higher brassicasterol levels impair immune recovery post-ART by promoting CD4[+] T cell hyperactivation. Hence, targeting microbial sterol metabolism-through Oscillibacter spp. enrichment or plant sterol modulation-may offer novel therapeutic strategies to optimize ART outcomes by balancing immune activation and resolution.IMPORTANCEThis study is the first to integrate non-cholesterol sterol profiling with gut microbiota analysis in people living with HIV (PLWH), uncovering a unique sterol dysregulation characterized by elevated cholesterol precursors and depleted plant sterols in this population. We demonstrate that Oscillibacter spp. were associated with these metabolic shifts and that specific sterols differentially affect immune recovery: plant sterols such as brassicasterol impede CD4[+] T cell restoration by promoting hyperactivation, whereas the cholesterol derivative lathosterol mitigates inflammation and supports immune reconstitution. These insights reveal novel microbiome-sterol interactions that can be leveraged to develop targeted microbiome- and sterol-based interventions aimed at enhancing antiretroviral therapy efficacy and long-term immune health in PLWH.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*HIV Infections/drug therapy/immunology/microbiology
Male
Leukocytes, Mononuclear/immunology
Adult
Female
*Sterols/metabolism
Middle Aged
CD4-Positive T-Lymphocytes/immunology
Dysbiosis/microbiology/immunology
Phytosterols/metabolism

@article {pmid40698938,
year = {2025},
author = {Lei, L and Li, X and Xiong, Z and Li, J and Liu, L and Chen, L and Zhong, Q and Jiang, H and Cheng, Z and Xiao, S},
title = {Distinctive structure of endophytic microbial communities in two species of wild and cultivated rice.},
journal = {Microbiology spectrum},
volume = {13},
number = {9},
pages = {e0297824},
pmid = {40698938},
issn = {2165-0497},
support = {202205AR070001-01//Yunnan seed Laboratory/ ; 202205AM340037//Science and technology personnel/ ; 2021YFD1200100//National Key Research and Development Program of China/ ; SKL-KF-202325//Open Research Fund of State Key Laboratory of Bioelectronics/ ; },
mesh = {*Oryza/microbiology/classification/growth & development ; *Endophytes/classification/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota/genetics ; China ; Plant Leaves/microbiology ; Metagenomics ; Phylogeny ; },
abstract = {Endophytic microbial communities play an important role in plant development, nutrient acquisition, and oxidative stress tolerance. Oryza officinalis and Oryza meyeriana are unique wild rice varieties in China with many high-quality resistance genes, rich endophyte diversity, and potential resources for sustainable agriculture. In the present study, the endophytic microbial community structures of O. officinalis, O. meyeriana, and cultivated rice were compared using metagenomic sequencing. Dechloromonas, Salmonella, Klebsiella, and Listeria were the core microbial groups in wild and cultivated rice. The relative abundances of Ligilactobacillus, Escherichia, and Bradyrhizobium in O. meyeriana were higher than those in cultivated rice. The relative abundances of Listeria, Acinetobacter, Escherichia, and Dechloromonas in O. officinalis were also higher. Compared to that of cultivated rice, the microbiota of wild rice had a more complex and stable community network. At the pathway level 2 based on the Kyoto Encyclopedia of Genes and Genomes classification system, the relative abundance of metabolic categories was dominant. Most pathways showed that the O. officinalis relative abundance was higher than those of the other two species. Our study revealed differences in the leaf endophyte community structure and function between wild and cultivated rice in the same habitat, demonstrating the potential of wild rice in recruiting specific microorganisms to improve crop performance and promote safe and sustainable food production.IMPORTANCEUnder the current climate change environment, plant-beneficial endophytes are of great significance for promoting food production. Modern cultivars may have lost many beneficial endophytes compared to their ancestors. However, relatively few studies have been conducted on the community structure and function of modern ancestral crop endophytes. In this study, the composition and function of the microbial communities of two wild rice species were analyzed; the differences between them and cultivated rice were determined; and the patterns of microbial interactions and their core microbiomes were determined. Our findings can aid in the exploration of the beneficial endophytes in wild rice and use them to improve crop stress resistance and sustainability. These results provide relevant insights into the role of endophytes in the mechanism of high-stress resistance in wild rice.},
}

*Oryza/microbiology/classification/growth & development
*Endophytes/classification/genetics/isolation & purification
*Bacteria/classification/genetics/isolation & purification
*Microbiota/genetics
China
Plant Leaves/microbiology
Metagenomics
Phylogeny

@article {pmid40614652,
year = {2025},
author = {Korotetskiy, I and Kuznetsova, T and Shilov, S and Zubenko, N and Ivanova, L and Korotetskaya, N and Izmailov, T},
title = {Metagenomic data insights into chicken microbiome diversity across various regions of Kazakhstan.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105488},
pmid = {40614652},
issn = {1525-3171},
mesh = {Animals ; Kazakhstan ; *Chickens/microbiology ; Metagenomics ; *Gastrointestinal Microbiome ; *Bacteria/isolation & purification/classification/genetics ; *Microbiota ; *Metagenome ; },
abstract = {Understanding the gut microbiome of poultry is essential for ensuring the health, productivity, and safety of poultry products. This study aimed to assess the regional diversity and composition of chicken microbiota in Kazakhstan using high-throughput metagenomic sequencing. Tracheal and cloacal swabs were collected from chickens on private farms in five geographic locations. Pooled DNA and RNA samples were sequenced using the Ion Torrent PGM platform, and taxonomic classification was performed using Kaiju, with subsequent alpha and beta diversity analyses in R. The results revealed considerable differences in the microbial profiles between regions. Notably, Chlamydia was abundant in the Shymkent samples (>48 %) but was nearly absent elsewhere. In contrast, Pseudomonas was disproportionately dominant in Almaty (32.7 %), suggesting possible dysbiosis. This study provides the first metagenomic characterization of poultry microbiota in Kazakhstan. This highlights region-specific microbial risks and underscores the importance of spatial microbiome monitoring in poultry health management. These findings provide a basis for future strategies aimed at preventing disease outbreaks and controlling zoonotic pathogens in poultry.},
}

Animals
Kazakhstan
*Chickens/microbiology
Metagenomics
*Gastrointestinal Microbiome
*Bacteria/isolation & purification/classification/genetics
*Microbiota
*Metagenome

@article {pmid40580838,
year = {2025},
author = {Mirzaei, S and Gorczyca, B and Uyaguari-Diaz, M and Sparling, R and Maksimova, E},
title = {Microbial consortia in full-scale pre-ozonated biologically active filters treating a high-DOC water: Effects of seasonal and operational variations.},
journal = {Water research},
volume = {285},
number = {},
pages = {124065},
doi = {10.1016/j.watres.2025.124065},
pmid = {40580838},
issn = {1879-2448},
mesh = {*Seasons ; *Water Purification/methods/instrumentation ; *Filtration/methods/instrumentation ; *Microbial Consortia ; Bacteria/genetics/metabolism/classification ; RNA, Ribosomal, 16S/genetics ; *Carbon ; Charcoal/chemistry ; },
abstract = {This study investigated the microbial dynamics in full-scale biologically active anthracite/silica sand (BAS) and granular activated carbon (BAC) filters used to treat high-DOC coagulated softened water. By analyzing these filter types across two seasons (winter and summer), we examined the impact of operational conditions-including temperature (1 °C vs. 25 °C), backwashing cycle (72 h vs. two weeks), and empty bed contact time (10 vs. 24 min in BAC and 4 vs. 10 min in BAS)-on organic matter removal, biological activity, and bacterial taxonomy and functionality. The highest DOC (19.1 %) and BDOC (34.8 %) removal rates were observed in BAC during summer and post-backwashing, whereas BAS in both seasons and BAC in the winter showed minimal effects on the organic matter concentration. No direct correlation was found between ATP levels, bacterial 16S rRNA bacterial gene copy numbers, and DOC/BDOC removal in BAC. However, an optimal condition of 13 × 10[-6] ATP per bacterial gene copy number in BAC during summer post-backwashing coincided with the highest DOC and BDOC removal. Bacterial taxa with established associations to DOC degradation accounted for over 60 % of the total bacterial orders identified in both BAS and BAC across seasons. The BAC environment appeared to selectively enrich consortia capable of transforming complex DOC fractions, likely facilitated by its greater surface area, extended EBCT, and less frequent backwashing. These conditions supported the persistence and activity of specific bacterial orders, including Actinomycetales, Myxococcales, Planctomycetales, and Rhizobiales. Subsystem-level metagenomic analysis indicated a significant enrichment of genes associated with metabolic functions linked to enzymes such as decarboxylase, N-methylhydantoinase A, cyclic beta-1,2-glucan synthase, carbon monoxide dehydrogenase, cell division protein FtsH, N-methylhydantoinase B, and UDP-glucose 4-epimerase in BAC samples. This study deepens our understanding of the BAF microbiome's role in natural organic matter removal and its relationship with operational parameters, addressing critical gaps in drinking water biological treatment.},
}

*Seasons
*Water Purification/methods/instrumentation
*Filtration/methods/instrumentation
*Microbial Consortia
Bacteria/genetics/metabolism/classification
RNA, Ribosomal, 16S/genetics
*Carbon
Charcoal/chemistry

@article {pmid40578104,
year = {2025},
author = {Li, X and Wang, H and Abdelrahman, HA and Kelly, AM and Roy, LA and Soto, E and Wang, L},
title = {Resistome and microbiome shifts in catfish rearing water: the influence of temperature and antibiotic treatments.},
journal = {Water research},
volume = {285},
number = {},
pages = {124074},
doi = {10.1016/j.watres.2025.124074},
pmid = {40578104},
issn = {1879-2448},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; Temperature ; *Catfishes/microbiology ; Aquaculture ; Bacteria/genetics ; },
abstract = {The increasing reliance on aquaculture for sustainable protein production highlights the need for responsible antibiotic use to manage bacterial infections, particularly in intensive farming systems. This study investigated the effects of three FDA-approved antibiotics (Aquaflor®, Romet®, Terramycin®) at common fish bacterial disease outbreak temperatures (20 °C, 25 °C, and 30 °C) on the microbiome and resistome of aquaculture water using a catfish model system. Metagenomic analyses evaluated the abundance, diversity, and mobility of antimicrobial resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). The impact of temperature on Aquaflor- and Romet-induced changes in ARG abundance, richness, and resistome composition followed a U-shaped trend, with the least effect observed at 25 °C. Of the three antibiotics tested, Terramycin exerted the most significant influence on the water microbiome and resistome, enriching tetracycline resistance genes and co-selecting for floR, sul, and dfrA genes. Temperature also induced notable shifts in the ARB population, with Mantel tests revealing strong correlations between ARG profiles and changes in the overall bacterial community and ARB populations. While certain ARG classes consistently remained associated with specific host phyla, others shifted, highlighting the potential for horizontal gene transfer (HGT) as a critical mechanism for disseminating resistance genes like tet(C), particularly after antibiotic treatment. This is further supported by the observed reduction in plasmid numbers following treatment, which coincided with increased HGT events. Our findings highlight the pivotal role of temperature in influencing resistome dynamics, emphasizing the importance of accounting for environmental factors when applying antibiotics to effectively mitigate antimicrobial resistance in aquaculture systems.},
}

Animals
*Anti-Bacterial Agents/pharmacology
*Microbiota/drug effects
Temperature
*Catfishes/microbiology
Aquaculture
Bacteria/genetics

@article {pmid40570497,
year = {2025},
author = {Thornton, M and Eder, G and Amman, F and Pantielieieva, A and Vierheilig, J and Bergthaler, A},
title = {Comparative wastewater virome analysis with different enrichment methods.},
journal = {Water research},
volume = {285},
number = {},
pages = {123985},
doi = {10.1016/j.watres.2025.123985},
pmid = {40570497},
issn = {1879-2448},
mesh = {*Wastewater/virology ; *Virome ; Ultrafiltration ; Viruses/isolation & purification ; },
abstract = {Wastewater-based epidemiology (WBE) has proven its value for public health. Physical concentration of virus particles is a crucial step for WBE to permit a sensitive and unbiased characterization of the catchment virome. Here we evaluate five different virion concentration techniques, including polyethylene glycol precipitation (PEG), vacuum-based direct capture (VDC), ultrafiltration (UF), NanoTrap® (NT), and membrane adsorption (MEM) for their suitability to concentrate a wide variety of viral taxa from raw wastewater for PCR detection and sequencing-based metagenomic readouts. We found that to capture a taxonomically diverse virome from wastewater, PEG and VDC outperform all other methods tested in enrichment rates, reproducibility, species detection, and captured nucleotide diversity. We observed that different methods exhibit variable concentration efficiencies across taxonomic groups in a reproducible manner, though we could not identify common physiochemical attributes driving this difference. We conclude that both PEG and VDC are equally capable at detecting and enriching a broad range of viral taxa, boosting the genomic information potential and reducing blind spots relative to other tested methods. These results advance WBE towards capturing the complex wastewater virome and help guide protocol choices for potential future viral threats.},
}

*Wastewater/virology
*Virome
Ultrafiltration
Viruses/isolation & purification

@article {pmid40561629,
year = {2025},
author = {Deng, Z and Xie, Y and Yu, H and Zhang, X and Tan, T and Kuang, W and Han, Z and Li, Y and Wang, H and Zhang, N and Zhang, C},
title = {Harnessing deep-sea cold seep microbiomes for reductive dehalogenation: from culturomics and genomics insights.},
journal = {Water research},
volume = {285},
number = {},
pages = {124072},
doi = {10.1016/j.watres.2025.124072},
pmid = {40561629},
issn = {1879-2448},
mesh = {*Microbiota ; Halogenation ; *Seawater/microbiology ; Genomics ; Biodegradation, Environmental ; Geologic Sediments/microbiology ; },
abstract = {Deep-sea cold seeps harbor a rich and diverse repertoire of reductive dehalogenase-encoding genes (rdhA), yet their potential for reductive dehalogenation remains largely unexplored. In this study, we investigated the microbial debromination of 2,4,6-tribromophenol (TBP) in cold seep sediment microcosms. By optimizing culture conditions with different nutrient sources and substrate concentrations, we established a highly efficient debrominating microbial consortium capable of completely degrading 50 μM TBP within 72 h. Metagenomic analysis revealed Bin3, a novel bacterium affiliated with Peptococcaceae, as a key dehalogenator harboring multiple rdhA genes. Microbial community analysis demonstrated that nutrient availability significantly influenced beta diversity (community composition) but had only a minor effect on alpha diversity. Through degradation kinetics, co-occurrence network analysis, normalized stochasticity ratio analysis, and metagenomic quantification, we found that supplementing lactate along with 0.05 % yeast extract significantly enhanced TBP degradation efficiency and facilitated the targeted enrichment of key dehalogenating microbes (with relative abundance increasing from <1 % to 32 %). Comparative genomic analysis indicated that Bin3 has undergone specific adaptations through expansion of gene families involved in pili formation, cell motility, nutrient acquisition, and diverse metabolic pathways, potentially enhancing its competitiveness in deep-sea cold seep environments. This study advances our understanding of deep-sea dehalogenating microbiomes and their adaptation to extreme environments, providing insights into their ecological significance and potential applications in pollutant bioremediation.},
}

*Microbiota
Halogenation
*Seawater/microbiology
Genomics
Biodegradation, Environmental
Geologic Sediments/microbiology

@article {pmid40544677,
year = {2025},
author = {Bortoluzzi, C and Watson, M and Iuspa, MA and Lumpkins, B and Mathis, G and Jones, M and Hofacre, C},
title = {Precision biotics enhance growth performance in broiler chickens by selectively modifying their intestinal microbiome to better respond to enteric challenges.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105454},
pmid = {40544677},
issn = {1525-3171},
mesh = {Animals ; *Chickens/growth & development/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Poultry Diseases/microbiology/prevention & control/parasitology ; Animal Feed/analysis ; Diet/veterinary ; Clostridium perfringens/physiology ; Dietary Supplements/analysis ; Coccidiosis/veterinary/prevention & control ; Clostridium Infections/veterinary/microbiology/prevention & control ; Eimeria/physiology ; *Enteritis/veterinary/microbiology/prevention & control ; *Polysaccharides/administration & dosage/metabolism ; Fatty Acids, Volatile/metabolism ; Random Allocation ; Male ; Necrosis/veterinary/microbiology ; Cecum/microbiology ; },
abstract = {Precision biotics (PB) are innovative feed additives designed to influence key metabolic pathways in the microbiome, particularly those involved in short-chain fatty acid (SCFA) production. These SCFAs are crucial for the healthy development and functionality of the gastrointestinal tract (GIT) in chickens. Our hypothesis was that adding a glycan-based PB to the diet would steer microbial metabolism towards increased SCFA production in the ceca, thereby reducing the adverse effects of necrotic enteritis (NE) in chickens. These studies evaluated the supplementation of PB on the cecal microbiome and growth performance in broiler chickens exposed to a necrotic enteritis (NE) challenge. Experiment 1: Day-old chicks were assigned to three treatment groups: a control, a challenged control, and a challenged group supplemented with PB. The birds were vaccinated for coccidiosis at day 0 and challenged with Clostridium perfringens. Cecal content was collected from one bird per pen on days 22 and 42 for microbiome analysis. Experiment 2: Day-old chicks were again assigned to three treatments: control, challenged control, and challenged with PB. All birds were vaccinated for coccidiosis and challenged with Eimeria maxima on day 14 and later with C. perfringens. On day 21, birds were euthanized for NE lesion scoring. In Exp. 1, the supplementation of PB significantly improved (P < 0.05) the growth performance of the challenged birds. An increased relative abundance of species related to SCFA production was observed on day 42, including several Faecalibacterium species (P < 0.05). This was paired with an increased relative abundance of both propionate (P<0.05) and butyrate pathways in birds with PB supplementation. In Exp. 2, on day 21, the challenge impaired growth performance, but the supplementation of PB counteracted this effect (P < 0.05). On day 42, the supplementation of PB improved BW by 10 % (P < 0.0001), and the FCR by 8.4 % (P < 0.0001) when compared to the challenged group. The supplementation of PB reduced NE associated mortality (5.5 vs 0.5 %; P = 0.002) and reduced the lesions characteristic of NE (P < 0.0001). Taken together, the microbiome metabolic shift observed with the supplementation of PB explains the improvement in growth performance, resilience to enteric stress and faster recovery of the intestine, which consequently improves welfare and the sustainability of poultry production.},
}

Animals
*Chickens/growth & development/microbiology
*Gastrointestinal Microbiome/drug effects
*Poultry Diseases/microbiology/prevention & control/parasitology
Animal Feed/analysis
Diet/veterinary
Clostridium perfringens/physiology
Dietary Supplements/analysis
Coccidiosis/veterinary/prevention & control
Clostridium Infections/veterinary/microbiology/prevention & control
Eimeria/physiology
*Enteritis/veterinary/microbiology/prevention & control
*Polysaccharides/administration & dosage/metabolism
Fatty Acids, Volatile/metabolism
Random Allocation
Male
Necrosis/veterinary/microbiology
Cecum/microbiology

@article {pmid40482531,
year = {2025},
author = {Yan, R and Manjunatha, V and Thomas, A and Shankar, V and Lumpkins, B and Hoerr, FJ and Greene, A and Jiang, X},
title = {Comparative effects of vegetarian diet and rendered animal by-product on the chicken gut health.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105360},
pmid = {40482531},
issn = {1525-3171},
mesh = {Animals ; *Chickens/physiology/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Animal Feed/analysis ; *Diet/veterinary ; *Diet, Vegetarian/veterinary ; Liver/pathology/drug effects ; Random Allocation ; Male ; Animal Nutritional Physiological Phenomena ; },
abstract = {Rendered animal proteins and fats can provide vital nutrients for poultry at affordable prices. With growing interest in reintroducing rendered animal by-products into poultry diets, this study investigated the effects of replacing a portion of soybean meal and vegetable fat with rendered animal proteins and fats in a standard vegetarian chicken diet. The study focused on the changes in gut and liver histopathology, and gut microbiome composition and functions. Five diet treatments were formulated to be isocaloric and isonitrogenous and balanced for amino acids, including a standard vegetarian control diet and four diets containing rendered animal by-products. A total of 15 pens with 50 chickens each were assigned one of the five diets from hatch to 42 days of age, with three replicate pens per treatment. On days 28 and 42, six birds were randomly selected from two pens per treatment and humanely euthanized by cervical dislocation. Cecal samples were collected for microbial enumeration and DNA extraction, while gut and liver histopathology analyses were conducted on day 42. Enumeration of Clostridium perfringens was performed under anaerobic conditions using selective media and metagenomic sequencing was used to assess taxonomic and functional profiles of the microbiome. Statistical analysis included data transformation, permutational multivariate analysis of variance, and differential abundance testing. No significant differences were observed between the vegetarian control and rendered animal by-product diets in gut or liver histopathology, C. perfringens levels, or microbiome composition, indicating that inclusion of animal by-products did not significantly affect broiler intestinal health or microbial functions over a 42-day period. These findings suggest that partially replacing soybean meal and vegetable fat with rendered animal by-products can be a safe and cost-effective alternative to plant-based ingredients in poultry diets.},
}

Animals
*Chickens/physiology/microbiology
*Gastrointestinal Microbiome/drug effects
*Animal Feed/analysis
*Diet/veterinary
*Diet, Vegetarian/veterinary
Liver/pathology/drug effects
Random Allocation
Male
Animal Nutritional Physiological Phenomena

@article {pmid40482059,
year = {2025},
author = {Rendina, M and Turnbaugh, PJ and Bradley, PH},
title = {Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome.},
journal = {G3 (Bethesda, Md.)},
volume = {15},
number = {9},
pages = {},
doi = {10.1093/g3journal/jkaf131},
pmid = {40482059},
issn = {2160-1836},
support = {R35GM151155/NH/NIH HHS/United States ; R01CA255116/NH/NIH HHS/United States ; R01HL122593/NH/NIH HHS/United States ; },
mesh = {Humans ; *Xenobiotics/metabolism ; *Gastrointestinal Microbiome/genetics ; Animals ; },
abstract = {Xenobiotics, including pharmaceutical drugs, can be metabolized by both host and microbiota, in some cases by homologous enzymes. We conducted a systematic search for all known human proteins with gut microbial homologs. Because gene fusion and fission can obscure homology detection, we built a pipeline to identify not only full-length homologs, but also cases where microbial homologs were split across multiple adjacent genes in the same neighborhood or operon ("split homologs"). We found that human proteins with full-length gut microbial homologs disproportionately participate in xenobiotic metabolism. While this included many different enzyme classes, short-chain and aldo-keto reductases were the most frequently detected, especially in prevalent gut microbes, while cytochrome P450 homologs were largely restricted to lower-prevalence facultative anaerobes. In contrast, human proteins with split homologs tended to play roles in central metabolism, especially of nucleobase-containing compounds. We identify twelve specific drugs that gut microbial split homologs may metabolize; 2 of these, 6-mercaptopurine by xanthine dehydrogenase and 5-fluorouracil by dihydropyrimidine dehydrogenase, have been recently confirmed in mouse models. This work provides a comprehensive map of homology between the human and gut microbial proteomes, indicates which human xenobiotic enzyme classes are most likely to be shared by gut microorganisms, and finally demonstrates that split homology may be an underappreciated explanation for microbial contributions to drug metabolism.},
}

Humans
*Xenobiotics/metabolism
*Gastrointestinal Microbiome/genetics
Animals

@article {pmid40892742,
year = {2025},
author = {Zhu, J and Chen, Y and Han, Y and Li, J},
title = {Mechanism of Huanglian Wendan Decoction in ameliorating non-alcoholic fatty liver disease via modulating gut microbiota-mediated metabolic reprogramming and activating the LKB1/AMPK pathway.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331303},
pmid = {40892742},
issn = {1932-6203},
mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/drug therapy/metabolism/microbiology/pathology ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology/therapeutic use/chemistry ; Rats ; Male ; *AMP-Activated Protein Kinases/metabolism ; Rats, Sprague-Dawley ; Signal Transduction/drug effects ; *Protein Serine-Threonine Kinases/metabolism ; Lipid Metabolism/drug effects ; Liver/metabolism/drug effects/pathology ; AMP-Activated Protein Kinase Kinases ; Disease Models, Animal ; Carnitine O-Palmitoyltransferase/metabolism ; Metabolic Reprogramming ; },
abstract = {BACKGROUND: Huanglian Wendan Decoction (HLWDD), a classical traditional Chinese medicine (TCM) formula, has shown therapeutic promise in treating metabolic disorders. However, its underlying mechanisms against non-alcoholic fatty liver disease (NAFLD) remain unclear.

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

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

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

CONCLUSION: HLWDD exerts its anti-NAFLD effects by enhancing Akkermansia-mediated aspartate metabolism, thereby activating the LKB1/AMPK axis and promoting lipid oxidation via CPT1A and PPARα. This study provides new mechanistic insight into the gut-liver axis in NAFLD and highlights HLWDD as a multi-targeted therapeutic approach for restoring metabolic balance.},
}

Animals
*Non-alcoholic Fatty Liver Disease/drug therapy/metabolism/microbiology/pathology
*Gastrointestinal Microbiome/drug effects
*Drugs, Chinese Herbal/pharmacology/therapeutic use/chemistry
Rats
Male
*AMP-Activated Protein Kinases/metabolism
Rats, Sprague-Dawley
Signal Transduction/drug effects
*Protein Serine-Threonine Kinases/metabolism
Lipid Metabolism/drug effects
Liver/metabolism/drug effects/pathology
AMP-Activated Protein Kinase Kinases
Disease Models, Animal
Carnitine O-Palmitoyltransferase/metabolism
Metabolic Reprogramming

@article {pmid40890888,
year = {2025},
author = {Wang, S and Zhao, Z and Cheng, R and Cui, L and Wang, J and Rubin-Blum, M and Zhang, Y and Liu, B and Chen, X and Baltar, F and Cao, X and Wen, X and Alain, K and Chen, Z and Liao, J and Jiang, L and Shao, Z},
title = {Phylogenetically and metabolically diverse active carbon-fixing microbes reside in mangrove sediments.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {194},
pmid = {40890888},
issn = {2049-2618},
support = {42306127//National Natural Science Foundation of China/ ; 42306127//National Natural Science Foundation of China/ ; 42176134//National Natural Science Foundation of China/ ; 42030412//National Natural Science Foundation of China/ ; 2024002//Scientific Research Foundation of Third Institute of Oceanography/ ; 2019021//Scientific Research Foundation of Third Institute of Oceanography/ ; },
mesh = {*Geologic Sediments/microbiology ; *Carbon Cycle ; Wetlands ; Phylogeny ; China ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Carbon/metabolism ; Metagenomics/methods ; Gammaproteobacteria/metabolism/genetics/classification/isolation & purification ; Microbiota ; },
abstract = {BACKGROUND: Mangroves are hotspots of carbon sequestration in transitional zones between marine and terrestrial ecosystems. Microbially driven dark carbon fixation (DCF) is prominent in sediments, yet our understanding of the DCF process across this continuum remains limited. In this study, we explored DCF activities and associated chemoautotrophs along the sediment depth of different mangrove sites in Fujian Province, China, using radiocarbon labeling and molecular techniques.

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

CONCLUSIONS: Overall, this study provides new insights into the understanding of biological carbon fixation and its ecological functions in mangrove sediments. Video Abstract.},
}

*Geologic Sediments/microbiology
*Carbon Cycle
Wetlands
Phylogeny
China
*Bacteria/classification/metabolism/genetics/isolation & purification
Carbon/metabolism
Metagenomics/methods
Gammaproteobacteria/metabolism/genetics/classification/isolation & purification
Microbiota

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

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

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

CONCLUSION: Our study revealed specific alterations in the gut microbiome and metabolome of Chinese CeD patients through a multi-omics integration strategy. We found that CeD individuals carrying CeD risk genes may possess a unique intestinal flora composition, and this intestinal flora may, to some extent, explain the pathogenesis of CeD beyond the contributions of genes and gluten intake.},
}

Adolescent
Adult
Female
Humans
Male
Middle Aged
Young Adult
Case-Control Studies
*Celiac Disease/ethnology/genetics/metabolism/microbiology
China/ethnology
*Feces/microbiology
Gastrointestinal Microbiome
*Metabolome
*Metabolomics
East Asian People

@article {pmid40719501,
year = {2025},
author = {Keskey, R and Bluiminck, S and Sangwan, N and Meltzer, R and Lam, A and Thewissen, R and Zaborin, A and van Goor, H and Zaborina, O and Alverdy, J},
title = {Dietary impact on the gut resistome: western diet independently increases the prevalence of antibiotic resistance genes within the gut microbiota.},
journal = {Microbiology spectrum},
volume = {13},
number = {9},
pages = {e0276624},
pmid = {40719501},
issn = {2165-0497},
support = {R01GMO62344-22//HHS | NIH | OSC | Common Fund (NIH Common Fund)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *Anti-Bacterial Agents/pharmacology ; *Diet, Western/adverse effects ; Cecum/microbiology ; *Bacteria/genetics/drug effects/isolation & purification ; *Drug Resistance, Bacterial/genetics ; Mice, Inbred C57BL ; Male ; },
abstract = {Approximately half of surgical site infections are caused by pathogens resistant to the antibiotics used for prophylaxis. We recently demonstrated that when mice are fed a western diet (WD) that is high in fat and low in fiber, exposed to antibiotics, and undergo an otherwise recoverable surgery, they develop lethal sepsis associated with dissemination of multi-drug-resistant pathogens. Here, we hypothesized that a WD alone can drive the intestinal microbiome to become populated by antibiotic-resistant bacteria independent of exposure to antibiotics. The cecal microbiota response to antibiotics was determined utilizing Biolog Phenotype Microarrays in the presence of 48 different antibiotics. WD-fed mice had a significant increase in antibiotic resistance within their microbiome compared to mice on a standard low-fat, high-fiber diet (SD) including aminoglycosides, tetracyclines, cephalosporins, fluoroquinolones, and sulfamethoxazole. By metagenomic sequencing, there was an increase in the antibiotic resistance genes (ARGs) within the WD cecal microbiota, including CfxA2, ErmG, TetQ, and LnuC. After just 7 days of WD, the ARGs ErmG and CfxA2 were detectable within the stool. WD independent of antibiotic exposure increases the presence of ARGs within the gut microbiota independent of antibiotic exposure.IMPORTANCEAntibiotic resistance is a major challenge in healthcare and results in significant morbidity and mortality. Currently, half of surgical site infections are caused by pathogens resistant to antibiotics used for prophylaxis. In this study, we demonstrate that a western diet alone has the ability to increase the presence of antibiotic resistance genes within the gut microbiome. By understanding dietary influences on the gut resistome, we may improve our understanding of infections with antibiotic-resistant organisms and one day develop personalized antibiotic regimens based on an individual's gut resistome.},
}

Animals
*Gastrointestinal Microbiome/drug effects/genetics
Mice
*Anti-Bacterial Agents/pharmacology
*Diet, Western/adverse effects
Cecum/microbiology
*Bacteria/genetics/drug effects/isolation & purification
*Drug Resistance, Bacterial/genetics
Mice, Inbred C57BL
Male

@article {pmid40711419,
year = {2025},
author = {Licata, AG and Zoppi, M and Dossena, C and Rossignoli, F and Rizzo, D and Marra, M and Gargari, G and Mantegazza, G and Guglielmetti, S and Bergamaschi, L and Nigro, O and Chiaravalli, S and Massimino, M and De Cecco, L},
title = {QIIME2 enhances multi-amplicon sequencing data analysis: a standardized and validated open-source pipeline for comprehensive 16S rRNA gene profiling.},
journal = {Microbiology spectrum},
volume = {13},
number = {9},
pages = {e0167325},
pmid = {40711419},
issn = {2165-0497},
support = {//Bain Capital Children's Fund Europe/ ; ID NET-2019-12371188//Italian Ministry of Health/Regione Lombardia/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; Feces/microbiology ; Software ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification/isolation & purification ; Child ; Gastrointestinal Microbiome/genetics ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Reproducibility of Results ; *Computational Biology/methods ; },
abstract = {Multi-amplicon sequencing is a cost-effective method for profiling multiple regions of the 16S rRNA gene, offering a more comprehensive view of microbial diversity. However, implementing such pipelines on open-source platforms (e.g., QIIME2) is often hindered by limited documentation and lack of validation against established tools. This lack of standardization poses challenges for researchers, particularly in clinical and experimental settings. This study aims to: (i) develop and benchmark a standardized, open-source QIIME2- and R-based pipeline for 16S rRNA gene profiling using semiconductor-based sequencing, comparing it with a commercial, closed-source software; and (ii) validate its effectiveness in a pediatric cancer cohort to examine parental influence on the microbiome and child-caregiver microbial relationships. We generated 16S rRNA profiles from 5 mock communities and 12 child-caregiver fecal sample pairs. Benchmarking against commercial software showed that the multi-region (V2-9) approach produced microbial profiles nearly identical to proprietary outputs, with higher sequencing depth and improved taxonomic resolution compared to single-region analyses. Both approaches demonstrated similar microbial richness, accurate mock community reconstruction, and high reproducibility (R = 0.99, P < 0.0001). These findings were further validated using fecal samples. Application of the pipeline to pediatric samples revealed distinct, differentially abundant Bifidobacterium bifidum and Bifidobacterium adolescentis variants in children whose microbiota closely resembled that of their caregivers. Overall, this study presents a validated, open-source QIIME2 and R pipeline for multi-amplicon sequencing, providing a standardized and reproducible framework for 16S rRNA gene profiling in clinical and research contexts.IMPORTANCEMulti-amplicon sequencing comprehensively characterizes microbial communities by targeting multiple regions of the 16S rRNA gene. However, analytical workflows and reference databases provided by commercial library preparation kits frequently rely on proprietary primers and closed-source pipelines, which can limit transparency, reproducibility, and adaptability. To address these limitations, we developed and validated an open-source bioinformatics pipeline utilizing QIIME2 and R. Our pipeline integrates data from all targeted 16S regions, generating microbial profiles comparable to those produced by proprietary software. Validation was performed using mock samples and fecal samples collected from pediatric cancer patients and their caregivers, confirming the pipeline's reliability and broad applicability. Furthermore, our pipeline enables detailed analysis of microbial variants, surpassing traditional genus-level restrictions and fully leveraging the enhanced coverage offered by multi-amplicon sequencing. Our findings highlight the necessity of adopting open-source solutions to ensure scientific reproducibility and adaptability to emerging methodologies.},
}

*RNA, Ribosomal, 16S/genetics
Humans
Feces/microbiology
Software
*High-Throughput Nucleotide Sequencing/methods
*Bacteria/genetics/classification/isolation & purification
Child
Gastrointestinal Microbiome/genetics
Microbiota/genetics
Sequence Analysis, DNA/methods
Reproducibility of Results
*Computational Biology/methods

@article {pmid40377870,
year = {2025},
author = {Amen, RA and Hassan, YM and Essmat, RA and Ahmed, RH and Azab, MM and Shehata, NR and Elgazzar, MM and El-Sayed, WM},
title = {Harnessing the Microbiome: CRISPR-Based Gene Editing and Antimicrobial Peptides in Combating Antibiotic Resistance and Cancer.},
journal = {Probiotics and antimicrobial proteins},
volume = {17},
number = {4},
pages = {1938-1968},
pmid = {40377870},
issn = {1867-1314},
mesh = {Humans ; *Gene Editing/methods ; *Neoplasms/microbiology/therapy/drug therapy ; *Microbiota ; *Antimicrobial Peptides/pharmacology ; CRISPR-Cas Systems ; Animals ; *Drug Resistance, Microbial ; Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {The growing crisis of antibiotic resistance and the increasing incidence of cancer have prompted the exploration of innovative approaches, such as gene editing and antimicrobial peptides (AMPs). The human microbiome is integral to various aspects of health, disease, and therapeutic development, influencing metabolic pathways, immune function, and pathogen resistance. Recent advances in gene editing technologies, particularly CRISPR (clustered regularly interspaced short palindromic repeats), have opened new avenues for leveraging the microbiome to address complex medical challenges, including combating multidrug-resistant pathogens and cancer. The microbiome plays a crucial role in combating antibiotic resistance by modulating microbial communities, influencing pathogen survival and susceptibility to treatments. This review explores the microbiome's dynamic role in metabolic regulation, its contribution to cancer management, and how AMPs help maintain homeostasis and exhibit emerging anticancer properties, supported by both preclinical findings and clinical evidence. Additionally, CRISPR-based microbiome engineering offers potential to enhance host-microbiome interactions, optimizing therapeutic outcomes. The integration of microbiome metagenomics and proteomics has led to the discovery of novel AMPs with targeted anticancer effects. Innovative strategies, such as engineered probiotics and CRISPR-based microbiome engineering, present exciting prospects for next-generation therapies. Despite these advances, the translation of microbiome-based therapies into clinical settings remains challenging due to ethical, regulatory, and ecological hurdles. This review underscores the transformative potential of microbiome-based interventions, emphasizing the role of personalized medicine in maximizing therapeutic efficacy. Furthermore, we also address critical research gaps, limitations, and future directions, including optimizing AMP stability, delivery, and bioavailability, as well as overcoming the regulatory and ethical challenges in clinical translation.},
}

Humans
*Gene Editing/methods
*Neoplasms/microbiology/therapy/drug therapy
*Microbiota
*Antimicrobial Peptides/pharmacology
CRISPR-Cas Systems
Animals
*Drug Resistance, Microbial
Clustered Regularly Interspaced Short Palindromic Repeats

@article {pmid39641861,
year = {2025},
author = {Leung, HKM and Lo, EKK and Chen, C and Zhang, F and Felicianna, and Ismaiah, MJ and El-Nezami, H},
title = {Probiotic Mixture Attenuates Colorectal Tumorigenesis in Murine AOM/DSS Model by Suppressing STAT3, Inducing Apoptotic p53 and Modulating Gut Microbiota.},
journal = {Probiotics and antimicrobial proteins},
volume = {17},
number = {4},
pages = {2227-2243},
pmid = {39641861},
issn = {1867-1314},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration & dosage/pharmacology ; *Colorectal Neoplasms/drug therapy/chemically induced/microbiology/metabolism ; Mice ; *Tumor Suppressor Protein p53/metabolism/genetics ; *STAT3 Transcription Factor/metabolism/genetics ; Apoptosis/drug effects ; Dextran Sulfate/adverse effects ; Azoxymethane/adverse effects ; Carcinogenesis/drug effects ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; },
abstract = {Colorectal cancer (CRC) is one of the most common cancers worldwide. The standard CRC chemo drug, 5-Fluorouracil (5-FU), has a poor response rate and chemoresistance, prompting the need for a more effective and affordable treatment. In this study, we aimed to evaluate whether Prohep, a novel probiotic mixture, would alleviate azoxymethane/dextran sodium sulfate (AOM/DSS)-induced colorectal tumorigenesis and enhance 5-FU efficacy and its mechanism. Our results suggested that Prohep showed stronger anti-tumorigenesis effects than 5-FU alone or when combined in the AOM/DSS model. Prohep significantly reduced the total tumor count, total tumor size, caecum weight, colonic crypt depth, colonic inflammation, and collagen fibrosis. Prohep downregulated pro-inflammatory TNF-α and proliferative p-STAT3 and upregulated apoptotic p53. Metagenomics analysis indicated that Prohep-enriched Helicobacter ganmani, Desulfovibrio porci, Helicobacter hepaticus, and Candidatus Borkfalkia ceftriaxoniphila were inversely correlated to the total tumor count. In addition, Prohep-enriched Prevotella sp. PTAC and Desulfovibrio porci were negatively correlated to AOM/DSS enriched bacteria, while forming a co-existing community with other beneficial bacteria. From KEGG analysis, Prohep downregulated CRC-related pathways and enhanced pathways related to metabolites suppressing CRC like menaquinone, tetrapyrrole, aminolevulinic acid, and tetrahydrofolate. From Metacyc analysis, Prohep downregulated CRC-related peptidoglycan, LPS, and uric acid biosynthesis, and conversion. Prohep elevated the biosynthesis of the beneficial L-lysine, lipoic acid, pyrimidine, and palmitate. Prohep also elevated metabolic pathways related to energy utilization of lactic acid-producing bacteria (LAB) and acetate producers. Similarly, fecal acetate concentration was upregulated by Prohep. To sum up, Prohep demonstrated exceptional anti-tumorigenesis effects in the AOM/DSS model, which revealed its potential to develop into a novel CRC therapeutic in the future.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Probiotics/administration & dosage/pharmacology
*Colorectal Neoplasms/drug therapy/chemically induced/microbiology/metabolism
Mice
*Tumor Suppressor Protein p53/metabolism/genetics
*STAT3 Transcription Factor/metabolism/genetics
Apoptosis/drug effects
Dextran Sulfate/adverse effects
Azoxymethane/adverse effects
Carcinogenesis/drug effects
Male
Mice, Inbred C57BL
Disease Models, Animal

@article {pmid40890565,
year = {2025},
author = {Ivanich, K and Yackzan, A and Flemister, A and Chang, YH and Xing, X and Chen, A and Yanckello, LM and Sun, M and Aware, C and Govindarajan, M and Kramer, S and Ericsson, A and Lin, AL},
title = {Ketogenic Diet Modulates Gut Microbiota-Brain Metabolite Axis in a Sex- and Genotype-Specific Manner in APOE4 Mice.},
journal = {Journal of neurochemistry},
volume = {169},
number = {9},
pages = {e70216},
doi = {10.1111/jnc.70216},
pmid = {40890565},
issn = {1471-4159},
support = {RF1AG062480/AG/NIA NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Diet, Ketogenic/methods ; Female ; *Apolipoprotein E4/genetics ; Mice ; Male ; *Brain/metabolism ; *Sex Characteristics ; Genotype ; Mice, Inbred C57BL ; Apolipoprotein E3/genetics ; Mice, Transgenic ; },
abstract = {The apolipoprotein E4 (APOE4) allele is the strongest genetic risk factor for late-onset Alzheimer's disease (AD), associated with early brain metabolic dysfunction and gut microbiome alterations. Targeting these early changes through dietary interventions may reduce AD risk in asymptomatic carriers. This study evaluated whether a ketogenic diet (KD) could reshape the gut microbiome and enhance key brain metabolite levels in young APOE4 mice, using APOE3 mice as a neutral-risk comparison. Male and female APOE3 and APOE4 mice were fed either a control diet or KD for 16 weeks, starting at 12 weeks of age. We used shotgun metagenomics and targeted brain metabolomics to identify microbe-metabolite signatures linked to neuroprotection. KD increased beneficial species such as Lactobacillus johnsonii and Lactobacillus reuteri while reducing pathogenic Bacteroides intestinalis. These microbial shifts correlated with improved brain metabolites related to mitochondrial function, neurotransmitter balance, redox homeostasis, and lipid metabolism. Notably, Lactobacillus species and B. intestinalis exhibited inverse correlations with key brain metabolite levels, suggesting their roles as both modulators and biomarkers of brain health. APOE4 females showed the greatest benefits, including restored microbiome diversity and normalization of brain metabolite levels. In contrast, APOE3 mice showed microbiome changes but limited brain metabolic responses. These findings highlight KD's potential to reprogram the gut-brain axis in a genotype- and sex-dependent manner, supporting its use as a precision nutrition strategy to reduce AD risk, particularly in asymptomatic female APOE4 carriers.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Diet, Ketogenic/methods
Female
*Apolipoprotein E4/genetics
Mice
Male
*Brain/metabolism
*Sex Characteristics
Genotype
Mice, Inbred C57BL
Apolipoprotein E3/genetics
Mice, Transgenic

@article {pmid40890119,
year = {2025},
author = {Yuan, B and Wang, S},
title = {Microbiome data integration via shared dictionary learning.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8147},
pmid = {40890119},
issn = {2041-1723},
support = {DBI-2243257//National Science Foundation (NSF)/ ; DMS-2515171//National Science Foundation (NSF)/ ; DBI-2243257//National Science Foundation (NSF)/ ; DMS-2515171//National Science Foundation (NSF)/ ; },
mesh = {Humans ; *Microbiota/genetics ; Metagenomics/methods ; Colorectal Neoplasms/microbiology/therapy ; Machine Learning ; Immunotherapy ; Gastrointestinal Microbiome ; Computational Biology/methods ; },
abstract = {Data integration is a powerful tool for facilitating a comprehensive and generalizable understanding of microbial communities and their association with outcomes of interest. However, integrating data sets from different studies remains a challenging problem because of severe batch effects, unobserved confounding variables, and high heterogeneity across data sets. We propose a new data integration method called MetaDICT, which initially estimates the batch effects by weighting methods in causal inference literature and then refines the estimation via novel shared dictionary learning. Compared with existing methods, MetaDICT can better avoid the overcorrection of batch effects and preserve biological variation when there exist unobserved confounding variables, data sets are highly heterogeneous across studies, or the batch is completely confounded with some covariates. Furthermore, MetaDICT can generate comparable embedding at both taxa and sample levels that can be used to unravel the hidden structure of the integrated data and improve the integrative analysis. Applications to synthetic and real microbiome data sets demonstrate the robustness and effectiveness of MetaDICT in integrative analysis. Using MetaDICT, we characterize microbial interaction, identify generalizable microbial signatures, and enhance the accuracy of outcome prediction in two real integrative studies, including an integrative analysis of colorectal cancer metagenomics studies and a meta-analysis of immunotherapy microbiome studies.},
}

Humans
*Microbiota/genetics
Metagenomics/methods
Colorectal Neoplasms/microbiology/therapy
Machine Learning
Immunotherapy
Gastrointestinal Microbiome
Computational Biology/methods

@article {pmid40889848,
year = {2026},
author = {Lin, X and Deng, C and Shu, Y and Li, S and Song, Y and Kong, H and Liang, Z and Liu, L and Rao, Y},
title = {Ecological presence and functional role of bacteriophages in fermented vegetables.},
journal = {Food microbiology},
volume = {133},
number = {},
pages = {104884},
doi = {10.1016/j.fm.2025.104884},
pmid = {40889848},
issn = {1095-9998},
mesh = {*Vegetables/microbiology/virology ; *Bacteriophages/genetics/isolation & purification/physiology/metabolism/classification ; Fermentation ; *Fermented Foods/virology/microbiology ; Microbiota ; *Bacteria/genetics/metabolism/virology/classification/isolation & purification ; Food Microbiology ; },
abstract = {Fermented vegetables are widely favored by consumers for their distinctive flavors and nutritional value, with their quality attributes being closely associated with microbiome dynamics. Recent advances in high-throughput sequencing technologies have revealed abundant bacteriophage resources within the fermented vegetable microbiome. These viral components significantly influence fermentation processes and product characteristics by modulating microbial community structure and function. However, research on optimizing vegetable fermentation processes through bacteriophage-mediated regulation remains in its nascent stage. This study systematically summarizes the compositional characteristics and dynamic patterns of microbial communities in fermented vegetables. We review the latest research progress on bacteriophage diversity and functional properties in fermented vegetables. Furthermore, by integrating multi-omics data, we provide insights into the complex interaction network among bacteriophages, host microbiota, and metabolic products. The results demonstrate that bacteriophages precisely regulate the fermentation process by mediating microbial community succession via lytic-lysogenic cycles and participating in the biosynthesis of key flavor compounds through encoded auxiliary metabolic genes. Finally, we sort out an integrated technical framework combining metagenomics and culturomics. This research provides novel insights into understanding the functional mechanisms of bacteriophages in fermented vegetables, offers a theoretical foundation for developing precision fermentation technologies based on bacteriophage regulation.},
}

*Vegetables/microbiology/virology
*Bacteriophages/genetics/isolation & purification/physiology/metabolism/classification
Fermentation
*Fermented Foods/virology/microbiology
Microbiota
*Bacteria/genetics/metabolism/virology/classification/isolation & purification
Food Microbiology

@article {pmid40889843,
year = {2026},
author = {Ren, F and Liu, M and Tan, B},
title = {Mycobiota of highly-preserved and easily-spoiled soybean pastes-what are their roles?.},
journal = {Food microbiology},
volume = {133},
number = {},
pages = {104876},
doi = {10.1016/j.fm.2025.104876},
pmid = {40889843},
issn = {1095-9998},
mesh = {*Glycine max/microbiology ; *Fungi/classification/genetics/isolation & purification/metabolism ; *Mycobiome ; Food Preservation ; Biodiversity ; },
abstract = {Effective preservation of fermented soybean pastes is critically dependent on their microbial communities. In this study, the fungal assemblages of highly-preserved (HP) and easily-spoiled (ES) soybean paste samples were analyzed and compared mainly with Illumina sequencing of both mycobiota ITS amplicon and metagenomic functional annotation. The results showed that fungal communities of two types soybean pastes were distinct and had different α-diversity and β-diversity characteristics. The phylum Ascomycota was predominant in all samples, with Candida, Aspergillus, and Penicillium being the most abundant genera. The HP group exhibited greater richness and diversity compared to ES samples, and the relative abundance of specific fungal taxa varied significantly between the two groups. Additionally, functional annotation revealed differences in metabolic categories, with HP samples having higher levels of functions related to amino acid transport and metabolism, cell cycle control, and signal transduction mechanisms. These results enhance the understanding of the fungal diversity and functional differences of soybean pastes, providing insights that could improve preservation methods, optimize production and storage processes, and ensure the quality of the products.},
}

*Glycine max/microbiology
*Fungi/classification/genetics/isolation & purification/metabolism
*Mycobiome
Food Preservation
Biodiversity

@article {pmid40888959,
year = {2025},
author = {Rajan, RJ and Sathyanathan, R and Rajnish, KN},
title = {Metabarcoding-Based Seasonal Assessment of Airborne Microbial Communities in PM10 Samples from a Semi-Urban Region in Tamil Nadu, India.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {9},
pages = {1069},
pmid = {40888959},
issn = {1573-2959},
mesh = {India ; *Air Microbiology ; Seasons ; *Environmental Monitoring/methods ; *Microbiota ; *Air Pollutants/analysis ; *Particulate Matter/analysis ; Bacteria/classification/genetics ; DNA Barcoding, Taxonomic ; Air Pollution/statistics & numerical data ; },
abstract = {Airborne microbial communities show marked seasonal variability, with implications for both environmental processes and public health. In this study, metagenomic sequencing was applied to characterize airborne microbiota across four distinct seasons in India-winter (Sw), summer (Ss), southwest monsoon (Ssw), and northeast monsoon (Sne). Distinct shifts in dominant bacterial taxa were observed. Sne was dominated by Pseudomonas (42.3%) alongside sulfur-oxidizing Thiobacillus and Stenotrophomonas, likely influenced by lower temperatures and anthropogenic inputs. In Ss, Thiobacillus (72.9%) prevailed, followed by Pseudomonas (8.06%) and Sphingosinicella (6.68%), reflecting adaptation to arid, UV-intense conditions. Ssw featured Thiobacillus (58%) and Pseudomonas (18.5%) with additional plant-associated Lactobacillus and Clostridium, suggesting enhanced biogenic emissions. Sw was distinct for Enterococcus (21.9%) dominance and reduced Thiobacillus (16.2%), associated with high humidity and precipitation. Species richness followed the order Ssw > Sw > Ss > Sne, with the highest diversity during Ssw and Sw as indicated by Chao1, Fisher, Shannon, and Simpson indices. Kruskal-Wallis tests revealed no statistically significant differences in alpha diversity across seasons. Canonical Correspondence Analysis (CCA) highlighted strong seasonal structuring linked to environmental parameters such as temperature, humidity, and UV exposure. Dendrogram clustering showed greatest dissimilarity between Sne and Sw, while Ss and Ssw formed a closely related group. Ordination analyses (PCA, PCoA, NMDS) further confirmed seasonal distinctions. Seasonal variations in dominant bacterial taxa indicate potential public health risks in semi-urban tropical environments. Thiobacillus, prevalent in summer and the southwest monsoon, is generally non-pathogenic. In contrast, Pseudomonas species, abundant during the northeast monsoon and winter, are metabolically versatile, encompassing environmental strains and opportunistic pathogens known to cause respiratory and wound infections, especially in immunocompromised individuals. Winter also saw the presence of Enterococcus faecalis, a gut commensal and opportunistic pathogen linked to hospital-acquired infections and notable for multi-drug resistance. These seasonal shifts highlight varying exposure risks, emphasizing the need for public health attention to airborne microbial dynamics across different seasons.},
}

India
*Air Microbiology
Seasons
*Environmental Monitoring/methods
*Microbiota
*Air Pollutants/analysis
*Particulate Matter/analysis
Bacteria/classification/genetics
DNA Barcoding, Taxonomic
Air Pollution/statistics & numerical data

@article {pmid40888678,
year = {2025},
author = {Zhou, R and Ng, SK and Sung, JJY and Wong, SH and Goh, WWB},
title = {Detecting and mitigating doppelgänger bias in microbiome data: impacts on machine learning and disease classification.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2554196},
doi = {10.1080/19490976.2025.2554196},
pmid = {40888678},
issn = {1949-0984},
mesh = {Humans ; *Machine Learning ; Clostridium Infections/microbiology ; Colorectal Neoplasms/microbiology ; Inflammatory Bowel Diseases/microbiology ; *Microbiota ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Obesity/microbiology ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Highly similar microbiome samples - so-called "doppelgänger pairs" - can distort analysis outcomes, yet are rarely addressed in microbiome studies. Here, we demonstrate that even a small proportion of such pairs (1-10% of samples) can substantially inflate machine learning performance across diverse disease cohorts including colorectal cancer (CRC), inflammatory bowel diseases (IBD), Clostridioides difficile infection (CDI), and obesity. Doppelgänger pairs also bias statistical tests and distort microbial network topology. In predictive models, classification accuracy was artificially boosted by 15-30% points across KNN, SVM, and Random Forest classifiers. In association testing, doppelgängers increased false-positive rates and decreased effect size stability; their removal reduced bootstrap variance by up to 28.3%. Moreover, the removal of doppelgängers yielded more stable networks. These effects were consistently observed across 16S, shotgun metagenomic, and simulated datasets. By accounting for highly similar samples, we reduce analytical noise and false discoveries, ultimately enabling more accurate and biologically meaningful microbiome insights.},
}

Humans
*Machine Learning
Clostridium Infections/microbiology
Colorectal Neoplasms/microbiology
Inflammatory Bowel Diseases/microbiology
*Microbiota
*Gastrointestinal Microbiome
Metagenomics/methods
Obesity/microbiology
Bacteria/classification/genetics/isolation & purification

@article {pmid40811873,
year = {2025},
author = {Simpson, AM and Chase, AB and Rodríguez-Verdugo, A and Martiny, JB},
title = {Investigating bacterial evolution in nature with metagenomics.},
journal = {Current opinion in microbiology},
volume = {87},
number = {},
pages = {102654},
doi = {10.1016/j.mib.2025.102654},
pmid = {40811873},
issn = {1879-0364},
mesh = {*Metagenomics/methods ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Genetic Variation ; *Evolution, Molecular ; *Biological Evolution ; },
abstract = {Metagenomic sequencing has revolutionized our ability to capture the vast genetic diversity of microbiomes. The technique provides an especially detailed characterization of intraspecific diversity, and a growing number of studies are using that information to investigate bacterial evolution in nature. Here, we review how these studies operationally define evolution, the sampling approaches and metrics used, and the interpretation of the observed evolutionary signatures. Current studies address three main themes: (1) the mechanisms that generate genetic diversity, (2) the spatiotemporal structure of that diversity, and (3) the evolutionary processes that determine its fate. While metagenomics provides enormous potential to investigate in situ evolution, the approach also introduces new questions, including whether populations defined by read mapping are meaningful proxies for biological units of evolution. Addressing these questions will facilitate investigation of the role of evolution relative to ecological shifts in shaping a microbiome's response to environmental change.},
}

*Metagenomics/methods
*Bacteria/genetics/classification
*Microbiota/genetics
Genetic Variation
*Evolution, Molecular
*Biological Evolution

@article {pmid40789383,
year = {2025},
author = {Rout, AK and Rout, SS and Panda, A and Tripathy, PS and Kumar, N and Parida, SN and Dey, S and Dash, SS and Behera, BK and Pandey, PK},
title = {Potential applications and future prospects of metagenomics in aquatic ecosystems.},
journal = {Gene},
volume = {967},
number = {},
pages = {149720},
doi = {10.1016/j.gene.2025.149720},
pmid = {40789383},
issn = {1879-0038},
mesh = {*Metagenomics/methods ; *Ecosystem ; Microbiota/genetics ; *Water Microbiology ; Environmental Monitoring/methods ; Computational Biology/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; },
abstract = {Metagenomics plays a vital role in advancing our understanding of microbial communities and their functional contributions in various ecosystems. By directly sequencing DNA from environmental samples such as soil, water, air, and the human body. Metagenomics enables the identification of previously uncultivable or unknown microorganisms, offering key insights into their ecological functions. Beyond taxonomic classification, metagenomic analyses reveal functional genes and metabolic pathways, facilitating the discovery of enzymes, bioactive compounds, and other molecules with applications in agriculture, biotechnology, and medicine. This review discusses the broad applications of metagenomics in environmental monitoring, encompassing sample collection, high-throughput sequencing, data analysis and interpretation. We review different sequencing platforms, library preparation methods, and advanced bioinformatics tools used for quality control, sequence assembly, and both taxonomic and functional annotation. Special focus is given to the role of metagenomics in evaluating microbial responses to environmental stress, contaminant degradation, disease emergence, and climate change. The use of microbial bioindicators for aquatic ecosystem monitoring and toxicological assessments is also examined. A comprehensive evaluation of current bioinformatics pipelines is provided for their effectiveness in processing large-scale metagenomic datasets. As global environmental pressures intensify, integrative meta-omics approaches, including whole-genome metagenomics, will become crucial for understanding the complexity, functions, and dynamics of microbiomes in both natural and affected ecosystems.},
}

*Metagenomics/methods
*Ecosystem
Microbiota/genetics
*Water Microbiology
Environmental Monitoring/methods
Computational Biology/methods
Humans
High-Throughput Nucleotide Sequencing/methods
Metagenome

@article {pmid40749752,
year = {2025},
author = {Von Tönnemann Pilati, G and da Silva Grisard, HB and Dorighello, RC and Filho, VB and Dahmer, M and Savi, BP and Elois, MA and Salles, GBC and Muniz, EC and Fongaro, G},
title = {Protocol for virome characterization in low-volume respiratory samples from broiler chickens.},
journal = {Journal of virological methods},
volume = {338},
number = {},
pages = {115233},
doi = {10.1016/j.jviromet.2025.115233},
pmid = {40749752},
issn = {1879-0984},
mesh = {Animals ; *Chickens/virology ; *Virome ; *Metagenomics/methods ; Brazil ; *Poultry Diseases/virology ; *Viruses/isolation & purification/genetics/classification ; Ultracentrifugation ; Trachea/virology ; Genome, Viral ; },
abstract = {The poultry industry is a major global source of animal protein but remains vulnerable to immunosuppressive viral infections that compromise bird health and productivity. This study evaluated five viral purification methods for metagenomic analysis of respiratory samples from broiler chickens in Santa Catarina, Brazil. Tracheal swabs from ten flocks (one per farm) were pooled, and 50 µL of a herpes simplex virus type 2 (HSV-2) and murine norovirus (MNV-1) mix was added as an internal positive control. The sample was centrifuged (2000 × g for 30 min), filtered (0.45 μm), and subjected to five purification methods. The filtrate was subjected to five different purification methods. Method 1 (M1) was based on nucleic acid direct genomic extraction of the supernatant. Method 2 (M2): a pre-treatment with DNase was used, followed by genomic extraction. Method 3 (M3) was performed using ultracentrifugation at 100,000 × g / 3 h at 4 °C, followed by genomic extraction. In Method 4 (M4), the sample was submitted to ultracentrifugation on a 25 % sucrose cushion at 100,000 × g / 3 h at 4 °C, followed by genomic extraction. Finally, in Method 5 (M5), the sample was ultracentrifuged on a 25 % sucrose cushion at 100,000 × g / 3 h at 4 °C, and the pellet was treated with DNase followed by genomic extraction. All genomic extractions were performed using the RNeasy Mini kit. Samples were reverse transcribed into cDNA and sequenced by the MiSeq Sequencing System. The efficiency of M1-5 was evaluated based on the yield of viral genetic material. All methodologies employed demonstrated varying rates of genome recovery from viruses identified in poultry production. Notable viruses included avian gyrovirus 2 (AGV-2), avian leukosis virus (ALV), and the avian endogenous retrovirus EAV-HP found within chicken genomes. However, M5 showed the best performance, recovering 9.32 % of viral sequences, 44 % of HSV-2, as internal viral control, 32 % of EAV-HP, 8 % of ALV, and 7 % of AGV-2. In conclusion, this study successfully evaluated and compared five distinct viral purification methods, contributing significantly to the characterization of avian viromes and enhancing comprehension of viral ecology.},
}

Animals
*Chickens/virology
*Virome
*Metagenomics/methods
Brazil
*Poultry Diseases/virology
*Viruses/isolation & purification/genetics/classification
Ultracentrifugation
Trachea/virology
Genome, Viral