@article {pmid40350492,
year = {2025},
author = {Ding, Y and Ke, J and Hong, T and Zhang, A and Wu, X and Jiang, X and Shao, S and Gong, M and Zhao, S and Shen, L and Chen, S},
title = {Microbial diversity and ecological roles of halophilic microorganisms in Dingbian (Shaanxi, China) saline-alkali soils and salt lakes.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {287},
pmid = {40350492},
issn = {1471-2180},
support = {STEP 2024QZKK02010//Supported by the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2208085MC39//Natural Science Foundation of Anhui Province, China/ ; },
mesh = {China ; *Lakes/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; *Archaea/classification/genetics/isolation & purification ; Phylogeny ; DNA, Archaeal/genetics ; Salinity ; *Biodiversity ; Alkalies/analysis ; Soil/chemistry ; High-Throughput Nucleotide Sequencing ; Sodium Chloride ; Sequence Analysis, DNA ; Bacteria/classification/genetics ; },
abstract = {Halophilic microorganisms abound in numerous hypersaline environments, such as salt lakes, salt mines, solar salterns, and salted seafood. In the northwest of Dingbian county (Shaanxi province, China), there exists a belt of hypersaline habitats extending from the west to the north consisting of saline-alkali soil and salt lakes. Theoretically, such a hypersaline environment has a high probability of containing abundant halophilic archaea communities. Nevertheless, there is nearly no systematic research on halophilic archaea in this area. Here, we employed a combination of culture-dependent and culture-independent methods to analyze the collected samples. The high-throughput sequencing results of the archaeal 16S rRNA gene indicated that the richness of halophilic archaea in saline-alkali soils was significantly higher than that in salt lakes. In saline-alkali soils, the Natronomonas genus of archaea was more predominant compared to other genera, while in salt lakes, the Halonotius, Halorubrum, and Haloarcula genera of archaea had relatively higher abundances. However, the dominant families of halophilic archaea in both environments were mainly Haloferacaceae (30.96-72%), Halomicrobiaceae (17-53.19%) and Nanosalinaceae (1-19.08%). Based on the outcomes of pure culture experiments, a total of 26 genera and 98 strains were identified. Among the identified halophilic microorganisms, the predominant species were Halorubrum and Fodinibius, accounting for 33.67% and 13.27%, respectively. The remainder were mostly low-abundance groups within the community, and 22 potential novel taxa were discovered. Additionally, metagenomic technology was employed in our research. The analysis results demonstrated that the microorganisms in this area possess metabolic pathways capable of degrading various pollutants such as atrazine, methane, and dioxins, suggesting that some microorganisms in this area play a positive role in environmental remediation. This study roughly reveals the diversity composition and dominant species of halophilic archaea in these hypersaline environments and provides a scientific basis for the possible ecological functions of microorganisms in this area during long-term survival. It also offers scientific evidence for the development and utilization of halophilic microbial resources and ecological protection.},
}

China
*Lakes/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
*Soil Microbiology
*Archaea/classification/genetics/isolation & purification
Phylogeny
DNA, Archaeal/genetics
Salinity
*Biodiversity
Alkalies/analysis
Soil/chemistry
High-Throughput Nucleotide Sequencing
Sodium Chloride
Sequence Analysis, DNA
Bacteria/classification/genetics

@article {pmid40350460,
year = {2025},
author = {Zhang, X and Zhong, R and Wu, J and Tan, Z and Jiao, J},
title = {Dietary selection of distinct gastrointestinal microorganisms drives fiber utilization dynamics in goats.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {118},
pmid = {40350460},
issn = {2049-2618},
support = {32372829, 31972992//National Natural Science Foundation of China/ ; 2023JJ10047//Hunan Provincial Natural Science Foundation of China/ ; 2022RC1158//The Science and Technology innovation Program of Hunan Province/ ; 2023382//Youth Innovation Promotion Association CAS/ ; },
mesh = {Animals ; *Goats/microbiology ; *Dietary Fiber/metabolism ; *Gastrointestinal Microbiome ; Rumen/microbiology/metabolism ; Animal Feed/analysis ; Metagenomics/methods ; Fermentation ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Fibrobacter/metabolism/genetics/isolation & purification ; Ruminococcus/metabolism/genetics/isolation & purification ; Diet/veterinary ; Cecum/microbiology/metabolism ; Cellulose/metabolism ; Fatty Acids, Volatile/metabolism ; Polysaccharides/metabolism ; *Gastrointestinal Tract/microbiology ; },
abstract = {BACKGROUND: Dietary fiber is crucial to animal productivity and health, and its dynamic utilization process is shaped by the gastrointestinal microorganisms in ruminants. However, we lack a holistic understanding of the metabolic interactions and mediators of intestinal microbes under different fiber component interventions compared with that of their rumen counterparts. Here, we applied nutritional, amplicon, metagenomic, and metabolomic approaches to compare characteristic microbiome and metabolic strategies using goat models with fast-fermentation fiber (FF) and slow-fermentation fiber (SF) dietary interventions from a whole gastrointestinal perspective.

RESULTS: The SF diet selected fibrolytic bacteria Fibrobacter and Ruminococcus spp. and enriched for genes encoding for xylosidase, endoglucanase, and galactosidase in the rumen and cecum to enhance cellulose and hemicellulose utilization, which might be mediated by the enhanced microbial ATP production and cobalamin biosynthesis potentials in the rumen. The FF diet favors pectin-degrading bacteria Prevotella spp. and enriched for genes encoding for pectases (PL1, GH28, and CE8) to improve animal growth. Subsequent SCFA patterns and metabolic pathways unveiled the favor of acetate production in the rumen and butyrate production in the cecum for SF goats. Metagenomic binning verified this distinct selection of gastrointestinal microorganisms and metabolic pathways of different fiber types (fiber content and polysaccharide chemistry).

CONCLUSIONS: These findings provide novel insights into the key metabolic pathways and distinctive mechanisms through which dietary fiber types benefit the host animals from the whole gastrointestinal perspective. Video Abstract.},
}

Animals
*Goats/microbiology
*Dietary Fiber/metabolism
*Gastrointestinal Microbiome
Rumen/microbiology/metabolism
Animal Feed/analysis
Metagenomics/methods
Fermentation
*Bacteria/classification/genetics/metabolism/isolation & purification
Fibrobacter/metabolism/genetics/isolation & purification
Ruminococcus/metabolism/genetics/isolation & purification
Diet/veterinary
Cecum/microbiology/metabolism
Cellulose/metabolism
Fatty Acids, Volatile/metabolism
Polysaccharides/metabolism
*Gastrointestinal Tract/microbiology

@article {pmid40350266,
year = {2025},
author = {Ohyama, Y and Miura, T and Furukawa, M and Shimamura, M and Asami, Y and Yamazoe, A and Uchino, Y and Kawasaki, H},
title = {A HPLC-based Method for Counting the Genome Copy Number of Cells Allows the Production of a High-quality Mock Community of Bacterial Cells.},
journal = {Microbes and environments},
volume = {40},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME24076},
pmid = {40350266},
issn = {1347-4405},
mesh = {Chromatography, High Pressure Liquid/methods ; *Bacteria/genetics/isolation & purification/classification ; Humans ; *Microbiota/genetics ; *Genome, Bacterial ; Metagenomics/methods ; Reproducibility of Results ; },
abstract = {Improving the reliability of a metagenomic sequencing ana-lysis requires the use of control samples, known as mock communities. Therefore, mock communities must be prepared with high accuracy and reproducibility, which is particularly challenging for cellular mock communities. In the present study, we prepared a cellular mock community consisting of bacterial strains representative of the human and surrounding environmental microbiomes to demonstrate the suitability of a HPLC-based method that measures the genome number of cells. This method proved to be more accurate and reproducible for preparing cellular mock communities than traditional cell counting-based enumeration methods.},
}

Chromatography, High Pressure Liquid/methods
*Bacteria/genetics/isolation & purification/classification
Humans
*Microbiota/genetics
*Genome, Bacterial
Metagenomics/methods
Reproducibility of Results

@article {pmid40349120,
year = {2025},
author = {Jiang, S and Huang, S and Zhang, Z and Ma, W and Han, Z and Song, Y and Huo, D and Cui, W and Zhang, J},
title = {Gut microbiota drives structural variation of exogenous probiotics to enhance colonization.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2503371},
pmid = {40349120},
issn = {1949-0984},
mesh = {*Probiotics/pharmacology ; *Gastrointestinal Microbiome/genetics ; Animals ; Mice ; *Lactobacillus plantarum/genetics/growth & development ; Gastrointestinal Tract/microbiology ; Bile Acids and Salts ; Metagenomics ; },
abstract = {Probiotics encounter colonization resistance from native gut microbiomes, affecting their effectiveness. Genetic engineering of probiotics lacks universal applicability, as gut microbiotas are highly individualized. Here, we employed probiotic Lactiplantibacillus plantarum HNU082 (Lp082) to test whether Lp082 gut-adapted mutants can resolve colonization resistance in a new gut environment. Relying on culture-based methods and metagenomics, two distinct evolutionary clades of Lp082 in mice gut were observed, where one clade, which acquired more mutations, exhibited a longer survival time. However, these Lp082 isolates carrying many single nucleotide variants (SNVs) still exhibited phenotypic inconsistencies, with 13 strains of enhanced acid resistance. Thus, nanopore sequencing was proposed to identify structural variations (SVs). Among them, 12 strains had the Cro/C1-type HTH DNA-binding domain insertion, which enhanced growth and reproduction under bile salt stress, thereby increasing colonization time and quantity in the gut. The gut domestication process can drive probiotics to undergo many SNVs and SVs, thereby enhancing their colonization ability, which provides new insights into the colonization mechanisms and offers an ecology-based strategy.},
}

*Probiotics/pharmacology
*Gastrointestinal Microbiome/genetics
Animals
Mice
*Lactobacillus plantarum/genetics/growth & development
Gastrointestinal Tract/microbiology
Bile Acids and Salts
Metagenomics

@article {pmid40348945,
year = {2025},
author = {Chen, J and Liu, J and Liu, S and Li, Z and Gao, C and Wang, Z and Huang, S and Jiang, Z and Yang, H},
title = {Multiomics reveals the synergistic response of gut microbiota and spider A. ventricosus to lead and cadmium toxicity.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {114},
number = {5},
pages = {77},
pmid = {40348945},
issn = {1432-0800},
support = {32001205//National Natural Science Foundation of China/ ; 2023JJ30299//Natural Science Foundation of Hunan Province/ ; 2019JJ50236//Natural Science Foundation of Hunan Province/ ; },
mesh = {Animals ; *Cadmium/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Lead/toxicity ; *Spiders/physiology/drug effects ; Metagenomics ; Multiomics ; },
abstract = {The potential crosstalk between the host and gut microbiota (GM) under heavy metal compound pollution remains unexplored. Herein, using comprehensive analysis of metagenomics, metabolomics, behavioral analysis, and cell morphology to investigate the causal relationship between GM and host responses to cadmium (Cd) and lead (Pb) toxicities. Results indicate that Pb and Cd pollution, alone or together, hinder spider predatory behavior and change the composition and function of GM. Combined exposure reduces protein and exogenous compound metabolism, while single exposure affects energy and lipid metabolism. Gut microbiota helps spider antioxidant activity by increasing glutathione, lipoic acid, and L-cysteine. Oxidative damage, increased Enterobacteriaceae (Salmonella), and lipopolysaccharide (LPS) may harm the midgut barrier. Upregulation of choline and acetylcholine, and downregulation of spermidine, may initiate neurotoxicity. Inhibiting actinomycetes might boost sodium gallate for detoxifying single contaminants. Combined pollution detoxification may involve downregulation of indole synthesis metabolic bacteria, tryptophan, indole metabolites, cytochrome P450 (CYP450), and an increase in Desulfobulbia could remove heavy metals and reduce oxidative stress. Combined pollution has a synergistic effect, making the toxicity of multiple pollutants greater than their individual effects, impacting metal resistance genes (MRGs), and antibiotic resistance ontology (AROs) which used for classifying and describing antibiotic resistance, midgut barrier integrity, oxidative stress, and detoxification. The results help to elucidate the interplay of GM and host's reactions, and aid in monitoring and bioremediation of heavy metal pollution.},
}

Animals
*Cadmium/toxicity
*Gastrointestinal Microbiome/drug effects
*Lead/toxicity
*Spiders/physiology/drug effects
Metagenomics
Multiomics

@article {pmid40338610,
year = {2025},
author = {Gan, X and Yu, Q and Hu, X and Qian, Y and Mu, X and Li, H},
title = {Metagenomic and metatranscriptomic analysis reveals the enzymatic mechanism of plant polysaccharide degradation through gut microbiome in plateau model animal (Ochotona curzoniae).},
journal = {FEMS microbiology letters},
volume = {372},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf045},
pmid = {40338610},
issn = {1574-6968},
support = {32471575//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Polysaccharides/metabolism ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; *Lagomorpha/microbiology/metabolism ; *Bacteria/genetics/classification/metabolism/enzymology/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Glycoside Hydrolases/genetics/metabolism ; Transcriptome ; Poaceae/metabolism ; Altitude ; Gene Expression Profiling ; Cellulase/genetics/metabolism ; },
abstract = {Herbivorous animals can obtain energy by decomposing plant polysaccharides through gut microbiota, but the mechanism of gut microbiota decomposing plant polysaccharides in high-altitude model animals is still unclear. Plateau pika (Ochotona curzoniae) is a key model animal native to the Qinghai-Tibet Plateau with a high intake of grass. Thus, Plateau pika is an excellent animal model for studying how herbivorous animals digest and metabolize grass polysaccharides. Here, we used 16S rDNA, 16S rRNA, metagenomic, and metatranscriptomic sequencing to characterize gut microbial composition, gene potential, and expressed function in pikas from different altitudes. Unlike total bacteria, Oscillospira and Ruminococcus were main active bacterial genera in pika's gut. The metabolic pathways of cellulose and hemicellulose were up-regulated in the middle and high-altitude groups; those genes encoding polysaccharide enzymes were enriched. Notably, the proportion of lignin metabolic genes expressed in pika's gut was the highest, followed by cellulase and hemicellulase genes. According to comparative metagenomics of different animals, the number and relative abundance of cellulase and hemicellulase genes in pika's gut were at a higher level compared with steer, etc. These results indicated that plateau pika obtained sufficient energy from grass-based diet by increasing the expression of related metabolic enzymes.},
}

Animals
*Polysaccharides/metabolism
*Gastrointestinal Microbiome/genetics
Metagenomics
*Lagomorpha/microbiology/metabolism
*Bacteria/genetics/classification/metabolism/enzymology/isolation & purification
RNA, Ribosomal, 16S/genetics
Glycoside Hydrolases/genetics/metabolism
Transcriptome
Poaceae/metabolism
Altitude
Gene Expression Profiling
Cellulase/genetics/metabolism

@article {pmid39876557,
year = {2025},
author = {Morsink, MC and van Schaik, EN and Bossers, K and Duijker, DA and Speksnijder, AGCL},
title = {Metagenomics education in a modular CURE format positively affects students' scientific discovery perception and data analytical skills.},
journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology},
volume = {53},
number = {3},
pages = {311-320},
doi = {10.1002/bmb.21888},
pmid = {39876557},
issn = {1539-3429},
mesh = {*Metagenomics/education ; *Students/psychology ; Humans ; Microbiota ; Animals ; Anthozoa/microbiology ; Computational Biology/education ; Curriculum ; },
abstract = {Targeted metagenomics is a rapidly expanding technology to analyze complex biological samples and genetic monitoring of environmental samples. In this research field, data analytical aspects play a crucial role. In order to teach targeted metagenomics data analysis, we developed a 4-week inquiry-driven modular course-based undergraduate research experience (mCURE) using publicly available Australian coral microbiome DNA sequencing data and associated metadata. Since an enormous amount of metadata was provided alongside the DNA sequencing data, groups of students were able to develop their own authentic research questions. Throughout the course, the student groups worked on these research questions and were supported with bioinformatics and statistics lessons. Additionally, practical aspects of data collection and analysis were addressed during hands-on field work on a nearby Dutch beach. Evaluation of the course indicated that the majority of students (1) achieved the intended metagenomics-based learning outcomes and (2) experienced scientific discovery while working on their research projects. In conclusion, the huge amount of data and metadata available in the coral microbiome data set facilitated the development of a strongly inquiry-driven course. Different groups of students were able to develop and conduct their own distinct microbiome research projects and our current mCURE format positively affected students' metagenomics data analytical skills and scientific discovery perception.},
}

*Metagenomics/education
*Students/psychology
Humans
Microbiota
Animals
Anthozoa/microbiology
Computational Biology/education
Curriculum

@article {pmid40348492,
year = {2025},
author = {Quigley, EMM},
title = {Microbial Influences on Irritable Bowel Syndrome.},
journal = {Gastroenterology clinics of North America},
volume = {54},
number = {2},
pages = {351-365},
doi = {10.1016/j.gtc.2024.12.003},
pmid = {40348492},
issn = {1558-1942},
mesh = {*Irritable Bowel Syndrome/microbiology ; Humans ; *Gastrointestinal Microbiome ; Feces/microbiology ; Metabolomics ; Metagenomics ; Dysbiosis ; },
abstract = {Since the description of postinfection irritable bowel syndrome (IBS), a role for gut microbes in the pathogenesis of IBS has been proposed. Molecular microbiological tools have now been applied to IBS, though data are largely derived from fecal samples with attendant limitations. Metagenomics, metabolomics, and other 'omics facilitate a comprehensive picture of the microbiome and its metabolic activity. Has a microbial signature characteristic of IBS been identified? The answer is no; this should not be a surprise given the heterogeneity of the phenotype and each individual's microbiome profile.},
}

*Irritable Bowel Syndrome/microbiology
Humans
*Gastrointestinal Microbiome
Feces/microbiology
Metabolomics
Metagenomics
Dysbiosis

@article {pmid40346812,
year = {2025},
author = {Pryor, JC and Nieva, C and Talley, NJ and Eslick, GD and Duncanson, K and Burns, GL and Hoedt, EC and Keely, S},
title = {Microbial-derived peptidases are altered in celiac disease, non-celiac gluten sensitivity, and functional dyspepsia: a systematic review and re-analysis of the duodenal microbiome.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2500063},
pmid = {40346812},
issn = {1949-0984},
mesh = {Humans ; *Celiac Disease/microbiology/enzymology ; *Gastrointestinal Microbiome ; *Glutens/metabolism ; *Duodenum/microbiology ; *Dyspepsia/microbiology ; *Peptide Hydrolases/metabolism/genetics ; *Bacteria/enzymology/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Dietary gluten triggers symptoms in patients with gluten-related disorders (GRDs) including celiac disease (CeD), non-celiac gluten sensitivity (NCGS), and subsets of patients with functional dyspepsia (FD). The gastrointestinal microbiota is altered in these patients when compared to healthy individuals. As the microbiota is crucial for the hydrolysis of gluten, we hypothesized that the capacity of the microbiota to digest gluten is reduced in these conditions. We systematically reviewed and re-analyzed published datasets to compare gastrointestinal microbiomes of GRD patients and identify signals explaining gluten responses. A systematic search of five databases was conducted to identify studies where the microbiota of CeD, NCGS, or FD patients was analyzed by 16S rRNA amplicon or shotgun metagenomic sequencing and compared to control populations. Where available, raw duodenal microbiota sequence data were re-analyzed with a consistent bioinformatic pipeline. Thirty articles met the inclusion criteria for this systematic review. Microbiota diversity metrics were not impacted by the diseases; however, genera including Streptococcus, Neisseria, and Lactobacillus were commonly altered in GRD patients. Re-analysis of duodenal 16S rRNA data was possible for five included articles but did not identify any consistent differentially abundant taxa. Predicted functional analysis of the microbiome revealed that peptidases including aminopeptidase, proline iminopeptidase, and Xaa-Pro dipeptidase are altered in CeD, NCGS, and FD, respectively. These microbial-derived peptidases hydrolyze bonds in proline-rich gluten peptides. While the gastrointestinal microbiota in patients with GRDs differ from controls, no distinct phenotype links them. However, alterations to the predicted functional capacity of the microbiome to produce gluten-hydrolyzing enzymes suggest that inappropriate digestion of gluten by the microbiome impacts host responses to dietary gluten in these conditions. These findings have implications for therapeutic management of GRDs, as treatment with gluten-degrading enzymes or tailored probiotics could improve disease outcomes by enhancing gluten digestion into non-reactive peptides.},
}

Humans
*Celiac Disease/microbiology/enzymology
*Gastrointestinal Microbiome
*Glutens/metabolism
*Duodenum/microbiology
*Dyspepsia/microbiology
*Peptide Hydrolases/metabolism/genetics
*Bacteria/enzymology/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics

@article {pmid40346542,
year = {2025},
author = {Gao, H and Xu, L and Liu, Y and Wang, X and Zhu, S and Lin, H and Gao, Y and Mao, D and Lu, X and Luo, Y},
title = {Whole genome comparisons reveal gut-to-lung translocation of Escherichia coli and Burkholderia cenocepacia in two cases of ventilator-associated pneumonia in ICU patients.},
journal = {Respiratory research},
volume = {26},
number = {1},
pages = {178},
pmid = {40346542},
issn = {1465-993X},
support = {2022BKY015//the Tianjin Graduate Research and Innovation Projects/ ; 42377426//the National Natural Science Foundation of China/ ; 18ZXDBSY00100//the Tianjin Science and Technology Plan Project/ ; 21JCYBJC01200//the Tianjin Municipal Natural Science Foundation/ ; 2023220//the Research Project on Integrated Traditional Chinese and Western Medicine of Tianjin Municipal Health Commission/ ; 2020YFC1806904//the National Key R&D Program of China/ ; 41831287//the Key Projects of the National Natural Science Foundation of China/ ; },
mesh = {Aged ; Animals ; Female ; Humans ; Male ; Mice ; Middle Aged ; *Bacterial Translocation/physiology/genetics ; *Burkholderia cenocepacia/genetics/isolation & purification/pathogenicity ; *Escherichia coli/genetics/isolation & purification/pathogenicity ; *Gastrointestinal Microbiome/genetics ; *Genome, Bacterial ; Intensive Care Units/trends ; *Lung/microbiology ; Mice, Inbred C57BL ; *Pneumonia, Ventilator-Associated/microbiology/diagnosis/genetics ; Whole Genome Sequencing/methods ; Case-Control Studies ; Adult ; Aged, 80 and over ; },
abstract = {BACKGROUND: Identifying the sources of pathogenic bacteria causing ventilator-associated pneumonia (VAP) in intensive care unit (ICU) patients is crucial for developing effective prevention and treatment strategies. However, the scarcity of reported cases with confirmed sources limits the ability to evaluate and manage VAP, which remains a major challenge for healthcare systems globally.

METHODS: Pathogens were isolated from endotracheal aspirate (ETA) samples of VAP patients using conventional culture techniques. Whole-genome comparisons, based on average nucleotide identity (ANI), were performed to identify genetically identical strains by comparing pulmonary isolate genomes with gut metagenome-derived bacterial genomes. Mouse models of pneumonia and colitis were used to validate the translocation of pathogenic bacteria from the gut to the lungs. Metagenomic analysis was performed to characterize the gut microbiome and resistome.

RESULTS: Pathogenic isolates were obtained from the ETA samples of seven VAP patients, with one isolate per sample. Among these, Escherichia coli (Ec1) and Burkholderia cenocepacia (Bc1) from two patients were genetically identical to strains in their respective gut microbiota, with ANI values above 99%, indicating gut-to-lung translocation. The Ec1 strain demonstrated increased resistance to cefazolin while remaining susceptible to gentamicin, amikacin, and kanamycin, compared to previously reported pneumonia-associated E. coli strains. The Bc1 strain showed elevated resistance to macrolides, chloramphenicols, and tetracyclines relative to pneumonia-associated B. cenocepacia strains. Metagenomic analysis revealed a highly individualized gut microbiota composition among VAP patients. Notably, the translocated bacteria were not dominant within their gut microbiota. Additionally, these patients showed a marked increase in the total abundance of antibiotic resistance genes (ARGs) in their gut microbiota. The translocation ability of the Ec1 strain was validated in a mouse pneumonia model, where it caused more severe lung damage. Furthermore, elevated levels of Escherichia-Shigella were detected in the lung tissues of colitis mice, suggesting that gut-to-lung bacterial translocation may occur in a severely inflamed host, potentially leading to pneumonia.

CONCLUSIONS: This study demonstrates the gut-to-lung translocation of E. coli and B. cenocepacia, highlighting their role in the development and progression of VAP in ICU patients. These findings provide valuable insights for implementing targeted prevention and treatment strategies for VAP in ICU settings.},
}

Aged
Animals
Female
Humans
Male
Mice
Middle Aged
*Bacterial Translocation/physiology/genetics
*Burkholderia cenocepacia/genetics/isolation & purification/pathogenicity
*Escherichia coli/genetics/isolation & purification/pathogenicity
*Gastrointestinal Microbiome/genetics
*Genome, Bacterial
Intensive Care Units/trends
*Lung/microbiology
Mice, Inbred C57BL
*Pneumonia, Ventilator-Associated/microbiology/diagnosis/genetics
Whole Genome Sequencing/methods
Case-Control Studies
Adult
Aged, 80 and over

@article {pmid40328090,
year = {2025},
author = {Xia, Y and Lan, Y and Xu, Y and Liu, F and Chen, X and Luo, J and Xu, H and Liu, Y},
title = {Effects of microplastics and tetracycline induced intestinal damage, intestinal microbiota dysbiosis, and antibiotic resistome: metagenomic analysis in young mice.},
journal = {Environment international},
volume = {199},
number = {},
pages = {109512},
doi = {10.1016/j.envint.2025.109512},
pmid = {40328090},
issn = {1873-6750},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Microplastics/toxicity ; *Anti-Bacterial Agents/toxicity ; *Tetracycline/toxicity ; *Dysbiosis/chemically induced ; Metagenomics ; *Intestines/drug effects ; *Drug Resistance, Microbial/genetics ; },
abstract = {Microplastics (MPs) and antibiotic tetracycline (TC) are widespread in the environment and constitute emerging combined contaminants. Young individuals are particularly vulnerable to agents that disrupt intestinal health and development. However, the combined effects of MPs and TC remain poorly understood. In this study, we developed a young mouse model exposed to polystyrene MPs, either alone or in combination with TC for 8 weeks to simulate real-life dietary exposure during early life. Our findings revealed that concurrent exposure to MPs and TC caused the most severe intestinal barrier dysfunction driven by inflammatory activation and oxidative imbalance. Moreover, exposure to MPs and TC reduced the abundance of potential probiotics while promoting the growth of opportunistic pathogens. Metagenomic analysis further indicated that co-exposure to MPs and TC enhanced the abundance of bacteria carrying either antibiotic resistance genes (ARGs) or virulence factor genes (VFGs), contributing to the widespread dissemination of potentially harmful genes. Finally, a strong positive correlation was observed between microbiota dysbiosis, ARGs, and VFGs. In general, this study highlighted the hazards of MPs and antibiotics to intestinal health in young mice, which provided a new perspective into the dynamics of pathogens, ARGs, and VFGs in early-life intestinal environments.},
}

Animals
Mice
*Gastrointestinal Microbiome/drug effects
*Microplastics/toxicity
*Anti-Bacterial Agents/toxicity
*Tetracycline/toxicity
*Dysbiosis/chemically induced
Metagenomics
*Intestines/drug effects
*Drug Resistance, Microbial/genetics

@article {pmid40327993,
year = {2025},
author = {Grafakou, ME and Pferschy-Wenzig, EM and Aziz-Kalbhenn, H and Kelber, O and Moissl-Eichinger, C and Bauer, R},
title = {Bidirectional interactions between St. John´s wort and gut microbiome: Potential implications on gut-brain-axis.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {187},
number = {},
pages = {118111},
doi = {10.1016/j.biopha.2025.118111},
pmid = {40327993},
issn = {1950-6007},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Hypericum/chemistry ; *Plant Extracts/pharmacology ; *Brain/drug effects/metabolism ; Male ; Adult ; Female ; Feces/microbiology ; Antidepressive Agents/pharmacology ; *Brain-Gut Axis/drug effects ; },
abstract = {Emerging evidence highlights the role of gut microbiome in mental health disorders, including depression, raising the question whether the action of antidepressants could be mediated, at least in part, via the microbiome-gut-brain axis. To explore this, we subjected a St. John's wort extract (STW 3-VI), clinically proven to be effective in mild to moderate depression, to a model of the upper and lower intestinal tract, including static in vitro predigestion followed by ex vivo incubation with human microbiota samples. To cover the interindividual diversity of gut microbiome composition, fecal samples from ten healthy volunteers were used. Although unchanged levels of most annotated compounds were observed during simulated upper intestinal tract digestion, incubation with fecal microbiota led to a significant change of the chemical profile of the extract. While hyperforins remained stable, flavonoids and hypericins were rapidly biotransformed, suggesting that they may act as prodrugs. Several metabolites were formed, many of which are known to be involved in gut-brain communication. Differential abundance analysis revealed significant changes in microbiome composition, particularly for taxa known to be potentially associated with depression. Among others, the Firmicutes/Bacteroidetes ratio, known to be lowered in depressive patients, was increased. Functional profiling revealed modulation of pathways involved in gut-brain communication, such as tyrosine and tryptophan metabolism. These bidirectional interactions suggest for the first time the gut microbiome as a potential mediator of the pharmacological effects of St. John's wort extracts via the microbiome-gut-brain axis.},
}

Humans
*Gastrointestinal Microbiome/drug effects/physiology
*Hypericum/chemistry
*Plant Extracts/pharmacology
*Brain/drug effects/metabolism
Male
Adult
Female
Feces/microbiology
Antidepressive Agents/pharmacology
*Brain-Gut Axis/drug effects

@article {pmid40216167,
year = {2025},
author = {Sangfuang, N and Xie, Y and McCoubrey, LE and Taub, M and Favaron, A and Mai, Y and Gaisford, S and Basit, AW},
title = {Investigating the bidirectional interactions between senotherapeutic agents and human gut microbiota.},
journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
volume = {209},
number = {},
pages = {107098},
doi = {10.1016/j.ejps.2025.107098},
pmid = {40216167},
issn = {1879-0720},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Quercetin/pharmacology ; *Senotherapeutics/pharmacology ; Dasatinib/pharmacology ; Sirolimus/pharmacology ; Flavonoids/pharmacology ; Bacteria/drug effects/genetics ; Adult ; Male ; Flavonols/pharmacology ; Female ; Middle Aged ; Aging/drug effects ; },
abstract = {Biological ageing is a time-dependent process that has implications for health and disease. Cellular senescence is a key driver in ageing and age-related diseases. Senotherapeutic agents have been shown to slow biological ageing by eliminating senescent mammalian cells. Given the increasing awareness of the gut microbiome in regulating human health, this study aimed to investigate the effects of senotherapeutic agents as pharmacological interventions on the human gut microbiota. In this study, the bidirectional effects of four senotherapeutic agents, quercetin, fisetin, dasatinib, and sirolimus, with the gut microbiota sourced from healthy human donors were investigated. The results revealed that quercetin was completely biotransformed by the gut microbiota within six hours, while dasatinib was the most stable of the four compounds. Additionally, metagenomic analysis confirmed that all four compounds increased the abundance of bacterial species associated with healthy ageing (e.g., Bacteroides fragilis, Bifidobacterium longum, and Veillonella parvula), and decreased the abundance of pathogenic bacteria primarily associated with age-related diseases (e.g., Enterococcus faecalis and Streptococcus spp.). The findings from this study provide a comprehensive understanding of the pharmacobiomics of senotherapeutic interventions, highlighting the potential of microbiome-targeted senolytics in promoting healthy ageing.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Quercetin/pharmacology
*Senotherapeutics/pharmacology
Dasatinib/pharmacology
Sirolimus/pharmacology
Flavonoids/pharmacology
Bacteria/drug effects/genetics
Adult
Male
Flavonols/pharmacology
Female
Middle Aged
Aging/drug effects

@article {pmid40147302,
year = {2025},
author = {Keneally, C and Chilton, D and Dornan, TN and Kidd, SP and Gaget, V and Toomes, A and Lassaline, C and Petrovski, R and Wood, L and Brookes, JD},
title = {Multi-omics reveal microbial succession and metabolomic adaptations to flood in a hypersaline coastal lagoon.},
journal = {Water research},
volume = {280},
number = {},
pages = {123511},
doi = {10.1016/j.watres.2025.123511},
pmid = {40147302},
issn = {1879-2448},
mesh = {*Floods ; Salinity ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology ; Metabolomics ; Microbiota ; Multiomics ; },
abstract = {Microorganisms drive essential biogeochemical processes in aquatic ecosystems and are sensitive to both salinity and hydrological changes. As climate change and anthropogenic activities alter hydrology and salinity worldwide, understanding microbial ecology and metabolism becomes increasingly important for managing aquatic ecosystems. Biogeochemical processes were investigated on sediment microbial communities during a significant flood event in the hypersaline Coorong lagoon, South Australia (the largest in the Murray-Darling Basin since 1956). Samples from six sites across a salinity gradient were collected before and during flooding in 2022. To assess changes in microbial taxonomy and metabolic function, 16S rRNA amplicon sequencing was employed alongside untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in microbial taxonomy and metabolic function. Results showed a decrease in microbial richness and diversity during flooding, especially in hypersaline conditions. Pre-flood communities were enriched with osmolyte-degrading and methanogenic taxa, alongside osmoprotectant metabolites, such as glycine betaine and choline. Flood conditions favored taxa such as Halanaerobiaceae and Beggiatoaceae, inducing inferred metagenomic shifts indicative of sulfur cycling and nitrogen reduction pathways, while also enriching a greater diversity of metabolites including Gly-Phe dipeptides and guanine. This study demonstrates that integrating metabolomics with microbial community analysis enhances understanding of ecosystem responses to disturbance. These findings suggest microbial communities rapidly change in response to salinity reductions while maintaining key biogeochemical functions. Such insights are valuable for ecosystem management and predictive modelling under environmental stressors such as flooding.},
}

*Floods
Salinity
RNA, Ribosomal, 16S/genetics
Geologic Sediments/microbiology
Metabolomics
Microbiota
Multiomics

@article {pmid40090144,
year = {2025},
author = {Deng, B and Ren, Z and Li, Q and Zhang, Z and Xu, C and Wang, P and Zhao, H and Yuan, Q},
title = {Black soldier fly larvae mediate Zinc and Chromium transformation through the ZnuCBA and citric acid cycle system.},
journal = {Water research},
volume = {280},
number = {},
pages = {123483},
doi = {10.1016/j.watres.2025.123483},
pmid = {40090144},
issn = {1879-2448},
mesh = {Animals ; Larva/metabolism ; *Zinc/metabolism ; *Chromium/metabolism ; *Citric Acid Cycle ; *Simuliidae/metabolism ; Gastrointestinal Microbiome ; },
abstract = {Intestinal microbiota and metal regulatory proteins (MRPs) underlie the transformation of heavy metals (HMs) by the black soldier fly larvae (BSFL), but the mechanisms involved are still not fully defined. Here, using 16S rRNA and metagenomics-assisted tracing, we found that zinc (Zn) and chromium (Cr) stress led to enrichment of Proteobacteria in the BSFL intestine. Support of Proteobacteria also led to increased levels of the Zn transporter proteins ZnuC/B/A and the Zn efflux proteins zntR/A. Meanwhile, the genes MltE, CitT, and SLT, which mediate the citric acid cycle, were also significantly up-regulated and involved in the cellular uptake of Cr. Although Zn and Cr stress affected the expression of antibiotic resistance genes and pathogenic genes, the BSFL intestine tended to form stable microbial communities (MCs) to transform HMs through a mechanism driven by ZupT and chrA. In addition, the expression of SCARB1 and LdcA was significantly down-regulated by acute HMs stimulation, but BSFL were still able to complete the life cycle. Therefore, we determined the protective role of MCs and MRPs on BSFL during the transformation of HMs.},
}

Animals
Larva/metabolism
*Zinc/metabolism
*Chromium/metabolism
*Citric Acid Cycle
*Simuliidae/metabolism
Gastrointestinal Microbiome

@article {pmid40343328,
year = {2025},
author = {McLamb, F and Vazquez, A and Olander, N and Vasquez, MF and Feng, Z and Malhotra, N and Bozinovic, L and Najera Ruiz, K and O'Connell, K and Stagg, J and Bozinovic, G},
title = {Comparative Three-Barcode Phylogenetics and Soil Microbiomes of Planted and Wild Arbutus Strawberry Trees.},
journal = {Plant direct},
volume = {9},
number = {5},
pages = {e70078},
pmid = {40343328},
issn = {2475-4455},
abstract = {Taxonomic identification of closely related plants can be challenging due to convergent evolution, hybridization, and overlapping geographic distribution. To derive taxonomic relationships among planted and wild Arbutus plants across a large geographic range, we complemented three standard plastid barcodes rbcL, matK, and trnH-psbA with soil and fruit chemistry, soil microbiome, and plant morphology analyses. Soil and plant sampling included planted Arbutus from manicured sites in Southern California, USA, wild plants from Southern and Northern California, and wild populations from Mediterranean island of Hvar, Croatia. We hypothesized that phenotypic variation within and between sites correlates with plants' genotype and geographic distribution. Similar fruit chemistry corresponds to geographical proximity and morphological resemblance, while bulk soil bacterial content defines three distinct clusters distinguishing planted versus wild trees and continent of origin. The soil microbiome of wild California Arbutus was characterized by an abundance of Nitrobacter, while the presence of Candidatus Xiphinematobacter was high in wild Hvar samples and most planted samples, but low in all wild California samples. Although all three barcodes resolved four main groups, the position of samples varies across barcodes. The rbcL phylogram is relatively unbalanced, suggesting slower diversification among wild California populations and exhibiting greater resolution than other barcodes among planted individuals. While our data demonstrate an overall agreement among standard plant barcodes relative to geo-distribution and plant morphology, sustained efforts on cost-effective global plant DNA barcode library standardization for closely related and geographically overlapping plants is recommended.},
}

@article {pmid40341642,
year = {2025},
author = {Humińska-Lisowska, K and Michałowska-Sawczyn, M and Kosciolek, T and Łabaj, PP and Kochanowicz, A and Mieszkowski, J and Proia, P and Cięszczyk, P and Zielińska, K},
title = {Gut microbiome and blood biomarkers reveal differential responses to aerobic and anaerobic exercise in collegiate men of diverse training backgrounds.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16061},
pmid = {40341642},
issn = {2045-2322},
support = {2018/29/N/NZ7/02800//Narodowe Centrum Nauki/ ; 2018/29/N/NZ7/02800//Narodowe Centrum Nauki/ ; },
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/physiology ; *Biomarkers/blood ; *Exercise/physiology ; Young Adult ; Feces/microbiology ; Exercise Test ; Athletes ; Anaerobiosis ; Adult ; },
abstract = {The gut microbiome influences physiological responses to exercise by modulating inflammatory markers and metabolite production. Athletes typically exhibit greater microbial diversity, which may be associated with improved performance, but the mechanisms linking different exercise modalities to the gut microbiome are not fully understood. In this study, blood and stool samples were collected from endurance athletes, strength athletes, and non-athletic controls performing two maximal exercise tests (the anaerobic Wingate test and the aerobic Bruce Treadmill Test) to integrate serum biomarker data with gut bacterial metagenomic profiles. While most biochemical markers showed similar post-exercise trends across groups, SPARC (secreted protein acidic and rich in cysteine) and adiponectin levels showed modality-specific responses. Strength-trained participants showed unique microbiome-biomarker associations after the Wingate test. In addition, baseline enrichment of certain bacterial taxa, including Clostridium phoceensis and Catenibacterium spp., correlated with reduced Bruce Treadmill test response in strength-trained individuals. These findings, while requiring further validation, indicate the complex interplay between exercise type, training background, and the gut microbiome, and suggest that specific microbial species may help shape recovery and adaptation.},
}

Humans
Male
*Gastrointestinal Microbiome/physiology
*Biomarkers/blood
*Exercise/physiology
Young Adult
Feces/microbiology
Exercise Test
Athletes
Anaerobiosis
Adult

@article {pmid40220715,
year = {2025},
author = {Chen, Y and Chen, Z and Liang, L and Li, J and Meng, L and Yuan, W and Xie, B and Zhang, X and Feng, L and Jia, Y and Fu, Z and Su, P and Tong, Z and Zhong, J and Liu, X},
title = {Multi-kingdom gut microbiota dysbiosis is associated with the development of pulmonary arterial hypertension.},
journal = {EBioMedicine},
volume = {115},
number = {},
pages = {105686},
pmid = {40220715},
issn = {2352-3964},
mesh = {*Dysbiosis/microbiology/complications ; *Gastrointestinal Microbiome ; Animals ; Rats ; Humans ; Fecal Microbiota Transplantation ; Male ; Disease Models, Animal ; *Pulmonary Arterial Hypertension/etiology/microbiology ; Metagenomics/methods ; Female ; Middle Aged ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: Gut microbiota dysbiosis has been implicated in pulmonary arterial hypertension (PAH). However, the exact roles and underlying mechanisms of multi-kingdom gut microbiota, including bacteria, archaea, and fungi, in PAH remain largely unclear.

METHODS: The shotgun metagenomics was used to analyse multi-kingdom gut microbial communities in patients with idiopathic PAH (IPAH) and healthy controls. Furthermore, fecal microbiota transplantation (FMT) was performed to transfer gut microbiota from IPAH patients or monocrotaline (MCT)-PAH rats to normal rats and from normal rats to MCT-PAH rats.

FINDINGS: Gut microbiota analysis revealed substantial alterations in the bacterial, archaeal, and fungal communities in patients with IPAH compared with healthy controls. Notably, FMT from IPAH patients or MCT-PAH rats induced PAH phenotypes in recipient rats. More intriguingly, FMT from normal rats to MCT-PAH rats significantly ameliorated PAH symptoms; restored gut bacteria, archaea, and fungi composition; and shifted the plasma metabolite profiles of MCT-PAH rats toward those of normal rats. In parallel, RNA-sequencing analysis demonstrated the expression of genes involved in key signalling pathways related to PAH. A panel of multi-kingdom markers exhibited superior diagnostic accuracy compared with single-kingdom panels for IPAH.

INTERPRETATION: Our findings established an association between multi-kingdom gut microbiota dysbiosis and PAH, thereby indicating the therapeutic potential of FMT in PAH. More importantly, apart from gut bacteria, gut archaea and fungi were also significantly associated with PAH pathogenesis, highlighting their indispensable role in PAH.

FUNDING: This work was supported by Noncommunicable Chronic Diseases-National Science and Technology Major Projects No. 2024ZD0531200, No. 2024ZD0531201 (Research on Prevention and Treatment of Cancer, Cardiovascular and Cerebrovascular Diseases, Respiratory Diseases, and Metabolic Diseases), the National Natural Science Foundation of China of China (No. 82170302, 82370432), Financial Budgeting Project of Beijing Institute of Respiratory Medicine (Ysbz2025004, Ysbz2025007), National clinical key speciality construction project Cardiovascular Surgery, Reform and Development Program of Beijing Institute of Respiratory Medicine (Ggyfz202417, Ggyfz202501), Clinical Research Incubation Program of Beijing Chaoyang Hospital Affiliated to Capital Medical University (CYFH202209).},
}

*Dysbiosis/microbiology/complications
*Gastrointestinal Microbiome
Animals
Rats
Humans
Fecal Microbiota Transplantation
Male
Disease Models, Animal
*Pulmonary Arterial Hypertension/etiology/microbiology
Metagenomics/methods
Female
Middle Aged
Bacteria/genetics/classification

@article {pmid40188743,
year = {2025},
author = {Deng, K and Wang, L and Nguyen, SM and Shrubsole, MJ and Cai, Q and Lipworth, L and Gupta, DK and Zheng, W and Shu, XO and Yu, D},
title = {A dietary pattern promoting gut sulfur metabolism is associated with increased mortality and altered circulating metabolites in low-income American adults.},
journal = {EBioMedicine},
volume = {115},
number = {},
pages = {105690},
pmid = {40188743},
issn = {2352-3964},
support = {R01 HL149779/HL/NHLBI NIH HHS/United States ; U01 CA202979/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome ; *Diet ; *Sulfur/metabolism ; Adult ; *Poverty ; *Metabolome ; Aged ; Black or African American ; Metabolomics/methods ; Biomarkers ; Prospective Studies ; United States/epidemiology ; White ; },
abstract = {BACKGROUND: Excessive hydrogen sulfide in the gut, generated by sulfur-metabolising bacteria from foods, has been linked to intestinal inflammation and human diseases. We aim to investigate the interplay between diet and sulphur-metabolising bacteria in relation to mortality and circulating metabolites in understudied populations.

METHODS: In the Southern Community Cohort Study (SCCS), a prospective cohort of primarily low-income American adults, habitual diets were assessed using a food frequency questionnaire at baseline (2002-2009). A sulfur microbial diet score (SMDS) was developed among 514 Black/African American participants by linking habitual dietary intakes with the abundance of sulfur-metabolising bacteria profiled by faecal shotgun metagenomics. The SMDS was then constructed among all eligible SCCS participants (50,114 Black/African American and 23,923 non-Hispanic White adults), and its associations with mortality outcomes were examined by Cox proportional hazards model and Fine-Grey subdistribution hazard model. The association between SMDS and 1110 circulating metabolites was examined by linear regression among 1688 SCCS participants with untargeted metabolomic profiling of baseline plasma samples.

FINDINGS: Over an average 13.9-year follow-up, SMDS was associated with increased all-cause mortality (HR [95% CI] for the highest vs. lowest quartiles: 1.21 [1.15-1.27]) and cardiovascular disease (1.18 [1.08-1.29]), cancer (1.13 [1.02-1.25]), and gastrointestinal cancer-specific (1.22 [1.00-1.49]) mortality among Black/African American participants (all P-trend<0.05). The associations were largely consistent across participant subgroups. Similar results were observed among non-Hispanic White participants. The SMDS was associated with 112 circulating metabolites, which mediated 36.15% of the SMDS-mortality association (P = 0.002).

INTERPRETATION: A dietary pattern promoting sulfur-metabolising gut bacteria may contribute to increased total and disease mortality in low-income American adults.

FUNDING: This study was funded by the National Institutes of Health, United States, to Vanderbilt University Medical Center, United States, and Anne Potter Wilson Chair endowment to Vanderbilt University, United States.},
}

Humans
Female
Male
Middle Aged
*Gastrointestinal Microbiome
*Diet
*Sulfur/metabolism
Adult
*Poverty
*Metabolome
Aged
Black or African American
Metabolomics/methods
Biomarkers
Prospective Studies
United States/epidemiology
White

@article {pmid40101514,
year = {2025},
author = {Zhang, X and Wu, L and Gu, L and Jiang, Q and He, Z and Qi, Y and Zheng, X and Xu, T},
title = {Dietary areca nut extract supplementation modulates the growth performance and immunity of Jiaji ducks (Cairina moschata).},
journal = {Poultry science},
volume = {104},
number = {5},
pages = {104971},
pmid = {40101514},
issn = {1525-3171},
mesh = {Animals ; *Ducks/growth & development/immunology ; Dietary Supplements/analysis ; Animal Feed/analysis ; Diet/veterinary ; *Plant Extracts/administration & dosage/metabolism ; Random Allocation ; *Areca/chemistry ; Gastrointestinal Microbiome/drug effects ; Nuts/chemistry ; *Immunity, Innate/drug effects ; },
abstract = {Areca nut extract (ANE) has a variety of pharmacological effects on animals. Here, we investigated the influence of ANE on the slaughter performance and immune function of Jiaji ducks. One hundred and fifty 42-day-old healthy Jiaji ducks were randomly divided into 2 groups (5 replicates of 15 ducks each), named DCK group (control) and DNT group (treatment), respectively. Ducks in the DCK group were fed a basal diet and ducks in the DNT group were fed a basal food supplemented with 0.08 g ANE per kg of basal diet. Additionally, using proteomics, untargeted metabolomics, and metagenomics, we analyzed the impact of ANE on the protein profile of the spleen, the composition of plasma metabolites, and the structure of the cecal microbiota. The results showed that the dietary inclusion of ANE significantly increased the slaughter rate of Jiaji ducks. Proteomic analysis revealed 78 differentially expressed proteins in the spleens of ANE-treated birds, including 54 proteins up-regulated and 24 proteins down-regulated in the DNT group, mainly enriched in cell adhesion molecules and glutathione metabolic pathways. Untargeted metabolomic analysis revealed that 117 serum metabolites were differentially regulated between the ANE and DCK groups; meanwhile, KEGG pathway analysis indicated that these metabolites were mainly involved in arachidonic acid metabolism, phospholipase D signaling pathway and eicosanoids. Furthermore, a metagenomic analysis showed that the genus Methanobrevibacter was significantly downregulated in the ANE supplementation group. Combined, the results of the metagenomic and metabolomic analyses showed that the relative abundance of Prevotella was significantly lower in the ANE group than in the DCK group and that Prevotella was negatively correlated with the levels of the anti-inflammatory compound hydrocinnamic acid and the lipid metabolism regulator ganoderic acid A. This study provides a reference for the application of ANE as a supplement in the diet of Jiaji ducks.},
}

Animals
*Ducks/growth & development/immunology
Dietary Supplements/analysis
Animal Feed/analysis
Diet/veterinary
*Plant Extracts/administration & dosage/metabolism
Random Allocation
*Areca/chemistry
Gastrointestinal Microbiome/drug effects
Nuts/chemistry
*Immunity, Innate/drug effects

@article {pmid38898177,
year = {2025},
author = {Enav, H and Paz, I and Ley, RE},
title = {Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution.},
journal = {Nature biotechnology},
volume = {43},
number = {5},
pages = {773-783},
pmid = {38898177},
issn = {1546-1696},
support = {Core//Max-Planck-Gesellschaft (Max Planck Society)/ ; NA//Max-Planck-Gesellschaft (Max Planck Society)/ ; },
mesh = {Polymorphism, Single Nucleotide/genetics ; Humans ; *Synteny/genetics ; *Microbiota/genetics ; *Evolution, Molecular ; Genome, Bacterial/genetics ; Metagenome/genetics ; Metagenomics/methods ; Software ; },
abstract = {Microbial species diversify into strains through single-nucleotide mutations and structural changes, such as recombination, insertions and deletions. Most strain-comparison methods quantify differences in single-nucleotide polymorphisms (SNPs) and are insensitive to structural changes. However, recombination is an important driver of phenotypic diversification in many species, including human pathogens. We introduce SynTracker, a tool that compares microbial strains using genome synteny-the order of sequence blocks in homologous genomic regions-in pairs of metagenomic assemblies or genomes. Genome synteny is a rich source of genomic information untapped by current strain-comparison tools. SynTracker has low sensitivity to SNPs, has no database requirement and is robust to sequencing errors. It outperforms existing tools when tracking strains in metagenomic data and is particularly suited for phages, plasmids and other low-data contexts. Applied to single-species datasets and human gut metagenomes, SynTracker, combined with an SNP-based tool, detects strains enriched in either point mutations or structural changes, providing insights into microbial evolution in situ.},
}

Polymorphism, Single Nucleotide/genetics
Humans
*Synteny/genetics
*Microbiota/genetics
*Evolution, Molecular
Genome, Bacterial/genetics
Metagenome/genetics
Metagenomics/methods
Software

@article {pmid40340756,
year = {2025},
author = {Laue, HE and Willis, AD and Wang, F and MacDougall, MC and Xu, Y and Karagas, MR and Madan, JC and Fleisch, AF and Lanphear, BP and Cecil, KM and Yolton, K and Chen, A and Buckley, JP and Braun, JM},
title = {Early-life and concurrent predictors of the healthy adolescent microbiome in a cohort study.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {50},
pmid = {40340756},
issn = {1756-994X},
support = {K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; R35GM133420/GM/NIGMS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Adolescent ; Female ; Male ; Child ; *Gastrointestinal Microbiome ; Feces/microbiology ; Cohort Studies ; Metagenomics/methods ; },
abstract = {BACKGROUND: The microbiome of adolescents is poorly understood, as are factors influencing its composition. We aimed to describe the healthy adolescent microbiome and identify early-life and concurrent predictors of its composition.

METHODS: We performed metagenomic sequencing of 247 fecal specimens from 167 adolescents aged 11-14 years participating in the Health Outcomes and Measures of the Environment (HOME) Study, a longitudinal pregnancy and birth cohort (Cincinnati, OH). We described common features of the adolescent gut microbiome and applied self-organizing maps (SOMs)-a machine-learning approach-to identify distinct microbial profiles (n = 4). Using prospectively collected data on sociodemographic characteristics, lifestyle, diet, and sexual maturation, we identified early-life and concurrent factors associated with microbial diversity and phylum relative abundance with linear regression models and composition with Kruskal-Wallis and Fisher's exact tests.

RESULTS: We found that household income and other sociodemographic factors were consistent predictors of the microbiome, with higher income associated with lower diversity and differential relative abundances of Firmicutes (increased) and Actinobacteria (decreased). Sexual maturation, distinct from chronological age, was related to higher diversity in females and differences in phylum relative abundances and compositional profiles in both males and females.

CONCLUSIONS: Our study suggests that adolescence is a unique window for gut microbial composition and that it may be shaped by both early-life and concurrent exposures, highlighting its potential in future epidemiologic research.},
}

Humans
Adolescent
Female
Male
Child
*Gastrointestinal Microbiome
Feces/microbiology
Cohort Studies
Metagenomics/methods

@article {pmid40324646,
year = {2025},
author = {Shen, H and Wang, D and Huang, Y and Yang, Y and Ji, S and Zhu, W and Liu, Q},
title = {2,3,7,8-tetrachlorodibenzofuran modulates intestinal microbiota and tryptophan metabolism in mice.},
journal = {Life sciences},
volume = {373},
number = {},
pages = {123679},
doi = {10.1016/j.lfs.2025.123679},
pmid = {40324646},
issn = {1879-0631},
mesh = {Animals ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome/drug effects ; Mice ; Male ; *Polychlorinated Dibenzodioxins/toxicity ; Mice, Inbred C57BL ; Environmental Pollutants/toxicity ; Indoles/metabolism/pharmacology ; Intestinal Mucosa/metabolism/drug effects ; *Benzofurans/toxicity ; },
abstract = {Persistent organic pollutants (POPs) are known to disrupt gut microbiota composition and host metabolism, primarily through dietary exposure. In this study, we investigate the impact of 2,3,7,8-tetrachlorodibenzofuran (TCDF) on gut microbiota and host metabolic processes. RNA-seq analysis revealed that TCDF exposure significantly affected tryptophan metabolism, lipid metabolic pathways, and immune system function. Metagenomic and metabolomic analyses further showed that TCDF reduced the abundance of Mucispirillum schaedleri and levels of two key tryptophan metabolites, indole-3-carboxaldehyde (3-IAld) and Indole acrylic acid (IA). Supplementation with 3-IAld and IA alleviated TCDF-induced liver toxicity in mouse, as evidenced by reduced Cyp1a1 expression, and mitigated intestinal inflammation, reflected by lower pro-inflammatory cytokines (Ifn-γ and Il-1β) in the colon. Additionally, 3-IAld and IA supplementation enhanced intestinal barrier function, as demonstrated by increased Mucin 2 (MUC2) expression in the gut mucosa of mouse. These findings suggest that TCDF exposure disrupts the gut microbiome and host metabolic balance, and highlight the potential therapeutic role of tryptophan-derived metabolites in mitigating environmental pollutant-induced damage.},
}

Animals
*Tryptophan/metabolism
*Gastrointestinal Microbiome/drug effects
Mice
Male
*Polychlorinated Dibenzodioxins/toxicity
Mice, Inbred C57BL
Environmental Pollutants/toxicity
Indoles/metabolism/pharmacology
Intestinal Mucosa/metabolism/drug effects
*Benzofurans/toxicity

@article {pmid40315837,
year = {2025},
author = {Baker, JS and Qu, E and Mancuso, CP and Tripp, AD and Conwill, A and Lieberman, TD},
title = {Intraspecies dynamics underlie the apparent stability of two important skin microbiome species.},
journal = {Cell host & microbe},
volume = {33},
number = {5},
pages = {643-656.e7},
doi = {10.1016/j.chom.2025.04.010},
pmid = {40315837},
issn = {1934-6069},
mesh = {Humans ; *Skin/microbiology ; *Microbiota/genetics ; *Staphylococcus epidermidis/genetics/isolation & purification/classification ; *Propionibacterium acnes/genetics/isolation & purification/classification ; Adult ; Metagenome ; Genome, Bacterial ; Phylogeny ; Male ; Skin Microbiome ; },
abstract = {Adult human facial skin microbiomes are remarkably similar at the species level, dominated by Cutibacterium acnes and Staphylococcus epidermidis, yet each person harbors a unique community of strains. Understanding how person-specific communities assemble is critical for designing microbiome-based therapies. Here, using 4,055 isolate genomes and 356 metagenomes, we reconstruct on-person evolutionary history to reveal on- and between-person strain dynamics. We find that multiple cells are typically involved in transmission, indicating ample opportunity for migration. Despite this accessibility, family members share only some of their strains. S. epidermidis communities are dynamic, with each strain persisting for an average of only 2 years. C. acnes strains are more stable and have a higher colonization rate during the transition to an adult facial skin microbiome, suggesting this window could facilitate engraftment of therapeutic strains. These previously undetectable dynamics may influence the design of microbiome therapeutics and motivate the study of their effects on hosts.},
}

Humans
*Skin/microbiology
*Microbiota/genetics
*Staphylococcus epidermidis/genetics/isolation & purification/classification
*Propionibacterium acnes/genetics/isolation & purification/classification
Adult
Metagenome
Genome, Bacterial
Phylogeny
Male
Skin Microbiome

@article {pmid40287117,
year = {2025},
author = {Lu, W and Liu, Z and Song, Z and Wang, C and Yu, Z and Peng, S and Tian, Z and Lyu, A and Ning, Z},
title = {Vinegar-processed frankincense ameliorates ulcerative colitis by targeting BSH-active bacteria preference-mediated GDCA hydrolysis.},
journal = {Journal of ethnopharmacology},
volume = {348},
number = {},
pages = {119845},
doi = {10.1016/j.jep.2025.119845},
pmid = {40287117},
issn = {1872-7573},
mesh = {*Colitis, Ulcerative/drug therapy/chemically induced/microbiology ; Animals ; Mice ; *Acetic Acid/chemistry/pharmacology ; Hydrolysis ; Male ; *Amidohydrolases/metabolism ; Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Dextran Sulfate ; Mice, Inbred C57BL ; Bacteria/drug effects ; },
abstract = {Frankincense, is extensively used in both traditional Chinese medicine (TCM) and Indian practices for the treatment of ulcerative colitis (UC). In TCM, it is typically subjected to process with vinegar, which is believed to enhance its therapeutic efficacy. However, the underlying mechanism has yet to be elucidated.

AIM OF THE STUDY: To elucidate the underlying mechanism of frankincense vinegar processing from the perspective of bile salt hydrolase (BSH)-active bacteria preference and glycodeoxycholic acid (GDCA) hydrolysis.

MATERIALS AND METHODS: Dextran sodium sulfate (DSS)-induced UC model was used to elucidate the superior improving effects of vinegar-processed frankincense (PF). 16S rRNA and metagenomic sequencing along with ultra-high performance liquid chromatography-triple quadrupole mass spectroscopy (UHPLC-TQ-MS) were employed to reveal the differential bacteria and its related disturbance of GDCA. The effects of PF and GDCA on BSH-active bacteria were confirmed using real-time quantitative polymerase chain reaction (RT-qPCR) and in vitro experiments. Finally, the pro-inflammatory effects of GDCA and the mechanisms by which PF ameliorates UC were verified by establishing a UC pseudo-sterile mice model with GDCA intervention.

RESULTS: PF exhibited remarkable mitigating effects on UC (P < 0.05 or P < 0.01). Specifically, PF enhanced the BSH activity of Bifidobacterium longum and Lactobacillus acidophilus (P < 0.01), thereby promoting their dissociation efficiency toward glycine-conjugated bile acids (G-CBAs), particularly GDCA (P < 0.01). Furthermore, PF reduced GDCA levels by regulating the dissociation efficiency of Bifidobacterium longum and Lactobacillus acidophilus toward GDCA, thereby alleviating GDCA-induced exacerbation of UC.

CONCLUSION: PF exhibits its superior amelioration effects on UC by enhancing the dissociation efficiency of Bifidobacteruum longum and Lactobacillus acidophilus towards G-CBAs, particularly GDCA.},
}

*Colitis, Ulcerative/drug therapy/chemically induced/microbiology
Animals
Mice
*Acetic Acid/chemistry/pharmacology
Hydrolysis
Male
*Amidohydrolases/metabolism
Gastrointestinal Microbiome/drug effects
Disease Models, Animal
Dextran Sulfate
Mice, Inbred C57BL
Bacteria/drug effects

@article {pmid40179570,
year = {2025},
author = {Zhang, P and Liu, Y and Xu, M and Zhang, J and Xia, J and Shi, Y and Wang, J and Han, B and Feng, G},
title = {Gut microbiota characteristics and prognostic value in patients with aneurysmal subarachnoid hemorrhage: A clinical study.},
journal = {Journal of clinical neuroscience : official journal of the Neurosurgical Society of Australasia},
volume = {136},
number = {},
pages = {111200},
doi = {10.1016/j.jocn.2025.111200},
pmid = {40179570},
issn = {1532-2653},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Subarachnoid Hemorrhage/microbiology/diagnosis ; Male ; Female ; Middle Aged ; Prognosis ; Adult ; Aged ; Feces/microbiology ; },
abstract = {BACKGROUND: This study aims to explore the characteristics of gut microbiota in the aneurysmal subarachnoid hemorrhage (aSAH) group and the healthy control group, as well as in the good prognosis group and the poor prognosis group. It also investigates the relationship between the severity of aSAH and gut microbiota, and the predictive value of gut microbiota for the prognosis outcome of patients with aSAH.

METHODS: Stool samples from 22 patients with aSAH and 11 healthy controls were subjected to metagenomic sequencing, and species annotations were obtained through the taxonomic information database corresponding to the NR database. The characteristics of the gut microbiota in the aSAH group versus the healthy control group, and the good prognosis group versus the poor prognosis group were analyzed.The correlations between differential microbiota and clinical hematology markers between the aSAH and control groups and between gut microbiota and aSAH severity were analyzed. The prognosis of patients with aSAH after three months was assessed. Finally, gut microbiota with significant effects were screened for potential as biomarkers, and the predictive value of gut microbiota for different prognostic outcomes in patients with aSAH was explored.

RESULTS: Gut microbiota composition, diversity, and abundance differed significantly between patients in the aSAH group and the control group. Additionally, the composition, diversity, and abundance differed between patients with good and poor prognosis. Five dominant genera--Bacillus, Eggerthia, Hominisplanchenecus, Carnobacterium, and Bifidobacterium were identified as potential biomarkers for predicting aSAH outcomes.

CONCLUSION: Patients with aSAH have altered gut microbiota composition, structure, and diversity compared with the healthy population. These alterations may be potential biomarkers for aSAH diagnosis and outcome prediction.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Subarachnoid Hemorrhage/microbiology/diagnosis
Male
Female
Middle Aged
Prognosis
Adult
Aged
Feces/microbiology

@article {pmid40340623,
year = {2025},
author = {Deng, J and Zhang, J and Su, M and Li, J and Su, Y and Zhong, Q and Hu, J and Chen, Y and Liao, S and Lin, D and Guo, X},
title = {Fusobacterium mortiferum and its metabolite 5-aminovaleric acid promote the development of colorectal cancer in obese individuals through Wnt/β-catenin pathway by DKK2.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2502138},
pmid = {40340623},
issn = {1949-0984},
mesh = {*Colorectal Neoplasms/metabolism/microbiology/genetics/pathology ; Animals ; Humans ; Mice ; Gastrointestinal Microbiome ; *Fusobacterium/metabolism ; *Wnt Signaling Pathway/drug effects ; *Obesity/microbiology/metabolism/complications ; *Intercellular Signaling Peptides and Proteins/metabolism/genetics ; Male ; Female ; Cell Line, Tumor ; Cell Proliferation ; Mice, Inbred C57BL ; },
abstract = {Colorectal cancer (CRC) is one of the most prevalent cancers worldwide, with high incidence and mortality rates. An increasing body of research suggests that obesity is a significant risk factor for the development of CRC. Moreover, recent findings have highlighted the close association between the gut microbiota and both obesity and CRC. Despite this, the specific mechanisms by which the gut microbiota influences obesity and CRC remain unclear. This study aims to explore the role of the gut bacterium Fusobacterium mortiferum and its metabolite 5-aminovaleric acid (5-AVA) in the development of obesity and CRC. Our study found that the metabolite 5-aminovaleric acid produced by Fusobacterium mortiferum significantly inhibits the expression of the tumor suppressor DKK2. This inhibition leads to enhanced proliferation of CRC cells. Furthermore, we discovered that Fusobacterium mortiferum and 5-AVA can activate the Wnt/β-catenin signaling pathway by inhibiting DKK2, thereby promoting tumor growth. This finding was validated in CRC mouse models and in vitro experiments. Additional mechanistic studies revealed that 5-AVA interacts with the demethylase KDM6B, affecting the demethylation process of DKK2 and subsequently activating the Wnt/β-catenin signaling pathway. Our study retrospectively collected fecal samples from patients who underwent gastrointestinal endoscopy at the Sixth Affiliated Hospital of Sun Yat-sen University over the past five years. Participants were stratified into a healthy control group and an adenoma group based on the outcomes of their colonoscopies. Following this, we conducted metagenomic analysis to identify differential bacteria, and based on the results, we performed bacterial cultivation and metabolomic profiling. The roles of the targeted bacteria and their metabolites were further validated through animal models and cellular assays, employing techniques such as Western Blot, qPCR, immunohistochemistry, molecular docking simulations, and gene overexpression studies. This study uncovers the potential carcinogenic effects of Fusobacterium mortiferum and 5-AVA in the development of obesity and CRC. Our research emphasizes the complex interplay between the gut microbiota and host metabolism and suggests new directions for future research to explore how modulation of the gut microbiota could prevent and treat CRC.},
}

*Colorectal Neoplasms/metabolism/microbiology/genetics/pathology
Animals
Humans
Mice
Gastrointestinal Microbiome
*Fusobacterium/metabolism
*Wnt Signaling Pathway/drug effects
*Obesity/microbiology/metabolism/complications
*Intercellular Signaling Peptides and Proteins/metabolism/genetics
Male
Female
Cell Line, Tumor
Cell Proliferation
Mice, Inbred C57BL

@article {pmid40335921,
year = {2025},
author = {Jia, S and Mi, H and Su, Y and Liu, Y and Ming, Z and Lin, J},
title = {Changes of intestinal microbiome and its relationship with painful diabetic neuropathy in rats.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {281},
pmid = {40335921},
issn = {1471-2180},
support = {22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Diabetic Neuropathies/microbiology/pathology ; Rats ; Male ; Rats, Sprague-Dawley ; Diabetes Mellitus, Experimental/microbiology/complications ; Interleukin-1beta/metabolism ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Tumor Necrosis Factor-alpha/metabolism ; Diabetes Mellitus, Type 2/microbiology/complications ; Colon/pathology/microbiology ; Spinal Cord/pathology/metabolism ; },
abstract = {OBJECTIVE: To analyze the gut bacterial microbiome in rats with painful diabetic neuropathy (PDN) compared to normal rats.

METHODS: Type 2 diabetes was induced in rats via a high-fat and high-sugar diet combined with a low dose of streptozotocin. Glucose metabolism and insulin sensitivity were evaluated using intraperitoneal glucose tolerance tests and insulin tolerance tests. The progression of peripheral neuropathy was assessed using the mechanical withdrawal threshold and thermal withdrawal latency. Histopathological analysis of rat colon tissues was performed using hematoxylin-eosin staining to observe morphological changes. The expression levels of pro-inflammatory cytokines TNF-α and IL-1β in spinal cord tissues were measured using enzyme-linked immunosorbent assay (ELISA). Fecal samples were then collected for metagenomic sequencing and analysis.

RESULT: Behavioral tests revealed reduced mechanical withdrawal threshold and thermal withdrawal latency in PDN rats. Histological analysis showed significant colonic mucosal damage and inflammatory cell infiltration, suggesting impaired intestinal barrier function. Elevated TNF-α and IL-1β levels in spinal cord tissues further highlight peripheral inflammation's role in PDN. Sequencing analysis revealed significant differences in gut microbiota composition between PDN and control rats, with altered Bacillota/Bacteroidota ratios and increased Lactobacillus abundance. Functional annotation analysis, based on the KEGG, EggNOG, and CAZy databases, indicated significant enrichment of metabolic pathways related to carbohydrate and amino acid metabolism, energy metabolism, and cell structure biogenesis in PDN rats. Cluster analysis identified higher functional clustering in Metabolism and Genetic Information Processing pathways in PDN rats.

CONCLUSION: This study demonstrates that PDN leads to altered gut microbiota composition, disrupted metabolic pathways, and increased inflammation, contributing to the pathological progression of diabetic neuropathy. This study provides new insights into the interplay between gut microbiota and diabetic neuropathy, offering potential avenues for therapeutic interventions targeting microbiome and metabolism.},
}

Animals
*Gastrointestinal Microbiome
*Diabetic Neuropathies/microbiology/pathology
Rats
Male
Rats, Sprague-Dawley
Diabetes Mellitus, Experimental/microbiology/complications
Interleukin-1beta/metabolism
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Tumor Necrosis Factor-alpha/metabolism
Diabetes Mellitus, Type 2/microbiology/complications
Colon/pathology/microbiology
Spinal Cord/pathology/metabolism

@article {pmid40335750,
year = {2025},
author = {Deepali, D and Tejoprakash, N and Sudhakara Reddy, M},
title = {Diversity of Bacterial Communities in Seleniferous Soils and Their Impact on Plant Growth and Selenium Toxicity.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {285},
pmid = {40335750},
issn = {1432-0991},
mesh = {*Selenium/toxicity/metabolism ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism/drug effects ; *Soil/chemistry ; *Zea mays/growth & development/microbiology/drug effects ; Biodiversity ; *Microbiota ; Plant Roots/microbiology/growth & development ; *Soil Pollutants/toxicity ; Phylogeny ; },
abstract = {The present study aimed to investigate the diversity of bacterial communities in seleniferous soils using Illumina Mi-Seq Next-Generation Sequencing. This study also compared seleniferous soils (SE) with non-seleniferous (NS) soils to evaluate Selenium (Se) impact on microbial communities and soil properties. Metagenomic analysis identified Proteobacteria as the predominant phylum in both environments, with SE soils exhibiting a higher dominance (48%) than NS soils (31%). The most dominant operational taxonomic unit (OTU) across both soil types belonged to the genus Bacillus. Se altered microbial community composition, increasing the abundance of the Bacillaceae family (30%) and Pseudomonadaceae family (25%) compared to NS soil. Bacillus was the dominant genus in the SE environment indicating its tolerance to selenium. Diversity indices indicated that control soils had higher species richness, while SE soils exhibited a more stressed microbial structure. A consortium of bacterial isolates (Proteus terrae Se3, Halopseudomonas formosensis Se5, and Corynebacterium glutamicum Se38) was inoculated in maize plants cultivated in natural seleniferous soils. Plants inoculated with bacterial consortium grew more healthy and had greater biomass in their roots, shoots, and seeds. Bacterial inoculation results in lesser selenium accumulation in the roots, shoots and seeds of maize plants compared to non-inoculated plants. These results suggest that bacterial species from seleniferous soils may be employed as biofertilizers to enhance plant growth and help plants tolerate Se toxicity in seleniferous soils.},
}

*Selenium/toxicity/metabolism
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism/drug effects
*Soil/chemistry
*Zea mays/growth & development/microbiology/drug effects
Biodiversity
*Microbiota
Plant Roots/microbiology/growth & development
*Soil Pollutants/toxicity
Phylogeny

@article {pmid40335510,
year = {2025},
author = {Zhi, J and Liang, Y and Zhao, W and Qiao, J and Zheng, Y and Peng, X and Li, L and Wei, X and Wang, W},
title = {Oral microbiome-derived biomarkers for non-invasive diagnosis of head and neck squamous cell carcinoma.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {74},
pmid = {40335510},
issn = {2055-5008},
support = {82403470//National Natural Science Foundation of China/ ; 82401333//National Natural Science Foundation of China/ ; 21JCYBJC01570//Tianjin Municipal Science and Technology Committee/ ; 24JCQNJC01170//Tianjin Municipal Science and Technology Project/ ; TJWJ2023XK013//Tianjin Municipal Health Commission/ ; TJYXZDXK-046A//Tianjin Municipal Health Commission/ ; },
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Squamous Cell Carcinoma of Head and Neck/diagnosis/microbiology ; *Microbiota ; Male ; Cross-Sectional Studies ; Middle Aged ; Female ; *Head and Neck Neoplasms/diagnosis/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Metagenomics ; Dysbiosis/microbiology ; *Mouth/microbiology ; Adult ; Biomarkers/analysis ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Machine Learning ; Biomarkers, Tumor ; },
abstract = {Mounting evidence suggests that sustained microbial dysbiosis is associated with the development of multiple cancers, while the species-level bacterial taxa and metabolic dysfunction of oral microbiome in patients with head and neck squamous cell carcinoma (HNSCC) remains unclear. In this cross-sectional study, comprehensive metagenomic and 16S rRNA amplicon sequencing analyses of oral swab samples from 172 patients were performed. Unsupervised clustering algorithms of relative microbial abundance profiles revealed three distinctive microbiome clusters. Based on the metagenomic and 16S rRNA amplicon sequencing data, machine learning-based methods were used to construct the HNSCC diagnostic classifier, which exhibited high area under the curve values of 0.78-0.89. Our study provided the first exhaustive metagenomic and 16S rRNA amplicon sequencing analyses to date, revealing that microbial-metabolic dysbiosis is a potential risk factor for HNSCC progression and therefore providing a robust theoretical basis for potential diagnostic and therapeutic strategies for HNSCC patients.},
}

Humans
RNA, Ribosomal, 16S/genetics
*Squamous Cell Carcinoma of Head and Neck/diagnosis/microbiology
*Microbiota
Male
Cross-Sectional Studies
Middle Aged
Female
*Head and Neck Neoplasms/diagnosis/microbiology
*Bacteria/classification/genetics/isolation & purification
Aged
Metagenomics
Dysbiosis/microbiology
*Mouth/microbiology
Adult
Biomarkers/analysis
DNA, Bacterial/genetics
Sequence Analysis, DNA
Machine Learning
Biomarkers, Tumor

@article {pmid40170118,
year = {2025},
author = {Li, J and Sun, W and Cao, Y and Wu, J and Duan, L and Zhang, M and Luo, X and Deng, Q and Peng, Z and Mou, X and Li, W and Wang, P},
title = {Increased temperature enhances microbial-mediated lignin decomposition in river sediment.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {89},
pmid = {40170118},
issn = {2049-2618},
support = {32200090//National Natural Science Foundation of China/ ; 91951205//National Natural Science Foundation of China/ ; 2023A1515012270//Guangdong Basic and Applied Basic Research Foundation, China/ ; },
mesh = {*Lignin/metabolism ; *Geologic Sediments/microbiology/chemistry ; *Rivers/microbiology/chemistry ; *Bacteria/metabolism/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Carbon Dioxide/metabolism ; Temperature ; Microbiota ; Carbon Isotopes ; Metagenomics ; Benzaldehydes/metabolism ; Carbon Cycle ; },
abstract = {BACKGROUND: Lignin, as the most abundant recalcitrant organic carbon in terrestrial ecosystems, plays a crucial role in the Earth's carbon cycle. After lignin entering aquatic environments, portion of it tends to accumulate in sediments, forming a stable carbon relatively reservoir. However, the increasing temperature caused by human activities may impact microbial-mediated lignin decomposition, thereby affecting sedimentary carbon reservoirs. Therefore, revealing how temperature affects microbial-mediated lignin decomposition in river sediment, a topic that remains elusive, is essential for comprehending the feedbacks between river carbon reservoirs and climate. To address this, we conducted stable isotope probing of river surface sediment using [13]C-lignin and [13]C-vanillin, and utilized a series of techniques, including CO2 production analysis, 16S rRNA gene amplicon sequencing, metagenomics, and metatranscriptomics, to identify the lignin-decomposing microbes and the effects of temperature on microbial-mediated lignin decomposition.

RESULTS: We found that elevated temperatures not only increased the total sediment respiration (total CO2) and the CO2 emissions from lignin/vanillin decomposition, but also enhanced priming effects. The [13]C-labled taxa, including Burkholderiales, Sphingomonadales, and Pseudomonadales, were identified as the main potential lignin/vanillin decomposers, and their abundances and activity significantly increased as temperature increased. Furthermore, we observed that increasing temperature significantly increased the activity of lignin decomposing pathways, including β-aryl ether fragments and 4,5-PDOG pathway. Additionally, as temperature increases, the transcriptional abundances of other carbon cycling related genes, such as pulA (starch decomposition) and xyla (hemicellulose decomposition), also exhibited increasing trends. Overall, our study elucidated the potential lignin-decomposing microbes and pathways in river sediment and their responses to temperature increasing.

CONCLUSIONS: Our study demonstrated that the temperature increasing can increase the rate of lignin/vanillin decomposition via affecting the activity of lignin-decomposing microbes. This finding indicates that the ongoing intensification of global warming may enhance the decomposition of recalcitrant organic carbon in river sediment, thereby impacting global carbon cycling. Video Abstract.},
}

*Lignin/metabolism
*Geologic Sediments/microbiology/chemistry
*Rivers/microbiology/chemistry
*Bacteria/metabolism/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Carbon Dioxide/metabolism
Temperature
Microbiota
Carbon Isotopes
Metagenomics
Benzaldehydes/metabolism
Carbon Cycle

@article {pmid40335465,
year = {2025},
author = {Romano, S and Wirbel, J and Ansorge, R and Schudoma, C and Ducarmon, QR and Narbad, A and Zeller, G},
title = {Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4227},
pmid = {40335465},
issn = {2041-1723},
support = {BB/R012490/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BBS/E/F/000PR10356//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; SEG 9093//European Molecular Biology Organization (EMBO)/ ; EMBO ALTF 1030-2022//European Molecular Biology Organization (EMBO)/ ; 395357507 - SFB 1371//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Parkinson Disease/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; Humans ; *Machine Learning ; Metagenome ; },
abstract = {There is strong interest in using the gut microbiome for Parkinson's disease (PD) diagnosis and treatment. However, a consensus on PD-associated microbiome features and a multi-study assessment of their diagnostic value is lacking. Here, we present a machine learning meta-analysis of PD microbiome studies of unprecedented scale (4489 samples). Within most studies, microbiome-based machine learning models accurately classify PD patients (average AUC 71.9%). However, these models are study-specific and do not generalise well across other studies (average AUC 61%). Training models on multiple datasets improves their generalizability (average LOSO AUC 68%) and disease specificity as assessed against microbiomes from other neurodegenerative diseases. Moreover, meta-analysis of shotgun metagenomes delineates PD-associated microbial pathways potentially contributing to gut health deterioration and favouring the translocation of pathogenic molecules along the gut-brain axis. Strikingly, microbial pathways for solvent and pesticide biotransformation are enriched in PD. These results align with epidemiological evidence that exposure to these molecules increases PD risk and raise the question of whether gut microbes modulate their toxicity. Here, we offer the most comprehensive overview to date about the PD gut microbiome and provide future reference for its diagnostic and functional potential.},
}

*Parkinson Disease/microbiology/diagnosis
*Gastrointestinal Microbiome/genetics
Humans
*Machine Learning
Metagenome

@article {pmid40335388,
year = {2025},
author = {Dwivedi, SL and Vetukuri, RR and Kelbessa, BG and Gepts, P and Heslop-Harrison, P and Araujo, ASF and Sharma, S and Ortiz, R},
title = {Exploitation of rhizosphere microbiome biodiversity in plant breeding.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.04.004},
pmid = {40335388},
issn = {1878-4372},
abstract = {Climate change-induced stresses are perceived by plants at the root-soil interface, where they are alleviated through interactions between the host plant and the rhizosphere microbiome. The recruitment of specific microbiomes helps mitigate stress, increases resistance to pathogens, and promotes plant growth, development, and reproduction. The structure of the rhizosphere microbiome is shaped by crop domestication and variations in ploidy levels. Here we list key genes that regulate rhizosphere microbiomes and host genetic traits. We also discuss the prospects for rigorous analysis of symbiotic interactions, research needs, and strategies for systematically utilizing microbe-crop interactions to improve crop performance. Finally, we highlight challenges of maintaining live rhizosphere microbiome collections and mining heritable variability to enhance interactions between host plants and their rhizosphere microbiomes.},
}

@article {pmid40333159,
year = {2025},
author = {Gao, Y and Lou, Y and Hui, Y and Chen, H and Sang, H and Liu, F},
title = {Characterization of the Gut Microbiota in Patients with Psoriasis: A Systematic Review.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40333159},
issn = {2076-0817},
support = {22LCYY-QH10//Jinling Hospital/ ; },
mesh = {Humans ; *Dysbiosis/microbiology/therapy ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Probiotics/administration & dosage ; *Psoriasis/microbiology/therapy ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Background: Psoriasis is a prevalent and persistent inflammatory disorder with systemic manifestations. Emerging evidence implicates the gut microbiota in regulating inflammatory responses, metabolic pathways, and immune homeostasis. This review synthesizes current evidence on gut microbiota dysbiosis in psoriasis and evaluates the therapeutic potential of probiotics and fecal microbiota transplantation (FMT) in disease management. Method: Following PRISMA guidelines, we systematically reviewed studies investigating gut microbiome profiles in psoriasis through the MEDLINE, EMBASE, and Web of Science databases (January 2015-December 2024). Included studies utilized 16S rRNA gene sequencing or metagenomic analyses for microbial characterization. Results: Comparative analyses revealed distinct gut microbiota patterns in psoriasis patients compared with healthy controls, although specific microbial signatures exhibited inconsistencies across studies. Notably, interventions modulating gut microbiota composition-particularly probiotic supplementation-demonstrated measurable improvements in psoriasis severity scores and inflammatory markers. Conclusions: Gut microbiome modulation represents a promising therapeutic strategy for psoriasis; however, current evidence highlights the need for standardized microbial analysis methodologies and larger longitudinal studies to establish causality. Future research should prioritize the functional characterization of microbiota-host interactions to optimize therapeutic applications.},
}

Humans
*Dysbiosis/microbiology/therapy
Fecal Microbiota Transplantation
*Gastrointestinal Microbiome
Probiotics/administration & dosage
*Psoriasis/microbiology/therapy
RNA, Ribosomal, 16S/genetics

@article {pmid40333054,
year = {2025},
author = {Matos, JSS and Demoliner, M and Gularte, JS and Filippi, M and de Abreu Góes Pereira, VM and da Silva, MS and Weber, MN and de Barros, MP and Spilki, FR},
title = {Virome of Terrestrial Mammals and Bats from Southern Brazil: Circulation of New Putative Members of the Togaviridae Family and Other Findings.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40333054},
issn = {2076-0817},
support = {405786/2022-0//CNPQ/ ; },
mesh = {Animals ; Brazil/epidemiology ; *Chiroptera/virology ; *Virome ; *Mammals/virology ; Phylogeny ; Metagenomics ; Humans ; },
abstract = {The surveillance of wildlife viromes is essential for identifying zoonotic threats within the One Health framework. This study analyzed rectal and oral swabs from 88 individuals representing 13 species as felids, wild rodents, marsupials and non-human primates in Southern Brazil using metagenomic sequencing. Akodon montensis (n = 15 individuals) and Coendou spinosus (n = 4) harbored Chikungunya virus (ChikV, Togaviridae), marking its first detection in these hosts. Molossus molossus (n = 17) presented Coronaviridae and Orthoherpesviridae, while Eptesicus furinalis (n = 1) also carried Coronaviridae. A broad virome diversity, including Togaviridae and Adenoviridae members, was identified in Didelphis albiventris (n = 43), with significant relevance to human health. Additional species, such as Callithrix jacchus (n = 1), Leopardus guttulus (n = 1), Myocastor coypus (n = 1), Monodelphis iheringi (n = 1), Thaptomys nigrita (n = 1), Sooretamys angouya (n = 1), Brucepattersonius iheringi (n = 1), and Lasiurus blossevillii (n = 1), contributed to insights into viral reservoirs. These results underscore the importance of virome studies in regions harboring high biodiversity, emphasizing genomic surveillance as a vital tool for monitoring zoonotic viruses and safeguarding global health.},
}

Animals
Brazil/epidemiology
*Chiroptera/virology
*Virome
*Mammals/virology
Phylogeny
Metagenomics
Humans

@article {pmid40330019,
year = {2025},
author = {Fang, P and Wen, Y and Deng, W and Liang, R and He, P and Wang, C and Fan, N and Huo, K and Zhao, K and Li, C and Bai, Y and Ma, Y and Hu, L and Guan, Y and Yang, S},
title = {Investigation of dynamic microbial migration patterns in the respiratory tract.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1542562},
pmid = {40330019},
issn = {2235-2988},
mesh = {Humans ; *Respiratory Tract Infections/microbiology ; Prospective Studies ; Male ; Female ; Middle Aged ; *Microbiota ; Sputum/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Respiratory System/microbiology ; Adult ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Oropharynx/microbiology ; Bayes Theorem ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: The role of the respiratory microbiome in lung diseases is increasingly recognized, with the potential migration of respiratory pathogens being a significant clinical consideration. Despite its importance, evidence elucidating this phenomenon remains scarce.

METHODS: This prospective study collected clinical samples from patients with suspected lower respiratory tract infections (LRTI), including oropharyngeal swabs (OPS), sputum, and bronchoalveolar lavage fluid (BALF). Metagenomic next-generation sequencing (mNGS) was employed to analyze respiratory microbial diversity, complemented by Bayesian source tracking and sequence alignment analyses to explore pathogen migration patterns.

RESULTS: A cohort of 68 patients was enrolled, with 56 diagnosed with LRTI and 12 with non-infectious respiratory conditions. A statistically significant disparity in respiratory microbiome diversity was observed between infected and non-infected groups (p < 0.05). Intriguingly, no significant variations in microbial community structure, including alpha and beta diversity, were detected across different respiratory tract sites within individuals. The Bayesian source tracking analysis revealed a pronounced migration pattern among pathogens compared to the overall microbial community, with migration ratios of 51.54% and 1.92%, respectively (p < 0.05). Sequence similarity analysis further corroborated these findings, highlighting a notable homology among specific migrating pathogens.

CONCLUSION: This study represents a pioneering effort in deducing pathogen migration patterns through microbial source tracking analysis. The findings provide novel insights that could significantly advance clinical diagnostics and therapeutic strategies for respiratory infections.},
}

Humans
*Respiratory Tract Infections/microbiology
Prospective Studies
Male
Female
Middle Aged
*Microbiota
Sputum/microbiology
Bronchoalveolar Lavage Fluid/microbiology
Aged
*Respiratory System/microbiology
Adult
High-Throughput Nucleotide Sequencing
Metagenomics
Oropharynx/microbiology
Bayes Theorem
*Bacteria/classification/genetics/isolation & purification

@article {pmid40329426,
year = {2025},
author = {Ren, L and Yang, J and Xiao, Y and Guo, L and Rao, J and Wu, C and Wang, X and Wang, Y and Zhang, L and Zhang, L and Jiang, X and Zhong, J and Zhong, J and Yang, W and Wang, C and Wang, J and Li, M},
title = {Transmission of the human respiratory microbiome and antibiotic resistance genes in healthy populations.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {115},
pmid = {40329426},
issn = {2049-2618},
support = {2020-I2M-2-013//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2023-I2M-2-001//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2023-I2M-2-001//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2019PT310029//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; 2022YFA1304300//National Key R&D Program of China/ ; 2022YFA1304300//National Key R&D Program of China/ ; NSFC82221004//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Microbiota/genetics ; Female ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Male ; Adult ; Metagenomics/methods ; *Oropharynx/microbiology ; Middle Aged ; *Drug Resistance, Microbial/genetics ; Family Characteristics ; Young Adult ; Metagenome ; },
abstract = {BACKGROUND: The human microbiome is transmissible between individuals, including pathogens and commensals with metabolic and immune-modulating effects, which could influence susceptibility, severity, and outcomes of both infection and non-infection diseases. However, limited studies of respiratory microbiome transmission within populations have been conducted. Herein, we performed species- and strain-level metagenomic analyses on oropharyngeal (OP) swabs from 1046 healthy urban dwellers across 13 districts, including 111 households with at least two cohabitants, to elucidate the transmission dynamics of the respiratory microbiome within households and communities.

RESULTS: We found that geographic districts accounted for the greatest variation in the OP microbiome, with unrelated individuals from the same district showing greater microbiome similarity and higher strain-sharing rates than those from different districts. Cohabitants, especially spouses and siblings, exhibited similar microbial abundances and shared more strains, with 16.7% (IQR 0.0-33.3%) of strains shared among cohabitants, compared to 0.0% (IQR 0.0-11.1%) in non-cohabiting pairs (p < 0.05). Both respiratory commensals and opportunistic pathogens were shared among cohabitants. In contrast, no evidence of vertical transmission was detected between mother-offspring pairs. Additionally, the OP microbiome contained diverse antibiotic resistance genes (ARGs), with 15.0% linked to mobile genetic elements (MGEs) or plasmids; the flanking sequences of these ARGs were more conserved across species than those of non-MGE-associated ARGs, suggesting horizontal transfer of ARGs among respiratory microorganisms.

CONCLUSIONS: In summary, we characterized the transmissible nature of the OP microbiome and the risk of ARG dissemination among respiratory microorganisms. These findings underscore the role of respiratory microbes and ARGs exchange in shaping the microbiome of healthy populations and emphasize their relevance to public health strategies for respiratory health management. Video Abstract.},
}

Humans
*Microbiota/genetics
Female
*Bacteria/genetics/classification/isolation & purification/drug effects
Male
Adult
Metagenomics/methods
*Oropharynx/microbiology
Middle Aged
*Drug Resistance, Microbial/genetics
Family Characteristics
Young Adult
Metagenome

@article {pmid40329425,
year = {2025},
author = {Vigneron, A and Cloarec, LA and Brochier-Armanet, C and Flandrois, JP and Troussellier, M and Bernard, C and Agogué, H and Oger, PM and Hugoni, M},
title = {Genomic characterisation of novel extremophile lineages from the thalassohaline lake Dziani Dzaha expands the metabolic repertoire of the PVC superphylum.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {48},
pmid = {40329425},
issn = {2524-6372},
support = {project SUBSILAKE, ANR-21-CE02-0027//Agence Nationale de la Recherche/ ; project MARWEL, ANR-21-CE20-0049//Agence Nationale de la Recherche/ ; project SUBSILAKE, ANR-21-CE02-0027//Agence Nationale de la Recherche/ ; },
abstract = {BACKGROUND: Extreme environments are useful systems to investigate limits of life, microbial biogeography and ecology, and the adaptation and evolution of microbial lineages. Many novel microbial lineages have been discovered in extreme environments, especially from the Planctomycetota-Verrucomicrobiota-Chlamydiota (PVC) superphyla. However, their evolutionary history and roles in ecosystem functioning and microbiome assemblage are poorly understood.

RESULTS: Applying a genome-centric approach on an 8-year metagenomic timeseries produced from the hypersaline and hyperalkaline waters of Lake Dziani Dzaha (Mayotte), we recovered 5 novel PVC extremophilic candidate lineages from the biosphere of the lake. Sibling to Elusimicrobia and Omnitrophota, these lineages represented novel halophilic clades, with global distributions bounded to soda lakes and hypersaline hydrosystems. Genome mining of these newly defined clades revealed contrasted, but ecologically relevant, catabolic capabilities involved in the carbon, hydrogen and iron/electron cycles of the Dziani Dzaha ecosystem. This also includes extracellular electron transfer for two of them, suggesting metal reduction or potential electron exchanges with other members of the lake community. By contrast, a putative extracellular giant protein with multiple carbohydrate binding domains and toxin-like structures, as observed in virulence factors, was identified in the genome of another of these clades, suggesting predatory capabilities.

CONCLUSIONS: Our results provided genomic evidences for original metabolism in novel extremophile lineages of the PVC superphyla, revealing unforeseen implications for members of this widespread and diverse bacterial radiation in aquatic saline ecosystems. Finally, monitoring the in-situ distribution of these lineages through the timeseries reveals the drastic effects of environmental perturbations on extreme ecosystem biodiversity.},
}

@article {pmid40329386,
year = {2025},
author = {Hou, L and Zhao, Z and Steger-Mähnert, B and Jiao, N and Herndl, GJ and Zhang, Y},
title = {Microbial metabolism in laboratory reared marine snow as revealed by a multi-omics approach.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {114},
pmid = {40329386},
issn = {2049-2618},
support = {42206098//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; 42125603//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; MELRS2327//State Key Laboratory of Marine Environmental Science/ ; I4978-B//Austrian Science Fund/ ; },
mesh = {*Snow/microbiology ; Gammaproteobacteria/metabolism/genetics/classification ; Metagenomics/methods ; Metagenome ; *Seawater/microbiology ; *Microbiota ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Phytoplankton/microbiology/metabolism ; Multiomics ; },
abstract = {BACKGROUND: Marine snow represents an organic matter-rich habitat and provides substrates for diverse microbial populations in the marine ecosystem. However, the functional diversity and metabolic interactions within the microbial community inhabiting marine snow remain largely underexplored, particularly for specific metabolic pathways involved in marine snow degradation. Here, we used a multi-omics approach to explore the microbial response to laboratory-reared phytoplankton-derived marine snow.

RESULTS: Our results demonstrated a dramatic shift in both taxonomic and functional profiles of the microbial community after the formation of phytoplankton-derived marine snow using a rolling tank system. The changes in microbial metabolic processes were more pronounced in the metaproteome than in the metagenome in response to marine snow. Fast-growing taxa within the Gammaproteobacteria were the most dominant group at both the metagenomic and metaproteomic level. These Gammaproteobacteria possessed a variety of carbohydrate-active enzymes (CAZymes) and transporters facilitating substrate cleavage and uptake, respectively. Analysis of metagenome-assembled genomes (MAGs) revealed that the response to marine snow amendment was primarily mediated by Alteromonas, Vibrio, and Thalassotalea. Among these, Alteromonas exclusively expressing auxiliary activities 2 (AA2) of the CAZyme subfamily were abundant in both the free-living (FL) and marine snow-attached (MA) microbial communities. Thus, Alteromonas likely played a pivotal role in the degradation of marine snow. The enzymes of AA2 produced by these Alteromonas MAGs are capable of detoxifying peroxide intermediates generated during the breakdown of marine snow into smaller poly- and oligomers, providing available substrates for other microorganisms within the system. In addition, Vibrio and Thalassotalea MAGs exhibited distinct responses to these hydrolysis products of marine snow in different size fractions, suggesting a distinct niche separation. Although chemotaxis proteins were found to be enriched in the proteome of all three MAGs, differences in transporter proteins were identified as the primary factor contributing to the niche separation between these two groups. Vibrio in the FL fraction predominantly utilized ATP-binding cassette transporters (ABCTs), while Thalassotalea MAGs in the MA fraction primarily employed TonB-dependent outer membrane transporters (TBDTs).

CONCLUSIONS: Our findings shed light on the essential metabolic interactions within marine snow-degrading microbial consortia, which employ complementary physiological mechanisms and survival strategies to effectively scavenge marine snow. This work advances our understanding of the fate of marine snow and the role of microbes in carbon sequestration in the ocean. Video Abstract.},
}

*Snow/microbiology
Gammaproteobacteria/metabolism/genetics/classification
Metagenomics/methods
Metagenome
*Seawater/microbiology
*Microbiota
*Bacteria/classification/metabolism/genetics/isolation & purification
Phytoplankton/microbiology/metabolism
Multiomics

@article {pmid40328944,
year = {2025},
author = {Kim, Y and Worby, CJ and Acharya, S and van Dijk, LR and Alfonsetti, D and Gromko, Z and Azimzadeh, PN and Dodson, KW and Gerber, GK and Hultgren, SJ and Earl, AM and Berger, B and Gibson, TE},
title = {Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain.},
journal = {Nature microbiology},
volume = {10},
number = {5},
pages = {1184-1197},
pmid = {40328944},
issn = {2058-5276},
support = {R35GM143056//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R21AI154075//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35GM149270//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01DK121822//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U19AI110818//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35GM141861//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {Humans ; *Microbiota/genetics ; Feces/microbiology ; Female ; *Metagenomics/methods ; Bayes Theorem ; Longitudinal Studies ; Escherichia coli/genetics/isolation & purification/classification ; Infant ; Algorithms ; Enterococcus faecalis/genetics/isolation & purification/classification ; Adult ; *Bacteria/genetics/classification/isolation & purification ; },
abstract = {The ability to detect and quantify microbiota over time from shotgun metagenomic data has a plethora of clinical, basic science and public health applications. Given these applications, and the observation that pathogens and other taxa of interest can reside at low relative abundance, there is a critical need for algorithms that accurately profile low-abundance microbial taxa with strain-level resolution. Here we present ChronoStrain: a sequence quality- and time-aware Bayesian model for profiling strains in longitudinal samples. ChronoStrain explicitly models the presence or absence of each strain and produces a probability distribution over abundance trajectories for each strain. Using synthetic and semi-synthetic data, we demonstrate how ChronoStrain outperforms existing methods in abundance estimation and presence/absence prediction. Applying ChronoStrain to two human microbiome datasets demonstrated its improved interpretability for profiling Escherichia coli strain blooms in longitudinal faecal samples from adult women with recurring urinary tract infections, and its improved accuracy for detecting Enterococcus faecalis strains in infant faecal samples. Compared with state-of-the-art methods, ChronoStrain's ability to detect low-abundance taxa is particularly stark.},
}

Humans
*Microbiota/genetics
Feces/microbiology
Female
*Metagenomics/methods
Bayes Theorem
Longitudinal Studies
Escherichia coli/genetics/isolation & purification/classification
Infant
Algorithms
Enterococcus faecalis/genetics/isolation & purification/classification
Adult
*Bacteria/genetics/classification/isolation & purification

@article {pmid40328731,
year = {2025},
author = {Wei, C and Xu, X and Zhang, J and Wang, X and Han, T and Zhang, Y and Pan, S and Ming, Z and Li, R and Lou, F and Cheng, Y and Xu, H and Sun, X and Geng, G and Pan, Y and Liu, Q and Qi, H and Yan, X and Dang, K and Zhou, J and Sun, C and Li, Y},
title = {Timing of unsaturated fat intake improves insulin sensitivity via the gut microbiota-bile acid axis: a randomized controlled trial.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4211},
pmid = {40328731},
issn = {2041-1723},
support = {Key Program 82030100//National Natural Science Foundation of China (National Science Foundation of China)/ ; Joint Fund Project U24A20768//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Male ; *Insulin Resistance/physiology ; Female ; *Bile Acids and Salts/metabolism ; Blood Glucose/metabolism ; Postprandial Period ; Insulin/blood/metabolism ; Double-Blind Method ; Aged ; *Dietary Fats, Unsaturated/administration & dosage ; Feces/microbiology/chemistry ; Adult ; Prediabetic State/metabolism/diet therapy/microbiology ; },
abstract = {The timing of dietary total fat intake influences glucose homeostasis, however, the impact of unsaturated fat (USFA) intake has yet to be explored. This 12-week, double-blind, randomized, controlled, 2 × 2 factorial-designed feeding trial investigated the effects of timing (lunch or dinner) and types of dietary USFA (high monounsaturated fat or polyunsaturated fat diet) intake on glucose metabolism in seventy prediabetes participants (mean age, 57 years). Sixty participants with completed fecal samples were included in the final analysis (n = 15 for each group). Postprandial serum glucose was first primary outcome, postprandial insulin levels and insulin sensitivity indices were co-primary outcomes Secondary outcomes were continuous glucose levels, serum fatty acid profile, gut microbiome (metagenomic sequencing) and fecal metabolites. Results showed no significant differences in postprandial glucose between groups. However, USFA intake at lunch (vs. dinner) improved insulin sensitivity and reduced postprandial insulin and serum free saturated fatty acid (Ptiming < 0.05, Ptype > 0.05, Pinteraction > 0.05), which was associated with alterations in gut microbiome and bile acid metabolism, regardless of USFA type. In summary, these results suggest that advancing timing of USFA intake improves insulin sensitivity through the gut microbiome and bile acid metabolism. Trial registration: ChiCTR2100045645.},
}

Humans
*Gastrointestinal Microbiome/physiology
Middle Aged
Male
*Insulin Resistance/physiology
Female
*Bile Acids and Salts/metabolism
Blood Glucose/metabolism
Postprandial Period
Insulin/blood/metabolism
Double-Blind Method
Aged
*Dietary Fats, Unsaturated/administration & dosage
Feces/microbiology/chemistry
Adult
Prediabetic State/metabolism/diet therapy/microbiology

@article {pmid40325616,
year = {2025},
author = {Xu, HY and Jiang, MT and Yang, YF and Huang, Y and Yang, WD and Li, HY and Wang, X},
title = {Microalgae-Based Fucoxanthin Attenuates Rheumatoid Arthritis by Targeting the JAK-STAT Signaling Pathway and Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {19},
pages = {11708-11719},
doi = {10.1021/acs.jafc.4c12474},
pmid = {40325616},
issn = {1520-5118},
mesh = {*Xanthophylls/administration & dosage ; *Arthritis, Rheumatoid/drug therapy/microbiology/genetics/metabolism/immunology ; *Gastrointestinal Microbiome/drug effects ; Humans ; Signal Transduction/drug effects ; Animals ; *Microalgae/chemistry ; Mice ; Male ; *Janus Kinases/genetics/metabolism/immunology ; *STAT Transcription Factors/genetics/metabolism/immunology ; *Diatoms/chemistry ; },
abstract = {Fucoxanthin, an abundant carotenoid in marine algae, has garnered attention for its diverse health benefits, including anti-inflammatory and anticancer properties. Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by joint inflammation and damage. This study investigated the therapeutic potential of fucoxanthin extracted from Phaeodactylum tricornutum in collagen-induced RA. Our results demonstrated that fucoxanthin significantly alleviated RA symptoms, including weight loss, joint swelling, and decreased appetite. Histological analysis revealed that fucoxanthin mitigated synovial inflammation, cartilage damage, and bone erosion. Mechanistically, transcriptomic analysis and cell experiments indicated that fucoxanthin suppressed the JAK-STAT signaling pathway by downregulating the expression of inflammatory cytokines, such as IL-6 and IL-1β. Furthermore, metagenomic analysis suggested that fucoxanthin restored the altered gut microbiota composition associated with RA. These findings highlight the therapeutic potential of fucoxanthin from P. tricornutum in the management of RA by targeting multiple pathways, including inflammation and gut microbiota.},
}

*Xanthophylls/administration & dosage
*Arthritis, Rheumatoid/drug therapy/microbiology/genetics/metabolism/immunology
*Gastrointestinal Microbiome/drug effects
Humans
Signal Transduction/drug effects
Animals
*Microalgae/chemistry
Mice
Male
*Janus Kinases/genetics/metabolism/immunology
*STAT Transcription Factors/genetics/metabolism/immunology
*Diatoms/chemistry

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

*Wetlands
*Mycorrhizae/drug effects/genetics/physiology
*Pesticides/toxicity
*Microbiota/drug effects
Soil Microbiology
Stress, Physiological
Bacteria/genetics

@article {pmid40250268,
year = {2025},
author = {Yang, JH and Huang, DQ and Wu, GG and Han, NN and Fan, NS and Jin, RC},
title = {Quorum sensing-mediated microecological homeostasis in anammox consortia.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138285},
doi = {10.1016/j.jhazmat.2025.138285},
pmid = {40250268},
issn = {1873-3336},
mesh = {*Quorum Sensing ; Homeostasis ; *Ammonium Compounds/metabolism ; *Microbial Consortia ; Oxidation-Reduction ; Nitrogen/metabolism ; 4-Butyrolactone/analogs & derivatives/pharmacology ; Bioreactors/microbiology ; Bacteria/metabolism/genetics ; Anaerobiosis ; },
abstract = {Quorum sensing (QS) mediated by signal molecules regulates bacterial communication and further affects the performance and microbial physiological characteristics of anaerobic ammonium oxidation (anammox) process. The potential application of low concentrations of typical exogenous signal molecules into maintaining the long-term homeostasis of anammox consortia were evaluated in this study. The results of 150-d continuous-flow experiment showed that 30 μg L[-1]N-hexanoyl-homoserine lactone (C6-HSL) and diffusible signaling factor (DSF) could maintain the stable nitrogen removal efficiency of anammox systems (90.3 ± 3.6 % and 90.2 ± 3.8 %). C6-HSL and DSF also significantly promoted the anammox activity and the production of extracellular polymeric substances (EPS). Microbial community analysis indicated that the relative abundance of Candidatus Kuenenia fluctuated and finally maintained at 27.0 % and 39.3 %, which was still significantly higher than that of initial phase. Meanwhile, the abundances of functional genes related to anammox process (hzsA, hdh and nirS) increased significantly. Metagenomic analysis revealed that the abundances of main functional genes involved in nitrogen metabolism, amino acid metabolism and QS were significantly upregulated. The interspecies interactions were also enhanced through QS-mediated intercellular communication, which was beneficial to microecological homeostasis in anammox systems. In contrast, DSF exhibited the more significant and longer-lasting promotion impact, while the effect of C6-HSL was rapid. These findings reveal the potential regulatory mechanism of exogenous signaling molecules on anammox consortia and drive the potential application of signaling molecules in the anammox process to treat real wastewater.},
}

*Quorum Sensing
Homeostasis
*Ammonium Compounds/metabolism
*Microbial Consortia
Oxidation-Reduction
Nitrogen/metabolism
4-Butyrolactone/analogs & derivatives/pharmacology
Bioreactors/microbiology
Bacteria/metabolism/genetics
Anaerobiosis

@article {pmid40207938,
year = {2025},
author = {Zhao, D and Salas-Leiva, DE and Williams, SK and Dunn, KA and Shao, JD and Roger, AJ},
title = {Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data.},
journal = {mBio},
volume = {16},
number = {5},
pages = {e0069925},
doi = {10.1128/mbio.00699-25},
pmid = {40207938},
issn = {2150-7511},
support = {FRN-142349//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Eukaryota/genetics ; *Computational Biology/methods ; *Blastocystis/genetics ; Gastrointestinal Microbiome/genetics ; Metagenome ; Whole Genome Sequencing ; Software ; },
abstract = {UNLABELLED: Whole-genome shotgun (WGS) metagenomic sequencing of microbial communities enables the discovery of the functions, physiologies, and evolutionary histories of prokaryotic and eukaryotic microbes. However, metagenomic studies of microbial eukaryotes lag due to challenges in identifying and assembling high-quality genomes from WGS data. To address this problem, we developed Eukfinder, a bioinformatics pipeline that identifies potential eukaryotic sequences from WGS metagenomic data, with a complementary binning workflow for recovering nuclear and mitochondrial genomes. Eukfinder uses two specialized databases for read/contig classification, customizable to specific data sets or environments. We tested Eukfinder on simulated gut microbiome data sets which included varying numbers of reads from the protist Blastocystis, a human gut commensal. We also applied Eukfinder to previously published human gut microbiome WGS metagenomic data to recover new genomes of Blastocystis. Compared to other workflows, Eukfinder offers the potential to recover high-quality, near-complete genomes of diverse eukaryotes, including different Blastocystis subtypes, without relying on a reference genome. With sufficient sequencing depth, Eukfinder outperforms similar tools for recovering eukaryotic genomes from metagenomic data. Eukfinder is a valuable tool for reference-independent and cultivation-free studies of eukaryotic microbial genomes from environmental WGS metagenomic samples.

IMPORTANCE: Advancements in next-generation sequencing have made whole-genome shotgun (WGS) metagenomic sequencing an efficient method for de novo reconstruction of microbial genomes from various environments. Thousands of new prokaryotic genomes have been characterized; however, the large size and complexity of protistan genomes have hindered the use of WGS metagenomics to sample microbial eukaryotic diversity. Eukfinder enables the recovery of eukaryotic microbial genomes from environmental WGS metagenomic samples. Retrieval of high-quality protistan genomes from diverse metagenomic samples increases the number of reference genomes available. This aids future metagenomic investigations into the functions, physiologies, and evolutionary histories of eukaryotic microbes in the gut microbiome and other ecosystems.},
}

*Metagenomics/methods
Humans
*Eukaryota/genetics
*Computational Biology/methods
*Blastocystis/genetics
Gastrointestinal Microbiome/genetics
Metagenome
Whole Genome Sequencing
Software

@article {pmid40188549,
year = {2025},
author = {Sun, J and Yang, W and Li, M and Zhang, S and Sun, Y and Wang, F},
title = {Metagenomic analysis reveals soil microbiome responses to microplastics and ZnO nanoparticles in an agricultural soil.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138164},
doi = {10.1016/j.jhazmat.2025.138164},
pmid = {40188549},
issn = {1873-3336},
mesh = {*Zinc Oxide/toxicity ; *Microplastics/toxicity ; *Soil Microbiology ; *Microbiota/drug effects ; *Soil Pollutants/toxicity ; Metagenomics ; *Nanoparticles/toxicity ; Bacteria/drug effects/genetics ; Agriculture ; Fungi/drug effects/genetics ; Soil/chemistry ; *Metal Nanoparticles/toxicity ; },
abstract = {Both microplastics (MPs) and engineered nanoparticles are pervasive emerging contaminants that can produce combined toxicity to terrestrial ecosystems, yet their effects on soil microbiomes remain inadequately understood. Here, metagenomic analysis was employed to investigate the impacts of three common MPs [i.e., polyethylene (PE), polystyrene (PS), and polylactic acid (PLA)] and zinc oxide nanoparticles (nZnO) on soil microbiomes. Both MPs and nZnO significantly altered the taxonomic, genetic, and functional diversity of soil microbes, with distinct effects depending on dosage or type. Archaea, fungi, and viruses exhibited more pronounced responses compared to bacteria. Higher doses of MPs and nZnO reduced gene abundance for nutrient cycles like C degradation and N cycling, but enhanced CO2 fixation and S metabolism. nZnO consistently decreased the complexity, connectivity, and modularity of microbial networks; however, these negative effects could be mitigated by co-existing MPs, particularly at elevated doses. Notably, PLA (10 %, w/w) exhibited greater harm to fungal communities and increased negative interactions between microbes and nutrient-cycling genes, posing unique risks compared to PE and PS. These findings demonstrate that MPs and nZnO interact synergistically, complicating ecological predictions and emphasizing the need to consider pollutant interactions in ecological risk assessments, particularly for biodegradable MPs.},
}

*Zinc Oxide/toxicity
*Microplastics/toxicity
*Soil Microbiology
*Microbiota/drug effects
*Soil Pollutants/toxicity
Metagenomics
*Nanoparticles/toxicity
Bacteria/drug effects/genetics
Agriculture
Fungi/drug effects/genetics
Soil/chemistry
*Metal Nanoparticles/toxicity

@article {pmid40168930,
year = {2025},
author = {Tang, GX and Huang, YH and Feng, LW and Hu, YC and Wei, JL and Lü, H and Liu, LH and Zhao, HM and Xiang, L and Li, H and Mo, CH and Li, YW and Cai, QY},
title = {New insights into rhizosphere bacterial community shaped by lettuce genotypes for divergent degradation efficiencies of phthalates.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138077},
doi = {10.1016/j.jhazmat.2025.138077},
pmid = {40168930},
issn = {1873-3336},
mesh = {*Rhizosphere ; *Lactuca/genetics/microbiology/metabolism ; Genotype ; *Soil Pollutants/metabolism ; *Bacteria/genetics/metabolism ; Soil Microbiology ; Biodegradation, Environmental ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology/metabolism ; *Diethylhexyl Phthalate/metabolism ; *Phthalic Acids/metabolism ; Microbiota ; },
abstract = {Rhizosphere dissipation of organic pollutants benefits safe utilization of the polluted agricultural soil. Nevertheless, dissipation variation of phthalates (PAEs) in rhizosphere among different vegetable genotypes and the related microbial mechanisms remain unknown. Here, twelve lettuce cultivars with different genetic relationships identified by 18S rRNA gene sequencing were cultivated in soil spiked with di-(2-ethylhexyl) phthalate (DEHP). Bacterial communities and function genes in rhizosphere of lettuce were analyzed by 16S rRNA gene and metagenomic sequencing. Results showed significant variations in DEHP concentrations of roots (2.8-15.3 mg/kg) and shoots (0.70-1.8 mg/kg) among 12 cultivars. Notably, cultivars L11 and L12 showed the lowest DEHP accumulation in roots and shoots, being lower by 82 % and 58 % than the highest accumulators (cultivars L5 and L6), respectively. This accumulation variation was closely connected with their genetic relationships and exhibited genotype-dependent trait. The significantly different bacterial community diversities and structures were recorded in rhizosphere among 12 cultivars. Especially, bacterial communities in rhizosphere of cultivars L11 and L12 (low-DEHP accumulators with high DEHP dissipation) strengthened their adaptation by enriching pollutant-resistant taxa, increasing extracellular polymeric substance contents and biofilm formation, as well as constructing complex ecological networks under DEHP pollution. Moreover, PAE-degrading bacteria and genes (e.g., hydrolase65, phtAb, and pcaI) in rhizosphere were enriched by low-DEHP accumulators, which benefited DEHP removal and subsequently safe agricultural products. This study provides new insights into microbial mechanisms on rhizosphere DEHP degradation and its correlation with accumulation variation among different crop genotypes.},
}

*Rhizosphere
*Lactuca/genetics/microbiology/metabolism
Genotype
*Soil Pollutants/metabolism
*Bacteria/genetics/metabolism
Soil Microbiology
Biodegradation, Environmental
RNA, Ribosomal, 16S/genetics
Plant Roots/microbiology/metabolism
*Diethylhexyl Phthalate/metabolism
*Phthalic Acids/metabolism
Microbiota

@article {pmid40131312,
year = {2025},
author = {Herazo-Álvarez, J and Mora, M and Cuadros-Orellana, S and Vilches-Ponce, K and Hernández-García, R},
title = {A review of neural networks for metagenomic binning.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
pmid = {40131312},
issn = {1477-4054},
support = {2022-21221825//National Agency for Research and Development/ ; EQM210185//Fondequip/ ; },
mesh = {*Metagenomics/methods ; *Neural Networks, Computer ; *Metagenome ; Humans ; Microbiota ; Machine Learning ; Deep Learning ; },
abstract = {One of the main goals of metagenomic studies is to describe the taxonomic diversity of microbial communities. A crucial step in metagenomic analysis is metagenomic binning, which involves the (supervised) classification or (unsupervised) clustering of metagenomic sequences. Various machine learning models have been applied to address this task. In this review, the contributions of artificial neural networks (ANN) in the context of metagenomic binning are detailed, addressing both supervised, unsupervised, and semi-supervised approaches. 34 ANN-based binning tools are systematically compared, detailing their architectures, input features, datasets, advantages, disadvantages, and other relevant aspects. The findings reveal that deep learning approaches, such as convolutional neural networks and autoencoders, achieve higher accuracy and scalability than traditional methods. Gaps in benchmarking practices are highlighted, and future directions are proposed, including standardized datasets and optimization of architectures, for third-generation sequencing. This review provides support to researchers in identifying trends and selecting suitable tools for the metagenomic binning problem.},
}

*Metagenomics/methods
*Neural Networks, Computer
*Metagenome
Humans
Microbiota
Machine Learning
Deep Learning

@article {pmid40086246,
year = {2025},
author = {Han, NN and Yang, JH and Wu, GG and Yang, JH and Jin, JA and Fan, NS and Jin, RC},
title = {Differential size-dependent response patterns and antibiotic resistance development mechanism in anammox consortia.},
journal = {Journal of hazardous materials},
volume = {491},
number = {},
pages = {137886},
doi = {10.1016/j.jhazmat.2025.137886},
pmid = {40086246},
issn = {1873-3336},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Sulfamethazine/pharmacology ; Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; Oxidation-Reduction ; *Ammonia/metabolism ; Anaerobiosis ; Pseudomonas/genetics/drug effects/metabolism ; *Microbial Consortia ; },
abstract = {Antibiotic resistance is a global threat to human and animal health. Anaerobic ammonia oxidation (anammox) is an efficient and innovative wastewater treatment technology, which can be served as a promising approach to teat antibiotic wastewater. This study systematically investigated effects of sulfamethazine on the performance, microbial community dynamics and the resistome in anammox systems inoculated with different-sized granular sludge. The activity and performance of small (< 0.5 mm) anammox granules were more susceptible to sulfamethazine stress than those of medium (0.5-1.0 mm) and large (1.0-2.0 mm) granules. Sulfamethazine addition greatly increased the diversity and abundance of mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs). Based on the metagenomic analysis, the horizontal transfer of ARGs in the anammox system was upregulated through bacterial oxidative stress, pili synthesis and type IV secretion system. In addition, two strains of sulfamethazine-resistant bacteria (Pseudomonas asiatica sp. nov. and Pseudomonas shirazica sp. nov.) were isolated from the anammox system. Their whole genome sequencing results showed that the most abundant plasmid was pkF7158B, which mediated the horizontal transfer of two main multidrug resistance genes (cpxR and mexB). This work provides a holistic insight into microbial heterogeneity of different-sized anammox granular sludge and their evolution and resistance development mechanism.},
}

*Anti-Bacterial Agents/pharmacology
*Sulfamethazine/pharmacology
Sewage/microbiology
*Drug Resistance, Microbial/genetics
Oxidation-Reduction
*Ammonia/metabolism
Anaerobiosis
Pseudomonas/genetics/drug effects/metabolism
*Microbial Consortia

@article {pmid40318372,
year = {2025},
author = {Chu, D and Zhang, H and Wang, Z and Ning, K},
title = {Microbial resources and interactions across three-dimensional space for a freshwater ecosystem.},
journal = {The Science of the total environment},
volume = {980},
number = {},
pages = {179522},
doi = {10.1016/j.scitotenv.2025.179522},
pmid = {40318372},
issn = {1879-1026},
mesh = {*Ecosystem ; *Fresh Water/microbiology ; China ; *Water Microbiology ; *Microbiota ; Bacteria ; Metagenome ; Lakes/microbiology ; *Environmental Monitoring ; },
abstract = {Freshwater ecosystems are important natural resources but face serious threats. Nevertheless, they host diverse microorganisms crucial for biosynthetic potential and global biochemical cycles. To fully understand the enrichment and interaction of species and functional resources in freshwater ecosystems, it is essential to profile the microbial resources in the whole three-dimensional space. We profiled 131 metagenomic samples to construct the Honghu Microbial Catalog, comprising 2617 metagenome-assembled genomes, 1718 candidate species, over 60 million non-redundant gene clusters, and 7396 biosynthetic gene clusters. We emphasized surface water may be the primary source of microbial species and ARGs for Honghu Lake. We also found the impact of surface water on groundwater had an "influence sphere". Furthermore, we have identified groundwater as a potential refuge for microbial resources, enriched with CPR bacteria and ARGs. These findings are crucial for the understanding, management, and protection of freshwater ecosystems.},
}

*Ecosystem
*Fresh Water/microbiology
China
*Water Microbiology
*Microbiota
Bacteria
Metagenome
Lakes/microbiology
*Environmental Monitoring

@article {pmid40315414,
year = {2025},
author = {Galperina, A and Lugli, GA and Milani, C and De Vos, WM and Ventura, M and Salonen, A and Hurwitz, B and Ponsero, AJ},
title = {The Aggregated Gut Viral Catalogue (AVrC): A unified resource for exploring the viral diversity of the human gut.},
journal = {PLoS computational biology},
volume = {21},
number = {5},
pages = {e1012268},
pmid = {40315414},
issn = {1553-7358},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Virome/genetics ; *Viruses/genetics/classification ; Computational Biology/methods ; Feces/virology ; Metagenome/genetics ; Infant ; Databases, Genetic ; },
abstract = {The growing interest in the role of the gut virome in human health and disease, has led to several recent large-scale viral catalogue projects mining human gut metagenomes each using varied computational tools and quality control criteria. Importantly, there has been to date no consistent comparison of these catalogues' quality, diversity, and overlap. In this project, we therefore systematically surveyed nine previously published human gut viral catalogues. While these catalogues collectively screened >40,000 human fecal metagenomes, 82% of the recovered 345,613 viral sequences were unique to one catalogue, highlighting limited redundancy between the ressources and suggesting the need for an aggregated resource bringing these viral sequences together. We further expanded these viral catalogues by mining 7,867 infant gut metagenomes from 12 large-scale infant studies collected in 9 different countries. From these datasets, we constructed the Aggregated Gut Viral Catalogue (AVrC), a unified modular resource containing 1,018,941 dereplicated viral sequences (449,859 species-level vOTUs). Using computational inference tools, annotations were obtained for each vOTU representative sequence quality, viral taxonomy, predicted viral lifestyle, and putative host. This project aims to facilitate the reuse of previously published viral catalogues by the research community and follows a modular framework to enable future expansions as novel data becomes available.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Virome/genetics
*Viruses/genetics/classification
Computational Biology/methods
Feces/virology
Metagenome/genetics
Infant
Databases, Genetic

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

Animals
*Food Hypersensitivity/immunology
*Diet, High-Fat/adverse effects
Mice
Mice, Inbred BALB C
Gastrointestinal Microbiome/drug effects
Ovalbumin/immunology
Immunoglobulin E/blood
*Microplastics/toxicity
Administration, Oral
*Polystyrenes/toxicity
Female

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

Animals
*Gastrointestinal Microbiome/physiology
*Deer/microbiology/metabolism
*Seasons
*Metabolome
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/metabolism/isolation & purification
Metagenomics
Fatty Acids, Volatile/metabolism
Tibet
Feces/microbiology
Metabolomics
Phylogeny

@article {pmid40172536,
year = {2025},
author = {Madison, JD and Osborne, OG and Ellison, A and Garvey Griffith, CN and Gentry, L and Gross, H and Gratwicke, B and Grayfer, L and Muletz-Wolz, CR},
title = {Probiotic colonization of Xenopus laevis skin causes short-term changes in skin microbiomes and gene expression.},
journal = {Infection and immunity},
volume = {93},
number = {5},
pages = {e0056924},
doi = {10.1128/iai.00569-24},
pmid = {40172536},
issn = {1098-5522},
support = {IOS-2131060//National Science Foundation/ ; IOS-2131061//National Science Foundation/ ; BB/W013517/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; *Skin/microbiology/immunology ; *Xenopus laevis/microbiology/immunology/genetics ; *Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; Batrachochytrium ; Transcriptome ; },
abstract = {Probiotic therapies have been suggested for amelioration efforts of wildlife disease such as chytridiomycosis caused by Batrachochytrium spp. in amphibians. However, there is a lack of information on how probiotic application affects resident microbial communities and immune responses. To better understand these interactions, we hypothesized that probiotic application would alter microbial community composition and host immune expression in Xenopus laevis. Accordingly, we applied three amphibian-derived and anti-Batrachochytrium bacteria strains (two Pseudomonas spp. and one Stenotrophomonas sp.) to X. laevis in monoculture and also as a cocktail. We quantified microbial community structure using 16S rRNA gene sequencing. We also quantified genes involved in X. laevis immune responses using quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) and skin transcriptomics over 1 and 3-week periods. All probiotic treatments successfully colonized X. laevis skin for 3 weeks, but with differential amplicon sequence variant (ASV) sequence counts over time. Bacterial community and immune gene effects were most pronounced at week 1 post-probiotic exposure and decreased thereafter. All probiotic treatments caused initial changes to bacterial community alpha and beta diversity, including reduction in diversity from pre-exposure anti-Batrachochytrium bacterial ASV relative abundance. Probiotic colonization by Pseudomonas probiotic strain RSB5.4 reduced expression of regulatory T cell marker (FOXP3, measured with RT-qPCR) and caused the greatest gene expression changes detected by transcriptomics. Single bacterial strains and mixed cultures, therefore, altered amphibian microbiome-immune interactions. This work will help to improve our understanding of the role of the microbiome-immune interface underlying both disease dynamics and emergent eco-evolutionary processes.IMPORTANCEAmphibian skin microbial communities have an important role in determining disease outcomes, in part through complex yet poorly understood interactions with host immune systems. Here we report that probiotic-induced changes to the Xenopus laevis frog skin microbial communities also result in significant alterations to these animals' immune gene expression. These findings underscore the interdependence of amphibian skin immune-microbiome interactions.},
}

Animals
*Probiotics/pharmacology/administration & dosage
*Skin/microbiology/immunology
*Xenopus laevis/microbiology/immunology/genetics
*Microbiota/drug effects
RNA, Ribosomal, 16S/genetics
Batrachochytrium
Transcriptome

@article {pmid39543873,
year = {2025},
author = {Saraswat, I and Goel, A},
title = {Therapeutic Modulation of the Microbiome in Oncology: Current Trends and Future Directions.},
journal = {Current pharmaceutical biotechnology},
volume = {26},
number = {5},
pages = {680-699},
pmid = {39543873},
issn = {1873-4316},
mesh = {Humans ; *Neoplasms/microbiology/therapy/immunology ; Probiotics/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Microbiota/drug effects ; },
abstract = {Cancer is a predominant cause of mortality worldwide, necessitating the development of innovative therapeutic techniques. The human microbiome, particularly the gut microbiota, has become a significant element in cancer research owing to its essential role in sustaining health and influencing disease progression. This review examines the microbiome's makeup and essential functions, including immunological modulation and metabolic regulation, which may be evaluated using sophisticated methodologies such as metagenomics and 16S rRNA sequencing. The microbiome influences cancer development by promoting inflammation, modulating the immune system, and producing carcinogenic compounds. Dysbiosis, or microbial imbalance, can undermine the epithelial barrier and facilitate cancer. The microbiome influences chemotherapy and radiation results by modifying drug metabolism, either enhancing or reducing therapeutic efficacy and contributing to side effects and toxicity. Comprehending these intricate relationships emphasises the microbiome's significance in oncology and accentuates the possibility for microbiome-targeted therapeutics. Contemporary therapeutic approaches encompass the utilisation of probiotics and dietary components to regulate the microbiome, enhance treatment efficacy, and minimise unwanted effects. Advancements in research indicate that personalised microbiome-based interventions, have the potential to transform cancer therapy, by providing more effective and customised treatment alternatives. This study aims to provide a comprehensive analysis of the microbiome's influence on the onset and treatment of cancer, while emphasising current trends and future possibilities for therapeutic intervention.},
}

Humans
*Neoplasms/microbiology/therapy/immunology
Probiotics/therapeutic use
*Gastrointestinal Microbiome/drug effects
Animals
*Microbiota/drug effects

@article {pmid40244062,
year = {2025},
author = {Stevens, EJ and Li, JD and Hector, TE and Drew, GC and Hoang, K and Greenrod, STE and Paterson, S and King, KC},
title = {Within-host competition causes pathogen molecular evolution and perpetual microbiota dysbiosis.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40244062},
issn = {1751-7370},
support = {COEVOPRO 802242//European Research Council Starting/ ; 802242//European Research Council Starting Grant/ ; //EPA Cephalosporin Junior Research Fellowship at Linacre College/ ; },
mesh = {Animals ; *Evolution, Molecular ; *Dysbiosis/microbiology ; *Microbiota ; *Staphylococcus aureus/genetics/pathogenicity/physiology ; Virulence ; Whole Genome Sequencing ; *Host-Pathogen Interactions ; Biofilms/growth & development ; Caenorhabditis elegans/microbiology ; },
abstract = {Pathogens newly invading a host must compete with resident microbiota. This within-host microbial warfare could lead to more severe disease outcomes or constrain the evolution of virulence. By passaging a widespread pathogen (Staphylococcus aureus) and a natural microbiota community across populations of nematode hosts, we show that the pathogen displaced microbiota and reduced species richness, but maintained its virulence across generations. Conversely, pathogen populations and microbiota passaged in isolation caused more host harm relative to their respective no-host controls. For the evolved pathogens, this increase in virulence was partly mediated by enhanced biofilm formation and expression of the global virulence regulator agr. Whole genome sequencing revealed shifts in the mode of selection from directional (on pathogens evolving in isolation) to fluctuating (on pathogens evolving in host microbiota). This approach also revealed that competitive interactions with the microbiota drove early pathogen genomic diversification. Metagenome sequencing of the passaged microbiota shows that evolution in pathogen-infected hosts caused a significant reduction in community stability (dysbiosis), along with restrictions on the co-existence of some species based on nutrient competition. Our study reveals how microbial competition during novel infection could determine the patterns and processes of evolution with major consequences for host health.},
}

Animals
*Evolution, Molecular
*Dysbiosis/microbiology
*Microbiota
*Staphylococcus aureus/genetics/pathogenicity/physiology
Virulence
Whole Genome Sequencing
*Host-Pathogen Interactions
Biofilms/growth & development
Caenorhabditis elegans/microbiology

@article {pmid40189243,
year = {2025},
author = {Chitcharoen, S and Sawaswong, V and Klomkliew, P and Chanchaem, P and Payungporn, S},
title = {Comparative analysis of human gut bacterial microbiota between shallow shotgun metagenomic sequencing and full-length 16S rDNA amplicon sequencing.},
journal = {Bioscience trends},
volume = {19},
number = {2},
pages = {232-242},
doi = {10.5582/bst.2024.01393},
pmid = {40189243},
issn = {1881-7823},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Feces/microbiology ; *Bacteria/genetics/classification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Metagenome ; Sequence Analysis, DNA/methods ; },
abstract = {The human gut microbiome is increasingly recognized as important to health and disease, influencing immune function, metabolism, mental health, and chronic illnesses. Two widely used, cost-effective, and fast approaches for analyzing gut microbial communities are shallow shotgun metagenomic sequencing (SSMS) and full-length 16S rDNA sequencing. This study compares these methods across 43 stool samples, revealing notable differences in taxonomic and species-level detection. At the genus level, Bacteroides was most abundant in both methods, with Faecalibacterium showing similar trends but Prevotella was more abundant in full-length 16S rDNA. Genera such as Alistipes and Akkermansia were more frequently detected by full-length 16S rDNA, whereas Eubacterium and Roseburia were more prevalent in SSMS. At the species level, Faecalibacterium prausnitzii, a key indicator of gut health, was abundant across both datasets, while Bacteroides vulgatus was more frequently detected by SSMS. Species within Parabacteroides and Bacteroides were primarily detected by 16S rDNA, contrasting with higher SSMS detection of Prevotella copri and Oscillibacter valericigenes. LEfSe analysis identified 18 species (9 species in each method) with significantly different detection between methods, underscoring the impact of methodological choice on microbial diversity and abundance. Differences in classification databases, such as Ribosomal Database Project (RDP) for 16S rDNA and Kraken2 for SSMS, further highlight the influence of database selection on outcomes. These findings emphasize the importance of carefully selecting sequencing methods and bioinformatics tools in microbiome research, as each approach demonstrates unique strengths and limitations in capturing microbial diversity and relative abundances.},
}

Humans
*Gastrointestinal Microbiome/genetics
*RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
Feces/microbiology
*Bacteria/genetics/classification
DNA, Bacterial/genetics
DNA, Ribosomal/genetics
Metagenome
Sequence Analysis, DNA/methods

@article {pmid40116459,
year = {2025},
author = {Blakeley-Ruiz, JA and Bartlett, A and McMillan, AS and Awan, A and Walsh, MV and Meyerhoffer, AK and Vintila, S and Maier, JL and Richie, TG and Theriot, CM and Kleiner, M},
title = {Dietary protein source alters gut microbiota composition and function.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf048},
pmid = {40116459},
issn = {1751-7370},
support = {7002782//USDA National Institute of Food and Agriculture, Hatch/ ; P30 DK034987/NH/NIH HHS/United States ; 7002782//USDA National Institute of Food and Agriculture/ ; P30 DK034987/NH/NIH HHS/United States ; },
mesh = {Animals ; *Dietary Proteins/metabolism/administration & dosage ; Mice ; *Gastrointestinal Microbiome/drug effects ; Metagenomics ; *Bacteria/classification/genetics ; Mice, Inbred C57BL ; Proteomics ; Diet ; Male ; Amino Acids/metabolism ; },
abstract = {The source of protein in a person's diet affects their total life expectancy. However, the mechanisms by which dietary protein sources differentially impact human health and life expectancy are poorly understood. Dietary choices impact the composition and function of the intestinal microbiota that ultimately modulate host health. This raises the possibility that health outcomes based on dietary protein sources might be driven by interactions between dietary protein and the gut microbiota. In this study, we determined the effects of seven different sources of dietary protein on the gut microbiota of mice using an integrated metagenomics-metaproteomics approach. The protein abundances measured by metaproteomics can provide microbial species abundances, and evidence for the molecular phenotype of microbiota members because measured proteins indicate the metabolic and physiological processes used by a microbial community. We showed that dietary protein source significantly altered the species composition and overall function of the gut microbiota. Different dietary protein sources led to changes in the abundance of microbial proteins involved in the degradation of amino acids and the degradation of glycosylations conjugated to dietary protein. In particular, brown rice and egg white protein increased the abundance of amino acid degrading enzymes. Egg white protein increased the abundance of bacteria and proteins usually associated with the degradation of the intestinal mucus barrier. These results show that dietary protein sources can change the gut microbiota's metabolism, which could have major implications in the context of gut microbiota mediated diseases.},
}

Animals
*Dietary Proteins/metabolism/administration & dosage
Mice
*Gastrointestinal Microbiome/drug effects
Metagenomics
*Bacteria/classification/genetics
Mice, Inbred C57BL
Proteomics
Diet
Male
Amino Acids/metabolism

@article {pmid40327160,
year = {2025},
author = {Li, N and Gao, G and Zhang, T and Zhao, C and Zhao, Y and Zhang, Y and Sun, Z},
title = {Co-variation of Host Gene Expression and Gut Microbiome in Intestine-Specific Spp1 Conditional Knockout Mice.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {282},
pmid = {40327160},
issn = {1432-0991},
support = {32325040//National Natural Science Foundation of China/ ; 2022BINCMCF007//Nutrition and Care of Maternal & Child Research Fund Project" of Biostime Institute of Nutrition & Care/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Osteopontin/genetics/metabolism ; Mice, Knockout ; Lipid Metabolism/genetics ; *Intestines/microbiology ; Mice, Inbred C57BL ; Transcriptome ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Osteopontin, which is a highly phosphorylated and glycosylated acidic secreted protein encoded by the secreted phosphoprotein 1 (Spp1) gene, plays a crucial role in immune regulation, inflammatory responses, and cell adhesion. However, its impact on intestinal gene expression and gut microbiota remains underexplored. In this study, we developed an Spp1 conditional knockout mouse model to investigate alterations in the intestinal transcriptome and microbiome, with particular emphasis on changes in gene expression and predicted metabolic pathways. Our findings demonstrated that Spp1 gene conditional knockout significantly modified the expression of genes involved in immune regulation and lipid metabolism. Moreover, metagenomic analysis revealed marked shifts in gut microbial diversity and predicted the metabolic pathways associated with digestion, absorption, and lipid metabolism. These results suggest that Spp1 is instrumental in maintaining gut microbial equilibrium and in regulating host lipid metabolism and immune responses. This study offers new insights into the role of Spp1 in host-microbiota interactions and the potential foundations for developing related therapeutic strategies.},
}

Animals
*Gastrointestinal Microbiome/genetics
Mice
*Osteopontin/genetics/metabolism
Mice, Knockout
Lipid Metabolism/genetics
*Intestines/microbiology
Mice, Inbred C57BL
Transcriptome
Bacteria/classification/genetics/isolation & purification

@article {pmid40325896,
year = {2025},
author = {Ikegwuoha, NPP and Hanekom, T and Booysen, E and Jason, C and Parker-Nance, S and Davies-Coleman, MT and van Zyl, LJ and Trindade, M},
title = {Fimsbactin Siderophores From a South African Marine Sponge Symbiont, Marinomonas sp. PE14-40.},
journal = {Microbial biotechnology},
volume = {18},
number = {5},
pages = {e70155},
pmid = {40325896},
issn = {1751-7915},
support = {//South African Medical Research Council (Self-Initiated grant)/ ; 87326//DSI/NRF SARChI research chair in Microbial Genomics/ ; 312184//European Union PharmaSea Consortium/ ; 129660//National Research Foundation/ ; },
mesh = {*Siderophores/chemistry/metabolism/genetics/isolation & purification ; Multigene Family ; Animals ; Biosynthetic Pathways/genetics ; *Porifera/microbiology ; Symbiosis ; Hydroxamic Acids/metabolism/chemistry ; },
abstract = {Low iron levels in marine habitats necessitate the production of structurally diverse siderophores by many marine bacterial species for iron acquisition. Siderophores exhibit bioactivities ranging from chelation for iron reduction in hemochromatosis sufferers to antimicrobial activity either in their own right or when coupled to known antibiotics for targeted delivery or for molecular imaging. Thus, marine environments are a sought-after resource for novel siderophores that could have pharmaceutical or industrial application. The fimsbactins A-F (1-6) are mixed catechol-hydroxamate siderophores that have only been reported to be produced by Acinetobacter species with the fimsbactin biosynthetic gene clusters (BGCs) widespread among species within this genus. Here, we identified a putative fimsbactin BGC from an uncharacterized marine isolate, Marinomonas sp. PE14-40. Not only was the gene synteny not conserved when comparing the pathway from Marinomonas sp. PE14-40 to the fimsbactin BGC from Acinetobacter sp., but five of the core biosynthetic genes found in the canonical fimsbactin BGC are located elsewhere on the genome and do not form part of the core cluster in Marinomonas sp. PE14-40, with four of these, fbsBCDL, colocalized. Through ESI-MS/MS analysis of extracts from Marinomonas sp. PE14-40, the known fimsbactin analogues 1 and 6 were identified, as well as two new fimsbactin analogues, 7 and 8, containing a previously unreported L-lysine-derived hydroxamate moiety, N1-acetyl-N1-hydroxycadaverine. Feeding experiments using stable isotope-label L-lysine provided further evidence of the N1-acetyl-N1-hydroxycadaverine moiety in 7 and 8. The study demonstrates functional conservation in seemingly disparate biosynthetic pathways and enzyme promiscuity's role in producing structurally diverse compounds.},
}

*Siderophores/chemistry/metabolism/genetics/isolation & purification
Multigene Family
Animals
Biosynthetic Pathways/genetics
*Porifera/microbiology
Symbiosis
Hydroxamic Acids/metabolism/chemistry

@article {pmid40302016,
year = {2025},
author = {Zhou, H and Tang, L and Fenton, KA and Song, X},
title = {Exploring and evaluating microbiome resilience in the gut.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {5},
pages = {},
doi = {10.1093/femsec/fiaf046},
pmid = {40302016},
issn = {1574-6941},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Host Microbial Interactions ; Bacteria/genetics/classification ; Probiotics ; *Gastrointestinal Tract/microbiology ; Animals ; },
abstract = {The gut ecosystem is closely related to human gastrointestinal health and overall wellness. Microbiome resilience refers to the capability of a microbial community to resist or recover from perturbations to its original state of balance. So far, there is no consensus on the criteria for assessing microbiome resilience. This article provides new insights into the metrics and techniques for resilience assessment. We discussed several potential parameters, such as microbiome structure, keystone species, biomarkers, persistence degree, recovery rate, and various research techniques in microbiology, metagenomics, biochemistry, and dynamic modeling. The article further explores the factors that influence the gut microbiome resilience. The microbiome structure (i.e. abundance and diversity), keystone species, and microbe-microbe interplays determine microbiome resilience. Microorganisms employ a variety of mechanisms to achieve the microbiome resilience, including flexible metabolism, quorum sensing, functional redundancy, microbial cooperation, and competition. Host-microbe interactions play a crucial role in maintaining microbiome stability and functionality. Unlike other articles, we focus on the regulation of host immune system on microbiome resilience. The immune system facilitates bacterial preservation and colonization, community construction, probiotic protection, and pathogen elimination through the mechanisms of immunological tolerance, immune-driven microbial compartmentalization, and immune inclusion and exclusion. Microbial immunomodulation indirectly modulates microbiome resilience.},
}

*Gastrointestinal Microbiome/physiology
Humans
Host Microbial Interactions
Bacteria/genetics/classification
Probiotics
*Gastrointestinal Tract/microbiology
Animals

@article {pmid40220806,
year = {2025},
author = {Ye, G and Li, M and Huang, H and Avellán-Llaguno, RD and Chen, J and Chen, G and Huang, Q},
title = {Polystyrene microplastic exposure induces selective accumulation of antibiotic resistance genes in gut microbiota and its potential health risks.},
journal = {International journal of biological macromolecules},
volume = {309},
number = {Pt 3},
pages = {142983},
doi = {10.1016/j.ijbiomac.2025.142983},
pmid = {40220806},
issn = {1879-0003},
mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Animals ; Rats ; *Polystyrenes/toxicity ; *Microplastics/toxicity ; *Drug Resistance, Microbial/genetics/drug effects ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Humans ; *Genes, Bacterial ; Male ; *Drug Resistance, Bacterial/genetics/drug effects ; Bacteria/genetics/drug effects ; },
abstract = {As emerging pollutants, antibiotic resistance genes (ARGs) and microplastics threaten the environment and human health. Gut microbiota is a hotspot for ARG emergence and spread. However, effects of microplastic exposure on the emergence and spread of gut microbial ARGs are unclear. Therefore, metagenomics was used to characterize polystyrene microplastics (PS)-induced ARG alterations in rat gut microbiota and their health risks, and to identify key ARG hosts and pathways as intervention targets. We found that PS exposure not only induced selective accumulation of glycopeptide and aminoglycoside ARGs, but also promoted mobility risks of glycopeptide and macrolide-lincosamide-streptogramin ARGs in gut microbiota. Metagenomic reassembly identified microbes belonging to Firmicutes (particularly order Clostridiales, such as speices Lachnospiraceae bacterium 3-1 and MD335) as major ARG hosts. Meanwhile, genera Enterococcus, Clostridioides and Streptococcus were main ARG hosts among human pathogens. Furthermore, glycopeptide and aminoglycoside ARGs were highly correlated with VanS/VanR signaling and its regulatory pathways of vancomycin resistance and peptidoglycan metabolism, amino sugar and nucleotide sugar metabolism, and CpxR signaling and its regulatory remodeling of cell envelope peptidoglycans and proteins in gut microbiota upon PS exposure. This study provides novel insights and intervention targets involved in PS-induced changes in gut microbial ARGs and their health risks.},
}

*Gastrointestinal Microbiome/drug effects/genetics
Animals
Rats
*Polystyrenes/toxicity
*Microplastics/toxicity
*Drug Resistance, Microbial/genetics/drug effects
Metagenomics
Anti-Bacterial Agents/pharmacology
Humans
*Genes, Bacterial
Male
*Drug Resistance, Bacterial/genetics/drug effects
Bacteria/genetics/drug effects

@article {pmid40053318,
year = {2025},
author = {Nihalani, R and Zola, J and Aluru, S},
title = {Disambiguating a Soft Metagenomic Clustering.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {32},
number = {5},
pages = {473-485},
doi = {10.1089/cmb.2024.0825},
pmid = {40053318},
issn = {1557-8666},
mesh = {*Metagenomics/methods ; Animals ; Cluster Analysis ; Rats ; Algorithms ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Gastrointestinal Microbiome/genetics ; },
abstract = {Clustering is a popular technique used for analyzing amplicon sequencing data in metagenomics. Specifically, it is used to assign sequences (reads) to clusters, each cluster representing a species or a higher level taxonomic unit. Reads from multiple species often sharing subsequences, combined with lack of a perfect similarity measure, make it difficult to correctly assign reads to clusters. Thus, metagenomic clustering methods must either resort to ambiguity, or make the best available choice at each read assignment stage, which could lead to incorrect clusters and potentially cascading errors. In this article, we argue for first generating an ambiguous clustering and then resolving the ambiguities collectively by analyzing the ambiguous clusters. We propose a rigorous formulation of this problem and show that it is NP-Hard. We then propose an efficient heuristic to solve it in practice. We validate our approach on several synthetically generated datasets and two datasets consisting of 16S rDNA sequences from the microbiome of rat guts.},
}

*Metagenomics/methods
Animals
Cluster Analysis
Rats
Algorithms
RNA, Ribosomal, 16S/genetics
Metagenome
Computational Biology/methods
Sequence Analysis, DNA/methods
Gastrointestinal Microbiome/genetics

@article {pmid40043973,
year = {2025},
author = {Liu, N and Dai, S and Fan, X and Li, B and Chen, M and Gong, P and Chen, X},
title = {In vitro fermentation of Auricularia auricula polysaccharides and their regulation of human gut microbiota and metabolism.},
journal = {International journal of biological macromolecules},
volume = {306},
number = {Pt 4},
pages = {141714},
doi = {10.1016/j.ijbiomac.2025.141714},
pmid = {40043973},
issn = {1879-0003},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Fermentation ; Fatty Acids, Volatile/metabolism ; *Auricularia/chemistry ; Feces/microbiology ; Prebiotics ; *Polysaccharides/pharmacology/metabolism ; *Fungal Polysaccharides/pharmacology/metabolism ; Bacteria/metabolism/genetics ; Metabolomics ; },
abstract = {Auricularia auricula is abundant in polysaccharides that received increasing attention due to their variety biological activities and prebiotic potential. In order to explore the role of A. auricula polysaccharides (AAP) in regulating human gut microbiota and metabolic health, this study employed metagenomic and metabolomic analyses to examine the impact of AAP on the gut microbiota via in vitro fecal fermentation experiments. After in vitro fermentation, the data indicated that gut microbiota utilized AAP to produce rich short-chain fatty acids (SCFAs) including acetic acid, propionic acid, butyric acid and modulate gut microbiota structure, such as increasing the proportion of Bacteroidetes to Firmicutes, elevating the abundance of beneficial bacteria, including Bacteroides, especially the Parabacteroides, and inhibiting the abundance of harmful bacteria such as Bilophila, Morganella, and Escherichia-Shigella. Furthermore, the metabolomic analysis indicated that AAP utilization by gut microbes substantially alters the metabolic profile, in which 26 potential biological biomarkers were found and affects tryptophan, bile acids, purines, and butyric acid pathways to promote host health. In conclusion, this research indicated that AAP has a prebiotic potential, which can regulate the gut microbiota and promote host health. Moreover, this study provided scientific evidence for using AAP as a functional food with prebiotic effect.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Fermentation
Fatty Acids, Volatile/metabolism
*Auricularia/chemistry
Feces/microbiology
Prebiotics
*Polysaccharides/pharmacology/metabolism
*Fungal Polysaccharides/pharmacology/metabolism
Bacteria/metabolism/genetics
Metabolomics

@article {pmid39961944,
year = {2025},
author = {Andraskar, J and Khan, D and Yadav, S and Kapley, A},
title = {Metagenomic Analysis of Microbial Community Associated with Food Waste Composting.},
journal = {Applied biochemistry and biotechnology},
volume = {197},
number = {5},
pages = {3503-3520},
pmid = {39961944},
issn = {1559-0291},
support = {DBT/JRF/BET-18/1/2018/AL/23//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {*Composting ; *Metagenomics ; *Bacteria/genetics ; *Food ; *Microbiota ; *Metagenome ; *Soil Microbiology ; Food Loss and Waste ; },
abstract = {Food waste is an increasing cause of concern in India. Its management through composting plays a vital role in managing the biodegradable fraction of municipal solid waste. However, the existing composting process has many challenges, such as the lack of optimum microenvironment and microbiome knowledge, which limits efficient outcomes. Therefore, the present study aims to bridge the gap by applying metagenomics to study microbial community dynamicity during different stages of composting. The bacterial community analysis showed that genus Marionobacter (9.4%) and Halomonas (7.4%) were prevalent during the mesophilic stage, whereas the Bacillus (12.2%) and Cellulomonas (0.1%) were prevalent during the thermophilic and maturation stage of composting. The functional profiling of metagenome indicated the abundance of genes involved in degradation of polymeric compounds such as carbohydrates, lipids, and proteins. The relative abundance of arginine and proline metabolisms increased during the thermophilic stage. Whereas the relative abundance of genes involved in fatty acid, tryptophan, galactose, and propanoate metabolisms declined. Similarly, the CAZyme tool predicted that the genes encoding for glycoside hydrolase (GH) families were higher during the mesophilic and thermophilic stages of composting. These enzymes play an important role in degradation of complex polysaccharides such as cellulose and hemicellulose. The data obtained from the present study could be utilized for the optimization and improving the composting process.},
}

*Composting
*Metagenomics
*Bacteria/genetics
*Food
*Microbiota
*Metagenome
*Soil Microbiology
Food Loss and Waste

@article {pmid39887373,
year = {2025},
author = {Byrd, DA and Damerell, V and Gomez Morales, MF and Hogue, SR and Lin, T and Ose, J and Himbert, C and Ilozumba, MN and Kahlert, C and Shibata, D and Toriola, AT and Li, CI and Figueiredo, J and Stephens, WZ and Warby, CA and Hardikar, S and Siegel, EM and Round, J and Ulrich, CM and Gigic, B},
title = {The gut microbiome is associated with disease-free survival in stage I-III colorectal cancer patients.},
journal = {International journal of cancer},
volume = {157},
number = {1},
pages = {64-73},
doi = {10.1002/ijc.35342},
pmid = {39887373},
issn = {1097-0215},
support = {01KD2101D//German Federal Ministry of Education and Research/ ; R01 AG083580/AG/NIA NIH HHS/United States ; //Stiftung LebensBlicke/ ; //ERA-NET on Translational Cancer Research (TRANSCAN)/ ; //Rahel Goitein-Straus-Program/ ; 01KT1503//German Federal Ministry of Education and Research/ ; //Matthias-Lackas Foundations/ ; U01 CA206110/NH/NIH HHS/United States ; //Heidelberger Stiftung Chirurgie, Heidelberg University Hospital/ ; R01 CA189184/NH/NIH HHS/United States ; //Medizinische Fakultät Heidelberg, Universität Heidelberg/ ; U01 CA206110/CA/NCI NIH HHS/United States ; R01 CA189184/NH/NIH HHS/United States ; U01 CA206110/NH/NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/microbiology/pathology/mortality ; Female ; Male ; Middle Aged ; Aged ; Feces/microbiology ; Disease-Free Survival ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Neoplasm Staging ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Colorectal cancer (CRC) is the second overall leading cause of cancer death in the United States, with recurrence being a frequent cause of mortality. Approaches to improve disease-free survival (DFS) are urgently needed. The gut microbiome, reflected in fecal samples, is likely mechanistically linked to CRC progression and may serve as a non-invasive biomarker. Accordingly, we leveraged baseline fecal samples from N = 166 stage I-III CRC patients in the ColoCare Study, a prospective cohort of newly diagnosed CRC patients. We sequenced the V3 and V4 regions of the 16S rRNA gene to characterize fecal bacteria. We calculated estimates of alpha diversity, beta diversity, and a priori- and exploratory-selected bacterial presence/absence and relative abundance. Associations of microbial metrics with DFS were estimated using multivariable Cox proportional hazards models. We found that alpha diversity was strongly associated with improved DFS, most strongly among rectal cancer patients (Shannon HRrectum = 0.40 95% CI = 0.19, 0.87; p = .02). Overall microbiome composition differences (beta diversity), as characterized by principal coordinate axes, were statistically significantly associated with DFS. Peptostreptococcus was statistically significantly associated with worse DFS (HR = 1.62, 95% CI = 1.13, 2.31; p = .01 per 1-SD) and Order Clostridiales was associated with improved DFS (HR = 0.62, 95% CI = 0.43-0.88; p = .01 per 1-SD). In exploratory analyses, Coprococcus and Roseburia were strongly associated with improved DFS. Overall, higher bacterial diversity and multiple bacteria were strongly associated with DFS. Metagenomic sequencing to elucidate species, gene, and functional level details among larger, diverse patient populations are critically needed to support the microbiome as a biomarker of CRC outcomes.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Colorectal Neoplasms/microbiology/pathology/mortality
Female
Male
Middle Aged
Aged
Feces/microbiology
Disease-Free Survival
RNA, Ribosomal, 16S/genetics
Prospective Studies
Neoplasm Staging
Bacteria/genetics/classification/isolation & purification

@article {pmid40325116,
year = {2025},
author = {Yiminniyaze, R and Zhang, Y and Zhu, N and Zhang, X and Wang, J and Li, C and Wumaier, G and Zhou, D and Xia, J and Li, S and Dong, L and Zhang, Y and Zhang, Y and Li, S},
title = {Characterizations of lung cancer microbiome and exploration of potential microbial risk factors for lung cancer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15683},
pmid = {40325116},
issn = {2045-2322},
support = {82241028//National Clinical Key Specialty Project Foundation/ ; 82270058//National Natural Science Foundation of China/ ; 22Y11900600//Shanghai Year 2022 Science and Technology Innovation Action Plan Medical Innovation Research Special Project/ ; },
mesh = {Humans ; *Lung Neoplasms/microbiology/pathology ; Male ; Female ; Risk Factors ; *Microbiota/genetics ; Middle Aged ; Aged ; Lung/microbiology/pathology ; High-Throughput Nucleotide Sequencing ; Adult ; Shewanella/isolation & purification/genetics ; },
abstract = {Recent studies have indicated that the lung microbiome may contribute to the development and progression of lung cancer, although the precise mechanisms remain to be fully elucidated. This study sought to delineate the microbial composition within lung cancer tissues and identify potential microbial risk factors. Tissue samples were collected from patients newly diagnosed with pulmonary opacities, and metagenomic next-generation sequencing was employed to analyze these samples. Tissue samples were collected from 130 patients with pulmonary opacities, categorized into lung cancer (50 cases), pulmonary infection (53 cases), and non-infectious pulmonary diseases (27 cases). The non-infectious group served as the primary control. The diversity of the lung microbiome in lung cancer tissues was found to be comparable to that observed in non-infectious benign pulmonary conditions. Specific phyla and genera exhibited increased abundance in lung cancer tissues. Additionally, correlations were established between certain microorganisms and clinical characteristics associated with lung cancer. Multivariate binary logistic regression analysis revealed that age and Shewanella were independent risk factors for lung cancer development. This study suggests that the composition of the lung microbiome differs significantly between individuals with lung cancer and those with benign pulmonary conditions, with certain microbes such as Shewanella potentially serving as risk factors for lung cancer progression.},
}

Humans
*Lung Neoplasms/microbiology/pathology
Male
Female
Risk Factors
*Microbiota/genetics
Middle Aged
Aged
Lung/microbiology/pathology
High-Throughput Nucleotide Sequencing
Adult
Shewanella/isolation & purification/genetics

@article {pmid40323477,
year = {2025},
author = {Kiran, NS and Chatterjee, A and Yashaswini, C and Deshmukh, R and Alsaidan, OA and Bhattacharya, S and Prajapati, BG},
title = {The gastrointestinal mycobiome in inflammation and cancer: unraveling fungal dysbiosis, pathogenesis, and therapeutic potential.},
journal = {Medical oncology (Northwood, London, England)},
volume = {42},
number = {6},
pages = {195},
pmid = {40323477},
issn = {1559-131X},
mesh = {Humans ; *Dysbiosis/microbiology ; *Mycobiome ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Inflammation/microbiology ; *Gastrointestinal Neoplasms/microbiology ; Fungi/pathogenicity ; Animals ; },
abstract = {The gastrointestinal mycobiome, comprising diverse fungal species, plays a significant role in gastrointestinal carcinogenesis and inflammatory bowel disease (IBD) pathogenesis. Recent studies have demonstrated that dysbiosis of the gut mycobiome, characterized by an overrepresentation of pathogenic fungi such as Candida albicans and Aspergillus, correlates with increased inflammation and cancer risk. For instance, C. albicans has been shown to induce colonic inflammation through the activation of pattern recognition receptors and the release of pro-inflammatory cytokines, exacerbating IBD symptoms and potentially facilitating tumorigenesis. Additionally, metagenomic analyses have revealed distinct fungal signatures in colorectal cancer tissues compared to adjacent healthy tissues, highlighting the potential of fungi as biomarkers for disease progression. Mechanistically, gut fungi contribute to disease through biofilm formation, mycotoxin secretion (e.g., aflatoxins, candidalysin), pro-inflammatory cytokine induction (e.g., IL-1β, IL-17), and disruption of epithelial barriers-creating a tumor-promoting and inflammation-prone environment. Furthermore, the interplay between fungi and the bacterial microbiome can amplify inflammatory responses, contributing to chronic inflammation and cancer development. Fungal interactions with bacterial communities also play a synergistic role in shaping mucosal immune responses and enhancing disease severity in both cancer and IBD contexts. As research continues to elucidate these complex fungal-host and fungal-bacterial interactions, targeting the gut mycobiome may offer novel therapeutic avenues for managing IBD and gastrointestinal cancers, emphasizing the need for integrated, mechanistically informed approaches to microbiome research.},
}

Humans
*Dysbiosis/microbiology
*Mycobiome
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/microbiology
*Inflammation/microbiology
*Gastrointestinal Neoplasms/microbiology
Fungi/pathogenicity
Animals

@article {pmid40323435,
year = {2025},
author = {Reynolds, J and Yoon, JY},
title = {Fluorescence-based spectrometric and imaging methods and machine learning analyses for microbiota analysis.},
journal = {Mikrochimica acta},
volume = {192},
number = {6},
pages = {334},
pmid = {40323435},
issn = {1436-5073},
mesh = {*Machine Learning ; *Microbiota ; Humans ; Spectrometry, Fluorescence/methods ; *Bacteria/isolation & purification/genetics ; },
abstract = {Most microbiota determination (skin, gut, soil, etc.) are currently conducted in a laboratory using expensive equipment and lengthy procedures, including culture-dependent methods, nucleic acid amplifications (including quantitative PCR), DNA microarray, immunoassays, 16S rRNA sequencing, shotgun metagenomics, and sophisticated mass spectrometric methods. In situ and rapid analysis methods are desirable for fast turnaround time and low assay cost. Fluorescence identification of bacteria and their mixtures is emerging to meet this demand, thanks to the recent development in various machine learning methods. High-dimensional spectroscopic or microscopic imaging data can be obtained to identify the bacterial makeup and its implications for human health and the environment. For example, we can classify healthy versus non-healthy skin microbiome, inflammatory versus non-inflammatory gut microbiome, degraded versus non-degraded soil microbiome, etc. This tutorial summarizes the various machine-learning algorithms used in bacteria identification and microbiota determinations. It also summarizes the various fluorescence spectroscopic methods used to identify bacteria and their mixtures, including fluorescence lifetime spectroscopy, fluorescence resonance energy transfer (FRET), and synchronous fluorescence (SF) spectroscopy. Finally, various fluorescence microscopic imaging methods were summarized that have been used to identify bacteria and their mixtures, including epi-fluorescence microscopy, confocal microscopy, two-photon/multi-photon microscopy, and super-resolution imaging methods (STED, SIM, PALM, and STORM). Finally, it discusses how these methods can be applied to microbiota determinations, what can be demonstrated in the future, opportunities and challenges, and future directions.},
}

*Machine Learning
*Microbiota
Humans
Spectrometry, Fluorescence/methods
*Bacteria/isolation & purification/genetics

@article {pmid38593566,
year = {2024},
author = {Pelpolage, SW and Kobayashi, H and Fukuma, N and Hoshizawa, M and Hamamoto, T and Han, KH and Fukushima, M},
title = {Temporal changes in the fermentation characteristics, bacterial community structure and the functionality of the predicted metagenome of a batch fermenter medium containing the upper gastrointestinal enzyme resistant fraction of white sorghum (Sorghum bicolor L. Moench).},
journal = {Food chemistry},
volume = {448},
number = {},
pages = {139102},
doi = {10.1016/j.foodchem.2024.139102},
pmid = {38593566},
issn = {1873-7072},
mesh = {*Sorghum/metabolism/chemistry/microbiology ; Fermentation ; Animals ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Swine ; *Gastrointestinal Microbiome ; *Gastrointestinal Tract/microbiology/metabolism/enzymology ; Metagenome ; Digestion ; Starch/metabolism ; },
abstract = {Sorghum is a potential prebiotic ascribed to the high native resistant starch (RS) content. Our previous studies on raw sorghum have revealed prominent amino acid fermentation despite the high RS content. Interestingly, autoclaved-freeze-dried sorghum fed rats exhibited beneficial microbial and biochemical profiles. Having a keen interest to reciprocally scrutinize the underlying mechanisms behind these contrasting outcomes, we used an in vitro porcine batch fermentation model. The fermentable substrates in raw and autoclaved-freeze-dried (three cycles) sorghum (AC) after in vitro gastrointestinal digestion fostered similar bacterial community structures, yet with significant differences in the characteristic amylolytic microbial taxa abundance and their temporal variation. Further, significant differences in the concentration of organic acids in raw and AC manifested the differences in the predicted abundance of the underlying pathways of carbohydrate and organic acid metabolism. Thus, this study highlights the propensity of the heat-moisture treatment of sorghum in modifying the fermentability of its RS.},
}

*Sorghum/metabolism/chemistry/microbiology
Fermentation
Animals
*Bacteria/genetics/metabolism/classification/isolation & purification
Swine
*Gastrointestinal Microbiome
*Gastrointestinal Tract/microbiology/metabolism/enzymology
Metagenome
Digestion
Starch/metabolism

@article {pmid38470044,
year = {2024},
author = {Liu, D and Xie, L-S and Lian, S and Li, K and Yang, Y and Wang, W-Z and Hu, S and Liu, S-J and Liu, C and He, Z},
title = {Anaerostipes hadrus, a butyrate-producing bacterium capable of metabolizing 5-fluorouracil.},
journal = {mSphere},
volume = {9},
number = {4},
pages = {e0081623},
pmid = {38470044},
issn = {2379-5042},
support = {2022YFA1304103//MOST | National Key Research and Development Program of China (NKPs)/ ; },
mesh = {Humans ; *Fluorouracil/metabolism ; *Butyrates/metabolism ; Metagenomics ; Gastrointestinal Microbiome ; *Clostridiales/metabolism/genetics ; Genome, Bacterial ; Colorectal Neoplasms/microbiology ; Inflammatory Bowel Diseases/microbiology ; Phylogeny ; },
abstract = {UNLABELLED: Anaerostipes hadrus (A. hadrus) is a dominant species in the human gut microbiota and considered a beneficial bacterium for producing probiotic butyrate. However, recent studies have suggested that A. hadrus may negatively affect the host through synthesizing fatty acid and metabolizing the anticancer drug 5-fluorouracil, indicating that the impact of A. hadrus is complex and unclear. Therefore, comprehensive genomic studies on A. hadrus need to be performed. We integrated 527 high-quality public A. hadrus genomes and five distinct metagenomic cohorts. We analyzed these data using the approaches of comparative genomics, metagenomics, and protein structure prediction. We also performed validations with culture-based in vitro assays. We constructed the first large-scale pan-genome of A. hadrus (n = 527) and identified 5-fluorouracil metabolism genes as ubiquitous in A. hadrus genomes as butyrate-producing genes. Metagenomic analysis revealed the wide and stable distribution of A. hadrus in healthy individuals, patients with inflammatory bowel disease, and patients with colorectal cancer, with healthy individuals carrying more A. hadrus. The predicted high-quality protein structure indicated that A. hadrus might metabolize 5-fluorouracil by producing bacterial dihydropyrimidine dehydrogenase (encoded by the preTA operon). Through in vitro assays, we validated the short-chain fatty acid production and 5-fluorouracil metabolism abilities of A. hadrus. We observed for the first time that A. hadrus can convert 5-fluorouracil to α-fluoro-β-ureidopropionic acid, which may result from the combined action of the preTA operon and adjacent hydA (encoding bacterial dihydropyrimidinase). Our results offer novel understandings of A. hadrus, exceptionally functional features, and potential applications.

IMPORTANCE: This work provides new insights into the evolutionary relationships, functional characteristics, prevalence, and potential applications of Anaerostipes hadrus.},
}

Humans
*Fluorouracil/metabolism
*Butyrates/metabolism
Metagenomics
Gastrointestinal Microbiome
*Clostridiales/metabolism/genetics
Genome, Bacterial
Colorectal Neoplasms/microbiology
Inflammatory Bowel Diseases/microbiology
Phylogeny

@article {pmid40322835,
year = {2025},
author = {Luo, Z and Lu, X and Zhang, T and Shi, S and Zhao, R and He, Y and Yao, H and Zhu, W and Zhang, C},
title = {Moxibustion Enhances Ovarian Function by Inhibiting the Th17/IL-17 Pathway and Regulating Gut Microbiota in POI Rats.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {93},
number = {5},
pages = {e70082},
doi = {10.1111/aji.70082},
pmid = {40322835},
issn = {1600-0897},
support = {BE2020624//Natural Science Foundation of Jiangsu Province/ ; },
mesh = {Animals ; Female ; *Moxibustion/methods ; *Gastrointestinal Microbiome/immunology ; Rats ; *Th17 Cells/immunology ; *Interleukin-17/metabolism ; *Primary Ovarian Insufficiency/therapy/immunology/chemically induced ; Rats, Sprague-Dawley ; *Ovary/physiology ; Signal Transduction ; Disease Models, Animal ; },
abstract = {PROBLEM: Premature ovarian insufficiency (POI) is a significant cause of female infertility, severely impacting physical and mental health. Current treatments, primarily hormone replacement therapy, fail to restore ovarian function and may cause adverse effects. Moxibustion, a traditional Chinese medicine therapy, has shown potential in treating POI, but its mechanisms remain unclear. This study investigated the therapeutic effects of moxibustion on POI rats and explored its underlying mechanisms.

METHOD OF STUDY: A POI rat model was established using cyclophosphamide, and moxibustion was applied daily to the CV4 and SP6 acupoints for 4 weeks. We analyzed hormone levels, estrous cycles, follicle count, and gut microbiota. Transcriptomic and metagenomic sequencing were performed to identify potential pathways. Network pharmacology was used to predict active components and targets.

RESULTS: Moxibustion restored estrous cycles, improved hormonal imbalances, and increased ovarian reserve function. Network pharmacology identified five active components in moxa, and based on the results of network pharmacology and transcriptome sequencing, we believe that the regulation of the IL-17 pathway is the key mechanism. Further experiments showed moxibustion downregulated the Th17/IL-17 pathway, reduced key proteins such as IL-17R, NF-κB, MMP3, IκBα, IL-1β, MMP9, TRAF6, and Cox2. Flow cytometry confirmed a decrease in Th17 cell proportion. Gut microbiota analysis revealed that moxibustion enhanced microbial diversity and modulated specific bacterial species, which correlated with improved hormone levels.

CONCLUSION: Moxibustion has a therapeutic effect on POI rats by regulating the Th17/IL17 pathway and gut microbiota, which provides evidence for the clinical application of moxibustion.},
}

Animals
Female
*Moxibustion/methods
*Gastrointestinal Microbiome/immunology
Rats
*Th17 Cells/immunology
*Interleukin-17/metabolism
*Primary Ovarian Insufficiency/therapy/immunology/chemically induced
Rats, Sprague-Dawley
*Ovary/physiology
Signal Transduction
Disease Models, Animal

@article {pmid40321823,
year = {2025},
author = {Yupanqui García, GJ and Badotti, F and Ferreira-Silva, A and da Cruz Ferraz Dutra, J and Martins-Cunha, K and Gomes, RF and Costa-Rezende, D and Mendes-Pereira, T and Delgado Barrera, C and Drechsler-Santos, ER and Góes-Neto, A},
title = {Microbial diversity of the remote Trindade Island, Brazil: a systematic review.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19305},
pmid = {40321823},
issn = {2167-8359},
mesh = {Brazil ; *Soil Microbiology ; *Biodiversity ; *Bacteria/genetics/classification/isolation & purification ; Islands ; *Fungi/genetics/classification/isolation & purification ; *Archaea/genetics/classification/isolation & purification ; Ecosystem ; *Microbiota ; },
abstract = {Trindade Island is a unique volcanic environment in the South Atlantic, characterized by acidic soils, rich organic matter and a high diversity of micro- and macroorganisms. Such diversity can represent a range of ecological niches and functions, potentially offering valuable ecosystem services. This systematic review aimed to synthesize the current knowledge of the island's microbial communities, focusing on their ecological roles and biotechnological potential. Following the PRISMA guidelines, a comprehensive search of the scientific literature was conducted to identify studies that performed DNA sequencing of samples collected on Trindade Island, Brazil. The selected studies used approaches, such as shotgun metagenomics and marker gene sequencing, including samples from microcosm experiments and culture-dependent samples. A total of eight studies were selected, but only six provided detailed taxonomic information, from which more than 850 genera of Bacteria, Archaea, and Fungi were catalogued. Soil communities were dominated by Actinobacteriota, Acidobacteriota, and Ascomycota (Fungi) while marine and coral environments showed high diversity of Pseudomonadota and Cyanobacteria. Microcosm experiments revealed adaptive responses to hydrocarbon contamination, mainly for Alcanivorax and Mortierella (Fungi). Compared to other ecosystems, such as the oligotrophic Galapagos Islands and the sea-restricted Cuatro Cienegas Basin, Cyanobacteria were shown to be more adaptive.},
}

Brazil
*Soil Microbiology
*Biodiversity
*Bacteria/genetics/classification/isolation & purification
Islands
*Fungi/genetics/classification/isolation & purification
*Archaea/genetics/classification/isolation & purification
Ecosystem
*Microbiota

@article {pmid40320520,
year = {2025},
author = {Liu, S and Wu, J and Cheng, Z and Wang, H and Jin, Z and Zhang, X and Zhang, D and Xie, J},
title = {Microbe-mediated stress resistance in plants: the roles played by core and stress-specific microbiota.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {111},
pmid = {40320520},
issn = {2049-2618},
support = {2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; },
mesh = {*Microbiota/physiology ; *Stress, Physiological ; *Plants/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Soil Microbiology ; Droughts ; },
abstract = {BACKGROUND: Plants in natural surroundings frequently encounter diverse forms of stress, and microbes are known to play a crucial role in assisting plants to withstand these challenges. However, the mining and utilization of plant-associated stress-resistant microbial sub-communities from the complex microbiome remains largely elusive.

RESULTS: This study was based on the microbial communities over 13 weeks under four treatments (control, drought, salt, and disease) to define the shared core microbiota and stress-specific microbiota. Through co-occurrence network analysis, the dynamic change networks of microbial communities under the four treatments were constructed, revealing distinct change trajectories corresponding to different treatments. Moreover, by simulating species extinction, the impact of the selective removal of microbes on network robustness was quantitatively assessed. It was found that under varying environmental conditions, core microbiota made significant potential contributions to the maintenance of network stability. Our assessment utilizing null and neutral models indicated that the assembly of stress-specific microbiota was predominantly driven by deterministic processes, whereas the assembly of core microbiota was governed by stochastic processes. We also identified the microbiome features from functional perspectives: the shared microbiota tended to enhance the ability of organisms to withstand multiple types of environmental stresses and stress-specific microbial communities were associated with the diverse mechanisms of mitigating specific stresses. Using a culturomic approach, 781 bacterial strains were isolated, and nine strains were selected to construct different SynComs. These experiments confirmed that communities containing stress-specific microbes effectively assist plants in coping with environmental stresses.

CONCLUSIONS: Collectively, we not only systematically revealed the dynamics variation patterns of rhizosphere microbiome under various stresses, but also sought constancy from the changes, identified the potential contributions of core microbiota and stress-specific microbiota to plant stress tolerance, and ultimately aimed at the beneficial microbial inoculation strategies for plants. Our research provides novel insights into understanding the microbe-mediated stress resistance process in plants. Video Abstract.},
}

*Microbiota/physiology
*Stress, Physiological
*Plants/microbiology
*Bacteria/classification/genetics/isolation & purification
Soil Microbiology
Droughts

@article {pmid40254113,
year = {2025},
author = {Bartáková, V and Bryjová, A and Polačik, M and Alila, DO and Nagy, B and Watters, B and Bellstedt, D and Blažek, R and Žák, J and Reichard, M},
title = {Phylogenomics and population genomics of Nothobranchius in lowland Tanzania: species delimitation and comparative genetic structure.},
journal = {Molecular phylogenetics and evolution},
volume = {208},
number = {},
pages = {108357},
doi = {10.1016/j.ympev.2025.108357},
pmid = {40254113},
issn = {1095-9513},
mesh = {Animals ; Tanzania ; *Phylogeny ; Polymorphism, Single Nucleotide ; *Genetics, Population ; Genetic Variation ; Sequence Analysis, DNA ; Metagenomics ; Killifishes ; },
abstract = {Annual killifishes of the genus Nothobranchius are widespread across East Africa, with a particularly high biodiversity in lowland Tanzania. While they are typically found in ephemeral pools, the pools vary greatly in size, connectivity and inundation patterns. It was previously suggested that main river channels formed significant barriers to Nothobranchius dispersal. Here, we study the distribution of genetic lineages in an equatorial part of their range where main river channels that may act as barriers occur and closely related lineages frequently coexist in secondary contact zones. We used single-nucleotide polymorphism (SNP) dataset from double-digest restriction site-associated DNA (ddRAD) sequencing to investigate how genetic diversity is structured in Nothobranchius species from the coastal lowlands of Tanzania. Our analyses resolved some uncertain phylogenetic relationships within the N. melanospilus and N. guentheri species groups and placed N. flammicomantis outside the Coastal clade. Rather than a shared intraspecific genetic diversity pattern across four coexisting and widely distributed species, we found highly diverse patterns of intra-specific genetic structure among N. eggersi, N. janpapi, N. melanospilus and N. ocellatus. Populations of Nothobranchius species from the humid coastal lowlands of Tanzania are therefore structured, but not constrained by barriers formed by river channels or by basins - in contrast to Nothobranchius species from the dry part of their distribution. Some of the genetic relationships determined call for a re-evaluation of taxonomic delimitations.},
}

Animals
Tanzania
*Phylogeny
Polymorphism, Single Nucleotide
*Genetics, Population
Genetic Variation
Sequence Analysis, DNA
Metagenomics
Killifishes

@article {pmid40175554,
year = {2025},
author = {Ryan, FJ and Clarke, M and Lynn, MA and Benson, SC and McAlister, S and Giles, LC and Choo, JM and Rossouw, C and Ng, YY and Semchenko, EA and Richard, A and Leong, LEX and Taylor, SL and Blake, SJ and Mugabushaka, JI and Walker, M and Wesselingh, SL and Licciardi, PV and Seib, KL and Tumes, DJ and Richmond, P and Rogers, GB and Marshall, HS and Lynn, DJ},
title = {Bifidobacteria support optimal infant vaccine responses.},
journal = {Nature},
volume = {641},
number = {8062},
pages = {456-464},
pmid = {40175554},
issn = {1476-4687},
mesh = {*Bifidobacterium/immunology/physiology/drug effects/isolation & purification ; Mice ; Infant ; Animals ; Humans ; Female ; *Pneumococcal Vaccines/immunology ; Infant, Newborn ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Feces/microbiology ; Male ; Haemophilus Vaccines/immunology ; *Immunogenicity, Vaccine/immunology/drug effects ; Gastrointestinal Microbiome/drug effects/immunology ; Germ-Free Life ; Prospective Studies ; Probiotics/administration & dosage ; Vaccines, Conjugate/immunology ; Vaccination ; Antibodies, Bacterial/immunology ; },
abstract = {Accumulating evidence indicates that antibiotic exposure may lead to impaired vaccine responses[1-4]; however, the mechanisms underlying this association remain poorly understood. Here we prospectively followed 191 healthy, vaginally born, term infants from birth to 15 months, using a systems vaccinology approach to assess the effects of antibiotic exposure on immune responses to vaccination. Exposure to direct neonatal but not intrapartum antibiotics was associated with significantly lower antibody titres against various polysaccharides in the 13-valent pneumococcal conjugate vaccine and the Haemophilus influenzae type b polyribosylribitol phosphate and diphtheria toxoid antigens in the combined 6-in-1 Infanrix Hexa vaccine at 7 months of age. Blood from infants exposed to neonatal antibiotics had an inflammatory transcriptional profile before vaccination; in addition, faecal metagenomics showed reduced abundance of Bifidobacterium species in these infants at the time of vaccination, which was correlated with reduced vaccine antibody titres 6 months later. In preclinical models, responses to the 13-valent pneumococcal conjugate vaccine were strongly dependent on an intact microbiota but could be restored in germ-free mice by administering a consortium of Bifidobacterium species or a probiotic already widely used in neonatal units. Our data suggest that microbiota-targeted interventions could mitigate the detrimental effects of early-life antibiotics on vaccine immunogenicity.},
}

*Bifidobacterium/immunology/physiology/drug effects/isolation & purification
Mice
Infant
Animals
Humans
Female
*Pneumococcal Vaccines/immunology
Infant, Newborn
*Anti-Bacterial Agents/adverse effects/pharmacology
Feces/microbiology
Male
Haemophilus Vaccines/immunology
*Immunogenicity, Vaccine/immunology/drug effects
Gastrointestinal Microbiome/drug effects/immunology
Germ-Free Life
Prospective Studies
Probiotics/administration & dosage
Vaccines, Conjugate/immunology
Vaccination
Antibodies, Bacterial/immunology

@article {pmid39978335,
year = {2025},
author = {Wang, Z and Tian, L and Jiang, Y and Ning, L and Zhu, X and Chen, X and Xuan, B and Zhou, Y and Ding, J and Ma, Y and Zhao, Y and Huang, X and Hu, M and Fang, JY and Shen, N and Cao, Z and Chen, H and Wang, X and Hong, J},
title = {Synergistic role of gut-microbial L-ornithine in enhancing ustekinumab efficacy for Crohn's disease.},
journal = {Cell metabolism},
volume = {37},
number = {5},
pages = {1089-1102.e7},
doi = {10.1016/j.cmet.2025.01.007},
pmid = {39978335},
issn = {1932-7420},
mesh = {*Crohn Disease/drug therapy/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Ustekinumab/therapeutic use/pharmacology ; Male ; Female ; *Ornithine/metabolism/pharmacology ; Adult ; Animals ; Mice ; Th17 Cells/immunology/metabolism/drug effects ; Middle Aged ; Faecalibacterium prausnitzii/metabolism ; Signal Transduction/drug effects ; Treatment Outcome ; Feces/microbiology ; Receptors, Interleukin/metabolism ; },
abstract = {The role of the intestinal microbiome in Crohn's disease (CD) treatment remains poorly understood. This study investigates microbe-host interactions in CD patients undergoing ustekinumab (UST) therapy. Fecal metagenome, metabolome, and host transcriptome data from 85 CD patients were analyzed using multi-omics integration and mediation analysis. Our findings reveal significant microbiome-metabolite-host interactions. Specifically, Faecalibacterium prausnitzii was linked to altered L-ornithine biosynthesis, resulting in higher L-ornithine levels in patients before UST therapy. In vivo and in vitro studies demonstrated that microbiome-derived L-ornithine enhances UST treatment sensitivity in CD by disrupting the host IL-23 receptor signaling and inhibiting Th17 cell stabilization through the IL-12RB1/TYK2/STAT3 axis. L-ornithine significantly enhances the therapeutic efficacy of UST in CD patients, as demonstrated in a prospective clinical trial. These findings suggest that targeting specific microbe-host metabolic pathways may improve the efficacy of inflammatory bowel disease (IBD) treatments.},
}

*Crohn Disease/drug therapy/microbiology/metabolism
Humans
*Gastrointestinal Microbiome/drug effects
*Ustekinumab/therapeutic use/pharmacology
Male
Female
*Ornithine/metabolism/pharmacology
Adult
Animals
Mice
Th17 Cells/immunology/metabolism/drug effects
Middle Aged
Faecalibacterium prausnitzii/metabolism
Signal Transduction/drug effects
Treatment Outcome
Feces/microbiology
Receptors, Interleukin/metabolism

@article {pmid39950813,
year = {2025},
author = {Seguel Suazo, K and Nierychlo, M and Kondrotaite, Z and Petriglieri, F and Peces, M and Singleton, C and Dries, J and Nielsen, PH},
title = {Diversity and abundance of filamentous and non-filamentous "Leptothrix" in global wastewater treatment plants.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {3},
pages = {e0148524},
pmid = {39950813},
issn = {1098-5336},
support = {13351//Villum Fonden (Villum Foundation)/ ; },
mesh = {*Wastewater/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics/analysis ; *Biodiversity ; Sewage/microbiology ; },
abstract = {Species belonging to the genus Leptothrix are widely distributed in the environment and in activated sludge (AS) wastewater treatment plants (WWTPs). They are commonly found in iron-rich environments and reported to cause filamentous bulking in WWTPs. In this study, the diversity, distribution, and metabolic potential of the most prevalent Leptothrix spp. found in AS worldwide were studied. Our 16S rRNA amplicon survey showed that Leptothrix belongs to the general core community of AS worldwide, comprising 32 species with four species being most commonly found. Their taxonomic classification was re-evaluated based on both 16S rRNA gene and genome-based phylogenetic analysis showing that three of the most abundant "Leptothrix" species represented species in three other genera, Rubrivivax, Ideonella, and the novel genus, Ca. Intricatilinea. New fluorescence in situ hybridization (FISH) probes revealed rod-shaped morphology for the novel Ca. Rubrivivax defluviihabitans and Ca. Ideonella esbjergensis, while filamentous morphology was found only for Ca. Intricatilinea gracilis. Analysis of high-quality metagenome-assembled genomes revealed metabolic potential for aerobic growth, fermentation, storage of intracellular polymers, partial denitrification, photosynthesis, and iron reduction. FISH in combination with Raman microspectroscopy confirmed the in situ presence of chlorophyll and carotenoids in Ca. Rubrivivax defluviihabitans and Ca. Intricatilinea gracilis. This study resolves the taxonomy of abundant but poorly classified "Leptothrix" species, providing important insights into their diversity, morphology, and function in global AS wastewater treatment systems.IMPORTANCEThe genus Leptothrix has been extensively studied and described since the 1880s, with six species currently described but with the majority uncultured and undescribed. Some species are assumed to have a filamentous morphology and can cause settling problems in wastewater treatment plants (WWTPs). Here, we revised the classification of the most abundant Leptothrix spp. present in WWTPs across the world, showing that most belong to other genera, such as Rubrivivax and Ideonella. Furthermore, most do not have a filamentous morphology and are not problematic in WWTPs as previously believed. Metabolic reconstruction, including some traits validated in situ by the application of new fluorescence in situ hybridization probes and Raman microspectroscopy, provided additional insights into their metabolism. The study has contributed to a better understanding of the diversity, morphology, and function of "Leptothrix," which belong to the abundant core community across global activated sludge WWTPs.},
}

*Wastewater/microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics/analysis
*Biodiversity
Sewage/microbiology

@article {pmid40316630,
year = {2025},
author = {Aya, V and Pardo-Rodriguez, D and Vega, LC and Cala, MP and Ramírez, JD},
title = {Integrating metagenomics and metabolomics to study the gut microbiome and host relationships in sports across different energy systems.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15356},
pmid = {40316630},
issn = {2045-2322},
support = {Small grant//Universidad del Rosario/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; *Energy Metabolism ; Adult ; Athletes ; Young Adult ; *Sports ; Feces/microbiology ; Female ; Lipidomics ; },
abstract = {The gut microbiome plays a critical role in modulating host metabolism, influencing energy production, nutrient utilization, and overall physiological adaptation. In athletes, these microbial functions may be further specialized to meet the unique metabolic demands of different sports disciplines. This study explored the role of the gut microbiome in modulating host metabolism among Colombian athletes by comparing elite weightlifters (n = 16) and cyclists (n = 13) through integrative omics analysis. Fecal and plasma samples collected one month before an international event underwent metagenomic, metabolomic, and lipidomic profiling. Metagenomic analysis revealed significant microbial pathways, including L-arginine biosynthesis III and fatty acid biosynthesis initiation. Key metabolic pathways, such as phenylalanine, tyrosine, and tryptophan biosynthesis; arginine biosynthesis; and folate biosynthesis, were enriched in both athlete groups. Plasma metabolomics and lipidomics revealed distinct metabolic profiles and a separation between athlete types through multivariate models, with lipid-related pathways such as lipid droplet formation and glycolipid synthesis driving the differences. Notably, elevated carnitine, amino acid, and glycerolipid levels in weightlifters suggest energy system-specific metabolic adaptations. These findings underscore the complex relationship between the gut microbiota composition and metabolic responses tailored to athletic demands, laying the groundwork for personalized strategies to optimize performance. This research highlights the potential for targeted modulation of the gut microbiota as a basis for tailored interventions to support specific energy demands in athletic disciplines.},
}

Humans
*Gastrointestinal Microbiome
*Metabolomics/methods
*Metagenomics/methods
Male
*Energy Metabolism
Adult
Athletes
Young Adult
*Sports
Feces/microbiology
Female
Lipidomics

@article {pmid40314681,
year = {2025},
author = {Li, X and Su, K and He, Y and Shao, S and Lan, L and Zhang, Q},
title = {Knowledge Mapping of International Microbiota Research: Analyzing Thirty-Year Citation Classics and Exploring Future Expectations.},
journal = {The new microbiologica},
volume = {48},
number = {1},
pages = {46-59},
pmid = {40314681},
issn = {1121-7138},
mesh = {Humans ; *Microbiota ; *Biomedical Research ; Bibliometrics ; Gastrointestinal Microbiome ; },
abstract = {Microbiota research has rapidly emerged as a pivotal field, with over 250,000 publications and more than ten million citations recorded in the Web of Science Core Collection database by 2024. There were 1682 original microbiota citation classics (each receiving 400 citations or more) identified over the past three decades, totaling 1,559,594 citations and averaging 927 citations per paper. Collaborative efforts in the production of these citation classics involved 87 out of 89 participating countries and 2107 out of 2142 institutions. The USA, various European countries, and China emerged as the leading contributors to this burgeoning research area. Jeffrey I. Gordon, Rob Knight, and Curtis Huttenhower were the prominent figures in microbiota research. Author keywords were analyzed, which revealed a notable shift in research focus from environmental microorganisms to human gut microbiota. Advances such as high-throughput 16S rRNA sequencing and metagenomics expanded the scope of investigations into host-microbiota interactions. Current research interests encompass exploring mechanisms underlying gut-X-axis conditions, including inflammatory bowel disease, obesity, diabetes, colorectal cancer, liver diseases, and neurological disorders. Moreover, environmental exposures have been evidenced to alter gut microbiota and metabolites, contributing a novel research direction. Future research direction is also anticipated to delve further into biosynthetic gene engineering technologies aimed at microbial interventions, including probiotics and fecal microbiota transplantation. This study outlines the evolving landscape of microbiota research and provides valuable insights to inform future investigations within the field.},
}

Humans
*Microbiota
*Biomedical Research
Bibliometrics
Gastrointestinal Microbiome

@article {pmid40313603,
year = {2025},
author = {Pu, Y and Zhou, X and Cai, H and Lou, T and Liu, C and Kong, M and Sun, Z and Wang, Y and Zhang, R and Zhu, Y and Ye, L and Zheng, Y and Zhu, B and Quan, Z and Zhao, G and Zheng, Y},
title = {Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {76-90},
pmid = {40313603},
issn = {2730-5848},
abstract = {UNLABELLED: In gut microbial research, DNA extraction remarkably influences study outcomes and biological interpretations. Rapid advancements in the research scale and technological upgrades necessitate evaluating new methods to ensure reliability and precision in microbial community profiling. We systematically evaluated the performance of eight recent and commonly used extraction methods using a microbial mock community (MMC) and fecal samples from two healthy volunteers, incorporating bacterial, archaeal, and fungal constituents. Performance metrics included nucleic acid assessment, microbial profile assessment, and scalability for large-scale studies, leveraging shotgun metagenomics for in-depth analysis. Despite variations in DNA quantity and quality, all methods yielded sufficient DNA for shotgun metagenomic sequencing. In the MMC microbial profile assessment, the QIAamp PowerFecal pro Kit (PF) and DNeasy PowerSoil HTP kit (PS) methods exhibited higher similarity with the theoretical composition and lower variability across technical replicates compared to other methods. For fecal samples, the extraction method accounted for 21.4% of the overall microbiome variation and significantly affected the abundances of 32% of detected microbial species. Methods using mechanical lysis with small beads, such as PF and PS, demonstrated better efficiency, indicated by increased microbial diversity in extracting DNA from Gram-positive bacteria. Furthermore, the PF and PS methods are notably simple to execute and automation-friendly, though relatively costly. Our study underscores the importance of maintaining consistency in DNA extraction methods for reliable comparative metagenomic analyses. We recommend PF and PS methods as optimal for expansive gut metagenomic research, emphasizing the critical role of mechanical lysis in DNA extraction.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-025-00232-x.},
}

@article {pmid40313461,
year = {2025},
author = {Bessa, LJ and Egas, C and Pires, C and Proença, L and Mascarenhas, P and Pais, RJ and Barroso, H and Machado, V and Botelho, J and Alcoforado, G and Mendes, JJ and Alves, R},
title = {Linking peri-implantitis to microbiome changes in affected implants, healthy implants, and saliva: a cross-sectional pilot study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1543100},
pmid = {40313461},
issn = {2235-2988},
mesh = {Humans ; *Peri-Implantitis/microbiology ; *Saliva/microbiology ; Pilot Projects ; Cross-Sectional Studies ; *Microbiota ; *Dental Implants/microbiology ; Male ; Female ; Biofilms/growth & development ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Metagenomics ; Adult ; },
abstract = {INTRODUCTION: The rising use of dental implants is accompanied by an expected increase in peri-implant diseases, particularly peri-implantitis (PI), which poses a significant threat to implant success and necessitates a thorough understanding of its pathogenesis for effective management.

METHODS: To gain deeper insights into the role and impact of the peri-implant microbiome in the pathogenesis and progression of PI, we analyzed 100 samples of saliva and subgingival biofilm from 40 participants with healthy implants (HI group) or with co-occurrence of diagnosed PI-affected implants and healthy implants (PI group) using shotgun metagenomic sequencing. We identified the most discriminative species distinguishing healthy from diseased study groups through log ratios and differential ranking analyses.

RESULTS AND DISCUSSION: Mogibacterium timidum, Schaalia cardiffensis, Parvimonas micra, Filifactor alocis, Porphyromonas endodontalis, Porphyromonas gingivalis and Olsenella uli were associated with the subgingival peri-implant biofilm. In contrast, Neisseria sp oral taxon 014, Haemophilus parainfluenzae, Actinomyces naeslundii, Rothia mucilaginosa and Rothia aeria were more prevalent in the healthy peri-implant biofilm. Functional pathways such as arginine and polyamine biosynthesis, including putrescine and citrulline biosynthesis, showed stronger correlations with PI-affected implants. In contrast, peri-implant health was characterized by the predominance of pathways involved in purine and pyrimidine deoxyribonucleotide de novo biosynthesis, glucose and glucose-1-phosphate degradation, and tetrapyrrole biosynthesis. Our findings reveal that healthy implants in PI-free oral cavities differ significantly in microbial composition and functional pathways compared to healthy implants co-occurring with PI-affected implants, which more closely resemble PI-associated profiles. This pattern extended to salivary samples, where microbial and functional biomarkers follow similar trends.},
}

Humans
*Peri-Implantitis/microbiology
*Saliva/microbiology
Pilot Projects
Cross-Sectional Studies
*Microbiota
*Dental Implants/microbiology
Male
Female
Biofilms/growth & development
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Aged
Metagenomics
Adult

@article {pmid40312907,
year = {2025},
author = {Zheng, CM and Kang, HW and Moon, S and Byun, YJ and Kim, WT and Choi, YH and Moon, SK and Piao, XM and Yun, SJ},
title = {Optimizing extraction of microbial DNA from urine: Advancing urinary microbiome research in bladder cancer.},
journal = {Investigative and clinical urology},
volume = {66},
number = {3},
pages = {272-280},
doi = {10.4111/icu.20240454},
pmid = {40312907},
issn = {2466-054X},
support = {2020R1I1A3062508/NRF/National Research Foundation of Korea/Korea ; RS-2023-00245919/NRF/National Research Foundation of Korea/Korea ; RS-2024-00342111/NRF/National Research Foundation of Korea/Korea ; 5199990614277/NRF/National Research Foundation of Korea/Korea ; /KHIDI/Korea Health Industry Development Institute/Korea ; },
mesh = {Humans ; *Microbiota/genetics ; *Urinary Bladder Neoplasms/microbiology/urine ; *DNA, Bacterial/isolation & purification/urine ; Male ; Female ; Middle Aged ; *Urine/microbiology ; Aged ; RNA, Ribosomal, 16S ; Reproducibility of Results ; },
abstract = {PURPOSE: This study aimed to evaluate and optimize microbial DNA extraction methods from urine, a non-invasive sample source, to enhance DNA quality, purity, and reliability for urinary microbiome research and biomarker discovery in bladder cancer.

MATERIALS AND METHODS: A total of 302 individuals (258 with genitourinary cancers and 44 with benign urologic diseases) participated in this study. Urine samples were collected via sterile catheterization, resulting in 445 vials for microbial analysis. DNA extraction was performed using three protocols: the standard protocol (SP), water dilution protocol (WDP), and chelation-assisted protocol (CAP). DNA quality (concentration, purity, and contamination levels) was assessed using NanoDrop spectrophotometry. Microbial analysis was conducted on 138 samples (108 cancerous and 30 benign) using 16S rRNA sequencing. Prior to sequencing on the Illumina MiSeq platform, Victor 3 fluorometry was used for validation.

RESULTS: WDP outperformed other methods, achieving significantly higher 260/280 and 260/230 ratios, indicating superior DNA purity and reduced contamination, while maintaining reliable DNA yields. CAP was excluded due to poor performance across all metrics. Microbial abundance was significantly higher in WDP-extracted samples (p<0.0001), whereas SP demonstrated higher alpha diversity indices (p<0.01), likely due to improved detection of low-abundance taxa. Beta diversity analysis showed no significant compositional differences between SP and WDP (p=1.0), supporting the reliability of WDP for microbiome research.

CONCLUSIONS: WDP is a highly effective and reliable method for microbial DNA extraction from urine, ensuring high-quality and reproducible results. Future research should address sample variability and crystal precipitation to further refine microbiome-based diagnostics and therapeutics.},
}

Humans
*Microbiota/genetics
*Urinary Bladder Neoplasms/microbiology/urine
*DNA, Bacterial/isolation & purification/urine
Male
Female
Middle Aged
*Urine/microbiology
Aged
RNA, Ribosomal, 16S
Reproducibility of Results

@article {pmid40307949,
year = {2025},
author = {Lee, JY and Jo, S and Lee, J and Choi, M and Kim, K and Lee, S and Kim, HS and Bae, JW and Chung, SJ},
title = {Distinct gut microbiome characteristics and dynamics in patients with Parkinson's disease based on the presence of premotor rapid-eye movement sleep behavior disorders.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {108},
pmid = {40307949},
issn = {2049-2618},
support = {RS-2024-00353952//Ministry of Science and ICT, South Korea/ ; RS-2023-00265588//the Ministry of Health and Welfare, Republic of Korea/ ; },
mesh = {Humans ; *Parkinson Disease/microbiology/complications ; *Gastrointestinal Microbiome/genetics ; Male ; *REM Sleep Behavior Disorder/microbiology ; Female ; Aged ; Middle Aged ; Disease Progression ; *Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Alpha-synuclein aggregation, a hallmark of Parkinson's disease (PD), is hypothesized to often begin in the enteric or peripheral nervous system in "body-first" PD and progresses through the vagus nerve to the brain, therefore REM sleep behavior disorder (RBD) precedes the PD diagnosis. In contrast, "brain-first" PD begins in the central nervous system. Evidence that gut microbiome imbalances observed in PD and idiopathic RBD exhibit similar trends supports body-first and brain-first hypothesis and highlights the role of microbiota in PD pathogenesis. However, further investigation is needed to understand distinct microbiome changes in body-first versus brain-first PD over the disease progression.

RESULTS: Our investigation involved 104 patients with PD and 85 of their spouses as healthy controls (HC), with 57 patients (54.8%) categorized as PD-RBD(+) and 47 patients (45.2%) as PD-RBD(-) based on RBD presence before the PD diagnosis. We evaluated the microbiome differences between these groups over the disease progression through taxonomic and functional differential abundance analyses and carbohydrate-active enzyme (CAZyme) profiles based on metagenome-assembled genomes. The PD-RBD(+) gut microbiome showed a relatively stable microbiome composition irrespective of disease stage. In contrast, PD-RBD(-) microbiome exhibited a relatively dynamic microbiome change as the disease progressed. In early-stage PD-RBD(+), Escherichia and Akkermansia, associated with pathogenic biofilm formation and host mucin degradation, respectively, were enriched, which was supported by functional analysis. We discovered that genes of the UDP-GlcNAc synthesis/recycling pathway negatively correlated with biofilm formation; this finding was further validated in a separate cohort. Furthermore, fiber intake-associated taxa were decreased in early-stage PD-RBD(+) and the biased mucin-degrading capacity of CAZyme compared to fiber degradation.

CONCLUSION: We determined that the gut microbiome dynamics in patients with PD according to the disease progression depend on the presence of premotor RBD. Notably, early-stage PD-RBD(+) demonstrated distinct gut microbial characteristics, potentially contributing to exacerbation of PD pathophysiology. This outcome may contribute to the development of new therapeutic strategies targeting the gut microbiome in PD. Video Abstract.},
}

Humans
*Parkinson Disease/microbiology/complications
*Gastrointestinal Microbiome/genetics
Male
*REM Sleep Behavior Disorder/microbiology
Female
Aged
Middle Aged
Disease Progression
*Bacteria/classification/genetics/isolation & purification
Feces/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid40164832,
year = {2025},
author = {Litichevskiy, L and Considine, M and Gill, J and Shandar, V and Cox, TO and Descamps, HC and Wright, KM and Amses, KR and Dohnalová, L and Liou, MJ and Tetlak, M and Galindo-Fiallos, MR and Wong, AC and Lundgren, P and Kim, J and Uhr, GT and Rahman, RJ and Mason, S and Merenstein, C and Bushman, FD and Raj, A and Harding, F and Chen, Z and Prateek, GV and Mullis, M and Deighan, AG and Robinson, L and Tanes, C and Bittinger, K and Chakraborty, M and Bhatt, AS and Li, H and Barnett, I and Davenport, ER and Broman, KW and Levy, M and Cohen, RL and Botstein, D and Freund, A and Di Francesco, A and Churchill, GA and Li, M and Thaiss, CA},
title = {Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice.},
journal = {Nature microbiology},
volume = {10},
number = {5},
pages = {1240-1257},
pmid = {40164832},
issn = {2058-5276},
mesh = {Animals ; *Aging/genetics/physiology ; *Gastrointestinal Microbiome/genetics ; Mice ; *Caloric Restriction ; *Metagenome ; Humans ; Male ; Mice, Inbred C57BL ; Female ; Longevity ; },
abstract = {The gut microbiome changes with age and has been proposed to mediate the benefit of lifespan-extending interventions such as dietary restriction. However, the causes and consequences of microbiome ageing and the potential of such interventions remain unclear. Here we analysed 2,997 metagenomes collected longitudinally from 913 deeply phenotyped, genetically diverse mice to investigate interactions between the microbiome, ageing, dietary restriction (caloric restriction and fasting), host genetics and a range of health parameters. Among the numerous age-associated microbiome changes that we find in this cohort, increased microbiome uniqueness is the most consistent parameter across a second longitudinal mouse experiment that we performed on inbred mice and a compendium of 4,101 human metagenomes. Furthermore, cohousing experiments show that age-associated microbiome changes may be caused by an accumulation of stochastic environmental exposures (neutral theory) rather than by the influence of an ageing host (selection theory). Unexpectedly, the majority of taxonomic and functional microbiome features show small but significant heritability, and the amount of variation explained by host genetics is similar to ageing and dietary restriction. We also find that more intense dietary interventions lead to larger microbiome changes and that dietary restriction does not rejuvenate the microbiome. Lastly, we find that the microbiome is associated with multiple health parameters, including body composition, immune components and frailty, but not lifespan. Overall, this study sheds light on the factors influencing microbiome ageing and aspects of host physiology modulated by the microbiome.},
}

Animals
*Aging/genetics/physiology
*Gastrointestinal Microbiome/genetics
Mice
*Caloric Restriction
*Metagenome
Humans
Male
Mice, Inbred C57BL
Female
Longevity

@article {pmid40140705,
year = {2025},
author = {Garrido-Sanz, D and Keel, C},
title = {Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation.},
journal = {Nature microbiology},
volume = {10},
number = {5},
pages = {1130-1144},
pmid = {40140705},
issn = {2058-5276},
mesh = {*Triticum/microbiology ; *Rhizosphere ; Soil Microbiology ; *Microbiota/genetics ; *Seeds/microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Plant Roots/microbiology ; },
abstract = {Microbial communities play a crucial role in supporting plant health and productivity. Reproducible, natural plant-associated microbiomes can help disentangle microbial dynamics across time and space. Here, using a sequential propagation strategy, we generated a complex and reproducible wheat rhizosphere microbiome (RhizCom) to study successional dynamics and interactions between the soil and heritable seed-borne rhizosphere microbiomes (SbRB) in a microcosm. Using 16S rRNA sequencing and genome-resolved shotgun metagenomics, we find that SbRB surpassed native soil microbes as the dominant rhizosphere-associated microbiome source. SbRB genomes were enriched in host-associated traits including degradation of key saccharide (niche partitioning) and cross-feeding interactions that supported partner strains (niche facilitation). In vitro co-culture experiments confirmed that helper SbRB strains facilitated the growth of partner bacteria on disaccharides as sole carbon source. These results reveal the importance of seed microbiota dynamics in microbial succession and community assembly, which could inform strategies for crop microbiome manipulation.},
}

*Triticum/microbiology
*Rhizosphere
Soil Microbiology
*Microbiota/genetics
*Seeds/microbiology
*Bacteria/genetics/classification/metabolism/isolation & purification
RNA, Ribosomal, 16S/genetics
Metagenomics
Plant Roots/microbiology

@article {pmid40307838,
year = {2025},
author = {Huang, L and Li, K and Peng, C and Gu, S and Huang, X and Gao, C and Ren, X and Cheng, M and He, G and Xu, Y and Jiang, Y and Wang, H and Wang, M and Shen, P and Wang, Q and He, X and Zhong, L and Wang, S and Wang, N and Zhang, G and Cai, H and Jiang, C},
title = {Elevated antibiotic resistance gene abundance of ICU healthcare workers, a multicentre, cross-sectional study.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {170},
pmid = {40307838},
issn = {1466-609X},
support = {LTGY24H190001//Zhejiang Provincial Natural Science Fund/ ; 82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; 82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; 2021YFA1301001//National Key Research and Development Program/ ; 2025C02090//"Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; WKJ-ZJ-2526//National Health Commission Scientific Research Fund - Zhejiang Provincial Health Major Science and Technology Plan Project/ ; },
mesh = {Humans ; Cross-Sectional Studies ; Male ; Female ; Intensive Care Units/organization & administration/statistics & numerical data ; Prospective Studies ; *Health Personnel/statistics & numerical data ; China ; Adult ; Middle Aged ; *Drug Resistance, Microbial/genetics ; Gastrointestinal Microbiome/genetics ; Feces/microbiology ; },
abstract = {OBJECTIVE: Studies suggest that the colonization of multidrug-resistant organism in the gut of healthcare workers is similar to that of healthy individuals. However, due to exposure to medical environments, is the abundance of antibiotic resistance genes (ARG) in the gut of ICU healthcare workers higher than that of healthy individuals?

DESIGN: Prospective, multicentre, cross-sectional study.

SETTING: Eight medical centers in China, recruiting from January 2024 to February 2024.

PARTICIPANTS: 303 Healthy people (201 ICU healthcare workers and 103 healthy controls) were screened and 290 Healthy people (191 ICU healthcare workers and 99 healthy controls) were included in analysis.

MAIN OUTCOME MEASURES: Fecal samples were collected and subjected to metagenomic sequencing. We compared the total ARG abundance, ARG diversity, and gut microbiome composition between the two groups.

RESULTS: After adjusting for age, sex, and body mass index, ICU healthcare workers exhibited a significantly higher total ARG abundance compared to healthy controls (fold change = 1.22, 95% CI: 1.12-1.34, p < 0.001). The β-diversity of ARG between the two groups differed significantly (p = 0.001). No significant linear or nonlinear relationship was observed between the duration of ICU occupational exposure and ARG abundance (p for overall = 0.96, p for nonlinear = 0.84).

CONCLUSION: In this prospective, multicenter study, we found that ICU healthcare workers exhibit significantly higher gut ARGs abundance compared to healthy controls. Meanwhile, ICU healthcare workers, including physicians, nurses, and nursing assistants, have a different composition of gut ARGs compared to healthy individuals.

TRIAL REGISTRATION: NCT06228248.},
}

Humans
Cross-Sectional Studies
Male
Female
Intensive Care Units/organization & administration/statistics & numerical data
Prospective Studies
*Health Personnel/statistics & numerical data
China
Adult
Middle Aged
*Drug Resistance, Microbial/genetics
Gastrointestinal Microbiome/genetics
Feces/microbiology

@article {pmid40307239,
year = {2025},
author = {Langwig, MV and Koester, F and Martin, C and Zhou, Z and Joye, SB and Reysenbach, AL and Anantharaman, K},
title = {Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4076},
pmid = {40307239},
issn = {2041-1723},
support = {DBI-2047598//National Science Foundation (NSF)/ ; OCE-2049478//National Science Foundation (NSF)/ ; },
mesh = {*Hydrothermal Vents/virology/microbiology ; *Viruses/genetics/classification/isolation & purification ; *Ecosystem ; Metagenome ; Genome, Viral ; Pacific Ocean ; Bacteriophages/genetics/classification ; Phylogeny ; Seawater/virology ; Gammaproteobacteria/virology ; Microbiota ; Virome ; },
abstract = {Viruses are ubiquitous in deep-sea hydrothermal vents, where they influence microbial communities and biogeochemistry. Yet, viral ecology and evolution remain understudied in these environments. Here, we identify 49,962 viruses from 52 globally distributed hydrothermal vent samples (10 plume, 40 deposit, and 2 diffuse flow metagenomes), and reconstruct 5708 viral metagenome-assembled genomes, the majority of which were bacteriophages. Hydrothermal viruses were largely endemic, however, some viruses were shared between geographically separated vents, predominantly between the Lau Basin and Brothers Volcano in the Pacific Ocean. Geographically distant viruses shared proteins related to core functions such as structural proteins, and rarely, proteins of auxiliary functions involved in processes such as fermentation and cobalamin biosynthesis. Common microbial hosts of viruses included members of Campylobacterota, Alpha-, and Gammaproteobacteria in deposits, and Gammaproteobacteria in plumes. Campylobacterota- and Gammaproteobacteria-infecting viruses reflected variations in hydrothermal chemistry and functional redundancy in their predicted microbial hosts, suggesting that hydrothermal geology is a driver of viral ecology and coevolution of viruses and hosts. Our results indicate that viral ecology and evolution in globally distributed hydrothermal vents is shaped by endemism and thus may have increased susceptibility to the negative impacts of deep-sea mining and anthropogenic change in ocean ecosystems.},
}

*Hydrothermal Vents/virology/microbiology
*Viruses/genetics/classification/isolation & purification
*Ecosystem
Metagenome
Genome, Viral
Pacific Ocean
Bacteriophages/genetics/classification
Phylogeny
Seawater/virology
Gammaproteobacteria/virology
Microbiota
Virome

@article {pmid40307209,
year = {2025},
author = {Song, X and Wang, Y and Wang, Y and Zhao, K and Tong, D and Gao, R and Lv, X and Kong, D and Ruan, Y and Wang, M and Tang, X and Li, F and Luo, Y and Zhu, Y and Xu, J and Ma, B},
title = {Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4048},
pmid = {40307209},
issn = {2041-1723},
support = {42277283//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41991334//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Rhizosphere ; *Arsenic/metabolism ; Oxidation-Reduction ; *Oryza/microbiology/virology/metabolism ; Soil Microbiology ; *Lysogeny/genetics ; Microbiota/genetics ; Gene Transfer, Horizontal ; Metagenome ; Plant Roots/microbiology/virology ; Oxidoreductases/genetics/metabolism ; Metabolic Reprogramming ; },
abstract = {The rhizosphere is a critical hotspot for metabolic activities involving arsenic (As). While recent studies indicate many functions for soil viruses, much remains overlooked regarding their quantitative impact on rhizosphere processes. Here, we analyze time-series metagenomes of rice (Oryza sativa L.)rhizosphere and bulk soil to explore how viruses mediate rhizosphere As biogeochemistry. We observe the rhizosphere favors lysogeny in viruses associated with As-oxidizing microbes, with a positive correlation between As oxidation and the prevalence of these microbial hosts. Moreover, results demonstrate these lysogenic viruses enrich both As oxidation and phosphorus co-metabolism genes and mediated horizontal gene transfers (HGTs) of As oxidases. In silico simulation with genome-scale metabolic models (GEMs) and in vitro validation with experiments estimate that rhizosphere lysogenic viruses contribute up to 25% of microbial As oxidation. These findings enhance our comprehension of the plant-microbiome-virome interplay and highlight the potential of rhizosphere viruses for improving soil health in sustainable agriculture.},
}

*Rhizosphere
*Arsenic/metabolism
Oxidation-Reduction
*Oryza/microbiology/virology/metabolism
Soil Microbiology
*Lysogeny/genetics
Microbiota/genetics
Gene Transfer, Horizontal
Metagenome
Plant Roots/microbiology/virology
Oxidoreductases/genetics/metabolism
Metabolic Reprogramming

@article {pmid40253770,
year = {2025},
author = {Zhu, Y and Tian, Q and Huang, Q and Wang, J},
title = {Bile-processed Rhizoma Coptidis alleviates type 2 diabetes mellitus through modulating the gut microbiota and short-chain fatty acid metabolism.},
journal = {International immunopharmacology},
volume = {156},
number = {},
pages = {114645},
doi = {10.1016/j.intimp.2025.114645},
pmid = {40253770},
issn = {1878-1705},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Diabetes Mellitus, Type 2/drug therapy/metabolism/microbiology ; Male ; *Drugs, Chinese Herbal/therapeutic use/pharmacology ; Rats ; *Fatty Acids, Volatile/metabolism ; Rats, Sprague-Dawley ; *Diabetes Mellitus, Experimental/drug therapy/metabolism ; *Hypoglycemic Agents/pharmacology/therapeutic use ; Bile/metabolism ; Diet, High-Fat ; Glucagon-Like Peptide 1/metabolism ; Insulin Resistance ; Blood Glucose/metabolism ; Coptis chinensis ; },
abstract = {BACKGROUND: Bile-Processed Rhizoma Coptidis (BPRC) is a processed products of Rhizoma Coptidis (RC) commonly used to treat type 2 diabetes mellitus (T2DM). However, the synergistic mechanism of its processing remains unknown. Current research indicates that the gut microbiota and its metabolites, such as short-chain fatty acids (SCFAs), are closely associated with the progression of T2DM.

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

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

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

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

Animals
*Gastrointestinal Microbiome/drug effects
*Diabetes Mellitus, Type 2/drug therapy/metabolism/microbiology
Male
*Drugs, Chinese Herbal/therapeutic use/pharmacology
Rats
*Fatty Acids, Volatile/metabolism
Rats, Sprague-Dawley
*Diabetes Mellitus, Experimental/drug therapy/metabolism
*Hypoglycemic Agents/pharmacology/therapeutic use
Bile/metabolism
Diet, High-Fat
Glucagon-Like Peptide 1/metabolism
Insulin Resistance
Blood Glucose/metabolism
Coptis chinensis

@article {pmid40058443,
year = {2025},
author = {Zhou, Y and Li, MY and Li, CY and Sheng, YJ and Ye, QT and Chen, RY and Zhou, KY and Zhang, Y and Shen, LF and Shou, D},
title = {Effective mechanism of polysaccharides from Erxian herbal pair in promoting bone repair in traumatic osteomyelitis by activating osteoblast GPR41 and inhibiting the MEK/ERK/MAPK signalling axis.},
journal = {International journal of biological macromolecules},
volume = {307},
number = {Pt 1},
pages = {141858},
doi = {10.1016/j.ijbiomac.2025.141858},
pmid = {40058443},
issn = {1879-0003},
mesh = {Animals ; *Polysaccharides/pharmacology/chemistry ; *Osteoblasts/drug effects/metabolism ; *Osteomyelitis/drug therapy/metabolism/pathology ; Rats ; *MAP Kinase Signaling System/drug effects ; *Receptors, G-Protein-Coupled/metabolism ; Male ; Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Bone Regeneration/drug effects ; Disease Models, Animal ; },
abstract = {Polysaccharides are the key components of natural products; however, their effects on bone repair haven't been fully evaluated. This study aimed to assess the efficacy and mechanism of polysaccharides in promoting bone repair. The Erxian herb pair polysaccharide (EHP) was isolated and purified using water extraction (1:20 (w/v); 100 ± 2 °C; 5 h) and alcohol precipitation (80 ± 2 %). A traumatic osteomyelitis (TO) rat model was established using lipopolysaccharide (LPS). The gut microbiota was analysed through intestinal flora and metagenomic sequencing. The results revealed that the yields of crude polysaccharide and purified polysaccharide EHP were 3.73 ± 0.34 % and 0.48 ± 0.06 %, respectively. The total sugar content of EHP was 83.53 ± 0.16 %. The EHP, with a molecular weight of 31.964 kDa, was primarily composed of mannose, rhamnose, glucose, galactose, and arabinose. In vivo experiments demonstrated that EHP intervention (300 mg/kg/day) significantly augmented bone density and enhanced the activity of alkaline phosphatase (ALP) (P < 0.01). EHP upregulated the abundance of probiotics and increased the production of butyric acid (P < 0.05). In vitro experiments revealed that butyric acid (500-1000 μM) enhanced osteoblast activity and inhibited the expression of mitogen-activated protein kinase kinase (MEK) and extracellular signal-regulated kinase (ERK) (P < 0.01). These findings indicate that polysaccharides may represent a promising therapeutic agent for bone-healing.},
}

Animals
*Polysaccharides/pharmacology/chemistry
*Osteoblasts/drug effects/metabolism
*Osteomyelitis/drug therapy/metabolism/pathology
Rats
*MAP Kinase Signaling System/drug effects
*Receptors, G-Protein-Coupled/metabolism
Male
Gastrointestinal Microbiome/drug effects
Rats, Sprague-Dawley
*Bone Regeneration/drug effects
Disease Models, Animal

@article {pmid40035787,
year = {2025},
author = {Tappauf, N and Lamers, Y and Sham, HP and Piper, HG},
title = {Multiomics profiling and parenteral nutrition weaning in pediatric patients with intestinal failure: A longitudinal cohort study.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {49},
number = {4},
pages = {451-459},
doi = {10.1002/jpen.2742},
pmid = {40035787},
issn = {1941-2444},
support = {//This study was funded through a 2021-2022 Healthy Starts Catalyst Grant, awarded by the BC Children's Hospital Research Institute in Vancouver, Canada./ ; },
mesh = {Humans ; Longitudinal Studies ; Male ; Female ; *Parenteral Nutrition ; *Gastrointestinal Microbiome ; Infant ; *Intestinal Failure/therapy/microbiology ; Child, Preschool ; Feces/microbiology ; *Weaning ; *Metabolomics ; Biomarkers/blood ; Cohort Studies ; Child ; Bacteria/classification/genetics ; Multiomics ; },
abstract = {BACKGROUND: Intestinal failure (IF) is a life-limiting condition that includes a variety of intestinal pathologies. Currently, there are few clinical biomarkers that reflect intestinal function or a patient's potential to wean off parenteral nutrition (PN), making it difficult to predict the clinical trajectory. By associating gut microbiome taxonomic and functional features and blood analytes with the proportion of daily energy delivered via PN-a proxy for intestinal function-our study aimed to discover potential predictors of intestinal function and PN weaning potential.

METHODS: In this longitudinal multiomics cohort study, we followed 18 pediatric patients with IF and PN support for ≤1.5 years. Fecal and stoma samples were analyzed using metagenomic shotgun sequencing to assess bacterial taxonomy and function and internal transcribed spacer 2 ribosomal RNA sequencing to characterize the fungal community. Targeted metabolomics was used to quantify 257 blood analytes. Linear mixed models were used to analyze the associations of PN dependence with microbiome features and blood analytes.

RESULTS: The bacterial and fungal taxonomic composition exhibited substantial interpatient and intrapatient variability, with no link to PN dependence. In contrast, bacterial functional analysis revealed 63 MetaCyc pathways significantly associated with PN dependence. Additionally, 32 blood analytes were associated with PN dependence.

CONCLUSION: In this exploratory study, we found that functional microbiome features and blood metabolomic profiles-particularly urea cycle metabolites, creatinine, asparagine, and tryptophan-derived metabolites-show promise for predicting intestinal function. Furthermore, they may have therapeutic implications for promoting intestinal adaptation. Confirmatory trials with larger sample sizes are needed to validate these findings.},
}

Humans
Longitudinal Studies
Male
Female
*Parenteral Nutrition
*Gastrointestinal Microbiome
Infant
*Intestinal Failure/therapy/microbiology
Child, Preschool
Feces/microbiology
*Weaning
*Metabolomics
Biomarkers/blood
Cohort Studies
Child
Bacteria/classification/genetics
Multiomics

@article {pmid39930064,
year = {2025},
author = {Eriksen, AMH and Rodríguez, JA and Seersholm, F and Hollund, HI and Gotfredsen, AB and Collins, MJ and Grønnow, B and Pedersen, MW and Gilbert, MTP and Matthiesen, H},
title = {Exploring DNA degradation in situ and in museum storage through genomics and metagenomics.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {210},
pmid = {39930064},
issn = {2399-3642},
mesh = {*Museums ; *Metagenomics/methods ; *Genomics/methods ; Animals ; *DNA/genetics ; Archaeology ; Microbiota ; Greenland ; DNA, Ancient/analysis ; *Specimen Handling ; Bone and Bones/microbiology ; DNA Damage ; Fossils ; },
abstract = {Understanding the environmental and microbial processes involved in DNA degradation from archaeological remains is a fundamental part of managing bone specimens. We investigated the state of DNA preservation in 33 archaeozoological caribou (Rangifer tarandus) ribs excavated from the same excavation trench at a former Inuit hunting camp in West Greenland, separated by 43 years: 1978 and 2021. Our findings show that DNA is better preserved in the most recently excavated samples, indicating a detrimental effect of museum storage on DNA integrity. Additionally, our data reveals a diverse microbiome in these bones, encoding genes relevant for bone degradation, such as enzymatic families relating to collagenases, peptidases and glycosidases. Microbes associated with bone degradation were present in both new and historical samples, with museum-stored bones showing significantly more DNA damage. Overall, our research sheds light on the nuanced dynamics governing the preservation of genomic material in archaeological contexts, underscoring the vital importance of careful considerations in museum curation practices for the sustainable conservation of invaluable skeletal records in museum repositories and in situ.},
}

*Museums
*Metagenomics/methods
*Genomics/methods
Animals
*DNA/genetics
Archaeology
Microbiota
Greenland
DNA, Ancient/analysis
*Specimen Handling
Bone and Bones/microbiology
DNA Damage
Fossils