@article {pmid40667647,
year = {2025},
author = {Yan, C and Li, XN and Peng, ZL and Wu, W and Wang, Z and Zhu, ZR and Liu, JC and Wang, Y and Ren, JL and Zhang, ZY and Li, JT},
title = {Hologenomics Reveals Specialized Dietary Adaptations in the Mengla Snail-Eating Snake.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e09999},
doi = {10.1002/advs.202509999},
pmid = {40667647},
issn = {2198-3844},
support = {2024NSFSC1181//Sichuan Science and Technology Program/ ; 2024YFHZ0294//Sichuan Science and Technology Program/ ; 32325011//National Natural Science Foundation of China/ ; 32220103004//National Natural Science Foundation of China/ ; 32370449//National Natural Science Foundation of China/ ; 32300351//National Natural Science Foundation of China/ ; },
abstract = {Serpents, as highly adaptable vertebrates, provide robust models for studying the mechanisms of dietary specialization. Using an integrative multi-omics approach, encompassing host genomic, transcriptomic, proteomic, gut metagenomic, and enzymatic analyses, the mechanisms underlying dietary adaptations in the Mengla snail-eating snake (Pareas menglaensis), a species specialized in consuming snails is investigated. Adaptations supporting this diet included evolution of infralabial glands secreting toxin homologs and digestive enzymes, facilitating molluscan predation and digestion. This specialization has driven adaptive evolution in the host genome and shaped the gut microbiota, addressing both nutritional challenges (e.g., lipid deficiency) and digestive requirements (e.g., mucus degradation) associated with snail consumption. Notably, the functional convergence in microbial gene functions between reptiles and mammals highlights parallel evolutionary pathways in dietary specialization. These findings elucidate the genomic foundations of dietary specialization in P. menglaensis, offering broader insights into evolutionary adaptation within a holobiome framework.},
}

@article {pmid40667420,
year = {2025},
author = {Orejudo, M and Gómez, MJ and Riestra, S and Rivero, M and Gutiérrez, A and Rodríguez-Lago, I and Fernández-Salazar, L and Ceballos, D and Benítez, JM and Aguas, M and Bastón-Rey, I and Bermejo, F and Casanova, MJ and Lorente-Poyatos, RH and Ber, Y and Ginard, D and Esteve, M and de Francisco, R and García, MJ and Francés, R and Rodríguez, A and Alcaide Suárez, N and Guerra Del Río, E and Soto, P and Nos, P and Barreiro-de Acosta, M and Guerra, I and Hervías Cruz, D and Domínguez Cajal, M and Royo, V and Aceituno, M and Aldars-García, L and Garre, A and Ramírez, C and Soleto, I and Schuppe-Koistinen, I and Engstrand, L and Baldán-Martín, M and Sánchez-Cabo, F and Gisbert, JP and Chaparro, M},
title = {Exploration of fecal microbiota in newly diagnosed patients with inflammatory bowel disease using shotgun metagenomics.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1595884},
pmid = {40667420},
issn = {2235-2988},
mesh = {Humans ; *Feces/microbiology ; *Metagenomics/methods ; Female ; Male ; Adult ; Middle Aged ; *Inflammatory Bowel Diseases/microbiology/diagnosis ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Crohn Disease/microbiology ; Colitis, Ulcerative/microbiology ; Young Adult ; Aged ; Computational Biology ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; },
abstract = {INTRODUCTION: Dysbiosis is a key mechanism in inflammatory bowel disease (IBD) pathophysiology. Previous microbiota studies in IBD generally have involved patients treated with immunosuppressive agents, which can affect the results. We aimed to elucidate the fecal microbiota composition in newly diagnosed treatment-naïve IBD patients.

METHODS: Microbiota from stool samples were investigated using shotgun metagenomics sequencing and subsequent bioinformatics analysis.

RESULTS: A total of 103 patients with Crohn's disease (CD), 144 with ulcerative colitis (UC), and 49 healthy controls (HC) were included. CD patients had significantly lower species-level diversity than those with UC and HC. CD subgroups with Ileocolonic location and stricturing behavior showed reduced diversity compared to HC. A negative correlation was observed between endoscopic severity and microbial diversity in CD patients. UC patients had similar microbial diversity to HC, which was unaffected by disease activity. Taxonomic abundance analysis revealed a tendency towards a higher relative abundance of Escherichia coli and a lower relative abundance of Faecalibacterium prausnitzii in IBD patients compared to HC. However, the most significant differences in these patients compared to HC were observed in less abundant species, such as Toxoplasma gondii, Gemella morbillorum, and several species of the Adlercreutzia genera. Functional analysis in these patients highlighted changes in carbohydrate and nucleotide pathways.

DISCUSSION: Our data suggest that newly diagnosed CD patients show significant microbiota composition disparities compared to UC patients and HC. Microbiota differences in these patients are linked to dysbiosis, characterized by a reduction in beneficial genera such as Gemella and Adlercreutzia, and a rise in pathogenic species.},
}

Humans
*Feces/microbiology
*Metagenomics/methods
Female
Male
Adult
Middle Aged
*Inflammatory Bowel Diseases/microbiology/diagnosis
Dysbiosis/microbiology
*Gastrointestinal Microbiome
Crohn Disease/microbiology
Colitis, Ulcerative/microbiology
Young Adult
Aged
Computational Biology
Bacteria/classification/genetics/isolation & purification
Biodiversity

@article {pmid40665424,
year = {2025},
author = {Yvenou, S and Le Moigne, M and Rouxel, O and Aubé, J and Trouche, B and Cathalot, C and Rinnert, E and Philippon, X and Chéron, S and Boissier, A and Guyader, V and Germain, Y and Godfroy, A and Roussel, EG and Alain, K},
title = {Sulfur-rich deposits associated with the deep submarine volcano Fani Maoré support broad microbial sulfur cycling communities.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {166},
pmid = {40665424},
issn = {2049-2618},
support = {ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; Sino-French IRP 1211 MicrobSea//CNRS-INEE/ ; Sino-French IRP 1211 MicrobSea//CNRS-INEE/ ; doi: 10.18715/MAYOTTE.REVOSIMA//REVOSIMA/ ; doi: 10.18715/MAYOTTE.REVOSIMA//REVOSIMA/ ; doi: 10.18715/MAYOTTE.REVOSIMA//REVOSIMA/ ; doi: 10.18715/MAYOTTE.REVOSIMA//REVOSIMA/ ; doi: 10.18715/MAYOTTE.REVOSIMA//REVOSIMA/ ; FR000063751 //876//TOTAL ENERGIES/ ; FR000063751 //876//TOTAL ENERGIES/ ; FR000063751 //876//TOTAL ENERGIES/ ; FR000063751 //876//TOTAL ENERGIES/ ; FR000063751 //876//TOTAL ENERGIES/ ; 20/1001730//IFREMER/ ; 20/1001730//IFREMER/ ; 20/1001730//IFREMER/ ; 20/1001730//IFREMER/ ; 20/1001730//IFREMER/ ; },
mesh = {*Sulfur/metabolism/analysis ; *Volcanic Eruptions/analysis ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota/genetics ; *Geologic Sediments/microbiology/chemistry ; Indian Ocean ; Metagenomics/methods ; Seawater/microbiology/chemistry ; Metagenome ; },
abstract = {BACKGROUND: In 2018, the island of Mayotte located in the western Indian ocean, has experienced a seismo-volcanic crisis linked to the birth of an impressive intraplate submarine volcano at the east of the island. This volcano, named Fani Maoré, which has not yet been the subject of microbiological studies, triggered the largest submarine eruptive event ever recorded. Close to the volcano's summit is a singular meter-size structure containing abundant native sulfur mineralizations. While a wide variety of ecosystems, with more or less well documented microbial communities, are found in active volcanoes on the ocean floor, knowledge on microbial communities hosted in habitats such as sulfur-rich intraplate volcanoes, that are not located on hotspots, remains limited. Genome-resolved metagenomics, culture-based functional approaches, geochemical and mineralogical analyses were combined to characterize the geological and physico-chemical constraints of the environment surrounding the yellow deposit part of this hotspot volcano and the composition and functions of its microbial community.

RESULTS: Geological and geochemical analyses indicated that this volcanic habitat had high concentrations in various sulfur species, including native sulfur, hydrogen sulfide and sulfate. Twenty-three Metagenome Assembled Genomes (MAGs) belonging to 8 different bacterial phyla, mainly Pseudomonadota, Bacteroidota and Campylobacterota, were reconstructed from the sulfur-rich deposit and analyzed. The vast majority of MAGs encoded genes for complete sulfur cycling metabolic pathways, in particular sulfur oxidation. Estimation of the cultivable microbial fraction revealed a diversity of microorganisms, with high growth rates for sulfur reduction, sulfate reduction with dihydrogen, and sulfur oxidation. Sulfur compound (S[0], SO3[2-] and S2O3[2-]) disproportionation was also observed in cultures. The versatile genus Sulfurimonas was prevalent in culture at 6 and 20 °C, in the presence of different sulfur redox couples.

CONCLUSIONS: Microbial communities, including taxa commonly found in ridge hydrothermal systems, were composed of autotrophic, heterotrophic or mixotrophic taxa using a large range of electron donors and acceptors to fuel their catabolism, particularly sulfur compounds in all common oxidation states. They had the genetic potential and physiological capacity to carry out all the metabolic reactions of the microbial sulfur cycle using the abiotic sulfur compounds present in their habitat. Representatives of the Sulfurimonas genus were among the main chemoautotrophs, since they predominated in eleven different temperature-redox pair culture combinations. Based on the observations, a conceptual model was proposed to describe the interactions in this sulfur-rich deposit that may occur between the microorganisms, the physico-chemical conditions and the sulfur compounds supplied by the environment. Video Abstract.},
}

*Sulfur/metabolism/analysis
*Volcanic Eruptions/analysis
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota/genetics
*Geologic Sediments/microbiology/chemistry
Indian Ocean
Metagenomics/methods
Seawater/microbiology/chemistry
Metagenome

@article {pmid40665409,
year = {2025},
author = {Lyu, L and Fan, Y and Vogt, JK and Clos-Garcia, M and Bonnefond, A and Pedersen, HK and Dutta, A and Koivula, R and Sharma, S and Allin, KH and Brorsson, C and Cederberg, H and Chabanova, E and De Masi, F and Dermitzakis, E and Elders, PJ and Blom, MT and Hollander, M and Eriksen, R and Forgie, I and Frost, G and Giordano, GN and Grallert, H and Haid, M and Hansen, TH and Jablonka, B and Kokkola, T and Mahajan, A and Mari, A and McDonald, TJ and Musholt, PB and Pavo, I and Prehn, C and Ridderstråle, M and Ruetten, H and Hart, LM' and Schwenk, JM and Stankevic, E and Thomsen, HS and Vangipurapu, J and Vestergaard, H and Viñuela, A and Walker, M and Hansen, T and Linneberg, A and Nielsen, HB and Brunak, S and McCarthy, MI and Froguel, P and Adamski, J and Franks, PW and Laakso, M and Beulens, JWJ and Pearson, E and Pedersen, O},
title = {The dynamics of the gut microbiota in prediabetes during a four-year follow-up among European patients-an IMI-DIRECT prospective study.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {78},
pmid = {40665409},
issn = {1756-994X},
support = {FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; },
mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Bacteria/classification/genetics ; Blood Glucose ; Europe ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Glucose Tolerance Test ; Metagenomics ; *Prediabetic State/microbiology/metabolism ; Prospective Studies ; },
abstract = {BACKGROUND: Previous case-control studies have reported aberrations of the gut microbiota in individuals with prediabetes. The primary objective of the present study was to explore the dynamics of the gut microbiota of individuals with prediabetes over 4 years with a secondary aim of relating microbiota dynamics to temporal changes of metabolic phenotypes.

METHODS: The study included 486 European patients with prediabetes. Gut microbiota profiling was conducted using shotgun metagenomic sequencing and the same bioinformatics pipelines at study baseline and after 4 years. The same phenotyping protocols and core laboratory analyses were applied at the two timepoints. Phenotyping included anthropometrics and measurement of fasting plasma glucose and insulin levels, mean plasma glucose and insulin under an oral glucose tolerance test (OGTT), 2-h plasma glucose after an OGTT, oral glucose insulin sensitivity index, Matsuda insulin sensitivity index, body mass index, waist circumference, and systolic and diastolic blood pressure. Measures of the dynamics of bacterial microbiota were related to concomitant changes in markers of host metabolism.

RESULTS: Over 4 years, significant declines in richness were observed in gut bacterial and viral species and microbial pathways accompanied by significant changes in the relative abundance and the genetic composition of multiple bacterial species. Additionally, bacterial-viral interactions diminished over time. Despite the overall reduction in bacterial richness and microbial pathway richness, 80 dominant core bacterial species and 78 core microbial pathways were identified at both timepoints in 99% of the individuals, representing a resilient component of the gut microbiota. Over the same period, individuals with prediabetes exhibited a significant increase in glycemia and insulinemia alongside a significant decline in insulin sensitivity. Estimates of the gut bacterial microbiota dynamics were significantly correlated with temporal impairments in host metabolic health.

CONCLUSIONS: In this 4-year prospective study of European patients with prediabetes, the gut microbiota exhibited major changes in taxonomic composition, bacterial species genetics, and microbial functional potentials, many of which paralleled an aggravation of host metabolism. Whether the temporal gut microbiota changes represent an adaptation to the progression of metabolic abnormalities or actively contribute to these in prediabetes cases remains unsettled.

TRIAL REGISTRATION: The Diabetes Research on Patient Stratification (DIRECT) study, an exploratory observational study initiated on October 15, 2012, was registered on ClinicalTrials.gov under the number NCT03814915.},
}

Adult
Aged
Female
Humans
Male
Middle Aged
Bacteria/classification/genetics
Blood Glucose
Europe
Follow-Up Studies
*Gastrointestinal Microbiome
Glucose Tolerance Test
Metagenomics
*Prediabetic State/microbiology/metabolism
Prospective Studies

@article {pmid40665020,
year = {2025},
author = {Liu, Y and Zhang, H and Cao, L and Fu, L and Lian, C and Guo, Y and Zhong, Z and Seim, I and Wang, M and Li, C},
title = {Methane filtration and metabolic cooperation of microbial communities in cold seep water columns from South China Sea.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1052},
pmid = {40665020},
issn = {2399-3642},
support = {42076091//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Methane/metabolism ; China ; *Seawater/microbiology ; *Bacteria/metabolism/genetics/classification ; *Microbiota ; Metagenome ; *Water Microbiology ; Oceans and Seas ; Metagenomics ; },
abstract = {Microbes in cold seep water columns are essential for methane sequestration and biogeochemical cycling, yet their structures and ecological functions, particularly at the bottom water interface (BWI), are poorly understood. Here, we performed metagenomic analyses to explore the microbial biodiversity and functions at the F-site cold seep in the South China Sea. Functional stratification revealed that photosynthetic autotrophs dominate surface zones, heterotrophs are prevalent in mesopelagic zones, and chemosynthetic bacteria are abundant at the BWI. We obtained 377 metagenome-assembled-genomes (MAGs) and constructed genome-scale metabolic models to unveil metabolic interactions facilitating the coupling of carbon, nitrogen, and sulfur among microbes, particularly at the BWI. Notably, methanotrophic bacteria with diverse metabolic capabilities distributed from the BWI zone to the deep mesopelagic regions, highlighting the broader influence of methane. In conclusion, our findings reveal a high degree of heterogeneity in the composition and function of microorganisms across the F-site cold seep water column. Our study also sheds light on the ecological interactions and environmental gradients that shape these microbial communities.},
}

*Methane/metabolism
China
*Seawater/microbiology
*Bacteria/metabolism/genetics/classification
*Microbiota
Metagenome
*Water Microbiology
Oceans and Seas
Metagenomics

@article {pmid40608492,
year = {2025},
author = {Ozuru, R and Yamagishi, J and Takeuchi, A and Date, Y and Fujii, T and Sugimoto, C and Nakajima, C and Suzuki, Y and Aoki, K and Fujii, J and Matsuba, T},
title = {Unification of symbiotic bacteria during larva-to-adult transition in Culicoides circumscriptus (Diptera: Ceratopogonidae).},
journal = {FEMS microbiology letters},
volume = {372},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf069},
pmid = {40608492},
issn = {1574-6968},
support = {24K13424//JSPS/ ; 18K16174//JSPS/ ; 21K16320//JSPS/ ; 24K10225//JSPS/ ; JP20wm0125008//Japan Agency for Medical Research and Development/ ; JP223fa62700//Japan Agency for Medical Research and Development/ ; },
mesh = {Animals ; *Ceratopogonidae/microbiology/growth & development ; Larva/microbiology/growth & development ; *Symbiosis ; Female ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Japan ; Microbiota ; Phylogeny ; },
abstract = {Blood-sucking midges such as Leptoconops and Culicoides are of medical importance due to their role in causing skin irritation and potentially transmitting pathogens. Investigating their bacterial communities, including possible endosymbionts, may help clarify ecological adaptations and interactions with hosts. Leptoconops nipponensis Tokunaga (Lnt) and Culicoides circumscriptus (Cc), blood-sucking midges, cause severe itching and inflammation in humans. Cc was collected from a small sample of an outbreak swarm of Lnt in the peninsula area of Yonago City, Tottori Prefecture, Japan. This study compared the bacterial flora of Lnt and Cc, revealing distinct bacterial diversity shifts in these insect species between life stages. We analyzed the bacterial communities of adult and larval females of Cc and Lnt using MiSeq sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Notably, alpha diversity in Cc adults was significantly reduced to 1.5 (n = 43), indicating that Cc adults were dominated by a single bacterial genus, compared to 14.9 in Cc larvae (n = 19). BLAST (Basic Local Alignment Search Tool) analysis identified this dominant genus in adult Cc as Rickettsia (Candidatus Tisiphisa), which is known for transovarial transmission in arthropod vectors. In contrast, the bacterial diversity of Lnt showed no significant difference between adults (18.1, n = 32) and larvae (n = 15). These findings suggest that the dominance of Rickettsia in Cc (Candidatus Tisiphisa) adults is linked to their emergence, potentially reflecting differences in reproductive biology and ecological adaptations between these two insect species. Further research is needed to elucidate the functional role of Rickettsia in the life cycle and physiology of Cc.},
}

Animals
*Ceratopogonidae/microbiology/growth & development
Larva/microbiology/growth & development
*Symbiosis
Female
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Japan
Microbiota
Phylogeny

@article {pmid40489211,
year = {2025},
author = {Gautam, P and Yadav, R and Vishwakarma, RK and Shekhar, S and Pathak, A and Singh, C},
title = {An Integrative Analysis of Metagenomic and Metabolomic Profiling Reveals Gut Microbiome Dysbiosis and Metabolic Alterations in ALS: Potential Biomarkers and Therapeutic Insights.},
journal = {ACS chemical neuroscience},
volume = {16},
number = {14},
pages = {2691-2706},
doi = {10.1021/acschemneuro.5c00254},
pmid = {40489211},
issn = {1948-7193},
mesh = {*Amyotrophic Lateral Sclerosis/metabolism/microbiology ; Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/metabolism/microbiology ; Male ; *Metabolomics/methods ; Female ; Middle Aged ; Biomarkers/metabolism ; Aged ; Metagenomics/methods ; Feces/microbiology ; },
abstract = {ALS is a severe neurodegenerative disorder characterized by motor neuron degeneration, gut dysbiosis, immune dysregulation, and metabolic disturbances. In this study, shotgun metagenomics and [1]H nuclear magnetic resonance (NMR)-based metabolomics were employed to investigate the altered gut microbiome and metabolite profiles in individuals with ALS, household controls (HCs), and nonhousehold controls (NHCs). The principal component analysis (PCA) explained 33% of the variance, and the partial least-squares discriminant analysis (PLS-DA) model demonstrate R[2] and Q[2] values of 0.97 and 0.84, respectively, indicating an adequate model fit. The relative bacterial abundance was 99.34% in the ALS group and 98.94% in the HC group. Among the ten identified genera, Bifidobacterium, Lactobacillus, and Enterococcus were more prevalent in ALS individuals, while Lactiplantibacillus and Klebsiella were more abundant in the HC group. We identified 70 metabolites, including short-chain fatty acids (SCFAs), branched-chain amino acids (BCAAs), carbohydrates, and aromatic compounds, using NMR. Orthogonal partial least-squares discriminant analysis (O-PLS-DA) explained 15.8% of the variance, with a clear separation between the ALS and HC groups. Univariate receiver operating characteristic (ROC) analysis identified three fecal metabolites with AUC values above 0.70, including butyrate (0.798), propionate (0.727), and citrate (0.719). These metabolites may serve as potential biomarkers for ALS. The statistical model for metabolic pathway analysis revealed interconnected pathways, highlighting the complexity of metabolic dysregulation, as well as potential microbial and metabolic biomarkers in ALS. These results highlight the role of gut microbiome alterations in ALS and suggest potential avenues for therapeutic intervention.},
}

*Amyotrophic Lateral Sclerosis/metabolism/microbiology
Humans
*Gastrointestinal Microbiome/physiology
*Dysbiosis/metabolism/microbiology
Male
*Metabolomics/methods
Female
Middle Aged
Biomarkers/metabolism
Aged
Metagenomics/methods
Feces/microbiology

@article {pmid40664945,
year = {2025},
author = {Jiang, W and Xi, R and Zhou, J and Pei, Y and Huang, P and Liu, M},
title = {16S rRNA and Metagenomic Datasets of Gastrointestinal Microbiota in Fetal and 7-Day-Old Goat Kids.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1234},
pmid = {40664945},
issn = {2052-4463},
mesh = {Animals ; *Goats/microbiology ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Metagenome ; Fetus/microbiology ; },
abstract = {The perinatal period (from late gestation to the neonatal stage) in ruminants is a critical phase for fetal organ maturation, where ecological succession of gastrointestinal microbial communities significantly impacts livestock production efficiency. However, research remains insufficient regarding the distribution patterns and functional annotation of microbial communities across different gastrointestinal compartments during this period. This study characterized early microbiota dynamics in Hutianshi Goats using 16S rRNA sequencing (4 fetal goats at 90 ± 10 gestational days) and metagenomics (3 7-day-old goat kids). The fetal goat group generated 852,694 valid reads, yielding 688,277 high-quality reads after chimera removal for downstream analysis. The 7-day-old goat kids group produced 1,081,588,182 final valid reads, after data processing and assembly, 8,561,345 contigs were generated. Gene prediction identified 6,095,352 genes. Multi-database annotations (NR, KEGG, CAZy, etc.) revealed functional potential and antimicrobial resistance traits. The public release of this dataset facilitates academic understanding of microbial community dynamics and host-microbe interactions during this developmental stage, providing both theoretical foundations and data resources for ruminant developmental biology and precision breeding regulation.},
}

Animals
*Goats/microbiology
*Gastrointestinal Microbiome
*RNA, Ribosomal, 16S/genetics
Metagenomics
*Metagenome
Fetus/microbiology

@article {pmid40661966,
year = {2025},
author = {Yao, C and Xue, X and Jia, Y and Li, M and Zhang, L and Yuan, H and Xue, H and Hu, R},
title = {Rosuvastatin ameliorates obesity-associated insulin resistance in high-fat diet-fed mice by modulating the gut microbiota and gut metabolites.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1593581},
pmid = {40661966},
issn = {2235-2988},
mesh = {Animals ; *Insulin Resistance ; *Gastrointestinal Microbiome/drug effects ; Diet, High-Fat/adverse effects ; *Obesity/drug therapy/complications/metabolism ; *Rosuvastatin Calcium/pharmacology/administration & dosage ; Mice, Inbred C57BL ; Male ; Mice ; Fatty Acids, Volatile/metabolism/analysis ; Disease Models, Animal ; Feces/microbiology/chemistry ; Metabolomics ; Metagenomics ; Bacteria/classification/genetics/drug effects ; },
abstract = {INTRODUCTION: Insulin resistance (IR) underlies metabolic diseases such as obesity and diabetes. Statins are lipid-lowering drugs that have also been studied to improve insulin resistance, but the mechanism is not well understood. Metagenomics and metabolomics were used to analyze the main species and metabolic pathways involved in intestinal microbes while improving insulin resistance in mice with rosuvastatin in this study.

METHODS: C57BL/6J male mice fed a high-fat diet were used to establish the insulin resistance (IR) mouse model. Rosuvastatin (RSV) was then administered for 8 weeks. Metagenomics and metabolomics were utilized to analyze the microbial composition and short chain fatty acid metabolites in intestinal feces of mice.

RESULTS: It was observed that insulin-resistant mice showed significant improvement in insulin resistance following treatment with RSV. In comparison to the HFD group, specific bacterial strains were significantly increased, and the levels of butyric acid, caproic acid, and isovaleric acid among the short-chain fatty acids were notably elevated in the RSV group. Through KEGG enrichment analysis, 19 dominant strains and 15 key enzymes involved in butyric acid metabolism were identified.

CONCLUSIONS: The results suggested that IR mice might enhance insulin sensitivity by promoting butyric acid synthesis via intestinal microbes following RSV treatment.},
}

Animals
*Insulin Resistance
*Gastrointestinal Microbiome/drug effects
Diet, High-Fat/adverse effects
*Obesity/drug therapy/complications/metabolism
*Rosuvastatin Calcium/pharmacology/administration & dosage
Mice, Inbred C57BL
Male
Mice
Fatty Acids, Volatile/metabolism/analysis
Disease Models, Animal
Feces/microbiology/chemistry
Metabolomics
Metagenomics
Bacteria/classification/genetics/drug effects

@article {pmid40661950,
year = {2025},
author = {Ma, Y and Suo, J and Sheng, S and Chen, L},
title = {PD-L1 deficiency exacerbates colitis severity by remodeling gut microbiota in inflammatory bowel disease.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1622744},
pmid = {40661950},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *B7-H1 Antigen/genetics/deficiency ; Mice ; Mice, Knockout ; *Colitis/pathology/microbiology/chemically induced/genetics/immunology/metabolism ; *Inflammatory Bowel Diseases/microbiology/immunology/pathology/genetics/metabolism ; Dysbiosis ; Disease Models, Animal ; Severity of Illness Index ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic autoimmune disorder driven by gut microbiota dysbiosis. As an essential immune checkpoint, Programmed death-ligand 1 (PD-L1) has been implicated in modulating gut microbiota composition. However, the precise role of PD-L1 in shaping metagenomic profiles during IBD-associated colitis remains unexplored.

METHODS: DSS-induced colitis was established in both PD-L1 knockout (Pdcd1lg1-/-) mice and wild-type (wt) control mice. Clinical parameters, including disease activity index (DAI), body weight changes, colon length, and histopathological alterations, were systematically evaluated using non-parametric Kruskal-Wallis tests and ANOVA to compare colitis severity between genotypes.

RESULTS: PD-L1 knockout mice exhibited exacerbated colitis, manifesting significantly greater weight loss (p<0.05 vs. wt_DSS), colonic shortening (p<0.05), and DAI scores (p<0.05) and inflammatory changes. PD-L1 knockout mice showed distinct dysbiosis, with enriched pathobionts (Escherichia coli, p=0.006; Bacteroides thetaiotaomicron, p=0.015) and depletion of commensals (Tritrichomonas foetus, p<0.001; Ligilactobacillus murinus). Alpha diversity analysis using Chao1 index revealed statistically significant differences between experimental groups (p=0.05). The transporters downregulate anti-inflammatory SCFA metabolism. KEGG enrichment analysis of differentially expressed genes (DEGs) revealed significant associations with immune and inflammatory pathways in PD-L1 knockout mice.

CONCLUSION: PD-L1 deficiency aggravates colitis by driving pathogenic microbiota alterations and impairing microbial metabolic homeostasis, highlighting its dual regulatory roles in immune homeostasis and microbiome dynamics.},
}

Animals
*Gastrointestinal Microbiome/immunology
*B7-H1 Antigen/genetics/deficiency
Mice
Mice, Knockout
*Colitis/pathology/microbiology/chemically induced/genetics/immunology/metabolism
*Inflammatory Bowel Diseases/microbiology/immunology/pathology/genetics/metabolism
Dysbiosis
Disease Models, Animal
Severity of Illness Index
Mice, Inbred C57BL
Dextran Sulfate
Male

@article {pmid40660333,
year = {2025},
author = {Yang, Z and Zhang, Y and Ran, S and Zhang, J and Gao, Y and Zhang, Y and Li, X and Ai, B and Wei, S and Tian, F and Jia, G and Lin, H and Chen, Z and Zhang, Z},
title = {Exposure to ambient air pollution over developmental stages induced neurodevelopmental impairment in mice offspring via microbiome-gut-brain axis.},
journal = {Particle and fibre toxicology},
volume = {22},
number = {1},
pages = {20},
pmid = {40660333},
issn = {1743-8977},
support = {2024A1515010465//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2022A1515010695//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 82203988//National Natural Science Foundation of China/ ; 2023A04J2071//Guangzhou Municipal Science and Technology Project/ ; 23qnpy107//Fundamental Research Funds for the Central Universities of Sun Yat-sen University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Female ; *Air Pollution/adverse effects ; Mice ; Male ; *Neurodevelopmental Disorders/chemically induced/microbiology ; Pregnancy ; *Prenatal Exposure Delayed Effects/chemically induced ; *Brain/drug effects/growth & development ; *Air Pollutants/toxicity ; Mice, Inbred C57BL ; Behavior, Animal/drug effects ; *Brain-Gut Axis/drug effects ; },
abstract = {Exposure to air pollution has been increasingly recognized as a risk factor for neurodevelopmental disorders, and gut microbiome may play a critical role. However, current evidence still remains scarce. In the present study, mice were exposed to real-time ambient air pollution from conception through young adulthood, with neurobehavioral performance and gut microbiome being assessed across different developmental stages. Neurodevelopmental changes including emotional and cognitive impairments were observed in behavioral tests, accompanied by pathological and inflammation changes in brain, which were more pronounced in adolescence than in young adulthood. Alterations in the compositions and functions of gut microbiome were also revealed by fecal metagenomic sequencing. Mediation analysis showed that gut microbiome alterations significantly contributed to the observed neurodevelopmental changes induced by air pollution. Furthermore, after antibiotic (ABX) intervention, the observed neurobehavioral, pathological and inflammatory differences between the exposed and control groups diminished. These findings indicate that the gut microbiome mediates the neurodevelopmental damage caused by exposure to air pollution during developmental stages, adding novel insights on the underlying mechanisms linking air pollution and neurodevelopmental disorders.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Female
*Air Pollution/adverse effects
Mice
Male
*Neurodevelopmental Disorders/chemically induced/microbiology
Pregnancy
*Prenatal Exposure Delayed Effects/chemically induced
*Brain/drug effects/growth & development
*Air Pollutants/toxicity
Mice, Inbred C57BL
Behavior, Animal/drug effects
*Brain-Gut Axis/drug effects

@article {pmid40659687,
year = {2025},
author = {Zhang, N and Zhao, Y and Zhang, Z and Zhan, M and Zhao, X and Zhang, Y and Sun, J and Zhang, Y and Teng, L and Liu, Z},
title = {Metagenomic and Transcriptomic Datasets of Plateau Brown Frogs (Rana kukunoris) from the Helan Mountains.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1219},
pmid = {40659687},
issn = {2052-4463},
support = {32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Transcriptome ; Metagenomics ; *Ranidae/genetics/microbiology ; *Metagenome ; Climate Change ; Microbiota ; China ; Adaptation, Physiological ; },
abstract = {Global climate change has become a primary driving factor behind the biodiversity crisis in amphibians, making it crucial to understand how climate change affects species and their potential responses. The plateau brown frog (Rana kukunoris) is often regarded as an ideal ecological indicator species, yet research on its environmental adaptation mechanisms based on transcriptomic and microbiomic studies remains limited. Therefore, this study investigates the adaptation strategies of the plateau brown frog to environmental changes, providing extensive transcriptomic and the first comprehensive metagenomic dataset from two distinctly different environmental regions (eastern and western slopes of the Helan Mountains). We gathered transcriptomic data from three tissues (blood, liver, and muscle), resulting in 294,962 unigenes and 570,192 transcripts. Metagenomic sequencing identified major bacterial groups, including Firmicutes, Proteobacteria, Bacteroidetes, Spirochetes, and Actinobacteria. In summary, the results of this study can be used to further explore the associations among microbiota, host, and environment, which are crucial for comprehending the mechanisms of environmental adaptation in this species and contributing to the conservation of amphibian biodiversity.},
}

Animals
*Transcriptome
Metagenomics
*Ranidae/genetics/microbiology
*Metagenome
Climate Change
Microbiota
China
Adaptation, Physiological

@article {pmid40376801,
year = {2025},
author = {Prisco, SZ and Blake, M and Kazmirczak, F and Moon, R and Kremer, BP and Hartweck, LM and Kim, M and Vogel, N and Mendelson, JB and Moutsoglou, D and Thenappan, T and Prins, KW},
title = {Lactobacillus Restructures the Micro/Mycobiome to Combat Inflammation-Mediated Right Ventricular Dysfunction in Pulmonary Arterial Hypertension.},
journal = {Circulation. Heart failure},
volume = {18},
number = {7},
pages = {e012524},
pmid = {40376801},
issn = {1941-3297},
mesh = {Animals ; *Ventricular Dysfunction, Right/physiopathology/microbiology/etiology/metabolism ; *Gastrointestinal Microbiome ; Male ; Rats ; *Pulmonary Arterial Hypertension/microbiology/physiopathology/therapy ; Humans ; Disease Models, Animal ; *Lacticaseibacillus rhamnosus ; *Ventricular Function, Right ; *Inflammation/microbiology ; Rats, Sprague-Dawley ; Middle Aged ; Female ; *Probiotics ; },
abstract = {BACKGROUND: Inflammation suppresses right ventricular (RV) function in pulmonary arterial hypertension (PAH). In particular, we showed GP130 (glycoprotein-130) signaling promotes pathological microtubule remodeling and RV dysfunction in rodent PAH. Emerging data demonstrate the intestinal microbiome regulates systemic inflammation, but the impact of modulating the gut microbiome on the GP130-microtubule axis in RV failure is unknown.

METHODS: Two weeks following monocrotaline injection, rats were administered daily Lactobacillus rhamnosus (4×10[7] colony-forming units) via oral gavage for 10 days. Next-generation metagenomics and internal transcribed spacer 2 sequencing delineated fecal bacterial and fungal compositions. SomaScan proteomics measured levels of 7596 serum proteins. RV immunoblots quantified protein abundances. Light or super resolution confocal microscopy assessed RV, lung, and jejunal morphology. Echocardiography and invasive closed-chest pressure-volume loops evaluated PAH severity and RV function. The relationship between Lactobacillus abundance and RV function was assessed in 65 patients with PAH.

RESULTS: Lactobacillus administration restructured both the intestinal micro- and mycobiome. The alteration in the gut ecosystem improved intestinal health as demonstrated by increased jejunal villus length and glycocalyx thickness and diminished intestinal permeability biomarkers. Serum proteomics revealed Lactobacillus modulated systemic inflammation and decreased circulating GP130 ligands. Lactobacillus-mediated suppression of GP130 signaling blunted pathological microtubule remodeling in RV cardiomyocytes. Microtubule-associated phenotypes, including RV cardiomyocyte and nuclear hypertrophy, transverse tubule integrity, and connexin-43 localization, were all corrected with Lactobacillus. These cellular changes manifested as improved RV function despite no significant alteration in PAH severity. Finally, patients with PAH and detectable fecal Lactobacillus had superior RV function despite similar mean pulmonary arterial pressure and pulmonary vascular resistance as compared with those without detectable Lactobacillus.

CONCLUSIONS: Lactobacillus supplementation restructures the gut micro/mycobiome, restores intestinal health, dampens systemic inflammation, and reduces GP130 ligands and associated RV cardiomyocyte microtubule remodeling. These data identify a novel microbiome-inflammation-microtubule axis that has therapeutic relevance for RV dysfunction.},
}

Animals
*Ventricular Dysfunction, Right/physiopathology/microbiology/etiology/metabolism
*Gastrointestinal Microbiome
Male
Rats
*Pulmonary Arterial Hypertension/microbiology/physiopathology/therapy
Humans
Disease Models, Animal
*Lacticaseibacillus rhamnosus
*Ventricular Function, Right
*Inflammation/microbiology
Rats, Sprague-Dawley
Middle Aged
Female
*Probiotics

@article {pmid40659674,
year = {2025},
author = {Ren, M and You, B and Gong, X and Zhang, P and Wang, J},
title = {Microbial genomic database of the Yangtze River, the third-longest river on Earth.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1222},
pmid = {40659674},
issn = {2052-4463},
support = {42372353, 42225708, 92251304, 92351303, 42002304//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Rivers/microbiology ; China ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; *Microbiota ; Metagenomics ; *Genome, Archaeal ; Databases, Genetic ; *Genome, Bacterial ; },
abstract = {Microbes play an important role in mediating the nutrient cycling in the river ecosystem as a hotspot for biogeochemical processes. Due to scattered sampling efforts, however, there is a lack of a systematic study of the diversity of prokaryotic genomes in the Yangtze River, the third longest river on Earth. Here, we collected 602 metagenomic datasets of water, sediment and riparian soil samples spanning the Upper, Middle, and Lower basins of the Yangtze River over a 6,300 km continuum. We reconstructed 8,110 qualified genomes represented by 927 species-level genomes at the 95% ANI threshold, spanning 31 bacterial and five archaeal phyla. We further showed that more than half of these species (61.3% ~ 82.4%) were novel according to the genomic comparison against the curated databases, greatly expanding the known diversity of river prokaryotes. This dataset depicts an overview of microbial genomic diversity in the Yangtze River and provides a resource for in-depth investigation of metabolic potential, ecology, and evolution of riverine microbiomes.},
}

*Rivers/microbiology
China
*Archaea/genetics/classification
*Bacteria/genetics/classification
*Microbiota
Metagenomics
*Genome, Archaeal
Databases, Genetic
*Genome, Bacterial

@article {pmid40657968,
year = {2025},
author = {Morandi, SC and Uldry, AC and Eldridge, N and Kreuzer, M and Herzog, EL and Zinkernagel, M and Zysset-Burri, DC},
title = {Toward the Characterization of the Human Core Ocular Surface Microbiome.},
journal = {Investigative ophthalmology & visual science},
volume = {66},
number = {9},
pages = {40},
doi = {10.1167/iovs.66.9.40},
pmid = {40657968},
issn = {1552-5783},
mesh = {Humans ; *Microbiota/genetics ; Middle Aged ; Adult ; *Tears/microbiology/metabolism ; *Conjunctiva/microbiology ; Female ; Male ; Tandem Mass Spectrometry ; *Eyelids/microbiology ; *Bacteria/genetics/isolation & purification ; Chromatography, Liquid ; Eye Proteins/metabolism ; },
abstract = {PURPOSE: The field of ocular surface microbiome (OSM) research suggests its involvement in ocular surface (OS) health and disease. However, existing OSM data are heterogeneous. This study aims to provide a whole-metagenome shotgun sequencing-based description of the healthy core ocular surface microbiome (COSM), encompassing all taxonomic kingdoms at species-level resolution.

METHODS: Swabs from the conjunctiva and lower lid margin, and tear fluid of 27 individuals without OS disease aged 40 to 60 years were collected at 3 time points. The OSM was sequenced and taxonomically and functionally profiled using Kraken2 and HUMAnN3, respectively. To validate sequencing results, human and microbial proteins of the tear fluid, termed the tear proteome (TP), were characterized by nano liquid chromatography-tandem mass spectrometry (nLC-MS/MS) and profiled by gene ontology. The COSM was defined as the microbiome present in most of the study population over time. Therefore, species present in > 50% of all samples across the three time points were considered to form the COSM.

RESULTS: At species level, Cutibacterium acnes, Malassezia restricta, and Staphylococcus epidermidis formed the COSM, with Corynebacterium segmentosum additionally being part of the core lid microbiome (LM). No significant differences in the OSM and human TP were observed between the left and right eyes on individual levels. However, the variance between subjects mostly exceeded that between eyes within subjects, suggesting an individual-specific COSM and TP.

CONCLUSIONS: The description of the COSM provides the basis for future OSM research and potential targets for preventive and therapeutic interventions of the OS and associated diseases.},
}

Humans
*Microbiota/genetics
Middle Aged
Adult
*Tears/microbiology/metabolism
*Conjunctiva/microbiology
Female
Male
Tandem Mass Spectrometry
*Eyelids/microbiology
*Bacteria/genetics/isolation & purification
Chromatography, Liquid
Eye Proteins/metabolism

@article {pmid40657495,
year = {2025},
author = {Bruins-van Sonsbeek, LGR and Verschuren, MCM and Kaal, S and Lindenburg, PW and Rodenburg, KCW and Clauss, M and Speksnijder, AGCL and Rutten, VPMG and Bonnet, BFJ and Wittink, F},
title = {Correction: Rhinoceromics: a multi-amplicon study with clinical markers to transferrin saturation levels in ex-situ black rhinoceros (Diceros bicornis michaeli).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1644681},
doi = {10.3389/fmicb.2025.1644681},
pmid = {40657495},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1515939.].},
}

@article {pmid40656756,
year = {2025},
author = {Huang, Y},
title = {Investigation of protists in Momoge wetland (China) through metagenomic next-generation sequencing.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e153721},
pmid = {40656756},
issn = {1314-2828},
abstract = {The Momoge wetland plays an important role in maintaining the ecosphere and protist is an indispensable component of it. In order to reveal community structure and diversity of protists in Momoge wetland, metagenomic next-generation sequencing (mNGS) was performed. The main results are as follows: 1) A total of 224 species were identified, belonging to 17 phyla, 32 classes, 75 orders, 94 families and 146 genera. Among them, Bacillariophyta, Evosea, Oomycota, Rhodophyta, Ciliophora, Haptophyta, and Salpingoecarosetta, Guillardiatheta, Polarellaglacialis, Cladocopiumgoreaui were the dominant phyla and species, respectively; 2) Most of them were species adapted to the saline-alkali environment, and the protists of Momoge wetland had higher diversity, fewer dominant species, and higher evenness than those of the harsher environment; 3) KEGG analysis showed that some protistan pathways were related to the saline-alkali environmental adaptation. This research is beneficial to ecological protection and provides valuable information for future studies.},
}

@article {pmid40653476,
year = {2025},
author = {Bi, BY and Lin, L and Huang, L and Zhou, J and Yan, WJ and Huang, L and Wang, J and Li, XB},
title = {Effects of arabinoxylan on BDNF/TrkB/p-CREB signaling pathway in the prefrontal cortex and intestinal microbiome in post-stroke depressed rats.},
journal = {BMC neuroscience},
volume = {26},
number = {1},
pages = {40},
pmid = {40653476},
issn = {1471-2202},
support = {No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; },
mesh = {Animals ; *Prefrontal Cortex/metabolism/drug effects ; *Brain-Derived Neurotrophic Factor/metabolism ; *Gastrointestinal Microbiome/drug effects ; Male ; Signal Transduction/drug effects ; Rats ; Receptor, trkB/metabolism ; *Depression/metabolism/drug therapy/etiology ; *Xylans/pharmacology ; Rats, Sprague-Dawley ; *Stroke/complications/metabolism ; Cyclic AMP Response Element-Binding Protein/metabolism ; },
abstract = {AIM: To explore the effects of arabinoxylan on the BDNF/TrkB/p-CREB signaling pathway in the prefrontal cortex of post-stroke depressed rats, and to explore its neuronal protective effects through the microbial-gut-brain axis in the regulation of this pathway.

METHODS: The rat model of post-stroke depression (PSD) was established by middle cerebral artery occlusion (MCAO) combined with chronic unpredictable mild stimulation (CUMS). They were randomly divided into 5 groups (blank control, post-stroke depression, arabinoxylan, fluoxetine hydrochloride, fluoxetine hydrochloride combined arabinoxylan). The rats were treated differently for 28 days according to their grouping. Body mass, sugar and water consumption experiments and open-field experiments were used to evaluate the behavior of rats. The pathological changes were observed by H&E staining. The expression levels of amine neurotransmitters were detected by ELISA. The expression levels of BDNF mRNA and BDNF, TrkB and p-CREB were detected by RT-PCR and Western blot. The analysis of intestinal metagenomics was conducted by 16 S rDNA sequencing.

RESULTS: Compared with the post-stroke depression group, the body weight, activity and sugar water consumption rate of the arabinoxylan group were increased. The expression levels of 5-HT in the prefrontal cortex, colon and serum levels of 5-HT, DA and NE were increased. The expression levels of BDNF mRNA and BDNF, TrkB and P-CREB in the prefrontal cortex were also upregulated. The number of neurons in the prefrontal cortex increased; Colon mucosal injury and inflammatory cell infiltration decreased, the intestinal microbial diversity increased; The relative abundance of probiotics such as bifidobacterium, Christensenia, Dubosiella New York and ruminococcus increased. The relative abundance of Prevotella NK3B31 group was reduced. The level of 5-HT in the prefrontal cortex was negatively correlated with the abundance of Prevotellaceae NK3B31 group.

CONCLUSION: Arabinoxylan improved depressive-like behavior in rats and its neuroprotective role was achieved by promoting the growth of intestinal probiotics, improving the intestinal barrier, affecting the BDNF/TrkB/p-CREB signaling pathway, and increasing the expression levels of monoamine neurotransmitters 5-HT, DA and NE.},
}

Animals
*Prefrontal Cortex/metabolism/drug effects
*Brain-Derived Neurotrophic Factor/metabolism
*Gastrointestinal Microbiome/drug effects
Male
Signal Transduction/drug effects
Rats
Receptor, trkB/metabolism
*Depression/metabolism/drug therapy/etiology
*Xylans/pharmacology
Rats, Sprague-Dawley
*Stroke/complications/metabolism
Cyclic AMP Response Element-Binding Protein/metabolism

@article {pmid40631381,
year = {2025},
author = {Huang, X and Gao, X and Fan, Y and Wang, D and Chen, X and Qi, X and Yang, Z and Wang, YE and Meng, J and Zou, G and Liu, Z and Li, X},
title = {Moderate altitude exposure impacts extensive host-microbiota multi-kingdom connectivity with serum metabolome and fasting blood glucose.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2530660},
doi = {10.1080/21505594.2025.2530660},
pmid = {40631381},
issn = {2150-5608},
mesh = {Humans ; *Altitude ; *Metabolome ; *Gastrointestinal Microbiome ; Male ; Female ; *Blood Glucose/analysis ; Adult ; Feces/microbiology ; Mycobiome ; Bacteriophages ; Fasting/blood ; Young Adult ; Bacteria/classification/genetics ; Metagenomics ; *Host Microbial Interactions ; China ; Middle Aged ; Archaea ; Fatty Acids, Volatile ; },
abstract = {The contributions and interactions of multi-kingdom microbiota (i.e. bacteriome, mycobiome, archaeome, and phageome) with serum metabolome and host phenome in healthy individuals under moderate altitude exposure remain unclear. We applied shotgun metagenomic sequencing in feces and targeted metabolomics technology in serum to explore how human gut multi-kingdom microorganisms influence the serum metabolome and phenome in healthy Chinese individuals following moderate altitude exposure. The results indicated that individuals with moderate altitude exposure exhibited more substantial alterations in gut bacteriome and phageome compared to those in mycobiome and archaeome. Both intra-kingdom and inter-kingdom correlations at baseline were denser than those following moderate altitude exposure. Bacteriophages-host interaction analysis revealed symbiosis between bacteriophages and Bacteroidetes, Proteobacteria, and short-chain fatty acids (SCFAs) producers. Furthermore, bacteriophage Shirahamavirus PTm1 (odds ratio (OR) = 3.82; 95% confidence interval (CI): 1.20-12.16), archaeon Crenarchaeota (OR = 3.70; 95% CI: 1.35-10.14) and bacterium Bacteroidetes (OR = 3.69; 95% CI: 1.34-10.15) showed a positive association with lowered fasting blood glucose (FBG) benefits, while bacteriophage Candidatus Nitrosopelagicus brevis (OR = 0.30; 95% CI: 0.10-0.89) and butyric acid (OR = 0.07; 95% CI: 0.01-0.37) exhibited a negative association with lowered FBG benefits. These findings suggest that targeting gut multi-kingdom microorganisms could serve as an alternative therapeutic approach to mitigate dysglycemia and its associated metabolic disorders.},
}

Humans
*Altitude
*Metabolome
*Gastrointestinal Microbiome
Male
Female
*Blood Glucose/analysis
Adult
Feces/microbiology
Mycobiome
Bacteriophages
Fasting/blood
Young Adult
Bacteria/classification/genetics
Metagenomics
*Host Microbial Interactions
China
Middle Aged
Archaea
Fatty Acids, Volatile

@article {pmid40652256,
year = {2025},
author = {Tang, Y and Zhan, P and Wu, Y and Zhang, T and Yin, D and Gao, Y and Yu, Y and Qiu, S and Zhao, J and Zhang, X and Ma, Z and Chen, Y and Zhao, L and Mao, S and Huang, J and Chen, WH and Liu, J},
title = {Landscape of mobile genetic elements and their functional cargo across the gastrointestinal tract microbiomes in ruminants.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {162},
pmid = {40652256},
issn = {2049-2618},
mesh = {Animals ; *Ruminants/microbiology ; *Gastrointestinal Microbiome/genetics ; *Interspersed Repetitive Sequences ; Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Plasmids/genetics ; Gene Transfer, Horizontal ; *Gastrointestinal Tract/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Mobile genetic elements (MGEs) drive horizontal gene transfer and microbial evolution, spreading adaptive genes across microbial communities. While extensively studied in other ecosystems, the role of MGEs in shaping ruminant gastrointestinal microbiomes-especially their impact on diversity, adaptation, and dietary responsiveness-remains largely unexplored. This study systematically profiles MGE distribution and functionality across gastrointestinal regions in multiple ruminant species to advance our understanding of microbial adaptation.

RESULTS: Across 2458 metagenomic samples from eight ruminant species, we identified 4,764,110 MGEs-a ~ 216-fold increase over existing MGE databases. These elements included integrative and conjugative elements, integrons, insertion sequences, phages, and plasmids, with mobilization patterns largely confined to closely related microbial lineages. The distribution of MGEs varied by GIT regions, often reflecting nutritional gradients. In a validation cohort, GH1-carrying plasmids enriched in carbohydrate-active enzymes were found to predominate in the stomach, showing notable responsiveness to forage-based diets. All annotated MGEs have been compiled into a publicly accessible database, rumMGE (https://rummge.liulab-njau.com), to support further research.

CONCLUSIONS: This study substantially expands the catalog of known MGEs in ruminants, revealing their diverse roles in microbial evolution and functional adaptation to dietary changes. The findings provide a valuable resource for advancing research on microbial functionality and offer insights with potential applications for enhancing ruminant health and productivity, through strategies aimed at modulating the microbiome in agricultural contexts. Video Abstract.},
}

Animals
*Ruminants/microbiology
*Gastrointestinal Microbiome/genetics
*Interspersed Repetitive Sequences
Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Plasmids/genetics
Gene Transfer, Horizontal
*Gastrointestinal Tract/microbiology
Metagenome

@article {pmid40650758,
year = {2025},
author = {Kearns, R},
title = {Gut modulation to regulate NF-κB in colorectal and gastric cancer therapy and inflammation.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {74},
number = {8},
pages = {264},
pmid = {40650758},
issn = {1432-0851},
mesh = {Humans ; *NF-kappa B/metabolism ; *Gastrointestinal Microbiome/immunology ; *Stomach Neoplasms/therapy/immunology/metabolism/microbiology/pathology ; *Inflammation/metabolism ; *Colorectal Neoplasms/therapy/immunology/metabolism/microbiology/pathology ; Animals ; Dysbiosis ; Fecal Microbiota Transplantation ; Signal Transduction ; },
abstract = {The nuclear factor-kappa B (NF-κB) pathway plays a pivotal role in cancer progression, immune regulation, and inflammation. Aberrant activation of this pathway, often driven by gut microbiota dysbiosis, contributes to tumorigenesis, therapy resistance, and chronic inflammation. Emerging evidence highlights the bidirectional interaction between gut microbiota and NF-κB signalling, suggesting that microbiota modulation may enhance cancer treatment efficacy and reduce treatment-induced inflammation. This review explores the mechanistic underpinnings of gut microbiota-mediated NF-κB regulation, focusing on microbial metabolites such as short-chain fatty acids (SCFAs) and microbial-associated molecular patterns, including lipopolysaccharides (LPS). It examines how conventional cancer treatments, chemotherapy, radiotherapy, and immune checkpoint inhibitors, exacerbate dysbiosis and NF-κB-driven inflammation, further complicating treatment outcomes. Additionally, this review evaluates the therapeutic potential of gut-targeted interventions, including probiotics, prebiotics, faecal microbiota transplantation (FMT), and dietary modifications, in restoring microbial homeostasis and modulating NF-κB signalling. Despite promising findings, challenges remain regarding the clinical translation of microbiota-based therapies, including the need for standardised microbiota profiling, regulatory frameworks, and long-term safety assessments. Advances in metagenomics and metabolomics are proposed as essential tools to personalise gut-targeted interventions and optimise cancer treatment strategies. Integrating gut modulation into oncology represents a paradigm shift, offering a holistic, patient-centric approach to cancer therapy. However, further research is required to validate these strategies and ensure their efficacy in clinical applications.},
}

Humans
*NF-kappa B/metabolism
*Gastrointestinal Microbiome/immunology
*Stomach Neoplasms/therapy/immunology/metabolism/microbiology/pathology
*Inflammation/metabolism
*Colorectal Neoplasms/therapy/immunology/metabolism/microbiology/pathology
Animals
Dysbiosis
Fecal Microbiota Transplantation
Signal Transduction

@article {pmid40650567,
year = {2025},
author = {Wallenius, AJ and Venetz, J and Zygadlowska, OM and Lenstra, WK and van Helmond, NAGM and Martins, PD and Slomp, CP and Jetten, MSM},
title = {A ubiquitous and diverse methanogenic community drives microbial methane cycling in eutrophic coastal sediments.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf075},
pmid = {40650567},
issn = {1574-6941},
abstract = {Coastal areas contribute over 75% of global marine methane emissions, a proportion predicted to increase with anthropogenic eutrophication and deoxygenation. Prolonged low oxygen and high organic matter input can disrupt the methane cycle, favoring methane production over oxidation. However, factors influencing this imbalance remain unclear. Here, we show that methanogenesis dominates microbial methane cycling in the anoxic sediments of eutrophic coastal marine Lake Grevelingen (NL) after summer stratification. A shallow sulfate-methane transition zone (SMTZ; 5-15 cm depth) was observed, with high methane concentrations below. Methane was produced in all investigated layers, while methane oxidation was restricted to the narrow SMTZ. Amplicon sequencing, metagenomics, and incubations revealed a metabolically and phylogenetically diverse methanogenic community with niche separation, and methylotrophic methanogenesis prevalent in all layers. Two clades of ANME archaea, ANME-2a/b and ANME-3, were restricted to a narrow zone together with their putative syntrophic sulfate-reducing bacteria, coinciding with the observed methane oxidation activity. Our results suggest that eutrophication and deoxygenation will further contribute to rising methane emissions, tilting the microbial methane cycle towards increased methanogenesis and decreasing the efficiency of the microbial methane filter.},
}

@article {pmid40650408,
year = {2025},
author = {Beau, A and Natividad, J and Benoit, B and Delerive, P and Duboux, S and Feng, Y and Jammes, M and Barnel, C and Sequino, G and Pinteur, C and Glorieux, G and Fouque, D and Vidal, H and Koppe, L},
title = {A specifically designed multi-biotic reduces uremic toxin generation and improves kidney function.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2531202},
doi = {10.1080/19490976.2025.2531202},
pmid = {40650408},
issn = {1949-0984},
mesh = {Humans ; *Uremic Toxins/metabolism ; *Renal Insufficiency, Chronic/microbiology/therapy ; Animals ; *Probiotics/administration & dosage ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; Male ; Cresols/metabolism ; *Kidney/physiology ; Prebiotics/administration & dosage ; Female ; Middle Aged ; Lactobacillus/metabolism/growth & development ; *Uremia ; Cellobiose/metabolism ; Rats ; Indican ; Bacteria/metabolism/genetics/classification ; Disease Models, Animal ; },
abstract = {Chronic kidney disease (CKD) is characterized by accumulation of uremic toxins (UTs), such as p-cresyl sulfate and indoxyl sulfate, generated through the transformation of tyrosine and tryptophan by the gut microbiota. Using an ex vivo Simulator of the Human Intestinal Microbial Ecosystem (SHIME) colonized with fecal samples from eight CKD patients or nine healthy volunteers, a higher bacterial generation of p-cresol and indoles post-amino acid enrichment, as well lower basal butyrate levels, in the feces of CKD patients were found. Through in silico data mining, we selected a probiotic strain lacking the capacity to produce UT, i.e. without genes for tryptophanase, tyrosinase and urease. In vitro, we confirmed the potential of cellobiose as a prebiotic supporting the growth of this strain. We further designed a novel specific multi-biotic for CKD (SynCKD) [containing a probiotic Lactobacillus johnsonii NCC533, a prebiotic (1% cellobiose), and a postbiotic (1% short and medium chain triglycerides C4-C8, a source of butyrate)]. SynCKD effectively curtailed UT precursor generation ex vivo. The in vivo efficacy of SynCKD (and the synergic effect) was established in two uremic rodent models, demonstrating lower plasma levels of UTs and enhancing kidney function after 6-8 weeks of treatment. These effects were linked to better gut microbial ecology. Metagenomic analysis revealed reduced microbial genes for tryptophan/tyrosine degradation. This study lays the foundation for SynCKD as a potential therapy to mitigate CKD progression.},
}

Humans
*Uremic Toxins/metabolism
*Renal Insufficiency, Chronic/microbiology/therapy
Animals
*Probiotics/administration & dosage
Feces/microbiology/chemistry
*Gastrointestinal Microbiome
Male
Cresols/metabolism
*Kidney/physiology
Prebiotics/administration & dosage
Female
Middle Aged
Lactobacillus/metabolism/growth & development
*Uremia
Cellobiose/metabolism
Rats
Indican
Bacteria/metabolism/genetics/classification
Disease Models, Animal

@article {pmid40649719,
year = {2025},
author = {Popov, IV and Manakhov, AD and Gorobets, VE and Diakova, KB and Lukbanova, EA and Malinovkin, AV and Venema, K and Ermakov, AM and Popov, IV},
title = {Metagenomic Investigation of Intestinal Microbiota of Insectivorous Synanthropic Bats: Densoviruses, Antibiotic Resistance Genes, and Functional Profiling of Gut Microbial Communities.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26135941},
pmid = {40649719},
issn = {1422-0067},
support = {23-14-00316//Russian Science Foundation/ ; 075-10-2025-017//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {Animals ; *Chiroptera/microbiology/virology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Phylogeny ; *Metagenome ; },
abstract = {Bats serve as key ecological reservoirs of diverse microbial communities, including emerging viruses and antibiotic resistance genes. This study investigates the intestinal microbiota of two insectivorous bat species, Nyctalus noctula and Vespertilio murinus, at the Rostov Bat Rehabilitation Center in Southern Russia using whole metagenome shotgun sequencing. We analyzed taxonomic composition, functional pathways, antibiotic resistance genes, and virulence factors. Densoviruses, especially those closely related to Parus major densovirus, were the most dominant viral sequences identified. Metagenome-assembled densovirus genomes showed high sequence similarity with structural variations and clustered phylogenomically with viruses from mealworms and birds, reflecting both dietary origins and the potential for vertebrate infection. Functional profiling revealed microbial pathways associated with cell wall biosynthesis, energy metabolism, and biofilm formation. A total of 510 antibiotic resistance genes, representing 142 unique types, mainly efflux pumps and β-lactamases, were identified. Additionally, 870 virulence factor genes were detected, with a conserved set of iron acquisition systems and stress response regulators across all samples. These findings highlight the ecological complexity of bat-associated microbiota and viromes and suggest that synanthropic bats may contribute to the circulation of insect-associated viruses and antimicrobial resistance in urban settings.},
}

Animals
*Chiroptera/microbiology/virology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Drug Resistance, Microbial/genetics
Phylogeny
*Metagenome

@article {pmid40647338,
year = {2025},
author = {Decembrino, N and Scuderi, MG and Betta, PM and Leonardi, R and Bartolone, A and Marsiglia, R and Marangelo, C and Pane, S and De Rose, DU and Salvatori, G and Grosso, G and Di Domenico, FM and Dotta, A and Putignani, L and Capolupo, I and Di Benedetto, V},
title = {Microbiota-Modulating Strategies in Neonates Undergoing Surgery for Congenital Gastrointestinal Conditions: A Narrative Review.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132234},
pmid = {40647338},
issn = {2072-6643},
mesh = {Humans ; Infant, Newborn ; *Gastrointestinal Microbiome/drug effects ; Probiotics/administration & dosage/therapeutic use ; Dysbiosis/microbiology/prevention & control ; Prebiotics/administration & dosage ; *Gastrointestinal Diseases/surgery/microbiology/congenital ; Anti-Bacterial Agents/therapeutic use ; Milk, Human ; *Digestive System Surgical Procedures ; Enteral Nutrition ; },
abstract = {Background/Objectives: The gut microbiota (GM) is pivotal for immune regulation, metabolism, and neurodevelopment. Infants undergoing surgery for congenital gastrointestinal anomalies are especially prone to microbial imbalances, with a paucity of beneficial bacteria (e.g., Bifidobacteria and Bacteroides) and diminished short-chain fatty acid production. Dysbiosis has been associated with severe complications, including necrotizing enterocolitis, sepsis, and feeding intolerance. This narrative review aims to critically examine strategies for microbiota modulation in this high-risk cohort. Methods: An extensive literature analysis was performed to compare the evolution of GM in healthy neonates versus those requiring gastrointestinal surgery, synthetizing strategies to maintain eubiosis, such as early nutritional interventions-particularly the use of human milk-along with antibiotic management and supplementary treatments including probiotics, prebiotics, postbiotics, and lactoferrin. Emerging techniques in metagenomic and metabolomic analysis were also evaluated for their potential to elucidate microbial dynamics in these patients. Results: Neonates undergoing gastrointestinal surgery exhibit significant alterations in microbial communities, characterized by reduced levels of eubiotic bacteria and an overrepresentation of opportunistic pathogens. Early initiation of enteral feeding with human milk and careful antibiotic stewardship are linked to improved microbial balance. Adjunctive therapies, such as the administration of probiotics and lactoferrin, show potential in enhancing gut barrier function and immune modulation, although confirmation through larger-scale studies remains necessary. Conclusions: Modulating the GM emerges as a promising strategy to ameliorate outcome in neonates with congenital gastrointestinal surgical conditions. Future research should focus on the development of standardized therapeutic protocols and the execution of rigorous multicenter trials to validate the efficacy and safety of these interventions.},
}

Humans
Infant, Newborn
*Gastrointestinal Microbiome/drug effects
Probiotics/administration & dosage/therapeutic use
Dysbiosis/microbiology/prevention & control
Prebiotics/administration & dosage
*Gastrointestinal Diseases/surgery/microbiology/congenital
Anti-Bacterial Agents/therapeutic use
Milk, Human
*Digestive System Surgical Procedures
Enteral Nutrition

@article {pmid40646273,
year = {2025},
author = {Mikolas, M and Fauszt, P and Petrilla, A and Nemeth, P and David, P and Szilagyi-Tolnai, E and Szilagyi-Racz, A and Stagel, A and Gal, F and Gal, K and Sohajda, R and Szoke, Z and Hossain, SA and Stundl, L and Biro, S and Remenyik, J and Paholcsek, M},
title = {Analysis of ICU resistome dynamics in patients, staff and environment for the identification of predictive biomarkers of sepsis and early mortality.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25080},
pmid = {40646273},
issn = {2045-2322},
mesh = {Humans ; *Intensive Care Units ; *Sepsis/mortality/microbiology ; Biomarkers/analysis ; Male ; Female ; Middle Aged ; Anti-Bacterial Agents/pharmacology ; Aged ; *Drug Resistance, Multiple, Bacterial ; Health Personnel ; Oropharynx/microbiology ; Bacteria/drug effects/genetics ; Microbiota ; Drug Resistance, Bacterial ; },
abstract = {Antimicrobial resistance (AMR) is a global crisis, posing a critical challenge to healthcare systems, particularly in intensive care units (ICUs), where multidrug-resistant organisms (MDROs) threaten patient survival. This study offers a unique, real-world perspective on AMR dynamics by analyzing 96 metagenomic samples from three key sources: oropharyngeal and rectal swabs of deceased ICU patients (both postadmission and antemortem), healthcare workers, and high-touch ICU surfaces. Findings revealed the ICU environment as a major AMR reservoir, with oropharyngeal swabs carrying the highest AMR burden. While healthcare staff facilitated MDRO spread, they were not primary sources. Staff microbiomes' MDRO pattern closely resembled environmental samples. Key AMR species included B. fragilis, E. coli, S. pneumoniae, S. aureus, with P. aeruginosa persisting on high-touch surfaces. Tetracycline resistance was the most prevalent, with common resistances comprising 36.1% of all detected AMR markers. Staff microbial community exhibited higher resistance to macrolides, fluoroquinolones, lincosamides, and cephamycins. A 10-day survival threshold distinguished early (EM) and late mortality (LM) groups. EM patients exhibited unique AMR species in the oropharynx, suggesting respiratory-driven infections, while LM patients showed greater gut-associated resistance. Higher rectal AMR counts correlated with prolonged survival. Notably, four key MDROs (L. monocytogenes, M. tuberculosis, S. haemolyticus, and S. agalactiae) were enriched in sepsis patients, suggesting early risk markers. Fewer new resistances emerged in rectal than oropharyngeal swabs, likely due to antibiotic selection pressure. Vancomycin and levofloxacin, frequently co-administered, exerted stronger selective pressure in the oropharynx, possibly explaining the high MRSA prevalence in patient and environmental samples.},
}

Humans
*Intensive Care Units
*Sepsis/mortality/microbiology
Biomarkers/analysis
Male
Female
Middle Aged
Anti-Bacterial Agents/pharmacology
Aged
*Drug Resistance, Multiple, Bacterial
Health Personnel
Oropharynx/microbiology
Bacteria/drug effects/genetics
Microbiota
Drug Resistance, Bacterial

@article {pmid40645966,
year = {2025},
author = {Kim, S and Park, MS and Kang, I and Cho, JC},
title = {Microbial metagenomes from Lake Soyang, the largest freshwater reservoir in South Korea.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1201},
pmid = {40645966},
issn = {2052-4463},
support = {NRF-2022R1A2C3008502//National Research Foundation of Korea (NRF)/ ; NRF-2022R1C1C2004070//National Research Foundation of Korea (NRF)/ ; },
mesh = {Republic of Korea ; *Lakes/microbiology ; *Metagenome ; *Microbiota ; Metagenomics ; Ecosystem ; Fresh Water/microbiology ; },
abstract = {Lake ecosystems play a fundamental role in the global biogeochemical cycling of essential elements such as carbon, nitrogen, and phosphorus. Microorganisms within these ecosystems mediate key processes that regulate these cycles. Metagenomic analyses provide valuable insights into the taxonomic and functional diversity of microbial communities in various environments, including freshwater habitats. Here, we present a comprehensive metagenomic dataset derived from Lake Soyang, the largest freshwater reservoir in South Korea. A total of 28 metagenomes were generated from water samples collected across two distinct sampling periods: the first set (n = 8) was obtained between April 2014 and January 2015 from two depths (1 m and 50 m) in four different seasons, while the second set (n = 20) was collected between January 2019 and November 2019 from five depths (1, 10, 20, 40, and 90 m) over four seasons. Metagenomic sequencing yielded 9.3-21.8 Gbp per sample. This dataset provides a valuable resource for future studies exploring the ecophysiological characteristics of microbial communities in pelagic freshwater environments.},
}

Republic of Korea
*Lakes/microbiology
*Metagenome
*Microbiota
Metagenomics
Ecosystem
Fresh Water/microbiology

@article {pmid40645948,
year = {2025},
author = {Calayag, AM and Priest, T and Oldenburg, E and Muschiol, J and Popa, O and Wietz, M and Needham, DM},
title = {Arctic Ocean virus communities and their seasonality, bipolarity, and prokaryotic associations.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6427},
pmid = {40645948},
issn = {2041-1723},
mesh = {Arctic Regions ; Seasons ; *Seawater/virology/microbiology ; Metagenome ; *Virome/genetics ; Oceans and Seas ; *DNA Viruses/genetics/classification/isolation & purification ; Biodiversity ; Bacteria/virology/genetics ; Host Microbial Interactions ; },
abstract = {Viruses of microbes play important roles in ocean environments as agents of mortality and genetic transfer, influencing ecology, evolution and biogeochemistry. However, we know little about the diversity, seasonality, and host interactions of viruses in polar waters. Here, we study dsDNA viruses in the Arctic Fram Strait across four years via 47 long-read metagenomes of the cellular size-fraction. Among 5662 vOTUs, 98% and 2% are Caudoviricetes and Megaviricetes, respectively. Viral coverage is, on average, 5-fold higher than cellular coverage, and 8-fold higher in summer. Viral community composition shows annual peaks in similarity and strongly correlates with prokaryotic community composition. Using network analysis, we identify putative virus-host interactions and six ecological modules associated with distinct environmental conditions. The network reveals putative novel cyanophages with time-lagged correlations to their hosts (in late summer) as well as diverse viruses correlated with Flavobacteriaceae, Pelagibacteraceae, and Nitrosopumilaceae. Via global metagenomes, we find that 42% of Fram Strait vOTUs peak in abundance in high latitude regions of both hemispheres, and encode proteins with biochemical signatures of cold adaptation. Our study reveals a rich diversity of polar viruses with pronounced seasonality, providing a foundation for understanding viral regulation and ecosystem impacts in changing polar oceans.},
}

Arctic Regions
Seasons
*Seawater/virology/microbiology
Metagenome
*Virome/genetics
Oceans and Seas
*DNA Viruses/genetics/classification/isolation & purification
Biodiversity
Bacteria/virology/genetics
Host Microbial Interactions

@article {pmid40640914,
year = {2025},
author = {Zhao, J and Kui, L and Huang, J and Deng, J and Liu, L and Zhu, C and Shi, Y and Li, C and Xiao, Y and Yu, J and Li, Q and Yang, B and Leng, B and Chan, H},
title = {Bifidobacterium animalis subsp. Lactis BX-BC08 modulates gut microbiota and secretes alpha-Ketoglutaric acid to alleviate MC903-induced atopic dermatitis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {768},
pmid = {40640914},
issn = {1479-5876},
support = {SL2024A04J01394//Guangzhou Municipal Science and Technology Bureau Young Doctor "Qihang" Program/ ; },
mesh = {Animals ; *Dermatitis, Atopic/microbiology/chemically induced/drug therapy ; *Gastrointestinal Microbiome ; *Bifidobacterium animalis/physiology/metabolism ; *Ketoglutaric Acids/metabolism ; Mice ; Disease Models, Animal ; Female ; Probiotics ; Mice, Inbred BALB C ; },
abstract = {OBJECTIVE: Bifidobacterium is known to be depleted in patients with atopic dermatitis (AD). This study aims to investigate the potential prophylactic effects of Bifidobacterium animalis subsp. lactis BX-BC08 (B. lactis BX-BC08) in a murine model of AD.

DESIGN: The immunosuppressive and anti-inflammatory effects of BX-BC08 were evaluated in a MC903-induced AD mouse model. Gut microbiota composition was analyzed by metagenomic sequencing, while high-performance liquid chromatography-mass spectrometry (HPLC-MS) was employed to identify anti-inflammatory molecules produced by B. lactis BX-BC08.

RESULTS: BX-BC08 significantly attenuated pro-inflammatory responses, scaling and swelling in the MC903-induced AD like murine model compared to controls. Fecal microbial profiling revealed an enrichment of probiotics and a reduction of pro-inflammatory bacteria in BX-BC08 treated mice. Metabolic analysis of BX-BC08 bacteria culture supernatant and treated mice identified a significant enrichment of alpha-Ketoglutaric acid (AKG). Functional validation in the murine AD model demonstrated that AKG strongly suppressed T helper 2 (Th2)-driven pro-inflammatory responses.

CONCLUSION: BX-BC08 mitigates AD-like inflammation by producing the anti-inflammatory metabolite AKG. BX-BC08 could serve as a novel prophylactic agent for AD prevention.},
}

Animals
*Dermatitis, Atopic/microbiology/chemically induced/drug therapy
*Gastrointestinal Microbiome
*Bifidobacterium animalis/physiology/metabolism
*Ketoglutaric Acids/metabolism
Mice
Disease Models, Animal
Female
Probiotics
Mice, Inbred BALB C

@article {pmid40571109,
year = {2025},
author = {Chen, H and Qiu, X and Lei, S and Zhao, Y and Zhang, M and Gao, M and Guo, R and Di, H and Huang, J and Yu, Z},
title = {Gut vs. vaginal microbiome in diabetes Progression: Key microbial shifts and implications.},
journal = {Microbial pathogenesis},
volume = {206},
number = {},
pages = {107833},
doi = {10.1016/j.micpath.2025.107833},
pmid = {40571109},
issn = {1096-1208},
mesh = {Humans ; Female ; *Diabetes Mellitus, Type 2/microbiology ; *Gastrointestinal Microbiome ; *Vagina/microbiology ; Middle Aged ; Feces/microbiology ; Disease Progression ; Metagenomics ; Aged ; Blood Glucose/analysis ; Glycated Hemoglobin/analysis ; Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Dysbiosis/microbiology ; Adult ; },
abstract = {BACKGROUND: Dysiosis in gut and vaginal microbiome is implicated in type 2 diabetes (T2D) pathogenesis, but their contributions remain unclear. This study aims to compare their alterations and clinical relevance in diabetes development.

METHODS: Metagenomic sequencing was performed on vaginal and fecal samples from T2D patients. Differential feature selection and correlation model were used to dissect microbial contributions to diabetic markers.

RESULTS: Gut microbiota exhibited reduced diversity in T2D patients, with enrichment of Desulfovibrio desulfuricans and Adlercreutzia equolifaciens validated in public cohorts. Vaginal microbiota diversity remained unaffected. Furthermore, structural equation modeling revealed stronger gut microbiota associations with blood glucose and HbA1c. Notably, Romboutsia ilealis-derived pgm was enriched in the diabetes group, which could catalyze the production of glucose, suggesting that it may be involved in the progression of T2D.

CONCLUSION: Our findings establish the gut microbiome as the dominant driver of T2D progression, with R. ilealis emerging as a potential therapeutic target. This highlights the priority of gut-centric microbiota interventions in diabetes management.},
}

Humans
Female
*Diabetes Mellitus, Type 2/microbiology
*Gastrointestinal Microbiome
*Vagina/microbiology
Middle Aged
Feces/microbiology
Disease Progression
Metagenomics
Aged
Blood Glucose/analysis
Glycated Hemoglobin/analysis
Bacteria/classification/genetics/isolation & purification
*Microbiota
Dysbiosis/microbiology
Adult

@article {pmid40571107,
year = {2025},
author = {Chen, J and Chen, Z and Xu, B and Huang, Z and Zhang, C},
title = {Skin microbiome of Asian elephants with skin diseases during seasonal transitions.},
journal = {Microbial pathogenesis},
volume = {206},
number = {},
pages = {107832},
doi = {10.1016/j.micpath.2025.107832},
pmid = {40571107},
issn = {1096-1208},
mesh = {Animals ; *Skin/microbiology ; *Microbiota/genetics ; *Elephants/microbiology ; Seasons ; Virulence Factors/genetics ; *Skin Diseases/microbiology/veterinary ; Metagenomics ; DNA, Bacterial/genetics ; Bacteria/genetics/classification/isolation & purification ; Staphylococcus/genetics/isolation & purification ; Computational Biology ; Sequence Analysis, DNA ; Skin Microbiome ; },
abstract = {INTRODUCTION: Wild Asian elephants (Elephas maximus), which are an endangered species, often suffer from skin diseases during seasonal transitions, which seriously affect their health. Understanding the pathogenesis of such skin diseases is critical for their prevention and treatment. It is known that skin microorganisms are closely related to host skin health.

OBJECTIVE: To compare the microbiotas and microbiomes of diseased and healthy skin of Asian elephants.

METHODS: DNA was extracted from skin swab samples from diseased and healthy Asian elephants for metagenomic sequencing. Various bioinformatic tools were used to process the raw sequencing data and identify gene sequences for functional annotation and species identification as well as to determine species abundance. Antibiotic resistance genes and virulence factors were also identified using DIAMOND.

RESULTS: Staphylococcus was highly enriched in the microbiota of diseased skin, whereas Leuconostoc predominated in that of healthy skin. Moreover, substantial differences existed between the two elephant skin groups in terms of metabolic pathways related to ATP-binding cassette transporters and TCSs and the abundance of antibiotic resistance genes and Staphylococcus-associated toxins. The substantial difference in Staphylococcus-related virulence factors was likely due to the significant enrichment of Staphylococcus in the diseased skin samples, suggesting that this bacterial genus is the causative agent of skin diseases in Asian elephants. Additionally, Leuconostoc mesenteroides, which was enriched in the healthy skin samples, has anti-inflammatory, antimicrobial, and other beneficial effects that have promising applications in the prevention, diagnosis, and treatment of skin diseases.

CONCLUSION: This study reveals the cause of skin diseases in Asian elephants and provides a theoretical basis for improving the skin health of wild animals and expanding wildlife conservation methods and technologies.},
}

Animals
*Skin/microbiology
*Microbiota/genetics
*Elephants/microbiology
Seasons
Virulence Factors/genetics
*Skin Diseases/microbiology/veterinary
Metagenomics
DNA, Bacterial/genetics
Bacteria/genetics/classification/isolation & purification
Staphylococcus/genetics/isolation & purification
Computational Biology
Sequence Analysis, DNA
Skin Microbiome

@article {pmid40562089,
year = {2025},
author = {Gu, P and Xu, Y and Li, X},
title = {Chronic low-dose cadmium exposure disrupts gut microbiota and lipid metabolism to induce liver injury.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {203},
number = {},
pages = {115603},
doi = {10.1016/j.fct.2025.115603},
pmid = {40562089},
issn = {1873-6351},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Lipid Metabolism/drug effects ; *Cadmium/toxicity/administration & dosage ; Mice ; Male ; Mice, Inbred C57BL ; Liver/drug effects/metabolism/pathology ; *Chemical and Drug Induced Liver Injury/metabolism/microbiology ; },
abstract = {Cadmium (Cd) is a widespread environmental pollutant linked to liver injury and metabolic dysfunction, yet the gut-liver axis mechanisms remain unclear. We investigated chronic low-dose Cd exposure (100 nM CdCl2, 12 weeks) in mice using integrated metagenomic and metabolomic profiling. Despite intact intestinal morphology, Cd exposure induced hepatic inflammation, steatosis, and elevated transaminases. Shotgun metagenomics revealed gut microbiota shifts, with enrichment of Prevotella and depletion of Turicibacter. Fecal metabolomics showed disrupted bile acid detoxification and lipid remodeling. Functional analysis indicated upregulation of microbial fatty acid metabolism genes, suggesting compensatory but dysregulated responses. These findings demonstrate that chronic Cd exposure perturbs gut microbiota and metabolic outputs, driving liver injury via microbiota-mediated mechanisms. Our study highlights the gut-liver axis as a key target of Cd toxicity and points to microbiota-based interventions as potential therapies.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Lipid Metabolism/drug effects
*Cadmium/toxicity/administration & dosage
Mice
Male
Mice, Inbred C57BL
Liver/drug effects/metabolism/pathology
*Chemical and Drug Induced Liver Injury/metabolism/microbiology

@article {pmid40532861,
year = {2025},
author = {Biswas, I and Mitra, D and Mallik, C and Das Mohapatra, PK},
title = {Characterization and toxicity assessment of metabiotic produced through natural tannin fermentation by newly isolated probiotic Lactiplantibacillus plantarum PKI15 and study of its effect on gut microbiome through metagenomics approach.},
journal = {Microbial pathogenesis},
volume = {206},
number = {},
pages = {107815},
doi = {10.1016/j.micpath.2025.107815},
pmid = {40532861},
issn = {1096-1208},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/metabolism ; Rats ; Fermentation ; Metagenomics ; Antioxidants/pharmacology/metabolism ; Molecular Docking Simulation ; Plant Extracts/metabolism/chemistry/pharmacology ; Terminalia/metabolism/chemistry ; Male ; Rats, Wistar ; Anti-Bacterial Agents/pharmacology/metabolism ; Liver/drug effects/pathology ; *Lactobacillus plantarum/metabolism ; Gallic Acid/metabolism ; Kidney/drug effects/pathology ; Spleen/drug effects/pathology ; },
abstract = {Metabiotic fabrication has been done by mixed plant fermentation of Terminalia bellirica and Phyllanthus emblica fruit extract with probiotic bacteria Lactiplantibacillus plantarum PKI15 and showed considerable tannase (0.36 U/ml), gallic caid and pyrogallol production. Fermentative end-product analysis through FTIR, LC-MS and GC-MS result indicates the presence of several bioactive compounds confirming the presence of gallic acid and pyrogallol respectively. Molecular docking analysis of the identified bioactive compounds with the protein myeloperoxidase denotes quercetin-3β-D-glucoside as the best ligand showing a binding score of -9.5 kcal/mol. The formulated metabiotic revealed potential antibacterial and antioxidant properties. In-vivo toxicity assessment was done on the laboratory rats. Results revealed reduced body weight, urea content and creatinine level. Increase in superoxide dismutase, catalase activity and reduced content of conjugated diene, glutamate pyruvate transaminase and glutamic-oxaloacetic transaminase further supports the antioxidative potential of the metabiotic. Further study through histological sectioning of liver, kidney and spleen showed no structural abnormalities. Finally, metagenomics analysis of the gut microbiome of the experimental rats was done to check the influence of the formulated metabiotic on the gut commensals and it was found that species of Bifidobacterium and Pseudomonas are the most prevalent members of the examined groups, while, the relative proportion of other bacterial genera, such as Lactobacillus, Lactococcus, and Bacillus, were found to vary among the groups. Thus, both the in vivo and in silico studies proved that the formulated metabiotic is non-toxic and safe in use.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Probiotics/metabolism
Rats
Fermentation
Metagenomics
Antioxidants/pharmacology/metabolism
Molecular Docking Simulation
Plant Extracts/metabolism/chemistry/pharmacology
Terminalia/metabolism/chemistry
Male
Rats, Wistar
Anti-Bacterial Agents/pharmacology/metabolism
Liver/drug effects/pathology
*Lactobacillus plantarum/metabolism
Gallic Acid/metabolism
Kidney/drug effects/pathology
Spleen/drug effects/pathology

@article {pmid40482930,
year = {2025},
author = {Adiningrat, A and Maulana, I and Fadhlurrahman, AG and Yumoto, H},
title = {Probiotic bacteria from asymptomatic necrotic tooth can regulate the microbiome homeostasis.},
journal = {Microbial pathogenesis},
volume = {206},
number = {},
pages = {107791},
doi = {10.1016/j.micpath.2025.107791},
pmid = {40482930},
issn = {1096-1208},
mesh = {Biofilms/growth & development/drug effects ; Humans ; *Probiotics/pharmacology ; *Microbiota ; Enterococcus faecalis/drug effects ; *Homeostasis ; *Bacteria/isolation & purification/classification/genetics ; Streptococcus mutans/drug effects ; *Dental Pulp Cavity/microbiology ; Metagenomics ; Microscopy, Electron, Scanning ; },
abstract = {OBJECTIVE: This study was performed to identify and isolate the dominant bacteria from a chronic asymptomatic necrotic root canal and investigate in vitro its potential postbiotics effect at the biofilm maturation maintaining root canal microbiome homeostasis.

METHODS: For bacterial identification of an in vivo root canal sample, metagenomic analysis was applied, followed by single colony isolation and PCR analysis. Cell free supernatant (CFS) was then cultivated through serial L paracasei culture procedures prior antibiofilm analysis. Antibiofilm effects of the CFS product were evaluated using in vitro biofilm analysis against S. mutans and E. faecalis. Biofilm mass analysis was measured by using colorimetric approach with cresyl-vast violet staining, morphological appearance was observed using both phase-contrast and scanning electron microscope (SEM). Shapiro-Wilk analysis was applied for normality test, followed by the ANOVA to compare multiple groups or a student t-test for independent two groups mean comparisons.

RESULTS: The isolated root canal bacteria produced biofilm mass that was similar to the Enterococcus faecalis control pathogenic biofilm. From the morphological analysis suggested that population of the isolated bacteria were predominantly occupied by rod-shaped rather than cocci-shaped inhabitants. Further metagenomic analysis indicated that the isolated dominant bacteria in the mixed culture were mainly identified as probiotic bacteria, Lacticaseibacillus paracasei. Moreover, the functional analysis revealed that the L. paracasei cell free supernatant product (CFS) exhibited a promising positive effect in biofilm structure integrity disturbances of S. mutans and E. faecalis.

CONCLUSIONS: The isolated Lacticaseibacillus paracasei from the root canal of a chronic asymptomatic necrotic tooth, produces potential postbiotic products that demonstrated a disruptive ability against Streptococcus mutans and Enterococcus faecalis biofilm integrity.},
}

Biofilms/growth & development/drug effects
Humans
*Probiotics/pharmacology
*Microbiota
Enterococcus faecalis/drug effects
*Homeostasis
*Bacteria/isolation & purification/classification/genetics
Streptococcus mutans/drug effects
*Dental Pulp Cavity/microbiology
Metagenomics
Microscopy, Electron, Scanning

@article {pmid40473125,
year = {2025},
author = {Darwiche, S and Gacesa, R and Ferraro, RB and Alwan, W and Oben, JA and Rashidghamat, E and Long, PF},
title = {Prevalence of skin fungi markedly declines in the lesions of two patients with moderate hidradenitis suppurativa.},
journal = {Microbial pathogenesis},
volume = {206},
number = {},
pages = {107778},
doi = {10.1016/j.micpath.2025.107778},
pmid = {40473125},
issn = {1096-1208},
mesh = {Humans ; *Hidradenitis Suppurativa/microbiology/pathology ; *Skin/microbiology/pathology ; *Fungi/isolation & purification/genetics/classification ; RNA, Ribosomal, 18S/genetics ; Male ; Adult ; DNA, Fungal/genetics ; Prevalence ; Female ; Metagenomics ; Mycobiome ; Malassezia/isolation & purification/genetics ; Sequence Analysis, DNA ; Middle Aged ; },
abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disorder affecting hair follicles in intertriginous regions, leading to painful nodules, sinus tracts, and scarring. The pathogenesis of HS is far from clear, but alterations in the bacterial community of the skin microbiome has been debated, yet the potential involvement of fungi - the mycobiome - has received almost no attention. Large areas of skin were sampled for amplicon metagenomics sequencing to negate the inference of low-sequence counts with the objective of examining the provenance of fungi between lesion and lesion-free skin from the same individuals. The DNA from skin swabs was isolated and the V4 region of the 18S rRNA gene was amplified and sequenced. Total fungal counts were inferred from taxonomic assignment of unique operational taxonomic units and absolute numbers then compared between skin sites. There were dramatically lower numbers of fungi in HS lesions with Malassezia dominance, as expected, across samples. This finding suggested, for the first time, that fungal depletion in lesions might be linked to HS pathology through disruption of normal skin barrier function and immunity, potentially due to reduced sebum production essential for fungal growth.},
}

Humans
*Hidradenitis Suppurativa/microbiology/pathology
*Skin/microbiology/pathology
*Fungi/isolation & purification/genetics/classification
RNA, Ribosomal, 18S/genetics
Male
Adult
DNA, Fungal/genetics
Prevalence
Female
Metagenomics
Mycobiome
Malassezia/isolation & purification/genetics
Sequence Analysis, DNA
Middle Aged

@article {pmid40451466,
year = {2025},
author = {Osogo, AK and Muyekho, F and Were, H and Okoth, P},
title = {Deciphering common bean (Phaseolus Vulgaris L.) microbiome assemblages reveal mechanistic insights into host-pathogen-microbiome interactions.},
journal = {Genomics},
volume = {117},
number = {4},
pages = {111064},
doi = {10.1016/j.ygeno.2025.111064},
pmid = {40451466},
issn = {1089-8646},
mesh = {*Phaseolus/microbiology/genetics ; *Microbiota ; *Host-Pathogen Interactions ; Bacteria/genetics/classification ; },
abstract = {Common bean (Phaseolus vulgaris L.) is the primary source of proteins and nutrients in most households in sub-Saharan Africa. However, production of this crop is constrained by several biotic factors. While research on common bean plant-pathogen interactions has predominantly focused on binary relationships, the diversity of microbes naturally inhabiting plant tissues and their interactions has often been overlooked. Recent findings, however, show that these resident microbes actively contribute to plant defense mechanisms, rather than merely acting as passive bystanders. This study aimed to document and explore potential interactions within the common bean microbiome assemblages through field investigations in selected locations across the western regions of Kenya. Common bean leaf samples were collected from farmer's fields along motorable roads 3-5 km apart. Shotgun metagenomic analysis identified a diverse range of microorganisms, including bacteria, fungi, yeast, phytoplasmas, viruses, and bacteriophages, across multiple taxonomic levels-spanning 4 Kingdoms, 136 Phyla, 168 Classes, 360 Orders, 792 Families, 2039 Genera, and 6130 Species-both epiphytic and endophytic, and pathogenic or non-pathogenic. Pseudomonadota consistently showed the highest taxonomic annotation for antimicrobial-resistant organisms, highlighting its central role in resistance across the studied area. The sequences obtained were mapped to the EggNOG, CAZy, and KEGG databases to explore, assign, and predict gene functions. The EggNOG database emphasized the importance of "Replication, recombination, and repair" processes in maintaining genomic stability, along with amino acid transport, energy production, and metabolism. CAZy analysis revealed a significant presence of glycosyltransferases, particularly from GT1 and GT32 families, and noted the role of enzymes like Glycoside Hydrolases in plant defense against pathogens. KEGG pathway analysis underscored the central role of metabolic processes such as energy metabolism, translation, and carbohydrate metabolism. Key pathways linked to plant defense and resilience, including 2-oxocarboxylic acid metabolism, amino acid biosynthesis, and secondary metabolite biosynthesis, were identified. These findings underscore the role of metabolic and enzymatic processes in strengthening plant defenses and stress tolerance while laying the groundwork for multidisciplinary research to advance sustainable agriculture and food safety.},
}

*Phaseolus/microbiology/genetics
*Microbiota
*Host-Pathogen Interactions
Bacteria/genetics/classification

@article {pmid40449763,
year = {2025},
author = {Liu, W and Chen, S and Yang, J and Chen, Y and Yang, Q and Lu, L and Li, J and Yang, T and Zhang, G and Hu, J},
title = {Characterization of blood and urine microbiome temporal variability in patients with acute myeloid leukemia.},
journal = {Microbial pathogenesis},
volume = {206},
number = {},
pages = {107734},
doi = {10.1016/j.micpath.2025.107734},
pmid = {40449763},
issn = {1096-1208},
mesh = {Humans ; *Leukemia, Myeloid, Acute/microbiology/blood/urine ; Male ; Middle Aged ; Female ; *Microbiota ; Longitudinal Studies ; Aged ; Adult ; *Urine/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; *Blood/microbiology ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Investigating the microbiota of blood and urine from acute myeloid leukemia (AML) patients is essential to unravel the complex role of microbiota in systemic host-microbe interactions and implications.

METHODS: We conducted a longitudinal observational study to characterize the temporal dynamics of blood and urine microbiota in 27 AML patients, utilizing metagenomic analysis pipeline for microbial identification to identify disease-associated microbial signatures.

RESULTS: The composition of blood and urine microbiota of AML was dominated by Proteobacteria phylum in blood, Firmicutes phylum in urine. The species and diversity of blood and urine microbiota did not have difference between AML patients and healthy controls. Restitution of alpha and beta diversity of blood microbiota and urine microbiota to resemble that of healthy controls occurred after cessation of treatment. Temporal variation of urine microbiome was higher than blood after treatment which was closely related to pathogenic bacteria and beneficial bacteria measured by coefficient of variation (CV) of alpha diversity. The temporal variability of urine microbiota was significantly correlated with platelet and exposure of levofloxacin. The variation of microbiome of AML patients with infection was found that the relative abundance of Burkholderia significantly enriched in blood and urine which had high accuracy and sensitivity. The correlation between blood microbiota and serum amino acid metabolites was similar to that between gut microbiota and serum metabolites.

CONCLUSION: This study represents the first comprehensive investigation to quantify the longitudinal variability of blood and urine microbiota in AML patients, revealing distinct patterns compared to gut microbiota and associations with adverse clinical outcomes. Our findings highlight the potential of leveraging stabilizing taxa as a target for microbiome restoration.},
}

Humans
*Leukemia, Myeloid, Acute/microbiology/blood/urine
Male
Middle Aged
Female
*Microbiota
Longitudinal Studies
Aged
Adult
*Urine/microbiology
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification
Metagenomics
*Blood/microbiology
Gastrointestinal Microbiome

@article {pmid40640502,
year = {2025},
author = {Liu, L and Firrman, JA and Narrowe, AB and Mahalak, KK and Lemons, JMS and Marzorati, M and Duysburgh, C and Rotsaert, C and Van de Wiele, T},
title = {Structural and functional characterization of a porcine intestinal microbial ecosystem developed in vitro.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24821},
pmid = {40640502},
issn = {2045-2322},
support = {8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; EOS-Homistasis project//FWO-FNR/ ; GOA-Microbes4Immunity//UGent-BOF/ ; },
mesh = {Animals ; Swine ; *Gastrointestinal Microbiome ; Metagenome ; Feces/microbiology ; *Bacteria/genetics/classification ; Metagenomics/methods ; Metabolomics ; *Intestines/microbiology ; Ecosystem ; },
abstract = {The mammalian digestive tract harbors a vast microbial community that has the potential to modulate numerous health-related processes. Multicompartment dynamic gut models have been developed to study microbial communities in a controlled environment. To verify the assumption that the experimental results produced in vitro in a mechanical device would be highly similar to those obtained from an in vivo study, in this study fecal samples from four pigs were inoculated in a simulator of the porcine intestinal microbial ecosystem (SPIME) and cultured until reaching steady state. The composition and structure of the resultant microbial communities, and the metabolites produced were compared with those harvested from the intestine of the same pigs. Taxonomic abundance identification based on shallow shotgun metagenomic sequencing revealed only 12.1% of species or 15% of metagenome-assembled genomes (MAGs) being shared across the colon compartments of the source pigs and the SPIME. Despite these overwhelming compositional shifts, higher functional conservation was indicated as measured by functional richness, MAG-level traits, CAZymes, and untargeted metabolomics. Environmental selection and bacterial functional redundancy were considered the two key elements in microbial compositional shifts and functional preservation.},
}

Animals
Swine
*Gastrointestinal Microbiome
Metagenome
Feces/microbiology
*Bacteria/genetics/classification
Metagenomics/methods
Metabolomics
*Intestines/microbiology
Ecosystem

@article {pmid40640272,
year = {2025},
author = {Xie, Y and Xiang, JY and Long, L and Ma, Y and Xing, Z and Wang, L and Shao, C and Liu, N and Li, F},
title = {Impact of different treatment methods and timings on soil microbial communities with transgenic maize straw return.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24820},
pmid = {40640272},
issn = {2045-2322},
support = {20230508091RC//Jilin Provincial Scientific and Technological Development Program/ ; 20230508091RC//Jilin Provincial Scientific and Technological Development Program/ ; },
mesh = {*Zea mays/genetics ; *Soil Microbiology ; *Plants, Genetically Modified ; *Microbiota ; Soil/chemistry ; Agriculture/methods ; Crops, Agricultural ; Metagenomics/methods ; },
abstract = {Understanding the impact of genetically modified (GM) crop straw return on soil ecosystems is crucial as GM crops become more prevalent. This study assesses the effects of straw mulching and deep tillage on soil microbial communities from GM and non-GM maize, highlighting potential ecological impacts. Shotgun metagenomic sequencing was utilized to analyze the microbial community structure and functional genes in soil samples collected at different times (30, 180, and 270 days) after straw mulching and deep tillage treatments. The study included insect-resistant transgenic maize varieties 2A-7 and CM8101 and their non-transgenic counterparts B73 and Zheng58. Different treatment methods significantly affect soil microbial alpha-diversity and beta-diversity, with deep tillage resulting in higher alpha-diversity compared to mulching, and the 180-day mark exhibiting the highest alpha-diversity across all sampling times. Early straw treatment prompted a rapid microbial response to nutrient availability, with notable changes in diversity and function over time. Straw treatments notably altered soil microbial functions, especially in carbon cycling and nutrient metabolism. Interestingly, the microbial effects of GM versus non-GM maize straw were similar, suggesting crop residue type under consistent soil management practices might not significantly alter microbial community structures. The methods and timing of straw treatments have a significant impact on soil microbial communities, surpassing the differences between GM and non-GM straw. These findings highlight the importance of straw management practices for sustainable agricultural ecosystem management.},
}

*Zea mays/genetics
*Soil Microbiology
*Plants, Genetically Modified
*Microbiota
Soil/chemistry
Agriculture/methods
Crops, Agricultural
Metagenomics/methods

@article {pmid40639969,
year = {2025},
author = {Shi, C and Wang, C and He, J and Zhang, M and Huang, W},
title = {Epichloë Endophytes Potentially Facilitate Host Plant Recruitment of Rhizosphere Microbiota Carrying Beneficial Traits.},
journal = {Physiologia plantarum},
volume = {177},
number = {4},
pages = {e70397},
doi = {10.1111/ppl.70397},
pmid = {40639969},
issn = {1399-3054},
support = {31760704//National Natural Science Foundation of China/ ; 2022D01A79//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 23XJTRZW07//Xinjiang Key Laboratory of Soil and Plant Ecological Processes/ ; },
mesh = {*Rhizosphere ; *Endophytes/physiology ; Plant Roots/microbiology ; *Epichloe/physiology ; *Microbiota/physiology ; Soil Microbiology ; Symbiosis ; },
abstract = {Plant-microbe symbiotic relationships drive ecosystem evolution. This study employed metabolomics and metagenomic technologies to investigate the effects of the aboveground-restricted endophytic fungus Epichloë guerinii in the host plant Melica transsilvanica on the rhizosphere microbial community structure and functional traits. Our results revealed that the presence of E. guerinii significantly increased the secretion of organic acids, amino acids, and sugar alcohols from the host root system. These exudates correlated strongly with abundant, plant growth-promoting rhizosphere microorganisms like Pseudomonas, Bradyrhizobium, and Nitrospira. Functional genes that were significantly enriched in the host rhizosphere microbiota were predominantly associated with biofilm formation and organic acid metabolic pathways. Co-enrichment analyses of rhizosphere soil metabolites and genes highlighted pathways such as flagellar assembly and carbon/nitrogen/sulfur metabolism. Notably, the abundance of key genes governing the flagellar motor MotA protein in the host rhizosphere, as well as those involved in the reductive tricarboxylic acid (rTCA) cycle, nitrification, and thiosulfate oxidation, were significantly elevated. This study demonstrates that E. guerinii positively regulates rhizosphere microbial community functions by reprogramming the composition of host root exudates. These findings deepen the mechanistic understanding of Epichloë-plant-rhizosphere microbe interactions.},
}

*Rhizosphere
*Endophytes/physiology
Plant Roots/microbiology
*Epichloe/physiology
*Microbiota/physiology
Soil Microbiology
Symbiosis

@article {pmid40639330,
year = {2025},
author = {Liu, K and Wang, Y},
title = {Metatranscriptomics catches gut microbes in the act.},
journal = {Cell host & microbe},
volume = {33},
number = {7},
pages = {1040-1042},
doi = {10.1016/j.chom.2025.06.004},
pmid = {40639330},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Humans ; *Transcriptome ; *Bacteria/genetics ; *Metagenome ; Animals ; Circadian Rhythm ; *Gastrointestinal Tract/microbiology ; },
abstract = {In this issue of Cell Host & Microbe, Flores Ramos et al.[1] employ metatranscriptomics to uncover diurnal microbial functional shifts in the gut microbiome driven by time-restricted feeding. Their work highlights the value of metatranscriptomics over metagenomics in capturing real-time microbial activity and guiding therapeutic bacterial engineering.},
}

*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Humans
*Transcriptome
*Bacteria/genetics
*Metagenome
Animals
Circadian Rhythm
*Gastrointestinal Tract/microbiology

@article {pmid40637407,
year = {2025},
author = {Chin, HS and Ravi Varadharajulu, N and Teo, KC and Cheong, PCH and Tang, S-L},
title = {Key findings from 15 years of Mangrovibacter research: a generalist bacterium beyond endophytes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0247924},
doi = {10.1128/aem.02479-24},
pmid = {40637407},
issn = {1098-5336},
abstract = {Since the discovery of Mangrovibacter plantisponsor in 2010, research on Mangrovibacters (MGBs) has stagnated. Although laboratories worldwide have isolated various MGB strains and deposited their 16S rDNA sequences in the NCBI database, a limited understanding of MGBs has resulted in only a few publications from these collections. Recent advancements in metagenomic technology have revealed the presence of MGBs in a broader range of habitats. Most microbiomes exhibit low MGB abundance (typically <1%). Even in environments with higher prevalence, such as salt-tolerant aerobic granular sludge (75%), the gut of superworms fed with polyurethane (22%), or fermented foods like mandai (16%), the functional roles of MGBs remain unclear. Through meticulous curation of publications and data from MicrobeAtlas and AMIBASE, MGBs can be classified as free living, endophytic, or zoonotic. Recent evidence suggests their presence in food sources and potential interactions with humans. Current studies confirm the coexistence of MGBs with humans. This review underscores the phenotypic features and genomic foundations of MGBs, highlighting attributes such as endophytic behavior, diverse metabolite utilization, tolerance to salinity and pH, metal homeostasis, biofilm formation, and bioremediation potential. Insights are derived from the analysis of four MGB genomes deposited in NCBI since 2014, along with three newly reported genomes in 2024. Experimental and genetic evidence suggests that MGBs act as "generalist microbes" capable of thriving in diverse nutrient sources and harsh environments. This review elucidates prospective research trajectories and highlights numerous potential commercial applications of MGBs, emphasizing the need for further investigation into their roles and benefits.},
}

@article {pmid40636496,
year = {2025},
author = {Ding, Z and Xu, Y and Wang, Y and Liu, M and Zhu, P and Cui, K and Yang, C and Xu, C and Feng, T and Liu, Q},
title = {Host-driven remodeling of rumen microbiota supports lactation metabolism in buffalo.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1617388},
pmid = {40636496},
issn = {1664-302X},
abstract = {INTRODUCTION: Rumen microbiota and host metabolites play a key role in regulating ruminant production performance and physiological adaptation. However, the interplay between host physiological status and rumen microbial-metabolite dynamics across lactation stages in buffaloes remains unclear.

METHODS: This study employed a multi-omics approach, integrating metagenomic and serum metabolomic analyses, to investigate microbial remodeling and metabolic adaptations in buffaloes during lactation and dry periods.

RESULTS: Metagenomic analysis revealed increased abundances of Anaerovibrio, Succiniclasticum, and Methanobrevibacter_A during lactation, associated with lipid hydrolysis, propionate production, and methanogenesis, respectively. Glycoside hydrolase families GH2, GH3, GH5, and GH13 were enriched, indicating elevated carbohydrate degradation potential. In contrast, Butyrivibrio, Fibrobacter, and Eubacterium_Q were predominant during the dry period, contributing to fiber degradation and butyrate synthesis. Functional pathways related to niacin metabolism, bicarbonate reabsorption, and neuroactive ligand-receptor interaction were significantly upregulated during lactation. Metabolomic profiling identified lactation-enriched metabolites such as indole-3-methylacetate, D-maltose, and gluconic acid, correlating with immune and metabolic indicators (e.g., IgA, glucose, LDL). Conversely, dry period metabolites such as 1-methylhistidine and 5-hydroxyindoleacetic acid indicated physiological shifts toward tissue repair and stress mitigation.

DISCUSSION: The integrative analysis revealed that host physiological demands during lactation coordinate rumen microbial restructuring to enhance triglyceride degradation, fatty acid biosynthesis, and energy mobilization, thereby supporting milk production. These findings provide novel insights into the host-driven microbiome-metabolite axis underlying lactation in buffaloes.},
}

@article {pmid40635073,
year = {2025},
author = {Zhao, GH and Zhou, BB and Cao, ZH and Xiao, T and Li, YN and Zhu, WJ and Sun, H and Xie, HH and Xie, XM and Zhang, JM and Wang, Q and Zhang, X and Xie, JJ and Dong, HJ and Xu, C and Yin, K},
title = {The development and excretion of Toxoplasma gondii oocyst manipulate the gut microbiota in its definitive host.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {273},
pmid = {40635073},
issn = {1756-3305},
support = {202401050157//The Health Science and Technology Development Program of Shandong Province/ ; 202401050156//The Health Science and Technology Development Program of Shandong Province/ ; 202201050466//The Health Science and Technology Development Program of Shandong Province/ ; ZR2023QH253//The Natural Science Foundation of Shandong Province/ ; ZR2022MH197//The Natural Science Foundation of Shandong Province/ ; tsqn202103186//The Taishan Scholars Project of Shandong Province/ ; 202407//Joint Innovation Team for Clinical & Basic Research/ ; },
mesh = {*Gastrointestinal Microbiome ; Animals ; *Toxoplasma/growth & development/physiology ; Cats ; *Oocysts/growth & development/physiology ; *Toxoplasmosis, Animal/parasitology/microbiology ; Bacteria/genetics/classification ; Metagenomics ; Feces/parasitology ; Host-Parasite Interactions ; },
abstract = {BACKGROUND: Oocysts serve as the primary source of Toxoplasma infection. Therefore, understanding oocyst development and exploring effective strategies to prevent oocyst excretion are crucial for controlling toxoplasmosis.

METHODS: In this study, shotgun metagenomics was employed to characterize the functional and compositional changes in the gut microbiota of cats during oocyst development. The Spearman correlation test was utilized to analyze the correlation between differential Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and carbohydrate-active enzymes (CAZymes) in key bacteria regulating oocyst excretion.

RESULTS: The results revealed that group A (sexual initiation stage) displayed a lower number of functional genes, which were restored to normal levels in group B (oocyst excretion stage), compared with group C (Toxoplasma-uninfected samples). The abundance of 39 KEGG pathways, 106 CAZymes, and 98 virulence factors (VFs) varied significantly among the three groups. The atrazine degradation pathway, associated with sexual development, was upregulated in group B. CAZymes involved in restoring the intestinal mucosal barrier and VFs related to iron metabolism, antibiotic resistance, and suppression of host immunity were enriched in group B. Sexual initiation and oocyst excretion resulted in reduced gut bacterial diversity and microbiota dysbiosis. Probiotics and bacteria related to linoleic acid (LA) uptake were dominant in both group A and group B. Bacteroides stercoris was the most significantly upregulated bacterium and could influence the expression of carbohydrate-binding modules (CBMs) and glycoside hydrolases (GHs) in group B.

CONCLUSIONS: During the oocyst development/excretion stage, the function and composition of the cat gut microbiota changed significantly. In addition, Bacteroides stercoris may play a crucial role in oocyst excretion by regulating key candidates of CBMs and GHs. Our findings lay the foundation for investigating the regulatory mechanisms of oocyst excretion.},
}

*Gastrointestinal Microbiome
Animals
*Toxoplasma/growth & development/physiology
Cats
*Oocysts/growth & development/physiology
*Toxoplasmosis, Animal/parasitology/microbiology
Bacteria/genetics/classification
Metagenomics
Feces/parasitology
Host-Parasite Interactions

@article {pmid40634275,
year = {2025},
author = {Özçam, M and Lin, DL and Gupta, CL and Li, A and Gomez, JC and Wheatley, LM and Baloh, CH and Sanda, S and Jones, SM and Lynch, SV},
title = {Gut microbial bile and amino acid metabolism associate with peanut oral immunotherapy failure.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6330},
pmid = {40634275},
issn = {2041-1723},
support = {AI128482//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI148104//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; UM1AI160040//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI089473//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/immunology/physiology ; *Bile Acids and Salts/metabolism ; *Peanut Hypersensitivity/therapy/immunology/microbiology ; Feces/microbiology/chemistry ; *Arachis/immunology ; *Amino Acids/metabolism ; Male ; Administration, Oral ; Female ; Child ; *Desensitization, Immunologic/methods ; Double-Blind Method ; Child, Preschool ; Treatment Failure ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Antigens, Plant/immunology ; },
abstract = {Peanut Oral Immunotherapy (POIT) holds promise for remission of peanut allergy, though treatment is protracted and successful in only a subset of patients. Because the gut microbiome has been linked to food allergy, we sought to identify fecal predictors of POIT efficacy and mechanistic insights into treatment response. Here, we conducted a secondary analysis of the IMPACT randomized, double-blind, placebo-controlled POIT trial (NCT01867671), using longitudinal fecal samples from 90 children, and performed 16S rRNA sequencing, shotgun metagenomics, and untargeted metabolomics. Integrated multi-omics analyses revealed a relationship between gut microbiome metabolic capacity and treatment outcomes. Five fecal bile acids present prior to treatment initiation predicted POIT efficacy (AUC 0.71). Treatment failure was associated with a specific bile acid profile, enhanced amino acid utilization, and higher copy number of the ptpA gene encoding a bacterial hydrolase that cleaves tripeptides containing proline residues - a feature of immunogenic peanut Ara h 2 proteins. In vitro, peanut-supplemented fecal cultures of children for whom POIT failed to induce remission evidenced reduced Ara h 2 concentrations. Thus, distal gut microbiome metabolism appears to contribute to POIT failure.},
}

Humans
*Gastrointestinal Microbiome/genetics/immunology/physiology
*Bile Acids and Salts/metabolism
*Peanut Hypersensitivity/therapy/immunology/microbiology
Feces/microbiology/chemistry
*Arachis/immunology
*Amino Acids/metabolism
Male
Administration, Oral
Female
Child
*Desensitization, Immunologic/methods
Double-Blind Method
Child, Preschool
Treatment Failure
RNA, Ribosomal, 16S/genetics
Metagenomics
Antigens, Plant/immunology

@article {pmid40592243,
year = {2025},
author = {Gao, Z and Liu, X and Yu, J and Li, Z and Shi, H and Zhang, G and Ling, J},
title = {Structural basis of immunomodulation by edible fungal polysaccharides: From molecular characteristics to action mechanisms.},
journal = {Carbohydrate research},
volume = {555},
number = {},
pages = {109591},
doi = {10.1016/j.carres.2025.109591},
pmid = {40592243},
issn = {1873-426X},
mesh = {Humans ; *Fungal Polysaccharides/chemistry/pharmacology ; Animals ; *Immunologic Factors/chemistry/pharmacology ; *Immunomodulation/drug effects ; Gastrointestinal Microbiome/drug effects ; *Immunomodulating Agents/chemistry/pharmacology ; },
abstract = {Edible Fungal polysaccharides as Immunomodulators: A Systematic Review at the Crossroads of Immunology, Natural Products Chemistry, and Microbiology. The chemical structure-specifically molecular weight, branching degree, and functional group modifications-directly dictates immunological activity. For instance, high-molecular-weight β-glucans activate macrophage surface receptors through triple-helix conformations, whereas sulfation enhances electrostatic interactions with immune cells. Mechanistically, polysaccharides regulate macrophage polarization, dendritic cell maturation, and T/B cell activation, therebyengaging core signaling pathways such as TLR4/MyD88/NF-κB, NLRP3 inflammasome, and MAPK, This orchestrates synergistic enhancement of innate and adaptive immunity. Recent research further demonstrate that polysaccharides can also reshape the gut microbiota-immune metabolic axis by promoting the production of short-chain fatty acids (SCFAs) and activating receptors (e.g., GPR43), indirectly modulating systemic immune responses. Clinically, polysaccharides from Ganoderma lucidum and Lentinus edodes demonstrate efficacy in cancer adjuvant therapy by enhancing immune function and reducing radiotherapy/chemotherapy side effects. However, species-specific receptor recognition heterogeneity and lack of standardized preparation protocols impede clinical translation. Therefore,the implementing an integrated strategy of "polysaccharide structure-immunometabolic reprogramming-precision delivery" to overcome the existing bottlenecks. Combining multi-omics approaches (e.g., gut metagenomics and metabolomics) will advance therapeutics targeting microbiota-immune crosstalk. Such strategies aim to address chronic inflammatory inflammation", malignancies, and related pathologies with enhanced mechanistic specificity.},
}

Humans
*Fungal Polysaccharides/chemistry/pharmacology
Animals
*Immunologic Factors/chemistry/pharmacology
*Immunomodulation/drug effects
Gastrointestinal Microbiome/drug effects
*Immunomodulating Agents/chemistry/pharmacology

@article {pmid40578342,
year = {2025},
author = {Wong, KK and Wu, BG and Chung, M and Li, Q and Darawshy, F and Tsay, JJ and Holub, M and Barnett, CR and Kwok, B and Kugler, MC and Chung, C and Natalini, JG and Singh, S and Li, Y and Schluger, R and Ficaro, L and Carpenito, J and Collazo, D and Perez, L and Kyeremateng, Y and Chang, M and Czachor, A and Singh, R and Mccormick, C and Campbell, CD and Keane, R and Askenazi, M and Hansbro, PM and Weiden, MD and Huang, YJ and Stringer, KA and Clemente, JC and Li, H and Jones, D and Ghedin, E and Segal, LN and Sulaiman, I},
title = {Microbial contribution to metabolic niche formation varies across the respiratory tract.},
journal = {Cell host & microbe},
volume = {33},
number = {7},
pages = {1073-1088.e6},
doi = {10.1016/j.chom.2025.06.002},
pmid = {40578342},
issn = {1934-6069},
mesh = {Animals ; Mice ; Humans ; *Microbiota ; Metabolome ; *Respiratory System/microbiology/metabolism ; Lung/microbiology/metabolism ; Prevotella/metabolism ; Female ; Mice, Inbred C57BL ; Male ; Methionine/metabolism ; Metagenome ; Streptococcus/metabolism ; *Bacteria/metabolism/classification/genetics ; Veillonella/metabolism ; Glutamic Acid/metabolism ; },
abstract = {Variations in the airway microbiome are associated with inflammatory responses in the lung and pulmonary disease outcomes. Regional changes in microbiome composition could have spatial effects on the metabolic environment, contributing to differences in the host response. Here, we profiled the respiratory microbiome (metagenome/metatranscriptome) and metabolome of a patient cohort, uncovering topographical differences in microbial function, which were further delineated using isotope probing in mice. In humans, the functional activity of taxa varied across the respiratory tract and correlated with immunomodulatory metabolites such as glutamic acid/glutamate and methionine. Common oral commensals, such as Prevotella, Streptococcus, and Veillonella, were more functionally active in the lower airways. Inoculating mice with these commensals led to regional increases in several metabolites, notably methionine and tyrosine. Isotope labeling validated the contribution of Prevotella melaninogenica in generating specific metabolites. This functional characterization of microbial communities reveals topographical changes in the lung metabolome and potential impacts on host responses.},
}

Animals
Mice
Humans
*Microbiota
Metabolome
*Respiratory System/microbiology/metabolism
Lung/microbiology/metabolism
Prevotella/metabolism
Female
Mice, Inbred C57BL
Male
Methionine/metabolism
Metagenome
Streptococcus/metabolism
*Bacteria/metabolism/classification/genetics
Veillonella/metabolism
Glutamic Acid/metabolism

@article {pmid40540838,
year = {2025},
author = {Conti Taguali, S and Pöter, R and Aloi, F and Fernández-Trujillo, C and Acedo, A and La Spada, F and Li Destri Nicosia, MG and Pane, A and Schena, L and Cacciola, SO},
title = {Influence of environmental and agronomic variables on soil microbiome in citrus orchards: A comparative analysis of organic and conventional farming system.},
journal = {Microbiological research},
volume = {299},
number = {},
pages = {128260},
doi = {10.1016/j.micres.2025.128260},
pmid = {40540838},
issn = {1618-0623},
mesh = {*Soil Microbiology ; *Citrus/microbiology/growth & development ; *Organic Agriculture/methods ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; Soil/chemistry ; *Agriculture/methods ; Sicily ; Biodiversity ; Plant Roots/microbiology ; Nitrogen Fixation ; },
abstract = {Crop health and productivity depend on the structure and functionality of soil microbiota associated with the root system of plants. The agricultural policy of the European Union promotes organic farming systems to ensure environmental sustainability and food safety. The objective of this study was to investigate the impact of organic farming on soil microbiome in citrus orchards. The soil microbiota of eight conventionally and seven organically managed commercial citrus orchards across eastern Sicily was characterised using Illumina sequencing and BeCrop® primers for PCR amplification. The structure (diversity and relative abundance) and functionality of soil bacterial and fungal communities depended primarily on the sampling site. Other variables influencing the soil microbiome included soil total carbon content, seasonality, rootstock genotype, soil tillage and irrigation system. The latter three exerted differential effects on either bacterial or fungal communities. Conversely, age and visible health status of the tree had negligible influence on both communities. The differences between organically and conventionally managed citrus orchards accounted for a significant proportion of the variability, indicating a relevant effect of the farming system on soil microbiome. Organically managed orchards compared to those managed conventionally exhibited higher microbial diversity and a unique composition of nutrient-cycling microbes. In particular, organic farming promoted beneficial microbial functions, such as nitrogen fixation and phosphorus solubilization. Findings provide insights into the dynamic and complex interactions between environmental variables and soil microbial communities in citrus orchards, confirming the potential of microbial diversity as an indicator of sustainability in agricultural systems.},
}

*Soil Microbiology
*Citrus/microbiology/growth & development
*Organic Agriculture/methods
*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
Soil/chemistry
*Agriculture/methods
Sicily
Biodiversity
Plant Roots/microbiology
Nitrogen Fixation

@article {pmid40480048,
year = {2025},
author = {Yang, J and Liu, J and Gu, H and Song, W and Zhang, H and Wang, J and Yang, P},
title = {Gut microbiota, metabolites, and pulmonary hypertension: Mutual regulation and potential therapies.},
journal = {Microbiological research},
volume = {299},
number = {},
pages = {128245},
doi = {10.1016/j.micres.2025.128245},
pmid = {40480048},
issn = {1618-0623},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Hypertension, Pulmonary/microbiology/therapy/metabolism ; Fatty Acids, Volatile/metabolism ; Methylamines/metabolism ; Animals ; Bile Acids and Salts/metabolism ; Bacteria/metabolism/classification/genetics ; Tryptophan/metabolism ; },
abstract = {Pulmonary hypertension is a progressive condition characterized by increased pulmonary vascular pressure and resistance, ultimately leading to right heart failure and death. Increasing evidence has underscored the importance of the gut-lung axis in the development of respiratory and cardiovascular diseases. Notably, significant changes in the gut microbiota, including altered microbial composition and function, have been observed in pulmonary hypertension. Specifically, microbiota-derived metabolites, including short chain fatty acids, trimethylamine N-oxide, bile acids and tryptophan, play a significant role in the development of pulmonary hypertension. The identification of key bacteria and metabolites, along with recent advances in gut microbiota-targeting technologies and metabolic pathway-targeting inhibitors/agonists, holds potential for developing diagnostic, prognostic, and therapeutic strategies for pulmonary hypertension. Emerging research directions include metagenomic analysis of viruses and fungi, artificial intelligence-aided prediction models, novel metabolites and their associated enzymes, drug-microbiota interactions, selective antibiotics, and advanced microbiota transplantation. This review synthesizes clinical and experimental evidence linking the gut microbiota to pulmonary hypertension, highlighting their interplay as a promising avenue for further investigation and translational applications.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Hypertension, Pulmonary/microbiology/therapy/metabolism
Fatty Acids, Volatile/metabolism
Methylamines/metabolism
Animals
Bile Acids and Salts/metabolism
Bacteria/metabolism/classification/genetics
Tryptophan/metabolism

@article {pmid40630933,
year = {2025},
author = {Takács, B and Jaksa, G and Qorri, E and Gyuris, Z and Pintér, L and Haracska, L},
title = {Advancing metagenomic classification with NABAS+: a novel alignment-based approach.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {3},
pages = {lqaf092},
pmid = {40630933},
issn = {2631-9268},
mesh = {Humans ; *Metagenomics/methods ; Algorithms ; *Software ; *Sequence Alignment/methods ; *Metagenome ; Microbiota/genetics ; },
abstract = {Microbiome research has expanded rapidly in the last decade due to advances in sequencing technology, resulting in larger and more complex data. This has also led to the development of a plethora of metagenomic classifiers applying different algorithmic principles to classify microorganisms. However, accurate metagenomic classification remains challenging due to false positives and the need for dataset-specific tuning, limiting the comparability of distinct studies and clinical use. In this study, we demonstrate the discrepancy between current, commonly used classifiers and propose a novel classifier, NABAS+ (Novel Alignment-based Biome Analyzing Software+). NABAS+ uses BWA (Burrows-Wheeler aligner) alignment with strict RefSeq curation to ensure one reliable genome per species and filters for genomes with only high-quality reads for precise species-level identification from Illumina shotgun data. The performance of our algorithm and three commonly used classifiers was evaluated on in silico datasets modelling human gastrooral communities, as well as on deeply sequenced microbial community standards. Additionally, we illustrated the usefulness of NABAS+ in detecting pathogens in real-world clinical data. Our results show that NABAS+, due to its extensive alignment process, is superior in accuracy and sensitivity compared to leading microbiome classifiers, particularly in reducing false positives in deep-sequenced microbial samples, making it suitable for clinical diagnosis.},
}

Humans
*Metagenomics/methods
Algorithms
*Software
*Sequence Alignment/methods
*Metagenome
Microbiota/genetics

@article {pmid40628728,
year = {2025},
author = {Arp, G and Jiang, AK and Dufault-Thompson, K and Levy, S and Zhong, A and Wassan, JT and Grant, MR and Li, Y and Hall, B and Jiang, X},
title = {Identification of gut bacteria reductases that biotransform steroid hormones.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6285},
pmid = {40628728},
issn = {2041-1723},
mesh = {*Gastrointestinal Microbiome/physiology/genetics ; Humans ; Phylogeny ; Male ; Female ; *Oxidoreductases/metabolism/genetics ; *Bacteria/enzymology/genetics/classification ; *Steroids/metabolism ; Biotransformation ; Pregnenolone/metabolism ; *Bacterial Proteins/metabolism/genetics ; },
abstract = {The metabolism of steroid hormones by the gut microbiome is increasingly recognized as a key factor in human health; however, the specific enzymes mediating these transformations remain largely unidentified. In this study, we identify Δ[4]-3-ketosteroid 5β-reductase, 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase, and Δ[6]-3-ketosteroid reductase enzyme families encoded by common human gut bacteria. Through phylogenetic reconstruction and mutagenesis, we show that 5β-reductase evolved to specialize in converting both natural and synthetic 3-ketosteroid hormones into their 5β-reduced derivatives, while Δ[6]-3-ketosteroid reductase adapted to produce Δ[6]-reduced derivatives. We also find that the novel 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase is fused with 5β-reductase in multiple species, streamlining the conversion of pregnenolone, a 3β-hydroxy-5-ene and steroid hormone precursor, into epipregnanolone. Through metagenomic analysis, we reveal that these enzymes are prevalent in healthy populations and enriched in females compared to males. These findings lay the groundwork for mechanistic investigations into how microbial steroid metabolism modulates host hormonal physiology.},
}

*Gastrointestinal Microbiome/physiology/genetics
Humans
Phylogeny
Male
Female
*Oxidoreductases/metabolism/genetics
*Bacteria/enzymology/genetics/classification
*Steroids/metabolism
Biotransformation
Pregnenolone/metabolism
*Bacterial Proteins/metabolism/genetics

@article {pmid40570246,
year = {2025},
author = {Ma, C and Bao, Y and Hereid, S and Zhang, H and Bai, X and Bai, Q and Zhao, L and Zhang, X and Lian, H and Dai, L and Bao, X and Bao, L},
title = {Mechanistic Elucidation of Tricholoma mongolicum Polysaccharides in Treating MAFLD via Regulation of the Gut Microbiota-Metabolite-Ferroptosis Axis: A Multi-Omics Perspective.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {27},
pages = {17040-17056},
doi = {10.1021/acs.jafc.5c05877},
pmid = {40570246},
issn = {1520-5118},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Polysaccharides/administration & dosage/chemistry ; Animals ; Mice ; Male ; Humans ; *Tricholoma/chemistry ; Bacteria/classification/genetics/isolation & purification/metabolism/drug effects ; Mice, Inbred C57BL ; Liver/metabolism/drug effects ; Iron/metabolism ; *Non-alcoholic Fatty Liver Disease/drug therapy/metabolism/microbiology/genetics ; *Plant Extracts/administration & dosage/chemistry ; *Fatty Liver/drug therapy/metabolism/microbiology/genetics ; Multiomics ; },
abstract = {This study aimed to elucidate the modulatory effects and underlying molecular mechanisms of Tricholoma mongolicum polysaccharide (TMP) in the context of metabolic dysfunction-associated fatty liver disease (MAFLD). High-performance gel permeation chromatography (HPGPC) analysis indicated a bimodal molecular weight distribution. Monosaccharide composition profiling revealed a predominance of glucose and galactose among other constituents. Scanning electron microscopy (SEM) illustrated a porous, aggregated colloidal microstructure. In a model of MAFLD, TMP intervention significantly attenuated serum levels of TC, TG, and AST, ALT, accompanied by notable histological improvements, including reduced hepatic steatosis and inflammatory cell infiltration. Metagenomic analysis demonstrated that TMP substantially enhanced gut microbial α-diversity, restructured microbial community composition, decreased the Firmicutes/Bacteroidetes ratio, enriched SCFAs-producing genera, and suppressed the excessive proliferation of pro-inflammatory bacterial genera. Integrated proteomic and lipidomic analyses revealed that TMP inhibited hepatic immune-inflammatory responses and ferroptosis pathways, enhanced pathways associated with metabolic homeostasis. Furthermore, TMP modulated hepatic iron metabolism by upregulating the Nrf2/GPx4 antioxidant axis and FPN1 while downregulating TFR1, thereby alleviating oxidative stress and iron overload. These findings demonstrate that TMP exerts therapeutic efficacy through a bidirectional gut-liver regulatory mechanism involving microbial modulation, ferroptosis inhibition, metabolic reprogramming, and activation of antioxidant defenses. This research provides novel insights and molecular targets for the development of natural polysaccharide-based interventions for MAFLD.},
}

*Gastrointestinal Microbiome/drug effects
*Polysaccharides/administration & dosage/chemistry
Animals
Mice
Male
Humans
*Tricholoma/chemistry
Bacteria/classification/genetics/isolation & purification/metabolism/drug effects
Mice, Inbred C57BL
Liver/metabolism/drug effects
Iron/metabolism
*Non-alcoholic Fatty Liver Disease/drug therapy/metabolism/microbiology/genetics
*Plant Extracts/administration & dosage/chemistry
*Fatty Liver/drug therapy/metabolism/microbiology/genetics
Multiomics

@article {pmid40556381,
year = {2025},
author = {Zhao, S and Xu, Q and Li, M and Chen, J and Francis, F and Dai, X and Tan, J and Kong, Z},
title = {Exploring the Impact of Dinotefuran Residue on Microbial Community and Flavor Generation in Huangjiu Fermentation.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {27},
pages = {17219-17232},
doi = {10.1021/acs.jafc.5c02308},
pmid = {40556381},
issn = {1520-5118},
mesh = {Fermentation ; *Flavoring Agents/metabolism/chemistry ; *Guanidines/analysis/metabolism ; *Bacteria/genetics/isolation & purification/classification/metabolism ; Microbiota/drug effects ; Volatile Organic Compounds/chemistry/metabolism ; *Nitro Compounds/analysis/metabolism ; Gas Chromatography-Mass Spectrometry ; *Neonicotinoids/analysis ; *Pesticide Residues/analysis ; Taste ; Odorants/analysis ; *Fermented Foods/microbiology/analysis ; Metagenomics ; *Brassica/microbiology/chemistry ; },
abstract = {Pesticide residues create food safety hazards while negatively affecting the quality of fermented foods, but the mechanisms of the deterioration response have been a mystery. In this study, headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) and metagenomics sequencing analyses were employed to investigate the effect of dinotefuran residue on the aroma profile and microbial community of Huangjiu. The presence of dinotefuran led to a reduction in the overall concentration of volatile compounds, and some floral, fruity, and sweet aromas such as piperitenol, citronellyl isobutyrate, and trans-2-decenal were no longer detected. Meanwhile, the levels of certain acidic volatiles, including formic acid, propionic acid, and heptanoic acid, increased and contributed to off-flavors. Dinotefuran affected the Huangjiu flavor by modifying the abundance and structure of key genera such as Saccharomyces, Lactococcus, and Cyberlindnera. These changes were associated with disturbances in 16 KEGG tertiary metabolic pathways, including glycolysis, pyruvate metabolism, and amino acid biosynthesis. These results provided some reference for further studies on how pesticide residues affect the flavor and microbial characteristics of traditional fermented beverages like Huangjiu.},
}

Fermentation
*Flavoring Agents/metabolism/chemistry
*Guanidines/analysis/metabolism
*Bacteria/genetics/isolation & purification/classification/metabolism
Microbiota/drug effects
Volatile Organic Compounds/chemistry/metabolism
*Nitro Compounds/analysis/metabolism
Gas Chromatography-Mass Spectrometry
*Neonicotinoids/analysis
*Pesticide Residues/analysis
Taste
Odorants/analysis
*Fermented Foods/microbiology/analysis
Metagenomics
*Brassica/microbiology/chemistry

@article {pmid40454811,
year = {2025},
author = {Millard, SA and Vendrov, KC and Young, VB and Seekatz, AM},
title = {Host origin of microbiota drives functional recovery and Clostridioides difficile clearance in mice.},
journal = {mBio},
volume = {16},
number = {7},
pages = {e0110825},
doi = {10.1128/mbio.01108-25},
pmid = {40454811},
issn = {2150-7511},
support = {P20GM146584, P20GM139769/NH/NIH HHS/United States ; K01-DK111794/NH/NIH HHS/United States ; AI124255, AI090871/NH/NIH HHS/United States ; },
mesh = {Animals ; *Clostridium Infections/therapy/microbiology ; *Fecal Microbiota Transplantation ; Mice ; *Clostridioides difficile/physiology ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Disease Models, Animal ; Mice, Inbred C57BL ; Female ; Male ; Metagenomics ; Metabolomics ; },
abstract = {UNLABELLED: Colonization resistance provided by the gut microbiota is essential for resisting both initial Clostridioides difficile infection (CDI) and potential recurrent infection (rCDI). Although fecal microbiota transplantation (FMT) has been successful in treating rCDI by restoring microbial composition and function, mechanisms underlying the efficacy of standardized stool-derived products remain poorly understood. Using a combination of 16S rRNA gene-based and metagenomic sequencing alongside metabolomics, we investigated microbiome recovery following FMT from human and murine donor sources in a mouse model of rCDI. We found that a human-derived microbiota was less effective in clearing C. difficile compared to a mouse-derived microbiota, despite recovery of taxonomic diversity, compositional changes, and bacterial functions typically associated with clearance. Metabolomic analysis revealed deficits in secondary metabolites compared to those that received murine FMT, suggesting a functional remodeling between human microbes in their new host environment. Collectively, our data revealed additional environmental, ecological, or host factors to consider in FMT-based recovery from rCDI.

IMPORTANCE: Clostridioides difficile is a significant healthcare-associated pathogen, with recurrent infections presenting a major treatment challenge due to further disruption of the microbiota after antibiotic administration. Despite the success of fecal microbiota transplantation (FMT) for the treatment of recurrent infection, the mechanisms mediating its efficacy remain underexplored. This study reveals that the effectiveness of FMT may be compromised by a mismatch between donor microbes and the recipient environment, leading to deficits in key microbial metabolites. These findings highlight additional factors to consider when assessing the efficacy of microbial-based therapeutics for C. difficile infection (CDI) and other conditions.},
}

Animals
*Clostridium Infections/therapy/microbiology
*Fecal Microbiota Transplantation
Mice
*Clostridioides difficile/physiology
*Gastrointestinal Microbiome
Humans
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Disease Models, Animal
Mice, Inbred C57BL
Female
Male
Metagenomics
Metabolomics

@article {pmid40285962,
year = {2025},
author = {Liao, J and Wei, JH and Liu, J and Ren, L and Zang, N and Liu, E},
title = {Respiratory virome in hospitalized children and analysis of its correlation with disease severity.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {44},
number = {7},
pages = {1643-1657},
pmid = {40285962},
issn = {1435-4373},
support = {Grant No. 82341111//The National Natural Science Foundation of China Special Project/ ; },
mesh = {Humans ; Male ; Female ; Child, Preschool ; Infant ; Child ; *Virome ; *Respiratory Tract Infections/virology/epidemiology ; Severity of Illness Index ; Bronchoalveolar Lavage Fluid/virology ; *Viruses/genetics/classification/isolation & purification ; Infant, Newborn ; Child, Hospitalized ; Sputum/virology ; High-Throughput Nucleotide Sequencing ; Adolescent ; *Virus Diseases/virology/epidemiology ; Metagenomics ; Hospitalization ; China/epidemiology ; },
abstract = {PURPOSE: To investigate the composition of respiratory viromes and their association with disease severity among hospitalized pediatric patients.

METHODS: Clinical data and metagenomic next-generation sequencing (mNGS) results were collected from pediatric patients hospitalized at the Children's Hospital of Chongqing Medical University between January 2022 and September 2023. The analyzed specimens included sputum and bronchoalveolar lavage fluid (BALF).

RESULTS: The study included 229 patients (65.07% male, median age 3 years) with 25 sputum and 204 BALF samples, of whom 40.17% met the WHO criteria for severe acute respiratory infection (SARI). Herpesviruses were detected in 166 cases (72.49%), including 85 cases of cytomegalovirus (CMV), 64 cases of Epstein-Barr virus (EBV), 34 cases of human herpesvirus-7 (HHV-7), 12 cases of human herpesvirus-6 (HHV-6), and 6 cases of herpes simplex virus type 1 (HSV-1). Additionally, 53 cases of torque teno virus (TTV) and 7 cases of torque teno mini virus (TLMV) were detected. CMV prevalence was highest in neonates, while EBV peaked in the 3-6 year group (37.78%). HSV-1 and HHV-6 were predominantly identified in severe infections.

CONCLUSION: Herpesviruses, particularly CMV and EBV, were the most frequently detected viruses, followed by anelloviruses. The age-specific viral distribution patterns provide novel epidemiological perspectives for understanding pediatric respiratory pathogenesis, though their clinical significance requires validation through mechanistic studies.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Humans
Male
Female
Child, Preschool
Infant
Child
*Virome
*Respiratory Tract Infections/virology/epidemiology
Severity of Illness Index
Bronchoalveolar Lavage Fluid/virology
*Viruses/genetics/classification/isolation & purification
Infant, Newborn
Child, Hospitalized
Sputum/virology
High-Throughput Nucleotide Sequencing
Adolescent
*Virus Diseases/virology/epidemiology
Metagenomics
Hospitalization
China/epidemiology

@article {pmid40625831,
year = {2025},
author = {Han, Y and Ding, PH},
title = {Advancing periodontitis microbiome research: integrating design, analysis, and technology.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1616250},
pmid = {40625831},
issn = {2235-2988},
mesh = {Humans ; *Periodontitis/microbiology ; *Microbiota ; Biofilms/growth & development ; Gingiva/microbiology ; Bacteria/genetics/classification ; },
abstract = {Periodontitis, a chronic inflammatory disease affecting 20%-50% of adults worldwide, is driven by polymicrobial synergy and dysbiosis. Despite numerous studies on the oral microbiota in periodontitis, significant heterogeneity exists between findings, posing challenges for treatment strategies. To understand the sources of this variability and establish standardized protocols, we reviewed the literature to identify potential factors contributing to these discrepancies. We found most studies focus on microbial communities in periodontal pockets, with fewer investigating microbial composition within gingival tissue. Research indicates that bacterial communities in gingival tissue exist as biofilms, potentially serving as reservoirs for persistent infection. Therefore, further exploration of the microbiome within periodontal tissues is needed, which may offer new insights for treatment strategies. Metatranscriptomics provides valuable insights into gene expression patterns of the oral microbiota, enabling the exploration of microbial activity at a functional level. Previous studies revealed that most upregulated virulence factors in periodontitis originate from species not traditionally considered major periodontal pathogens. However, current studies have not fully identified or revealed the functional changes in key symbiotic microbes in periodontitis. We reviewed the analytical paradigms of metatranscriptomics and found that current analysis is largely limited to assessing functional changes in known periodontal pathogens, highlighting the need for a functional-driven approach. Beyond the limitations of current analytical paradigms, the metatranscriptomics also has inherent constraints. We suggested integrating emerging high-throughput microbial sequencing technologies with functional-driven analytical strategies to provide a more comprehensive and higher-resolution insight for microbiome reconstruction in periodontitis.},
}

Humans
*Periodontitis/microbiology
*Microbiota
Biofilms/growth & development
Gingiva/microbiology
Bacteria/genetics/classification

@article {pmid40624949,
year = {2025},
author = {Wu, M and Zhang, T and Han, S and Huan, S and Jiang, Y and Wang, Y and Cai, Z and Zhou, J},
title = {Structure and Function Features of Abundant and Rare Prokaryotic Communities Along Nearshore to Offshore Transitions.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70144},
doi = {10.1111/1462-2920.70144},
pmid = {40624949},
issn = {1462-2920},
support = {42476137//National Natural Science Foundation of China/ ; KCXFZ20230731093402005//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; SGDX20220530111204028//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; RCJC20200714114433069//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; ZDSYS20230626091459009//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; 2023KCXTD052//Innovation Team Project for Guangdong's Universities/ ; 2025A1515010643//Natural Science Foundation of Guangdong Province/ ; 2025A1515010519//Natural Science Foundation of Guangdong Province/ ; },
mesh = {Biodiversity ; *Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Phylogeny ; *Microbiota ; Metagenome ; Metagenomics ; *Archaea/genetics/classification/isolation & purification ; },
abstract = {Abundant and rare taxa are crucial members of the marine microbial community. However, their biodiversity, assembly mechanisms, functional characteristics and ecological response strategies remain poorly understood. In this study, 16S rRNA and metagenomic sequencing were carried out to reveal the structural and functional features of abundant and rare taxa across the transition from nearshore to offshore. The results showed that the biodiversity of both abundant and rare taxa decreased with increasing distance from shore, with rare taxa exhibiting relatively higher diversity indices than abundant ones. Neutral model analysis revealed that the assembly process gradually changed from deterministic to stochastic from nearshore to offshore among abundant taxa. In contrast, among rare taxa, a stochastic process dominated nearshore, whereas a deterministic process was predominant in the offshore environment. Meanwhile, the proportion of variance that could be explained by environmental factors was relatively higher among abundant communities than among rare ones. A co-occurrence network analysis indicated that rare communities displayed greater complexity and a higher degree of modularity than abundant communities. Functionally, abundant communities tended to favour an r-strategy, whereas rare communities leaned towards a K-strategy. Our results strengthen the understanding of the ecological mechanisms controlling microbial community patterns along coastal-to-open water transitions.},
}

Biodiversity
*Seawater/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Phylogeny
*Microbiota
Metagenome
Metagenomics
*Archaea/genetics/classification/isolation & purification

@article {pmid40624695,
year = {2025},
author = {Li, Q and Huang, J and Zhou, Y and Wu, Q and Zhou, J and He, F and He, L and Shi, Y and Guo, C and Dai, J},
title = {Virome profiling of Aedes albopictus across urban ecosystems in Guangdong reveals sex-specific diversity.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {264},
pmid = {40624695},
issn = {1756-3305},
support = {2024HK037//Scientific Research Project of General Administration of Customs/ ; 2024M760629//China Postdoctoral Science Foundation/ ; 2022YFC2302700//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Aedes/virology ; *Virome/genetics ; Female ; Male ; China ; *Mosquito Vectors/virology ; Phylogeny ; Ecosystem ; Metagenomics ; Cities ; Sex Factors ; Arboviruses/genetics/isolation & purification ; },
abstract = {BACKGROUND: Aedes albopictus mosquitoes are key vectors for arboviruses such as Dengue virus, Zika virus, and Chikungunya virus, posing significant global public health risks. Guangdong Province, a densely populated subtropical region in southern China, has experienced recurrent outbreaks of mosquito-borne diseases. However, sex- and geography-specific virome profiles of Aedes albopictus populations in this area remain uncharacterized, limiting the development of targeted surveillance strategies and precise risk assessment.

METHODS: We performed a metagenomic analysis of 1269 adult Aedes albopictus collected from five cities across Guangdong Province during autumn 2021. Mosquito pools underwent viral particle enrichment followed by DNA and RNA sequencing. Bioinformatic analyses were employed to characterize viral communities, evaluate alpha/beta diversity, and conduct phylogenetic reconstruction.

RESULTS: A comparative analysis of virome profiles in male and female Aedes albopictus across five regions of Guangdong Province (Chaozhou, Guangzhou, Shaoguan, Shenzhen, Zhanjiang) revealed significant viral distribution patterns influenced by both sex and geographic location. Female mosquitoes predominantly hosted vertebrate-associated arboviruses, including Flavivirus, consistent with their blood-feeding behavior. RNA virome composition showed significant sex-specific clustering (permutational multivariate analysis of variance, PERMANOVA, P = 0.008), with coastal cities (Shenzhen, Zhanjiang) being dominated by RNA viruses, whereas inland areas (Shaoguan) exhibited a predominance of DNA viruses. DNA virome profiles displayed divergence between sexes but marked regional variation. Guangzhou emerged as an outlier, exhibiting exceptional bacteriophage diversity distinct from other regions. Phylogenetic analysis identified zoonotic pathogens with signatures of cross-species transmission and region-specific evolutionary adaptation. These findings highlight the interplay between mosquito ecology, geographic factors, and viral evolution in shaping virome diversity.

CONCLUSIONS: This study presents the inaugural comparative analysis of DNA/RNA viromes in Aedes albopictus populations across Guangdong Province, revealing distinct sex-specific and geographic patterns in viral composition. The identification of vertebrate-associated viruses in female mosquitoes reinforces their epidemiological significance as arboviral vectors, while male-specific environmental viral signatures suggest potential pathways for ecological spillover. Coastal-inland and urban-rural disparities in viral communities emphasize the need for regionally tailored surveillance. These findings provide essential baseline virome data for forecasting emerging arboviral threats and informing strategies to mitigate zoonotic spillover in subtropical urban ecosystems.},
}

Animals
*Aedes/virology
*Virome/genetics
Female
Male
China
*Mosquito Vectors/virology
Phylogeny
Ecosystem
Metagenomics
Cities
Sex Factors
Arboviruses/genetics/isolation & purification

@article {pmid40624638,
year = {2025},
author = {Yan, X and Lin, X and Wu, J and Zheng, L and Liu, Y and Wu, F and Lin, Y and Lu, Y and Huang, C and Shen, B and Liu, H and Huang, R and Hou, F and Zhou, Q and Song, M and Liu, K and Zhu, F and Li, S and Lin, Y and Wang, W and Li, P and Liao, W and Zhi, F},
title = {Mitigation of chemotherapy-induced gut dysbiosis and diarrhea by supplementation with heat-killed Bacteroides fragilis.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {408},
pmid = {40624638},
issn = {1741-7015},
support = {Y20190159//Study on the Mechanism of FUT7 regulating CD15s+eTreg cells in the Pathogenesis of Ulcerative Colitis/ ; NO.2024B03J1282//Key Technology Project in Guangzhou/ ; NO. 201809010014//Innovation Leading Team Project in Guangzhou/ ; },
mesh = {Animals ; *Dysbiosis/chemically induced/therapy/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects ; Humans ; *Diarrhea/chemically induced/microbiology/therapy ; Mice ; *Bacteroides fragilis ; Mice, Inbred C57BL ; *Probiotics/therapeutic use ; Mice, Inbred BALB C ; *Antineoplastic Agents/adverse effects ; Middle Aged ; Fluorouracil/adverse effects ; Feces/microbiology ; Female ; Aged ; },
abstract = {BACKGROUND: The role of gut microbial dysbiosis in chemotherapy-induced diarrhea (CID) pathogenesis remains unclear in humans. This study investigates gut microbiota alterations in CID patients and evaluates the therapeutic potential of probiotic supplementation.

METHODS: To establish a paired cohort for longitudinal comparison and minimize confounding factors in assessing CID-related microbiota changes, strict inclusion/exclusion criteria were applied to gastrointestinal cancer patients. Fecal samples from eligible participants underwent shotgun metagenomic sequencing to comprehensively profile the gut microbiome composition and function. To evaluate probiotic efficacy and mechanisms, we utilized 6-8-week-old male BALB/c and C57BL/6 mice in established 5-FU- or CPT-11-induced CID models. Probiotic efficacy was assessed using primary (diarrhea severity) and secondary endpoints (body weight change, intestinal permeability). Mechanistic studies were conducted in murine models, complemented by IEC-6 cells and intestinal organoid experiments to elucidate microbiota-host interactions.

RESULTS: Analysis of paired fecal samples (pre- and post-chemotherapy) from 30 gastrointestinal cancer patients (n = 60) revealed chemotherapy-induced reduction of Bacteroides fragilis (B. f) via metagenomics sequencing, with baseline B. f relative abundance negatively correlating with CID severity (r =  - 0.93, p = 3.1e - 12). Building on these clinical observations, in 5-FU/CPT-11-induced CID murine models, oral gavage of heat-killed B. f (hk-B. f) outperformed live bacteria in diarrhea alleviation. Mechanistically, B. f-derived succinate exacerbated diarrhea, while its capsular polysaccharide (PSA) ameliorated mice diarrhea. This discovery explains the discrepant therapeutic effect between hk-B. f and live B. f. Fluorescence tracing confirmed hk-B. f transiently localized to the upper gastrointestinal tract without extraintestinal colonization. hk-B. f preserved epithelial integrity, mitochondrial function, and intestinal organoid development (higher budding count and larger organoid surface area). Moreover, hk-B. f upregulated the expression of BCL2 and downregulated the expression of BAX. Shifting the balance between BCL2 and BAX alleviates intestinal epithelial apoptosis. Caspase-3 inhibition or BCL2 silencing abrogated hk-B. f's anti-apoptotic effects in IEC-6 cells.

CONCLUSIONS: Pathological process of CID can be partially explained by compositional alterations in the gut microbiota. Supplementation with hk-B. f reduces 5-FU-stimulated epithelial injury through mitochondrial apoptotic pathway in CID murine models. These preclinical findings suggest hk-B. f merits further investigation as a potential strategy for improving CID, pending clinical validation.},
}

Animals
*Dysbiosis/chemically induced/therapy/microbiology
Male
*Gastrointestinal Microbiome/drug effects
Humans
*Diarrhea/chemically induced/microbiology/therapy
Mice
*Bacteroides fragilis
Mice, Inbred C57BL
*Probiotics/therapeutic use
Mice, Inbred BALB C
*Antineoplastic Agents/adverse effects
Middle Aged
Fluorouracil/adverse effects
Feces/microbiology
Female
Aged

@article {pmid40624612,
year = {2025},
author = {De, T and Ma, T and Wang, W and An, X and Liu, D and Yin, H and Wang, Q and Zhao, T and Wang, H},
title = {Intestinal microbiota in adults with cholangiocarcinoma identifies the dysregulated Blautia species and bile acid metabolic pathways.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {506},
pmid = {40624612},
issn = {1471-230X},
support = {XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; },
mesh = {Humans ; *Cholangiocarcinoma/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Bile Duct Neoplasms/microbiology/metabolism ; *Bile Acids and Salts/metabolism ; Male ; Middle Aged ; Female ; Metabolic Networks and Pathways ; *Dysbiosis/microbiology ; *Clostridiales/genetics/isolation & purification ; Aged ; Case-Control Studies ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: Cholangiocarcinoma (CCA) represents a significant global health concern. The gut and bile microbiota, which can influence the gut-liver axis and disease progression, have not been thoroughly characterized in CCA patients.

METHODS: We selected two clinical centers at our hospital and collected stool samples from CCA patients and healthy controls (HC). These samples underwent whole-genome metagenomic shotgun sequencing, followed by analysis using both marker gene-based and assembly-based methods. Additionally, KEGG pathway enrichment was performed using the cholangiocarcinoma (CHOL) RNA-seq samples.

RESULTS: Our results revealed distinct dysbiosis of the gut microbiota in our regional CCA patients. The results revealed greater heterogeneity in the gut microbiome of CCA patients compared to HC samples. We found Blautia species to be significantly less abundant in CCA samples, and can distinguish CCA patients from HC. Blautia can also play a role in influencing the modification of secondary bile acids. Additionally, down-regulation of arachidonic acid and linoleic acid metabolism was observed in the tumor tissues of CHOL patients. In summary, the results revealed significant heterogeneity difference in the gut microbiome of CCA patients compared to HC samples, and detected the specifically decreased Blautia species in CCA patients, suggesting that Blautia may influence bile acid metabolic pathways. Further investigation is warranted to explore Blautia as a potential biomarker for CCA.},
}

Humans
*Cholangiocarcinoma/microbiology/metabolism
*Gastrointestinal Microbiome
*Bile Duct Neoplasms/microbiology/metabolism
*Bile Acids and Salts/metabolism
Male
Middle Aged
Female
Metabolic Networks and Pathways
*Dysbiosis/microbiology
*Clostridiales/genetics/isolation & purification
Aged
Case-Control Studies
Adult
Feces/microbiology

@article {pmid40624564,
year = {2025},
author = {Zhu, J and Jiang, MZ and Chen, X and Li, M and Wang, YL and Liu, C and Liu, SJ and Chen, WH},
title = {Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {161},
pmid = {40624564},
issn = {2049-2618},
support = {2022YFA1304100//Ministry of Science and Technology of the People's Republic of China/ ; 2022YFA1304100//Ministry of Science and Technology of the People's Republic of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bacteria/classification/isolation & purification/genetics/growth & development/metabolism ; *Microbial Interactions ; Coculture Techniques ; Metagenome ; Healthy Volunteers ; Feces/microbiology ; China ; },
abstract = {BACKGROUND: Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, there is a lack of large-scale experiments focusing on bacterial interactions within the human gut microbiome.

METHODS: We investigated the pairwise interactions of 113 bacterial strains isolated from healthy Chinese volunteers, selected for their high abundance and functional representation of the human gut microbiome. Using mGAM agar plates, a rich medium designed to maintain community structure, we established the "PairInteraX" dataset, which includes 3233 pair combinations of culturable human gut bacteria. This dataset was analyzed to identify interaction patterns and the key factors influencing these patterns.

RESULTS: Our analysis revealed that negative interactions were predominant among the bacteria in the PairInteraX dataset. When combined with in vivo gut metagenome datasets, we noted a diminishing mutualism and an increasing competition as microbial abundances increased; consequently, the maintenance of community diversity requires the participation of various types of interactions, especially the negative interactions. We also identified key factors influencing these interaction patterns including metabolic capacity and motility.

CONCLUSIONS: This study provides a comprehensive overview of pairwise bacterial interactions within the human gut microbiome, revealing a dominance of negative interactions. Besides, metabolic capacity and motility were identified as the key factors to influence the pairwise interaction patterns. This large-scale dataset and analysis offer valuable insights for further research on microbial community dynamics and their implications for host health. Video Abstract.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Bacteria/classification/isolation & purification/genetics/growth & development/metabolism
*Microbial Interactions
Coculture Techniques
Metagenome
Healthy Volunteers
Feces/microbiology
China

@article {pmid40624535,
year = {2025},
author = {Zhao, Y and Niu, X and Zhang, Y and Zhao, L and Zhang, L and He, J and Zhang, Q and Mao, Y and Wang, F and Zhao, X and Wang, R},
title = {Impact of supplementing Limosilactobacillus fermentum MN-LF23 on the eradication of Helicobacter pylori with 14-day standard quadruple therapy: a randomized, double-blind, placebo-controlled trial.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {106},
pmid = {40624535},
issn = {1475-2891},
support = {2022YFF1100100//National Key Research and Development Program of China/ ; 2022YFF1100100//National Key Research and Development Program of China/ ; 2022YFF1100100//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Probiotics/administration & dosage/therapeutic use ; Male ; Female ; *Helicobacter pylori/drug effects ; *Helicobacter Infections/drug therapy/microbiology/therapy ; Double-Blind Method ; Middle Aged ; Adult ; *Limosilactobacillus fermentum ; Drug Therapy, Combination ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; Feces/microbiology ; Treatment Outcome ; Gastrointestinal Microbiome ; Dietary Supplements ; Dyspepsia ; },
abstract = {BACKGROUND: The effect of probiotics on Helicobacter pylori (Hp) infection demonstrates considerable heterogeneity. This study aims to elucidate the role of Limosilactobacillus fermentum MN-LF23 (MN-LF23) in Hp-infected populations.

METHODS: A total of 94 adult patients with confirmed Hp infection were enrolled in this study and randomly allocated to the placebo or MN-LF23 group. Patients initially received either placebo or probiotics along with standard quadruple therapy for 2 weeks, followed by continued administration of either placebo or probiotics for an additional 4 weeks. The eradication of Hp, serum levels of inflammatory factors, and alterations in gastrointestinal symptoms were assessed at weeks 0, 2, and 6, while fecal samples were collected for metagenomic sequencing.

RESULTS: The results showed no significant difference (P = 1) in the eradication rate between the placebo group (85.11%) and the probiotic group (82.98%). Following treatment, the incidence of constipation, dyspepsia, and Gastrointestinal Symptom Rating Scale (GSRS) scores in the probiotic group were markedly lower (P < 0.05) compared to those observed in the placebo group. Throughout the treatment process, there were no significant differences in TNF-α and IL-1β levels between the two groups. Compared to the placebo group, the probiotic group exhibited a significant increase in beneficial bacteria such as Limosilactobacillus fermentum, Lactiplantibacillus plantarum, Bifidobacterium longum, Coprococcus caltus, and Clostridium butyricum.

CONCLUSION: MN-LF23 supplementation did not improve the eradication rate of standard quadruple therapy. However, it significantly reduced the overall GSRS score, improved digestive and constipation symptoms, and promoted the proliferation of beneficial bacteria in the intestine.},
}

Humans
*Probiotics/administration & dosage/therapeutic use
Male
Female
*Helicobacter pylori/drug effects
*Helicobacter Infections/drug therapy/microbiology/therapy
Double-Blind Method
Middle Aged
Adult
*Limosilactobacillus fermentum
Drug Therapy, Combination
Anti-Bacterial Agents/therapeutic use/administration & dosage
Feces/microbiology
Treatment Outcome
Gastrointestinal Microbiome
Dietary Supplements
Dyspepsia

@article {pmid40624250,
year = {2025},
author = {Fukuda, T and Takagaki, M and Kaimori, J and Motooka, D and Nakamura, S and Kawabata, S and Nakamura, H and Ozaki, T and Nakagawa, R and Matsumura, T and Teranishi, K and Yamazaki, H and Isaka, Y and Kishima, H},
title = {Differences in gut microbiome between autosomal dominant polycystic kidney disease with and without intracranial aneurysms.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24204},
pmid = {40624250},
issn = {2045-2322},
support = {22K09282//Japan Society for the Promotion of Science/ ; 21K09072//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Polycystic Kidney, Autosomal Dominant/microbiology/complications ; *Gastrointestinal Microbiome ; *Intracranial Aneurysm/microbiology/complications ; Female ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Adult ; Feces/microbiology ; Aged ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder characterized by cyst formation in the kidneys, and is associated with an elevated risk of intracranial aneurysms (IAs). Although a family history is a recognized risk factor for IAs in patients with ADPKD, emerging research suggests that gut microbiome composition may influence IA development. We investigated the relationship between the gut microbiome and the development of IA in patients with ADPKD. We recruited patients with ADPKD with (IA group) and without (non-IA group) IA from Osaka University between October 2021 and December 2023. Fecal samples were analyzed using 16S rRNA sequencing. Data were processed using the QIIME 2 pipeline to determine microbial diversity and composition. We included 60 patients: 26 in the IA and 34 in the non-IA groups. There were significant differences in microbial beta diversity between the groups. The IA group had higher abundances of Eubacterium siraeum group, Oscillibacter, Fournierella, Negativibacillus, Colidextribacter, and Adlercreutzia. The non-IA group had higher abundances of Bifidobacterium, Megamonas, Acidaminococcus, Megasphaera, and Merdibacter. There was a significant association between the gut microbiome composition and the presence of IAs in patients with ADPKD. Specific bacterial taxa were differentially abundant between patients with ADPKD with and without IAs, suggesting a potential role of the gut microbiome in the pathogenesis of IAs in this genetically predisposed population.},
}

Humans
*Polycystic Kidney, Autosomal Dominant/microbiology/complications
*Gastrointestinal Microbiome
*Intracranial Aneurysm/microbiology/complications
Female
Male
Middle Aged
RNA, Ribosomal, 16S/genetics
Adult
Feces/microbiology
Aged
Bacteria/genetics/classification/isolation & purification

@article {pmid40624236,
year = {2025},
author = {Wu, D and Niu, J and Hu, J and Wang, H and Kuang, H},
title = {Metabolomics combined with metagenomics analysis reveals the potential mechanism of Zhejiang psyllium polysaccharides against hyperuricemia in rats.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24180},
pmid = {40624236},
issn = {2045-2322},
mesh = {Animals ; *Hyperuricemia/drug therapy/metabolism/chemically induced/blood/pathology ; *Metagenomics/methods ; *Metabolomics/methods ; Rats ; Uric Acid/blood ; Gastrointestinal Microbiome/drug effects ; Male ; *Psyllium/pharmacology/chemistry ; *Polysaccharides/pharmacology/therapeutic use ; Rats, Sprague-Dawley ; Kidney/pathology/drug effects/metabolism ; Blood Urea Nitrogen ; Creatinine/blood ; },
abstract = {This study aimed to assess the anti-hyperuricemia efficacy of Zhejiang psyllium polysaccharides (ZPP) in rats and to explore its underlying mechanism. Hyperuricemia was induced by intragastric administration of potassium oxonate, hypoxanthine, and adenine. The serum levels of uric acid (UA), creatinine (Cr), and blood urea nitrogen (BUN) were measured, and kidney pathology was examined. Serum metabolomics was employed to monitor metabolic alterations following ZPP intervention. Metagenomic analysis was conducted to investigate the impact of ZPP on the intestinal flora of hyperuricemia rats. The results showed that ZPP could significantly reduce the serum UA level in hyperuricemia rats and exhibited a certain renal protective effect. The metabolomics results indicated that ZPP regulates uric acid levels in rats with hyperuricemia and ameliorates renal pathological changes by modulating biomarkers associated with purine metabolism, amino acid metabolism, and lipid metabolism. Metagenomic research also found that ZPP could increase the relative abundance of uric acid metabolism-related probiotics, such as Limosilactobacillus reuteri and Lactobacillus murinus, thereby improving intestinal flora imbalance in rats with hyperuricemia.},
}

Animals
*Hyperuricemia/drug therapy/metabolism/chemically induced/blood/pathology
*Metagenomics/methods
*Metabolomics/methods
Rats
Uric Acid/blood
Gastrointestinal Microbiome/drug effects
Male
*Psyllium/pharmacology/chemistry
*Polysaccharides/pharmacology/therapeutic use
Rats, Sprague-Dawley
Kidney/pathology/drug effects/metabolism
Blood Urea Nitrogen
Creatinine/blood

@article {pmid40557789,
year = {2025},
author = {Jones, KS and Pilliod, DS and Aunins, AW},
title = {Metabarcoding Analysis of Arthropod Pollinator Diversity: A Methodological Comparison of eDNA Derived From Flowers and DNA Derived From Bulk Samples of Insects.},
journal = {Molecular ecology},
volume = {34},
number = {14},
pages = {e70003},
doi = {10.1111/mec.70003},
pmid = {40557789},
issn = {1365-294X},
support = {//U.S. Bureau of Land Management/ ; //U.S. Geological Survey/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Pollination ; *Flowers/genetics ; Bees/genetics/classification ; *Biodiversity ; *DNA, Environmental/genetics ; *Arthropods/genetics/classification ; Sequence Analysis, DNA ; *Insecta/genetics/classification ; },
abstract = {Limitations of traditional insect sampling methods have motivated the development and optimisation of new non-lethal methods capable of quantifying diverse arthropod communities. Environmental DNA (eDNA) metabarcoding using arthropod-specific primers has recently been investigated as a novel way to characterise arthropod communities from the DNA they deposit on the surface of plants. This sampling method has had demonstrated success, but pollinators-especially bees-are oddly underrepresented in these studies. To evaluate this inconsistency, we investigated the limitations of eDNA metabarcoding for bees and other pollinators. We compared pollinator diversity derived from eDNA extracted from flowers and DNA extracted from pulverised bulk samples of insects collected from vane traps deployed at the same sites using three metabarcoding primers, two of which target arthropods generally (COI-Jusino and 16S-Marquina) and one that targets bumblebees (Bombus spp., COI-Milam). Across methods, we detected 77 insect families from 9 orders. The COI-Jusino marker amplified the highest taxonomic diversity compared to 16S-Marquina and COI-Milam. More amplicon sequence variants (ASVs) were recovered from vane traps (blue: 1357, yellow: 1542) than flowers (245), but only 23% of families and 13% of genera were shared among methods, indicating that flowers and blue and yellow vane traps may each sample different parts of the available arthropod community. Of 29 flower samples with known bee visitations, only 10 samples had bee detections from eDNA, and incomplete reference databases hindered assignment to species. Although our study provides additional evidence for the usefulness of eDNA metabarcoding for characterising arthropod communities, significant challenges remain when using eDNA metabarcoding methods to identify and quantify pollinator communities, especially bees.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Pollination
*Flowers/genetics
Bees/genetics/classification
*Biodiversity
*DNA, Environmental/genetics
*Arthropods/genetics/classification
Sequence Analysis, DNA
*Insecta/genetics/classification

@article {pmid40415184,
year = {2025},
author = {Sheyn, U and Poff, KE and Eppley, JM and Leu, AO and Bryant, JA and Li, F and Romano, AE and Burger, A and Barone, B and DeLong, EF},
title = {Mesoscale eddies shape Prochlorococcus community structure and dynamics in the oligotrophic open ocean.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf106},
pmid = {40415184},
issn = {1751-7370},
mesh = {*Prochlorococcus/genetics/classification/growth & development ; *Seawater/microbiology/chemistry ; Phylogeny ; Pacific Ocean ; Ecosystem ; Temperature ; *Microbiota ; Ecotype ; },
abstract = {Mesoscale eddies, horizontally rotating currents sometimes referred to as "ocean weather," influence open ocean macronutrient distributions, primary production, and microbial community structure. Such eddies impact ecosystems like the North Pacific Subtropical Gyre, where year-round thermal stratification limits the mixing of subsurface macronutrients with surface waters. Populations of the dominant primary producer Prochlorococcus in the North Pacific Subtropical Gyre consist of genetic variants with differential adaptive traits to light intensity, temperature, and macronutrient availability. How Prochlorococcus population variants respond to transient, localized environmental changes, however, remains an open question. Leveraging microbial community phylogenetic, metagenomic, and metatranscriptomic data, we report here a consistent, specific enrichment of Prochlorococcus high-light I ecotypes around the deep chlorophyll maximum (DCM) in cyclonic eddies, but not adjacent anticyclonic eddies. The shallower DCM depths of cyclones had lower temperatures, higher light intensities, and elevated nutrient concentrations compared to adjacent anticyclones, which favored Prochlorococcus high-light I ecotype proliferation. Prochlorococcus high-light I ecotypes in the cyclone DCM exhibited unique genetic traits related to nitrogen metabolism and were enriched in gene transcripts associated with energy production, cell replication, and proliferation. Prochlorococcus gene transcripts involved in amino acid transport, metabolism, and biosynthesis were also elevated in the cyclone. These results suggest the potential importance of nitrogen metabolism in Prochlorococcus high-light I ecotype proliferation in cyclonic eddies. Our findings demonstrate how mesoscale eddies shape microbial community structure in the oligotrophic ocean and how Prochlorococcus communities respond to short-term localized environmental variability.},
}

*Prochlorococcus/genetics/classification/growth & development
*Seawater/microbiology/chemistry
Phylogeny
Pacific Ocean
Ecosystem
Temperature
*Microbiota
Ecotype

@article {pmid40624115,
year = {2025},
author = {Liu, L and Wei, L and Mou, FX and Zhang, W and Wang, RF and Wang, Q and Wang, F},
title = {Oral microbiome dysbiosis in women with a history of pregnancy loss: a metagenomic cross-sectional study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24242},
pmid = {40624115},
issn = {2045-2322},
support = {Grant No. YJS-BD-19//the Special Fund for Doctoral Student Training of The Second Hospital of Lanzhou University in 2019/ ; Grant No. 071100107//The Science Foundation of Lanzhou University/ ; },
mesh = {Humans ; Female ; *Dysbiosis/microbiology ; Pregnancy ; Adult ; Cross-Sectional Studies ; Metagenomics/methods ; *Microbiota/genetics ; *Abortion, Spontaneous/microbiology ; Mouth Mucosa/microbiology ; Metagenome ; *Mouth/microbiology ; Young Adult ; },
abstract = {Pregnancy loss is a prevalent condition among women of reproductive age, significantly affecting fertility and psychological well-being. Despite advances in understanding the etiology of pregnancy loss, the role of the oral microbiome-its composition and metabolic activity-in influencing pregnancy outcomes remains underexplored. Previous studies have suggested that imbalances in the microbiota may contribute to adverse health outcomes, but few have investigated its association with pregnancy loss specifically. A total of 182 women of childbearing age were recruited for this study and divided into two groups: those with a history of pregnancy loss (n = 70) and a control group with no history of adverse pregnancy outcomes (n = 112). Clinical data and buccal mucosa samples were collected for metagenomic analysis. The inclusion of participants was based on their reproductive history, with particular attention to selecting women with at least one confirmed pregnancy loss and those with at least one successful live birth to serve as controls. The oral microbiota of women in the pregnancy loss group exhibited significantly lower richness and diversity compared to the control group (p < 0.05). Notably, specific genera such as Faecalibacterium, Roseburia, and Bacteroides were positively correlated with pregnancy loss, whereas Pseudomonas and Leptotrichia were correlated with it. These findings suggest a potential microbial dysbiosis associated with pregnancy loss. Our study identifies significant oral microbiota dysbiosis in women with pregnancy loss, characterized by reduced diversity and altered metabolic pathways. These findings underscore the potential role of oral microbial imbalance in adverse pregnancy outcomes. While our cross-sectional design and sample heterogeneity limit causal inference, they highlight the need for longitudinal cohorts and mechanistic studies. Future research integrating multi-niche microbiome profiling (e.g., gut and vaginal microbiota) is essential to unravel systemic interactions and advance targeted interventions for reproductive health.},
}

Humans
Female
*Dysbiosis/microbiology
Pregnancy
Adult
Cross-Sectional Studies
Metagenomics/methods
*Microbiota/genetics
*Abortion, Spontaneous/microbiology
Mouth Mucosa/microbiology
Metagenome
*Mouth/microbiology
Young Adult

@article {pmid40624015,
year = {2025},
author = {Wang, C and Zhang, L and Kan, C and He, J and Liang, W and Xia, R and Zhu, L and Yang, J and Jiang, X and Ma, W and Liang, Z and Xiao, Z and Zhang, J and Zhong, J and Sun, X and Chang, D and Wang, Z and Zhang, G and Li, M},
title = {Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {130},
pmid = {40624015},
issn = {2055-5008},
support = {Z211100002121135//Beijing Nova Program/ ; 32100098//National Natural Science Foundation of China/ ; 2021097//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; KCXFZ20211020163545004//Shenzhen Scientific and Technological Foundation/ ; SZZYSM202311009//Sanming Project of Medicine in Shenzen Municipality/ ; 2022YFA1304300//National Key Research and Development Program of China/ ; },
mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; *Respiratory Tract Infections/microbiology/diagnosis ; Oropharynx/microbiology ; *Respiratory System/microbiology ; },
abstract = {Metagenomic sequencing for respiratory pathogen detection faces two challenges: efficient host DNA depletion and the representativeness of upper respiratory samples for lower tract infections. In this study, we benchmarked seven host depletion methods, including a new method (F_ase), using bronchoalveolar lavage fluid (BALF), oropharyngeal swab (OP), and mock samples. All methods significantly increased microbial reads, species richness, genes richness, and genome coverage while reduced bacterial biomass, introduced contamination, and altered microbial abundance. Some commensals and pathogens, including Prevotella spp. and Mycoplasma pneumoniae, were significantly diminished. F_ase demonstrated the most balanced performance. High-resolution microbiomes profiling revealed distinct microbial niche preferences and microbiome disparities between the upper and lower respiratory tract. In pneumonia patients, 16.7% of high-abundance species (>1%) in BALF were underrepresented (<0.1%) in OP, highlighting OP's limitations as lower respiratory proxies. This study underscores both the potential and challenges of metagenomic sequencing in advancing microbial ecology and clinical research.},
}

Humans
Bronchoalveolar Lavage Fluid/microbiology
*Microbiota/genetics
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
*Respiratory Tract Infections/microbiology/diagnosis
Oropharynx/microbiology
*Respiratory System/microbiology

@article {pmid40621956,
year = {2025},
author = {Huang, X and Yang, L and Zhou, S and Zhong, L and Xu, G and Bi, M and Yang, X and Su, X and Rillig, MC},
title = {Plastic Biofilms as Hotspots of Nitrogen Cycling in Estuarine Ecosystems: Comparative Ecological, Genomic, and Transcriptomic Analysis Across Substrates.},
journal = {Global change biology},
volume = {31},
number = {7},
pages = {e70329},
doi = {10.1111/gcb.70329},
pmid = {40621956},
issn = {1365-2486},
support = {42021005//National Natural Science Foundation of China/ ; U23A20145//National Natural Science Foundation of China/ ; 2021-DST-004//Ningbo Municipal Science and Technology Innovative Research Team/ ; ANSO-PA-2023-18//Alliance of International Science Organizations/ ; },
mesh = {*Biofilms/growth & development ; *Plastics ; *Nitrogen Cycle ; *Estuaries ; Transcriptome ; Nitrogen/metabolism ; Ecosystem ; Seawater/microbiology ; Bacteria/metabolism/genetics ; Gene Expression Profiling ; Metagenome ; },
abstract = {Biofilms represent a ubiquitous microbial lifestyle that facilitates colonization, symbiosis, and nutrient cycling, shaping environmental chemical transformations. In the Anthropocene, the proliferation of artificial surfaces, particularly plastics, has introduced novel and artificial ecological niches for microbial colonization. However, the biogeochemical potential of biofilms on these emerging artificial substrates remains largely unknown. Here, using [15]N tracing, amplicon, metagenome, and metatranscriptomic sequencing, we explore nitrogen (N) potential biogeochemistry across artificial and natural biofilms as well as the bulk seawater. Our results reveal that plastic biofilms exhibit enhanced N transformation potential, including elevated nitrification (2~45-fold), denitrification (5~44-fold), and N2O production (3~13-fold) rates, compared to natural biofilms and ambient seawater. This functional shift corresponds to distinct microbial community structures, driven by active N-cycling taxa and metabolic pathway reconfigurations on plastic surfaces. We also observe that carbohydrate metabolism pathways, such as glycolysis and the pentose phosphate pathway, were highly expressed in plastic biofilms, with transcriptional levels of glk (encoding glucokinase) and PGK (encoding phosphoglycerate kinase) increased by 6- and 2-fold, respectively. Our findings depict the role of plastic biofilms as active participants in estuarine N cycling and underscore the broader implications of plastic pollution on ecosystem biogeochemistry.},
}

*Biofilms/growth & development
*Plastics
*Nitrogen Cycle
*Estuaries
Transcriptome
Nitrogen/metabolism
Ecosystem
Seawater/microbiology
Bacteria/metabolism/genetics
Gene Expression Profiling
Metagenome

@article {pmid40619813,
year = {2025},
author = {Sabih Ur Rehman, S and Nasar, MI and Mesquita, CS and Al Khodor, S and Notebaart, RA and Ott, S and Mundra, S and Arasardanam, RP and Muhammad, K and Alam, MT},
title = {Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/bib/bbaf323},
pmid = {40619813},
issn = {1477-4054},
support = {G00005310//UAEU-ZU/ ; G00004960//UPAR/ ; G00004540//UPAR/ ; G00004152//UPAR/ ; },
mesh = {Humans ; *Dysbiosis/microbiology ; *Systems Biology/methods ; *Microbiota ; Metagenomics ; Metabolomics ; Proteomics ; },
abstract = {Microbiomes are crucial for human health and well-being, with microbial dysbiosis being linked to various complex diseases. Therefore, understanding the structural and functional changes in the microbiome, along with the underlying mechanisms in disease conditions, is essential. In this review, we outline the structure and function of different human microbiomes and examine how changes in their composition may contribute to diseases. We highlight critical information associated with microbial dysbiosis and explore various therapeutic strategies for restoring a healthy microbiome, including microbiota transplantation, phage therapy, probiotics, prebiotics, dietary interventions, and drug-based approaches. Further, to better understand microbiome dysbiosis, we discuss multi-omics approaches including metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics, alongside computational modeling approaches such as ecological and metabolic network analysis. We outline key challenges associated with multi-omics techniques and emphasize the importance of integrative systems biology approaches that combine multi-omics data with computational modeling. These approaches are crucial for effectively analyzing microbiome data, providing deeper insights into species interactions and microbiome dynamics. Finally, we offer insights into future research directions in the field of microbiome research. This review makes a unique contribution to microbiome research by presenting a holistic framework that integrates multi-omics data with multi-scale modeling to elucidate microbial interactions, microbiome dysbiosis, and their modulation in disease-associated contexts.},
}

Humans
*Dysbiosis/microbiology
*Systems Biology/methods
*Microbiota
Metagenomics
Metabolomics
Proteomics

@article {pmid40617811,
year = {2025},
author = {Zhu, B and Liang, L and Chen, S and Li, H and Huang, Y and Wang, W and Zhang, H and Zhou, J and Xiong, D and Li, X and Li, J and Ning, Y and Shi, X and Wu, F and Wu, K},
title = {Multi-kingdom microbial changes and their associations with the clinical characteristics in schizophrenia patients.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {228},
pmid = {40617811},
issn = {2158-3188},
mesh = {Humans ; *Schizophrenia/microbiology/metabolism/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; Feces/microbiology ; Case-Control Studies ; Metabolic Networks and Pathways ; Fungi ; },
abstract = {Accumulating evidence has highlighted alterations in the gut microbiome in schizophrenia (SZ); however, the role of multi-kingdom microbiota in SZ remains inadequately understood. In this study, we performed metagenomic sequencing of fecal samples from 36 SZ patients and 55 healthy controls (HC) to profile bacterial, fungal, archaeal, and viral communities, along with functional pathways. We also conducted co-occurrence network analysis to explore the relationships among differential microbial species and metabolic pathways separately. Additionally, we assessed the associations of these differential species and functional pathways with clinical characteristics. Our findings revealed significant differences in species between SZ patients and HC, identifying not only 17 bacterial species, but also 8 fungal, 26 archaeal, and 19 viral species. Functional pathway analysis revealed 21 metabolic pathways significantly altered in SZ patients, including an increase in tryptophan metabolism, while biosynthesis of amino acids was decreased. Network analysis further uncovered more complex inter-kingdom interactions in SZ patients, with specific fungal species appearing exclusively in the SZ network. Importantly, significant associations were observed between microbial species and functional pathways with clinical characteristics, including symptom severity, cognitive function, and clinical biochemical marker. For instance, the abundance of Streptococcus vestibularis was positively correlated with homocysteine levels; the ubiquinone and other terpenoid-quinone biosynthesis was positively correlated with both symptom severity and C-reactive protein. Our findings reveal the intricate microbial dysbiosis present in SZ patients, suggesting multi-kingdom microbial interactions play a crucial role in SZ patients, highlighting promising avenues for potential diagnostic and therapeutic applications.},
}

Humans
*Schizophrenia/microbiology/metabolism/physiopathology
Male
Female
*Gastrointestinal Microbiome
Adult
Middle Aged
Feces/microbiology
Case-Control Studies
Metabolic Networks and Pathways
Fungi

@article {pmid40615957,
year = {2025},
author = {Durand, K and Ogier, JC and Nam, K},
title = {The evaluation of shotgun sequencing and rpoB metabarcoding for taxonomic profiling of bacterial communities.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {413},
pmid = {40615957},
issn = {1471-2180},
support = {ANR-10-LABX-04-01//Agence Nationale de la Recherche/ ; ANR-10-LABX-001-01//Agence Nationale de la Recherche/ ; ANR-16-IDEX-0006//Agence Nationale de la Recherche,France/ ; Resistome//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Bacteria/genetics/classification ; *DNA-Directed RNA Polymerases/genetics ; *Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; Computational Biology/methods ; Phylogeny ; *Microbiota/genetics ; Metagenomics/methods ; Bacterial Proteins/genetics ; High-Throughput Nucleotide Sequencing/methods ; Shotgun Sequencing ; },
abstract = {BACKGROUND: The importance of microbial community profiling has been increasingly recognized in biological and environmental research. While metabarcoding has been widely used for such analysis by targeting specific DNA sequences as markers, shotgun sequencing has been proposed as an alternative method because the analysis of whole genomes can potentially reduce biases introduced by targeted approaches. However, it is largely unknown whether shotgun sequencing may provide improved precision for qualitative taxonomic identification and quantitative abundance estimation compared with metabarcoding with housekeeping gene markers, such as the rpoB gene. Furthermore, the comparative performance of various bioinformatics pipelines for shotgun data analysis remains uncertain. In this study, we evaluated the performance of rpoB metabarcoding and shotgun sequencing coupled to various bioinformatic pipelines to describe the bacterial diversity of artificially generated mock bacterial communities, which included eukaryote gDNA intentional contamination or whole-genome amplification. For shotgun sequencing, the Assembly-Binning-Method and k-mer-based approaches were evaluated.

RESULTS: For taxonomic profiling, the Assembly-Binning-Method and rpoB metabarcoding exhibited comparable sensitivity and precision, whereas k-mer approaches produced a notably high number of false negatives. In some cases, the Assembly-Binning-Method improved taxonomic resolution compared with rpoB metabarcoding by identifying taxa at the species level rather than the genus level. Regarding the quantification of microbial composition, the Assembly-Binning-Method consistently showed a higher correlation with expected values ​​and a lower dissimilarity index than rpoB metabarcoding. The use of three sets of reference genomes to calculate depth coverage did not systematically affect the precision of the Assembly-Binning-Method.

CONCLUSIONS: These results demonstrate that although shotgun sequencing and rpoB metabarcoding have nearly equivalent accuracy in taxonomic profiling, shotgun sequencing has better taxonomic resolution and outperforms rpoB metabarcoding in quantitative estimation of microbial community abundance using the Assembly-Binning approach.},
}

*DNA Barcoding, Taxonomic/methods
*Bacteria/genetics/classification
*DNA-Directed RNA Polymerases/genetics
*Sequence Analysis, DNA/methods
DNA, Bacterial/genetics
Computational Biology/methods
Phylogeny
*Microbiota/genetics
Metagenomics/methods
Bacterial Proteins/genetics
High-Throughput Nucleotide Sequencing/methods
Shotgun Sequencing

@article {pmid40499078,
year = {2025},
author = {Xue, K and Wang, P and Lin, Q and Xie, J and Cong, L and Yan, Z},
title = {Uncovering the Single Amino-Acid Polymorphisms of the Human Gut Ecosystem.},
journal = {Journal of proteome research},
volume = {24},
number = {7},
pages = {3429-3446},
doi = {10.1021/acs.jproteome.5c00108},
pmid = {40499078},
issn = {1535-3907},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Polymorphism, Single Nucleotide ; *Amino Acids/genetics ; Metagenome/genetics ; Inflammatory Bowel Diseases/microbiology/genetics ; Diabetes Mellitus, Type 1/microbiology/genetics ; Proteome/genetics ; },
abstract = {Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation in the gut microbial metagenome and the host genome, but they could not adequately represent the protein-level variants. Single amino-acid polymorphisms (SAP) derived from nonsynonymous SNPs can cause functional changes of proteins and are important forces of adaption. However, SAP remains quite unexplored for the human gut microbiome. Here, we present a comprehensive large-scale analysis of SAP in the gut ecosystem, introducing a rigorous computational pipeline for detecting such protein variation from 992 published human metaproteomes. We find varied yet elaborate SAP patterns, capturing both known and novel functions and adaptive strategies of gut microbes. Microbial SAP is enriched in the outermost shell, motility devices, and ribosomes. Generally, gut microbial SAP is more convergent in metabolic subpathway regions and is enriched in the initial steps of carbohydrate metabolism pathways that catalyze the formation and isomerization of phosphorylated sugars. Furthermore, microbial and host mutant peptide patterns were altered and exhibited significant correlations in both inflammatory bowel disease and type 1 diabetes. Our results highlight the functional and clinically relevant implications and potential host-microbial interactions of gut ecosystem SAP.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Polymorphism, Single Nucleotide
*Amino Acids/genetics
Metagenome/genetics
Inflammatory Bowel Diseases/microbiology/genetics
Diabetes Mellitus, Type 1/microbiology/genetics
Proteome/genetics

@article {pmid40456384,
year = {2025},
author = {Nayyar, J and Bedu-Ferrari, C and Patangia, D and Hurley, E and Feeley, L and Ross, RP and Stanton, C and Brady, P},
title = {Gut and oral microbial profile associations to oral cancer.},
journal = {Journal of dentistry},
volume = {160},
number = {},
pages = {105848},
doi = {10.1016/j.jdent.2025.105848},
pmid = {40456384},
issn = {1879-176X},
mesh = {Humans ; *Mouth Neoplasms/microbiology/pathology ; Saliva/microbiology ; Male ; Female ; Middle Aged ; *Mouth/microbiology ; Aged ; *Microbiota ; *Gastrointestinal Microbiome ; Adult ; Fusobacterium nucleatum/isolation & purification ; Biomarkers, Tumor/analysis ; },
abstract = {The human microbiome is widely known to be associated with health and disease. The oral microbiome has been linked with oral diseases and infections, though not many studies have explored the relation between oral and gut microbiome with oral cancer based on lesion histology METHODS: This study uniquely explores the oral and gut microbiota in 30 participants (n = 30) divided into three groups based on histology; Benign (B) (n = 15), Potentially Malignant (PM) (n = 8), and Malignant (M) (n = 7) oral lesions. Using shotgun metagenomic sequencing, we analysed microbiota profiles to determine their potential as biomarkers for oral malignancy RESULTS: Distinct gut microbial profiles were observed between Benign and Malignant groups and the association of specific microbes in oral saliva, such as Haemophilus parainfluenzae, Veillonella parvula, Fusobacterium nucleatum and Rothia mucilaginosa were strongly associated with malignancy CONCLUSION: The data from this exploratory study suggest that oral and gut microbiomes could act as possible biomarkers and aid in early detection and assessment of oral cancer risk. With regard to potentially malignant lesions, future research could study individual Oral Potentially Malignant Disorders (OPMDs) as distinct entities due to the wide variation in clinical and histological presentation. Further research is required to develop definitive biomarkers in both potentially malignant and malignant oral lesions CLINICAL SIGNIFICANCE: While smoking and alcohol are known risk factors for oral cancer, a biomarker such as the saliva/stool microbiome profile could help identify a risk indicator or a potential risk factor. Additionally such a biomarker could help identify patients with OPMDs that are likely to undergo malignant transformation.},
}

Humans
*Mouth Neoplasms/microbiology/pathology
Saliva/microbiology
Male
Female
Middle Aged
*Mouth/microbiology
Aged
*Microbiota
*Gastrointestinal Microbiome
Adult
Fusobacterium nucleatum/isolation & purification
Biomarkers, Tumor/analysis

@article {pmid40015949,
year = {2025},
author = {Hu, M and Xu, Y and Wang, Y and Huang, Z and Wang, L and Zeng, F and Qiu, B and Liu, Z and Yuan, P and Wan, Y and Ge, S and Zhong, D and Xiao, S and Luo, R and He, J and Sun, M and Zhuang, X and Guo, N and Cui, C and Gao, J and Zhou, H and He, X},
title = {Gut microbial-derived N-acetylmuramic acid alleviates colorectal cancer via the AKT1 pathway.},
journal = {Gut},
volume = {74},
number = {8},
pages = {1230-1245},
doi = {10.1136/gutjnl-2024-332891},
pmid = {40015949},
issn = {1468-3288},
mesh = {*Colorectal Neoplasms/metabolism/microbiology ; Animals ; Humans ; *Gastrointestinal Microbiome/physiology ; Mice ; *Proto-Oncogene Proteins c-akt/metabolism ; *Muramic Acids/metabolism/pharmacology ; Male ; Signal Transduction ; Female ; Peptidoglycan/metabolism ; Disease Models, Animal ; Carcinogenesis ; Feces/chemistry/microbiology ; },
abstract = {BACKGROUND: Gut microbial metabolites are recognised as critical effector molecules that influence the development of colorectal cancer (CRC). Peptidoglycan fragments (PGFs) produced by microbiota play a crucial role in maintaining intestinal homeostasis, but their role in CRC remains unclear.

OBJECTIVE: Here, we aimed to explore the potential contribution of PGFs in intestinal tumourigenesis.

DESIGN: The relative abundance of peptidoglycan synthase and hydrolase genes was assessed by metagenomic analysis. Specific PGFs in the faeces and serum of CRC patients were quantified using targeted mass spectrometry. The effects of PGF on intestinal tumourigenesis were systematically evaluated using various murine models of CRC and organoids derived from CRC patients. Downstream molecular targets were screened and evaluated using proteome microarray, transcriptome sequencing and rescue assays.

RESULTS: Metagenomic analysis across seven independent cohorts (n=1121) revealed a comprehensive reduction in peptidoglycan synthase gene relative abundance in CRC patients. Targeted mass spectrometry identified significant depletion of a specific PGF, N-acetylmuramic acid (NAM) in CRC patients, which decreased as tumours progressed (p<0.001). NAM significantly inhibits intestinal tumourigenesis in various models, including Apc [Min/+], AOM/DSS-treated and MC38 tumour-bearing mice. Additionally, NAM inhibits the growth of patient-derived CRC organoids in a concentration-dependent manner. Mechanistically, NAM inhibits the activation of AKT1 by directly binding to it and blocking its phosphorylation, which is a partial mediator of NAM's anticancer effects.

CONCLUSION: The PGF NAM protects against intestinal tumourigenesis by targeting the AKT1 signalling pathway. NAM may serve as a novel potential preventive and therapeutic biomarker against CRC.},
}

*Colorectal Neoplasms/metabolism/microbiology
Animals
Humans
*Gastrointestinal Microbiome/physiology
Mice
*Proto-Oncogene Proteins c-akt/metabolism
*Muramic Acids/metabolism/pharmacology
Male
Signal Transduction
Female
Peptidoglycan/metabolism
Disease Models, Animal
Carcinogenesis
Feces/chemistry/microbiology

@article {pmid40615853,
year = {2025},
author = {Li, S and Xu, Z and Diao, H and Zhou, A and Tu, D and Wang, S and Feng, Y and Feng, X and Lai, Y and Yang, S and Tang, B},
title = {Gut microbiome alterations and hepatic encephalopathy post-TIPS in liver cirrhosis patients.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {745},
pmid = {40615853},
issn = {1479-5876},
mesh = {Humans ; *Hepatic Encephalopathy/microbiology/etiology/blood ; *Liver Cirrhosis/microbiology/surgery/complications ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *Portasystemic Shunt, Transjugular Intrahepatic/adverse effects ; Ammonia/blood ; Aged ; },
abstract = {BACKGROUND: The transjugular intrahepatic portosystemic shunt (TIPS), a crucial tool for treating complications related to portal hypertension in patients with liver cirrhosis, is often associated with an increased risk of postoperative complications such as hepatic encephalopathy. Accurate preoperative prediction of the risk of developing hepatic encephalopathy is critical for optimizing the rational clinical application of TIPS.

METHODS: In this study, stool samples from 67 patients were collected preoperatively and 1 month postoperatively and metagenomic sequencing was performed to assess the composition of the gut microbiota. The differential abundances of species and MetaCyc pathways were analyzed using microbiome multivariate associations with linear models. Correlations between variables, including species abundance, the MetaCyc pathway, and clinical characteristics, were assessed using the Pearson correlation test. Prognostic models were developed from metagenomic sequencing cohorts to predict hepatic encephalopathy (HE) and elevated blood ammonia levels.

RESULTS: We demonstrated that the abundance of Phocaeicola vulgatus increased after TIPS, and the urea cycle decreased. A positive correlation was observed between P.vulgatus and elevated blood ammonia levels (P < 0.05). Patients exhibiting increased blood ammonia after TIPS showed significant enrichment of P.vulgatus (LDA > 2.5), accompanied by a reduction in the urea cycle (P < 0.05) and associated enzymes (P < 0.05). Similar microbiota alterations were identified in patients who experienced postoperative hepatic encephalopathy. Furthermore, a comprehensive genetic profile of P.vulgatus was developed, highlighting its ability to increase amino acid metabolism. Many models have shown that the use of gut microbiota characteristics has greater predictive performance.

CONCLUSION: Multiple machine learning models revealed that P.vulgatus may serve as a significant predictive microbe for hepatic encephalopathy after TIPS, which may be closely related to its ability to metabolize ammonia. These findings establish a microbiome-based framework for postoperative complication risk stratification and personalized preoperative interventions and offer unexplored targets for future research.},
}

Humans
*Hepatic Encephalopathy/microbiology/etiology/blood
*Liver Cirrhosis/microbiology/surgery/complications
*Gastrointestinal Microbiome/genetics
Male
Female
Middle Aged
*Portasystemic Shunt, Transjugular Intrahepatic/adverse effects
Ammonia/blood
Aged

@article {pmid40570762,
year = {2025},
author = {Pateriya, D and Malwe, AS and Sharma, VK},
title = {CRCpred: An AI-ML tool for colorectal cancer prediction using gut microbiome.},
journal = {Computers in biology and medicine},
volume = {195},
number = {},
pages = {110592},
doi = {10.1016/j.compbiomed.2025.110592},
pmid = {40570762},
issn = {1879-0534},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Colorectal Neoplasms/microbiology/diagnosis ; *Machine Learning ; Deep Learning ; Algorithms ; },
abstract = {Colorectal cancer (CRC) is a leading cause of death worldwide. A plethora of research shows the alteration of the gut microbiome and the association of bacterial taxa with CRC. Gaining insights into the health status through microbiome-based diagnosis is a rapidly growing area of research. Many studies have utilized machine learning (ML) to leverage gut microbial dysbiosis for CRC screening, yet most have been limited by their training data and algorithms. Here, using 1728 publicly available metagenomic samples from 11 studies across eight countries, we developed a web-based tool, "CRCpred," employing ML and deep learning-based hybrid algorithms for CRC prediction. The XGBoost algorithm demonstrated the highest performance, achieving an average area under the curve (AUC) of 0.90 on the test and 0.91 on the validation datasets. Our results highlight the utility of CRCpred in predicting CRC and healthy status using gut bacterial species relative abundance profile. CRCpred is publicly available at https://metabiosys.iiserb.ac.in/crcpred.},
}

*Gastrointestinal Microbiome
Humans
*Colorectal Neoplasms/microbiology/diagnosis
*Machine Learning
Deep Learning
Algorithms

@article {pmid40615598,
year = {2025},
author = {Shah, M and Sieber, G and Deep, A and Beisser, D and Boenigk, J},
title = {Unravelling the temporal dynamics of community functions in protists induced by treated wastewater exposure using metatranscriptomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23957},
pmid = {40615598},
issn = {2045-2322},
mesh = {*Wastewater/microbiology ; *Transcriptome ; Ecosystem ; Fresh Water/microbiology ; *Eukaryota/genetics ; },
abstract = {The discharge of treated wastewater (TWW) into freshwater ecosystems poses a significant impact on microbial communities, particularly protists, which play a crucial role in nutrient cycling and ecosystem stability. While the ecological effects of TWW on microbial diversity have been studied, understanding the functional responses of protist communities remains limited. This study employs metatranscriptomics to unravel the temporal dynamics of protist community functions in response to TWW exposure. Using mesocosm experiment, water samples were analyzed over a ten-day period to monitor shifts in metabolic pathways and community interactions. Our results indicate that processed metatranscriptomic data, focusing on treatment-significant pathways, is more sensitive than traditional methods, such as meta-barcoding, and non-target screening, in detecting wastewater-induced perturbations. Early exposure to TWW significantly altered expression of pathways associated with signal transduction and environmental interaction, while general metabolic pathways showed resilience. Over time, the protist community showed signs of adaptation with expression levels stabilizing towards the end of the experiment. This study underscores the importance of focussing on functional shifts rather than just taxonomic changes for assessing wastewater impacts on freshwater ecosystems. Our findings advocate for the use of metatranscriptomics as a robust indicator for TWW detection, aiding in development of targeted environmental management strategies.},
}

*Wastewater/microbiology
*Transcriptome
Ecosystem
Fresh Water/microbiology
*Eukaryota/genetics

@article {pmid40615445,
year = {2025},
author = {Di Gloria, L and Casbarra, L and Lotti, T and Ramazzotti, M},
title = {Testing the limits of short-reads metagenomic classifications programs in wastewater treating microbial communities.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23997},
pmid = {40615445},
issn = {2045-2322},
mesh = {*Wastewater/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Sewage/microbiology ; *Metagenome ; },
abstract = {Biological wastewater treatment processes, such as activated sludge (AS) and aerobic granular sludge (AGS), have proven to be crucial systems for achieving both efficient waste purification and the recovery of valuable resources like poly-hydroxy-alkanoates. Gaining a deeper understanding of the microbial communities underpinning these technologies would enable their optimization, ultimately reducing costs and increasing efficiency. To support this research, we quantitatively compared classification methods differing in read length (raw reads, contigs and MAGs), overall search approach (Kaiju, Kraken2, RiboFrame and kMetaShot), as well as source databases to assess the classification performances at both the genus and species levels using an in silico-generated mock community designed to provide a simplified yet comprehensive representation of the complex microbial ecosystems found in AS and AGS. Particular attention was given to the misclassification of eukaryotes as bacteria and vice versa, as well as the occurrence of false negatives. Notably, Kaiju emerged as the most accurate classifier at both the genus and species levels, followed by RiboFrame and kMetaShot. However, our findings highlight the substantial risk of misclassification across all classifiers and databases, which could significantly hinder the advancement of these technologies by introducing noises and mistakes for key microbial clades.},
}

*Wastewater/microbiology
*Metagenomics/methods
*Bacteria/genetics/classification
*Microbiota/genetics
Sewage/microbiology
*Metagenome

@article {pmid40613581,
year = {2025},
author = {Dang, T and Lysenko, A and Boroevich, KA and Tsunoda, T},
title = {VBayesMM: variational Bayesian neural network to prioritize important relationships of high-dimensional microbiome multiomics data.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/bib/bbaf300},
pmid = {40613581},
issn = {1477-4054},
support = {JP20H03240//JSPS KAKENHI/ ; JP24K15175//JSPS KAKENHI/ ; JPMJCR2231//JST CREST/ ; },
mesh = {Bayes Theorem ; *Microbiota ; *Neural Networks, Computer ; *Metagenomics/methods ; Humans ; *Computational Biology/methods ; Algorithms ; Multiomics ; },
abstract = {The analysis of high-dimensional microbiome multiomics datasets is crucial for understanding the complex interactions between microbial communities and host physiological states across health and disease conditions. Despite their importance, current methods, such as the microbe-metabolite vectors approach, often face challenges in predicting metabolite abundances from microbial data and identifying keystone species. This arises from the vast dimensionality of metagenomics data, which complicates the inference of significant relationships, particularly the estimation of co-occurrence probabilities between microbes and metabolites. Here we propose the variational Bayesian microbiome multiomics (VBayesMM) approach, which aims to improve the prediction of metabolite abundances from microbial metagenomics data by incorporating a spike-and-slab prior within a Bayesian neural network. This allows VBayesMM to rapidly and precisely identify crucial microbial species, leading to more accurate estimations of co-occurrence probabilities between microbes and metabolites, while also robustly managing the uncertainty inherent in high-dimensional data. Moreover, we have implemented variational inference to address computational bottlenecks, enabling scalable analysis across extensive multiomics datasets. Our large-scale comparative evaluations demonstrate that VBayesMM not only outperforms existing methods in predicting metabolite abundances but also provides a scalable solution for analyzing massive datasets. VBayesMM enhances the interpretability of the Bayesian neural network by identifying a core set of influential microbial species, thus facilitating a deeper understanding of their probabilistic relationships with the host.},
}

Bayes Theorem
*Microbiota
*Neural Networks, Computer
*Metagenomics/methods
Humans
*Computational Biology/methods
Algorithms
Multiomics

@article {pmid40613164,
year = {2025},
author = {Zhang, QL and Dong, LL and Zhang, LL and Wu, YJ and Li, M and Bo, J and Wang, LL and Jing, Y and Dou, LP and Liu, DH and Gu, ZY and Gao, CJ},
title = {[Characteristics of Gut Microbiota Changes and Their Relationship with Infectious Complications During Induction Chemotherapy in AML Patients].},
journal = {Zhongguo shi yan xue ye xue za zhi},
volume = {33},
number = {3},
pages = {738-744},
doi = {10.19746/j.cnki.issn.1009-2137.2025.03.017},
pmid = {40613164},
issn = {1009-2137},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Leukemia, Myeloid, Acute/drug therapy/microbiology ; *Induction Chemotherapy ; Feces/microbiology ; Male ; Female ; Middle Aged ; },
abstract = {OBJECTIVE: To investigate the characteristics of gut microbiota changes in patients with acute myeloid leukemia (AML) undergoing induction chemotherapy and to explore the relationship between infectious complications and gut microbiota.

METHODS: Fecal samples were collected from 37 newly diagnosed AML patients at four time points: before induction chemotherapy, during chemotherapy, during the neutropenic phase, and during the recovery phase. Metagenomic sequencing was used to analyze the dynamic changes in gut microbiota. Correlation analyses were conducted to assess the relationship between changes in gut microbiota and the occurrence of infectious complications.

RESULTS: During chemotherapy, the gut microbiota α-diversity (Shannon index) of AML patients exhibited significant fluctuations. Specifically, the diversity decreased significantly during induction chemotherapy, further declined during the neutropenic phase (P < 0.05, compared to baseline), and gradually recovered during the recovery phase, though not fully returning to baseline levels.The abundances of beneficial bacteria, such as Firmicutes and Bacteroidetes, gradually decreased during chemotherapy, whereas the abundances of opportunistic pathogens, including Enterococcus, Klebsiella, and Escherichia coli, progressively increased.Analysis of the dynamic changes in gut microbiota of seven patients with bloodstream infections revealed that the bloodstream infection pathogens could be detected in the gut microbiota of the corresponding patients, with their abundance gradually increasing during the course of infection. This finding suggests that bloodstream infections may be associated with opportunistic pathogens originating from the gut microbiota.Compared to non-infected patients, the baseline samples of infected patients showed a significantly lower relative abundance of Bacteroidetes (P < 0.05). Regression analysis indicated that Bacteroidetes abundance is an independent predictive factor for infectious complications (P < 0.05, OR =13.143).

CONCLUSION: During induction chemotherapy in AML patients, gut microbiota α-diversity fluctuates significantly, and the abundance of opportunistic pathogens increase, which may be associated with bloodstream infections. Patients with lower baseline Bacteroidetes abundance are more prone to infections, and its abundance can serve as an independent predictor of infectious complications.},
}

Humans
*Gastrointestinal Microbiome
*Leukemia, Myeloid, Acute/drug therapy/microbiology
*Induction Chemotherapy
Feces/microbiology
Male
Female
Middle Aged

@article {pmid40604345,
year = {2025},
author = {Kang, JW and Khatib, LA and Heston, MB and Dilmore, AH and Labus, JS and Deming, Y and Schimmel, L and Blach, C and McDonald, D and Gonzalez, A and Bryant, M and Ulland, TK and Johnson, SC and Asthana, S and Carlsson, CM and Chin, NA and Blennow, K and Zetterberg, H and Rey, FE and , and Kaddurah-Daouk, R and Knight, R and Bendlin, BB},
title = {Gut microbiome compositional and functional features associate with Alzheimer's disease pathology.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {7},
pages = {e70417},
doi = {10.1002/alz.70417},
pmid = {40604345},
issn = {1552-5279},
support = {U01AG061359/AG/NIA NIH HHS/United States ; U19AG063744/AG/NIA NIH HHS/United States ; R01AG070973/AG/NIA NIH HHS/United States ; R01AG083883/AG/NIA NIH HHS/United States ; #S10 OD026929/GF/NIH HHS/United States ; //Vilas Early-Career Investigator Award/ ; #2023-00356//Swedish Research Council/ ; #2022-01018//Swedish Research Council/ ; #2019-02397//Swedish Research Council/ ; #101053962//European Union's Horizon Europe research and innovation programme/ ; #ALFGBG-71320//Swedish State Support for Clinical Research/ ; #201809-2016862//Alzheimer Drug Discovery Foundation (ADDF)/ ; #ADSF-21-831376-C//AD Strategic Fund and the Alzheimer's Association/ ; #ADSF-21-831381-C//AD Strategic Fund and the Alzheimer's Association/ ; #ADSF-21-831377-C//AD Strategic Fund and the Alzheimer's Association/ ; #ADSF-24-1284328-C//AD Strategic Fund and the Alzheimer's Association/ ; #22HLT07//European Partnership on Metrology co-financed from the European Union's Horizon Europe Research and Innovation Programme and by the Participating States/ ; //Bluefield Project/ ; //Cure Alzheimer's Fund/ ; //Olav Thon Foundation/ ; //Erling-Persson Family Foundation/ ; #FO2022-0270//Familjen Rönströms Stiftelse, Stiftelsen för Gamla Tjänarinnor, Hjärnfonden, Sweden/ ; #860197//European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie/ ; JPND2021-00694//European Union Joint Programme-Neurodegenerative Disease Research/ ; UKDRI-1003//NIH and Care Research University College London Hospitals Biomedical Research Centre and the UK Dementia Research Institute at UCL/ ; },
mesh = {Humans ; *Alzheimer Disease/microbiology/pathology/cerebrospinal fluid ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Aged ; Biomarkers/cerebrospinal fluid ; Feces/microbiology ; Metagenomics ; Amyloid beta-Peptides/cerebrospinal fluid ; Aged, 80 and over ; },
abstract = {BACKGROUND: The gut microbiome is a potentially modifiable risk factor for Alzheimer's disease (AD); however, understanding of its composition and function regarding AD pathology is limited.

METHODS: Shallow-shotgun metagenomics was used to analyze the fecal microbiome of participants in the Wisconsin Microbiome in Alzheimer's Risk Study, leveraging clinical data and cerebrospinal fluid (CSF) biomarkers. Differential abundance and ordinary least squares regression analyses were performed to find differentially abundant gut microbiome features and their associations with CSF biomarkers of AD and related pathologies.

RESULTS: Gut microbiome composition and function differed between individuals with and without AD dementia. The compositional difference was replicated in an independent cohort. Differentially abundant gut microbiome features were associated with CSF biomarkers of AD and related pathologies.

DISCUSSION: These findings enhance our understanding of alterations in gut microbial composition and function in AD, and suggest that gut microbes and their pathways are linked to AD pathology.

HIGHLIGHTS: Gut microbiome composition and function differ between people with Alzheimer's disease (AD) dementia and cognitively unimpaired (CU) individuals. Co-occurring gut microbes show differential abundance across AD-related groups (AD vs CU, amyloid status+ vs amyloid status-, and apolipoprotein E (APOE) ε4 status+ vs APOE ε4 status-). Gut microbiome composition also differs between people with AD dementia and CU individuals in a larger validation cohort. Differentially abundant gut microbiome composition and function between AD and CU groups are correlated with cerebrospinal fluid biomarkers for AD and related pathologies.},
}

Humans
*Alzheimer Disease/microbiology/pathology/cerebrospinal fluid
*Gastrointestinal Microbiome/physiology
Male
Female
Aged
Biomarkers/cerebrospinal fluid
Feces/microbiology
Metagenomics
Amyloid beta-Peptides/cerebrospinal fluid
Aged, 80 and over

@article {pmid40604089,
year = {2025},
author = {Das, B and Desai, M and Bhagora, NJ and Koringa, P and Pathan, M and Thakor, JC and Savaliya, FP and Adil, S and Hati, S},
title = {Influence of fermented whey protein fractions on the growth performance, haematological traits, serum biochemistry, faecal and caeca microbiota of broiler chickens.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23678},
pmid = {40604089},
issn = {2045-2322},
mesh = {Animals ; *Chickens/growth & development/microbiology/blood ; *Whey Proteins/pharmacology/metabolism ; *Feces/microbiology ; Fermentation ; Animal Feed ; *Gastrointestinal Microbiome/drug effects ; Dietary Supplements ; *Cecum/microbiology ; Male ; Limosilactobacillus fermentum/metabolism ; Female ; },
abstract = {Nowadays researchers and consumers are concerned about antibiotic resistance in poultry products causing antibiotic-resistant pathogens. Here, we investigated the effects of fermented whey peptides (FWP) with Limosilactobacillus fermentum (M4) as a nutraceutical supplement on growth performance, blood parameters, relative organs, and metagenomic analysis of broiler chickens, aiming to develop substitute for antibiotics in poultry feeds. An active culture of Lactobacillus fermentum (M4, GenBank Accession Number: MF951096) was inoculated into sterilized cheese whey at a rate of 2% (v/v) (10[7] CFU/ml) and incubated at 37 °C for 48 h. Ninety-six one-day-old mixed-sex commercial broiler chicks were randomly assigned in a Completely Randomized Design (CRD) experiment with four treatments, each having four replicates of six broiler chickens (6 × 4 × 4). One millilitre of liquid FWP fractions (> 10 kDa, < 10 kDa, and < 3 kDa) was freshly prepared and administered daily to the respective groups along with the basal diet from the 8th to the 15th day. Our current study revealed that supplementation with FWPs to broiler diets had no significant (p < 0.05) impact on body weight and FCR but numerically FCR value was high in control group. Blood cholesterol was significantly reduced in FWP fed groups. FWP had no significant impact on various blood parameters but influenced leukocytes and platelets. Metagenomic analysis showed no significant differences in microbial proportions. Histological analysis revealed no organ toxicity. The current findings suggest that broiler diets can substitute FWP for antibiotics to improve the growth performance and birds' health, without posing any biohazards. Furthermore, FWPs provide a variety of health benefits, potentially improving the health of humans who consume broiler meat or eggs.},
}

Animals
*Chickens/growth & development/microbiology/blood
*Whey Proteins/pharmacology/metabolism
*Feces/microbiology
Fermentation
Animal Feed
*Gastrointestinal Microbiome/drug effects
Dietary Supplements
*Cecum/microbiology
Male
Limosilactobacillus fermentum/metabolism
Female

@article {pmid40604039,
year = {2025},
author = {Meng, K and Bao, Y and Chen, G and Qu, J and Liang, S and An, S and Chen, Y and Liu, X and Fu, X},
title = {Metagenomics and transcriptomics analysis of aspartame's impact on gut microbiota and glioblastoma progression in a mouse model.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23298},
pmid = {40604039},
issn = {2045-2322},
support = {GNK2023ZX06//Guangxi Academy of Agricultural Science and Technology Development Project/ ; GK-AA22117015-3//the Guangxi Major Science and Technology Program/ ; GNK2021YT117//Guangxi Academy of Agricultural Sciences Basic Research Project/ ; 2019E016//Guangdong 3D Orthopedics Biomimetic Translational Medicine Engineering Technology Research Center/ ; },
mesh = {Animals ; *Aspartame/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Glioblastoma/pathology/genetics/microbiology ; Mice ; Disease Models, Animal ; *Metagenomics/methods ; Disease Progression ; Gene Expression Profiling ; *Transcriptome/drug effects ; *Brain Neoplasms/pathology/genetics/microbiology ; Humans ; Gene Expression Regulation, Neoplastic/drug effects ; Male ; Sweetening Agents/pharmacology ; },
abstract = {Aspartame, a widely used artificial sweetener, has been extensively studied for its potential health effects. Emerging evidence suggests that aspartame intake may directly impact the composition and function of the intestinal microbiota, which could subsequently influence the risk, progression, and treatment of glioblastoma multiforme (GBM) within the tumor microenvironment. However, it remains unclear whether aspartame intake affects intestinal flora, gene expression, and epigenetic regulation during tumor progression. To address these gaps in knowledge, we conducted a comprehensive metagenomics and transcriptomics analysis of aspartame's impact on gut microbiota and glioblastoma progression in a mouse model. Using a well-established mouse model and a rigorous metagenomics and transcriptomics approach, our results demonstrated that although the aspartame diet did not significantly affect tumor growth, it induced changes in the composition of the gut microbiota, particularly a decrease in the relative abundance of the Rikenellaceae family. Additionally, key N6-methyladenosine (m[6]A)-regulated genes, such as cyclin-dependent kinase inhibitor 1A (CDKN1A), MYC (myelocytomatosis) oncogene, and transforming growth factor-β (TGFB1), were significantly upregulated in GBM tumors exposed to aspartame. Notably, the expression of TGFB1 (transforming growth factor-β) suggested a critical role in the progression of GBM mediated by aspartame-induced m[6]A modifications. Our integrative analysis offered novel perspectives on the intricate interplay between dietary aspartame intake, gut microbiota, and tumor biology.},
}

Animals
*Aspartame/pharmacology
*Gastrointestinal Microbiome/drug effects/genetics
*Glioblastoma/pathology/genetics/microbiology
Mice
Disease Models, Animal
*Metagenomics/methods
Disease Progression
Gene Expression Profiling
*Transcriptome/drug effects
*Brain Neoplasms/pathology/genetics/microbiology
Humans
Gene Expression Regulation, Neoplastic/drug effects
Male
Sweetening Agents/pharmacology

@article {pmid40603380,
year = {2025},
author = {Wang, R and Wang, J and Wang, L and Cai, Y and Wang, Y and Luo, H and Chen, B and Chen, J and Fang, J and Song, Z},
title = {A novel eco-friendly Acinetobacter strain A1-4-2 for bioremediation of aquatic pollutants.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23207},
pmid = {40603380},
issn = {2045-2322},
support = {2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; },
mesh = {*Acinetobacter/metabolism/genetics/isolation & purification/classification ; *Biodegradation, Environmental ; Animals ; *Water Pollutants, Chemical/metabolism ; Zebrafish ; Phylogeny ; Metagenomics ; },
abstract = {The increasing accumulation of hydrocarbons and aromatic compounds in aquatic ecosystems, stemming from anthropogenic activities, poses severe ecological challenges, including disrupting biodiversity and threatening human health through the food chain. This study presents Acinetobacter strain A1-4-2, isolated from a hairy crab farming base, which could represent a novel Acinetobacter species. The metagenomic analysis of approximately 12,000 publicly available datasets revealed that this novel Acinetobacter species is widely distributed across various environments, particularly in those with high organic matter content, such as sludge, feces, and wastewater. Strain A1-4-2 exhibited exceptional metabolic capabilities, effectively degrading a diverse range of substrates, including amino acids, organic acids, oils, n-alkanes, lignin, and aromatic monomers. Genomic analysis, coupled with biological experiments, revealed that strain A1-4-2 exhibited resistance to a very limited kind of antibiotics. Moreover, the strain's biosafety, affirmed through zebrafish toxicity assays, underscores its suitability for environmental release. Additionally, the feasibility of genetic manipulation of strain A1-4-2 gives it the potential to become a chassis cell, enabling it to degrade organic pollutants more efficiently through genetic engineering. Our findings elucidate the strain's genomic and metabolic attributes, offering insights into its biodegradation potentials and developing effective strategies for ecological restoration in face of pollution.},
}

*Acinetobacter/metabolism/genetics/isolation & purification/classification
*Biodegradation, Environmental
Animals
*Water Pollutants, Chemical/metabolism
Zebrafish
Phylogeny
Metagenomics

@article {pmid40555791,
year = {2025},
author = {Lin, S and Sun, Z and Zhu, X and Wang, M and Zhang, Q and Qian, J and Zhang, H and Mei, Z and Pu, Y and Kong, M and Guo, P and Zhou, X and Li, J and Sun, X and Ma, L and Zhang, X and Zhao, F and Nie, J and Hong, S and Chen, J and Wang, X and Li, X and Zheng, Y},
title = {Segatella copri and gut microbial ammonia metabolism contribute to chronic kidney disease pathogenesis.},
journal = {Nature microbiology},
volume = {10},
number = {7},
pages = {1684-1697},
pmid = {40555791},
issn = {2058-5276},
mesh = {*Ammonia/metabolism ; *Renal Insufficiency, Chronic/microbiology/pathology/metabolism ; *Gastrointestinal Microbiome/physiology ; Animals ; Mice ; Humans ; Aged ; Aged, 80 and over ; Escherichia coli/genetics/metabolism ; Male ; Female ; Metagenome ; Kidney ; Mice, Inbred C57BL ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Alterations in gut microbiota have been linked to chronic kidney disease (CKD), but large-scale studies and mechanistic insights are limited. Here we analysed gut metagenome data from 1,550 older individuals (aged 65-93 years) with comprehensive kidney function measurements. Segatella copri was positively associated with kidney function through microbial ammonia metabolism-related pathways and the asnA gene, which encodes an ammonia-assimilating enzyme. These associations were replicated in two external studies. In mice, ammonia supplementation increased serum levels of creatinine and blood urea nitrogen, accelerating CKD progression. In vitro cultures of S. copri or asnA-overexpressing Escherichia coli reduced ammonia concentrations, which was markedly attenuated in asnA-knockout S. copri. Gavage of either S. copri or asnA-overexpressing E. coli, but not asnA-knockout S. copri, mitigated ammonia-induced CKD progression in mice. These findings highlight the role of gut microbial ammonia metabolism in CKD pathogenesis and underscore the therapeutic potential of microbial-based interventions.},
}

*Ammonia/metabolism
*Renal Insufficiency, Chronic/microbiology/pathology/metabolism
*Gastrointestinal Microbiome/physiology
Animals
Mice
Humans
Aged
Aged, 80 and over
Escherichia coli/genetics/metabolism
Male
Female
Metagenome
Kidney
Mice, Inbred C57BL
Bacterial Proteins/genetics/metabolism

@article {pmid40542287,
year = {2025},
author = {Fierer, N and Leung, PM and Lappan, R and Eisenhofer, R and Ricci, F and Holland, SI and Dragone, N and Blackall, LL and Dong, X and Dorador, C and Ferrari, BC and Goordial, J and Holmes, SP and Inagaki, F and Korem, T and Li, SS and Makhalanyane, TP and Metcalf, JL and Nagarajan, N and Orsi, WD and Shanahan, ER and Walker, AW and Weyrich, LS and Gilbert, JA and Willis, AD and Callahan, BJ and Shade, A and Parkhill, J and Banfield, JF and Greening, C},
title = {Guidelines for preventing and reporting contamination in low-biomass microbiome studies.},
journal = {Nature microbiology},
volume = {10},
number = {7},
pages = {1570-1580},
pmid = {40542287},
issn = {2058-5276},
support = {SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; RGY0058/2022//Human Frontier Science Program (HFSP)/ ; },
mesh = {*Microbiota/genetics ; Humans ; Biomass ; *Metagenomics/methods/standards ; Specimen Handling/standards/methods ; *DNA Contamination ; Guidelines as Topic ; },
abstract = {Numerous important environments harbour low levels of microbial biomass, including certain human tissues, the atmosphere, plant seeds, treated drinking water, hyper-arid soils and the deep subsurface, with some environments lacking resident microbes altogether. These low microbial biomass environments pose unique challenges for standard DNA-based sequencing approaches, as the inevitability of contamination from external sources becomes a critical concern when working near the limits of detection. Likewise, lower-biomass samples can be disproportionately impacted by cross-contamination and practices suitable for handling higher-biomass samples may produce misleading results when applied to lower microbial biomass samples. This Consensus Statement outlines strategies to reduce contamination and cross-contamination, focusing on marker gene and metagenomic analyses. We also provide minimal standards for reporting contamination information and removal workflows. Considerations must be made at every study stage, from sample collection and handling through data analysis and reporting to reduce and identify contaminants. We urge researchers to adopt these recommendations when designing, implementing and reporting microbiome studies, especially those conducted in low-biomass systems.},
}

*Microbiota/genetics
Humans
Biomass
*Metagenomics/methods/standards
Specimen Handling/standards/methods
*DNA Contamination
Guidelines as Topic

@article {pmid40387372,
year = {2025},
author = {Lei, Z and Zhang, H and Liu, W and Sheng, J and Zhang, H and Wang, Y and Tang, Y and Wang, H and Ding, C and Qiao, W and Zhu, Y and Yang, G and Zhang, Y and Liu, Z and Zhou, N and Hu, C and Zhao, X},
title = {Dynamic and Stable Core Microbiota Assist Plants in Enriching Selenium and Reducing Cadmium Absorption.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {12},
number = {25},
pages = {e00862},
pmid = {40387372},
issn = {2198-3844},
support = {2023YFD1900904//National Key Research and Development Program of China/ ; SKLEG2024225//State Key Laboratory of Environmental Geochemical/ ; 23567601H//State Key Laboratory of North China Crop Improvement and Regulation, S&T Program of Hebei/ ; 24XJTRZW13//Xinjiang Key Laboratory of Soil and Plant Ecological Processes/ ; WY22B04//Wuhan Municipal Health Commission/ ; Grants KJ2025-5//2025 Science and Technology Project of Hubei Geological Bureau/ ; Grants 2023AFD215//Hubei Provincial Natural Science Foundation and Hubei Geological Bureau of China/ ; D20234501//Science and Technology Research Project of Hubei Province/ ; 23xjz05R//Hubei Polytechnic University/ ; },
mesh = {*Selenium/metabolism ; *Cadmium/metabolism ; Rhizosphere ; *Microbiota/physiology/genetics ; Soil Microbiology ; *Brassica napus/metabolism/microbiology ; Soil/chemistry ; Plant Roots/metabolism/microbiology ; Metagenomics ; },
abstract = {Rhizosphere microbiome is crucial for regulating rhizosphere complex nutrient dynamics. However, mechanisms by which plants regulate rhizosphere microbes to manage nutrient availability under coexisting beneficial and harmful elements remain unclear. This study focuses on the rhizosphere microbiome of Brassica napus in different naturally selenium (Se)-cadmium (Cd)-rich soils, the functionality of this rhizosphere, and the changes in the availability of rhizosphere nutrients. Microbiome analysis, metagenomics, genomic analysis, strain isolation, and functional validation are performed to investigate these relationships. Results show that a significant negative correlation is observed between the rhizosphere available Se and Cd content across the plant whole growth cycle and identified a group of core microbiota that are highly positively correlated with available Se and negatively correlated with available Cd. Genomics and metagenomics analyses reveal that the core microbiota has a higher substrate preference for amino acids related to the glutathione metabolic pathway. Key glutathione-related-amino acids and synthetic microbial community significantly improve the expression of glutathione anabolism and related amino acid transport genes and enhance Se uptake and reduce Cd absorption in plants grown in various Se-Cd-rich soils. This study provides insights into the mechanisms of root-associated microbes responding to complex soil nutrients during plant growth.},
}

*Selenium/metabolism
*Cadmium/metabolism
Rhizosphere
*Microbiota/physiology/genetics
Soil Microbiology
*Brassica napus/metabolism/microbiology
Soil/chemistry
Plant Roots/metabolism/microbiology
Metagenomics

@article {pmid40329496,
year = {2025},
author = {Rose, S and Johnson, H and Cartozzo, C and Swall, J and Simmons, T and Singh, B},
title = {Testing the efficacy of surface swab sampling to determine postmortem submersion interval (PMSI), using the microbiome colonization of skeletal remains.},
journal = {Journal of forensic sciences},
volume = {70},
number = {4},
pages = {1261-1273},
pmid = {40329496},
issn = {1556-4029},
mesh = {Animals ; *Postmortem Changes ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Swine ; *Specimen Handling/methods ; *Immersion ; DNA, Bacterial ; *Water Microbiology ; Models, Animal ; *Bone and Bones/microbiology ; },
abstract = {Postmortem interval (PMI) estimation contributes valuable information in the medicolegal investigation of decomposed human remains, and estimating the postmortem submersion interval (PMSI) can specifically aid investigations involving victims discovered in aquatic environments. Microbial succession-driven models in long-term decomposition studies have utilized the abundant colonizing bacterial community of skeletal remains to estimate the PMSI using bone powder. This study investigates the use of bone surface swabbing as an effective alternative method that minimizes time and resources required for bone sampling and also provides a highly replicable method for decomposition studies. Skeletal porcine (Sus scrofa) remains were caged and submerged in both lentic and lotic environments (Henley Lake in White Hall and James River at the Rice Rivers Center in Charles City, respectively) in Central Virginia from November 2017 to November 2018. Bone surface swabs and water samples were analyzed at 500 accumulated degree days (ADD) intervals, from baseline (0 ADD) to 4500 ADD. Variable region 4 (V4) of 16S rDNA was amplified and sequenced using the Illumina MiSeq Sequencing platform and analyzed using Mothur (v.1.39.5) and R (v.4.04). Analysis of Molecular Variance (AMOVA) indicated a significant difference in bacterial community structure among and between the swab, bone, and water samples (p < 0.001, F = 7.92331), and among and between lake and river samples (p < 0.001, F = 9.38829). PMSI models were constructed using random forest models for lake swabs (R[2] = 0.83, RMSE = 623.24) and river swabs (R[2] = 0.83, RMSE = 580.2). Swab samples from both aquatic environments predicted PMSI, albeit slightly less accurately than those previously reported from bone powder (lake: R[2] = 0.96, 334.1; river: R[2] = 0.94, 498.47).},
}

Animals
*Postmortem Changes
RNA, Ribosomal, 16S/genetics
*Microbiota
Swine
*Specimen Handling/methods
*Immersion
DNA, Bacterial
*Water Microbiology
Models, Animal
*Bone and Bones/microbiology

@article {pmid40170447,
year = {2025},
author = {Veríssimo, J and Lopes-Lima, M and Amaral, F and Chaves, C and Fernandes, V and Kemanja, M and Teixeira, A and Martins, FMS and Beja, P},
title = {Navigating Methodological Trade-Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14082},
pmid = {40170447},
issn = {1755-0998},
support = {2020.03608.CEECIND//Fundação para a Ciência e a Tecnologia/ ; COVID/BD/152600/2022//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/133159/2017//Fundação para a Ciência e a Tecnologia/ ; UIDP/50027/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0048/2020//Fundação para a Ciência e a Tecnologia/ ; NORTE-01-0246-FEDER-000063//European Regional Development Fund (ERDF)/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Animals ; *DNA, Environmental/genetics ; *Metagenomics/methods ; Mediterranean Region ; *Vertebrates/classification/genetics ; *Environmental Monitoring/methods ; },
abstract = {Environmental DNA (eDNA) metabarcoding technologies promise significant advances in biodiversity monitoring, yet their application requires extensive optimisation and standardisation. Recent research demonstrated that increased sampling and analytical efforts are needed to improve biodiversity estimates, though fully optimising study designs is often hindered by resource constraints. Consequently, researchers must carefully navigate methodological trade-offs to design effective eDNA metabarcoding monitoring studies. We conducted a water eDNA survey of vertebrates in a Mediterranean watershed to identify key methodological factors influencing species richness and composition estimates. We examined the impacts of using high- versus low-capacity filtration capsules, varying levels of biological and technical replication, and the pooling of PCR replicates before indexing. The primary sources of variation identified were capsule filtration capacity and site replication across the watershed. While biological replication within sites and PCR replication also improved biodiversity estimates, their effects were comparatively smaller. Pooling PCR replicates before indexing performed more poorly than analysing them independently. Methodological impacts were stronger on terrestrial than on aquatic species. Based on these results, we recommend that priority should be given to high-capacity filtration and sampling across multiple sites. Site-level replication deserves lower priority, especially when filtering large water volumes. PCR replication is crucial for detecting rare species but should be balanced with increased site sampling and eventually site-level replication. Avoiding the pooling of PCR replicates is important to enhance sensitivity for rare species. Overall, we stress the importance of balancing methodological choices with resource constraints and monitoring goals, and we emphasise the need for research assessing methodological trade-offs in different study systems.},
}

*DNA Barcoding, Taxonomic/methods
*Biodiversity
Animals
*DNA, Environmental/genetics
*Metagenomics/methods
Mediterranean Region
*Vertebrates/classification/genetics
*Environmental Monitoring/methods

@article {pmid40079420,
year = {2025},
author = {Jurburg, SD},
title = {Short Read Lengths Recover Ecological Patterns in 16S rRNA Gene Amplicon Data.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14102},
pmid = {40079420},
issn = {1755-0998},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Metagenomics/methods ; Microbiota ; Animals ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {16S rRNA gene metabarcoding, the study of amplicon sequences of the 16S rRNA gene from mixed environmental samples, is an increasingly popular and accessible method for assessing bacterial communities across a wide range of environments. As metabarcoding sequence data archives continue to grow, data reuse will likely become an important source of novel insights into the ecology of microbes. While recent work has demonstrated the benefits of longer read lengths for the study of microbial communities from 16S rRNA gene segments, no studies have explored the use of shorter (< 200 bp) read lengths in the context of data reuse. Nevertheless, this information is essential to improve the reuse and comparability of metabarcoding data across existing datasets. This study reanalyzed nine 16S rRNA datasets targeting aquatic, animal-associated and soil microbiomes, and evaluated how processing the sequence data across a range of read lengths affected the resulting taxonomic assignments, biodiversity metrics and differential (i.e., before-after treatment) analyses. Short read lengths successfully recovered ecological patterns and allowed for the use of more sequences. Limited increases in resolution were observed beyond 150 bp reads across environments. Furthermore, abundance-weighted diversity metrics (e.g., Inverse Simpson index, Morisita-Horn dissimilarities or weighted Unifrac distances) were more robust to variation in read lengths. Read lengths alone contributed to consistent increases in the total number of ASVs detected, highlighting the need to consider metabarcoding-derived diversity estimates within the context of the bioinformatics parameters selected. This study provides evidence-based guidelines for the processing of short reads.},
}

*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
*Metagenomics/methods
Microbiota
Animals
*DNA Barcoding, Taxonomic/methods
Biodiversity
Computational Biology/methods
Sequence Analysis, DNA/methods

@article {pmid40071381,
year = {2025},
author = {da Silva, LP and Porto, M and Amorim, F and Beja, P and Mata, VA},
title = {Beware of Plant DNA in Animal Dietary Metabarcoding: Lessons From a Strictly Insectivorous Bat.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14100},
doi = {10.1111/1755-0998.14100},
pmid = {40071381},
issn = {1755-0998},
support = {CEECIND/02064/2017//Fundação para a Ciência e a Tecnologia/ ; CEECIND/02547/2020//Fundação para a Ciência e a Tecnologia/ ; DL57/2016/CP1440/CP1646/CT0018//Fundação para a Ciência e a Tecnologia/ ; NORTE-01-0246-FEDER-000063//European Regional Development Fund/ ; SR20/1575//British Ecological Society/ ; },
mesh = {*Chiroptera/physiology ; Animals ; *DNA Barcoding, Taxonomic/methods ; *DNA, Plant/genetics/isolation & purification ; Feces/chemistry ; *Plants/genetics/classification ; *Diet ; *Metagenomics/methods ; Arthropods ; },
abstract = {DNA metabarcoding is increasingly used in dietary studies, but it has limitations, such as detecting nonfood taxa. This issue is frequently mentioned in the literature but poorly understood, limiting interpretation of results and mitigation strategies. We evaluate the extent and sources of nonfood plant DNA in dietary metabarcoding, based on 281 faecal samples of a strictly insectivorous bat. We modelled plant taxa detections in relation to pollination syndromes, flowering and fruiting phenology and habitat associations, and we estimated co-occurrences between plants and arthropods. The bat arthropod diet was consistent with previous studies. Plants were detected in 82.9% of samples, representing 148 taxa, and all pollination syndromes evaluated. Plant detections were more frequent during their flowering periods, particularly for those with mixed pollination syndromes, suggesting a relationship between flowering and detectability. Fruiting had a positive, albeit weaker, effect. There was a tendency for more frequent detection of forest plants and less frequent detection of plants associated with riparian and agricultural habitats. Co-occurrences between arthropods and plants were weak and inconsistent. Our results highlight the potential for widespread detection of nonfood plant DNA in metabarcoding studies, calling for great care when analysing the plant component of diets. Specifically, we recommend: (i) implementing strategies for reducing plant contamination during field sampling; (ii) using multiple field and lab negative controls; and (iii) using ancillary information (e.g., sample visual inspection and literature review) to aid interpretation of metabarcoding results. Moreover, we recommend that studies reporting plant consumption results greatly diverging from dietary patterns obtained through other methods should include detailed explanations of methodological steps taken to exclude the confounding effects of nonfood plant DNA.},
}

*Chiroptera/physiology
Animals
*DNA Barcoding, Taxonomic/methods
*DNA, Plant/genetics/isolation & purification
Feces/chemistry
*Plants/genetics/classification
*Diet
*Metagenomics/methods
Arthropods