@article {pmid41138002,
year = {2025},
author = {Yarahmadi, A and Emrahoglu, S and Afkhami, H and Mehdipour, A and Aghaali, M},
title = {Integrative insights into the oral microbiome's role in systemic diseases: novel therapeutic strategies and future directions.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {178},
pmid = {41138002},
issn = {1572-9699},
mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; Periodontal Diseases/microbiology/therapy ; Dental Caries/microbiology/therapy ; Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The oral microbiome, which is known as the diverse and abundant microbial community within the human oral cavity, is an integral part of the human body. The investigation of its composition and functions in both wellness and illness has received notable attention from researchers in recent times. The presence of oral bacteria directly impacts the disease condition of dental caries and periodontal diseases. The oral microbiota interacts dynamically with the host to influence immune regulation and metabolic processes. Advances in sequencing technologies, including whole-metagenome shotgun sequencing, the examination of 16S ribosomal RNA, and meta-transcriptomes, we now possess the capability to comprehensively explore the diversity and functionalities of oral microorganisms, encompassing those that are not amenable to cultivation. As research advances, there is a growing body of evidence suggesting the notable contribution of the oral microbiome to various health conditions, extending beyond ailments solely associated with the oral cavity. This review advances current understanding by presenting a systemic, integrative perspective on the oral microbiome's role in chronic diseases, offering novel hypotheses and therapeutic directions beyond those explored in prior literature.},
}

Humans
*Microbiota
*Mouth/microbiology
Periodontal Diseases/microbiology/therapy
Dental Caries/microbiology/therapy
Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics

@article {pmid41137523,
year = {2025},
author = {Tegegne, HA and Savidge, TC},
title = {Gut microbiome metagenomics in clinical practice: bridging the gap between research and precision medicine.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2569739},
doi = {10.1080/19490976.2025.2569739},
pmid = {41137523},
issn = {1949-0984},
mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Precision Medicine/methods ; },
abstract = {Gut microbiome metagenomics is emerging as a cornerstone of precision medicine, offering exceptional opportunities for improved diagnostics, risk stratification, and therapeutic development. Advances in high-throughput sequencing have uncovered robust microbial signatures linked to infectious, inflammatory, metabolic, and neoplastic diseases. Clinical applications now include pathogen detection, antimicrobial resistance profiling, microbiota-based therapies, and enterotype-guided patient stratification. However, translation into routine care is hindered by significant barriers including methodological variability, limited functional annotation, lack of bioinformatics standardization, and underrepresentation of global populations. This review synthesizes current translational strategies, emphasizing the need for hypothesis-driven designs, multi-omic integration, longitudinal and multi-center cohorts, and mechanistic validation. We also examine critical ethical, regulatory, and equity considerations shaping the clinical landscape. Realizing the full potential of microbiome-informed care will require globally harmonized standards, cross-sector collaboration, and inclusive frameworks that ensure scientific rigor and equitable benefit.},
}

Humans
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Precision Medicine/methods

@article {pmid41137517,
year = {2025},
author = {Bayne, J and Charavaryamath, C and Hu, Y and Yousefi, F and Murphy, M and Law, A and Michael, A and Muyyarikkandy, MS and Nibbering, B and Smits, WK and Kuijper, E and Opriessnig, T and Sauer, M and Scaria, J and Sponseller, B and Ramirez, A and Mooyottu, S},
title = {The swine IsoLoop model of the gut host-microbiota interface enables intra-animal treatment comparisons to advance 3R principles.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2568706},
doi = {10.1080/19490976.2025.2568706},
pmid = {41137517},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Swine ; Ileum/microbiology/surgery ; *Host Microbial Interactions ; Humans ; Feces/microbiology ; Clostridioides difficile/physiology ; Fecal Microbiota Transplantation ; Bacteria/classification/genetics/isolation & purification ; Models, Animal ; Disease Models, Animal ; },
abstract = {Understanding gut-host microbiota interactions requires models that replicate human physiology while providing region-specific resolution, translational precision, and minimal animal use. To this end, we developed the IsoLoop model, a swine gut loop platform enabling intra-animal, multi-treatment comparisons. Microbiota-depleted ileal loops were surgically created in pigs, maintaining neurovascular integrity while isolating them from the anastomosed digestive tract. In Experiment 1, loops were inoculated with human fecal microbiota (HFM) or HFM combined with Peptacetobacter hiranonis. In Experiment 2, they were inoculated with Clostridioides difficile. Host-microbiota interactions were compared with respective controls in each experiment. The IsoLoop model reduced animal use by 75% compared to conventional whole-animal designs. Following antibiotic-induced depletion, loops re-established microbial diversity by day 5, despite reduced richness and loss of taxa, including Lactobacillus. HFM transplantation in microbiota-depleted loops induced robust transcriptomic recovery, enriched Akkermansia and Bifidobacterium, and restored specific metabolic pathways, although taxonomic and metabolic restoration remained incomplete and divergent. P. hiranonis promoted normal ileum-like metagenomic functional convergence, activated epithelial repair pathways, and increased specific secondary bile acids. C. difficile challenge recapitulated early infection pathology in IsoLoops. The IsoLoop model offers an ethical and precise platform for investigating host-microbiota crosstalk, localized enteric pathologies, and therapeutic interventions.},
}

Animals
*Gastrointestinal Microbiome/physiology
Swine
Ileum/microbiology/surgery
*Host Microbial Interactions
Humans
Feces/microbiology
Clostridioides difficile/physiology
Fecal Microbiota Transplantation
Bacteria/classification/genetics/isolation & purification
Models, Animal
Disease Models, Animal

@article {pmid41137068,
year = {2025},
author = {Asin, ICA and Egana, JMC and Paul, RE and Bautista, MAM},
title = {Virome sequencing and analysis of Aedes aegypti and Aedes albopictus from ecologically different sites in the Philippines.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {426},
pmid = {41137068},
issn = {1756-3305},
mesh = {Animals ; *Aedes/virology ; Philippines ; *Virome/genetics ; *Mosquito Vectors/virology ; Metagenomics ; Phylogeny ; *Insect Viruses/genetics/classification/isolation & purification ; },
abstract = {BACKGROUND: Aedes aegypti and Aedes albopictus are important vectors of arthropod-borne viruses (arboviruses) such as dengue, chikungunya, and Zika. Changes in land use have long been considered a factor in the emergence of infectious diseases; thus, it is imperative to look at how the diversity of viruses is also affected by land use.

METHODS: Viral metagenomics was used to determine the virome compositions of 260 Ae. aegypti and 75 Ae. albopictus collected from the three study sites in Los Baños, Laguna, Philippines, that differ in topography and land use transformations.

RESULTS: The virome of Ae. aegypti and Ae. albopictus revealed virus sequences belonging to 12 different taxon groups, dominated by insect-specific viruses (ISVs) such as Phasi Charoen-like phasivirus (PCLV), Humaita Tubiacanga virus (HTV), and Wenzhou sobemo-like virus 4 (WSLV4). Both species were found to share the majority of identified viruses. Moreover, a relatively higher number of viral families were observed in sites that had undergone transformation from agriculture to bare and built-up areas, compared with a forest site.

CONCLUSIONS: The findings of this study underscore the vast diversity of Ae. aegypti and Ae. albopictus viruses from the selected sites in the Philippines generated by viromics. Results also impact the understanding that land use may contribute to virus diversity. The prevalence of ISVs and nondetection of arboviruses in the virome composition of Ae. aegypti and Ae. albopictus were notable, suggesting further examination of the roles of ISVs in arbovirus transmission.},
}

Animals
*Aedes/virology
Philippines
*Virome/genetics
*Mosquito Vectors/virology
Metagenomics
Phylogeny
*Insect Viruses/genetics/classification/isolation & purification

@article {pmid41136898,
year = {2025},
author = {Junier, T and Palmieri, F and Ubags, ND and Trompette, A and Koutsokera, A and Junier, P and Pagni, M and Neuenschwander, S},
title = {Prevalence of oxalotrophy in the human microbiome.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {954},
pmid = {41136898},
issn = {1471-2164},
support = {40B2-0_194701//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; GRS-064/18//Gebert Rüf Stiftung/ ; },
mesh = {Humans ; *Oxalates/metabolism ; *Microbiota/genetics ; Metagenome ; Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; },
abstract = {BACKGROUND: Incomplete degradation of oxalate, a compound commonly found in the diet, can lead to disease in humans, particularly affecting the kidneys. The concentration of oxalate in the body depends on several factors, one of which is intestinal absorption-an aspect influenced by oxalotrophy among enteric bacteria. Despite its potential significance, oxalotrophy in the human microbiome remains poorly understood.

RESULTS: In this study, we conducted a systematic search for the co-occurrence of three key oxalotrophy genes-frc, oxc, and oxlT. We developed and validated specific conservation models for each gene and applied them to genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. Our analysis revealed that oxalotrophy, defined as the capacity to use oxalate as an energy source, is a rare metabolic trait predominantly confined to the gut. We also found evidence that this capacity can be acquired via horizontal gene transfer.

CONCLUSIONS: While oxalotrophy is relatively uncommon, the broader capacity for oxalate degradation is more widespread. Notably, the genes frc and oxc are frequently found in close proximity within genomes, suggesting a selective advantage for organisms possessing this capability. Incomplete degradation of oxalate, a compound commonly found in the diet, can cause disease in humans, particularly affecting the kidney. Its concentration in the body depends on several factors, one of which is intestinal absorption, which is itself affected by oxalotrophy among enteric bacteria. Oxalotrophy in the human microbiome is poorly known. In this study, we perform a systematic search for the simultaneous presence of the three oxalotrophy genes, namely frc, oxc and oxlT. Thanks to the construction and validation of specific conservation models for all three genes, we were able to search for oxalotrophy in genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. We report that oxalotrophy-the capacity to use oxalate as an energy source-is a rare metabolic trait, mostly confined to the gut, and also find evidence that it can be acquired by horizontal gene transfer. By contrast, the capacity for oxalate degradation is more widespread, and two genes responsible for it (frc and oxc) are almost always close together in the genome, suggesting selection pressure.},
}

Humans
*Oxalates/metabolism
*Microbiota/genetics
Metagenome
Gene Transfer, Horizontal
*Bacteria/genetics/metabolism

@article {pmid40848995,
year = {2025},
author = {Wang, J and Xue, L and Zhang, M and Shen, P and Zhao, W and Tong, Q and Wu, S and Dai, W and Yang, X and Wang, H},
title = {Colonoscopic fecal microbiota transplantation for Mild-to-Moderate Parkinson's Disease: A randomized controlled trial.},
journal = {Brain, behavior, and immunity},
volume = {130},
number = {},
pages = {106086},
doi = {10.1016/j.bbi.2025.106086},
pmid = {40848995},
issn = {1090-2139},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; Male ; Female ; Middle Aged ; *Parkinson Disease/therapy/microbiology ; Aged ; Double-Blind Method ; Quality of Life ; *Colonoscopy/methods ; Feces/microbiology ; Treatment Outcome ; Gastrointestinal Microbiome/physiology ; Constipation ; },
abstract = {OBJECTIVE: Growing evidence supports the efficacy and safety of fecal microbiota transplantation (FMT) in treating Parkinson's disease (PD). Fecal microbiota are commonly transplanted via oral capsules, a nasojejunal tube, or colonoscopy, but freezing often decreases the diversity and viability of transplanted microbiota. This single-center, double-blind, randomized, placebo-controlled trial aims to explore the efficacy and safety of fresh FMT via colonoscopy in dealing with PD.

METHODS: Thirty patients with mild-to-moderate PD (Hoehn-Yahr stage I-III) were randomly assigned into the FMT group (fresh FMT via colonoscopy) and placebo group (saline injection via colonoscopy) in a 1:1 ratio. Motor and non-motor symptoms, constipation, quality of life, cognitive function, emotional state and sleep quality were assessed using relevant scales. Fecal samples were harvested before and at 4, 8 and 12 weeks after treatment for metagenomic and metabolomics analyses.

RESULTS: A total of 30 patients with mild-to-moderate PD were enrolled in the present study, involving 18 males and 12 females with a median age of 68 years, a median age of onset of 63.5 years, and a median disease duration of 3 years. At 12 weeks, scores of the UPDRS Ⅲ (group × time effect, B =  - 8.80 [-13.79, -3.81]), PAC-QOL (group × time effect, B =  - 29.67 [-45.35, -13.98]), UPDRS Ⅱ (group × time effect, B =  - 5.07 [-8.85, -1.28]), NMSS (group × time effect, B =  - 35.60 [-53.59, -17.61]), PDQ-39 (group × time effect, B =  - 17.80 [-28.21, -7.39]), HAMA (group × time effect, B =  - 1.66 [-2.92, -0.40]), and HAMD (group × time effect, B =  - 1.33 [-2.49, -0.16]) were significantly reduced in the FMT group, while CSBM per week (group × time effect, B = 3.03 [1.42, 4.63]) and the Bristol Stool Scale score (group × time effect, B = 1.95 [0.12, 3.79]) significantly increased (all P < 0.05). Significant alterations were seen in the gut microbiota and fecal metabolites in the FMT group. No adverse events were observed during the follow-up period.

CONCLUSION: Fresh FMT via colonoscopy is a safe and well-tolerated procedure for treating mild-to-moderate PD. It effectively alleviates motor and non-motor symptoms, thus facilitating defecation and improving the quality of life. These effects can be maintained for a minimum of 12 weeks and may be attributed to the optimization of gut microbiota and fecal metabolites.},
}

Humans
*Fecal Microbiota Transplantation/methods
Male
Female
Middle Aged
*Parkinson Disease/therapy/microbiology
Aged
Double-Blind Method
Quality of Life
*Colonoscopy/methods
Feces/microbiology
Treatment Outcome
Gastrointestinal Microbiome/physiology
Constipation

@article {pmid40835054,
year = {2025},
author = {Wu, Y and Tao, S and Xiao, L and Zhang, J and Tang, Y and Zhang, M and Liu, S and Huang, Y and Liu, Y and Xie, M and Zhao, Z and Lv, Q and Cai, J and Pei, K and Ma, Q and Yin, Y and Dai, M and Wei, M and Chen, Y and Wang, Q},
title = {Gut virome alterations in schizophrenia: identifying viral biomarkers associated with schizophrenia and treatment response.},
journal = {Brain, behavior, and immunity},
volume = {130},
number = {},
pages = {106080},
doi = {10.1016/j.bbi.2025.106080},
pmid = {40835054},
issn = {1090-2139},
mesh = {Humans ; *Schizophrenia/virology/drug therapy/microbiology ; Male ; Female ; Adult ; *Gastrointestinal Microbiome/physiology ; *Virome/physiology ; Feces/virology ; Biomarkers ; Treatment Outcome ; Young Adult ; Antipsychotic Agents/therapeutic use ; },
abstract = {BACKGROUND: The gut virome is an important component of the microbiome with potential implications for schizophrenia. However, its role in disease pathology and treatment response remains unclear.

METHODS: We performed metagenomic sequencing on fecal samples from 49 first-episode schizophrenia patients and 49 healthy controls. Viral diversity and taxonomic profiles were compared between groups. Within patients, we assessed associations between viral alpha diversity and symptom severity, as well as between specific viral taxa and treatment outcomes, including short- and long-term PANSS reduction and response trajectories. Response trajectories were identified by clustering patients based on the longitudinal PANSS reduction patterns.

RESULTS: There were no significant differences in alpha diversity between schizophrenia patients and healthy controls. Among patients, higher viral diversity was associated with more severe negative symptoms. Although several viral taxa showed nominal associations with schizophrenia, none remained significant after FDR correction. Regarding treatment outcomes, the abundance of Brigitvirus was negatively associated with the 6-week symptom reduction rate (FDR = 0.012), and two viral species were reduced in the low-response trajectory group.

CONCLUSIONS: Although virome differences between patients with schizophrenia and healthy controls were modest, associations between viral features and both symptom severity and treatment response indicate potential clinical relevance.},
}

Humans
*Schizophrenia/virology/drug therapy/microbiology
Male
Female
Adult
*Gastrointestinal Microbiome/physiology
*Virome/physiology
Feces/virology
Biomarkers
Treatment Outcome
Young Adult
Antipsychotic Agents/therapeutic use

@article {pmid41136439,
year = {2025},
author = {Xue, W and Liu, Z and Zhang, Y and Raza, W and Li, Y and Jiang, L and Tao, Y and Qian, J and Alexandre, J and Zhao, FJ and Xu, Y and Sedlazeck, F and Shen, Q and Jiang, G and Wei, Z},
title = {LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9353},
pmid = {41136439},
issn = {2041-1723},
mesh = {*Metagenome/genetics ; *Metagenomics/methods ; *Microbiota/genetics ; Humans ; Cluster Analysis ; Gastrointestinal Microbiome/genetics ; *Software ; Algorithms ; },
abstract = {Long-read sequencing has transformed metagenomics and improved the quality of metagenome-assembled genomes (MAGs). However, current binning methods struggle with identifying unknown species and managing imbalanced species distributions. Here, we present LorBin, an unsupervised binner specially designed to reconstruct MAGs in natural microbiomes. LorBin deploys a two-stage multiscale adaptive DBSCAN and BIRCH clustering with evaluation decision models using single-copy genes to maximize MAG recovery. LorBin outperforms six competing binners in both simulated and real microbiomes, including oral, gut, and marine samples. LorBin generated 15-189% more high-quality MAGs with high serendipity and identified 2.4-17 times more novel taxa than state-of-the-art binning methods. Together, LorBin is a promising long-read metagenomic binner for accessing species-rich samples containing unknown taxa and is efficient at retrieving more complete genomes from imbalanced natural microbiomes.},
}

*Metagenome/genetics
*Metagenomics/methods
*Microbiota/genetics
Humans
Cluster Analysis
Gastrointestinal Microbiome/genetics
*Software
Algorithms

@article {pmid41131658,
year = {2025},
author = {Li, Z and Luo, W and Xie, H and Mo, C and Qin, B and Zhao, Y and Chen, X and Zhang, S and Zhao, Y and Wang, M and Yang, Y and Cai, J and Wang, B and Liu, X and Shi, Y},
title = {Reovirus infection results in rice rhizosphere microbial community reassembly through metabolite-mediated recruitment and exclusion.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {214},
pmid = {41131658},
issn = {2049-2618},
mesh = {*Oryza/virology/microbiology ; *Rhizosphere ; *Reoviridae/physiology/pathogenicity ; Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota ; Metagenomics/methods ; *Plant Diseases/virology/microbiology ; Metabolomics/methods ; },
abstract = {BACKGROUND: Microbial assembly plays a critical role in ecosystem function and biodiversity. While numerous studies have explored the effect of abiotic factors on the belowground community assembly, much less is known about the role of biotic interactions, particularly viral infections, in shaping microbial communities. Southern rice black-streaked dwarf virus (SRBSDV), a member of the Fijivirus genus in the Reoviridae family, has caused severe yield losses in rice due to its rapid transmission. However, its specific effects on rhizosphere microbiota and the dynamics of microbial community changes have not been fully elucidated.

RESULTS: By leveraging metabolomics with amplicon and metagenomics, this study provided a comprehensive understanding of the effect of SRBSDV infection on the rhizosphere microbial community and their functions. The results revealed that SRBSDV invasion led to significant changes in rhizosphere metabolites and microbial assembly processes. Specifically, the estimated overdispersion of cations sharply decreased following viral infection, while anion levels decreased markedly during early infection and then increased rapidly after 15 days. Key taxa, such as methanotrophs (e.g., Methylomicrobium), nitrifiers (e.g., Nitrospira), and iron-cycling bacteria (e.g., Sideroxydans), not only increased in abundance but also showed strong involvement in the microbial assembly processes. These key microbes were closely linked to specific metabolites and organized into two distinct network modules. Both modules predominantly recruited beneficial microbes, but one module also actively excluded potentially harmful taxa (e.g., Salmonella), which could disrupt community stability. Further experiments with exogenous metabolites confirmed the vital role of quercetin in attracting beneficial microbes while repelling harmful ones.

CONCLUSION: The findings indicate that arboviruses can strongly influence the belowground rhizosphere microbial assembly processes by modulating metabolite profiles to selectively recruit or exclude key microbial species. These taxa, in turn, play fundamental roles in rhizosphere functions. These insights lay the groundwork for strategies to enhance rice immunity against viral infections by managing the rhizosphere microbial community. Video Abstract.},
}

*Oryza/virology/microbiology
*Rhizosphere
*Reoviridae/physiology/pathogenicity
Soil Microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota
Metagenomics/methods
*Plant Diseases/virology/microbiology
Metabolomics/methods

@article {pmid41131656,
year = {2025},
author = {Chen, X and Xu, J and Zhang, L and Xie, B and Ren, J and He, J and Liu, T and Liu, Q and Dong, Y and He, X and Yao, J and Wu, S},
title = {Altered ruminal microbiome tryptophan metabolism and their derived 3-indoleacetic acid inhibit ruminal inflammation in subacute ruminal acidosis goats.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {215},
pmid = {41131656},
issn = {2049-2618},
support = {2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; },
mesh = {Animals ; Goats/microbiology ; *Rumen/microbiology/metabolism ; *Acidosis/veterinary/microbiology/metabolism ; Animal Feed/analysis ; *Tryptophan/metabolism ; *Indoleacetic Acids/metabolism ; *Gastrointestinal Microbiome ; *Inflammation ; *Goat Diseases/microbiology/metabolism ; Diet ; Female ; Metagenomics ; Bacteria/classification/genetics/metabolism/isolation & purification ; Fermentation ; Metagenome ; },
abstract = {BACKGROUND: Subacute ruminal acidosis (SARA) is a digestive disorder that often severely jeopardizes the health and lactation performance of ruminants fed a high-energy diet. Different dairy ruminants exhibit varying degrees of inflammation accompanied by variations in the rumen microbiota when SARA occurs. Our understanding of the occurrence of SARA and varying degrees of rumen epithelial inflammation is lacking. Hence, we performed rumen metagenomic, metagenome-assembled genome and metabolomic analyses, with transcriptome and single-nucleus RNA sequence analyses, to explore the microbial mechanism of SARA occurrence and different degrees of inflammation.

RESULTS: A total of 36 goats fed two diets with gradually increasing levels of rumen-degradable starch (RDS) were included in this study, and SARA goats fed 70% concentrate diets supplemented with whole corn (HGW-SARA) and SARA goats fed 70% concentrate diets supplemented with crushed corn (HGC-SARA) were identified. Moreover, 11 goats fed a control basal diet, named LGW-CON, were also included. Compared with those in the LGW-CON group, the rumen fermentation capacity was enhanced, accompanied by ruminal epithelial and systemic inflammation, in goats from HGW-SARA and HGC-SARA. Between them, HGC-SARA goats presented less inflammation. Notably, the ruminal inflammation-related pathways were increased only in the HGW-SARA group but not in the HGC-SARA group. Metagenomic analysis revealed that the β diversity of SARA goats was significantly different from that of LGW-CON goats. Ruminococcus significantly increased in both SARA groups, whereas Prevotella and Bacteroidales significantly decreased, which was accompanied by a decrease in cellulose and hemicellulose enzymes and an increase in lysozymes and lipopolysaccharide synthesis enzymes. Multi-omics analysis of the ruminal contents and tissues suggested that epithelial inflammation was caused by disturbed ruminal microbiome-induced Th17 cell differentiation and IL-17 signalling pathway activation. Comparative analyses between the HGW-SARA and HGC-SARA groups highlighted the importance of Selenomonas and Bifidobacterium, as well as bacterial tryptophan metabolism, in the production of 3-indoleacetic acid, which mitigated ruminal epithelial inflammation by modulating Th17 cells and inhibiting IL-17 signalling. Ruminal microbiota transplantation from HGW-SARA goats to healthy dairy goats and mice revealed the role of microbes in epithelial inflammation. Additionally, 3-indoleacetic acid supplementation reduced rumen inflammation and the IL-17 concentration in the serum, improved VFAs absorption, and enhanced milk production.

CONCLUSIONS: This study unveiled that after SARA was induced by high-concentrate feeding, the rumen homeostasis was disrupted, and rumen fiber degradation capacity of dairy goats decreased, but the LPS synthesis capacity increased, and inflammation of the rumen epithelium was observed. However, the ruminal microbial species from the Bifidobacterium and Selenomonas genera and bacterial 3-indole acetic acid are pivotal in mitigating ruminal epithelial inflammation during SARA in dairy goats. This could potentially be attributed to the modulation of ruminal Th17 cell proportions and the inhibition of IL-17 signalling pathways. Video Abstract.},
}

Animals
Goats/microbiology
*Rumen/microbiology/metabolism
*Acidosis/veterinary/microbiology/metabolism
Animal Feed/analysis
*Tryptophan/metabolism
*Indoleacetic Acids/metabolism
*Gastrointestinal Microbiome
*Inflammation
*Goat Diseases/microbiology/metabolism
Diet
Female
Metagenomics
Bacteria/classification/genetics/metabolism/isolation & purification
Fermentation
Metagenome

@article {pmid41131583,
year = {2025},
author = {Lou, Y and Lv, Y and Wang, X and Luo, Y and Lou, J and Yu, Y and Gu, W and Yu, J and Fang, Y and Zhao, H and Peng, K and Chen, J and Ni, Y},
title = {Ruminococcus torques ameliorates the inflammation bowel disease and gut barrier dysfunction by modulating gut microbiota and bile acid metabolism.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1162},
pmid = {41131583},
issn = {1479-5876},
support = {No. CCCF-QF-2022B04-4//the China Crohn's & Colitis Foundation/ ; 2024KY1171//Medical Science and Technology Project of Zhejiang Province/ ; 82170583//National Natural Science Foundation of China/ ; U23A20167//National Natural Science Foundation of China/ ; 82400595//National Natural Science Foundation of China/ ; 2025C02085//the Key R&D Program of Zhejiang/ ; 2021YFC2701900//the National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Animals ; Male ; *Bile Acids and Salts/metabolism ; *Inflammatory Bowel Diseases/microbiology ; *Ruminococcus/physiology ; *Intestinal Mucosa/pathology/microbiology ; Child ; Colitis/pathology/microbiology ; Mice ; Female ; Mice, Inbred C57BL ; Crohn Disease/microbiology ; Adolescent ; },
abstract = {BACKGROUND: Recent advances in microbiome-targeted therapies have uncovered immunomodulatory bacterial taxa with strain-specific therapeutic potential; however, the microbial signatures driving exclusive enteral nutrition (EEN) efficacy, particularly protective microbiota, and their mechanistic links to therapeutic outcomes remain uncharacterized in pediatric inflammatory bowel disease (IBD). Elucidating these microbial determinants and their functional pathways is critical for advancing targeted probiotic strategies in children.

METHODS: A cohort of treatment-naïve pediatric Crohn's disease (CD) patients and age-matched healthy controls (HC) were enrolled. Fecal samples were collected from both HC and CD patients during active phase and remission following EEN therapy. Metagenomic sequencing, qPCR validation, and targeted bile acid (BA) analysis were conducted to identify candidate protective strains and potential impacts on BA homeostasis. Mechanistic investigations were conducted using dextran sulfate sodium (DSS)- and trinitrobenzene sulfonic acid (TNBS)-induced colitis model in male mice.

RESULTS: The relative abundance of Ruminococcus torques (R. torques) demonstrated significant depletion in active CD cases (p = 0.02) compared to HC, which was restored after EEN treatment at remission status (p < 0.001). Its level was negatively correlated with the disease severity index (PCDAI r=-0.64; CDEIS r=-0.70) and positively correlated with the secondary to primary BA ratio (r = 0.27). In murine models, R. torques supplementation attenuated colitis severity through enhancing epithelial integrity (claudin-3, 3.3-fold; occludin, 7.5-fold), suppressing pro-inflammatory mediators (TNF-α, -44%; IL-6, -71%), regulating BA metabolism (secondary/unconjugated BAs, 29%) and autophagy pathway (LC3-II/LC3-I ratio, -1.8-fold).

CONCLUSIONS: Our findings demonstrated R. torques as a novel microbial therapeutic candidate for IBD management. The anti-colitis mechanisms involve the modulation of BA metabolic homeostasis, epithelial barrier reinforcement, and inflammation resolution.},
}

Humans
*Gastrointestinal Microbiome
Animals
Male
*Bile Acids and Salts/metabolism
*Inflammatory Bowel Diseases/microbiology
*Ruminococcus/physiology
*Intestinal Mucosa/pathology/microbiology
Child
Colitis/pathology/microbiology
Mice
Female
Mice, Inbred C57BL
Crohn Disease/microbiology
Adolescent

@article {pmid41131465,
year = {2025},
author = {Hamdene, I and Bez, C and Bertani, I and López-Menchero, JR and Yahyaoui, A and Venturi, V and Sadfi-Zouaoui, N},
title = {Endophytic bacterial communities associated with halophytic plants in kebili and Gabes regions of Southern Tunisia.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {683},
pmid = {41131465},
issn = {1471-2180},
mesh = {Tunisia ; *Salt-Tolerant Plants/microbiology ; *Endophytes/classification/isolation & purification/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Soil Microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; DNA, Bacterial/genetics ; Soil/chemistry ; *Microbiota ; Salinity ; Biodiversity ; Sequence Analysis, DNA ; Amaranthaceae/microbiology ; },
abstract = {In the arid regions of southern Tunisia, soil and irrigation water salinity represent major challenges to agricultural sustainability. Despite the increasing interest in plant-associated microbes, the role of endophytic bacteria in conferring salt tolerance remains largely unexplored in this context. To address this gap, twenty-two halophytic plants and their associated soils were sampled from five distinct sites across the Kebili and Gabes governorates. Significant differences in soil physicochemical properties were observed between sampling sites. The soils are generally poorly developed, non-fertile (with very low organic matter and high CaCO3 levels), and highly saline, leading to limited cultivation potential. Molecular identification of plants revealed nine different families and 14 genera, with the Amaranthaceae family being the most prominent, including Atriplex spp. (2), Bassia spp. (2), Suaeda spp. (4), and Halocnemum spp. (1). Bacterial community studies were conducted of both culturable and non-culturable endophyte communities inhabiting the green and root compartments of different halotolerant plants. Endophytic microbiome compositions differed between above-ground and below-ground tissues within the same plant family. A higher prevalence of three phyla Proteobacteria (67.80%), Firmicutes (14.06%), and Actinobacteria (6.57%) was detected across all samples. At the genus level, Acinetobacter, Halomonas, Kushneria, Pseudomonas, Psychrobacter, Stenotrophomonas, and Streptomyces formed the common core microbiome. Functional predictions of endophytic bacteria in halophytes highlighted multiple KEGG functional pathways, indicating recruitment of beneficial bacterial taxa to adapt to extreme hypersaline conditions, including plant growth-promoting, biocontrol, and halophilic bacteria.},
}

Tunisia
*Salt-Tolerant Plants/microbiology
*Endophytes/classification/isolation & purification/genetics
*Bacteria/classification/genetics/isolation & purification
*Soil Microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics
Plant Roots/microbiology
DNA, Bacterial/genetics
Soil/chemistry
*Microbiota
Salinity
Biodiversity
Sequence Analysis, DNA
Amaranthaceae/microbiology

@article {pmid41101029,
year = {2025},
author = {Ma, L and Liu, F and Zhou, M and Zhang, M and Zheng, J and Wang, Z and He, Z and Yan, Q and Wu, B and Wang, C and Shu, L},
title = {Amoebae contribute to the diversity and fate of antibiotic resistance genes in drinking water system.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109867},
doi = {10.1016/j.envint.2025.109867},
pmid = {41101029},
issn = {1873-6750},
mesh = {*Drinking Water/microbiology/parasitology ; *Amoeba/genetics/physiology ; *Drug Resistance, Microbial/genetics ; Symbiosis ; *Water Microbiology ; Bacteria/genetics ; Microbiota ; },
abstract = {Free-living amoebae represent a significant eukaryotic group that thrives in drinking water systems, posing considerable risks to water quality due to their inherent pathogenicity and associations with various microorganisms. However, the symbiotic microbial profiles of different amoeba species and the impact of amoeba-bacteria interactions on the antibiotic resistome within drinking water systems remain poorly understood. In this study, we obtained 24 amoeba isolates from tap water, encompassing diverse phyla within the amoeba lineage. Through metagenome sequencing, we uncovered variations in symbiotic microbiome composition across different amoeba species and strains. Notably, amoebae acted as vectors for human pathogens, including bacteria and viruses. The majority of symbionts carried multiple antibiotic-resistance genes and virulence factors. Furthermore, dominant symbiotic species could be cultured independently, underscoring the critical role of amoebae in preserving and transmitting antibiotic-resistant opportunistic pathogens in drinking water systems. Disinfection experiments demonstrated highly diverse viability of amoebae and their protective capabilities for symbionts against chlorine disinfection. Our findings expand the germplasm bank for amoebae and symbiotic bacteria derived from tap water and emphasize the necessity for further research on amoeba-bacteria symbiosis to ensure drinking water quality and public health safety.},
}

*Drinking Water/microbiology/parasitology
*Amoeba/genetics/physiology
*Drug Resistance, Microbial/genetics
Symbiosis
*Water Microbiology
Bacteria/genetics
Microbiota

@article {pmid40889349,
year = {2025},
author = {Moraitou, M and Richards, JL and Bolyos, C and Saliari, K and Gilissen, E and Timmons, Z and Kitchener, AC and Pauwels, OSG and Sabin, R and Kokkini, P and Portela Miguez, R and Guschanski, K},
title = {Host Traits Impact the Outcome of Metagenomic Library Preparation From Dental Calculus Samples Across Diverse Mammals.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70039},
doi = {10.1111/1755-0998.70039},
pmid = {40889349},
issn = {1755-0998},
support = {2019-00275//Svenska Forskningsrådet Formas/ ; },
mesh = {*Metagenomics/methods ; *Dental Calculus/microbiology ; *Mammals/microbiology/classification ; Animals ; *Microbiota ; *Gene Library ; Metagenome ; Computational Biology ; },
abstract = {Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study, we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. Although we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly because of both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was ~74%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.},
}

*Metagenomics/methods
*Dental Calculus/microbiology
*Mammals/microbiology/classification
Animals
*Microbiota
*Gene Library
Metagenome
Computational Biology

@article {pmid40885278,
year = {2025},
author = {Bastón-Paz, N and Moreno-Blanco, A and Palacios, E and Olavarrieta, L and Galeano, J and Garriga, M and Máiz, L and Vicente-Santamaría, S and Oteo-Iglesias, J and López-Causapé, C and Fuentes, I and Oliver, A and Cantón, R and Del Campo, R and de Dios-Caballero, J},
title = {Exploring the complexities of intestinal and pulmonary microbiota in cystic fibrosis: A multi-omics approach.},
journal = {Respiratory medicine},
volume = {248},
number = {},
pages = {108331},
doi = {10.1016/j.rmed.2025.108331},
pmid = {40885278},
issn = {1532-3064},
mesh = {Humans ; *Cystic Fibrosis/microbiology/physiopathology ; Male ; Female ; Feces/microbiology ; Sputum/microbiology ; Adult ; *Gastrointestinal Microbiome/genetics ; *Lung/microbiology ; Metagenomics/methods ; Adolescent ; Fatty Acids, Volatile/metabolism/analysis ; Child ; Young Adult ; *Microbiota ; Multiomics ; },
abstract = {BACKGROUND: We aimed to elucidate the cystic fibrosis (CF) microbiota composition (shotgun metagenomics) and functionality (short-chain fatty acids, SCFAs).

METHODS: Fecal and sputum samples were recruited from 39 clinically stable CF subjects.

RESULTS: Bacillota and Pseudomonadota were dominant in both gut and lung compartments, whereas Ascomycota were the most abundant fungi in feces, and Basidiomycota, especially Malassezia globosa, in sputum. Viruses accounted for 0.4 % of the relative abundance in the gut and 0.6 % in lungs. Mycobacteroides abscessus was genetically identified in 10 individuals, although only 2 had positive cultures. Patients with higher levels of Pseudomonas filamentous phages had negative cultures for P. aeruginosa. The protozoan Toxoplasma gondii was detected in all sputum samples, accounting for 0.25 % of the metagenomic reads, with further PCR-confirmation in 50 % of subjects, including children. No correlation was found between SCFA and lung function or microbial composition. The resistome of the fecal compartment was higher than that of the lungs, and a greater abundance of SCFAs in the intestine was associated with poorer lung function.

CONCLUSIONS: Patients with normal-mild lung function had higher alpha diversity in the respiratory microbiota; however, beta diversity in the stool was statistically different compared with the group with poorer lung function. Although there were no differences in SCFA concentrations, butyrate-producing bacteria were more abundant in the sputum of the group with better lung function. In fecal samples, resistome to tetracyclines, glycopeptides, and aminoglycosides predominated, whereas in sputum an enrichment of ARGs related to tetracyclines, beta-lactams, and macrolides was observed.},
}

Humans
*Cystic Fibrosis/microbiology/physiopathology
Male
Female
Feces/microbiology
Sputum/microbiology
Adult
*Gastrointestinal Microbiome/genetics
*Lung/microbiology
Metagenomics/methods
Adolescent
Fatty Acids, Volatile/metabolism/analysis
Child
Young Adult
*Microbiota
Multiomics

@article {pmid40755083,
year = {2025},
author = {Koseki, Y and Takeshima, H and Yoneda, R and Katayanagi, K and Ito, G and Yamanaka, H},
title = {gmmDenoise: A New Method and R Package for High-Confidence Sequence Variant Filtering in Environmental DNA Amplicon Analysis.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70023},
doi = {10.1111/1755-0998.70023},
pmid = {40755083},
issn = {1755-0998},
support = {JP21K12329//Japan Society for the Promotion of Science/ ; JP22K14908//Japan Society for the Promotion of Science/ ; JP25K02038//Japan Society for the Promotion of Science/ ; },
mesh = {*DNA, Environmental/genetics ; *DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; *Genetic Variation ; *Metagenomics/methods ; *Software ; Sequence Analysis, DNA/methods ; },
abstract = {Assessing and monitoring genetic diversity is vital for understanding the ecology and evolution of natural populations but is often challenging in animal and plant species due to technically and physically demanding tissue sampling. Although environmental DNA (eDNA) metabarcoding is a promising alternative to the traditional population genetic monitoring based on biological samples, its practical application remains challenging due to spurious sequences present in the amplicon data, even after data processing with the existing sequence filtering and denoising (error correction) methods. Here we developed a novel amplicon filtering approach that can effectively eliminate such spurious amplicon sequence variants (ASVs) in eDNA metabarcoding data. A simple simulation of eDNA metabarcoding processes was performed to understand the patterns of read count (abundance) distributions of true ASVs and their polymerase chain reaction (PCR)-generated artefacts (i.e., false-positive ASVs). Based on the simulation results, the approach was developed to estimate the abundance distributions of true and false-positive ASVs using Gaussian mixture models and to determine a statistically based threshold between them. The developed approach was implemented as an R package, gmmDenoise and evaluated using single-species metabarcoding datasets in which all or some true ASVs (i.e., haplotypes) were known. Example analyses using community (multi-species) metabarcoding datasets were also performed to demonstrate how gmmDenoise can be used to derive reliable intraspecific diversity estimates and population genetic inferences from noisy amplicon sequencing data. The gmmDenoise package is freely available in the GitHub repository (https://github.com/YSKoseki/gmmDenoise).},
}

*DNA, Environmental/genetics
*DNA Barcoding, Taxonomic/methods
*Computational Biology/methods
*Genetic Variation
*Metagenomics/methods
*Software
Sequence Analysis, DNA/methods

@article {pmid40580061,
year = {2025},
author = {Rathour, R and Ma, Y and Xiong, J and Wang, XW and Petersen, J and Zhang, X},
title = {Hemolymph microbiota and host immunity of crustaceans and mollusks.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf133},
pmid = {40580061},
issn = {1751-7370},
support = {//Synthetic Biology Research Centre of Shenzhen University/ ; //Austrian Science Fund/ ; //ERC Starting Grant EvoLucin/ ; 42476113//National Natural Science Foundation of China/ ; JCYJ20241202124403006//Shenzhen Science and Technology Program/ ; 2025A1515010475//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; },
mesh = {Animals ; *Hemolymph/microbiology/immunology ; *Microbiota/immunology ; Immunity, Innate ; *Mollusca/microbiology/immunology ; *Crustacea/microbiology/immunology ; },
abstract = {Crustaceans and mollusks have major economic importance and are also key players in aquatic biogeochemical cycles. However, disease outbreaks, temperature fluctuations, pollutants, and other stressors have severely threatened their global production. Invertebrates generally rely on their innate immune system as the primary defense mechanism, operating at cellular and humoral levels to protect against pathogens. The hemolymph plays a vital role in immune responses, containing microbial communities that interact with the host's immune processes. Significant advances in molecular methods such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics have revealed the presence of a resident hemolymph microbiome and delineated its potentially vital role in immune homeostasis and overall host health. Accordingly, understanding the composition and role of the hemolymph microbiota, alongside innate immune responses, has become a key focus in recent research aimed at unraveling disease resistance mechanisms and supporting sustainable aquaculture practices. Here, we summarize the latest advancements in understanding the host and environmental factors that shape hemolymph microbiota diversity in various crustacean and mollusk species. We also consider the innate immune responses of the hosts, as these modulate interactions between hosts, microbes, and environments. Interactions within the hemolymph microbiome significantly affect host health, providing critical insights for advancing sustainable aquaculture.},
}

Animals
*Hemolymph/microbiology/immunology
*Microbiota/immunology
Immunity, Innate
*Mollusca/microbiology/immunology
*Crustacea/microbiology/immunology

@article {pmid41131078,
year = {2025},
author = {Chen, R and Guo, X and Wu, M and Zheng, T and Chen, S and He, B},
title = {Bacillus velezensis ES2-4 modulates root exudation and microbiome remodeling to enhance soybean resistance against gray mold.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37098},
pmid = {41131078},
issn = {2045-2322},
support = {32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; },
mesh = {*Bacillus/physiology ; *Glycine max/microbiology/metabolism/immunology ; *Plant Roots/microbiology/metabolism ; *Botrytis/pathogenicity ; *Microbiota ; *Plant Diseases/microbiology/prevention & control ; Rhizosphere ; *Disease Resistance ; Soil Microbiology ; },
abstract = {Gray mold, caused by Botrytis cinerea, represents a significant threat to soybean productivity, while conventional chemical control strategies raise concerns regarding long-term sustainability. Plant-associated beneficial microbes, such as Bacillus velezensis, have been proposed as environmentally sustainable alternatives; however, their specific roles in modulating root-microbe interactions remain insufficiently characterized. This study investigated the mechanisms by which B. velezensis ES2-4 enhances soybean resistance by modulating root exudate composition and restructuring rhizosphere microbial communities. Metabolomic and metagenomic analyses indicated that ES2-4 inoculation led to the upregulation of antifungal metabolites (e.g., oxalic acid, eicosane) in root exudates, which facilitated the recruitment of beneficial bacteria while inhibiting B. cinerea proliferation. Pathogen infection was associated with disruptions in rhizosphere microbial diversity; however, ES2-4 application restored bacterial richness, particularly within the Alphaproteobacteria and Streptomyces lineages, while reducing the relative abundance of fungal pathogens. Co-occurrence network analysis further demonstrated that ES2-4 inoculation promoted microbial interactions associated with stress-responsive pathways, including two-component signaling systems and fatty acid metabolism, while downregulating pathogen-associated metabolic functions. These findings elucidate a dual mechanism through which ES2-4 enhances plant immunity via metabolite-mediated microbiome modulation, highlighting its potential as a sustainable biocontrol agent against soybean gray mold.},
}

*Bacillus/physiology
*Glycine max/microbiology/metabolism/immunology
*Plant Roots/microbiology/metabolism
*Botrytis/pathogenicity
*Microbiota
*Plant Diseases/microbiology/prevention & control
Rhizosphere
*Disease Resistance
Soil Microbiology

@article {pmid41130610,
year = {2025},
author = {Karim, DM and Papp, M and Fehérvári, P and Turan, C and Hegyi, P and Molnar, Z and Madách, K},
title = {No difference in microbial diversity between bronchoalveolar lavage and tracheal sampling: a systematic review and meta-analysis.},
journal = {BMJ open respiratory research},
volume = {12},
number = {1},
pages = {},
doi = {10.1136/bmjresp-2025-003456},
pmid = {41130610},
issn = {2052-4439},
mesh = {Humans ; *Trachea/microbiology ; *Microbiota ; *Bronchoalveolar Lavage Fluid/microbiology ; *Bronchoalveolar Lavage/methods ; *Specimen Handling/methods ; },
abstract = {INTRODUCTION: The respiratory microbiome has a vital role in maintaining respiratory health and preventing pathogen colonisation, but traditional diagnostic methods fail to capture a complete picture of it. Metagenomic sequencing has improved our understanding of microbial ecosystems in both acute and chronic pathologies. However, its results have not been systematically compared between different respiratory sampling techniques, as has been done with traditional methods. Our study aims to compare the microbial diversity in bronchoalveolar lavage (BAL) and tracheal samples using microbiome sequencing.

METHODS: A systematic search was conducted in Medline, Embase and CENTRAL databases to identify studies where lower respiratory tract microbiome specimens were collected simultaneously using BAL and tracheal sampling and diversity was analysed postsequencing. Risk of bias was assessed with our specifically tailored tool. A random-effects model was used for data synthesis, analysing pooled Shannon, Chao1 and Simpson indices.

RESULTS: We screened 1050 potentially relevant publications, 10 of which were included. No significant difference was found in microbial alpha diversity between BAL and tracheal samples. The subgroup analysis of tracheal sample types, including sputum and endotracheal aspirate, revealed no significant differences compared with BAL.

CONCLUSIONS: Tracheal sampling methods offer a viable and less invasive alternative to BAL for characterising microbiome alpha diversity in clinical or research settings where segmental sampling is not required. However, further high-quality comparative studies are needed to confirm these findings.

PROSPERO REGISTRATION NUMBER: CRD42023436934.},
}

Humans
*Trachea/microbiology
*Microbiota
*Bronchoalveolar Lavage Fluid/microbiology
*Bronchoalveolar Lavage/methods
*Specimen Handling/methods

@article {pmid41130083,
year = {2025},
author = {Tripathy, B and Singh, S and Behera, ID and Mishra, S and Das, AP},
title = {Metagenomic profiling of diversified marine microbiome across microplastic-contaminated niches of Bay of Bengal, India.},
journal = {Marine pollution bulletin},
volume = {222},
number = {Pt 3},
pages = {118872},
doi = {10.1016/j.marpolbul.2025.118872},
pmid = {41130083},
issn = {1879-3363},
abstract = {Diverse microorganisms in the marine sediment share a significant section of the global marine ecosystem and play a dominant role in marine biogeochemistry. The present study is the first to report an evaluation of shotgun metagenomic sequencing of microplastic-contaminated marine water and sediment samples from the coastal shores of the Bay of Bengal, India, across a stretch of 25 km, which houses a plethora of ubiquitous and uncultured microbial biodiversity coexisting with multitudinous human interventions. Illumina Nova sequencing 6000 suggested the presence of 88,539 scaffolds of data containing 132,568 identified genes of marine microorganisms. Taxonomic identification with the assistance of curated global databases ensued in the presence of Proteobacteria (53.12 %), Bacteroidetes (7.13 %), Actinobacteria (5.87 %), and miscellaneous (33.86 %) in abundance. Azonexus hydrophillus, Mycobacteroides abscessus, and Acidaminobacter hydrogenoformans were identified in profusion from the sequenced samples of the study area. The adaptation, sustenance, and survivability in the presence of plastic pollutants confirm the presence of microplastic-degrading enzymes in the microorganisms. The functional annotations revealed 54.32 % and 58.34 % similarities in genes with KEGG and COG databases, revealing the heavy presence of inorganic and amino acid transport channels. Further metabolic profiling of the identified novel microorganisms will assist in engineering the enhancement of microbial enzymes, such as cutinases, lipases, and esterases, leading to microplastic degradation activity. The present research work signifies the analysis and documentation of native microbiota of the marine shores of the Bay of Bengal and their interactive potentialities with microplastic-contaminated anthropogenic environments.},
}

@article {pmid41032862,
year = {2025},
author = {Ghosh Chowdhury, M and Singh, AA and Bhattacharyya, M and Muthukumar, V and Kapoor, S and Srivastava, A and Kumar, H and Shard, A},
title = {Thiazole-Based Tumor Pyruvate Kinase M2 Inhibitors: A Paradigm-Shifting Therapeutic Strategy Targeting Metabolic and Microbial Synergy in Colorectal Cancer.},
journal = {Journal of medicinal chemistry},
volume = {68},
number = {20},
pages = {21786-21806},
doi = {10.1021/acs.jmedchem.5c02169},
pmid = {41032862},
issn = {1520-4804},
mesh = {Humans ; *Thiazoles/pharmacology/chemistry/chemical synthesis ; *Colorectal Neoplasms/drug therapy/pathology/metabolism/microbiology ; Gastrointestinal Microbiome/drug effects ; *Antineoplastic Agents/pharmacology/chemistry/chemical synthesis ; *Pyruvate Kinase/antagonists & inhibitors/metabolism ; *Membrane Proteins/antagonists & inhibitors/metabolism ; Cell Line, Tumor ; *Thyroid Hormones/metabolism ; Thyroid Hormone-Binding Proteins ; *Carrier Proteins/antagonists & inhibitors/metabolism ; Cell Proliferation/drug effects ; Structure-Activity Relationship ; Animals ; *Enzyme Inhibitors/pharmacology/chemistry ; },
abstract = {Colorectal cancer (CRC) remains a major global health burden, with current treatments primarily focused on eradicating cancer cells. However, chemotherapy-induced gut dysbiosis exacerbates inflammation and disease progression, necessitating innovative therapeutic strategies. While various metabolic inhibitors and microbiome-modulating approaches have been explored separately, no reported agent to date simultaneously targets both cancer cell survival and gut microbiome restoration. We designed thiazole-based pyruvate kinase M2 (PKM2) inhibitors, hypothesizing that selective modulation may suppress tumor growth while restoring gut microbial balance. 10j selectively inhibited PKM2 in a cell-free assay (0.01 ± 0.0009 μM) and in CRC cells (4.21 ± 0.04 μM), disrupting key pathways driving CRC progression. Remarkably, metagenomic analysis revealed that 10j restored gut microbiota balance. These findings suggest that dual-function anticancer agents, which kill cancer cells while simultaneously restoring gut microbiota, represent an unexplored therapeutic avenue. Thiazole-based PKM2 inhibitors are pioneering this novel strategy in CRC treatment.},
}

Humans
*Thiazoles/pharmacology/chemistry/chemical synthesis
*Colorectal Neoplasms/drug therapy/pathology/metabolism/microbiology
Gastrointestinal Microbiome/drug effects
*Antineoplastic Agents/pharmacology/chemistry/chemical synthesis
*Pyruvate Kinase/antagonists & inhibitors/metabolism
*Membrane Proteins/antagonists & inhibitors/metabolism
Cell Line, Tumor
*Thyroid Hormones/metabolism
Thyroid Hormone-Binding Proteins
*Carrier Proteins/antagonists & inhibitors/metabolism
Cell Proliferation/drug effects
Structure-Activity Relationship
Animals
*Enzyme Inhibitors/pharmacology/chemistry

@article {pmid41002268,
year = {2025},
author = {Aminu, S and Ascandari, A and Benhida, R and Daoud, R},
title = {GRUMB: a genome-resolved metagenomic framework for monitoring urban microbiomes and diagnosing pathogen risk.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {10},
pages = {},
doi = {10.1093/bioinformatics/btaf548},
pmid = {41002268},
issn = {1367-4811},
support = {//Mohammed VI Polytechnic University/ ; //African Supercomputing Center at UM6P/ ; },
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Software ; *Metagenome ; Machine Learning ; Humans ; Cities ; },
abstract = {SUMMARY: Urban infrastructure hosts dynamic microbial communities that complicate biosurveillance and AMR monitoring. Existing tools rarely combine genome-resolved reconstruction with ecological modeling and batch-aware analytics tailored to infrastructure-scale studies. We present GRUMB (Genome-Resolved Urban Microbiome Biosurveillance), an open-source, SLURM-compatible pipeline that reconstructs high-quality metagenome-assembled genomes (MAGs) from shotgun sequencing reads and integrates taxonomic/functional annotation (CARD, VFDB), batch-aware normalization, ecological diagnostics and machine learning classification of environment types with uncertainty and risk scoring. GRUMB accepts either SRA project accessions or paired-end FASTQ files with metadata, and produces assemblies, MAGs, taxonomic and functional profiles, ecological outputs and risk-informed classification. Its modular design enables reproducible, infrastructure-scale biosurveillance across diverse environments.

GRUMB is freely available under the MIT License at: https://github.com/SuleimanAminu/genome-resolved-urban-microbiome-biosurveillance; Zenodo DOI: https://doi.org/10.5281/zenodo.15505402. Requirements: Linux (Ubuntu 20.04+), Python 3.11, R 4.2+, SLURM. Issues and feature requests are tracked on GitHub.},
}

*Microbiota/genetics
*Metagenomics/methods
*Software
*Metagenome
Machine Learning
Humans
Cities

@article {pmid40613917,
year = {2025},
author = {Zakerska-Banaszak, O and Ladziak, K and Kruszka, D and Maciejewski, K and Wolko, L and Krela-Kazmierczak, I and Zawada, A and Vibeke Vestergaard, M and Dobrowolska, A and Skrzypczak-Zielinska, M},
title = {New potential biomarkers of ulcerative colitis and disease course - integrated metagenomic and metabolomic analysis among Polish patients.},
journal = {Journal of gastroenterology},
volume = {60},
number = {11},
pages = {1384-1399},
pmid = {40613917},
issn = {1435-5922},
support = {2020/04/X/NZ2/02172//Narodowe Centrum Nauki/ ; 2021/02//Institute of Human Genetics, Polish Academy of Sciences, in Poznan, Poland/ ; },
mesh = {Humans ; *Colitis, Ulcerative/microbiology/metabolism ; Male ; Female ; Adult ; *Gastrointestinal Microbiome/genetics ; Biomarkers/blood/metabolism ; Middle Aged ; Metagenomics/methods ; Metabolomics/methods ; Poland ; Feces/microbiology/chemistry ; Case-Control Studies ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Metabolome ; Disease Progression ; Young Adult ; Remission Induction ; },
abstract = {BACKGROUND & AIM: The course of ulcerative colitis (UC) involves successive periods of remission and exacerbation but is difficult to predict. Gut dysbiosis in UC has already been intensively investigated. However, are periods of exacerbation and remission associated with specific disturbances in the composition of the intestinal microbiota and its metabolome? Our goal was to answer this question and to identify bacteria and metabolites necessary to maintain the remission.

METHODS: We enrolled 65 individuals, including 20 UC patients in remission, 15 in exacerbation, and 30 healthy controls. Metagenomic profiling of the gut microbial composition was performed based on 16S rRNA V1-V9 sequencing. Stool and serum metabolic profiles were studied by chromatography combined with mass spectrometry.

RESULTS: We revealed significant differences in the gut bacterial and metabolic composition between patients in active UC and those in remission, as well as in healthy controls. As associated with UC remission we have identified following bacteria: Akkermansia, Agathobacter, Anaerostipes, Enterorhabdus, Coprostanoligenes, Colinsella, Ruminococcus, Subdoligranulum, Lachnoclostridium, Coriobacteriales, Erysipelotrichaceae, and Family XII, and compounds - 1-hexadecanol, phytanic acid, squalene, adipic acid, cis-gondoic acid, nicotinic acid, tocopherol gamma, ergosterol and lithocholic acid. Whereas, in the serum lithocholic acid, indole and xanthine were found as potential candidates for biomarkers of UC remission.

CONCLUSION: We have demonstrated that specific bacteria, metabolites, and their correlations could be crucial in the remission of UC among Polish patients. Our results provide valuable insights and a significant source for developing new hypotheses on host-microbiome interactions in diagnosis and course of UC.},
}

Humans
*Colitis, Ulcerative/microbiology/metabolism
Male
Female
Adult
*Gastrointestinal Microbiome/genetics
Biomarkers/blood/metabolism
Middle Aged
Metagenomics/methods
Metabolomics/methods
Poland
Feces/microbiology/chemistry
Case-Control Studies
Dysbiosis/microbiology
RNA, Ribosomal, 16S/genetics
Metabolome
Disease Progression
Young Adult
Remission Induction

@article {pmid41122951,
year = {2025},
author = {Vilonen, L and Thompson, A and Adams, B and Ayres, E and Franco, ALC and Wall, DH},
title = {Characterising Soil Eukaryotic Diversity From NEON Metagenomics Datasets.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70062},
doi = {10.1111/1755-0998.70062},
pmid = {41122951},
issn = {1755-0998},
support = {//U.S. National Science Foundation/ ; },
abstract = {Belowground eukaryotic diversity serves a vital role in soil ecosystem functioning, yet the composition, structure, and macroecology of these communities are significantly under-characterized. The National Ecological Observatory Network (NEON) provides publicly available datasets from long-term surveillance of numerous taxa and ecosystem properties. However, this dataset is not routinely evaluated for its eukaryotic component, likely because analyzing metagenomes for eukaryotic sequences is hampered by low relative sequence abundance, large genomes, poorer eukaryote representation in public reference databases, and is not yet mainstream. We mined the NEON soil metagenome datasets for 18S rRNA sequences using a custom-built pipeline and produced a preliminary assessment of biodiversity trends in North American soil eukaryotes. We extracted ~800 18S rRNA reads per sample (~22,000 reads per site) from 1455 samples from 495 plots across 45 NEON sites in 11 biomes, which corresponded to 5183 genera in 35 phyla. To our knowledge, this represents the first large-scale soil eukaryote analysis of NEON data. We asked whether taxonomic richness paralleled patterns previously established ecological trends and found that eukaryotic richness was negatively correlated with pH, managed sites lowered eukaryotic richness by 47%, most biomes had a distinct eukaryotic community, and fire decreased eukaryotic richness. These findings parallel generally accepted ecological trends and support the notion that NEON soil metagenome datasets can and should be used to explore spatiotemporal patterns in soil eukaryote diversity, its association with ecosystem functioning, and its response to environmental changes in North America.},
}

@article {pmid41122237,
year = {2025},
author = {Terra Machado, D and Bernardes Brustolini, OJ and Dos Santos Corrêa, E and Ribeiro Vasconcelos, AT},
title = {Prediction of sporulating Firmicutes from uncultured gut microbiota using SpoMAG, an ensemble learning tool.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20232},
pmid = {41122237},
issn = {2167-8359},
mesh = {*Gastrointestinal Microbiome/genetics ; *Machine Learning ; *Spores, Bacterial/genetics ; Animals ; Humans ; *Firmicutes/genetics/physiology ; Cattle ; Feces/microbiology ; Metagenome ; Swine ; Phylogeny ; Ensemble Learning ; },
abstract = {Sporulation represents a key adaptive strategy among Firmicutes, facilitating bacterial persistence under environmental stress while mediating host colonization, transmission dynamics, and microbiome stability. Despite the recognized ecological and biomedical significance of spore-forming Bacilli and Clostridia, most taxa remain uncultivated, limiting phenotypic characterization of their sporulation capacity. To bridge this knowledge gap, we developed SpoMAG, an ensemble machine learning framework that predicts sporulation potential of metagenome-assembled genomes (MAGs) through supervised classification models trained on the presence/absence of 160 sporulation-associated genes. This R-based tool integrates Random Forest and support vector machine algorithms, achieving probabilistic predictions with high performance (AUC = 92.2%, F1-score = 88.2%). Application to fecal metagenomes from humans, cattle, poultry, and swine identified 63 putatively spore-forming MAGs exhibiting distinct host- and order-specific patterns. Bacilli MAGs from Bacillales and Paenibacillales orders showed high sporulation probabilities and gene richness, while Clostridia MAGs exhibited more heterogeneous profiles. Predictions included undercharacterized families in the spore-forming perspective, such as Acetivibrionaceae, Christensenellaceae, and UBA1381, expanding the known phylogenetic breadth of sporulation capacity. Nine genes were consistently present across all predicted spore-formers (namely pth, yaaT, spoIIAB, spoIIIAE, spoIIIAD, ctpB, ftsW, spoVD, and lgt), suggesting conserved genetic elements across uncultivated Firmicutes for future research. Average nucleotide identity (ANI) analysis revealed seven cases of species-level sharing (ANI value > 95%) among hosts, including a putative novel Acetivibrionaceae species, suggesting possible cross-host transmission facilitated by sporulation. In all 63 genomes predicted to sporulate, we identified nine genes across sporulation steps. In addition, SHapley Additive exPlanations (SHAP) analysis indicated 16 consensus genes consistently contributing to predictions (namely lytH, cotP, spoIIIAG, spoIIR, spoVAD, gerC, yabP, yqfD, gerD, spoVAA, gpr, ytaF, gdh, ypeB, spoVID, and ymfJ), bringing biologically meaningful features across sporulation stages. By combining gene annotation with interpretable machine learning, SpoMAG provides a reproducible and accessible framework to infer sporulation potential in uncultured microbial taxa. This tool enhances targeted investigations into microbial survival strategies and supports research in microbiome ecology, probiotic discovery, food safety, and public health surveillance. SpoMAG is freely available as an R package and expands current capabilities for functional inference in metagenomic datasets.},
}

*Gastrointestinal Microbiome/genetics
*Machine Learning
*Spores, Bacterial/genetics
Animals
Humans
*Firmicutes/genetics/physiology
Cattle
Feces/microbiology
Metagenome
Swine
Phylogeny
Ensemble Learning

@article {pmid41121668,
year = {2025},
author = {Enagbonma, BJ and Modise, DM and Babalola, OO},
title = {Effects of Legume‒Cereal Rotation on Sorghum Rhizosphere Microbial Community Structure and Nitrogen-Cycling Functions.},
journal = {MicrobiologyOpen},
volume = {14},
number = {5},
pages = {e70085},
doi = {10.1002/mbo3.70085},
pmid = {41121668},
issn = {2045-8827},
support = {//This study was supported by the ICGEB Research Project (CRP/ZAF22-03) awarded to O.O.B./ ; },
mesh = {*Sorghum/microbiology/growth & development ; *Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Fabaceae/growth & development/microbiology ; Nitrogen/metabolism ; *Nitrogen Cycle ; Soil/chemistry ; Zea mays/microbiology/growth & development ; *Edible Grain/growth & development/microbiology ; Agriculture/methods ; },
abstract = {Legumes form mutualistic interactions with specific soil microbiomes that fix atmospheric nitrogen and improve soil fertility. However, legume-based rotations influence on soil microorganisms and their correlations with soil physicochemical parameters during subsequent crop development are not yet clear. We examined the shifts in microbial community structure and nitrogen genes via shotgun sequencing across cowpea-sorghum, soybean-sorghum, maize-sorghum rotations, and sorghum without precrops. Precropping in rotation significantly affected N-NO3, clay, and silt, and caused a shift in the rhizosphere microbiome. Actinomycetota was the most predominant bacteria across all the cropping systems, followed by Pseudomonadota, whose composition differed across the cropping systems. Legume in rotation increased the relative abundance of Streptomyces and reduced the relative abundances of Pyxidicoccus, Microbacterium, and Microvirga. Nocardioides and Solirubrobacter predominated in the soil after the maize crops. Shannon index, non-metric multidimensional scaling, and permutational multivariate analysis of variance revealed that crop rotation caused significant differences in both the alpha and beta diversity of the microbial community and the nitrogen-cycling functional genes. The relative abundances of amoC, narH, gltB, glnA, ureC, napA, and napA significantly increased in legume monocrops in rotation. The relative abundances of glnA, gltB, narZ, and narH increased in the soil after maize cropping, whereas sorghum without precrops significantly increased the relative abundances of glnA, narZ, and ureC. Several soil physicochemical parameters drive microbial communities. *S, Na, N-NH4, N-NH3, and P were the most significant environmental variables regulating microbiome and nitrogen-cycling genes by crop rotation. This study supports sustainable agricultural practices and promotes sorghum development through rhizosphere microbiome optimization.},
}

*Sorghum/microbiology/growth & development
*Rhizosphere
*Soil Microbiology
*Microbiota
*Bacteria/classification/genetics/metabolism/isolation & purification
*Fabaceae/growth & development/microbiology
Nitrogen/metabolism
*Nitrogen Cycle
Soil/chemistry
Zea mays/microbiology/growth & development
*Edible Grain/growth & development/microbiology
Agriculture/methods

@article {pmid41121093,
year = {2025},
author = {Jia, Y and He, M and Wang, F and Zhan, Y and Deng, Q and Shen, J and Wang, X and Ran, Q and Huang, W and Ling, Y and Wen, S},
title = {Indole-3-lactic acid protects the gut vascular barrier following intestinal ischemia injury through AhR/Nrf2/STAT3 mediated claudin 2 downregulation.},
journal = {Cell communication and signaling : CCS},
volume = {23},
number = {1},
pages = {447},
pmid = {41121093},
issn = {1478-811X},
support = {82302457//National Natural Science Foundation of China/ ; 82372187//National Natural Science Foundation of China/ ; 82272223//National Natural Science Foundation of China/ ; 23qnpy134//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Animals ; *Receptors, Aryl Hydrocarbon/metabolism ; *NF-E2-Related Factor 2/metabolism ; Mice ; *Reperfusion Injury/metabolism/pathology/drug therapy ; *Down-Regulation/drug effects ; *STAT3 Transcription Factor/metabolism ; *Indoles/pharmacology ; *Intestinal Mucosa/metabolism/drug effects/pathology ; Male ; Mice, Inbred C57BL ; Gastrointestinal Microbiome/drug effects ; *Basic Helix-Loop-Helix Transcription Factors/metabolism ; Tryptophan ; *Intestines/pathology/blood supply/drug effects ; *Protective Agents/pharmacology ; Signal Transduction/drug effects ; },
abstract = {BACKGROUND & AIMS: Dysfunction of the intestinal epithelial barrier (IEB) and gut vascular barrier (GVB) contributes to the development of intestinal ischemia/reperfusion (IR) injury. Tryptophan (TRP), an essential amino acid, plays a crucial role in maintaining intestinal homeostasis, yet its regulatory effects on the GVB following IR remain unexplored. We aimed to better define the role of TRP in intestinal IR in vivo and in vitro.

METHODS: Mice underwent intestinal ischemia/reperfusion (IR) and were fed control, TRP-recommended (TRP-r), or TRP-sufficient (TRP-s) diets. Fecal metagenomic sequencing analyzed microbial composition, and targeted metabolomics quantified tryptophan and its metabolites in intestinal and serum samples. ILA's effects on barrier integrity were assessed via tight junction protein expression and FITC-dextran permeability assays. RNA sequencing of intestinal endothelial cells elucidated mechanisms by which ILA modulated GVB function. The STAT3-claudin 2 relationship was validated in vitro by ChIP-qPCR.

RESULTS: TRP supplementation significantly reshaped the gut microbiota, mitigated tissue damage and enhanced the integrity of both the IEB and GVB. Indole-3-lactic acid (ILA), a key tryptophan metabolite, was identified as an important factor in preserving GVB function. Mechanistically, our results show that the aryl hydrocarbon receptor (AhR)/Nrf2/signal transducer and activator of transcription 3 (STAT3) pathway is essential for ILA-mediated improvement of GVB integrity and downregulation of the pore-forming protein claudin 2.

CONCLUSIONS: Our findings highlight the dual role of ILA in reinforcing both IEB and GVB functions and shed light on the molecular mechanisms underlying ILA's GVB-protective effects. This study implicates that ILA or other AhR-activating metabolites may serve as promising pharmacological agents for alleviating IR-induced intestinal damage.},
}

Animals
*Receptors, Aryl Hydrocarbon/metabolism
*NF-E2-Related Factor 2/metabolism
Mice
*Reperfusion Injury/metabolism/pathology/drug therapy
*Down-Regulation/drug effects
*STAT3 Transcription Factor/metabolism
*Indoles/pharmacology
*Intestinal Mucosa/metabolism/drug effects/pathology
Male
Mice, Inbred C57BL
Gastrointestinal Microbiome/drug effects
*Basic Helix-Loop-Helix Transcription Factors/metabolism
Tryptophan
*Intestines/pathology/blood supply/drug effects
*Protective Agents/pharmacology
Signal Transduction/drug effects

@article {pmid41005300,
year = {2025},
author = {Zhao, CN and Li, SS and Yau, T and Chen, WQ and Ji, R and Guan, XY and Kong, FS},
title = {Phocaeicola vulgatus induces immunotherapy resistance in hepatocellular carcinoma via reducing indoleacetic acid production.},
journal = {Cell reports. Medicine},
volume = {6},
number = {10},
pages = {102370},
doi = {10.1016/j.xcrm.2025.102370},
pmid = {41005300},
issn = {2666-3791},
mesh = {*Carcinoma, Hepatocellular/microbiology/therapy/immunology/metabolism/pathology ; Humans ; *Indoleacetic Acids/metabolism ; *Liver Neoplasms/microbiology/therapy/immunology/metabolism/pathology ; Animals ; *Immunotherapy/methods ; Mice ; CD8-Positive T-Lymphocytes/immunology ; *Drug Resistance, Neoplasm ; Male ; Cell Line, Tumor ; Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Programmed Cell Death 1 Receptor/antagonists & inhibitors ; *Enterobacteriaceae ; Female ; },
abstract = {Immunotherapy has made remarkable achievements in various cancers, but response rates in hepatocellular carcinoma (HCC) remain highly variable. Understanding mechanisms behind this heterogeneity and identifying responsive patients are urgent clinical challenges. In this study, the metagenomic analysis of 65 HCC patients reveals distinct gut microbiota profiles distinguishing responders (Rs) from non-responders (NRs). These findings are further validated through fecal microbiota transplantation (FMT) in mouse models. Notably, Phocaeicola vulgatus (P. vulgatus) is enriched in NRs and diminishes anti-PD-1 efficacy in both syngeneic and orthotopic tumor models. Mechanistically, P. vulgatus suppresses the production of indoleacetic acid (IAA), thereby weakening interferon (IFN)-γ[+] and granzyme B (GzmB)[+]CD8[+] T cells and impairing the antitumor immune response. Furthermore, supplementation with IAA restores CD8[+] T cell cytotoxicity and counteracts the immune-suppressive effects of P. vulgatus. Our findings establish a causal relationship between P. vulgatus and anti-PD-1 resistance in HCC, highlighting IAA as a potential therapeutic target to enhance immunotherapy outcomes.},
}

*Carcinoma, Hepatocellular/microbiology/therapy/immunology/metabolism/pathology
Humans
*Indoleacetic Acids/metabolism
*Liver Neoplasms/microbiology/therapy/immunology/metabolism/pathology
Animals
*Immunotherapy/methods
Mice
CD8-Positive T-Lymphocytes/immunology
*Drug Resistance, Neoplasm
Male
Cell Line, Tumor
Gastrointestinal Microbiome
Mice, Inbred C57BL
Programmed Cell Death 1 Receptor/antagonists & inhibitors
*Enterobacteriaceae
Female

@article {pmid40985733,
year = {2025},
author = {Romero, JL and Ratliff, JH and Carlson, CJ and Griffiths, DR and Miller, CS and Mosier, AC and Roane, TM},
title = {Community and functional stability in a working bioreactor degrading 1,4-dioxane at the Lowry Landfill Superfund Site.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {10},
pages = {e0057425},
doi = {10.1128/aem.00574-25},
pmid = {40985733},
issn = {1098-5336},
mesh = {*Dioxanes/metabolism ; Biodegradation, Environmental ; *Bioreactors/microbiology ; *Bacteria/metabolism/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics/analysis ; Waste Disposal Facilities ; *Water Pollutants, Chemical/metabolism ; *Microbiota ; Phylogeny ; },
abstract = {UNLABELLED: 1,4-dioxane (dioxane) is an emerging contaminant that poses risks to human and environmental health. Bacterial dioxane degradation is increasingly being studied as a method to remove dioxane from contaminated water. However, there is a lack of studies on microbial community structures and functions within efficient, large-scale, biodegradation-based remediation technologies. The Lowry Landfill Superfund Site (Colorado, USA) uses an on-site, pump-and-treat facility to remove dioxane from contaminated groundwater by biodegradation. Here, 16S rRNA gene and shotgun metagenomic sequencing were used to describe microbial community composition, soluble di-iron monooxygenase (SDIMO) alpha hydroxylases, and potential for dioxane degradation and horizontal gene transfer in bioreactor support media from the facility. Support media showed diverse microbial communities dominated by Nitrospiraceae, Nitrososphaeraceae, and Nitrosomonadaceae. Pseudonocardia was also detected, suggesting a potential presence of known dioxane-degraders. Candidate SDIMOs belonged mostly to Group V, followed by Groups IV, II, and I (based on read depth). The most abundant Group V clade contained 38 proteins that were phylogenetically related to DxmA-like proteins, including that of Pseudonocardia dioxanivorans CB1190 (a known dioxane degrader). Seventeen Lowry contigs containing DxmA-like proteins contained protein-coding genes potentially involved in chemical degradation, transcriptional regulation, and chemical transport. Interestingly, these contigs also included evidence of potential horizontal gene transfer, including toxin-antitoxin proteins, phage integrase proteins, putative transposases, and putative miniature inverted-repeat transposable elements. These findings improve our understanding of potential dioxane biodegradation mechanisms in a functioning remediation system. Further studies are needed to definitively confirm microbial activity and enzymatic activity toward dioxane removal in this site.

IMPORTANCE: As an environmental contaminant, 1,4-dioxane poses risks for water quality and human health. Used as a solvent and chemical stabilizer in a variety of manufacturing and industrial applications, microbiological methods of detoxification and mitigation are of interest. The degradation of 1,4-dioxane by the bacterium Pseudonocardia spp. is the best understood example; however, these studies are largely based on single isolate, bench-scale, or in silico experiments. Consequently, a knowledge gap exists on bacterial degradation of 1,4-dioxane at environmentally relevant concentrations using functioning remediation technologies at scale. This study addresses this gap directly by describing microbial taxa, enzymes, and potential horizontal gene transfer mechanisms associated with an active treatment plant located on a 1,4-dioxane-impacted U.S. Environmental Protection Agency (EPA) superfund site. As 1,4-dioxane contamination gains more attention, these findings may prove useful for future facilities aiming to promote and optimize removal by biodegradation.},
}

*Dioxanes/metabolism
Biodegradation, Environmental
*Bioreactors/microbiology
*Bacteria/metabolism/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics/analysis
Waste Disposal Facilities
*Water Pollutants, Chemical/metabolism
*Microbiota
Phylogeny

@article {pmid40981429,
year = {2025},
author = {Ferretti, P},
title = {The gut remembers: the long-lasting effect of medication use on the gut microbiome.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0107625},
doi = {10.1128/msystems.01076-25},
pmid = {40981429},
issn = {2379-5077},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; Anti-Bacterial Agents/pharmacology/adverse effects ; Electronic Health Records ; Proton Pump Inhibitors/pharmacology ; Feces/microbiology ; },
abstract = {Growing evidence suggests that antibiotics and many human-targeted medications can alter the gut microbiome composition, but the persistence of these effects remains unclear. In their article, Aasmets and colleagues (O. Aasmets, N. Taba, K. L. Krigu, R. Andreson, et al., mSystems e00541-25, 2025, https://doi.org/10.1128/msystems.00541-25) leveraged electronic health records (EHR) and stool metagenomic data from 2,509 individuals to assess the impact of past medication use (up to 5 years prior to sampling) on the gut microbiome composition. They found that nearly half of the 186 tested drugs had long-term effects, with antibiotics, beta-blockers, benzodiazepine derivatives, proton-pump inhibitors, and antidepressants associated with microbiome changes that persisted for years after intake. For some medications, the effects were additive, with greater impact observed after repeated use. Overall, the authors highlight how medication use in the years preceding sample collection represents an often overlooked confounding factor in microbiome studies and emphasize the utility of combining EHR with microbiome data to assess the impact of past medication use.},
}

*Gastrointestinal Microbiome/drug effects
Humans
Anti-Bacterial Agents/pharmacology/adverse effects
Electronic Health Records
Proton Pump Inhibitors/pharmacology
Feces/microbiology

@article {pmid40980873,
year = {2025},
author = {Lai, W and Alberdi, A and Leu, A and de Leon, AVP and Kobel, CM and Aho, VTE and Roehe, R and Pope, PB and Hvidsten, TR},
title = {Metabolic capabilities of key rumen microbiota drive methane emissions in cattle.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0060125},
doi = {10.1128/msystems.00601-25},
pmid = {40980873},
issn = {2379-5077},
support = {0054575-SuPAcow//Novo Nordisk Fonden/ ; 101000213//HORIZON EUROPE European Research Council/ ; FT230100560//Australian Research Council/ ; },
mesh = {Animals ; Cattle/microbiology ; *Methane/metabolism ; *Rumen/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; Animal Feed ; Bacteria/metabolism/genetics/classification ; },
abstract = {UNLABELLED: The rumen microbiome plays a critical role in determining feed conversion and methane emissions in cattle, with significant implications for both agricultural productivity and environmental sustainability. In this study, we applied a hierarchical joint species distribution model to predict directional associations between biotic factors and abundances of microbial populations determined via metagenome-assembled genomes (MAGs). Our analysis revealed distinct microbial differences, including 191 MAGs significantly more abundant in animals with a higher methane yield (above 24 g/kg dry matter intake [DMI]; high-emission cattle), and 220 MAGs more abundant in low-emission cattle. Interestingly, the microbiome community of the low-methane-emission rumen exhibited higher metabolic capacity but with lower functional redundancy compared to that of high-methane-emission cattle. Our findings also suggest that microbiomes associated with low methane yields are prevalent in specific functionalities such as active fiber hydrolysis and succinate production, which may enhance their contributions to feed conversion in the host animal. This study provides an alternate genome-centric means to investigate the microbial ecology of the rumen and identify microbial and metabolic intervention targets that aim to reduce greenhouse gas emissions in livestock production systems.

IMPORTANCE: Ruminant livestock are major contributors to global methane emissions, largely through microbial fermentation in the rumen. Understanding how microbial communities vary between high- and low-methane-emitting animals is critical for identifying mitigation strategies. This study leverages a genome-centric approach to link microbial metabolic traits to methane output in cattle. By reconstructing and functionally characterizing hundreds of microbial genomes, we observe that a low-methane-emission rumen harbors well-balanced, "streamlined" microbial communities characterized by high metabolic capacity and minimal metabolic overlap across populations (low functional redundancy). Our results demonstrate the utility of genome-level functional profiling in uncovering microbial community traits tied to climate-relevant phenotypes.},
}

Animals
Cattle/microbiology
*Methane/metabolism
*Rumen/microbiology/metabolism
*Gastrointestinal Microbiome
*Microbiota
Metagenome
Animal Feed
Bacteria/metabolism/genetics/classification

@article {pmid40960303,
year = {2025},
author = {Qie, J and Cao, M and Xu, M and Zhang, Y and Luo, L and Sun, C and Ke, D and Yuan, S and Jia, W and Qiu, T and Li, T and Du, X and Xiao, C and Hong, Z and Zhang, B},
title = {Multi-cohort analysis unveils novel microbial targets for the treatment of hyperuricemia and gout.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0109125},
doi = {10.1128/msystems.01091-25},
pmid = {40960303},
issn = {2379-5077},
mesh = {Humans ; *Hyperuricemia/microbiology/therapy ; *Gout/microbiology/therapy ; *Gastrointestinal Microbiome/genetics ; Male ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Female ; Cohort Studies ; Uric Acid/metabolism ; Adult ; Aged ; Bacteria/genetics/classification ; Metagenomics ; },
abstract = {The gut microbiota plays a crucial role in the development of hyperuricemia (HUA) and gout. However, the variability in study designs and analytical methods has led to inconsistent conclusions across different studies. Here, we conducted a comprehensive analysis of the gut microbiota associated with HUA and gout by examining 368 16S rRNA sequencing data from four Chinese cohorts, including 159 healthy controls (HC), 136 HUA patients, and 73 gout patients. Our findings indicate that there were significant differences in the gut microbiota composition between the three groups. Specifically, the HUA and gout groups demonstrated an increased abundance of pro-inflammatory bacteria, such as Fusobacterium and Bilophila, while beneficial bacteria known for their anti-inflammatory properties and metabolic benefits, including Christensenellaceae R-7 group, Anaerostipes, and Collinsella, are relatively reduced. Additionally, we developed a predictive model using microbial markers that achieved a high accuracy (area under the curve [AUC] > 0.8) in distinguishing between the HC, HUA, and gout groups. Notably, further metagenomic analysis identified a species-level genome bin (SGB), designated as Phil1 sp00194085, belonging to the order Christensenellales. For the first time, we discovered that this SGB carries a uric acid metabolic gene cluster and possesses enzymes associated with purine metabolism, suggesting its potential role in uric acid metabolism. Overall, our study deepens the understanding of the gut microbiota's role in HUA and gout and lays a foundation for developing innovative therapeutic strategies to effectively control uric acid levels through gut microbiota modulation.In this study, we conducted a comprehensive analysis of gut microbiota across multiple cohorts, identifying distinct microbial signatures in healthy controls, hyperuricemia (HUA), and gout patients. We observed an increase in pro-inflammatory bacteria and a decrease in beneficial bacteria for host metabolism in both the HUA and gout groups. Additionally, we developed a predictive model with high accuracy (area under the curve [AUC] > 0.8) based on microbial markers and discovered a novel species with potential for uric acid metabolism, providing new therapeutic targets for HUA and gout.},
}

Humans
*Hyperuricemia/microbiology/therapy
*Gout/microbiology/therapy
*Gastrointestinal Microbiome/genetics
Male
RNA, Ribosomal, 16S/genetics
Middle Aged
Female
Cohort Studies
Uric Acid/metabolism
Adult
Aged
Bacteria/genetics/classification
Metagenomics

@article {pmid40960301,
year = {2025},
author = {Yan, Y and Zhao, X and Liang, X and Xue, Y and Niu, Q and Li, D and Zhou, X and Li, Y and Dong, S and Gai, Y},
title = {Global wastewater microbiome reveals core bacterial community and viral diversity with regional antibiotic resistance patterns.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0142824},
doi = {10.1128/msystems.01428-24},
pmid = {40960301},
issn = {2379-5077},
support = {BLX202162//Central University Basic Research Fund of China/ ; },
mesh = {*Wastewater/microbiology/virology ; *Microbiota/genetics ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Drug Resistance, Microbial/genetics ; Humans ; Metagenome ; *Viruses/genetics/classification/isolation & purification ; Metagenomics ; Drug Resistance, Bacterial ; Biodiversity ; },
abstract = {Municipal wastewater treatment plants (WWTPs) serve as global repositories for diverse and dynamic microbial communities, reflecting the complex interplay of human activities, environmental conditions, and public health challenges. Despite their importance, a comprehensive understanding of the global distribution, composition, and functional roles of these microbial ecosystems has remained elusive. Here, we present a comprehensive analysis of bacterial and viral diversities in global wastewater systems by examining 575 sampling sites across 74 cities in 60 countries. Through metagenomic analysis, we reconstructed 12,758 non-redundant bacterial metagenome-assembled genomes (MAGs) spanning 70 phyla, with 4,499 MAGs representing novel species. Despite considerable regional variation, we identified a consistent core microbiome present across 70% of global samples predominantly comprising Proteobacteria. We further assembled 1.7 million viral genomes, revealing unprecedented viral diversity with over 1.5 million species-level viral operational taxonomic units (vOTUs). Network analysis demonstrated that transport proteins play crucial roles in maintaining WWTP functional resilience against disturbances. Machine learning approaches effectively predicted continental origins of wastewater samples based on microbial signatures, confirming that microbial communities reflect local environmental and socioeconomic conditions while maintaining functional conservation. We observed significant variation in the antibiotic resistance gene (ARG) distribution, with elevated prevalence in certain African and Asian regions compared to Europe and North America. Our results establish wastewater microbiomes as important indicators of human activity and provide critical insights for advancing environmental monitoring, antimicrobial resistance surveillance, and wastewater-based epidemiology.IMPORTANCEIntensifying urbanization and human activities have dramatically increased global wastewater generation, creating complex microbial ecosystems that significantly impact environmental and public health. This study presents the first large-scale, comprehensive characterization of bacterial and viral communities in wastewater treatment systems worldwide. By analyzing samples from diverse geographical, climatic, and socioeconomic contexts, we reveal how wastewater microbiomes serve as microbial fingerprints of human society, reflecting regional characteristics while maintaining functional conservation. Our findings demonstrate that these communities function as ecological extensions of human gut microbiota in the external environment, with important implications for the spread of antibiotic resistance and pathogens. The identification of viruses as key metabolic regulators in these systems provides new perspectives on microbial community dynamics. This global-scale analysis advances our understanding of wastewater microbiology and offers valuable insights for improving wastewater management, enhancing environmental monitoring systems, and strengthening public health surveillance through wastewater-based epidemiology.},
}

*Wastewater/microbiology/virology
*Microbiota/genetics
*Bacteria/genetics/classification/drug effects/isolation & purification
*Drug Resistance, Microbial/genetics
Humans
Metagenome
*Viruses/genetics/classification/isolation & purification
Metagenomics
Drug Resistance, Bacterial
Biodiversity

@article {pmid40956075,
year = {2025},
author = {Yu, D and Mai, Y and Zhang, L and Xiao, Y and Zhang, M and Shao, B and Chen, B and Wang, T and Zhang, K and Zhang, L and Gao, N and Zhang, J and Yan, J},
title = {Viral community succession during cadaver decomposition and its potential for estimating postmortem intervals.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {10},
pages = {e0145325},
doi = {10.1128/aem.01453-25},
pmid = {40956075},
issn = {1098-5336},
support = {82030058//National Natural Science Foundation of China/ ; 82101977//National Natural Science Foundation of China/ ; },
mesh = {Cadaver ; Animals ; Rats ; *Postmortem Changes ; *Viruses/classification/genetics/isolation & purification ; *Microbiota ; Metagenomics ; },
abstract = {UNLABELLED: Microbial communities play a vital role in cadaver decomposition and serve as reliable tools for postmortem interval (PMI) estimation. However, current research focuses primarily on bacterial/fungal communities, though viruses-as Earth's most abundant biological entities-play key roles in biogeochemical cycles by regulating bacterial communities via lysis-lysogeny switching. Viral succession patterns during decomposition remain insufficiently characterized, and their PMI biomarker potential is unexamined. We present metagenomic analysis of viral succession during 35-day decomposition of buried rat cadavers, revealing stage-specific dynamics: early dominance of Peduoviridae (0-3 days), mid-stage proliferation of Herelleviridae (7-21 days), and late-stage resurgence of Peduoviridae (28-35 days). Viral α-diversity exhibits a fluctuating downward trend. β-Diversity analysis (PCoA, ANOSIM, PERMANOVA; P < 0.001) confirmed PMI as a major structural driver (27% variance explained). Nine viral families exhibited significant PMI correlations (P < 0.05): Zierdtviridae, Casjensviridae, Schitoviridae, and Ackermannviridae showed strong negative correlations (r = -0.82 to -0.78), while Straboviridae correlated positively (r = 0.59). Using integrated viral abundance data, our Extremely Randomized Trees model achieved exceptional PMI prediction accuracy (test set: R[2] = 0.96, MAE = 2.54 days). Spearman correlations between dominant bacterial phyla (Bacteroidota, Bacillota, etc.) and viral families, combined with Procrustes analysis (M[2] =0.3385, P = 0.001) and Mantel tests (r = 0.8059, P = 0.001), confirmed strong virus-bacteria community consistency. This indicates viruses may regulate decomposition by targeting bacteria for lysis, releasing nutrients (e.g., organic nitrogen/phosphorus) to drive bacterial succession. Our study establishes a novel virus-based PMI prediction tool and discusses ecological drivers of decomposition.

IMPORTANCE: We present a viral succession-based framework for estimating PMI in buried remains. Our study identifies stage-specific viral biomarkers and identified nine viral families significantly correlated with PMI. By combining metagenomics and machine learning, we developed an Extremely Randomized Trees (ERT) model that achieved a low prediction error (test set: R² = 0.96, MAE = 2.54 days). Furthermore, our findings demonstrate that viral and bacterial communities exhibit significant consistency and correlation during cadaver decomposition. This study not only provides a novel tool for the accurate estimation of forensic PMI but also advances our insight into viral regulation of bacteria and their interactions during cadaver decomposition.},
}

Cadaver
Animals
Rats
*Postmortem Changes
*Viruses/classification/genetics/isolation & purification
*Microbiota
Metagenomics

@article {pmid40952003,
year = {2025},
author = {Sun, T and Zheng, Q and Huang, R and Yang, L and Liu, Z and Zhang, Z and Liu, X and Yang, H and Li, X and Tong, J and Zhu, L},
title = {Exploring cervicovaginal microbiome differences between single and multiple endometrial polyps: implications for non-invasive classification.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0002325},
doi = {10.1128/msystems.00023-25},
pmid = {40952003},
issn = {2379-5077},
support = {2022-PUMCH-A-264//National High Level Hospital Clinical Reasearch Fungding/ ; 2022-PUMCH-A-042//National High Level Hospital Clinical Reasearch Fungding/ ; L232074//Natural Science Foundation of Beijing Municipality/ ; 2021-12M-C&TA-008//CAMS Innovation Funds for Medical Sciences/ ; 2022-PUMCH-C-031//National High Level Hospital Clinical Resarch Funding/ ; 2022-PUMCH-C-060//National High Level Hospital Clinical Research Funding/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; *Microbiota/genetics ; Adult ; *Polyps/microbiology/classification ; *Cervix Uteri/microbiology ; Metagenomics/methods ; Endometrium/microbiology/pathology ; Middle Aged ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Single and multiple endometrial polyps (EP) are common gynecological conditions with differing recurrence rates, influencing clinical treatment decisions. This study aimed to characterize the reproductive tract microbiome in both subtypes to support the development of methods for the non-invasive categorization of EPs. Using metagenomic sequencing, we analyzed vaginal and cervical samples from 27 reproductive-aged patients with single EP and 22 with multiple EP. Compared with controls and multiple EP cases, single EP vaginal and cervical samples exhibited a lower percentage of community state types (CST) I and II. Sneathia amnii was identified as a characteristic species in both the vagina (P = 0.0051) and cervix (P = 0.0398) of single EP patients compared with controls. Mesorhizobium sp. (vaginal P = 0.0110, cervical P = 0.0210), Acinetobacter baumannii (vaginal P = 8.0 × 10[-5], cervical P = 0.0314), and Pasteurella multocida (vaginal P = 0.0173, cervical P = 0.0210) were enriched in single EP compared with multiple EP. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of vaginal microbiome revealed unique pathways in single EP, including aminoacyl-tRNA biosynthesis, pantothenate and coenzyme A (CoA) synthesis, pyrimidine metabolism, glycolysis/gluconeogenesis, and biosynthesis of phenylalanine, tyrosine, and tryptophan. Using a random forest model, we further selected microbiota and clinical parameters to differentiate single and multiple EPs, thus achieving an area under curve (AUC) of 0.861. Our findings characterized the composition of the cervicovaginal microbiota of single and multiple EPs and proposed biomarkers for their non-invasive classification based on a random forest model.IMPORTANCEThe prevalence rate of endometrial polyps (EPs), a common gynecological condition, varies between 7.8% and 34.9%. Multiple EPs are associated with higher recurrence rates and chronic endometritis than single EPs and thus require more aggressive clinical interventions. However, only laparoscopic surgery can accurately identify single and multiple polyps. Non-invasive adjunctive diagnostic methods can aid in altering surgical indications preoperatively. Using metagenomic sequencing, we thoroughly analyzed the vaginal and cervical samples of 27 single EP and 22 multiple EP patients of reproductive age. We then identified distinct microbial patterns in the single and multiple samples, which were crucial for understanding EP pathogenesis and its association with gynecological health. Using a random forest model, key bacterial taxa that differentiate single and multiple EPs were identified with high accuracy. These could potentially serve as non-invasive diagnostic biomarkers. This research delineates the cervicovaginal microbiome of the reproductive tract in EP patients, offering a basis for developing non-invasive diagnostic tools and personalized treatment strategies.},
}

Humans
Female
*Vagina/microbiology
*Microbiota/genetics
Adult
*Polyps/microbiology/classification
*Cervix Uteri/microbiology
Metagenomics/methods
Endometrium/microbiology/pathology
Middle Aged
Bacteria/classification/genetics/isolation & purification

@article {pmid40952001,
year = {2025},
author = {Raich, SS and Majzoub, ME and Haifer, C and Paramsothy, S and Shamim, MMI and Borody, TJ and Leong, RW and Kaakoush, NO},
title = {Bacterial taxonomic and functional changes following oral lyophilized donor fecal microbiota transplantation in patients with ulcerative colitis.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0099125},
doi = {10.1128/msystems.00991-25},
pmid = {40952001},
issn = {2379-5077},
support = {988415//Crohn's and Colitis Foundation/ ; APP2011047//National Health and Medical Research Council/ ; Investigator grant//National Health and Medical Research Council/ ; Scientia fellowship//University of New South Wales/ ; },
mesh = {Humans ; *Colitis, Ulcerative/therapy/microbiology ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Freeze Drying ; Female ; Male ; Administration, Oral ; Double-Blind Method ; Feces/microbiology ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; },
abstract = {UNLABELLED: Oral lyophilized fecal microbiota transplantation (FMT) can induce remission in patients with active ulcerative colitis (UC); however, our understanding of how this form of FMT alters the patient microbiome remains limited. Here, we analyzed data from a recent randomized, double-blind, placebo-controlled clinical trial of FMT in UC to assess donor species colonization and factors responsible for efficacy using this form of therapy. The gut microbiome of donors and patients was profiled longitudinally using deep shotgun metagenomic sequencing, and microbiome diversity, species-genome bin presence, functional profiles, and the resistome were studied. The gut microbiome of patients treated with oral lyophilized FMT significantly increased in species-genome bin richness and shifted in composition toward the donor profiles; this was not observed in patients receiving placebo. While species-genome bin richness was not associated with clinical response in this trial, we identified donor- and patient-specific features associated with the induction of remission and maintenance of response. However, the presence of a Clostridium species-genome bin, as well as L-citrulline biosynthesis contributed by Alistipes spp., was seen in responders treated by either donor. Several of the above outcomes were found to be consistent when data were analyzed at the level of metagenome-assembled genomes. FMT was also found to deplete the resistome within patients treated with antibiotics to levels lower than the UC baseline. Single donor oral lyophilized FMT substantially modifies taxonomic diversity and composition as well as microbiome function and the resistome in patients with UC, with several features identified as strongly linked to response regardless of the donor used.

IMPORTANCE: There is a limited amount of work examining the effects of oral lyophilized fecal microbiota transplantation (FMT) on the microbiome of patients with ulcerative colitis (UC), and less so studies examining species-level dynamics and functional changes using this form of FMT. We performed deep shotgun metagenomic sequencing to provide an in-depth species-genome bin-level analysis of the microbiome of patients with UC receiving oral lyophilized FMT from a single donor. We identified key taxonomic and functional features that transferred into patients and were associated with clinical response. We also determined how FMT impacts the resistome of patients with UC. We believe these findings will be important in ongoing efforts to not only improve the efficacy of FMT in UC but also allow for the transition to defined microbial therapeutics, foregoing the need for FMT donors.},
}

Humans
*Colitis, Ulcerative/therapy/microbiology
*Fecal Microbiota Transplantation/methods
*Gastrointestinal Microbiome
Freeze Drying
Female
Male
Administration, Oral
Double-Blind Method
Feces/microbiology
Adult
*Bacteria/classification/genetics/isolation & purification
Middle Aged

@article {pmid40928232,
year = {2025},
author = {Allman, HM and Bernate, EP and Franck, E and Oliaro, FJ and Hartmann, EM and Crofts, TS},
title = {Preparation of functional metagenomic libraries from low biomass samples using METa assembly and their application to capture antibiotic resistance genes.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0103925},
doi = {10.1128/msystems.01039-25},
pmid = {40928232},
issn = {2379-5077},
mesh = {*Metagenomics/methods ; *Gene Library ; *Drug Resistance, Microbial/genetics ; Metagenome ; Biomass ; Bacteria/genetics ; Humans ; Microbiota/genetics ; },
abstract = {A significant challenge in the field of microbiology is the functional annotation of novel genes from microbiomes. The increasing pace of sequencing technology development has made solving this challenge in a high-throughput manner even more important. Functional metagenomics offers a sequence-naive and cultivation-independent solution. Unfortunately, most methods for constructing functional metagenomic libraries require large input masses of metagenomic DNA, putting many sample types out of reach. Here, we show that our functional metagenomic library preparation method, METa assembly, can be used to prepare useful libraries from much lower input DNA quantities. Standard methods of functional metagenomic library preparation generally call for 5-60 µg of input metagenomic DNA. We demonstrate that the threshold for input DNA mass can be lowered at least to 30.5 ng, a 3-log decrease from prior art. We prepared functional metagenomic libraries using between 30.5 ng and 100 ng of metagenomic DNA and found that despite their limited input mass, they were sufficient to link MFS transporters lacking substrate-specific annotations to tetracycline resistance and capture a gene encoding a novel GNAT family acetyltransferase that represents a new streptothricin acetyltransferase, satB. Our preparation of functional metagenomic libraries from aquatic samples and a human stool swab demonstrates that METa assembly can be used to prepare functional metagenomic libraries from microbiomes that were previously incompatible with this approach.IMPORTANCEBacterial genes in microbial communities, including those that give resistance to antibiotics, are often so novel that sequencing-based approaches cannot predict their functions. Functional metagenomic libraries offer a high-throughput, sequence-naive solution to this problem, but their use is often held back due to their need for large quantities of metagenomic DNA. We demonstrate that our functional metagenomic library preparation method, METa assembly, can prepare these libraries using as little as ~30 ng of DNA, approximately 1,000-fold less than other methods. We use METa assembly to prepare functional metagenomic libraries from low-biomass aquatic and fecal swab microbiomes and show that they are home to novel tetracycline efflux pumps and a new family of streptothricin resistance gene, respectively. The efficiency of the METa assembly library preparation method makes many otherwise off-limits, low-biomass microbiome samples compatible with functional metagenomics.},
}

*Metagenomics/methods
*Gene Library
*Drug Resistance, Microbial/genetics
Metagenome
Biomass
Bacteria/genetics
Humans
Microbiota/genetics

@article {pmid40928220,
year = {2025},
author = {Dong, L and Yang, J and Wu, H and Sun, Y and Liu, J and Yuan, H and Wang, M and Dai, Y and Teng, F and Jing, G and Yang, F},
title = {Metagenomic research on the structural difference of plaque microbiome from different caries stages and the construction of a caries diagnostic model.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0004425},
doi = {10.1128/msystems.00044-25},
pmid = {40928220},
issn = {2379-5077},
support = {No. 81670979,No. 31300424//National Natural Science Foundation of China/ ; 24-4-4-zrjj-158-jch//Natural Science Foundation of Qingdao Municipality/ ; ZR2024MH235//Natural Science Foundation of Shandong Province/ ; tsqn201909126//Taishan Scholar Award For Young Expert/ ; 202408010669//Shandong Medical and Health Technology Development Project/ ; },
mesh = {*Dental Caries/microbiology/diagnosis ; Humans ; *Dental Plaque/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Child ; Female ; Male ; Child, Preschool ; },
abstract = {Development of dental caries is a dynamic process; yet, there is limited knowledge on microbial differences at various stages of caries at higher resolution. To investigate the shifting microbiome profiles across different caries stages, 30 children were enrolled in this study, including 15 caries-active patients and 15 caries-free individuals. Plaque samples were collected from the buccal surface of caries-free subjects, defined as confident health (CH; n = 15). For caries-active individuals, plaque samples were collected from non-cavitated surfaces (defined as relative health [RH], n = 15), enamel caries (EC; n = 15), and dentin caries samples (DC; n = 15). All the above samples were sequenced through the 2bRAD sequencing platform to reveal the microbial community structures in each group. We identified significant differences in microbial community structures from different caries stages. First, the CH group showed the highest species richness (P < 0.05), and then followed by the RH and EC groups with lower richness, and the lowest richness was found in the DC group, yet no significant difference was found among the last three groups (P > 0.05). Second, the microbial structure exhibited the greatest difference between CH and DC groups, followed by the distance between RH/EC and DC groups, and the smallest difference was found between RH and EC groups. Third, specific species were found with a significant difference during the different caries stages. Therefore, we developed a diagnostic model using deep learning methods based on neural networks to diagnose different caries stages with an AUC of over 98%. This may provide methodological support for the understanding of the etiological factor in the pathological progression of dental caries.IMPORTANCEThe diagnosis and treatment of dental caries are crucial for human oral health. Previous studies have focused on the microbial differences between caries and healthy teeth, but there was not enough knowledge on the microbial differences at different stages of dental caries. Our findings could provide a high-resolution understanding of the microbial divergencies among different stages of dental caries and thus build microbial-based diagnostic models for differentiating dental caries status using deep learning methods with an accuracy of over 98%. This may provide methodological support for the understanding of the etiological factor in the pathological progression of dental caries.},
}

*Dental Caries/microbiology/diagnosis
Humans
*Dental Plaque/microbiology
*Microbiota/genetics
*Metagenomics/methods
Child
Female
Male
Child, Preschool

@article {pmid40919923,
year = {2025},
author = {Francis, JD and Yanaç, K and Uyaguari-Diaz, MI},
title = {Seasonal patterns of viromes in urban aquatic environments of Manitoba.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {10},
pages = {e0040824},
doi = {10.1128/aem.00408-24},
pmid = {40919923},
issn = {1098-5336},
support = {RGPIN-2022-04508//Natural Sciences and Engineering Research Council of Canada/ ; ALLRP 553987//Natural Sciences and Engineering Research Council of Canada/ ; 322388//University of Manitoba/ ; },
mesh = {Seasons ; Manitoba ; *Virome ; *Wastewater/virology ; *Rivers/virology ; *Water Microbiology ; Metagenomics ; *RNA Viruses/isolation & purification/genetics/classification ; Cities ; *DNA Viruses/isolation & purification/genetics/classification ; },
abstract = {UNLABELLED: Although wastewater treatment plants harbor many pathogens, traditional methods that monitor the microbial quality of surface water and wastewater have not changed since the early 1900s and often disregard the presence of other types of significant waterborne pathogens such as viruses. We used metagenomics and quantitative PCR to assess the taxonomy, functional profiling, and seasonal patterns of DNA and RNA viruses, including the virome distribution in aquatic environments receiving wastewater discharges. Environmental water samples were collected at 11 locations in Winnipeg, Manitoba, along the Red and Assiniboine rivers during the Spring, Summer, and Fall 2021. Samples were filtered and underwent skimmed milk flocculation for viral concentration. The taxonomy of classified DNA was primarily bacteriophages such as Autographiviridae, Kyanoviridae, and Peduoviridae, which were abundant to a lesser extent. Phage-related functionalities such as portal proteins and bacteriophage T4 major head proteins accounted for approximately 20%-40% of aquatic samples across seasons, which may possibly correspond to the DNA phages that were previously identified. RNA viruses went unclassified in the study; however, similar to DNA viruses, many were found to be non-enveloped or "naked viruses" such as Partiviridae, Picobirnaviridae, Tombusviridae, and Picornaviridae, which accounted for 3%-30% of RNA viruses in the study locations across season. Interestingly, aquatic samples were revealed to maintain an abundance of RNA phage-related functionalities such as long tail fiber protein and putative tail proteins, which accounted for approximately 2%-5% of aquatic samples during the Fall of 2021.

IMPORTANCE: Municipal wastewater effluents discharged into the Red and Assiniboine rivers of Winnipeg, Manitoba, rely on traditional methods that monitor the microbial quality of effluents and receiving surface waters focus solely on the detection of coliforms, which are not necessarily good indicators of viruses or other pathogens. There is also a lack of current wastewater system effluent regulations at the federal and provincial level. Furthermore, previous literature has shown that when viral DNA and RNA sequences are blasted against current genomic databases, approximately 50% of the viral reads are classified as unknown. The significance of our research in characterizing the virome distribution in aquatic environments addresses a knowledge gap in the current effluent guidelines and a need for regulatory practices. In the long run, fecal indicator bacteria, combined with the detection of enteric viruses, may complement assessment of water quality in effluents discharged into rivers.},
}

Seasons
Manitoba
*Virome
*Wastewater/virology
*Rivers/virology
*Water Microbiology
Metagenomics
*RNA Viruses/isolation & purification/genetics/classification
Cities
*DNA Viruses/isolation & purification/genetics/classification

@article {pmid40910778,
year = {2025},
author = {Aasmets, O and Taba, N and Krigul, KL and Andreson, R and , and Org, E},
title = {A hidden confounder for microbiome studies: medications used years before sample collection.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0054125},
doi = {10.1128/msystems.00541-25},
pmid = {40910778},
issn = {2379-5077},
support = {PRG1414//Eesti Teadusagentuur/ ; Installation grant 3573//European Molecular Biology Organization/ ; //Biocodex Microbiota Foundation/ ; 16-0125//Estonian Center of Genomics/Roadmap II/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Anti-Bacterial Agents/pharmacology/adverse effects ; Female ; Retrospective Studies ; Middle Aged ; Metagenomics/methods ; Adult ; Electronic Health Records ; Antidepressive Agents ; Aged ; Microbiota/drug effects ; },
abstract = {Medication usage is a known contributor to the inter-individual variability of the gut microbiome. However, medications are often used repeatedly and for long periods, a notion yet unaccounted for in microbiome studies. Recently, we and others showed that not only the usage of antibiotics and antidepressants at sampling, but also past consumption, is associated with the gut microbiome. This effect can be "additive"-the more a medication is used, the stronger the impact on the microbiome. Here, by utilizing retrospective medication usage data from the electronic health records and the observational Estonian microbiome cohort shotgun metagenomics data set (n = 2,509), we systematically evaluate the long-term effects of antibiotics and human-targeted medications on the gut microbiome. We show that past usage of medications is associated with the gut microbiome. For example, the effects of antibiotics, psycholeptics, antidepressants, proton pump inhibitors, and beta-blockers are detectable several years after use. Furthermore, by analyzing a subcohort (n = 328) with a second microbiome characterization, we show that similar changes in the gut microbiome occur after treatment initiation or discontinuation, possibly indicating causal effects.IMPORTANCEThis is the first study using detailed retrospective medication usage data from electronic health records to systematically assess the long-term effects of medication usage on the gut microbiome. We identified carryover and additive effects on the gut microbiome for a range of antibiotics and non-antibiotic medications, such as benzodiazepine derivatives, antidepressants and glucocorticoids, among others. These findings highlight a collateral effect of diverse drug classes on the gut microbiome, which warrants accounting for long-term medication usage history when assessing disease-microbiome associations.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Male
Anti-Bacterial Agents/pharmacology/adverse effects
Female
Retrospective Studies
Middle Aged
Metagenomics/methods
Adult
Electronic Health Records
Antidepressive Agents
Aged
Microbiota/drug effects

@article {pmid41120531,
year = {2025},
author = {Brito, B and DeMaere, M and Lean, I and Hazelton, M and O'Rourke, BA and Holmes, EC and House, JK and Rowe, S and Myers, GSA and Roy Chowdhury, P},
title = {Leveraging metatranscriptomics for the characterisation of bovine blood viromes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36670},
pmid = {41120531},
issn = {2045-2322},
mesh = {Animals ; Cattle ; *Virome/genetics ; *Transcriptome ; *Cattle Diseases/virology/blood/genetics ; Kenya ; *Viruses/genetics/classification ; Gene Expression Profiling ; },
abstract = {Understanding the diversity of the bovine virome is essential for assessing their potential impact on cattle health and transmission risks. Viruses present in the blood comprise both those that establish persistent infections in blood cells and those present during transient viremia. Farm management practices, such as the reuse of syringes for treatments, vaccinations, and supplements, may inadvertently contribute to the spread of blood-borne pathogens, emphasizing the need for improved biosecurity measures. Herein, we used a metatranscriptomic approach to analyse 20 bovine blood transcriptomes from dairy cows in New South Wales, Australia, along with 577 publicly available blood transcriptomes from studies in Australia and Kenya. Our analysis identified several viruses that are known to infect blood cells, transmitted either by direct contact or by vectors, including bovine viral diarrhea virus, bovine gammaherpesvirus 6, hepacivirus, foamy virus, ephemeroviruses and a new species of a coltivirus. Our findings highlight the complexity of the bovine blood virome and underscore the importance of sustained surveillance to identify emerging pathogens and assess their potential role in cattle health. This study provides a framework for integrating transcriptomic data into disease monitoring efforts, ultimately contributing to improved cattle management and biosecurity practices.},
}

Animals
Cattle
*Virome/genetics
*Transcriptome
*Cattle Diseases/virology/blood/genetics
Kenya
*Viruses/genetics/classification
Gene Expression Profiling

@article {pmid41117817,
year = {2025},
author = {Gogoi, R and Bora, SS and Gogoi, B and Naorem, RS and Barooah, M},
title = {Insights into the microbial diversity and functionalities of potential hydrocarbon-degrading bioremediation agents in oil spill sludge of Assam, India.},
journal = {Archives of microbiology},
volume = {207},
number = {12},
pages = {325},
pmid = {41117817},
issn = {1432-072X},
mesh = {India ; Biodegradation, Environmental ; *Hydrocarbons/metabolism ; *Petroleum Pollution/analysis ; *Sewage/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Surface-Active Agents/metabolism ; RNA, Ribosomal, 16S/genetics ; Petroleum/metabolism ; Phylogeny ; Biodiversity ; },
abstract = {Oil spill contamination poses a significant threat to environmental and ecological health, particularly in crude oil-rich regions such as Assam, a north-eastern state of India. This study explores the microbial diversity and functional potential of hydrocarbon-degrading bacteria in crude oil-contaminated sludge. Sludge samples were collected from three contaminated sites in Assam and analyzed for microbial diversity by culture dependent and independent (using 16 S rRNA amplicon sequencing) approaches. Metagenomic analysis revealed a diverse microbial community, with Proteobacteria and Planctomycetes dominating the metagenomes. Seven bacterial isolates, including Diaphorobacter nitroreducens, Lysinibacillus capsici, and Pseudomonas otitidis, were isolated and identified as potential hydrocarbon degraders. The isolates were screened and evaluated for biosurfactant production, hydrocarbon adhesion, and key enzymatic activities involved in degradation. These isolates exhibited significant biosurfactant-producing abilities, with Diaphorobacter nitroreducens MBRG1 showing the highest emulsification index (79%) and strong adherence to hydrocarbons. The enzymatic activities of alkane hydroxylase and alcohol dehydrogenase confirmed the metabolic capabilities of the isolates in hydrocarbon degradation. Optimal growth conditions for biosurfactant production were determined to be pH 7, 30 °C, 2% sucrose as the carbon source, and 3% yeast extract as the nitrogen source. The study highlights the potential of these indigenous bacterial isolates in bioremediation strategies to mitigate oil contamination. Future studies should focus on large-scale bioreactor studies, field trials, and strain improvement of these bacteria to enhance their degradation efficiency and adaptability to varied environmental conditions.},
}

India
Biodegradation, Environmental
*Hydrocarbons/metabolism
*Petroleum Pollution/analysis
*Sewage/microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
Surface-Active Agents/metabolism
RNA, Ribosomal, 16S/genetics
Petroleum/metabolism
Phylogeny
Biodiversity

@article {pmid40897099,
year = {2025},
author = {Ma, X and Zhai, T and Bao, X and Wu, Z and Yang, Y and Yin, R and Cai, C and Liu, G},
title = {Salinity-driven trade-offs between nitrogen removal and microbiome dynamics in Fe-C-CWs toward saline aquaculture tailwater management.},
journal = {Water research},
volume = {287},
number = {Pt B},
pages = {124519},
doi = {10.1016/j.watres.2025.124519},
pmid = {40897099},
issn = {1879-2448},
mesh = {*Salinity ; *Nitrogen ; *Microbiota ; *Aquaculture ; Iron ; Denitrification ; },
abstract = {Salinity-driven nitrogen removal mechanisms in iron-carbon CWs (Fe-C-CWs) remain poorly understood for aquaculture tailwater management. Through a 155-day trial under four salinities (designated as S0, S10, S20, and S30), result showed that S20 achieved optimal removals of total nitrogen (84.9 ± 3.1 %), nitrate (81.8 ± 2.5 %), and ammonium (79.3 ± 3.0 %), significantly outperforming other groups (P < 0.05). Metagenomics revealed that S20 significantly enriched denitrifying taxa (Halothiobacillus, Prolixibacter) and upregulated nitrogen cycling genes (nirB, nrfA, nrfH, hao) and iron cycling genes (feoA, feoB), highlighting the functional synergy between microbial composition and biogeochemical cycling processes. Dual isotope signatures (δ[15]NNO2/ δ[18]ONO2) first applied in Fe-C-CWs confirmed salinity-mediated pathway shifts: nitrite oxidation dominated in saline groups, especially in S20 versus reduction in S0. Enzymatic profiling substantiated the concurrent operation of nitrification, denitrification, and anammox pathways across all groups, with activities exhibiting significant salinity-dependent modulation. S20 demonstrated remarkable enzymatic potentiation, where core nitrogen-cycling enzymes including nitrite oxidoreductase (NXR: 8.79 ± 0.67 U/g), nitrate reductase (NAR: 18.13 ± 1.19 U/g), and nitrite reductase (NIR: 6.74 ± 0.47 U/g) showed 16.00∼32.18 % higher than S0 (P < 0.01). This enzymatic synergy suggests salinity-optimized coupling between dissimilatory iron reduction and nitrogen transformation processes. Ecological network analysis revealed significant interactions among microbial phyla, particularly between Proteobacteria and Planctomycetota. This study demonstrates that S20 can enhance interaction between Fe-C matrix and microorganisms, thereby improving the efficiency of Fe-C-CWs in removing nitrogen pollutants from aquaculture tailwater. These findings offer theoretical insights for further understanding the internal operational mechanisms of the Fe-C-CWs.},
}

*Salinity
*Nitrogen
*Microbiota
*Aquaculture
Iron
Denitrification

@article {pmid40882565,
year = {2025},
author = {Cheng, S and Hu, Y and Gu, X and Xu, X and Duan, X and Li, X and Liu, Z and Jian, Q and Oleskowicz-Popiel, P and Shen, P and Zhou, A and Xue, G and Makinia, J},
title = {Magnetite-enhanced chain elongation via endogenous electron donors through a novel fungi-bacteria microbiome.},
journal = {Water research},
volume = {287},
number = {Pt B},
pages = {124478},
doi = {10.1016/j.watres.2025.124478},
pmid = {40882565},
issn = {1879-2448},
mesh = {*Microbiota ; Bacteria/metabolism ; *Ferrosoferric Oxide ; Fungi/metabolism ; Fermentation ; Fatty Acids/metabolism ; },
abstract = {Anaerobic fermentation of organic waste stream into medium-chain fatty acids (MCFA) through chain elongation (CE) has emerged as a sustainable and eco-friendly approach for resource recovery. Co-culture of yeast with chain elongator achieved a promising endogenous electron donor (ED)-driven CE but was limited by the weak yeast-bacteria synergy. This study presents a novel approach to optimizing the CE process through the regulation of magnetite (0-15 g/L). Results indicated that the 5 g/L of magnetite (Mag-5) achieved MCFA production at 8.42±0.67 g COD/L, which was 2.01 times greater than the blank. In-situ ethanol and lactate served as the ED to drive the CE. Under the optimal condition (Mag-5), Streptococcus (55.83%) and Candida (57.52%) were the dominant ED-producing microorganisms, and Clostridium_sensu_stricto_12 (22.70%) was the dominant chain elongator. In addition, metagenome analysis demonstrated the enhancement in reverse β-oxidization for MCFA production. Furthermore, the truncated tricarboxylic acid cycle was enhanced by magnetite amendment to provide more reduced energy, potentially accelerating the electron transfer within the mixed fungi-bacteria consortia. Finally, the constructed network of fungi and bacteria discerned the substrate competition between yeast and bacteria, and the cooperation among chain elongators, yeast, and mold. This study first proposed to regulate the mixed fungi-bacteria microbiome with magnetite to enhance the in-situ ED-driven CE process, providing a viable approach to the bioconversion of organic streams into high-value products.},
}

*Microbiota
Bacteria/metabolism
*Ferrosoferric Oxide
Fungi/metabolism
Fermentation
Fatty Acids/metabolism

@article {pmid40834728,
year = {2025},
author = {Bains, A and Dahal, S and Manna, B and Lyte, M and Yang, L and Singhal, N},
title = {L-norepinephrine induces community shift, oxidative stress response, metabolic reprogramming, and virulence potential in wastewater microbiomes.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124353},
doi = {10.1016/j.watres.2025.124353},
pmid = {40834728},
issn = {1879-2448},
mesh = {*Oxidative Stress/drug effects ; *Wastewater/microbiology ; Virulence/drug effects ; *Microbiota/drug effects ; *Bacteria/drug effects/pathogenicity/genetics/metabolism ; },
abstract = {Neuroendocrine compounds discharged into wastewater systems represent an emerging challenge at the intersection of human physiology and environmental microbiology. l-norepinephrine (L-NE), which has been recognized to potentiate growth of human and animal bacterial pathogens, is discharged in sewage through urine and faeces. While extensive pure culture studies have established l-NE's capacity to modulate bacterial virulence through iron acquisition and quorum sensing pathways, its impact on complex microbial communities, where intricate metabolic networks and interspecies interactions dominate, remains largely unexplored. This knowledge gap is particularly critical as urbanization drives increasing neuroendocrine compound loads in wastewater influents in metropolitan areas. Through parallel treatments of l-NE (1 × 10[-5] M to 1 × 10[-4] M), dextrose, and H2O2 in municipal and agricultural wastewater communities, we uncovered sophisticated metabolic and regulatory mechanisms that challenge the conventional understanding of microbial substrate utilization. Despite containing 10-fold less carbon, l-NE treatments achieved superior growth (10[8] CFU mL[-1]) while maintaining Pseudomonadaceae-dominated communities. Targeted metaproteomics revealed coordinated upregulation of oxidative stress genes (oxyR, soxRS) and antioxidant enzymes, while proteome-constrained metabolic modeling demonstrated distinct pathway modulation in central carbon and nitrogen metabolism. Notably, when compared to dextrose-supplemented controls, representing typical carbon substrate utilization, l-NE treatments showed similar taxonomic profiles without preferential enrichment of known pathogenic families. However, l-NE significantly enhanced autoinducer gene (luxS, qseC) expression, suggesting increased virulence potential through community-level metabolic reprogramming. These findings reveal l-NE as a potent modulator of microbial community dynamics in engineered ecosystems, with important implications for treatment process stability and downstream environmental impacts.},
}

*Oxidative Stress/drug effects
*Wastewater/microbiology
Virulence/drug effects
*Microbiota/drug effects
*Bacteria/drug effects/pathogenicity/genetics/metabolism

@article {pmid40784283,
year = {2025},
author = {Zhao, J and Wang, Q and Zhao, Y and Guo, J and Ji, Z and Huang, Y and Shen, Q and Liu, Y and Bai, Y and Qi, W and Liu, H and Chen, Y},
title = {Chronic exposure to environmentally-relevant sulfamethoxazole alters ammonia-oxidizing microbial communities in managed aquifer recharge systems.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124298},
doi = {10.1016/j.watres.2025.124298},
pmid = {40784283},
issn = {1879-2448},
mesh = {*Sulfamethoxazole/pharmacology ; *Ammonia/metabolism ; *Groundwater/microbiology ; Archaea/drug effects ; Oxidation-Reduction ; Bacteria/metabolism/drug effects ; Anti-Bacterial Agents ; Microbiota/drug effects ; },
abstract = {Managed aquifer recharge (MAR) is a critical technology for water resource management and purification, yet its capacity to remove antibiotics remains limited. Understanding the response of ammonia-oxidizing microorganisms (AOMs) to antibiotics exposure is essential for optimizing MAR-based antibiotic mitigation strategies. This study investigated the long-term effects of sulfamethoxazole (SMX, ∼500 ng/L) on AOM communities through a 20-month controlled MAR column experiment. Results showed that AOMs (0.4-3.7 % of total microbial abundance) were dominated by ammonia-oxidizing archaea (AOA, 10.2-82.9 %) and complete ammonia oxidizers (comammox, 15.4-89.7 %), with negligible ammonia-oxidizing bacteria (AOB, <2.4 %). Chronic effects of SMX resulted in a 60-67 % reduction in amoA genes across AOA, AOB, and comammox populations, indicating a significant threat to nitrogen cycling. Specifically, SMX suppressed 2-7 AOA metagenome-assembled genomes (MAGs) (e.g., Nitrosotenuis) by 57-95 % and 4-5 comammox MAGs (e.g., Nitrospira) by 23-82 %. Conversely, SMX increased 4-7 AOA MAGs (e.g., Nitrosarchaeum) by 1.4-24.3-fold and 2 comammox MAGs (e.g., Nitrospira) by 1.9-2.0-fold, revealing taxon-specific tolerance. Notably, AOA lineages demonstrated superior resilience to SMX compared to comammox. These findings advance our understanding of antibiotic-driven microbial community dynamics in MAR systems and provide valuable insights for enhancing their performance in antibiotic-polluted environments.},
}

*Sulfamethoxazole/pharmacology
*Ammonia/metabolism
*Groundwater/microbiology
Archaea/drug effects
Oxidation-Reduction
Bacteria/metabolism/drug effects
Anti-Bacterial Agents
Microbiota/drug effects

@article {pmid41115930,
year = {2025},
author = {Fitzjerrells, RL and Meza, LA and Yadav, M and Olalde, H and Hoang, J and Paullus, M and Cherwin, C and Cho, TA and Brown, G and Ganesan, SM and Mangalam, AK},
title = {Multiple sclerosis patients exhibit oral dysbiosis with decreased early colonizers and lower hypotaurine level.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {199},
pmid = {41115930},
issn = {2055-5008},
support = {F31DE033564/DE/NIDCR NIH HHS/United States ; T90DE023520/DE/NIDCR NIH HHS/United States ; R03DE030527/DE/NIDCR NIH HHS/United States ; 1P20NR018081-01/NR/NINR NIH HHS/United States ; 1RO1AI137075//National Institute of Allergy and Infectious Diseases/ ; 1I01CX002212//U.S. Department of Veterans Affairs/ ; P30 ES005605/ES/NIEHS NIH HHS/United States ; },
mesh = {Humans ; *Dysbiosis/microbiology ; Female ; Male ; Adult ; *Taurine/analogs & derivatives/analysis/metabolism ; Middle Aged ; Metagenomics ; *Mouth/microbiology ; *Multiple Sclerosis, Relapsing-Remitting/microbiology ; Metabolomics ; *Bacteria/classification/genetics/isolation & purification ; Microbiota ; Fusobacterium nucleatum/isolation & purification ; Metabolome ; *Multiple Sclerosis/microbiology ; Actinomyces/isolation & purification ; Porphyromonas gingivalis/isolation & purification ; },
abstract = {Although gut microbiome dysbiosis is implicated in the pathobiology of multiple sclerosis (MS), the role of the oral microbiome (OM), the second largest microbiome, remains poorly understood. Additionally, while the salivary metabolome has been linked to other neurodegenerative diseases; its role in people with Relapsing-Remitting MS (pwRRMS), the most prevalent form of MS, is unknown. Combining shotgun metagenomics with untargeted metabolomics, we identified a reduced abundance of several early colonizing species including Streptococcus and Actinomyces in pwRRMS and an enrichment of bacteria with pathogenic potential including Fusobacterium nucleatum, Porphyromonas gingivalis, and several Prevotella species. pwRRMS had an altered metabolite profile including a decreased hypotaurine compared to healthy controls. Thus we report altered oral microbiome and metabolome in pwRRMS which might contribute to MS pathobiology. These findings offer potential microbiome-metabolome based diagnostic biomarkers for MS and pave the way for novel therapeutic interventions to improve disease management and patient outcomes.},
}

Humans
*Dysbiosis/microbiology
Female
Male
Adult
*Taurine/analogs & derivatives/analysis/metabolism
Middle Aged
Metagenomics
*Mouth/microbiology
*Multiple Sclerosis, Relapsing-Remitting/microbiology
Metabolomics
*Bacteria/classification/genetics/isolation & purification
Microbiota
Fusobacterium nucleatum/isolation & purification
Metabolome
*Multiple Sclerosis/microbiology
Actinomyces/isolation & purification
Porphyromonas gingivalis/isolation & purification

@article {pmid41115834,
year = {2025},
author = {Facey, FSB and Maharjan, R and Dinh, H and Buchanan, JS and Connal, LA and Tay, AP and Paulsen, IT and Cain, AK},
title = {Characterising the Multiple-Plastic Degrading Strain of Bacillus subtilis GM_03 From the Galleria mellonella Microbiome.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70216},
doi = {10.1111/1758-2229.70216},
pmid = {41115834},
issn = {1758-2229},
support = {W911NF2320155//US Department of Defense/ ; FT220100152//Australian Research Council Future Fellowship/ ; 20235185//FSBF was supported by Macquarie University Research Excellence Scholarship Programme/ ; },
mesh = {Animals ; *Bacillus subtilis/metabolism/genetics/isolation & purification/classification ; Larva/microbiology ; *Moths/microbiology ; Biodegradation, Environmental ; *Plastics/metabolism ; *Microbiota ; Polyethylene/metabolism ; Polyurethanes/metabolism ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; Gastrointestinal Microbiome ; },
abstract = {Plastic waste is a mounting global problem with over 400 million tons of plastic produced annually and over 50% ending up in landfill after its intended use. Two types of plastics are particularly problematic and are difficult to recycle: low-density polyethylene (LDPE) and polyurethane (PU). Fortuitously, nature may offer a potential solution; Galleria mellonella larvae can digest various plastics, including LDPE, which is believed to be driven by microbes in their gut microbiome. Although some studies have examined their gut microbiota on a metagenomic level, little is known about their ability to degrade plastics. Here, we isolated six bacterial strains from G. mellonella larvae feeding on LDPE. One of them, identified as Bacillus subtilis GM_03, has the capacity to break down commercial PU (Impranil), in addition to LDPE. This bacterium encodes a suite of genes required for plastic degradation. Directed evolution was used to enhance this strain's plastic degrading rate by over six-fold. Sequencing of the evolved culture revealed four genes, srfAB, fadD, appA and citS, associated with this increased PU degradation rate. This is the first time that B. subtilis isolated from G. mellonella larvae has been shown to be capable of degrading multiple types of plastics.},
}

Animals
*Bacillus subtilis/metabolism/genetics/isolation & purification/classification
Larva/microbiology
*Moths/microbiology
Biodegradation, Environmental
*Plastics/metabolism
*Microbiota
Polyethylene/metabolism
Polyurethanes/metabolism
Phylogeny
Bacterial Proteins/genetics/metabolism
Gastrointestinal Microbiome

@article {pmid41112778,
year = {2025},
author = {Dong, Y and Fan, S and He, S and Zhao, W and Lancuo, Z and Sharshov, K and Li, Y and Wang, W},
title = {Comparative analysis of fecal DNA viromes in Large-billed crows and Northern ravens reveals diverse viral profiles.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20170},
pmid = {41112778},
issn = {2167-8359},
mesh = {Animals ; *Crows/virology ; *Feces/virology ; *Virome/genetics ; *DNA, Viral/genetics ; *DNA Viruses/genetics/isolation & purification/classification ; Metagenomics ; },
abstract = {As facultative scavenger birds, crows carry various parasites, viruses, and bacteria, making them significant infection hosts and transmission vectors. In this study, we employed viral metagenomics to enrich viral particles from three fecal samples of the Northern ravens (Corvus corax) and four fecal samples of the Large-billed crows (Corvus macrorhynchos). Viral DNA was then extracted, and seven sequencing libraries were constructed. The composition and characteristics of the DNA viromes in the feces of these two facultative scavenging bird species were analyzed using the Illumina NovaSeq platform (PE150 mode). The results showed that the fecal DNA viruses carried by Northern ravens mainly belonged to Parvoviridae (31.49%), Caudoviricetes_Unclassified (21.91%), Microviridae (21.57%), and Genomoviridae (18.2%), while those carried by Large-billed crows were predominantly Genomoviridae (29.7%), Parvoviridae (26.15%), and Caudoviricetes_Unclassified (22.15%). Diversity analysis using Richness, Shannon, and Simpson indices showed no significant differences in viral composition between the two crow species. Additionally, principal coordinate analysis (PCoA) (F = 1.079, P = 0.155) and non-metric multidimensional scaling (NMDS) (F = 1.079, P = 0.154) analyses demonstrated no distinct separation between the two groups. Moreover, the KEGG-enriched pathways in both crow species were primarily associated with metabolic and genetic information processing functions. The selection of the Large-billed crows and Northern ravens in this study was based on their widespread distribution, close association with human settlements, and distinctive scavenging behavior. Comparative analysis of the diversity and composition of their DNA viral communities offers a basis for evaluating the zoonotic risks associated with these scavenger birds.},
}

Animals
*Crows/virology
*Feces/virology
*Virome/genetics
*DNA, Viral/genetics
*DNA Viruses/genetics/isolation & purification/classification
Metagenomics

@article {pmid41112578,
year = {2025},
author = {Chen, J and Xu, Q and Zhang, L and Zhang, D and Wu, X},
title = {Enrichment of prevotella melaninogenica in the lower respiratory tract links to checkpoint inhibitor pneumonitis and radiation pneumonitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1594460},
pmid = {41112578},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; Middle Aged ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; *Radiation Pneumonitis/microbiology ; *Prevotella/isolation & purification/genetics/classification ; Microbiota ; Lung Neoplasms/drug therapy ; *Immune Checkpoint Inhibitors/adverse effects ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Pneumonia/microbiology ; Lung/microbiology ; },
abstract = {BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) and radiation pneumonitis (RP) lead to anti-cancer therapy discontinuation and poor diagnosis. The human microbiome is related to various respiratory diseases. However, the role of the lung microbiome in CIP and RP remains unknown. Our study aimed to explore the lower respiratory tract (LRT) microbiome in CIP/RP patients.

METHODS: The study enrolled 61 patients with pneumonitis or pneumonia, including 23 with CIP/RP, and 38 with lung cancer with pneumonia (LC-P). Metagenomic next-generation sequencing (mNGS) was performed to identify the microbiota in bronchoalveolar lavage fluid (BALF), and bioinformatics methods were used to compare the microbial differences between CIP/RP and LC-P groups. Correlation analysis was conducted to explore the relationship between LRT microbiota and clinical features.

RESULTS: The Prevotella was the dominant genus in both groups. The Prevotella melaninogenica, which belongs to the Prevotella genus, was the dominant species in the CIP/RP group and the second most abundant species in the LC-P group. Compared to the LC-P group, the CIP/RP group had significantly high levels of Prevotella melaninogenica species and lymphocyte percentage in BALF but significantly low levels of lymphocytes, eosinophils and albumin in peripheral blood. In addition, the Prevotella melaninogenica species had a negative correlation with peripheral blood lymphocytes.

CONCLUSION: The enrichment of Prevotella melaninogenica species in LRT and a decreased level of peripheral blood lymphocytes are associated with CIP/RP.},
}

Humans
Male
Female
Middle Aged
Aged
Bronchoalveolar Lavage Fluid/microbiology
*Radiation Pneumonitis/microbiology
*Prevotella/isolation & purification/genetics/classification
Microbiota
Lung Neoplasms/drug therapy
*Immune Checkpoint Inhibitors/adverse effects
High-Throughput Nucleotide Sequencing
Metagenomics
*Pneumonia/microbiology
Lung/microbiology

@article {pmid41112258,
year = {2025},
author = {Filippi Xavier, L and Gacesa, R and da Rocha, GHO and Broering, MF and Scharf, P and Lima, FDS and Faber, KN and Harmsen, H and Hoffmann, C and Farsky, SHP},
title = {Annexin A1 levels affect microbiota in health and DSS-induced colitis/inflammatory bowel disease development.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1679071},
pmid = {41112258},
issn = {1664-3224},
mesh = {Animals ; *Annexin A1/genetics/metabolism ; *Gastrointestinal Microbiome ; Humans ; Mice ; Mice, Knockout ; *Colitis/chemically induced/microbiology/metabolism ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; *Inflammatory Bowel Diseases/microbiology/metabolism ; Female ; Disease Models, Animal ; Dysbiosis ; Feces/microbiology ; Adult ; Middle Aged ; },
abstract = {BACKGROUND: Inflammatory Bowel Diseases (IBDs) are characterized by intestinal dysbiosis and immune dysregulation. Annexin A1 (AnxA1) promotes epithelial repair and inhibits immune responses during IBD. However, AnxA1's impact on gut microbiota during IBD remains unclear. Here, we experimentally investigated the microbiota profile during colitis in wild-type (WT) and AnxA1-deficient mice (AnxA1[-/-]), and evaluated an observational cohort in IBD patients with high or low AnxA1 expression.

METHODS: Colitis was induced in C57BL/6 WT and AnxA1 [[-]/[-]] mice via oral administration of 2% DSS for six days. Fecal samples were collected at baseline, peak inflammation (day 6), and during the recovery phase (day 10) for 16S rRNA sequencing. Human microbiota data from the Lifelines Dutch Microbiome Project cohort, including IBD and healthy subjects, were analyzed for AnxA1 expression using R software.

RESULTS: Healthy AnxA1[-/-] mice exhibited reduced microbial richness and a distinct gut microbiota composition, marked by increased Proteobacteria and Parasutterella, and reduced Deferribacterota, Campylobacterota, and Verrucomicrobiota. During DSS-induced colitis, AnxA1[-/-] mice showed greater weight loss and heightened inflammation, displaying earlier and more pronounced microbial shifts, including increased Proteobacteria, Cyanobacteria, Parabacteroides, Bacteroides, and Escherichia-Shigella. In contrast, WT mice exhibited delayed changes, with expansion of Alloprevotella, Akkermansia, and Faecalibaculum after day 6. In human IBD samples, Crohn's disease (CD) patients with low AnxA1 expression and active inflammation presented an altered microbiota enriched in Lachnoclostridium and Parabacteroides, while ulcerative colitis (UC) patients showed phylum-level shifts modulated by AnxA1 levels. Notably, non-inflamed CD and UC patients with low AnxA1 differed significantly in microbiota composition. Moreover, inflamed CD patients with high AnxA1 expression showed microbial profiles resembling those of healthy controls, while low AnxA1 expression was associated with a more pronounced dysbiotic state.

CONCLUSION: AnxA1 is implicated in microbiota control under healthy and IBD conditions. Accordingly, the microbiota of healthy AnxA1[-/-] mice, colitic AnxA1[-/-] mice, and IBD patients with low AnxA1 expression exhibit dysbiosis compared to their respective controls. Together, these unprecedented findings reveal AnxA1 as a potential regulatory protein in the immune-microbiota axis involved in IBD pathogenesis.},
}

Animals
*Annexin A1/genetics/metabolism
*Gastrointestinal Microbiome
Humans
Mice
Mice, Knockout
*Colitis/chemically induced/microbiology/metabolism
Mice, Inbred C57BL
Dextran Sulfate
Male
*Inflammatory Bowel Diseases/microbiology/metabolism
Female
Disease Models, Animal
Dysbiosis
Feces/microbiology
Adult
Middle Aged

@article {pmid41112045,
year = {2025},
author = {Zhang, Y and Gilbert, JA and Liu, X and Nie, L and Xu, X and Gao, G and Lyu, L and Ma, Y and Fan, K and Yang, T and Zhang, Y and Zhang, J and Chu, H},
title = {SynCom-mediated herbicide degradation activates microbial carbon metabolism in soils.},
journal = {iMeta},
volume = {4},
number = {5},
pages = {e70058},
pmid = {41112045},
issn = {2770-596X},
abstract = {Extensive herbicide residues in the black soil of northeastern China are considered a significant agricultural pollution threat, yet effective bioremediation of this complex and persistent mixture remains a challenge. We identified 16 bacterial species that associated with these herbicide residues in situ, nine of which were culturable and could degrade multiple herbicides. From these strains, we constructed a four-member synthetic microbial community (SynCom) that degrades multiple herbicides, stabilizes colonization, increases soil bacterial biodiversity, and alters soil enzyme activity. Under laboratory conditions, the SynCom degraded eight herbicides within 48 h with >60% efficiency, and accumulated carbon on the cell surface of the constituent species. In black soil microcosm trials, the SynCom achieved 60%-99% degradation efficiency of the endogenous herbicides over 35 days and was able to consistently maintain biomass above 10[4] cfu/g soil. Additionally, SynCom application resulted in an accumulation of carbohydrate-active enzymes and microbial necromass-associated carbon, which suggests activation of soil microbial carbon metabolism. In support of this, metagenomic analyses identified a significant increase in the abundance of genes involved in the tricarboxylic acid cycle, pyruvate metabolism, and glycolysis. This SynCom represents a compelling bioremediation solution that simultaneously improves soil microbial carbon metabolism activity in polluted soils.},
}

@article {pmid40812483,
year = {2025},
author = {Han, Q and Xia, S and Huang, X and He, J and Yin, Y and Yin, J},
title = {Age-Related Differences in the Gut Microbiota of Pigs Influence Fat Deposition in the Mouse.},
journal = {The Journal of nutrition},
volume = {155},
number = {10},
pages = {3547-3561},
doi = {10.1016/j.tjnut.2025.07.022},
pmid = {40812483},
issn = {1541-6100},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; Swine ; Feces/microbiology ; Age Factors ; Lipid Metabolism ; *Adipose Tissue/metabolism ; RNA, Ribosomal, 16S/genetics ; *Aging ; Male ; Fecal Microbiota Transplantation ; },
abstract = {BACKGROUND: The gut microbiota significantly influences lipid metabolism, but the impact of its developmental patterns at different growth stages on fat deposition remains unclear.

OBJECTIVES: This study aimed to explore the dynamic changes in microbial diversity and composition during the growth of pig models and assess their involvement in fat deposition.

METHODS: Forty-five Duroc-Landrace-Yorkshire (DLY) crossbred pigs were killed at 5 ages: 90, 120, 150, 180, and 210 d of age (n = 9). Fecal samples were collected 1 and 15 d before each killing, and the fecal microbiota were detected by 16S rRNA sequencing. The backfat thickness, serum lipid concentrations, intramuscular fat, and fatty acid content in the longissimus dorsi muscle of pigs were measured to assess lipid metabolism. Fecal microbiota transplantation (FMT) from DLY pigs of different ages to antibiotics-challenged mice (n = 8) was used to confirm the effects of microbial development on fat deposition. Metagenomic sequencing was conducted on feces from pigs aged 150 and 180 d and their corresponding transplanted mice to identify key strains involved in fat deposition.

RESULTS: We observed marked alterations and an increase in intestinal microbial α-diversity with age, peaking at 150 d of age in DLY pigs (P < 0.05). Spearman correlation analyses indicated that 20 genera significantly correlated with the muscle fatty acid contents (P < 0.05). FMT further confirmed that the developmental patterns of the gut microbiota affected host fat deposition, with notable differences observed between the fecal microbiota at day 150 and 180 of age in pigs. Schaalia canis was identified as a potential key microbial strain involved in the developmental patterns of the gut microbiota-governed fat deposition, and its colonization in mice reduced fat deposition by downregulating of LXRα/β gene expressions (P < 0.05).

CONCLUSIONS: Gut microbiota development impacts fat deposition in pigs, with S canis capable of inhibiting fat deposition.},
}

Animals
*Gastrointestinal Microbiome/physiology
Mice
Swine
Feces/microbiology
Age Factors
Lipid Metabolism
*Adipose Tissue/metabolism
RNA, Ribosomal, 16S/genetics
*Aging
Male
Fecal Microbiota Transplantation

@article {pmid40790086,
year = {2025},
author = {Wu, L and Lian, W and Bai, R and Chen, H and Wu, J and Li, H and Zhao, L},
title = {METTL3 facilitates colorectal cancer growth through altering the abundance of intestinal Akkermansia muciniphila.},
journal = {Cancer gene therapy},
volume = {32},
number = {10},
pages = {1098-1106},
pmid = {40790086},
issn = {1476-5500},
support = {82203607//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2022M721540//China Postdoctoral Science Foundation/ ; 2021A1515111186//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; 2024A04J6605//Guangzhou Municipal Science and Technology Project/ ; },
mesh = {*Colorectal Neoplasms/pathology/genetics/metabolism/microbiology ; Animals ; Mice ; Humans ; *Gastrointestinal Microbiome ; *Methyltransferases/metabolism/genetics ; Akkermansia ; Cell Line, Tumor ; },
abstract = {Colorectal cancer (CRC) is a prevalent malignant tumor that poses a significant threat to human health; however, the precise mechanism underlying its onset remains elusive. In this study, we utilized metagenomic sequencing to reveal the dysregulation of intestinal microbiota caused by CRC. Single-cell sequencing data showed elevated mRNA expression of methyltransferase-like protein 3 (METTL3) in CRC, which was correlated with the abundance of intestinal microbiota. Furthermore, we found that METTL3 promotion of CRC progression is microbiota-dependent. Using induced METTL3[fl/fl] Vil1-cre[+/-] mice, we identified the microbiota regulated by METTL3 in CRC. Our research indicates that METTL3 leads to high expression of HIF1α, which promotes the expression of lipocalin 2 (LCN2) in CRC cells, inhibiting the abundance of Akkermansia muciniphila, thereby promoting CRC progression.},
}

*Colorectal Neoplasms/pathology/genetics/metabolism/microbiology
Animals
Mice
Humans
*Gastrointestinal Microbiome
*Methyltransferases/metabolism/genetics
Akkermansia
Cell Line, Tumor

@article {pmid41038565,
year = {2025},
author = {Habiba, U and Noor, M and Kayani, MUR and Huang, L},
title = {Horizontal gene transfers differentially shape the functional potential of the infant gut metagenome.},
journal = {Life sciences},
volume = {381},
number = {},
pages = {124006},
doi = {10.1016/j.lfs.2025.124006},
pmid = {41038565},
issn = {1879-0631},
mesh = {Humans ; *Gene Transfer, Horizontal ; *Gastrointestinal Microbiome/genetics ; Infant ; Female ; Infant, Newborn ; *Metagenome/genetics ; Cesarean Section ; Male ; Delivery, Obstetric ; Feces/microbiology ; Pregnancy ; },
abstract = {Horizontal gene transfer (HGT) is a major driver of microbial evolution, influencing the metabolic potential of microbial communities. Despite its significance, the consequences of HGT in shaping the microbial metabolic potential remain poorly understood, particularly in complex environments such as the human gut. This study aimed to assess the impact of HGT in infant gut microbiome from Caesarean section (CSD) and vaginal delivery (VD) groups during the first year of life. At Month 0, CSD infants exhibited a higher number of HGT events than VD infants. However, the numbers converged around Month 2 and remained comparable until Month 9, with no significant differences between groups (p > 0.05). HGT in VD was primarily driven by Coprococcus catus and Ruminococcus sp_5_1_39BFAA, while in CSD, Salmonella enterica and Klebsiella pneumoniae were dominant donors and acceptors. Functional analysis revealed that HGT in VD enriched genes related to carbohydrate metabolism and immune responses, whereas CSD was enriched for metabolic processes and biofilm formation. Additionally, HGT events were associated with Neonatal Intensive Care Unit Admission and diet transitions. These results suggest that HGT events in the VD and CSD groups differently shape the functional potential of the infant gut microbiome, with possible health implications that require further investigation. However, experimental validation is needed to establish a causal link.},
}

Humans
*Gene Transfer, Horizontal
*Gastrointestinal Microbiome/genetics
Infant
Female
Infant, Newborn
*Metagenome/genetics
Cesarean Section
Male
Delivery, Obstetric
Feces/microbiology
Pregnancy

@article {pmid40992653,
year = {2025},
author = {Sharma, SP and Cha, MG and Kwon, GH and Song, SH and Park, JH and Kim, MJ and Eom, JA and Lee, KJ and Yoon, SJ and Park, H and Won, SM and Oh, KK and Ham, YL and Baik, GH and Kim, DJ and Suk, KT},
title = {Phocaeicola plebeius oral treatment improve fibrosis by reversing cirrhosis-related hepatic gene dysregulation.},
journal = {Life sciences},
volume = {381},
number = {},
pages = {123979},
doi = {10.1016/j.lfs.2025.123979},
pmid = {40992653},
issn = {1879-0631},
mesh = {Animals ; *Liver Cirrhosis/genetics/microbiology/drug therapy ; Humans ; Mice ; Male ; Gastrointestinal Microbiome/drug effects ; Female ; Gene Expression Regulation/drug effects ; Liver/metabolism/pathology ; Middle Aged ; Administration, Oral ; Dysbiosis ; *Bacteroidetes ; Feces/microbiology ; },
abstract = {BACKGROUND: Bacteroides-centric gut dysbiosis reported to exacerbates liver cirrhosis via inflammation and fibrosis, therefore utilizing Bacteroides species as microbiome-based therapeutic logical to mitigate disease progression.

MATERIALS AND METHODS: Feces were collected from 52 Healthy and 144 Liver cirrhosis individuals for V3-V4 dependent 16rRNA-bsed comparative metagenomics analysis, followed a by microbiome depleted and non-depleted DDC mice model to explain the role of Bacteroidetes phylum classified microbial species P. plebeius in liver fibrosis pathophysiological pathways.

RESULTS: Bacteroides presented cirrhosis-dependent decrease in human and animal microbiome, and negatively correlated to key molecular pattern associated with cirrhosis. P. plebeius significantly reduced in abundance and identified as a microbial biomarker for cirrhosis (AUC = 0.73) and treatment with P. plebeius significantly improved the levels of cirrhosis-related phenotypical and biochemical markers in the microbiome-depleted cirrhosis group. P. plebeius decrease the expression of S100a9, CCR1, ADAM8, TREM2, ITGAM, and MYO5A which are primarily responsible for inducing inflammation in liver cirrhosis. P. plebeius downregulated the fibrosis related genes expression including CD51, PLAT, ITGA3, CXCR4, and TGFBR1 and gene related to extracellular matrix formation including COL1A1, LTBP2, S100A6, and SMCO2. Additionally, P. plebeius treatment decreased the expression of hepatotoxicity-related genes including LPL, KRT18, ALDOA, and MCM10, and increased the expression of FABP1 and RDX. Additionally, P. plebeius normalized the expression of genes connected to two pathophysiological process including TIMP4, TGFB3, S100A8, PLSCR1, MMP8, CXCL4, and BMP.

CONCLUSIONS: Our study revealed P. plebeius as a multifaceted bio-therapeutic candidate that normalized dysregulated gene expression and reversed hepatic inflammation, fibrogenesis, and hepatotoxicity.},
}

Animals
*Liver Cirrhosis/genetics/microbiology/drug therapy
Humans
Mice
Male
Gastrointestinal Microbiome/drug effects
Female
Gene Expression Regulation/drug effects
Liver/metabolism/pathology
Middle Aged
Administration, Oral
Dysbiosis
*Bacteroidetes
Feces/microbiology

@article {pmid41102734,
year = {2025},
author = {Lv, Y and Zhang, L and Zhang, Y},
title = {Clear niche partitioning of nitrite-oxidizing bacteria from the bottom and the slope of Mariana Trench.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {208},
pmid = {41102734},
issn = {2049-2618},
support = {42306104//National Natural Science Foundation of China/ ; 42122043//National Natural Science Foundation of China/ ; 2023M742237//China Postdoctoral Science Foundation/ ; HRSJ-ZSZX-008//Project of Hainan Research Institute/ ; 21TQ1400201//Shanghai Jiao Tong University, Shanghai Pilot Program for Basic Research-Shanghai Jiao Tong University/ ; 2023YFC2812800//National Key Research and Development Program of China/ ; },
mesh = {*Nitrites/metabolism ; Oxidation-Reduction ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Geologic Sediments/microbiology ; Metagenome ; Ecosystem ; Microbiota ; Metagenomics/methods ; Phylogeny ; Nitrogen Cycle ; },
abstract = {BACKGROUND: The hadal zone, characterized by extreme hydrostatic pressure and geographic isolation, hosts microbial communities uniquely adapted to these harsh conditions. While niche partitioning has been observed in other deep-sea environments, its existence within hadal trench ecosystems remains controversial. Focusing on the Mariana Trench, we investigated whether nitrite-oxidizing bacteria (NOB) exhibit depth-stratified ecological specialization between slope (6000-10,000 m) and bottom (> 10,000 m) sediments. By analysing the genomic features and ecological interactions of NOB, we aimed to resolve their functional roles in nitrogen cycling under distinct hadal microniches.

RESULTS: We reconstructed 8 high-quality NOB metagenome-assembled genomes (MAGs) from 58 sediment metagenomes, revealing stark niche differentiation between depth zones. Slope-dominant NOB harboured expanded genetic arsenals for antioxidation (e.g. superoxide dismutase) and osmoprotection (compatible solute transporters), Suggesting enhanced adaptive capacity to pressure-adjacent stresses. Metatranscriptomics revealed 1.48 × (nxrA) and 1.28 × (aclA) greater expression of nitrite oxidation and carbon fixation genes in slope communities than in their bottom counterparts. Network analysis identified slope NOB as keystone taxa with elevated among-module connectivity and intramodule linkages, in contrast with bottom NOB, which exhibited localized nitrate-production gene networks. Functional profiling revealed complementary biogeochemical roles: slope NOB primarily consumed nitrite, whereas bottom populations dominated nitrate synthesis.

CONCLUSION: Our multiomics analysis revealed depth-dependent niche partitioning among hadal NOB, with transcriptional and network evidence supporting distinct pressure adaptation strategies and biogeochemical functions. The slope-bottom differentiation in stress response systems and nitrogen transformation pathways highlights how micron-scale environmental gradients drive microbial specialization in Earth's deepest ecosystems. These findings establish NOB as critical mediators of hadal biogeochemical cycles and provide a framework for understanding microbial resilience in extreme biospheres. Video Abstract.},
}

*Nitrites/metabolism
Oxidation-Reduction
*Bacteria/metabolism/genetics/classification/isolation & purification
*Geologic Sediments/microbiology
Metagenome
Ecosystem
Microbiota
Metagenomics/methods
Phylogeny
Nitrogen Cycle

@article {pmid40846194,
year = {2025},
author = {Han, Y and Cui, J and Guo, P and Yang, S},
title = {Remediation effects of straw combined with microbial agents on cinnamon soils with varying degradation based on metagenomics and untargeted metabolome.},
journal = {Environmental research},
volume = {285},
number = {Pt 5},
pages = {122649},
doi = {10.1016/j.envres.2025.122649},
pmid = {40846194},
issn = {1096-0953},
mesh = {*Soil Microbiology ; Metagenomics ; *Cinnamomum zeylanicum ; *Metabolome ; Soil/chemistry ; Biodegradation, Environmental ; *Environmental Restoration and Remediation/methods ; *Soil Pollutants/metabolism ; Microbiota ; },
abstract = {Microbial agents show potential for improving soil quality and crop yield. However, in the context of different soil degraded degrees, the effects of straw combined with microbial agents on soil microbial communities and their associated metabolic processes remain insufficiently explored. Here, we conducted pot experiments using cinnamon soils at three degradation levels (highly, moderately, and non-degraded), applying straw alone or straw combined with microbial agents during alfalfa cultivation. In this study, we combined metagenomic sequencing and untargeted metabolomics to study the effects of straw and straw combined with microbial agents on soil quality and plant biomass, and metabolites as well as on the network complexity and stability of soil microbial communities. Our findings showed that both straw and straw-microbial agent combinations enhanced the soil quality and alfalfa yield, as well as on the complexity and stability of bacterial networks in highly degraded soils. Meanwhile, the straw-microbial agent combination significantly altered key metabolic pathways (e.g., steroid hormone biosynthesis, cofactor biosynthesis, and nucleotide metabolism) and differentially regulated metabolites (e.g., amino acids/peptides, organosulfur compounds, and alkaloids) compared to straw alone, with distinct effects observed across degradation levels. Overall, the microbial community and their metabolites shaped by straw and straw combined with microbial agents promoted the remediation of degraded soils, ultimately enhancing soil quality and plant biomass. These findings advance the understanding of straw and microbial agents as a synergistic remediation strategy for modulating soil microbial communities and offer practical insights for soil health restoration.},
}

*Soil Microbiology
Metagenomics
*Cinnamomum zeylanicum
*Metabolome
Soil/chemistry
Biodegradation, Environmental
*Environmental Restoration and Remediation/methods
*Soil Pollutants/metabolism
Microbiota

@article {pmid40774558,
year = {2025},
author = {Li, Y and Dai, L and Zhang, L and Shen, X and Zhang, X and Yang, Y and Guan, Y},
title = {Metagenomic insights into the changes of runoff water quality in a deep tunnel drainage system.},
journal = {Environmental research},
volume = {285},
number = {Pt 3},
pages = {122509},
doi = {10.1016/j.envres.2025.122509},
pmid = {40774558},
issn = {1096-0953},
mesh = {*Water Quality ; China ; Water Pollutants, Chemical/analysis ; Rain ; Metagenomics ; Environmental Monitoring ; Microbiota ; *Water Microbiology ; *Metagenome ; Nitrogen ; },
abstract = {Deep tunnel retrofitting of conventional urban drainage systems represents a pivotal strategy for mitigating stormwater pollution and combating flooding. While microbial-driven biogeochemical cycles in stormwater are constrained by taxonomic diversity and environmental variability, the interplay between hydrogeochemical dynamics and microbial functional genes during storage remains poorly characterized. In this study, an in situ stormwater self-purification system was constructed to investigate seasonal water quality evolution, microbial community dynamics, and functional gene regulation in Shenzhen, China. Compared with continuous rainfall events, initial postdrought stormwater events resulted in significantly elevated pollutant loads. Dissolved organic matter analysis revealed that endogenous contaminants accounted for 76 % of the total contaminants, characterized by high microbial bioavailability and low humification after 14 days of storage. The storage of samples favors the enrichment of functional microorganisms such as Plancomycetota, Verrucomicrobiota and Proteobacteria. A quantitative assessment of 62 functional genes linked to carbon (C)/nitrogen (N)/sulfur (S) cycling identified temperature, oxidation‒reduction potential ammonia nitrogen, chemical oxygen demand and total nitrogen as critical drivers of microbial community succession and gene abundance. N cycle genes presented heightened sensitivity to environmental fluctuations, with increased stability and metabolic activity observed in wet season samples. Comparative analysis demonstrated that deep tunnel samples presented more stable functional gene profiles and enriched microbial consortia relative to their surface counterparts. These findings elucidate the mechanistic relationships between hydrogeochemical variables and microbial functional resilience in stormwater storage systems. This work advances the process-level understanding of biochemical cycles mediated by C, N and S transformations, offering actionable insights for optimizing urban drainage infrastructure and microbial-mediated pollution control strategies.},
}

*Water Quality
China
Water Pollutants, Chemical/analysis
Rain
Metagenomics
Environmental Monitoring
Microbiota
*Water Microbiology
*Metagenome
Nitrogen

@article {pmid40617568,
year = {2025},
author = {Tian, G and Zhang, R and Zhao, M and Ye, Z and Dai, T and Chen, D and Zeng, Y and Yang, Y and Zhou, J and Zhang, B and Guo, X},
title = {Biogeochemical stratification governs microbial hydrocarbon degradation potential in a petrochemical contaminated site.},
journal = {Environmental research},
volume = {285},
number = {Pt 1},
pages = {122286},
doi = {10.1016/j.envres.2025.122286},
pmid = {40617568},
issn = {1096-0953},
mesh = {Biodegradation, Environmental ; *Hydrocarbons/metabolism ; *Soil Pollutants/metabolism/analysis ; *Soil Microbiology ; *Petroleum/metabolism ; Groundwater/chemistry/microbiology ; Petroleum Pollution ; Microbiota ; Bacteria/metabolism ; },
abstract = {The success of in situ bioremediation at petrochemical-contaminated sites (defined as those impacted by petrochemical production or accidental release) depends on the structure and functional capacities of indigenous microbial communities, as well as the physicochemical gradients that shape their metabolic potential. While microbial degradation mechanisms are well-documented in homogeneous environments, systematic evaluations of microbial dynamics across environmental compartments (e.g., surface/middle/deep soil vs. groundwater) remain scarce. In this study, we combined chemical profiling with shotgun metagenomic sequencing to characterize layer-specific microbial assemblages and hydrocarbon degradation pathways at a historically contaminated petrochemical site. Total petroleum hydrocarbons (TPHs) were markedly higher in the middle and deep soil layers compared to the surface. In subsurface layers, elevated organic carbon and moisture limited oxygen diffusion, and high concentrations of hydrophobic hydrocarbons imposed toxic stress, together creating a reducing environment that favored anaerobic taxa and pathways such as benzoyl-CoA reductase. In contrast, surface soils, with greater aeration and lower pollutant levels, harbored approximately 50 % greater microbial α-diversity (P < 0.05) and supported more diverse and complex metabolic capabilities. Groundwater showed an 83 % detection frequency of naphthalene, and its high solubility and toxicity selected for specialized degraders. Principal Coordinates Analysis (PCoA) revealed distinct depth-dependent community clustering of microbial communities (P < 0.001), with middle/deep soil microbiomes showing significantly reduced metabolic versatility for xenobiotics (BTEX, PAHs, and derivatives) compared to surface soils and groundwater at the community level. Functional gene annotation identified rate-limiting enzymes in aerobic/anaerobic degradation pathways (dmpK [benzene], badA [ethylbenzene], nahA [naphthalene], and fadA [fatty acid β-oxidation]), and Metagenome-Assembled Genomes (MAGs)-based reconstructions revealed a systemic bias towards anaerobic degradation. These mechanistic insights guide layer-specific in situ bioremediation, integrate environmental gradients with microbial functional potential for targeted treatments, and provide a framework for predicting community succession and functional resilience at petrochemical-contaminated sites.},
}

Biodegradation, Environmental
*Hydrocarbons/metabolism
*Soil Pollutants/metabolism/analysis
*Soil Microbiology
*Petroleum/metabolism
Groundwater/chemistry/microbiology
Petroleum Pollution
Microbiota
Bacteria/metabolism

@article {pmid40209695,
year = {2025},
author = {Yamane, T and Masaoka, T and Ishii, C and Masuoka, H and Suda, W and Kurokawa, S and Kishimoto, T and Mikami, Y and Fukuda, S and Kanai, T},
title = {Factors Contributing to the Efficacy of Fecal Microbiota Transplantation for Diarrhea-Dominant Functional Bowel Disorders.},
journal = {Digestion},
volume = {106},
number = {5},
pages = {469-479},
doi = {10.1159/000545183},
pmid = {40209695},
issn = {1421-9867},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Diarrhea/therapy/microbiology/etiology ; Female ; Feces/microbiology/chemistry ; Male ; Middle Aged ; Adult ; Treatment Outcome ; Gastrointestinal Microbiome ; *Irritable Bowel Syndrome/therapy/microbiology ; Dysbiosis/therapy/microbiology ; Aged ; },
abstract = {INTRODUCTION: In cases of effective fecal microbiota transplantation (FMT) for irritable bowel syndrome (IBS), donor feces have been observed to be enriched in Bifidobacterium spp. Moreover, FMT for functional bowel disease can improve psychiatric symptoms. Although intestinal dysbiosis has received attention as one of the pathophysiologies of IBS, the efficacy of FMT for IBS has not yet been established. In this study, we performed a post hoc analysis of the efficacy of FMT, focusing on metabolites in donor feces.

METHODS: FMT was performed in 12 patients, 8 with refractory diarrhea-predominant IBS and 4 with functional diarrhea (FDr), who were refractory to medical therapy. The donors were family members within a second degree of kinship and differed for each transplant. Fecal characteristics were evaluated before and 12 weeks after transplantation using the Bristol stool scale (BS). BS scores of 3-5 at 12 weeks after transplantation were considered to indicate responders, while BS scores of 6 and 7 indicated nonresponders. Metagenomic and metabolomic analyses of all 12 donor fecal samples were performed to compare the responder and nonresponder groups.

RESULTS: Before transplantation, all patients had BS scores of 6-7, but 12 weeks after transplantation, 6 were considered responders and 6 were nonresponders. Metagenomic analysis showed that effective donor feces contained significantly higher levels of Prevotella than did the ineffective donor feces. Metabolomic analysis showed that effective donor feces contained significantly higher levels of propionate and butyrate and significantly lower lactate levels than did ineffective donor feces.

CONCLUSION: Propionate-, butyrate-, or Prevotella-rich donor feces may contribute to successful FMT in patients with diarrhea-dominant functional gastrointestinal disorders.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Diarrhea/therapy/microbiology/etiology
Female
Feces/microbiology/chemistry
Male
Middle Aged
Adult
Treatment Outcome
Gastrointestinal Microbiome
*Irritable Bowel Syndrome/therapy/microbiology
Dysbiosis/therapy/microbiology
Aged

@article {pmid41102233,
year = {2025},
author = {Kwak, MJ and Park, J and Park, H and Yoon, J and Lee, J and Hahnke, RL and Lee, SW and Kwon, SK and Song, JY and Kim, JF},
title = {Polyphasic and comparative genomic characterization of a novel Mariniflexile species in the rhizosphere microbiome of tomato resistant to bacterial wilt.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36158},
pmid = {41102233},
issn = {2045-2322},
support = {918011-4//Ministry of Agriculture, Food and Rural Affairs/ ; NRF-2023R1A2C3004496//Ministry of Science and ICT, South Korea/ ; NRF-2018R1A6A1A03025607//Ministry of Education, South Korea/ ; },
mesh = {*Solanum lycopersicum/microbiology ; *Rhizosphere ; Phylogeny ; *Plant Diseases/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Genome, Bacterial ; Ralstonia solanacearum ; Soil Microbiology ; Genomics ; Disease Resistance ; },
abstract = {A plethora of microbes resides in the plant rhizosphere, and some play roles in host health and disease. We previously isolated a Gram-negative, aerobic, rod-shaped rhizobacterium, TRM1-10, that contributes to bacterial wilt resistance of tomato caused by Ralstonia solanacearum. In this study, we characterized TRM1-10 through physiological and biochemical analyses, complemented by whole genome sequencing and comparative genomic analyses. Phylogenetic analysis using the 16S rRNA gene and genome sequences revealed that TRM1-10 belongs to the genus Mariniflexile and represents a new lineage. TRM1-10 also exhibits noticeable differences in physiological and biochemical characteristics compared to other Mariniflexile species. Thus, based on phylogenetic affiliation and chemotaxonomic characteristics, we propose this bacterium as a novel species in the genus, Mariniflexile rhizosphaerae sp. nov. (type strain TRM1-10[T] = KCTC 18646P[T] = DSM 33122[T]). Comparative genome analyses revealed that TRM1-10 harbors more genes linked to soil adaptation compared to other phylogenetically related Mariniflexile species, most of which are associated with marine habitats. The genomic features of TRM1-10 and other strains in the species may allow the taxon to adapt to the soil and rhizosphere, compete effectively with the resident soil microbiota, and contribute to plant health.},
}

*Solanum lycopersicum/microbiology
*Rhizosphere
Phylogeny
*Plant Diseases/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Genome, Bacterial
Ralstonia solanacearum
Soil Microbiology
Genomics
Disease Resistance

@article {pmid41100443,
year = {2025},
author = {Shi, F and Zou, D and Zhang, L and Guo, N and Yu, J and Degen, AA and Tang, X and Ren, S and Ru, Y and Zheng, S and Zhang, Y and Wang, D},
title = {Increased urea nitrogen salvaging by a remodeled gut microbiota helps nonhibernating pikas maintain protein homeostasis during winter.},
journal = {PLoS biology},
volume = {23},
number = {10},
pages = {e3003436},
doi = {10.1371/journal.pbio.3003436},
pmid = {41100443},
issn = {1545-7885},
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Nitrogen/metabolism ; *Urea/metabolism ; Seasons ; *Lagomorpha/metabolism/microbiology/physiology ; Homeostasis ; *Proteostasis/physiology ; Feces/microbiology ; Diet, Protein-Restricted ; Male ; Liver/metabolism ; Herbivory ; Fecal Microbiota Transplantation ; },
abstract = {Nitrogen balance is a major challenge for herbivores when consuming a low-nitrogen diet. Gut microbiota-mediated urea nitrogen recycling facilitates protein homeostasis during times of nitrogen deficiency, yet its relevance to wild nonhibernating small mammals remains unclear. Here, through a combination of isotope tracing, metagenomics, targeted short-chain fatty acid analysis, and fecal microbiota transplantation, we investigated the effects of protein restriction in winter on urea nitrogen recycling in plateau pikas (Ochotona curzoniae) of the Qinghai-Tibetan Plateau. Hepatic urea-cycle metabolism was downregulated during winter protein restriction, accompanied by increases in beneficial bacteria with ureolytic capacity (such as the genus Alistipes), gut urease activity, and urea transporters, and acetate production, with a consequent increase in nitrogen reincorporation into the pika's protein pool. Critically, supplementing a low-protein diet with yak fecal microbiota enhanced the ureolytic capacity by increasing Alistipes abundance, revealing a critical mechanism whereby interspecies horizontal microbial transfer between sympatric species enhances host protein homeostasis. Our results reveal a functional role for the gut microbiota in urea nitrogen recycling to maintain protein balance in winter-active herbivorous small mammals and contribute to our understanding of species coexistence and mammalian adaptation to high-altitude environments. Our findings establish that microbiota-driven urea nitrogen recycling is a key adaptive strategy for protein homeostasis in winter-active herbivores. This work provides new insights into the mechanisms of mammalian adaptation to high-altitude environments and the dynamics of interspecies coexistence.},
}

*Gastrointestinal Microbiome/physiology
Animals
*Nitrogen/metabolism
*Urea/metabolism
Seasons
*Lagomorpha/metabolism/microbiology/physiology
Homeostasis
*Proteostasis/physiology
Feces/microbiology
Diet, Protein-Restricted
Male
Liver/metabolism
Herbivory
Fecal Microbiota Transplantation

@article {pmid41099510,
year = {2025},
author = {Wallace, BA and Varona, NS and Stiffler, AK and Vermeij, MJA and Silveira, C},
title = {High microbial diversity, functional redundancy, and prophage enrichment support the success of the yellow pencil coral, Madracis mirabilis, in Curaçao's coral reefs.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0120825},
doi = {10.1128/msystems.01208-25},
pmid = {41099510},
issn = {2379-5077},
abstract = {UNLABELLED: Coral reefs have undergone extensive coral loss and shifts in community composition worldwide. Despite this, some coral species appear naturally more resistant, such as Madracis mirabilis (herein Madracis). Madracis has emerged as the dominant hard coral in Curaçao, comprising 26% of coral cover in reefs that declined by 78% between 1973 and 2015. Although life history traits and competitive mechanisms contribute to Madracis's success, these factors alone may not fully explain it, as other species with similar traits have not shown comparable success. Here, we investigated the potential role of microbial communities in the success of Madracis on Curaçao reefs by leveraging a low-bias bacterial and viral enrichment method for metagenomic sequencing of coral samples, resulting in 77 unique bacterial metagenome-assembled genomes and 2,820 viral genomic sequences. Our analyses showed that Madracis-associated bacterial and viral communities are 12% and 20% richer than the communities of five sympatric coral species combined. The Madracis-associated bacterial community was dominated by Ruegeria and Sphingomonas, genera that have previously been associated with coral health, defense against pathogens, and bioremediation. These communities also displayed higher functional redundancy, which is often associated with ecological resilience. The viral community exhibited a 50% enrichment of proviruses relative to other corals. These proviruses had the genomic capacity to laterally transfer genes involved in antibiotic resistance, central metabolism, and oxidative stress responses, potentially enhancing the adaptive capacity of the Madracis microbiome and contributing to Madracis's success on Curaçao's reefs.

IMPORTANCE: Understanding why some coral species persist and thrive while most are in fast decline is critical. Madracis mirabilis is increasingly dominant on degraded reefs in Curaçao, yet the role of microbial communities in its success remains underexplored. This study highlights the potential role of Madracis-associated bacterial and viral communities in supporting coral resilience and competitive success. By identifying key microbial partners and viral genes that may enhance host stress tolerance and defense against pathogens, we broaden the understanding of how the coral holobiont contributes to species persistence under environmental stress. These insights are valuable for predicting key microbial community players in reef interactions and may inform microbiome-based strategies to support coral conservation and restoration.},
}

@article {pmid41097145,
year = {2025},
author = {Tuigunov, D and Sinyavskiy, Y and Nurgozhin, T and Zholdassova, Z and Smagul, G and Omarov, Y and Dolmatova, O and Yeshmanova, A and Omarova, I},
title = {Precision Nutrition and Gut-Brain Axis Modulation in the Prevention of Neurodegenerative Diseases.},
journal = {Nutrients},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/nu17193068},
pmid = {41097145},
issn = {2072-6643},
support = {Grant No. AP23489983//This research is funded by the Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {Humans ; *Neurodegenerative Diseases/prevention & control/microbiology ; *Gastrointestinal Microbiome/physiology ; *Brain ; *Precision Medicine/methods ; *Brain-Gut Axis/physiology ; Prebiotics/administration & dosage ; Probiotics/administration & dosage ; },
abstract = {In the recent years, the accelerating global demographic shift toward population aging has been accompanied by a marked increase in the prevalence of neurodegenerative disorders, notably Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and multiple sclerosis. Among emerging approaches, dietary interventions targeting the gut-brain axis have garnered considerable attention, owing to their potential to modulate key pathogenic pathways underlying neurodegenerative processes. This review synthesizes current concepts in precision nutrition and elucidates neurohumoral, immune, and metabolic regulatory mechanisms mediated by the gut microbiota, including the roles of the vagus nerve, cytokines, short-chain fatty acids, vitamins, polyphenols, and microbial metabolites. Emerging evidence underscores that dysbiotic alterations contribute to compromised barrier integrity, the initiation and perpetuation of neuroinflammatory responses, pathological protein aggregations, and the progressive course of neurodegenerative diseases. Collectively, these insights highlight the gut microbiota as a pivotal target for the development of precision-based dietary strategies in the prevention and mitigation of neurodegenerative disorders. Particular attention is devoted to key bioactive components such as prebiotics, probiotics, psychobiotics, dietary fiber, omega-3 fatty acids, and polyphenols that critically participate in regulating the gut-brain axis. Contemporary evidence on the contribution of the gut microbiota to the pathogenesis of Alzheimer's disease, Parkinson's disease, and multiple sclerosis is systematically summarized. The review further discusses the prospects of applying nutrigenomics, chrononutrition, and metagenomic analysis to the development of personalized dietary strategies. The presented findings underscore the potential of integrating precision nutrition with targeted modulation of the gut-brain axis as a multifaceted approach to reducing the risk of neurodegenerative diseases and preserving cognitive health.},
}

Humans
*Neurodegenerative Diseases/prevention & control/microbiology
*Gastrointestinal Microbiome/physiology
*Brain
*Precision Medicine/methods
*Brain-Gut Axis/physiology
Prebiotics/administration & dosage
Probiotics/administration & dosage

@article {pmid41094699,
year = {2025},
author = {Serrana, JM and Dessirier, B and Nascimento, FJA and Broman, E and Posselt, M},
title = {Microbial hydrocarbon degradation potential of the Baltic Sea ecosystem.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {204},
pmid = {41094699},
issn = {2049-2618},
support = {Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; },
mesh = {*Hydrocarbons/metabolism ; Biodegradation, Environmental ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Ecosystem ; Metagenome ; Petroleum/metabolism ; Microbiota ; Metagenomics/methods ; *Water Pollutants, Chemical/metabolism ; Oceans and Seas ; },
abstract = {BACKGROUND: The Baltic Sea receives petroleum hydrocarbons from various point sources. The degradation of these contaminants in the environment is typically facilitated by a variety of microorganisms that possess a range of genes and metabolic functions related to the degradation of various hydrocarbon substrates. However, our understanding of natural attenuation and the microbial capacity to degrade these contaminants within the Baltic Sea ecosystem remains limited. In this study, we compiled metagenomes from the benthic and pelagic ecosystems across the Baltic Sea to identify microorganisms and characterize their genes and metabolic functions involved in the degradation of hydrocarbon compounds.

RESULTS: Known hydrocarbon-degrading phyla, i.e., Pseudomonadota, Myxococcota A, Actinomycetota, and Desulfobacterota, were identified within the Baltic Sea metagenome-assembled genomes (MAGs). Notably, 80% of the MAGs exhibited multiple hydrocarbon degradation gene annotations (> 10 reads per kilobase million). Aerobic degradation was the predominant pathway for hydrocarbon degradation across environmental samples. Hydrocarbon degradation gene abundances varied among samples and Baltic Sea subbasins, with long-chain alkanes and dibenzothiophene compounds being the preferred substrates. Species richness and diversity of both benthic and pelagic microorganisms positively correlated with hydrocarbon degradation gene diversity, with the pelagic ecosystem exhibiting significantly higher richness and diversity compared to the benthic ecosystem. Additionally, the composition of the hydrocarbon degradation genes across the Baltic Sea subbasins was influenced by oil spill history, with areas that experienced higher spill volumes showing lower microbial diversity, suggesting potential enrichment of specific hydrocarbon degraders. Among the environmental factors assessed, depth played a significant role in shaping the composition of genes involved in hydrocarbon degradation within the Baltic Sea.

CONCLUSIONS: Using metagenomics, we profiled the native microorganisms associated with hydrocarbon degradation in the Baltic Sea. This knowledge will aid in understanding the natural capacities of microbial communities, potentially linked to the natural attenuation of hydrocarbon pollutants in the area. Insights into microbial degradation potential can enhance predictions of petroleum pollutant persistence and accumulation, support mitigation strategies for marine pollution, and reveal the ecological resilience of native microbial communities in marine ecosystems. Video Abstract.},
}

*Hydrocarbons/metabolism
Biodegradation, Environmental
*Seawater/microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
Ecosystem
Metagenome
Petroleum/metabolism
Microbiota
Metagenomics/methods
*Water Pollutants, Chemical/metabolism
Oceans and Seas

@article {pmid41093983,
year = {2025},
author = {Zhang, J and Sekela, JJ and Hutchinson, LE and Yang, J and Sellers, RS and Bhatt, AP and Redinbo, MR},
title = {Sex-dependent responses in mice to indomethacin-induced organ injury and gut microbiome-targeted alleviation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36025},
pmid = {41093983},
issn = {2045-2322},
support = {NIH R35 award GM152079/NH/NIH HHS/United States ; },
mesh = {Animals ; *Indomethacin/adverse effects/toxicity ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred C57BL ; *Anti-Inflammatory Agents, Non-Steroidal/adverse effects/toxicity ; Sex Factors ; Spleen/drug effects/pathology ; Liver/drug effects/pathology ; Colon/drug effects/pathology ; RNA, Ribosomal, 16S/genetics ; Glucuronidase/antagonists & inhibitors/metabolism ; Sex Characteristics ; },
abstract = {Nonsteroidal anti-inflammatory drugs (NSAIDs) are used widely but produce gastrointestinal (GI) toxicities in both short- and long-term users. Previous studies have shown that the intestinal microbiota play an important role in gut damage and that gut microbial β-glucuronidase (GUS) inhibitors can alleviate NSAID-induced injury in male mice by blocking the GI reactivation of NSAID-glucuronides. Here, in both male and female C57BL/6 mice, we examine the effects of indomethacin alone and with the GUS inhibitor UNC10201652. Oral delivery of 5 mg/kg body weight indomethacin over 5 days decreased body weight, induced colonic and hepatic inflammatory cytokine gene expression, and enlarged the spleens of both male and female mice. However, sex-specific inflammatory responses to indomethacin were observed, with males demonstrating more colonic injury while females presented greater splenic and hepatic toxic responses. Females also showed a unique indomethacin-induced bloom of fecal Verrucomicrobia as measured by 16S rRNA metagenomic sequencing. UNC10201652 alleviated aspects of these indomethacin-induced toxicities, including features of the male-specific colonic damage and the female-specific compositional changes and spleen and liver toxicities. Thus, GI and non-GI tissues in male and female mice respond distinctly to indomethacin-induced damage. These findings advance our understanding of how sex impacts systemic responses to xenobiotic exposure and may lead to improved therapeutic outcomes with these widely used drugs.},
}

Animals
*Indomethacin/adverse effects/toxicity
Female
Male
*Gastrointestinal Microbiome/drug effects
Mice
Mice, Inbred C57BL
*Anti-Inflammatory Agents, Non-Steroidal/adverse effects/toxicity
Sex Factors
Spleen/drug effects/pathology
Liver/drug effects/pathology
Colon/drug effects/pathology
RNA, Ribosomal, 16S/genetics
Glucuronidase/antagonists & inhibitors/metabolism
Sex Characteristics

@article {pmid40915146,
year = {2025},
author = {Leonard, SR and Mammel, MK and Brassill, N and Champ, C and Lacher, DW and Saber, B and Kase, JA and Kataoka, A and Bell, RL and Brown, EW and Rock, CM and Musser, SM},
title = {Air microbiomes reveal presence of Shiga toxin-producing Escherichia coli in airborne cattle pen soil adjacent to large feedlot.},
journal = {The Science of the total environment},
volume = {1000},
number = {},
pages = {180375},
doi = {10.1016/j.scitotenv.2025.180375},
pmid = {40915146},
issn = {1879-1026},
mesh = {Animals ; Cattle ; *Shiga-Toxigenic Escherichia coli/isolation & purification ; *Air Microbiology ; *Soil Microbiology ; *Microbiota ; *Environmental Monitoring ; Animal Husbandry ; },
abstract = {Cattle are a reservoir for the zoonotic human foodborne pathogen Shiga toxin-producing Escherichia coli (STEC), the causative agent of many disease outbreaks associated with contaminated fresh leafy greens. Concentrated animal feeding operations (CAFOs) housing cattle generate fugitive dust, however the potential risk of STEC movement by means of the aerosolized dust is not well known. In this investigation, we used metagenome sequencing of air samples collected in an agricultural setting to investigate airborne transfer of STEC from a large CAFO to the surrounding area. Shiga toxin genes and other E. coli virulence genes were observed in air metagenomes, and their presence was positively correlated with abundance of cattle mitochondrial DNA (mtDNA). Air bacterial community composition differed based on STEC presence, and source tracking utilizing the air metagenomes indicated that cattle feedlot soil contributed to the air bacterial communities. Moreover, a novel biomarker for cattle pen soil, Corynebacterium maris, was identified that correlated with both E. coli virulence gene presence and cattle mtDNA abundance. Overall, our results demonstrate a definitive link between aerosolized cattle feedlot dust and airborne STEC transfer to adjacent and nearby agricultural fields. This work highlights the importance of including the potential for airborne transmission of pathogens in risk assessments for contamination by human foodborne pathogens of fresh produce grown in proximity to CAFOs.},
}

Animals
Cattle
*Shiga-Toxigenic Escherichia coli/isolation & purification
*Air Microbiology
*Soil Microbiology
*Microbiota
*Environmental Monitoring
Animal Husbandry

@article {pmid40812705,
year = {2025},
author = {Gao, H and Guo, Z and Huang, F and Li, S and He, X and Fernio, JU and Lv, W and Zhou, L and Du, S and Shen, M and Xu, R},
title = {Core microbiota with antimonite oxidation coupled nitrogen fixation traits persist in the rhizosphere of pioneer plants in antimony tailings.},
journal = {Environmental research},
volume = {285},
number = {Pt 4},
pages = {122586},
doi = {10.1016/j.envres.2025.122586},
pmid = {40812705},
issn = {1096-0953},
mesh = {*Antimony/metabolism ; *Rhizosphere ; *Nitrogen Fixation ; *Microbiota ; Oxidation-Reduction ; *Soil Pollutants/metabolism ; *Soil Microbiology ; *Poaceae/microbiology ; Mining ; Bacteria ; },
abstract = {Antimony (Sb) tailings pose a dual challenge to plant colonization, combining high metal(loid) toxicity with nitrogen (N) limitation, both of which constrain pioneer plant establishment and hinder ecological restoration. Rhizosphere microbiota, particularly Sb(III) oxidation coupled with nitrogen fixation (SbNF) taxa, are critical in mitigating such stresses. However, the composition and persistence of these functional microbes may vary across plant species, leading to untargeted selection. Here, we investigated the rhizosphere microbiomes of two pioneer species-Miscanthus sinensis (herbaceous) and Boehmeria nivea (shrubby)-in Sb tailings. A shared core microbiota (>20 % of the genera) was identified, within which certain taxa exhibited SbNF capabilities with plant growth-promoting (PGP) potential. Through integrated metagenomic binning, culture-based isolation, and functional validation, we identified core genera, such as Pseudomonas and Streptomyces, that were consistently enriched across plant types and exhibited robust SbNF capacities, versatile PGP traits, and community assembly interactions. These findings reveal a conserved assembly mechanism of functional rhizobacteria in Sb-stressed environments and offer promising microbial candidates for the development of bioinoculants to support phytoremediation in metalloid-contaminated ecosystems.},
}

*Antimony/metabolism
*Rhizosphere
*Nitrogen Fixation
*Microbiota
Oxidation-Reduction
*Soil Pollutants/metabolism
*Soil Microbiology
*Poaceae/microbiology
Mining
Bacteria

@article {pmid40455595,
year = {2025},
author = {Fetters, AM and Cantalupo, PG and Robles, MTS and Pipas, JM and Ashman, TL},
title = {Sharing Pollinators and Viruses: Virus Diversity of Pollen in a Co-Flowering Community.},
journal = {Integrative and comparative biology},
volume = {65},
number = {4},
pages = {942-954},
doi = {10.1093/icb/icaf073},
pmid = {40455595},
issn = {1557-7023},
support = {KA2017-91786//Charles E. Kaufman Foundation/ ; //Kenneth P. Dietrich School of Arts and Sciences/ ; },
mesh = {*Pollination ; *Pollen/virology ; *Plant Viruses/physiology ; *Biodiversity ; Animals ; *Magnoliopsida/virology/physiology ; Flowers/virology ; },
abstract = {Co-flowering plant species frequently share pollinators, flower-inhabiting bacteria, and fungi, but whether pollen-associated viruses are shared is unknown. Given that pollen-associated viruses are sexually transmitted diseases, their diversity is expected to increase with pollinator sharing. We conducted a metagenomic study to identify pollen-associated viruses from 18 co-flowering plant species to determine whether (1) life history, floral traits, or pollination generalism were associated with viral richness, and (2) plants shared pollen-associated viruses. We demonstrated that pollination generalism influences pollen-associated virus richness and the extent of pollen virus sharing between plant species. We also revealed that perenniality, multiple flowers, and bilateral floral symmetry were associated with high pollen viral richness locally, confirming and extending patterns observed previously at a continental scale. Our results highlight the importance of plant-pollinator interactions as drivers of plant-viral interaction diversity.},
}

*Pollination
*Pollen/virology
*Plant Viruses/physiology
*Biodiversity
Animals
*Magnoliopsida/virology/physiology
Flowers/virology

@article {pmid41091222,
year = {2025},
author = {Tajdozian, H and Seo, H and Kim, S and Rahim, MA and Park, HA and Sarafraz, F and Yoon, Y and Kim, H and Barman, I and Park, CE and Ghorbanian, F and Lee, S and Jeong, HR and Song, HY},
title = {Microbiome therapeutic PMC101 inhibits the translocation of carbapenem-resistant Klebsiella while enhancing eubiosis in antibiotic-induced dysbiosis mice.},
journal = {Medical microbiology and immunology},
volume = {214},
number = {1},
pages = {49},
pmid = {41091222},
issn = {1432-1831},
support = {No. RS-2023-00219563//Ministry of Science and ICT, South Korea/ ; P248400003//Korea Institute for Advancement of Technology/ ; },
mesh = {Animals ; *Dysbiosis/chemically induced/microbiology/therapy ; *Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; *Klebsiella Infections/microbiology/therapy ; *Bacterial Translocation/drug effects ; Carbapenems/pharmacology ; Humans ; Mice, Inbred C57BL ; Feces/microbiology ; },
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE), known for their extensive antibiotic resistance, pose a severe global medical threat. Therefore, developing novel therapeutics beyond conventional antibiotics is urgently needed, and the importance of microbiome therapeutics is increasingly being recognized. This study explores the expanded systemic efficacy of PMC101, a microbiome therapeutic, beyond intestinal CRE infections and investigates its mechanism of action from a microbiome perspective. First, the genetic characteristics of the novel strain were identified through whole-genome analysis, and a scalable cultivation process was established as part of the overall development of this microbiome therapeutic. PMC101 increased the survival rate to 100%, significantly reduced disease severity scores, and prevented weight loss in CRE-infected mice treated with antibiotics. These effects are attributed to the inhibition of CRE growth in stool and the reduced detection of CRE in the lungs and kidneys, indicating suppression of systemic translocation. Metagenomic analysis revealed that PMC101 prevented the reduction in microbial population caused by antibiotics and CRE infection, restored species diversity indices, and mitigated dysbiosis while promoting eubiosis. This CRE translocation suppression was closely associated with increased CRE translocation-microbiome index, defined as the ratio of Bacteroidetes to Proteobacteria. This relationship was further confirmed through simulations using a human intestinal microbial ecosystem model. Additionally, increases in short-chain fatty acids, reductions in excessive inflammatory responses, and decreases in tissue damage were observed, all of which contribute to preventing CRE translocation. Finally, pathogen inhibition effects and safety tests were conducted, confirming the prophylactic potential of PMC101 as a microbiome therapeutic. These findings strongly support PMC101 as a promising candidate for future microbiome-based therapies against CRE infections.},
}

Animals
*Dysbiosis/chemically induced/microbiology/therapy
*Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology
*Anti-Bacterial Agents/adverse effects/pharmacology
Mice
*Gastrointestinal Microbiome/drug effects
Disease Models, Animal
*Klebsiella Infections/microbiology/therapy
*Bacterial Translocation/drug effects
Carbapenems/pharmacology
Humans
Mice, Inbred C57BL
Feces/microbiology

@article {pmid41089454,
year = {2025},
author = {Hu, X and He, Z and Liu, C and Zhang, Y and Mu, D and Guskov, VY and Wang, K and Yao, Y and Jin, D and Lu, J and Ning, Y and Jiang, G},
title = {Revealing Amur tiger family pedigrees based on age identification using fecal microbiome and kinship analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1666201},
pmid = {41089454},
issn = {1664-302X},
abstract = {INTRODUCTION: The construction of a species' family pedigree is crucial for understanding population structure, assessing genetic diversity, and conserving the genetic resources of endangered species. However, developing non-invasive and reliable methods for age identification in wild individuals remains a significant challenge in family pedigree establishments.

METHODS: In this study, we employed 16S rRNA sequencing and metagenomic analysis to examine 30 fecal samples collected from captive Amur tigers across three distinct age groups, aiming to identify the age-specific biomarker, which could subsequently facilitate age determination of wild individuals and support the construction of species pedigree.

RESULTS: Our results demonstrate that, through 16S rRNA high-throughput sequencing, 16 potential microbial age biomarkers were identified in fecal samples from captive Amur tigers, and the ages of 17 captive individuals were distinguished. Notably, f_Erysipelotrichaceae_Unclassified and Paraclostridium, identified as potential age-associated bacterial markers in captive Amur tigers, were also detected in fecal samples from wild individuals of this species. To explore their potential application in age inference for Amur tigers, we integrated genetic relationship analysis with these potential age-specific biomarkers to construct a comprehensive pedigree of wild Amur tigers.

DISCUSSION: This study established a comprehensive scientific framework for pedigree reconstruction based on age determination in Amur tigers and developed a scalable, non-invasive methodology offering opportunities for population structure and promoting the precision of conservation for wild tigers.},
}

@article {pmid41088378,
year = {2025},
author = {Chen, Z and Jia, Y and Li, H and Fan, R and Cao, Y and Ni, L and Yang, L and Yuan, Z and Zhu, K and Gao, Y and Lin, Y},
title = {Effects of zacopride and multidimensional impacts of cross-kingdom symbiosis: gut microbiota modulates coronary microvascular dysfunction via the chlorophyll/heme-tryptophan metabolic axis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1097},
pmid = {41088378},
issn = {1479-5876},
support = {20210302123485//Fundamental Research Program of Shanxi Province/ ; BYJL065//Shanxi Province Higher Education "Billion Project" Science and Technology Guidance Project/ ; NSFC-82102104//National Natural Science Foundation of China/ ; 2021M702054//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Tryptophan/metabolism ; Male ; *Symbiosis/drug effects ; *Benzamides/pharmacology/therapeutic use ; *Coronary Vessels/drug effects/physiopathology ; *Microvessels/drug effects/physiopathology ; Rats ; *Microcirculation/drug effects ; },
abstract = {BACKGROUND: Coronary Microvascular Dysfunction (CMD) represents a critical pathological substrate for ischemic heart disease and is strongly associated with major adverse cardiovascular events. Zacopride, known for its dual cardiovascular regulatory properties targeting the 5-HT4 receptor and Kir2.1 channel, lacks evidence regarding its systemic impact on the gut microbiota-metabolism axis. Therefore, this study aims to elucidate the structural and metabolic characteristics of gut bacteria and fungi in CMD, and to explore the multidimensional therapeutic mechanisms of Zacopride through "microbial remodeling-metabolic regulation-microcirculation repair."

METHODS: Sixty Sprague-Dawley rats were randomized into three groups: coronary microvascular dysfunction (CMD), healthy control (NC), and Zacopride intervention (ZAC). CMD and ZAC groups received high-fat diet plus streptozotocin (STZ, 35 mg/kg) for modeling. ZAC rats were orally administered 5 mg/kg Zacopride daily for 7 days. Transthoracic Doppler echocardiography measured left anterior descending coronary artery resting/stress peak flow velocity and coronary flow reserve (CFR). Ileocecal contents underwent bacterial-fungal metagenomic sequencing to identify differential metabolic pathways. Spearman's correlation assessed cross-kingdom ecological interactions. Nine machine learning algorithms constructed classification models, with Random Forest (RF) and an optimal model identifying key genera. Linear Discriminant Analysis Effect Size validated microbial biomarkers.

RESULTS: Zacopride partially restored the CFR in CMD rats, demonstrating a therapeutic effect, and exerted a beneficial influence on the structure and diversity of the gut microbiota. The CMD state significantly reduced the expression levels of the Chlorophyll a and tryptophan metabolic pathways in the gut microbiota. Zacopride specifically restored the Chlorophyll a pathway but did not significantly recover the tryptophan metabolic pathway. RF and Elastic Net (ENET) identified JC017, Chromelosporium, and Barnesiella as biomarker microbiota for CMD. Notably, JC017 primarily mediate the therapeutic effects of Zacopride via direct or indirect modulation of the Chlorophyll a metabolic pathway. Chromelosporium, acting as an interactive hub between fungi and bacteria, formed a cross-kingdom symbiotic relationship with Bradyrhizobium. Additionally, the reduction in Barnesiella abundance constitutes a distinctive feature of gut microbial dysbiosis in CMD.

CONCLUSION: This study provides the first evidence that the gut microbiota modulates the pathogenesis of CMD through the "chlorophyll/heme-tryptophan metabolic axis." Furthermore, we demonstrate that Zacopride exerts therapeutic effects by remodeling microbiota-host interactions and regulating this metabolic axis, revealing a novel mechanistic link between microbial metabolism and CMD progression.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Rats, Sprague-Dawley
*Tryptophan/metabolism
Male
*Symbiosis/drug effects
*Benzamides/pharmacology/therapeutic use
*Coronary Vessels/drug effects/physiopathology
*Microvessels/drug effects/physiopathology
Rats
*Microcirculation/drug effects

@article {pmid41088296,
year = {2025},
author = {Tang, A and Chen, Y and Ding, J and Li, Z and Xu, C and Hu, S and Lai, J},
title = {Gut microbiota remodeling and sensory-emotional functional disruption in adolescents with bipolar depression.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1083},
pmid = {41088296},
issn = {1479-5876},
support = {82201676//National Natural Science Foundation of China/ ; 82471542//National Natural Science Foundation of China/ ; No. JNL-2023001B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; 2023YFC2506200//National Key Research and Development Program of China/ ; 2023ZFJH01-01//Fundamental Research Funds for the Central Universities/ ; 2024ZFJH01-01//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; Adolescent ; *Bipolar Disorder/microbiology/physiopathology/drug therapy/psychology ; Male ; Female ; *Emotions ; Quetiapine Fumarate/therapeutic use/pharmacology ; Magnetic Resonance Imaging ; Case-Control Studies ; Brain/physiopathology/diagnostic imaging ; Neuroimaging ; },
abstract = {BACKGROUND: Adolescence is the peak period of newly-onset bipolar disorder (BD). Accumulating studies have revealed disturbed gut microbiota can interfere with neurodevelopment in adolescents. In this study, we aimed to characterize the gut microbiota in adolescents with BD and its correlation with brain dysfunction.

METHODS: Thirty unmedicated BD adolescents within depressive episode were recruited and underwent four-week quetiapine treatment. Twenty-five age-, gender-, and BMI-matched healthy controls (HCs) were recruited. Fecal samples were collected from HCs and all BD adolescents before and after treatment and analyzed by metagenomic sequencing. Resting-state cranial functional magnetic images were collected from 21 BD adolescents before treatment. Random forest models were used to evaluate the discriminative power of gut microbiota and neuroimaging data for BD and the predictive power of treatment effect.

RESULTS: Although no significant difference was found in alpha-diversity, intra- and inter-group differences in beta-diversity were observed among HCs, pre- and post-treatment patients. Compared to HCs, unmedicated BD adolescents presented a differentiated gut microbial communities, which correlated to the short-chain fatty acids, choline, lipids, vitamins, polyamines, aromatic amino acids metabolic pathways. Four-week quetiapine treatment improved the abundance of specific genus, such as Odoribacter splanchnicus, Oribacterium sinus, Hafnia alvei, Fusobacterium periodonticum, Acidaminococcus interstini and Veillonella rogosae. Neuroimaging analysis revealed sensor-emotional brain regions were associated with BD severity. Finally, random forest models based on gut microbial biomarkers can well distinguish unmedicated BD from HCs (AUC = 91.12%) and predict the treatment effect (AUC = 91.84%). The random forest model integrating gut microbiota and neuroimaging data exhibited a better predictive efficacy than using microbiota data alone.

CONCLUSION: This study first characterized the gut microbiota architecture in adolescent BD. Combining gut microbiota and brain function biomarkers may benefit disease diagnosis and predict treatment outcome. Nonetheless, these findings should be carefully interpreted considering the limitations of a modest sample size and the absence of detailed mechanistic explorations. Trial registration NCT05480150. Registered 29 July 2022-Retrospectively registered, https://clinicaltrials.gov/study/NCT05480150 .},
}

Humans
*Gastrointestinal Microbiome/drug effects/physiology
Adolescent
*Bipolar Disorder/microbiology/physiopathology/drug therapy/psychology
Male
Female
*Emotions
Quetiapine Fumarate/therapeutic use/pharmacology
Magnetic Resonance Imaging
Case-Control Studies
Brain/physiopathology/diagnostic imaging
Neuroimaging

@article {pmid41087898,
year = {2025},
author = {Zheng, N and Wang, D and Xing, G and Gao, Y and Li, S and Liu, J and Kang, J and Sha, S and Cheng, L and Fan, S and Yu, J and Yan, Q and Jiang, C},
title = {Characterization of the gut mycobiome in patients with non-alcoholic fatty liver disease and correlations with serum metabolome.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {660},
pmid = {41087898},
issn = {1471-2180},
mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/microbiology/blood/metabolism ; *Mycobiome ; *Gastrointestinal Microbiome ; *Metabolome ; Male ; Female ; Middle Aged ; *Fungi/classification/genetics/isolation & purification ; Feces/microbiology ; Adult ; Bacteria/classification/genetics/isolation & purification ; Aged ; Metagenomics ; },
abstract = {BACKGROUND: Emerging evidence suggests that the gut microbiome plays a key role in metabolic diseases such as non-alcoholic fatty liver disease, yet the contribution of the gut mycobiome remains largely overlooked.

METHODS: We performed a comprehensive analysis of publicly available fecal metagenomic sequencing data and matched serum metabolomic profiles from 90 non-alcoholic fatty liver disease patients and 90 healthy controls. A curated fungal genome database was constructed for taxonomic profiling. We integrated fungal, bacterial, and metabolomic data to assess taxon-specific associations, cross-kingdom interactions, and predictive potential.

RESULTS: Although overall fungal diversity showed no significant differences between groups, four fungal species-Pseudopithomyces sp. c174, Mucor sp. c176, Aspergillus sp. c25, and Ascochyta c213-were significantly enriched in non-alcoholic fatty liver disease patients. The gut mycobiome explained 38.2% of the variance in serum metabolomic profiles, with several species displaying strong correlations with non-alcoholic fatty liver disease relevant metabolites. For instance, Pseudopithomyces sp. c174 was positively associated with protective metabolites such as glycoursodeoxycholic acid and alpha-linolenic acid, while Aureobasidium c170 and Basipetospora c193 were linked to phenylacetic acid, a metabolite implicated in hepatic lipid accumulation. Network analysis revealed altered fungal-bacterial co-abundance patterns in non-alcoholic fatty liver disease, with fungal taxa such as Alternaria alternata c42 and Malassezia c303 emerging as key hubs. A random forest classifier integrating 42 bacterial and fungal features achieved an AUC of 0.772 for distinguishing non-alcoholic fatty liver disease from controls, highlighting the predictive value of the mycobiome.

CONCLUSIONS: Our findings reveal that gut fungal communities are functionally and ecologically altered in non-alcoholic fatty liver disease and contribute to shaping the host metabolic environment. These results underscore the need to incorporate the gut mycobiome into future microbiome-based strategies for non-alcoholic fatty liver disease diagnosis and treatment.},
}

Humans
*Non-alcoholic Fatty Liver Disease/microbiology/blood/metabolism
*Mycobiome
*Gastrointestinal Microbiome
*Metabolome
Male
Female
Middle Aged
*Fungi/classification/genetics/isolation & purification
Feces/microbiology
Adult
Bacteria/classification/genetics/isolation & purification
Aged
Metagenomics

@article {pmid41087864,
year = {2025},
author = {Chen, H and Wang, Z and Su, W and Li, S and Ye, Q and Zhang, G and Zhou, X},
title = {Helicobacter pylori infection impairs glucose homeostasis through gut microbiota dysbiosis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {663},
pmid = {41087864},
issn = {1471-2180},
support = {82100594//National Natural Science Foundation of China,China/ ; },
mesh = {Animals ; *Helicobacter Infections/microbiology/metabolism/complications ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/metabolism ; *Helicobacter pylori/physiology ; Mice ; Humans ; Mice, Inbred C57BL ; *Homeostasis ; *Diabetes Mellitus, Type 2/microbiology/metabolism ; Male ; Retrospective Studies ; *Glucose/metabolism ; Glucagon-Like Peptide 1/metabolism ; Female ; Middle Aged ; Colon/microbiology/metabolism ; Fecal Microbiota Transplantation ; Anti-Bacterial Agents ; Insulin Resistance ; Diabetes Mellitus, Experimental/microbiology ; Feces/microbiology ; },
abstract = {BACKGROUND: Epidemiological data show that Helicobacter pylori (H. pylori) infection is not only the most important risk factor for gastric cancer, but is also associated with poor glycemic control in patients with diabetes. However, the direct causal and functional relationship between H. pylori infection and dysglycemia is unclear.

METHOD: A retrospective cohort study was conducted to examine the association between H. pylori infection and glycemic levels in individuals with Type 2 diabetes. C57BL/6 diabetic mice were infected with H. pylori, and the resulting changes in colonic inflammation and intestinal Glucagon-like peptide-1 (GLP-1) secretion were thoroughly examined using immunohistochemistry, RNA sequencing, metagenomic sequencing, and targeted metabolomics. The microbial and metabolomics profiles were analyzed and compared in antibiotic-treated mice through fecal transfer experiments.

RESULTS: H. pylori infection aggravated insulin resistance in diabetic individuals and mice. We identified a unique H. pylori-induced epithelial inflammation and reduced intestinal GLP-1 secretion in the colon. H. pylori infection also interrupts the normal microbial composition in the colon, leading to a decrease in SCFA-producing bacteria and a reduction in acetic and propionate acids. Similar changes were observed in antibiotic-treated mice after receiving fecal transplants from H. pylori-infected diabetic mice. In vitro studies revealed that the intestinal flora of H. pylori-positive diabetic mice inhibited proglucagon transcription, cAMP levels, and GLP-1 secretion in colonic endocrine cells, with SCFA supplementation reversing this effect on GLP-1 production. These microbial, metabolic, and GLP-1 alterations were also seen in antibiotic-treated mice after receiving fecal transplants from H. pylori-infected diabetic mice. H. pylori eradication with antibiotics improved glucose metabolism and GLP-1 secretion to levels comparable to uninfected controls.

CONCLUSION: Our studies offer evidence that H. pylori infection significantly contributes to the progression of glucose impairment and insulin resistance. Therefore, incorporating H. pylori status into preventive strategies for diabetes should be taken into account. (Chinese Clinical Trial Registry Center, ChiCTR2200063489, Registered 08 September 2022, https://www.chictr.org.cn/showproj.html?proj=178102).},
}

Animals
*Helicobacter Infections/microbiology/metabolism/complications
*Gastrointestinal Microbiome
*Dysbiosis/microbiology/metabolism
*Helicobacter pylori/physiology
Mice
Humans
Mice, Inbred C57BL
*Homeostasis
*Diabetes Mellitus, Type 2/microbiology/metabolism
Male
Retrospective Studies
*Glucose/metabolism
Glucagon-Like Peptide 1/metabolism
Female
Middle Aged
Colon/microbiology/metabolism
Fecal Microbiota Transplantation
Anti-Bacterial Agents
Insulin Resistance
Diabetes Mellitus, Experimental/microbiology
Feces/microbiology

@article {pmid41043233,
year = {2025},
author = {Sun, C and Liu, X and Wang, M and Zhang, Q and Geng, H and Ji, X and Wang, H and Li, S and Jin, E and Zhang, F},
title = {Metagenome-metabolome responses to linarin alleviate hepatic inflammatory response, oxidative damage, and apoptosis in an ETEC-challenged weaned piglet model.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119145},
doi = {10.1016/j.ecoenv.2025.119145},
pmid = {41043233},
issn = {1090-2414},
mesh = {Animals ; Swine ; Oxidative Stress/drug effects ; Apoptosis/drug effects ; Enterotoxigenic Escherichia coli/physiology ; Gastrointestinal Microbiome/drug effects ; Liver/drug effects ; *Metabolome/drug effects ; *Metagenome/drug effects ; *Escherichia coli Infections/veterinary/drug therapy ; Inflammation ; Weaning ; },
abstract = {Enterotoxigenic Escherichia coli (ETEC), present in contaminated food, water, and environments, can induce hepatic injury via the gut-liver axis, posing a serious threat to ecological systems and public health. Linarin, a flavonoid extracted from Chrysanthemum indicum, exhibits anti-inflammatory and antioxidant properties, but its protective effects against ETEC-induced hepatic injury remain unclear. In this study, 24 weaned piglets were randomly assigned to four groups: BD+NB (basal diet + nutrient broth), LN+NB (basal diet + 150 mg/kg linarin + nutrient broth), BD+ETEC (basal diet + ETEC challenge), and LN+ETEC (basal diet + 150 mg/kg linarin + ETEC challenge). Dietary linarin significantly increased ADFI and the genes related to oxidative damage and bile acid metabolism, while decreasing F:G ratio, liver index, serum liver function-related parameters, and the genes related to inflammatory response and apoptosis. It also significantly altered the relative abundances of gut microbiota, which were closely associated with key hepatic metabolic pathways, including nicotinate and nicotinamide metabolism and fatty acid biosynthesis. Our study suggests that linarin alleviated ETEC-induced hepatic inflammation and apoptosis, enhanced antioxidant capacity, and regulated bile acid metabolism. The potential mechanism involves linarin modulating gut microbiota-mediated key hepatic metabolic pathways to exert protective effects. In contrast to previous flavonoid-ETEC studies that primarily focused on the gut, this study, based on the gut-liver axis, investigates the potential mechanisms by which linarin is associated with the alleviation of ETEC-induced hepatic injury through integrated analysis of gut microbiome metagenomics and liver metabolomics.},
}

Animals
Swine
Oxidative Stress/drug effects
Apoptosis/drug effects
Enterotoxigenic Escherichia coli/physiology
Gastrointestinal Microbiome/drug effects
Liver/drug effects
*Metabolome/drug effects
*Metagenome/drug effects
*Escherichia coli Infections/veterinary/drug therapy
Inflammation
Weaning

@article {pmid41015306,
year = {2026},
author = {Hou, DJ and Guo, WL and Yang, HW and Liu, QR and Fan, NS and Jin, RC},
title = {Behaviors and adaptive strategies of anammox microbiota in response to typical ionic liquid: Metabolic compensation and gene regulation.},
journal = {Bioresource technology},
volume = {439},
number = {},
pages = {133395},
doi = {10.1016/j.biortech.2025.133395},
pmid = {41015306},
issn = {1873-2976},
mesh = {*Ionic Liquids/pharmacology ; *Microbiota/drug effects/genetics ; *Ammonium Compounds/metabolism ; Wastewater/microbiology ; Oxidation-Reduction ; Anaerobiosis ; *Gene Expression Regulation, Bacterial/drug effects ; Bacteria/metabolism/genetics/drug effects ; Molecular Docking Simulation ; },
abstract = {Ionic liquids (ILs) have been used to replace organic solvents, thereby causing challenges for wastewater treatment. Anaerobic ammonium oxidation (anammox) had been recognized to treat high-strength ammonium wastewater, but its response to ILs remains unclear. Metagenomic sequencing, granule characterization and molecular docking simulation were employed to investigate the comprehensive effects of 1-ethyl-3-methylimidazolium acetate ([EMIM][Ac]) on anammox consortia. [EMIM][Ac] of 2 mg L[-1] reduced the specific anammox activity (SAA) by 46.0 %. [EMIM][Ac] also induced oxidative stress. The higher abundance of denitrifying bacteria and functional genes (nirK and nirS) compensated for the reduced nitrogen removal efficiency. In P2, the total abundance of nirK and nirS in R1 was 16.2 % higher than its initial value, and also 9.6 % higher than that in R0. This study elucidated how anammox microbiota resisted ILs via metabolic regulation and EPS secretion, providing a theoretical support for improving the feasibility and efficiency of anammox-based wastewater treatment systems.},
}

*Ionic Liquids/pharmacology
*Microbiota/drug effects/genetics
*Ammonium Compounds/metabolism
Wastewater/microbiology
Oxidation-Reduction
Anaerobiosis
*Gene Expression Regulation, Bacterial/drug effects
Bacteria/metabolism/genetics/drug effects
Molecular Docking Simulation

@article {pmid40914221,
year = {2025},
author = {Geng, J and Zhang, W and Christie-Oleza, JA and Abdolahpur Monikh, F and Yang, Q and Yang, Y},
title = {Succession-driven potential functional shifts in microbial communities in the tire-plastisphere: Comparison of pristine and scrap tire.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {385},
number = {},
pages = {127074},
doi = {10.1016/j.envpol.2025.127074},
pmid = {40914221},
issn = {1873-6424},
mesh = {*Microbiota ; *Microplastics/analysis ; Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; Ecosystem ; Bacteria ; Lakes/microbiology ; },
abstract = {Tire microplastics (TMPs) represent a major contributor to microplastic pollution, posing threats to aquatic ecosystems. As carbon-rich substrates, TMPs influence microbial colonization and ecological functions. This study investigates the impacts of pristine (P-TMPs) and scrap (S-TMPs) TMPs from the same brand on microbial communities within the tire-plastisphere. We incubated wood particles, P-TMPs, and S-TMPs in situ in a lake environment for 60 days. Utilizing amplicon and metagenome sequencing, we analyzed structural and potential functional changes in microbial communities across five colonization time points. Our findings reveal that TMPs establish distinct ecological niches, functioning as hotspots of microbial activity in aquatic environments. Both niche specificity and colonization time significantly shape microbial community structure. During the early adaptation stage, we observed clustering patterns in both microbial composition and functional genes associated with the particles. Over time, divergent succession in community composition and potential function emerged, primarily driven by differences in substrate availability between niches. Notably, the substrate availability of S-TMPs promoted microbial community shifts, whereas the P-TMPs posed challenges to microbial adaptation. This study elucidates the long-term adaptive processes exhibited by microbial communities when colonizing the contrasting ecological niches represented by these two TMP states (pristine vs. scrap), documenting the progression from community structural change to functional adaptation. The results underscore the complexity of TMP impacts on microbial ecology and highlight the critical need for long-term monitoring to fully understand their environmental implications.},
}

*Microbiota
*Microplastics/analysis
Environmental Monitoring
*Water Pollutants, Chemical/analysis
Ecosystem
Bacteria
Lakes/microbiology

@article {pmid40896895,
year = {2025},
author = {Jiang, Z and Yang, S and Pang, Q and Abdalla, M and Karbin, S and Qi, S and Hu, J and Qiu, H and Song, X and Smith, P},
title = {Metagenomic insights into the influence of soil microbiome on greenhouse gas emissions from paddy fields under varying irrigation and fertilisation regimes.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127129},
doi = {10.1016/j.jenvman.2025.127129},
pmid = {40896895},
issn = {1095-8630},
mesh = {*Greenhouse Gases ; Fertilizers ; *Agricultural Irrigation ; *Soil Microbiology ; Soil/chemistry ; *Microbiota ; China ; Agriculture ; Oryza ; Methane ; },
abstract = {Integration of diverse fertilisation strategies with water-saving irrigation techniques presents a promising sustainable agricultural practice, offering the potential to reduce greenhouse gases (GHGs) emissions, enhance carbon sequestration and boost crop yields. However, existing research on the influence of soil microorganisms on biogeochemical processes of GHGs is limited. Herein, we explored the microbial mechanisms influencing GHGs emissions through a 3-year field experiment and metagenomic sequencing conducted in southeastern China. We investigated two irrigation patterns (controlled irrigation [CI] and flooded irrigation [FI]) and three fertilisation strategies (chemical fertiliser [F], straw returning [S] and manure substitution [M]). Results indicated that irrigation patterns significantly affected the microbial community structure in paddy soil. The key environmental factors affecting microorganisms at the phylum level included soil pH, moisture content, total nitrogen content and CH4 emissions. Random forest analysis further identified Cyanobacteria, Nitrospirae, Kiritimatiellaeota, Proteobacteria, and Balneolaeota as dominant phyla driving the differences in microbial communities across treatments. Under CI, an increase in N2O emissions was observed, which was driven by key genes, such as nirS, nirK, nosZ and norB. Compared with CF (CI with F), S increased the abundance of nirS and nirK, leading to higher N2O emissions, whereas M increased the abundance of nosZ, thereby reducing N2O emissions. The genes mcrA, pmoA and pmoC were responsible for elevated CH4 emissions through straw incorporation and manure application. Structural equation model analysis revealed that the irrigation pattern significantly affected CH4 emissions and rice yield, while the fertilisation type mainly influenced soil pH and rice yield. Organic input, particularly manure, resulted in higher C emissions owing to the presence of more CH4-producing gene mcrA in the soil. Overall, the combination of CI and manure is recommended for reducing GHGs emissions, enhancing C sequestration and boosting rice yields.},
}

*Greenhouse Gases
Fertilizers
*Agricultural Irrigation
*Soil Microbiology
Soil/chemistry
*Microbiota
China
Agriculture
Oryza
Methane

@article {pmid40882272,
year = {2025},
author = {Wang, K and Xu, J and Luo, X and Yu, Z and Tang, A and Peng, K and Song, J and Chen, X and Ren, M},
title = {Insights into microalgal-bacterial consortia in sustaining denitrification via algal-derived organic matter in harsh low-C/N wastewater.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127108},
doi = {10.1016/j.jenvman.2025.127108},
pmid = {40882272},
issn = {1095-8630},
mesh = {*Denitrification ; *Wastewater/chemistry ; *Microalgae/metabolism ; Carbon ; Nitrates ; Bacteria/metabolism ; Nitrogen ; Microbial Consortia ; },
abstract = {Conventional nitrate removal processes are often hampered by insufficient carbon sources for remediating low-C/N wastewater. Herein, a microalgal-bacterial (MB) consortia system was constructed to leverage algal-derived organic matter for sustaining denitrification. The system demonstrated superior nitrate removal performance when assisted by algal-derived organic matter, achieving a 168.62 ± 4.17 % enhancement in nitrate removal capacity compared to the sole bacterial system. Furthermore, Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) analysis of algal-derived organic matter revealed that specific components facilitating nitrate elimination included unsaturated aliphatic compounds, aliphatic/peptide-like/amino sugars, lignin-like, and tannin-like substances. Notably, the consortia showed preferential utilization of unsaturated aliphatic (35.21 %) and aliphatic/amino sugars over aliphatic/peptide-like/amino acids (31.05 %) and aliphatic/peptide-like compounds (31.31 %) within the CHO, CHON, CHON2, and CHON3 classes, respectively. Metagenomic analysis identified notable disparities in microbial community composition between the bacterial and MB consortia systems. Moreover, the MB consortia exhibited higher abundances of genes encoding nitrate removal enzymes, including those involved in denitrification, assimilatory/dissimilatory reduction, and L-glutamate synthesis pathways. Genes associated with lignin degradation were also detected, suggesting potential indirect contributions to nitrate elimination. Besides, the MB symbiotic microspheres were successfully fabricated and achieved efficient nitrate removal. These findings provide novel insights into the development of innovative MB symbiotic systems for nitrate removal under harsh carbon-limited conditions.},
}

*Denitrification
*Wastewater/chemistry
*Microalgae/metabolism
Carbon
Nitrates
Bacteria/metabolism
Nitrogen
Microbial Consortia

@article {pmid40882267,
year = {2025},
author = {Davis, BC and Linz, D and McMinn, BR and Korajkic, A},
title = {Limited ARG removal but stable resistome dynamics in a surface flow constructed wetland.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {126986},
doi = {10.1016/j.jenvman.2025.126986},
pmid = {40882267},
issn = {1095-8630},
mesh = {*Wetlands ; Wastewater/microbiology ; Bacteria/genetics ; Microbiota ; Anti-Bacterial Agents ; },
abstract = {Improperly treated wastewater and surface runoff can degrade water quality by introducing microbial contaminants, including antibiotic-resistant bacteria (ARB) and their genes (ARGs). Constructed treatment wetlands (CTWs) offer a low-resource solution for managing impaired watersheds. However, their ability to mitigate microbial contaminants, particularly ARGs, requires further study. In this study, 62 water samples from Banklick Creek CTW (BCTW) were shotgun sequenced to assess ARG dynamics and removal characteristics. Results showed minimal resistome attenuation, likely due to the wetland's horizontal surface flow design with short, variable hydraulic residence times (0.48-3.1 days). Despite this, 198 low-abundance ARGs were removed, accounting for a median of 0.52 % (0-3.1 %) of total ARG abundance upstream. The core resistome, comprising 95.6 ± 1.9 % of total ARG abundance, was stable and mainly consisted of multidrug efflux systems carried by bacterioplankton and macrophyte symbionts, indicating a native resistome reflective of regional pollution history. Resistome and microbiome structures were highly correlated (R[2] = 0.808), with ARGs rarely co-occurring with mobile genetic elements, indicating limited intercellular transfer potential. No significant correlations were found between resistome dynamics and human fecal (HF183, crAssphage) or avian (GFD) biomarkers. Although several class-one integron-integrase (intI1) contigs were enriched in treatment channels, gene cassette cargo was void of ARGs. As detection of intI1 via qPCR is generally considered indicative of resistome mobility potential, this finding carries important implication for intI1 qPCR assay selection (i.e., targeting clinical intI1 mosaics) and over-interpretation of ARG spread in the environment.},
}

*Wetlands
Wastewater/microbiology
Bacteria/genetics
Microbiota
Anti-Bacterial Agents

@article {pmid40834570,
year = {2025},
author = {Ansari, SA and Ramteke, A and Sawarkar, R and Kumar, T and Khan, D and Agashe, A and Patil, MP and Singh, L},
title = {"Innovative approaches in microbial community engineering for food waste management: A comprehensive review".},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127000},
doi = {10.1016/j.jenvman.2025.127000},
pmid = {40834570},
issn = {1095-8630},
mesh = {*Waste Management/methods ; Biodegradation, Environmental ; *Microbial Consortia ; Metabolic Engineering ; Fermentation ; },
abstract = {Food waste (FW) is a critical global issue, exacerbating environmental degradation and resource scarcity. Traditional FW management methods are often inefficient and unsustainable. This review highlights advances in microbial community engineering for FW valorization, focusing on synthetic biology, metagenomics, metabolic engineering, and electro-fermentation. Engineered microbial consortia enhance the breakdown of complex organics while producing bioenergy, bioplastics, and organic acids. Metagenomics enables precise metabolic optimizations, and electro-fermentation improves bioconversion yields. These systems outperform conventional methods in reducing greenhouse gases, recovering nutrients, and promoting a circular bioeconomy. Challenges persist, including microbial stability, scalability, and incomplete knowledge of interspecies interactions. Future research should integrate AI and machine learning to design robust synthetic consortia and optimize metabolic pathways. Scaling electrochemical technologies (e.g., microbial electrosynthesis) requires further validation. Standardized biosafety protocols, techno-economic analyses, and supportive policies are essential for industrial adoption. Interdisciplinary collaboration is crucial to address these gaps. In conclusion, microbial engineering offers a sustainable FW management solution, improving biodegradation efficiency and resource recovery. Future efforts must prioritize scalable, stable systems with real-time monitoring and ecological safety. Overcoming these challenges will enable engineered microbes to mitigate environmental impacts, generate renewable energy, and advance a resource-efficient future.},
}

*Waste Management/methods
Biodegradation, Environmental
*Microbial Consortia
Metabolic Engineering
Fermentation

@article {pmid40796326,
year = {2025},
author = {Patel, SM and Farirai, J and Patel, MZ and Boiditswe, S and Tawe, L and Lekalake, S and Matshaba, M and Steenhoff, AP and Arscott-Mills, T and Feemster, KA and Shah, SS and Thielman, N and Cunningham, CK and David, LA and Murdoch, DM and Kelly, MS},
title = {Alterations of the Upper Respiratory Microbiome Among Children Living With HIV Infection in Botswana.},
journal = {The Journal of infectious diseases},
volume = {232},
number = {4},
pages = {815-825},
doi = {10.1093/infdis/jiaf429},
pmid = {40796326},
issn = {1537-6613},
support = {T32 HL 007538//Institutional Training Grant in Pulmonary and Critical Care Medicine/ ; D43 TW009337/TW/FIC NIH HHS/United States ; K23-HL166022//NIH Career Development Award/ ; //Duke University Center for AIDS Research/ ; 5P30-AI064518//NIH-funded program/ ; K23-AI135090//NIH-funded program/ ; //NIH/ ; P30-AI045008//Penn Center for AIDS Research/ ; },
mesh = {Humans ; *HIV Infections/microbiology/complications ; Botswana/epidemiology ; Female ; Male ; Cross-Sectional Studies ; *Microbiota ; *Nasopharynx/microbiology ; Child, Preschool ; *Respiratory Tract Infections/microbiology/epidemiology ; Infant ; },
abstract = {Children living with HIV (CLWH) are at high risk of colonization and infection by respiratory pathogens, though this risk can be reduced by other microbes in the upper respiratory microbiome. The impact of HIV infection on the pediatric upper respiratory microbiome is poorly understood, and we sought to address this knowledge gap by identifying associations between HIV infection and the nasopharyngeal microbiomes of Batswana children. We enrolled Batswana CLWH (<5 years) and age- and sex-matched HIV-exposed, uninfected and HIV-unexposed, uninfected children in a cross-sectional study. We used shotgun metagenomic sequencing to compare nasopharyngeal microbiomes by HIV status. Among the 143 children in this study, HIV and HIV-associated immunosuppression were associated with alterations in nasopharyngeal microbiome composition, including lower abundances of Corynebacterium species associated with resistance to bacterial pathogen colonization. These findings suggest that the upper respiratory microbiome may contribute to the high risk of respiratory infections among CLWH.},
}

Humans
*HIV Infections/microbiology/complications
Botswana/epidemiology
Female
Male
Cross-Sectional Studies
*Microbiota
*Nasopharynx/microbiology
Child, Preschool
*Respiratory Tract Infections/microbiology/epidemiology
Infant

@article {pmid40795737,
year = {2025},
author = {Zhao, J and Kou, X and Liu, H and Wu, T and Li, J and Wang, Y and Xie, H and Wang, M and Wu, L and Wen, L and Wang, L},
title = {Microbial community responses and functional shifts in carbon degradation driven by water-salt gradients in lakeshore wetlands of semi-arid lakes.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {126893},
doi = {10.1016/j.jenvman.2025.126893},
pmid = {40795737},
issn = {1095-8630},
mesh = {*Wetlands ; *Lakes ; *Carbon/metabolism ; Soil/chemistry ; Salinity ; Soil Microbiology ; Microbiota ; Ecosystem ; },
abstract = {Wetlands, especially lakeshore ecosystems, play an essential role in global carbon (C) cycling and are strongly influenced by dynamic water-salt gradients. However, the mechanisms by which these gradients shape microbial communities and affect soil organic C (SOC) degradation remain incompletely understood. Here, we aimed to elucidate microbial mechanisms driving C degradation shifts along water-salt gradients. We investigated microbially mediated SOC degradation potential in Daihai Lake wetlands by metagenomic profiling of carbohydrate-active enzyme (CAZyme) genes. Our results demonstrated a significant shift in CAZyme gene abundances across the gradients. Genes involved in plant-derived C (cellulose, hemicellulose, lignin) degradation decreased with increasing soil salinity and moisture, while those related to microbial-derived C (chitin, peptidoglycan, glucans) decomposition were significantly enriched. Concurrently, the microbial community composition shifted toward greater abundance of salt-tolerant taxa, notably Proteobacteria and Bacteroidetes, while Actinobacteria and Firmicutes declined under higher water-salt conditions. Statistical analyses revealed strong correlations between key environmental factors (soil salinity (EC), soil moisture (SM), and pH) and both microbial community structure and CAZyme gene abundances (p < 0.001). Random Forest analysis further identified EC and SM as primary factors influencing C-degrading microbial functions. This study highlights the importance of water-salt gradients in regulating microbial-mediated C cycling in wetlands, providing critical insights into microbial adaptation strategies and their implications for wetland C dynamics under environmental change.},
}

*Wetlands
*Lakes
*Carbon/metabolism
Soil/chemistry
Salinity
Soil Microbiology
Microbiota
Ecosystem

@article {pmid40581627,
year = {2025},
author = {Nørgaard, JC and Marandi, RZ and Ilett, EE and Gulay, A and Paredes, R and Lundgren, JD and Jørgensen, M and Sengeløv, H},
title = {The Gut Microbiome and Its Resistome as Predictors of Clinical Infections and Phenotypic Antibiotic Resistance in Hematopoietic Stem Cell Transplant Recipients.},
journal = {The Journal of infectious diseases},
volume = {232},
number = {4},
pages = {806-814},
doi = {10.1093/infdis/jiaf330},
pmid = {40581627},
issn = {1537-6613},
support = {DNRF126//Danish National Research Foundation/ ; R167-A108665-17-S2//Danish Cancer Society/ ; R218-2016-1482//Lundbeck Foundation/ ; NNF15OC0014158//Novo Nordisk Foundation/ ; //Svend Anderson Foundation/ ; RD16/0025/0041//RED de SIDA/ ; //European Regional Development Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Male ; Female ; Middle Aged ; Adult ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Enterococcus faecium/drug effects/isolation & purification ; Enterococcus faecalis/drug effects/isolation & purification ; Metagenomics ; *Drug Resistance, Bacterial ; Young Adult ; Escherichia coli/drug effects/isolation & purification ; Aged ; Gram-Positive Bacterial Infections/microbiology ; Transplant Recipients ; },
abstract = {A relationship among the gut microbiome composition, its resistome, and risk of clinical infections may exist and was explored here by using 663 shotgun-sequenced fecal samples from 276 stem cell transplants. Enterococcus faecium, Escherichia coli, and Enterococcus faecalis were the 3 most prevalent causes of clinical infection, with vancomycin resistance in E faecium as the most common antibiotic resistance feature. Associations among the gut microbiome, resistome, and clinical infections were tested, with significant findings (false discovery rate <0.05) evaluated in multivariable analysis. A 10% increase in gut abundance of E faecium was positively associated with subsequent clinical infection with E faecium (odds ratio, 1.14; P = .02). Additionally, a 1% increase in vanA gene abundance was positively associated with vancomycin-resistant E faecium infection (odds ratio, 1.27; P < .01). Here we used metagenomics to enhance the understanding of infectious sources and to identify patients at risk of clinical infection with antibiotic-resistant bacterial strains.},
}

Humans
*Gastrointestinal Microbiome
*Hematopoietic Stem Cell Transplantation/adverse effects
Male
Female
Middle Aged
Adult
Feces/microbiology
Anti-Bacterial Agents/pharmacology
Enterococcus faecium/drug effects/isolation & purification
Enterococcus faecalis/drug effects/isolation & purification
Metagenomics
*Drug Resistance, Bacterial
Young Adult
Escherichia coli/drug effects/isolation & purification
Aged
Gram-Positive Bacterial Infections/microbiology
Transplant Recipients

@article {pmid40468098,
year = {2025},
author = {Srivastava, A and Rai, PK and Agnihotri, VK and Choure, K and Vishvakarma, R},
title = {Metagenomic analysis of viral communities in the polluted Varuna River reveals site-specific diversity patterns associated with environmental aspects.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {28},
number = {7},
pages = {2129-2150},
pmid = {40468098},
issn = {1618-1905},
mesh = {*Rivers/virology ; Metagenomics ; *Viruses/genetics/classification/isolation & purification ; *Biodiversity ; Phylogeny ; *Virome ; },
abstract = {Varuna River, which is native to Varanasi, is of great importance as a water reservoir for the people and is contaminated with heavy pollutants due to urbanization. In this study, four sites (VR1, VR2, VR3, and VR4) of Varuna River water were sampled to assess the viral diversity. The metagenomics approach was used to study the viral diversity and functional analysis, suggesting the overall quality of the water at the sampled location. The analysis shows that VR1 had the most species richness (3000 species), followed by VR3 (2500), VR2 (2000), and VR4 (1500). The PCA analysis revealed distinct spatial patterns and community differentiation where VR2 and VR4 clustered while VR1 and VR3 were distant.Diversity analysis showed that Negarnaviricota dominated all samples at the phylum level. Yunchangviricetes, a non-reported virus, and Insthoviricetes were the dominant classes. Pakpunavirus was the leading genus, followed by the human pathogen Mimivirus. The highest species abundance in VR1 and VR2 was Mimivirus, Megavirus, chilensis, while VR3 and VR4 had Hpunavirus and Pseudomonas phage O4, indicating human involvement. Functional analyses of enzymatic activity and KEGG Orthology in microbial communities from VR1 to VR4 samples showed that VR4 exhibited maximal enzymatic activity, genetic flexibility, and advanced regulatory control compared to the other samples. The increased presence of transporter genes alongside signal transduction proteins and metabolic enzymes in VR4 indicates enhanced functional diversity, which aids in coping with environmental stresses. On the basis of viral species, ecological, biotechnological aspects were also interpreted. This study concluded that the Negarnaviricota plays a key role in maintaining the overall water quality and there is an urgent need for remediation of the Varuna River especially at site VR4 (25° 19' 46.7″ N 83° 02' 38.3″ E).},
}

*Rivers/virology
Metagenomics
*Viruses/genetics/classification/isolation & purification
*Biodiversity
Phylogeny
*Virome

@article {pmid40439813,
year = {2025},
author = {Biktasheva, L and Galitskaya, P and Kuryntseva, P and Shipaeva, M and Selivanovskaya, S},
title = {Challenges and distortions in microbial community analysis of oil reservoirs: a case study with heavy crude oil from the Romashkino field.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {28},
number = {7},
pages = {2095-2103},
pmid = {40439813},
issn = {1618-1905},
support = {075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Oil and Gas Fields/microbiology ; *Petroleum/microbiology/analysis ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Microbiota ; DNA, Bacterial/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Anaerobiosis ; },
abstract = {The study of the microbial community of wells is a methodologically complex, but urgent problem. In the course of our work, five samples of oil wells were selected from one deposit of the Romashkino field. The samples were subjected to nucleic acid extraction using three methods-direct DNA extraction, and after enrichment using aerobic and anaerobic cultivation methods. In three samples from wells W1-W3, extraction after anaerobic enrichment was successful. Effective aerobic cultivation was possible in all five samples. All three of these samples represented the aqueous part of the produced fluid; samples from wells W4 and W5, where extraction was difficult, represented the oil part. During the analysis of the microbial community in enrichment cultures from wells W1-W3, exogenous microorganisms such as Desulfovibrio, Acetobacterium, Bacillus, and Georgenia were discovered, which can be explained by the long-term exploitation of this section of the field. In one sample from well W1, community information was obtained using direct extraction and anaerobic enrichment. It was found that the microbial community changed significantly after enrichment, and its diversity decreased. At the same time, however, the functional profile of microorganisms has not changed, and sulfate-reducing microorganisms dominate in both samples. Thus, the results of the work allow us to make an assumption about the physicochemical parameters of samples in which the study of the microbial community is possible. In addition, it became known that well W1 needs to control the process of biological acidification and has a high risk of equipment corrosion.},
}

*Oil and Gas Fields/microbiology
*Petroleum/microbiology/analysis
*Bacteria/classification/genetics/isolation & purification/metabolism
*Microbiota
DNA, Bacterial/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Anaerobiosis

@article {pmid40411710,
year = {2025},
author = {Chen, L and Chen, C and Bai, Y and Li, C and Wei, C and Wei, R and Luo, R and Li, R and Ma, Q and Geng, Y},
title = {Evaluation of the effects of different formulations of protectants on the preservation of the microbiota in fecal microbiota transplantation.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {28},
number = {7},
pages = {2057-2079},
pmid = {40411710},
issn = {1618-1905},
mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; Mice ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Bacteria/drug effects/genetics/growth & development ; *Protective Agents/pharmacology/chemistry ; Microbial Viability/drug effects ; *Preservation, Biological/methods ; Freeze Drying ; Male ; },
abstract = {BACKGROUND: With the increasing indications for fecal microbiota transplantation for the treatment of diseases, there is a growing demand for the preparation of frozen or lyophilized fecal microbiota products that are viable and can stably colonize the recipient. The addition of protective agents plays an important role in the preparation. However, there has been no systematic evaluation of the protective agents used in fecal microbiota sample transplantation preparation for transplantation.

METHODS: We were used the donor bacterial flora containing 10 different formulations of protective agents were frozen, lyophilized, and stored. Plate counting, CCK8 assay, flow cytometry after LIVE/DEAD staining, and fluorescence intensity were used to assess viable bacteria in vitro. In addition, the donor bacterial flora samples containing different formulations protective agents were transplanted into antibiotic-treated SPF mice, with 3 mice in each group and a total of 5 groups. Fecal samples were collected for metagenomic sequencing to observe the colonization of the bacterial flora in the recipient mice.

RESULTS: The preliminary screening results showed that the survival rate of bacteria in the 5% trehalose (T) groups, and 5% sucrose, 5% inulin, and 1% cysteine hydrochloride (SI) groups was slightly higher than that in the other groups. SI groups tended to be more protective against anaerobes than T groups. The donor gut microbiota containing the SI groups protective agent exhibited the best colonization of the recipient mice. The protective effects of different formulations of protective agents on the colonized probiotic strains and the metabolic function of the bacterial flora in recipient mice were found to be species specific.

CONCLUSIONS: SI groups can not only better protect the activity of anaerobic bacteria in the intestine, but also effectively promote the effective colonization of donor intestinal bacteria in the recipient mice, and the effect of frozen storage method is less, and can be used at the same time as frozen and freeze-dried preparation. It can be used as a reference for the selection of protective agents in the preparation of fecal microbiota transplantation samples.},
}

Animals
*Fecal Microbiota Transplantation/methods
Mice
*Feces/microbiology
*Gastrointestinal Microbiome/drug effects
Bacteria/drug effects/genetics/growth & development
*Protective Agents/pharmacology/chemistry
Microbial Viability/drug effects
*Preservation, Biological/methods
Freeze Drying
Male

@article {pmid40402820,
year = {2025},
author = {Alberdi, A and Limborg, MT and Groussin, M and Aizpurua, O and Gilbert, MTP},
title = {Metagenomic spaces: a framework to study the effect of microbiome variation on animal ecology and evolution.},
journal = {Journal of evolutionary biology},
volume = {38},
number = {10},
pages = {1285-1298},
doi = {10.1093/jeb/voaf063},
pmid = {40402820},
issn = {1420-9101},
support = {DNRF143//Danish National Research Foundation/ ; R250-2017-1351//Lundbeckfonden/ ; CF20-0460//Carlsbergfondet/ ; H2020-SFS-2018-1//European Union/ ; HoloFood-817729//European Union/ ; 901436//Norwegian Seafood Research Fund/ ; 1182//German Science Foundation/ ; 261376515-SFB 1182//German Science Foundation/ ; },
mesh = {Animals ; *Biological Evolution ; *Microbiota ; *Metagenomics ; *Vertebrates/microbiology ; Host Microbial Interactions ; },
abstract = {Microorganisms are essential for the normal functioning of most vertebrates. Hence, identifying and measuring the factors that shape host-associated microbial communities is necessary to understand the ecological and evolutionary implications of host-microbiota associations. We propose a framework, built on the so-called "metagenomic space" concept, which incorporates multiple definitions and quantifiable features relating to the variation of microbial communities that are associated with vertebrate hosts. By drawing on diverse theories and concepts developed in different fields of biology, our framework sets a conceptual landscape that transcends the mere characterization of microbial communities. This provides the basis to study more complex attributes, such as "potential metagenomic space" and "fundamental metagenomic space," "metagenomic plasticity," and "metagenomic evolvability," which we argue are essential for understanding the microbial contribution to vertebrate host ecology and evolution-and hold considerable promise for advancing applied research and innovation. In doing so, we hope to contribute to an improved understanding of the impact of spatiotemporal variation of vertebrate host-microbiota associations, and inspire new approaches to address testable hypotheses related to ecological, evolutionary, and applied processes.},
}

Animals
*Biological Evolution
*Microbiota
*Metagenomics
*Vertebrates/microbiology
Host Microbial Interactions

@article {pmid40266232,
year = {2025},
author = {Zhang, M and Shi, S and Feng, Y and Zhang, F and Xiao, Y and Li, X and Pan, X and Feng, Y and Liu, D and Guo, Y and Hu, Y},
title = {Synthetic microbial community improves chicken intestinal homeostasis and provokes anti-Salmonella immunity mediated by segmented filamentous bacteria.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf076},
pmid = {40266232},
issn = {1751-7370},
support = {2024TZXD026//Shandong Provincial Key Research and Development Program of China/ ; 2022YFA1304201//National Key Research and Development Program of China/ ; //Shandong Provincial Key Research and Development Program of China/ ; //National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Chickens/microbiology/immunology ; *Gastrointestinal Microbiome ; *Homeostasis ; *Intestines/microbiology/immunology ; *Bacteria/genetics/classification ; *Salmonella Infections, Animal/immunology/prevention & control/microbiology ; Phylogeny ; Poultry Diseases/immunology/microbiology ; *Salmonella/immunology ; },
abstract = {Applying synthetic microbial communities to manipulate the gut microbiota is a promising manner for reshaping the chicken gut microbial community. However, it remains elusive the role of a designed microbial community in chicken physiological metabolism and immune responses. In this study, we constructed a 10-member synthetic microbial community (SynComBac10) that recapitulated the phylogenetic diversity and functional capability of adult chicken intestinal microbiota. We found that early-life SynComBac10 exposure significantly enhanced chicken growth performance and facilitated the maturation of both the intestinal epithelial barrier function and the gut microbiota. Additionally, SynComBac10 promoted the pre-colonization and growth of segmented filamentous bacteria (SFB), which in turn induced Th17 cell-mediated immune responses, thereby conferring resistance to Salmonella infection. Through metagenomic sequencing, we assembled the genomes of two distinct species of SFB from the chicken gut microbiota, which displayed common metabolic deficiencies with SFB of other host origins. In silico analyses indicated that the SynComBac10-stimulated early establishment of SFB in the chicken intestine was likely through SynComBac10-derived metabolite cross-feeding. Our study demonstrated the pivotal role of a designed microbial consortium in promoting chicken gut homeostasis and anti-infection immunity, providing a new avenue for engineering chicken gut microbiota.},
}

Animals
*Chickens/microbiology/immunology
*Gastrointestinal Microbiome
*Homeostasis
*Intestines/microbiology/immunology
*Bacteria/genetics/classification
*Salmonella Infections, Animal/immunology/prevention & control/microbiology
Phylogeny
Poultry Diseases/immunology/microbiology
*Salmonella/immunology

@article {pmid40134271,
year = {2025},
author = {Orme, W and Grimm, SL and Vella, DSN and Fowler, JC and Frueh, BC and Weinstein, BL and Petrosino, J and Coarfa, C and Madan, A},
title = {Relationships of Personality Traits With the Taxonomic Composition of the Gut Microbiome Among Psychiatric Inpatients.},
journal = {The Journal of neuropsychiatry and clinical neurosciences},
volume = {37},
number = {4},
pages = {349-358},
doi = {10.1176/appi.neuropsych.20240126},
pmid = {40134271},
issn = {1545-7222},
support = {P30 ES030285/ES/NIEHS NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Adult ; Middle Aged ; Inpatients ; *Personality/physiology ; *Mental Disorders/microbiology ; Machine Learning ; Feces/microbiology ; Young Adult ; *Personality Disorders/microbiology ; },
abstract = {OBJECTIVE: Through the brain-gut-microbiome axis, myriad psychological functions that affect behavior share a dynamic, bidirectional relationship with the intestinal microbiome. Little is known about the relationship between personality-a stable construct that influences social- and health-related behaviors-and the bacterial ecosystem. The authors of this exploratory study examined the relationship between general and maladaptive personality traits and the composition of the gut microbiome.

METHODS: In total, 105 psychiatric inpatients provided clinical data and fecal samples. Personality traits were measured with the five-factor model of personality, the Structured Clinical Interview for DSM-IV Axis II Personality Disorders, and the Personality Inventory for DSM-5; 16S ribosomal DNA sequencing and whole-genome shotgun sequencing methods were used on fecal samples. Machine learning (ML) was used to identify personality traits associated with bacterial variability and specific taxa.

RESULTS: Supervised ML techniques were used to classify traits of social detachment (maximum area under the receiver operating characteristic curve [AUROC]=0.944, R[2]>0.20), perceptual disturbance (maximum AUROC=0.763, R[2]=0.301), and hoarding behaviors (maximum AUROC=0.722) by using limited sets of discriminant bacterial species or genera. Established bacterial genera associated with psychosis (e.g., Peptococcus and Coprococcus) were associated with traits of perceptual disturbance. Hoarding behaviors were associated with a defined gut microbial composition that included Streptococcus, a known contributor to the development of pediatric autoimmune neuropsychiatric disorders.

CONCLUSIONS: Observations from this study are consistent with recent findings demonstrating person-to-person interactions as a mode of gut microbiome transmission. This study adds to the emerging literature on the intricate connections between brain and gut function, expanding the interdisciplinary field of psychiatric microbiology.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
Female
Adult
Middle Aged
Inpatients
*Personality/physiology
*Mental Disorders/microbiology
Machine Learning
Feces/microbiology
Young Adult
*Personality Disorders/microbiology

@article {pmid41087370,
year = {2025},
author = {Balachandran, KRS and Mani, G and Sidharthan, AT and Mary Leema, JT and Senthilkumar, R and Gopal, D},
title = {Unearthing the genetic resources of Arabian sea seamount and metagenomic insights into phosphate cycling genes for next generation plant biostimulants.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35782},
pmid = {41087370},
issn = {2045-2322},
mesh = {*Metagenomics/methods ; *Metagenome ; *Phosphates/metabolism ; *Geologic Sediments/microbiology ; Bacteria/genetics ; Microbiota/genetics ; Phosphoric Monoester Hydrolases/genetics/metabolism ; },
abstract = {Deep-sea encompasses a wide diversity of microbiomes including bacteria, fungi and viruses which play crucial significant roles in nutrient biogeochemical cycling thereby imparting majorly to functional biodiversity of these hotspots. Sea mounts harboring microbes with extremophilic properties found in deep oceans could be conserved as living repository by functional metagenomics approach which is a potent source to screen bioactive compounds and novel enzymes thereby could address biological question on developing next generation plant biostimulants. This study outlines construction of fosmid metagenome library and adapted combined strategy of functional and nanopore sequence-based metagenomic screening to unveil phosphatase enzymes from Arabian Sea seamount sediment. About 9068 metagenomic clones were generated with an average insert size of 38 kb and stored in pools of 1024 clones, out of which 42 were found to be positive for phosphatase. Five clones with high phosphatase activity were further characterized and NIOT F41 showed the greatest specific activity for phosphatase (41.2 U/mg). Gluconic (1041 mg/L), oxalic (327 mg/L), and succinic acids (610 mg/L) were the predominant organic acids produced by recombinant clones. Fosmid DNA were extracted from five potential clones for nanopore-based metagenomics sequencing which generated an average of 6,00,786 reads. Taxonomic analysis revealed an abundance of Proteobacteria and Firmicutes phyla harboring phosphate-solubilising bacteria Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus warneri. Furthermore, functional annotation using phosphorus cycling database (PCycDB) predicted variation in relative abundance of phosphatase gene clusters encoding alkaline phosphatase (PhoD, PhoX and PhoA) and acid phosphatase (OlpA, PhoNand PhoC) produced by recombinant clones. In the pot assay, potential metagenomic clones exhibited positive impacts on shoot length (9.1 ± 1.1 cm, p < 0.05), root length (2.05 ± 0.05 cm, p < 0.05), wet biomass (39.3 ± 0.65 mg, p < 0.05), and dry biomass (5.1 ± 1.15 mg, p < 0.05) compared to the negative control indicating significant effect on promoting plant growth. The advanced nanopore sequencing and functional metagenomics methods employed in this study could serve as a marine biodiversity conservation approach for deep-sea microbes hidden in sea mount sediments towards harnessing potential next generation plant biostimulants with promising biotechnological application for sustainable agriculture.},
}