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

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

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

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

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

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

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

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

@article {pmid40240456,
year = {2025},
author = {Bahetjan, K and Yu-Xia, and Lin, S and Aili, N and Yang, H and Du, S},
title = {Analysis of the bronchoalveolar lavage fluid microbial flora in COPD patients at different lung function during acute exacerbation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13179},
pmid = {40240456},
issn = {2045-2322},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Female ; Aged ; Middle Aged ; *Microbiota ; Bacteria/classification/genetics/isolation & purification ; *Lung/microbiology/physiopathology ; Dysbiosis/microbiology ; },
abstract = {There is a correlation between the dysbiosis of the respiratory microbiota and the occurrence, severity, frequency, and mortality of Chronic Obstructive Pulmonary Disease (COPD). However, it is not unclear if there are differences in the bronchoalveolar lavage fluid (BALF) microbiota among patients at differente lung function. In this study, BALF samples were collected from 70 COPD patients experiencing acute exacerbations (AECOPD). The patients were divided into a mild group (FEV1/pre ≥ 50; PFT I, n = 50) and a severe group (FEV1/pre < 50; PFT II, n = 20) according to the lung function: or a frequent exacerbation (FE, n = 41) group and a non-frequent exacerbation (NFE, n = 29) group according to their exacerbation history. Microbiota analysis of BALF samples was conducted using mNGS and bioinfromatic analysis. Compared to PFT I group, PFT II group exhibited a significant decrease in species diversity (Shannon index), as well as a significant reduction in total species count and richness (Chao1, ACE indices). NFE group demonstrated diversity similar to that of FE group. Conversely, the microbial diversity of NFE group was comparable to that of FE group. The most abundant bacterial genera were Streptococcus, Prevotella, Veillonella, Rod-shaped Bacillus, and Rothia. Aspergillus was the most dominant fungal genus in AECOPD. Lymphocryptovirus was the most prevalent virus in AECOPD.Compared to the PFT I group, Corynebacterium's abundance significantly increased in PFT II group. Furthermore, FE group showed a notable increase in Streptococcus mitis abundance relative to NFE group. Bubble plot analysis revealed a significant increase in Moraxella, Fusobacterium, Haemophilus, Pseudomonas, Streptomyces, and Klebsiella in PFT II group, including a notable increase in typical Veillonella, Actinomyces, and Gordonia. The NFE group exhibited a significant increase in Bacteroides and Prevotella's relative abundance. Spearman correlation analysis revealed strong positive correlations among certain microbial communities. There exists a significant variation in microbial composition across groups of AECOPD patients at different lung function. Specifically, patients with severe airflow limitations exhibit a significant reduction in microbial diversity. Additionally, distinct bacterial taxa are enriched in patients characterized by varying levels of airflow limitation and exacerbation frequency. These observations offer vital insights into the pathogenesis of AECOPD, suggesting a potentially crucial role for the microbiota in its development. Such findings pave the way for identifying potential therapeutic targets and intervention strategies, ultimately aiming to improve treatment outcomes for AECOPD patients.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology
*Bronchoalveolar Lavage Fluid/microbiology
Male
Female
Aged
Middle Aged
*Microbiota
Bacteria/classification/genetics/isolation & purification
*Lung/microbiology/physiopathology
Dysbiosis/microbiology

@article {pmid40240384,
year = {2025},
author = {Pinto, OHB and Biazotti, BB and de Souza, RSC and Yassitepe, JÉCT and Arruda, P and Dante, RA and Gerhardt, IR},
title = {Seasonal bacterial profiles of Vellozia with distinct drought adaptations in the megadiverse campos rupestres.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {636},
pmid = {40240384},
issn = {2052-4463},
support = {2022/08797-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; 2022/08797-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; },
mesh = {*Droughts ; Seasons ; *Soil Microbiology ; Brazil ; RNA, Ribosomal, 16S/genetics ; Adaptation, Physiological ; *Microbiota ; Bacteria/genetics/classification ; },
abstract = {Microbial communities can vary as a function of seasonal precipitation and the phenotypic characteristics of the prevailing plant species in an ecosystem. The Brazilian campos rupestres (CRs) host a unique flora adapted to harsh conditions, including severe droughts and nutrient-poor soils. Velloziaceae, a dominant angiosperm family in CRs, exhibit contrasting drought adaptive strategies, prominently desiccation tolerance and dehydration avoidance. Here, we created a comprehensive dataset of microbial composition and dynamics of bulk soil and distinct plant compartments (leaf blade, dry sheath, aerial root, and underground root) from two desiccation-tolerant and two dehydration-avoiding, non-desiccation-tolerant Vellozia species, across four seasons (beginning and end of rainy and dry seasons) through 16S rRNA gene sequencing of 374 samples. This dataset also includes 38 soil metagenomes encompassing dry and rainy seasons from both drought adaptive strategies. Exploring an overlooked aspect of CRs biology offers significant potential for understanding plant-microbial associations and adaptations to water availability in tropical regions. The genetic data and metadata support further research for hypothesis testing and cross-study comparisons.},
}

*Droughts
Seasons
*Soil Microbiology
Brazil
RNA, Ribosomal, 16S/genetics
Adaptation, Physiological
*Microbiota
Bacteria/genetics/classification

@article {pmid40238917,
year = {2025},
author = {Trepka, KR and Kidder, WA and Kyaw, TS and Halsey, T and Olson, CA and Ortega, EF and Noecker, C and Upadhyay, V and Stanfield, D and Steiding, P and Guthrie, BGH and Spanogiannopoulos, P and Dumlao, D and Turnbaugh, JA and Stachler, MD and Van Blarigan, EL and Venook, AP and Atreya, CE and Turnbaugh, PJ},
title = {Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity.},
journal = {Science translational medicine},
volume = {17},
number = {794},
pages = {eadq8870},
doi = {10.1126/scitranslmed.adq8870},
pmid = {40238917},
issn = {1946-6242},
mesh = {Animals ; Humans ; *Operon/genetics ; *Fluorouracil/therapeutic use/toxicity/adverse effects ; Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *Colorectal Neoplasms/drug therapy/microbiology ; *Pyrimidines/toxicity ; *Bacteria/genetics/drug effects ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; },
abstract = {Dose-limiting toxicities remain a major barrier to drug development and therapy, revealing the limited predictive power of human genetics. Here, we demonstrate the utility of a more comprehensive approach to studying drug toxicity through longitudinal profiling of the human gut microbiome during colorectal cancer (CRC) treatment (NCT04054908) coupled to cell culture and mouse experiments. Substantial shifts in gut microbial community structure during oral fluoropyrimidine treatment across multiple patient cohorts, in mouse small and large intestinal contents, and in patient-derived ex vivo communities were revealed by 16S rRNA gene sequencing. Metagenomic sequencing revealed marked shifts in pyrimidine-related gene abundance during oral fluoropyrimidine treatment, including enrichment of the preTA operon, which was sufficient for the inactivation of active metabolite 5-fluorouracil (5-FU). preTA[+] bacteria depleted 5-FU in gut microbiota grown ex vivo and in the mouse distal gut. Germ-free and antibiotic-treated mice experienced increased fluoropyrimidine toxicity, which was rescued by colonization with the mouse gut microbiota, preTA[+] Escherichia coli, or preTA-high stool from patients with CRC. Last, preTA abundance was negatively associated with fluoropyrimidine toxicity in patients. Together, these data support a causal, clinically relevant interaction between a human gut bacterial operon and the dose-limiting side effects of cancer treatment. Our approach may be generalizable to other drugs, including cancer immunotherapies, and provides valuable insights into host-microbiome interactions in the context of disease.},
}

Animals
Humans
*Operon/genetics
*Fluorouracil/therapeutic use/toxicity/adverse effects
Gastrointestinal Microbiome/drug effects/genetics
Mice
*Colorectal Neoplasms/drug therapy/microbiology
*Pyrimidines/toxicity
*Bacteria/genetics/drug effects
RNA, Ribosomal, 16S/genetics
Female
Male

@article {pmid40238748,
year = {2025},
author = {da Silva-Álvarez, E and Gómez-Arrones, V and Correa-Fiz, F and Martín-Cano, FE and Gaitskell-Phillips, G and Carrasco, JJ and Rey, J and Aparicio, IM and Peña, FJ and Alonso, JM and Ortega-Ferrusola, C},
title = {Metagenomic and proteomic analyses reveal similar reproductive microbial profiles and shared functional pathways in uterine immune regulation in mares and jennies.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0321389},
doi = {10.1371/journal.pone.0321389},
pmid = {40238748},
issn = {1932-6203},
mesh = {Animals ; Female ; Horses/microbiology/immunology ; *Uterus/microbiology/immunology/metabolism ; Proteomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Vagina/microbiology/immunology ; Bacteria/genetics/classification ; Proteome ; },
abstract = {This study aims to unveil potential differences in the vaginal and uterine microbiomes in mares and jennies, and to identify possible mechanisms involved in uterine immune homeostasis. The microbiota was characterized using 16S rRNA sequencing, and the uterine proteome was analyzed using UHPLC/MS/MS in 18 samples from healthy mares and 14 from jennies. While taxonomic analysis revealed high interspecies similarities, β-diversity analysis showed distinct clustering, with only two vaginal taxa and five uterine taxa differing between species. Despite compositional differences, PICRUSt analysis suggested minimal variations in predicted functional pathways across species. Comparing vaginal and uterine microbiota within the same species revealed overlapping bacterial taxa, but significant differences in α- and β-diversity and functional pathways. The uterine microbiota of both species was dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with abundant taxa like Streptococcus, Pseudomonas, Bacillus, Corynebacterium, and Staphylococcus, many of which are frequently associated with endometritis. The presence of Lactobacillus in the equine reproductive tract was minimal or non-existent. KEGG functional pathway analysis predicted that uterine microbiota of both species utilize metabolic pathways with potential immunomodulatory effects. Proteomic enrichment analysis showed that numerous overexpressed uterine proteins in both species are linked to adaptive and innate immune regulation and defense mechanisms against symbionts. Gene enrichment analysis identified several enriched Gene Ontology terms, including response to bacterial stimuli, humoral immune regulation, and TGF-beta receptor signaling, underscoring microbial-host interactions. The uterine microbiota may play a vital role in maintaining immune balance. Further research is required to confirm its interaction with the uterine immune system and clarify the mechanisms involved.},
}

Animals
Female
Horses/microbiology/immunology
*Uterus/microbiology/immunology/metabolism
Proteomics/methods
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
*Metagenomics
Vagina/microbiology/immunology
Bacteria/genetics/classification
Proteome

@article {pmid40238740,
year = {2025},
author = {Wang, J and Yin, J and Liu, X and Liu, Y and Jin, X},
title = {Gut commensal bacterium Bacteroides vulgatus exacerbates helminth-induced cardiac fibrosis through succinate accumulation.},
journal = {PLoS pathogens},
volume = {21},
number = {4},
pages = {e1013069},
doi = {10.1371/journal.ppat.1013069},
pmid = {40238740},
issn = {1553-7374},
mesh = {Animals ; *Succinic Acid/metabolism ; Mice ; Fibrosis ; *Gastrointestinal Microbiome/physiology ; *Trichinellosis/complications/metabolism/pathology ; *Trichinella spiralis ; *Bacteroides/metabolism ; Mice, Inbred C57BL ; Receptors, G-Protein-Coupled/metabolism ; Myocardium/pathology/metabolism ; Male ; },
abstract = {Trichinella spiralis (Ts) is known to cause cardiac fibrosis, which is a critical precursor to various heart diseases, and its progression is influenced by metabolic changes. However, the metabolic mechanisms remain unclear. Here, we observed that Ts-infected mice exhibited cardiac fibrosis along with elevated succinate levels in the heart using metabolomic analysis. Administration of succinate exacerbated fibrosis during Ts infection, while deficiency in succinate receptor 1 (Sucnr1) alleviated the condition, highlighting the role of the succinate-Sucnr1 axis in fibrosis development. Furthermore, metagenomics sequencing showed that Ts-infected mice had a higher abundance ratio of succinate-producing bacteria to succinate-consuming bacteria in the intestines. Notably, the succinate-producer Bacteroides vulgatus was enriched in Ts group. Oral supplementation with B. vulgatus aggravated Ts-induced cardiac fibrosis. In summary, our findings underscore the succinate-Sucnr1 axis as a critical pathway in helminth-induced cardiac fibrosis and highlight the potential of targeting this axis for therapeutic interventions. This study presents novel insights into the gut-heart axis, revealing innovative strategies for managing cardiovascular complications associated with helminth infections.},
}

Animals
*Succinic Acid/metabolism
Mice
Fibrosis
*Gastrointestinal Microbiome/physiology
*Trichinellosis/complications/metabolism/pathology
*Trichinella spiralis
*Bacteroides/metabolism
Mice, Inbred C57BL
Receptors, G-Protein-Coupled/metabolism
Myocardium/pathology/metabolism
Male

@article {pmid40237336,
year = {2025},
author = {Naspolini, NF and Schüroff, PA and Vanzele, PAR and Pereira-Santos, D and Valim, TA and Bonham, KS and Fujita, A and Passos-Bueno, MR and Beltrão-Braga, PCB and Carvalho, ACPLF and Klepac-Ceraj, V and Polanczyk, GV and Campos, AC and Taddei, CR},
title = {Exclusive breastfeeding is associated with the gut microbiome maturation in infants according to delivery mode.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2493900},
doi = {10.1080/19490976.2025.2493900},
pmid = {40237336},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Breast Feeding ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Brazil ; Feces/microbiology ; Metagenomics ; *Delivery, Obstetric/methods ; Cohort Studies ; Infant, Newborn ; },
abstract = {Exclusive breastfeeding (EBF) plays a crucial role in infant gut microbiome assembly and development. However, few studies have investigated the effects of EBF in restoring a perturbed microbiome. In this study, we applied whole metagenomic sequencing to assess the gut microbiome assembly in 525 Brazilian infants from 3 to 9 months of age of the Germina Cohort, demonstrating the early determinants of microbial taxonomy and function modulation. Our analysis shows that EBF alters the relative abundance of genes related to the microbiome taxonomy and function, with effects varying by delivery mode. EBF alters the pattern of carbohydrates, lipid metabolism, and cell structure pathways depending on the delivery mode. The microbiome age is closer to chronological infant age in EBF than in non-EBF infants, meaning a lower microbiome maturation index (MMI). Using a complementary machine learning approach, we show that Escherichia coli, Ruminococcus gnavus, and Clostridium neonatale, as well as vitamin K and o-antigen pathways contribute strongly to EBF prediction. Moreover, EBF influences the microbiome maturation in early life, toward a microbiome age more similar to the chronological infant's age.},
}

Humans
*Gastrointestinal Microbiome
Infant
*Breast Feeding
Female
*Bacteria/classification/genetics/isolation & purification
Male
Brazil
Feces/microbiology
Metagenomics
*Delivery, Obstetric/methods
Cohort Studies
Infant, Newborn

@article {pmid40234093,
year = {2025},
author = {Block, MS and Nelson, GD and Chen, J and Johnson, S and Yang, L and Flotte, TJ and Grewal, EP and McWilliams, RR and Kottschade, LA and Domingo-Musibay, E and Markovic, SN and Dimou, A and Montane, HN and Piltin, MA and Price, DL and Khariwala, SS and Hui, JYC and Erskine, CL and Strand, CA and Zahrieh, D and Dong, H and Hieken, TJ},
title = {Neoadjuvant cobimetinib and atezolizumab with or without vemurafenib for stage III melanoma: outcomes and the impact of the microbiome from the NeoACTIVATE trial.},
journal = {Journal for immunotherapy of cancer},
volume = {13},
number = {4},
pages = {},
doi = {10.1136/jitc-2025-011706},
pmid = {40234093},
issn = {2051-1426},
mesh = {Humans ; *Melanoma/drug therapy/pathology/mortality ; Female ; Male ; *Azetidines/therapeutic use/pharmacology ; *Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; Middle Aged ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; *Neoadjuvant Therapy/methods ; *Piperidines/pharmacology/therapeutic use ; *Vemurafenib/pharmacology/therapeutic use ; Aged ; Neoplasm Staging ; Adult ; Gastrointestinal Microbiome ; Treatment Outcome ; *Skin Neoplasms/drug therapy ; },
abstract = {BACKGROUND: Neoadjuvant treatment has become standard for patients with high-risk operable stage III melanoma, but the optimal regimen is unknown. Targeted therapy approaches yield high pathological response rates, while immunotherapy regimens show favorable recurrence-free survival (RFS). NeoACTIVATE was designed to address whether a neoadjuvant combination of both targeted therapy and immunotherapy might leverage the benefits of each.

METHODS: We tested neoadjuvant treatment with 12 weeks of vemurafenib, cobimetinib, and atezolizumab for patients with BRAF-mutated (BRAFm) melanoma (cohort A) and cobimetinib and atezolizumab for patients with BRAF-wild-type (BRAFwt) melanoma (cohort B), regimens which we have shown generate a substantial major pathological response. After therapeutic lymph node dissection, patients received 24 weeks of adjuvant atezolizumab. Here, we report survival outcomes and their association with biomarkers assayed among the gut microbiome and peripheral blood immune subsets.

RESULTS: With 49 months median follow-up, the median RFS was not reached for cohort A and was 40.8 months for cohort B. At 24 months after operation, 2 of 14 cohort A patients and 4 of 13 cohort B patients had experienced distant relapse. Key findings from correlative analyses included diversity, taxonomic and functional metagenomic gut microbiome signals associated with distant metastasis-free survival at 2 years. Notably, we observed a strong correlation between low microbial arginine biosynthesis (required for T-cell activation and effector function) and early distant recurrence (p=0.0005), which correlated with taxonomic differential abundance findings. Peripheral blood immune monitoring revealed increased double-positive (CD4+CD8+) T cells in patients with early recurrence.

CONCLUSIONS: Neoadjuvant treatment with cobimetinib and atezolizumab±vemurafenib was associated with a low rate of distant metastasis in patients with high-risk stage III melanoma. Freedom from early distant metastasis was highly associated with taxonomic differences in gut microbiome structure and with functional pathway alterations known to modulate T cell immunity. Identification of predictive biomarkers will permit optimization of neoadjuvant therapy regimens for individual patients.

TRIAL REGISTRATION NUMBER: NCT03554083.},
}

Humans
*Melanoma/drug therapy/pathology/mortality
Female
Male
*Azetidines/therapeutic use/pharmacology
*Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use
Middle Aged
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology
*Neoadjuvant Therapy/methods
*Piperidines/pharmacology/therapeutic use
*Vemurafenib/pharmacology/therapeutic use
Aged
Neoplasm Staging
Adult
Gastrointestinal Microbiome
Treatment Outcome
*Skin Neoplasms/drug therapy

@article {pmid40233938,
year = {2025},
author = {Kolokotronis, SO and Bhattacharya, C and Panja, R and Quate, I and Seibert, M and Jorgensen, E and Mason, CE and Hénaff, EM},
title = {Metagenomic interrogation of urban Superfund site reveals antimicrobial resistance reservoir and bioremediation potential.},
journal = {Journal of applied microbiology},
volume = {136},
number = {4},
pages = {},
doi = {10.1093/jambio/lxaf076},
pmid = {40233938},
issn = {1365-2672},
support = {80NSSC24K0728/NASA/NASA/United States ; R01AI125416/NH/NIH HHS/United States ; 1758800//National Science Foundation/ ; },
mesh = {Biodegradation, Environmental ; Metagenomics ; *Microbiota/genetics ; Metals, Heavy/metabolism ; *Geologic Sediments/microbiology ; *Bacteria/genetics/metabolism/drug effects/isolation & purification/classification ; Water Pollutants, Chemical/metabolism ; Polychlorinated Biphenyls/metabolism ; *Drug Resistance, Bacterial/genetics ; Metagenome ; },
abstract = {AIMS: We investigate the bioremediation potential of the microbiome of the Gowanus Canal, a contaminated waterway in Brooklyn, NY, USA, designated a Superfund site by the US Environmental Protection Agency due to high concentrations of contaminants, including polychlorinated biphenyls, petrochemicals, and heavy metals.

METHODS AND RESULTS: We present a metagenomic analysis of the Gowanus Canal sediment, consisting of a longitudinal study of surface sediment and a depth-based study of sediment core samples. We demonstrate that the resident microbiome includes 455 species, including extremophiles across a range of saltwater and freshwater species, which collectively encode 64 metabolic pathways related to organic contaminant degradation and 1171 genes related to heavy metal utilization and detoxification. Furthermore, our genetic screening reveals an environmental reservoir of antimicrobial resistance markers falling within 8 different classes of resistance, as well as de-novo characterization of 2319 biosynthetic gene clusters and diverse groups of secondary metabolites with biomining potential.

CONCLUSION: The microbiome of the Gowanus Canal is a biotechnological resource of novel metabolic functions that could aid in efforts for bioremediation, AMR reservoir mapping, and heavy metal mitigation.},
}

Biodegradation, Environmental
Metagenomics
*Microbiota/genetics
Metals, Heavy/metabolism
*Geologic Sediments/microbiology
*Bacteria/genetics/metabolism/drug effects/isolation & purification/classification
Water Pollutants, Chemical/metabolism
Polychlorinated Biphenyls/metabolism
*Drug Resistance, Bacterial/genetics
Metagenome

@article {pmid40233768,
year = {2025},
author = {Tinker, KA and Anthony, W and Brandi, M and Flett, S and Bagwell, CE and Smallwood, C and Davis, R and Gulliver, D},
title = {Identifying Potential Geochemical and Microbial Impacts of Hydrogen Storage in a Deep Saline Aquifer.},
journal = {Environmental microbiology reports},
volume = {17},
number = {2},
pages = {e70076},
doi = {10.1111/1758-2229.70076},
pmid = {40233768},
issn = {1758-2229},
support = {//U.S. Department of Energy's (DOE) Office of Fossil Energy and Carbon Management's Hydrogen with Carbon Management Program and executed through the National Energy Technology Laboratory (NETL) Research & Innovation Center's Natural Gas Decarbonization and Hydrogen Technologies Multi-Year Research Plan/ ; },
mesh = {*Hydrogen/metabolism ; *Groundwater/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Illinois ; Methane/metabolism ; Microbiota ; Metagenomics ; },
abstract = {Hydrogen is valuable commodity and a promising energy carrier for variable energy production. Storage of hydrogen may occur through injection of hydrogen or a hydrogen/methane gas blend in subsurface reservoirs. However, the geochemical and biological reactions that may impact the stored hydrogen are not yet understood. Therefore, we collected samples from a deep storage aquifer located in the St. Peter Formation in southern Illinois. The reservoir material was primarily quartz with sulphur and iron deposits, while the major constituents of the fluid were chloride and sulphate. 16S rRNA gene amplicon sequencing revealed a low biomass microbial community that contained no obvious hydrogen-consuming bacteria. Next, we enriched a field sample to increase the biomass and completed a metagenomic analysis, finding a low number of genes present that are associated with hydrogen consumption. Then, we completed a series of reactor experiments under reservoir conditions with 15% H2/85% CH4 gas simulating a short-term hydrogen storage, high withdrawal scenario. We found minimal changes in the geochemistry or microbiology for the reactor experiments. This work suggests that short-term storage may be highly successful, although significant additional work needs to be completed in order to accurately evaluate the risks associated with long-term hydrogen storage scenarios. It is essential we continue to expand our understanding of the dynamics present in saline aquifers and provide new insights into how hydrogen storage may impact underground geological storage environments.},
}

*Hydrogen/metabolism
*Groundwater/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/metabolism/classification/isolation & purification
Illinois
Methane/metabolism
Microbiota
Metagenomics

@article {pmid40233040,
year = {2025},
author = {Pomej, K and Frick, A and Scheiner, B and Balcar, L and Pajancic, L and Klotz, A and Kreuter, A and Lampichler, K and Regnat, K and Zinober, K and Trauner, M and Tamandl, D and Gasche, C and Pinter, M},
title = {Study protocol: Fecal Microbiota Transplant combined with Atezolizumab/Bevacizumab in Patients with Hepatocellular Carcinoma who failed to achieve or maintain objective response to Atezolizumab/Bevacizumab - the FAB-HCC pilot study.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0321189},
doi = {10.1371/journal.pone.0321189},
pmid = {40233040},
issn = {1932-6203},
mesh = {Humans ; *Liver Neoplasms/therapy/drug therapy ; *Carcinoma, Hepatocellular/therapy/drug therapy ; Pilot Projects ; *Fecal Microbiota Transplantation/methods ; *Bevacizumab/therapeutic use/administration & dosage ; *Antibodies, Monoclonal, Humanized/therapeutic use/administration & dosage ; Male ; Female ; Gastrointestinal Microbiome ; Middle Aged ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Aged ; },
abstract = {BACKGROUND: The gut microbiota is often altered in chronic liver diseases and hepatocellular carcinoma (HCC), and increasing evidence suggests that it may influence response to cancer immunotherapy. Strategies to modulate the gut microbiome (i.e., fecal microbiota transplant (FMT)) may help to improve efficacy of immune checkpoint inhibitors (ICIs) or even overcome resistance to ICIs. Here, we describe the design and rationale of FAB-HCC, a single-center, single-arm, phase II pilot study to assess safety, feasibility, and efficacy of FMT from patients with HCC who responded to PD-(L)1-based immunotherapy or from healthy donors to patients with HCC who failed to achieve or maintain a response to atezolizumab plus bevacizumab.

METHODS: In this single-center, single-arm, phase II pilot study (ClinicalTrials.gov identifier: NCT05750030), we plan to include 12 patients with advanced HCC who failed to achieve or maintain a response to atezolizumab/bevacizumab. Patients will receive a single FMT via colonoscopy from donors with HCC who responded to PD-(L)1-based immunotherapy or from healthy individuals, followed by atezolizumab/bevacizumab every 3 weeks. The primary endpoint is safety, measured by incidence and severity of treatment-related adverse events. The main secondary endpoint is efficacy, as assessed by best radiological response according to RECISTv1.1 and mRECIST. Additional exploratory endpoints include data on the effect of FMT on recipient gut microbiota, as well as metagenomic analysis of stool samples, analyses of circulating immune cells and serum and stool proteomic, metabolomic and lipidomic signatures.

DISCUSSION: The results of this study will help to define the potential of FMT as add-on intervention in the systemic treatment of advanced HCC, with the potential to improve efficacy of immunotherapy or even overcome resistance.

TRIAL REGISTRATION: EudraCT Number: 2022-000234-42 Clinical trial registry & ID: ClinicalTrials.gov identifier: NCT05750030 (Registration date: 16.01.2023).},
}

Humans
*Liver Neoplasms/therapy/drug therapy
*Carcinoma, Hepatocellular/therapy/drug therapy
Pilot Projects
*Fecal Microbiota Transplantation/methods
*Bevacizumab/therapeutic use/administration & dosage
*Antibodies, Monoclonal, Humanized/therapeutic use/administration & dosage
Male
Female
Gastrointestinal Microbiome
Middle Aged
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use
Aged

@article {pmid40232948,
year = {2025},
author = {Leech, SM and Barrett, HL and Dorey, ES and Mullins, T and Laurie, J and Nitert, MD},
title = {Consensus approach to differential abundance analysis detects few differences in the oral microbiome of pregnant women due to pre-existing type 2 diabetes mellitus.},
journal = {Microbial genomics},
volume = {11},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001385},
pmid = {40232948},
issn = {2057-5858},
mesh = {Humans ; Female ; Pregnancy ; *Diabetes Mellitus, Type 2/microbiology/complications ; *Microbiota/genetics ; Adult ; *Diabetes, Gestational/microbiology ; Saliva/microbiology ; *Mouth/microbiology ; Metagenomics/methods ; Dysbiosis/microbiology ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {Oral microbiome dysbiosis has been proposed as a potential contributing factor to rising rates of diabetes in pregnancy, with oral health previously associated with an increased risk of numerous chronic diseases and complications in pregnancy, including gestational diabetes mellitus (GDM). However, whilst most studies examining the relationship between GDM and the oral microbiome identify significant differences, these differences are highly variable between studies. Additionally, no previous research has examined the oral microbiome of women with pre-existing type 2 diabetes mellitus (T2DM), which has greater risks of complications to both mother and baby. In this study, we compared the oral microbiome of 11 pregnant women with pre-existing T2DM with 28 pregnant normoglycaemic controls. We used shotgun metagenomic sequencing to examine buccal swab and saliva rinse samples at two time points between 26 and 38 weeks of gestation. To reduce variation caused by the choice of differential abundance analysis tool, we employed a consensus approach to identify differential taxa and pathways due to diabetes status. Differences were identified at the late time point only. In swab samples, there was increased Flavobacteriaceae, Capnocytophaga, Capnocytophaga gingivalis SGB2479, Capnocytophaga leadbetteri SGB2492 and Neisseria elongata SGB9447 abundance in T2DM as well as increased Shannon diversity and richness. In rinse samples, there was an increased abundance of Haemophilus, Pasteurellaceae, Pasteurellales and Proteobacteria. In contrast to studies of the oral microbiome in T2DM or GDM that use a single differential abundance analysis tool, our consensus approach identified few differences between pregnant women with and without T2DM.},
}

Humans
Female
Pregnancy
*Diabetes Mellitus, Type 2/microbiology/complications
*Microbiota/genetics
Adult
*Diabetes, Gestational/microbiology
Saliva/microbiology
*Mouth/microbiology
Metagenomics/methods
Dysbiosis/microbiology
*Bacteria/classification/genetics/isolation & purification

@article {pmid40229213,
year = {2025},
author = {Hoops, SL and Moutsoglou, D and Vaughn, BP and Khoruts, A and Knights, D},
title = {Metagenomic source tracking after microbiota transplant therapy.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2487840},
doi = {10.1080/19490976.2025.2487840},
pmid = {40229213},
issn = {1949-0984},
mesh = {Humans ; *Metagenomics/methods ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/genetics ; Colitis, Ulcerative/therapy/microbiology ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Metagenome ; Bayes Theorem ; Feces/microbiology ; },
abstract = {Reliable engraftment assessment of donor microbial communities and individual strains is an essential component of characterizing the pharmacokinetics of microbiota transplant therapies (MTTs). Recent methods for measuring donor engraftment use whole-genome sequencing and reference databases or metagenome-assembled genomes (MAGs) to track individual bacterial strains but lack the ability to disambiguate DNA that matches both donor and patient microbiota. Here, we describe a new, cost-efficient analytic pipeline, MAGEnTa, which compares post-MTT samples to a database comprised MAGs derived directly from donor and pre-treatment metagenomic data, without relying on an external database. The pipeline uses Bayesian statistics to determine the likely sources of ambiguous reads that align with both the donor and pre-treatment samples. MAGEnTa recovers engrafted strains with minimal type II error in a simulated dataset and is robust to shallow sequencing depths in a downsampled dataset. Applying MAGEnTa to a dataset from a recent MTT clinical trial for ulcerative colitis, we found the results to be consistent with 16S rRNA gene SourceTracker analysis but with added MAG-level specificity. MAGEnTa is a powerful tool to study community and strain engraftment dynamics in the development of MTT-based treatments that can be integrated into frameworks for functional and taxonomic analysis.},
}

Humans
*Metagenomics/methods
*Fecal Microbiota Transplantation
*Gastrointestinal Microbiome/genetics
Colitis, Ulcerative/therapy/microbiology
*Bacteria/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
*Metagenome
Bayes Theorem
Feces/microbiology

@article {pmid40156579,
year = {2025},
author = {Sanghani, A and Antaliya, K and Patel, R and Dave, S and Tipre, D},
title = {Revealing microbial functionalities and ecological roles in Rajpardi lignite mine: insights from metagenomics analysis.},
journal = {Letters in applied microbiology},
volume = {78},
number = {4},
pages = {},
doi = {10.1093/lambio/ovaf048},
pmid = {40156579},
issn = {1472-765X},
mesh = {*Metagenomics ; India ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Mining ; *Soil Microbiology ; Phylogeny ; *Microbiota ; },
abstract = {The present study employs a metagenomics approach to evaluate microbial communities' ecological functions and potential within the Rajpardi lignite mine of Gujarat, India. Through whole genome shotgun sequencing on the Illumina Miseq platform, we obtained 10 071 318 sequences, which unveiled a diverse and abundant microbial community primarily composed of Proteobacteria, Acidobacteria, and Nitrospirae. Comprehensive taxonomic profiling and gene prediction was carried out using the SqueezeMeta pipline, which highlighted significant contributions to carbohydrate, amino acid, and energy metabolism. The detection of antimicrobial resistance and stress resistance genes, such as blaTEM and merA, suggests that these microbes possess the ability to adapt to harsh environmental conditions. Genome binning revealed species such as Acidiphilum sp. 20-67-58, emphasizing the nature of these communities as they adapted to an acidic environment. This finding highlights the crucial role of microbes in biogeochemical cycles, emphasizing their potential in bioremediation, pollutant degradation, and ecosystem restoration.},
}

*Metagenomics
India
*Bacteria/genetics/classification/isolation & purification/metabolism
Mining
*Soil Microbiology
Phylogeny
*Microbiota

@article {pmid40056517,
year = {2025},
author = {Choonut, A and Wongfaed, N and Wongthong, L and Poolpol, A and Chaikitkaew, S and Sittijunda, S and Reungsang, A},
title = {Microbial degradation of polypropylene microplastics and concomitant polyhydroxybutyrate production: An integrated bioremediation approach with metagenomic insights.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137806},
doi = {10.1016/j.jhazmat.2025.137806},
pmid = {40056517},
issn = {1873-3336},
mesh = {*Polypropylenes/metabolism ; Biodegradation, Environmental ; *Microplastics/metabolism ; *Hydroxybutyrates/metabolism ; Microbial Consortia ; Metagenomics ; Bacteria/metabolism/genetics ; *Polyesters/metabolism ; Polyhydroxybutyrates ; },
abstract = {The persistence of plastics, particularly polypropylene (PP), and their conversion into microplastics (MPs), specifically PP-MPs, have emerged as serious ecological threats to soil and aquatic environments. In the present study, we aimed to isolate a microbial consortium capable of degrading PP-MPs. The results revealed that three microbial consortia (CPP-KKU1, CPP-KKU2, and CPP-KKU3) exhibited the ability to degrade PP-MPs, achieving weight losses ranging from 11.6 ± 0.2 % to 17.8 ± 0.5 % after 30 days. Fourier transform infrared (FTIR) spectroscopy analysis confirmed the degradation through oxidation, as evidenced by the presence of new functional groups (-OH and -C=O). In particular, CPP-KKU3 showed the highest degradation efficiency, with scanning electron microscopy (SEM) analysis revealing surface cracking after treatment. Additionally, gas chromatography-mass spectrometry (GC-MS) analysis identified various intermediate compounds, including heterocyclic aromatic compounds, phenyl groups, methylthio derivatives, and ethoxycarbonyl derivatives, indicating complex biochemical processes that were likely mediated by microbial enzymes. Furthermore, polyhydroxybutyrate (PHB) production by these consortia was also investigated. The result showed that both CPP-KKU2 and CPP-KKU3 successfully produced PHB, with CPP-KKU3 demonstrating superior performance in terms of PP-MP degradation and PHB production. Metagenomic analysis of CPP-KKU3 revealed abundant carbohydrate-active enzymes (CAZymes), particularly glycosyl transferases and glycoside hydrolases, which are associated with MP digestion. This study presents a promising bioremediation approach that addresses plastic waste degradation and sustainable bioplastic production, offering a potential solution for environmental plastic pollution.},
}

*Polypropylenes/metabolism
Biodegradation, Environmental
*Microplastics/metabolism
*Hydroxybutyrates/metabolism
Microbial Consortia
Metagenomics
Bacteria/metabolism/genetics
*Polyesters/metabolism
Polyhydroxybutyrates

@article {pmid40043390,
year = {2025},
author = {Li, F and Zeng, Z and Wu, Y and Wang, Y and Shen, L and Huang, X and Wang, X and Sun, Y},
title = {Characteristics of microplastics in typical poultry farms and the association of environment microplastics colonized-microbiota, waterfowl gut microbiota, and antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137808},
doi = {10.1016/j.jhazmat.2025.137808},
pmid = {40043390},
issn = {1873-3336},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; *Microplastics/analysis/toxicity ; *Drug Resistance, Microbial/genetics ; Poultry ; Farms ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; },
abstract = {Microplastics (MPs) pollution is a growing global environmental concern. MPs serve as ecological niches for microbial communities, which may accelerate the spread of antibiotic resistance genes (ARGs), posing risks to the breeding industry. While studies on MPs in aquatic organisms are common, research on farmed poultry is limited. This study investigates MPs in poultry farm environments and waterfowl intestines for the first time. MPs were isolated via density separation and analyzed for characterization in soil, pond water, and waterfowl intestines. Metagenomics was used to investigate the association between environment MPs colonized-microbiota and waterfowl gut microbiota. Our findings reveal that MPs are abundant in soil (6.75 ± 2.78 items/g d.w.), pond water (0.94 ± 0.28 items/g w.w.), and poultry intestines (45.35 ± 19.52 items/g w.w.), primarily appearing as fragmented particles sized 20-50 μm. MPs abundance in intestines correlates with environmental levels. Colonized-microbiota on MPs are linked to poultry intestinal microbiota, with greater diversity and microbial functions. Network analysis reveals that Corynebacterium plays a key role in MPs and poultry intestinal. Polymyxin resistance exhibits high clustering. Procrustes analysis reveals correlations between MPs, bacteria, and ARGs in the farming environment. Overall, MPs in poultry farms may facilitate pathogen and ARGs transmission, posing risks to animal gut health.},
}

Animals
*Gastrointestinal Microbiome/drug effects/genetics
*Microplastics/analysis/toxicity
*Drug Resistance, Microbial/genetics
Poultry
Farms
*Water Pollutants, Chemical/analysis
Environmental Monitoring

@article {pmid40024121,
year = {2025},
author = {Woo, SY and Park, SB and Lee, SY and Sul, WJ and Chun, HS},
title = {Mycotoxin and microbiome profiling for aflatoxin control in the Korean traditional fermented soybean paste Doenjang.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137777},
doi = {10.1016/j.jhazmat.2025.137777},
pmid = {40024121},
issn = {1873-3336},
mesh = {*Aflatoxins/analysis ; *Microbiota ; Republic of Korea ; Aspergillus/genetics/isolation & purification ; *Glycine max/microbiology ; Penicillium/genetics ; *Food Contamination/prevention & control/analysis ; *Soy Foods/analysis/microbiology ; Fermentation ; *Fermented Foods/microbiology/analysis ; Food Microbiology ; },
abstract = {Mycotoxin contamination is an important concern in producing traditional fermented soybean paste, though no effective control strategy has been developed. This study investigated the mycotoxin profiles of the intermediate (fermented soybean brick, known as "Meju" in South Korea) and final soybean paste products ("Doenjang") to identify major contaminants and describe microbial diversity with the mycotoxins. Profiling of 323 Meju and Doenjang samples revealed severe aflatoxin (AF) contamination. Metagenomic analysis revealed that the species richness and phylogenetic diversity were significantly higher in AF-free than in AF-contaminated Meju and Doenjang. Certain Aspergillus and Penicillium species were more abundant in AF-free than in AF-contaminated Meju and Doenjang. To control AF levels, we developed a novel mycotoxin-reduction approach that preserves the indigenous microbiome by backslopping fermentation of Meju in both Aspergillus-dominant and Penicillium-dominant modes. Both treatments reduced AF levels by > 95 % at a backslopping rate of > 2.5 %. Our results suggested that backslopping fermentation can effectively reduce AF contamination in traditional soybean fermentation, maintaining food safety standards and artisanal practices.},
}

*Aflatoxins/analysis
*Microbiota
Republic of Korea
Aspergillus/genetics/isolation & purification
*Glycine max/microbiology
Penicillium/genetics
*Food Contamination/prevention & control/analysis
*Soy Foods/analysis/microbiology
Fermentation
*Fermented Foods/microbiology/analysis
Food Microbiology

@article {pmid40020294,
year = {2025},
author = {Zhao, Y and Li, L and Tan, J and Zhao, H and Wang, Y and Zhang, A and Jiang, L},
title = {Metagenomic insights into the inhibitory effect of phytochemical supplementation on antibiotic resistance genes and virulence factors in the rumen of transition dairy cows.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137717},
doi = {10.1016/j.jhazmat.2025.137717},
pmid = {40020294},
issn = {1873-3336},
mesh = {Animals ; Cattle ; *Rumen/microbiology ; Metagenomics ; *Virulence Factors/genetics ; *Phytochemicals/pharmacology ; *Dietary Supplements ; *Drug Resistance, Microbial/genetics/drug effects ; Female ; *Flavanones/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Microbiota/drug effects ; Gastrointestinal Microbiome/drug effects ; Bacteria/genetics/drug effects ; Animal Feed ; },
abstract = {Antimicrobial resistance (AMR) is a major global health concern, with the rumen microbiota of dairy cows serving as an important reservoir for antibiotic resistance genes (ARGs) and virulence factors (VFs). This study explores the impact of dietary phytochemical supplementation on the rumen resistome and virulome of transition dairy cows using metagenomic sequencing. Naringin supplementation reduced the abundance of ARGs by up to 9.0 % and VFs by up to 7.2 % during the transition period, as indicated by metagenomic analysis (P < 0.05). Clinically high-risk ARGs, including those conferring resistance to beta-lactams (mecA), tetracyclines (tetM, tetO), and aminoglycosides (rmtF), were notably downregulated (P < 0.05). Virulence factors associated with adherence, secretion systems, and toxins were also significantly decreased (P < 0.05). Naringin altered the microbial community structure, particularly reducing the abundance of Proteobacteria, a key phylum harboring ARGs and VFs. Despite inducing increased ARG-VF network complexity, naringin supplementation promoted a less pathogenic microbiome with reduced resistance potential. These findings demonstrate the potential of naringin as a natural dietary strategy to mitigate AMR by reducing the risk of ARG and VF dissemination into the environment, while supporting rumen microbiota stability in transition dairy cows.},
}

Animals
Cattle
*Rumen/microbiology
Metagenomics
*Virulence Factors/genetics
*Phytochemicals/pharmacology
*Dietary Supplements
*Drug Resistance, Microbial/genetics/drug effects
Female
*Flavanones/pharmacology
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Genes, Bacterial
Microbiota/drug effects
Gastrointestinal Microbiome/drug effects
Bacteria/genetics/drug effects
Animal Feed

@article {pmid39420836,
year = {2024},
author = {Qu, W and Xu, Y and Yang, J and Shi, H and Wang, J and Yu, X and Chen, J and Wang, B and Zhuoga, D and Luo, M and Liu, R},
title = {Berberine alters the gut microbiota metabolism and impairs spermatogenesis.},
journal = {Acta biochimica et biophysica Sinica},
volume = {57},
number = {4},
pages = {569-581},
doi = {10.3724/abbs.2024174},
pmid = {39420836},
issn = {1745-7270},
mesh = {Male ; *Gastrointestinal Microbiome/drug effects ; *Berberine/pharmacology ; Animals ; *Spermatogenesis/drug effects ; Mice ; Testosterone/blood ; Testis/drug effects/metabolism ; Fecal Microbiota Transplantation ; Mice, Inbred C57BL ; },
abstract = {Berberine (BBR) is used to treat diarrhea clinically. However, its reproductive toxicity is unclear. This study aims to investigate the impact of BBR on the male reproductive system. Intragastric BBR administration for 14 consecutive days results in a significant decrease in the serum testosterone concentration, epididymal sperm concentration, mating rate and fecundity of male mice. Testicular treatment with testosterone propionate (TP) partially reverses the damage caused by BBR to the male reproductive system. Mechanistically, the decrease in Muribaculaceae abundance in the gut microbiota of mice is the principal cause of the BBR-induced decrease in the sperm concentration. Both fecal microbiota transplantation (FMT) and polyethylene glycol (PEG) treatment demonstrate that Muribaculaceae is necessary for spermatogenesis. The intragastric administration of Muribaculaceae intestinale to BBR-treated mice restores the sperm concentration and testosterone levels. Metabolomic analysis reveals that BBR affects arginine and proline metabolism, of which ornithine level is downregulated. Combined analysis via 16S rRNA metagenomics sequencing and metabolomics shows that Muribaculaceae regulates ornithine level. The transcriptomic results of the testes indicate that the expressions of genes related to the low-density lipoprotein receptor (LDLR)-mediated testosterone synthesis pathway decrease after BBR administration. The transcriptional activity of the Ldlr gene in TM3 cells is increased with increased ornithine supplementation in the culture media, leading to increased testosterone synthesis. Overall, this study reveals an association between a BBR-induced decrease in Muribaculaceae abundance and defective spermatogenesis, providing a prospective therapeutic approach for addressing infertility-related decreases in serum testosterone triggered by changes in the gut microbiota composition.},
}

Male
*Gastrointestinal Microbiome/drug effects
*Berberine/pharmacology
Animals
*Spermatogenesis/drug effects
Mice
Testosterone/blood
Testis/drug effects/metabolism
Fecal Microbiota Transplantation
Mice, Inbred C57BL

@article {pmid40226542,
year = {2025},
author = {Cao, J and Wang, S and Ding, R and Liu, Y and Yuan, B},
title = {Comparative analyses of the gut microbiome of two sympatric rodent species, Myodes rufocanus and Apodemus peninsulae, in northeast China based on metagenome sequencing.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19260},
pmid = {40226542},
issn = {2167-8359},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; China ; *Arvicolinae/microbiology ; *Murinae/microbiology ; *Metagenome ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Proteobacteria/genetics/isolation & purification ; Firmicutes/genetics/isolation & purification ; Sympatry ; Bacteroidetes/genetics/isolation & purification ; },
abstract = {The gut microbiota is integral to an animal's physiology, influencing nutritional metabolism, immune function, and environmental adaptation. Despite the significance of gut microbiota in wild rodents, the Korean field mouse (Apodemus peninsulae) and the gray red-backed vole (Myodes rufocanus) remain understudied. To address this, a metagenomic sequencing analysis of the gut microbiome of these sympatric rodents in northeast China's temperate forests was conducted. Intestinal contents were collected from A. peninsulae and M. rufocanus within the Mudanfeng National Nature Reserve. High-throughput sequencing elucidated the gut microbiome's composition, diversity, and functional pathways. Firmicutes, Bacteroidetes, and Proteobacteria were identified as the dominant phyla, with M. rufocanus showing greater microbiome diversity. Key findings indicated distinct gut bacterial communities between the species, with M. rufocanus having a higher abundance of Proteobacteria. The gut microbiota of A. peninsulae and M. rufocanus differed marginally in functional profiles, specifically in the breakdown of complex carbohydrates, which might reflect their distinct food preferences albeit both being herbivores with a substantial dietary overlap. The investigation further elucidated gut microbiota's contributions to energy metabolism and environmental adaptation mechanisms. This study aligns with information on rodent gut microbiota in literature and highlights the two understudied rodent species, providing comparative data for future studies investigating the role of gut microbiota in wildlife health and ecosystem functioning.},
}

Animals
*Gastrointestinal Microbiome/genetics
China
*Arvicolinae/microbiology
*Murinae/microbiology
*Metagenome
Metagenomics
High-Throughput Nucleotide Sequencing
Proteobacteria/genetics/isolation & purification
Firmicutes/genetics/isolation & purification
Sympatry
Bacteroidetes/genetics/isolation & purification

@article {pmid40223273,
year = {2025},
author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW},
title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2412001},
doi = {10.4014/jmb.2412.12001},
pmid = {40223273},
issn = {1738-8872},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods/trends ; *Metabolomics/methods ; *Genomics/methods ; Proteomics/methods ; Precision Medicine ; Host Microbial Interactions ; Multiomics ; },
abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods/trends
*Metabolomics/methods
*Genomics/methods
Proteomics/methods
Precision Medicine
Host Microbial Interactions
Multiomics

@article {pmid40223231,
year = {2025},
author = {Lin, H and Chen, Y and Zhou, M and Wang, H and Chen, L and Zheng, L and Wang, Z and Zheng, X and Lu, S},
title = {Comprehensive analysis of faecal metagenomic and serum metabolism revealed the role of gut microbes and related metabolites in detecting colorectal lateral spreading tumours.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2489154},
doi = {10.1080/21505594.2025.2489154},
pmid = {40223231},
issn = {2150-5608},
mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology/pathology/metabolism/blood ; *Gastrointestinal Microbiome ; *Feces/microbiology/chemistry ; Male ; Female ; Middle Aged ; Metagenomics ; Aged ; Metabolomics ; Dysbiosis/microbiology ; Bacteria/classification/genetics/metabolism/isolation & purification ; Metabolic Networks and Pathways ; Case-Control Studies ; Adult ; },
abstract = {Colorectal lateral spreading tumours (LST), early-stage lesions of colorectal cancer (CRC), are associated with gut microbiota dysbiosis. However, the functional alterations in gut microbiota and their metabolic pathways remain inadequately understood. This study employed propensity score matching to compare 35 LST patients with 35 healthy controls. Metagenomic and metabolomic analyses revealed notable differences in gut microbiota composition and metabolic pathways. LST patients exhibited a marked reduction in short-chain fatty acid (SCFA)-producing probiotics, such as Roseburia, Clostridium, and Butyricicoccus sp-OF13-6, alongside anti-inflammatory metabolites. In contrast, potential intestinal pathogens linked to inflammatory bowel disease (IBD), including Escherichia and Citrobacter amalonaticus, were significantly enriched. Orthogonal partial least squares discriminant analysis (OPLS-DA) highlighted significant metabolic disparities between the groups, with enrichment in pathways associated with cholesterol metabolism, choline metabolism in cancer, and amino acid metabolism - all relevant to cancer progression. Key biomarkers identified for LST included fumarate, succinate, glutamic acid, glycine, and L-aspartic acid, which were closely linked to these pathways. Functional studies demonstrated that these metabolites promoted the proliferation and invasion of HCT-116 and SW480 human colorectal cancer cells in vitro. Metagenomic and metabolomic analysis revealed a strong positive correlation between Escherichia and Ruminococcus sp-AM41-2AC abundance and the enriched pathways, whereas reductions in Roseburia species, including Roseburia-OF03-24 and Roseburia intestinalis_CAG13-exhibited negative correlations. These results suggest that gut microbiota and metabolite alterations in LST contribute to intestinal inflammation and CRC development, underscoring their potential as biomarkers for early detection and therapeutic targets.},
}

Humans
*Colorectal Neoplasms/diagnosis/microbiology/pathology/metabolism/blood
*Gastrointestinal Microbiome
*Feces/microbiology/chemistry
Male
Female
Middle Aged
Metagenomics
Aged
Metabolomics
Dysbiosis/microbiology
Bacteria/classification/genetics/metabolism/isolation & purification
Metabolic Networks and Pathways
Case-Control Studies
Adult

@article {pmid40221653,
year = {2025},
author = {Babalola, OO and Adebayo, AA and Enagbonma, BJ},
title = {Shotgun metagenomics dataset of the core rhizo-microbiome of monoculture and soybean-precedent carrot.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {26},
pmid = {40221653},
issn = {2730-6844},
mesh = {*Daucus carota/microbiology ; *Metagenomics/methods ; *Rhizosphere ; *Glycine max/microbiology/growth & development ; *Microbiota ; Soil Microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {OBJECTIVES: Carrot is a significant vegetable crop contributing to agricultural diversity and food security, but less is known about the core microbiome associated with its rhizosphere. More so, the effect of preceding crop and cropping history on the composition and diversity of carrot rhizo-microbiome remains largely unknown. With shotgun metagenomics, the study unveils how cropping systems direct rhizo-microbiome structure and functions, previously limited by other methods.

DATA DESCRIPTION: Metagenomic-DNA molecule was extracted from four replicates each (12 samples) of a distant bulk soil and the rhizosphere soils from monoculture and soybean-precedent carrots, with the Power soil® DNA Isolation kit. The DNA samples were subjected to Next Generation Sequencing using the Illumina Novaseq X Plus (PE 150) platform. Raw sequencing reads were assembled and annotated with MEGAHIT and LCA algorithms in MEGAN software respectively, before a quality control check was done with FASTP. CD-Hit was used to de-replicate the sequences and the removal of host genomic-DNA and contaminant sequences was done with Bowtie2. The clean sequence data, in FastQ files, were analyzed for taxonomic classification and functional diversity of the rhizosphere microbiome using the Micro_NR and KEGG database respectively. The findings provide insights into microbiome dynamics, with potential implications for sustainable agricultural practices.},
}

*Daucus carota/microbiology
*Metagenomics/methods
*Rhizosphere
*Glycine max/microbiology/growth & development
*Microbiota
Soil Microbiology
High-Throughput Nucleotide Sequencing

@article {pmid40175313,
year = {2025},
author = {Fortin, SG and Uhlig, K and Hale, RC and Song, B},
title = {Microplastic biofilms as potential hotspots for plastic biodegradation and nitrogen cycling: a metagenomic perspective.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {5},
pages = {},
doi = {10.1093/femsec/fiaf035},
pmid = {40175313},
issn = {1574-6941},
support = {//Virginia Water Resources Research Center/ ; 1737258//National Science Foundation/ ; },
mesh = {*Biofilms/growth & development ; *Microplastics/metabolism ; Biodegradation, Environmental ; *Nitrogen Cycle ; *Bacteria/genetics/metabolism/classification ; Metagenomics ; *Plastics/metabolism ; Metagenome ; Nitrification ; Microbiota ; Water Pollutants, Chemical/metabolism ; Petroleum/metabolism ; Polyesters ; },
abstract = {Microplastics are an emerging contaminant worldwide, with the potential to impact organisms and facilitate the sorption and release of chemicals. Additionally, they create a novel habitat for microbial communities, forming biofilms known as the plastisphere. While the plastisphere has been studied in select aquatic environments, those in estuarine ecosystems merit additional attention due to their proximity to plastic debris sources. Additionally, the role plastisphere communities play in nutrient cycling has rarely been examined. This study used metagenomic analysis to investigate the taxonomic composition and functional genes of developing plastisphere communities living on petroleum-based (polyethylene and polyvinyl chloride) and biopolymer-based (polylactic acid) substrates. Isolated metagenome-assembled genomes (MAGs) showed plastisphere communities have the genes necessary to perform nitrification and denitrification and degrade petroleum and biopolymer-based plastics. The functions of these plastispheres have implications for estuarine nitrogen cycling and provide a possible explanation for the plastisphere microbes' competitiveness in biofilm environments. Overall, microplastics in the estuarine system provide a novel habitat for microbial communities and associated nitrogen cycling, facilitating the growth of microbes with plastic-degrading capabilities.},
}

*Biofilms/growth & development
*Microplastics/metabolism
Biodegradation, Environmental
*Nitrogen Cycle
*Bacteria/genetics/metabolism/classification
Metagenomics
*Plastics/metabolism
Metagenome
Nitrification
Microbiota
Water Pollutants, Chemical/metabolism
Petroleum/metabolism
Polyesters

@article {pmid40126388,
year = {2025},
author = {Zhang, Q and Su, T and Pan, Y and Wang, X and Zhang, C and Qin, H and Li, M and Li, Q and Li, X and Guo, J and Wu, L and Qin, L and Liu, T},
title = {Malus hupehensis leaves: a functional beverage for alleviating hepatic inflammation and modulating gut microbiota in diabetic mice.},
journal = {Food & function},
volume = {16},
number = {8},
pages = {2972-2990},
doi = {10.1039/d4fo05325g},
pmid = {40126388},
issn = {2042-650X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; Plant Leaves/chemistry ; *Plant Extracts/pharmacology/administration & dosage ; *Diabetes Mellitus, Type 2/drug therapy ; Male ; *Malus/chemistry ; Liver/drug effects/immunology/metabolism ; Mice, Inbred C57BL ; Beverages/analysis ; Functional Food ; Inflammation ; },
abstract = {Malus hupehensis leaves (MHL), consumed as a daily beverage in Chinese folk tradition and recently recognized as a new food material, are abundant in polyphenols and bioactive compounds that demonstrate hypoglycemic, lipid-lowering, and anti-inflammatory effects. However, the antidiabetic mechanisms have not been fully elucidated. This study aimed to investigate the protective mechanisms of Malus hupehensis leaves' extract (MHLE) against type 2 diabetes mellitus (T2DM). The results showed that MHLE effectively ameliorated glucose and lipid metabolic abnormalities in db/db mice, and attenuated hepatic macrophage activation. Transcriptomic analysis of the liver revealed that MHLE primarily affects genes involved in inflammatory responses and inhibited the TLR4/MAPK pathway to reduce hepatic inflammation. Metagenomic sequencing identified changes in gut microbiota composition and showed that MHLE restored the abundance of Lachnospiraceae bacterium, Oscillospiraceae bacterium, and Clostridia bacterium while reducing the abundance of Escherichia coli, thereby ameliorating gut dysbiosis. The integrated regulation of metabolism, immune response, and the microbial environment by MHLE significantly alleviated symptoms of T2DM. This study offers strong scientific evidence for the potential use of MHL as a functional food.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
Plant Leaves/chemistry
*Plant Extracts/pharmacology/administration & dosage
*Diabetes Mellitus, Type 2/drug therapy
Male
*Malus/chemistry
Liver/drug effects/immunology/metabolism
Mice, Inbred C57BL
Beverages/analysis
Functional Food
Inflammation

@article {pmid40221512,
year = {2025},
author = {Yong, Y and Zhou, L and Zhang, X and Ran, X and Guo, Y and Gai, W and Chen, Y},
title = {The clinical value of metagenomic next-generation sequencing in the diagnosis of pulmonary tuberculosis and the exploration of lung microbiota characteristics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12568},
pmid = {40221512},
issn = {2045-2322},
support = {82104236//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Male ; Female ; Middle Aged ; *Lung/microbiology ; *Microbiota/genetics ; Adult ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Metagenomics/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; },
abstract = {The lung microbiota plays a critical role in many important physiological processes and is linked with various pulmonary infectious diseases. The present study aimed to characterize the lung microbiota in patients with pulmonary tuberculosis (PTB), and to explore the association between the abundance of Mycobacterium tuberculosis complex (MTBC) and the lung microbiota. This retrospective study included 190 patients with MTBC infection. The enrolled patients were classified into three groups based on the abundance results of bronchoalveolar lavage fluid (BALF) mNGS: low [reads per ten million (RPTM) = 1 ~ 1000], medium (RPTM = 1001 ~ 10000) and high (RPTM > 10000). In the high-abundance group, there were more bilateral lobar involvement and symptoms of cavitation. In addition to mNGS, the highest positivity rates were T-spot (92.36%), GeneXpert (71.58%), culture (68.95%) and AFB smear (17.84%). The positive rates of culture, AFB smear and GeneXpert increased with the increase of MTBC abundance, and the positive rates were highest in the high-abundance MTBC group. Both the alpha and beta diversity showed significant difference between the three groups, with the high-abundance MTBC groups showed lowest alpha diversity. The increased abundance of MTBC positively associated with the longer time of hospital stay. To sum up, the lung microbiota of patients with PTB were significantly distinct between groups with different abundant levels of MTBC. Combined with imaging features, a high abundance of MTBC suggests the patient is more severely ill and has a poorer prognosis.},
}

Humans
*Tuberculosis, Pulmonary/diagnosis/microbiology
Male
Female
Middle Aged
*Lung/microbiology
*Microbiota/genetics
Adult
*Mycobacterium tuberculosis/genetics/isolation & purification
*High-Throughput Nucleotide Sequencing/methods
Retrospective Studies
*Metagenomics/methods
Bronchoalveolar Lavage Fluid/microbiology
Aged

@article {pmid40221450,
year = {2025},
author = {Kim, KS and Noh, J and Kim, BS and Koh, H and Lee, DW},
title = {Refining microbiome diversity analysis by concatenating and integrating dual 16S rRNA amplicon reads.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {57},
pmid = {40221450},
issn = {2055-5008},
support = {RS-2021-NR056579//National Research Foundation of Korea (NRF)/ ; RS-2023-KH141436//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; 200118770//Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; Colitis, Ulcerative/microbiology ; DNA, Bacterial/genetics ; Republic of Korea ; Phylogeny ; Feces/microbiology ; Biodiversity ; High-Throughput Nucleotide Sequencing ; },
abstract = {Understanding the role of human gut microbiota in health and disease requires insights into its taxonomic composition and functional capabilities. This study evaluates whether concatenating paired-end reads enhances data output for gut microbiome analysis compared to the merging approach across various regions of the 16S rRNA gene. We assessed this approach in both mock communities and Korean cohorts with or without ulcerative colitis. Our results indicate that using the direct joining method for the V1-V3 or V6-V8 regions improves taxonomic resolution compared to merging paired-end reads (ME) in post-sequencing data. While predicting microbial function based on 16S rRNA sequencing has inherent limitations, integrating sequencing reads from both the V1-V3 and V6-V8 regions enhanced functional predictions. This was confirmed by whole metagenome sequencing (WMS) of Korean cohorts, where our approach improved taxa detection that was lost using the ME method. Thus, we propose that the integrated dual 16S rRNA sequencing technique serves as a valuable tool for microbiome research by bridging the gap between amplicon sequencing and WMS.},
}

*RNA, Ribosomal, 16S/genetics
Humans
*Gastrointestinal Microbiome/genetics
*Bacteria/classification/genetics/isolation & purification
*Metagenomics/methods
Sequence Analysis, DNA/methods
Metagenome
Colitis, Ulcerative/microbiology
DNA, Bacterial/genetics
Republic of Korea
Phylogeny
Feces/microbiology
Biodiversity
High-Throughput Nucleotide Sequencing

@article {pmid40216789,
year = {2025},
author = {Shekarriz, S and Szamosi, JC and Whelan, FJ and Lau, JT and Libertucci, J and Rossi, L and Fontes, ME and Wolfe, M and Lee, CH and Moayyedi, P and Surette, MG},
title = {Detecting microbial engraftment after FMT using placebo sequencing and culture enriched metagenomics to sort signals from noise.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3469},
pmid = {40216789},
issn = {2041-1723},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Metagenomics/methods ; *Colitis, Ulcerative/therapy/microbiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; Placebos ; Adult ; Middle Aged ; },
abstract = {Fecal microbiota transplantation (FMT) has shown efficacy for the treatment of ulcerative colitis but with variable response between patients and trials. The mechanisms underlying FMT's therapeutic effects remains poorly understood but is generally assumed to involve engraftment of donor microbiota into the recipient's microbiome. Reports of microbial engraftment following FMT have been inconsistent between studies. Here, we investigate microbial engraftment in a previous randomized controlled trial (NCT01545908), in which FMT was sourced from a single donor, using amplicon-based profiling, shotgun metagenomics, and culture-enriched metagenomics. Placebo samples were included to estimate engraftment noise, and a significant level of false-positive engraftment was observed which confounds the prediction of true engraftment. We show that analyzing engraftment across multiple patients from a single donor enhances the accuracy of detection. We identified a unique set of genes engrafted in responders to FMT which supports strain displacement as the primary mechanism of engraftment in our cohort.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Metagenomics/methods
*Colitis, Ulcerative/therapy/microbiology
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Male
Female
Placebos
Adult
Middle Aged

@article {pmid40158829,
year = {2025},
author = {Liu, Y and Zhang, Q and Lu, L and Qian, Y and Wu, Y and Hu, D and Xu, Y and Xu, H and Ji, G},
title = {Huang-qin decoction alleviates deoxycholic acid-induced colorectal cancer in mice by regulating gut microbiota.},
journal = {Journal of ethnopharmacology},
volume = {346},
number = {},
pages = {119715},
doi = {10.1016/j.jep.2025.119715},
pmid = {40158829},
issn = {1872-7573},
mesh = {Animals ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/chemically induced/drug therapy/microbiology/pathology ; Mice ; Deoxycholic Acid/toxicity ; Male ; Mice, Inbred C57BL ; Protein Interaction Maps/drug effects ; Network Pharmacology ; Apoptosis/drug effects ; Astragalus propinquus ; },
abstract = {Huangqin Decoction (HQD), a traditional Chinese medicine (TCM) formula documented in Shang Han Lun, has demonstrated safety and efficacy in the treatment of ulcerative colitis (UC). Recent studies also suggest that HQD exerts therapeutic effects on colorectal cancer (CRC). However, the underlying mechanisms remain unclear.

AIMS OF THE STUDY: This study aimed to investigate the therapeutic effects of HQD on CRC and explore its potential mechanisms of action.

METHODS: The active ingredients and potential targets of HQD were identified through network pharmacology-based analyses. The CRC-related targets were compared with those of HQD. Shared targets were subjected to Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and a protein-protein interaction (PPI) network was constructed. Additionally, APC[min/+] mice were treated with 0.2 % deoxycholic acid (DCA) and gavaged with low or high doses of HQD. Tumor morphology was assessed using hematoxylin and eosin (HE) staining. Immunohistochemical staining was performed to evaluate the expression of Ki-67, Caspase-3, and MUC2 in the intestine. Periodic acid-Schiff (PAS) and PAS-alcian blue (PAS-AB) staining were utilized to detect mucin distribution and the number of goblet cells in the intestines of the mice. The mRNA expression levels of interleukin 6 (IL-6), mitogen-activated protein kinase 8 (MAPK8), vascular endothelial growth factor A (VEGFA), epidermal growth factor receptor (EGFR), albumin (ALB), and Caspase 3 (CASP3) were quantified using quantitative reverse-transcription PCR (qRT-PCR). Immunofluorescence was employed to assess the degree of apoptosis. Additionally, 16S ribosomal RNA gene sequencing, sequence curation and annotation, and metagenomic sequencing were performed to analyze changes in the composition of the mouse intestinal microbiota and related functions and signaling pathways.

RESULTS: The active ingredients of HQD were identified. GO and KEGG pathway enrichment analyses indicated that the shared targets were primarily involved in tumor suppression. HQD effectively treated DCA-induced CRC in mice. Furthermore, positive PAS and PAS-AB staining was significantly increased in the intestines of mice treated with HQD. HQD enhanced the abundance of Lachnospiraceae, Firmicutes, Fusobacteria, and Clostridium, while reducing the abundance of Eggerthellales. Additionally, HQD modulated secondary bile acid metabolism, carbohydrate synthesis, and other energy metabolism pathways, which may underlie its therapeutic effects.

CONCLUSION: HQD effectively treated CRC in mice, and its mechanisms of action may be related to the regulation of the gut microbiota.},
}

Animals
*Drugs, Chinese Herbal/pharmacology/therapeutic use
*Gastrointestinal Microbiome/drug effects
*Colorectal Neoplasms/chemically induced/drug therapy/microbiology/pathology
Mice
Deoxycholic Acid/toxicity
Male
Mice, Inbred C57BL
Protein Interaction Maps/drug effects
Network Pharmacology
Apoptosis/drug effects
Astragalus propinquus

@article {pmid39961991,
year = {2025},
author = {Booth, ME and Wood, HM and Travis, MA and , and Quirke, P and Grabsch, HI},
title = {The relationship between the gastric cancer microbiome and clinicopathological factors: a metagenomic investigation from the 100,000 genomes project and The Cancer Genome Atlas.},
journal = {Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association},
volume = {28},
number = {3},
pages = {358-371},
pmid = {39961991},
issn = {1436-3305},
mesh = {Humans ; *Stomach Neoplasms/microbiology/pathology/genetics ; Male ; Female ; Middle Aged ; Microsatellite Instability ; Metagenomics/methods ; Aged ; *Gastrointestinal Microbiome ; Adult ; },
abstract = {BACKGROUND: Findings from previous gastric cancer microbiome studies have been conflicting, potentially due to patient and/or tumor heterogeneity. The intratumoral gastric cancer microbiome and its relationship with clinicopathological variables have not yet been characterized in detail. We hypothesized that variation in gastric cancer microbial abundance, alpha diversity, and composition is related to clinicopathological characteristics.

METHODS: Metagenomic analysis of 529 GC samples was performed, including whole exome sequencing data from The Cancer Genome Atlas (TCGA) and whole genome sequencing data from the 100,000 Genomes Project. Microbial abundance, alpha diversity, and composition were compared across patient age, sex, tumor location, geographic origin, pathological depth of invasion, pathological lymph node status, histological phenotype, microsatellite instability status, and TCGA molecular subtype.

RESULTS: Gastric cancer microbiomes resembled previous results, with Prevotella, Selenomonas, Stomatobaculum, Streptococcus, Lactobacillus, and Lachnospiraceae commonly seen across both cohorts. Within the TCGA cohort, microbial abundance and alpha diversity were greater in gastric cancers with microsatellite instability, lower pathological depth of invasion, intestinal-type histology, and those originating from Asia. Microsatellite instability status was associated with microbiome composition in both cohorts. Sex and pathological depth of invasion were associated with microbiome composition in the TCGA cohort.

CONCLUSION: The intratumoral gastric cancer microbiome appears to differ according to clinicopathological factors. Certain clinicopathological factors associated with favourable outcomes in gastric cancer were observed to be associated with greater microbial abundance and diversity. This highlights the need for further work to understand the underlying biological mechanisms behind the observed microbiome differences and their potential clinical and therapeutic impact.},
}

Humans
*Stomach Neoplasms/microbiology/pathology/genetics
Male
Female
Middle Aged
Microsatellite Instability
Metagenomics/methods
Aged
*Gastrointestinal Microbiome
Adult

@article {pmid39536756,
year = {2025},
author = {Poulsen, CE and Vinding, R and Rasmussen, MA and Shah, S and Trivedi, U and Rodriguez, CL and Widdowson, ML and Jiang, J and Poulsen, CS and Eliasen, A and Chawes, B and Bønnelykke, K and Hansen, CHF and Sørensen, SJ and Thorsen, J and Stokholm, J},
title = {No association between the early-life gut microbiota and childhood body mass index and body composition.},
journal = {Med (New York, N.Y.)},
volume = {6},
number = {4},
pages = {100538},
doi = {10.1016/j.medj.2024.10.015},
pmid = {39536756},
issn = {2666-6340},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Body Mass Index ; Female ; *Body Composition ; Male ; Child, Preschool ; Infant ; Child ; *Pediatric Obesity/microbiology/epidemiology ; Prospective Studies ; Feces/microbiology ; Infant, Newborn ; Denmark/epidemiology ; RNA, Ribosomal, 16S ; Adiposity ; Overweight/epidemiology ; },
abstract = {BACKGROUND: The gut microbiota has been implicated in adult obesity, but the causality is still unclear. It has been hypothesized that an obesity-prone gut microbiota can be established in infancy, but only few studies have examined the early-life gut microbiota in relation to obesity in childhood, and no consistent associations have been reported. Here, we examine the association between the early-life gut microbiota and body mass index (BMI) development and body composition throughout childhood.

METHODS: Gut microbiota from stool were collected from 700 children in the Copenhagen Prospective Studies on Asthma in Childhood2010 (COPSAC2010) cohort at ages of 1 week, 1month, 1 year, 4 years, and 6 years and analyzed by 16S rRNA gene sequencing. Outcomes included BMI World Health Organization (WHO) Z scores (zBMI), overweight (zBMI > 1.04) and obesity (zBMI > 1.64) (0-10 years), and adiposity rebound and body composition from dual-energy X-ray absorptiometry at 6 years.

FINDINGS: The early-life gut microbiota diversity, overall composition, and individual taxon abundances in unsupervised and supervised models were not consistently associated with either current or later BMI Z scores, overweight, obesity, adiposity rebound, or body composition in childhood.

CONCLUSIONS: In a deeply characterized longitudinal birth cohort, we did not observe any consistent associations between the early-life gut microbiota and BMI or risk of obesity in later childhood. While this does not conclusively rule out a relationship, it suggests that if such associations exist, they may be more complex and potentially influenced by factors emerging later in life, including lifestyle changes.

FUNDING: COPSAC is funded by private and public research funds (all listed on www.copsac.com).},
}

Humans
*Gastrointestinal Microbiome
*Body Mass Index
Female
*Body Composition
Male
Child, Preschool
Infant
Child
*Pediatric Obesity/microbiology/epidemiology
Prospective Studies
Feces/microbiology
Infant, Newborn
Denmark/epidemiology
RNA, Ribosomal, 16S
Adiposity
Overweight/epidemiology

@article {pmid40216686,
year = {2025},
author = {Fan, Q and Zhang, Y and Lian, J and Liang, D and Yu, J and Liu, X and Zhang, N},
title = {Screening and community succession and functional prediction of high-efficiency degradation microbial communities for rice straw at low-temperature.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {2},
pages = {20},
pmid = {40216686},
issn = {1433-4909},
support = {2023YFD2100803//National Key R&D Programme Project of China/ ; },
mesh = {*Oryza/microbiology/metabolism ; *Microbiota ; *Cold Temperature ; Lignin/metabolism ; },
abstract = {Traditional straw return relies on microbial degradation, but cold winters delay it, risking crops. Therefore, a microbial community adapted to rice straw degradation in cold regions was constructed by restrictive consecutively sub-cultured under low-temperature limitations. The capabilities of the microbial community, such as adaptability, stability, and degradation power, were evaluated by analyzing straw degradation features, Characterization experiments and lignocellulose enzyme activities across multiple generations. 16S amplicon sequencing was used to monitor the changes in its structure over generations. Metagenomic sequencing uses CAZy and KEGG to classify gene functions. The results showed that the highest degradation efficiencies and enzyme activities were observed in the E and F generations, dominated by Proteobacteria, Bacteroidetes, and Fungi The stable microbial community was designated as LJ-7. Metagenomic analysis showed that functional genes of LJ-7 were mainly concentrated in glycoside hydrolase (GHs) and glycosyl transferase (GTs) related genes which contained many fiber and lignin-degrading enzyme genes. It is speculated that microbial enzymes degrade straw by breaking down its complex structure into monosaccharides or metabolizing quinone compounds for energy. This experiment successfully screened a microbial community capable of degrading rice straw at low temperatures, thus offering novel research insights and pathways for straw degradation in cold conditions.},
}

*Oryza/microbiology/metabolism
*Microbiota
*Cold Temperature
Lignin/metabolism

@article {pmid40212922,
year = {2025},
author = {Wang, C and Li, C and You, F and Zhou, Y and Tu, G and Liu, R and Yi, P and Wu, X and Nie, H},
title = {Multi-Omics Analysis of Gut Microbiome and Host Metabolism in Different Populations of Chinese Alligators (alligator sinensis) During Various Reintroduction Phases.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71221},
pmid = {40212922},
issn = {2045-7758},
abstract = {Reintroduction plays a significant role in the self-maintenance and reconstruction of wild animal populations, serving as a communication bridge between captive and wild animals. The Chinese alligator (Alligator sinensis) is a distinct and endangered reptile species found in China. The mechanisms by which artificially bred Chinese alligators adapt following their release into the wild remain poorly understood. This study aims to elucidate the alterations in gut microbiomes and metabolic phenotypes of Chinese alligators during their reintroduction. During the Chinese alligator's reintroduction, Fusobacterium and Cetobacterium became more abundant, while typical pathogens declined significantly. The gut type of the Chinese alligator changed from Acinetobacter to Cetobacterium. The construction of the gut microbial community was dominated by neutral (random) processes and shifted towards deterministic processes with the progression of reintroduction. In terms of species function, reintroduction significantly upregulated the expression of host immune-related genes and significantly decreased the expression of gut bacterial pathogenic genes and antibiotic resistance genes. Metagenomic and metabolomic KEGG enrichment analyses indicate that glucoside hydrolase families 13 and 23-alongside glycolysis and gluconeogenesis pathways-may play pivotal roles in energy metabolism, host-pathogen interactions, and homeostasis maintenance for Chinese alligators. Differential metabolite analysis identified significant upregulation of metabolites related to neuroendocrine immune modulation and significant down-regulation of anti-inflammatory metabolites during Chinese alligator reintroduction. Association analysis showed that there were significant co-metabolic effects between microorganisms and metabolites, which coordinated host adaptive interaction. This study provides insights into the synergistic mechanisms of host adaptation and wild environment adaptation for Chinese alligators.},
}

@article {pmid40211121,
year = {2025},
author = {Polizel, GHG and Diniz, WJS and Cesar, ASM and Ramírez-Zamudio, GD and Cánovas, A and Dias, EFF and Fernandes, AC and Prati, BCT and Furlan, É and Pombo, GDV and Santana, MHA},
title = {Impacts of prenatal nutrition on metabolic pathways in beef cattle: an integrative approach using metabolomics and metagenomics.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {359},
pmid = {40211121},
issn = {1471-2164},
support = {2021/03265-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/12105-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 307593/2021-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {Animals ; Cattle ; Female ; *Metabolomics/methods ; Pregnancy ; *Metabolic Networks and Pathways ; *Metagenomics/methods ; Male ; Metabolome ; Rumen/microbiology ; Microbiota ; *Prenatal Nutritional Physiological Phenomena ; *Animal Nutritional Physiological Phenomena ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: This study assessed the long-term metabolic effects of prenatal nutrition in Nelore bulls through an integrated analysis of metabolome and microbiome data to elucidate the interconnected host-microbe metabolic pathways. To this end, a total of 126 cows were assigned to three supplementation strategies during pregnancy: NP (control)- only mineral supplementation; PP- protein-energy supplementation during the last trimester; and FP- protein-energy supplementation throughout pregnancy. At the end of the finishing phase, blood, fecal, and ruminal fluid samples were collected from 63 male offspring. The plasma underwent targeted metabolomics analysis, and fecal and ruminal fluid samples were used to perform 16 S rRNA gene sequencing. Metabolite and ASV (amplicon sequence variant) co-abundance networks were constructed for each treatment using the weighted gene correlation network analysis (WGCNA) framework. Significant modules (p ≤ 0.1) were selected for over-representation analyses to assess the metabolic pathways underlying the metabolome (MetaboAnalyst 6.0) and the microbiome (MicrobiomeProfiler). To explore the metabolome-metagenome interplay, correlation analyses between host metabolome and microbiome were performed. Additionally, a holistic integration of metabolic pathways was performed (MicrobiomeAnalyst 2.0).

RESULTS: A total of one and two metabolite modules associated with the NP and FP were identified, respectively. Regarding fecal microbiome, three, one, and two modules for the NP, PP, and FP were identified, respectively. The rumen microbiome demonstrated two modules correlated with each of the groups under study. Metabolite and microbiome enrichment analyses revealed the main metabolic pathways associated with lipid and protein metabolism, and regulatory mechanisms. The correlation analyses performed between the host metabolome and fecal ASVs revealed 13 and 12 significant correlations for NP and FP, respectively. Regarding the rumen, 16 and 17 significant correlations were found for NP and FP, respectively. The NP holistic analysis was mainly associated with amino acid and methane metabolism. Glycerophospholipid and polyunsaturated fatty acid metabolism were over-represented in the FP group.

CONCLUSIONS: Prenatal nutrition significantly affected the plasma metabolome, fecal microbiome, and ruminal fluid microbiome of Nelore bulls, providing insights into key pathways in protein, lipid, and methane metabolism. These findings offer novel discoveries about the molecular mechanisms underlying the effects of prenatal nutrition.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Animals
Cattle
Female
*Metabolomics/methods
Pregnancy
*Metabolic Networks and Pathways
*Metagenomics/methods
Male
Metabolome
Rumen/microbiology
Microbiota
*Prenatal Nutritional Physiological Phenomena
*Animal Nutritional Physiological Phenomena
Gastrointestinal Microbiome

@article {pmid40210868,
year = {2025},
author = {Fu, Y and Guzior, DV and Okros, M and Bridges, C and Rosset, SL and González, CT and Martin, C and Karunarathne, H and Watson, VE and Quinn, RA},
title = {Balance between bile acid conjugation and hydrolysis activity can alter outcomes of gut inflammation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3434},
pmid = {40210868},
issn = {2041-1723},
support = {1R01DK140854//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; },
mesh = {Animals ; *Bile Acids and Salts/metabolism ; Humans ; Gastrointestinal Microbiome/genetics ; Mice, Knockout ; Mice ; Amidohydrolases/metabolism/genetics ; Hydrolysis ; Acyltransferases/genetics/metabolism ; Taurocholic Acid/pharmacology/metabolism ; Disease Models, Animal ; *Colitis/metabolism/pathology/microbiology ; Male ; Inflammatory Bowel Diseases/metabolism/microbiology ; Female ; Mice, Inbred C57BL ; Clostridiales/metabolism/genetics ; Crohn Disease/metabolism/microbiology/genetics ; },
abstract = {Conjugated bile acids (BAs) are multi-functional detergents in the gastrointestinal (GI) tract produced by the liver enzyme bile acid-CoA:amino acid N-acyltransferase (BAAT) and by the microbiome from the acyltransferase activity of bile salt hydrolase (BSH). Humans with inflammatory bowel disease (IBD) have an enrichment in both host and microbially conjugated BAs (MCBAs), but their impacts on GI inflammation are not well understood. We investigated the role of host-conjugated BAs in a mouse model of colitis using a BAAT knockout background. Baat[-/-] KO mice have severe phenotypes in the colitis model that were rescued by supplementation with taurocholate (TCA). Gene expression and histology showed that this rescue was due to an improved epithelial barrier integrity and goblet cell function. However, metabolomics also showed that TCA supplementation resulted in extensive metabolism to secondary BAs. We therefore investigated the BSH activity of diverse gut bacteria on a panel of conjugated BAs and found broad hydrolytic capacity depending on the bacterium and the amino acid conjugate. The complexity of this microbial BA hydrolysis led to the exploration of bsh genes in metagenomic data from human IBD patients. Certain bsh sequences were enriched in people with Crohn's disease particularly that from Ruminococcus gnavus. This study shows that both host and microbially conjugated BAs may provide benefits to those with IBD, but this is dictated by a delicate balance between BA conjugation/deconjugation based on the bsh genes present.},
}

Animals
*Bile Acids and Salts/metabolism
Humans
Gastrointestinal Microbiome/genetics
Mice, Knockout
Mice
Amidohydrolases/metabolism/genetics
Hydrolysis
Acyltransferases/genetics/metabolism
Taurocholic Acid/pharmacology/metabolism
Disease Models, Animal
*Colitis/metabolism/pathology/microbiology
Male
Inflammatory Bowel Diseases/metabolism/microbiology
Female
Mice, Inbred C57BL
Clostridiales/metabolism/genetics
Crohn Disease/metabolism/microbiology/genetics

@article {pmid40101486,
year = {2025},
author = {Sun, J and Geng, L and Zhou, D and Teng, X and Chen, M},
title = {Gut microbiota participates in polystyrene microplastics-induced defective implantation through impairing uterine receptivity.},
journal = {Journal of environmental management},
volume = {380},
number = {},
pages = {124997},
doi = {10.1016/j.jenvman.2025.124997},
pmid = {40101486},
issn = {1095-8630},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Mice ; Female ; *Microplastics/toxicity ; *Polystyrenes/toxicity ; Uterus/drug effects ; },
abstract = {Microplastics (MPs) are widespread in global ecosystems and could pose risks to human health. However, crucial information on the impact of MP exposure on female reproductive health remains insufficient. In this study, we constructed an MP-exposure mice model through oral administration of polystyrene microplastics (PS-MPs) and found that it resulted in impaired uterine receptivity and defective implantation. An accumulation of plastic particles was detected in MP mice intestines. Metagenomic sequencing of feces samples indicated a structural and functional alteration of gut microbiota. Alistipes played a prominent role in MP biodegradation, while among the biodegradable functional genes, ACSL made the greatest contribution. Both had a significant increase in MP group, suggesting a potential occurrence of ferroptosis. Ferroptosis, a form of programmed cell death, is closely associated with uterine receptivity impairment and defective implantation. We detected MDA contents and ferroptosis-related proteins, and the results indicated the activation of ferroptosis in the process. Our research is the first to elucidate that exposure to MPs impairs uterine receptivity and results in deficient implantation, while also providing initial evidence that gut microbiota plays a critical role in this process.},
}

*Gastrointestinal Microbiome/drug effects
Animals
Mice
Female
*Microplastics/toxicity
*Polystyrenes/toxicity
Uterus/drug effects

@article {pmid40048849,
year = {2025},
author = {Bargheet, A and Noordzij, HT and Ponsero, AJ and Jian, C and Korpela, K and Valles-Colomer, M and Debelius, J and Kurilshikov, A and Pettersen, VK},
title = {Dynamics of gut resistome and mobilome in early life: a meta-analysis.},
journal = {EBioMedicine},
volume = {114},
number = {},
pages = {105630},
pmid = {40048849},
issn = {2352-3964},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Metagenomics/methods ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Metagenome ; Female ; Interspersed Repetitive Sequences ; *Drug Resistance, Bacterial/genetics ; Computational Biology/methods ; },
abstract = {BACKGROUND: The gut microbiota of infants harbours a higher proportion of antibiotic resistance genes (ARGs) compared to adults, even in infants never exposed to antibiotics. Our study aims to elucidate this phenomenon by analysing how different perinatal factors influence the presence of ARGs, mobile genetic elements (MGEs), and their bacterial hosts in the infant gut.

METHODS: We searched MEDLINE and Embase up to April 3rd, 2023, for studies reporting infant cohorts with shotgun metagenomic sequencing of stool samples. The systematic search identified 14 longitudinal infant cohorts from 10 countries across three continents, featuring publicly available sequencing data with corresponding metadata. For subsequent integrative bioinformatic analyses, we used 3981 high-quality metagenomic samples from 1270 infants and 415 mothers.

FINDINGS: We identified distinct trajectories of the resistome and mobilome associated with birth mode, gestational age, antibiotic use, and geographical location. Geographical variation was exemplified by differences between cohorts from Europe, Southern Africa, and Northern America, which showed variation in both diversity and abundance of ARGs. On the other hand, we did not detect a significant impact of breastfeeding on the infants' gut resistome. More than half of detected ARGs co-localised with plasmids in key bacterial hosts, such as Escherichia coli and Enterococcus faecalis. These ARG-associated plasmids were gradually lost during infancy. We also demonstrate that E. coli role as a primary modulator of the infant gut resistome and mobilome is facilitated by its increased abundance and strain diversity compared to adults.

INTERPRETATION: Birth mode, gestational age, antibiotic exposure, and geographical location significantly influence the development of the infant gut resistome and mobilome. A reduction in E. coli relative abundance over time appears as a key factor driving the decrease in both resistome and plasmid relative abundance as infants grow.

FUNDING: Centre for Advanced Study in Oslo, Norway. Centre for New Antibacterial Strategies through the Tromsø Research Foundation, Norway.},
}

Humans
*Gastrointestinal Microbiome/genetics
Infant
Metagenomics/methods
Infant, Newborn
Anti-Bacterial Agents/pharmacology/therapeutic use
Metagenome
Female
Interspersed Repetitive Sequences
*Drug Resistance, Bacterial/genetics
Computational Biology/methods

@article {pmid39168909,
year = {2025},
author = {Wang, X and Li, Y and Kang, L and Zhang, Z and Zhang, D and Li, P and Zhang, Q and Ma, X and Wang, J and Hou, Y and Li, Q and Fu, J and Hong, M},
title = {Diversity, functions, and antibiotic resistance genes of bacteria and fungi are examined in the bamboo plant phyllosphere that serve as food for the giant pandas.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {28},
number = {4},
pages = {751-763},
pmid = {39168909},
issn = {1618-1905},
support = {2019QZKK05010502//by the Second Qinghai-Tibet Plateau Comprehensive Scientific Survey/ ; KCXTD2022-7//the Innovation Team Funds of China West Normal University/ ; },
mesh = {*Ursidae/microbiology ; *Fungi/genetics/drug effects/classification/isolation & purification ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Animals ; RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Poaceae/microbiology ; Biodiversity ; Gastrointestinal Microbiome ; },
abstract = {The phyllosphere of bamboo is rich in microorganisms that can disrupt the intestinal microbiota of the giant pandas that consume them, potentially leading to their death. In the present study, the abundance, diversity, biological functions (e.g., KEGG and CAZyme), and antibiotic resistance genes (ARGs) of bacteria and fungi in two bamboo species phyllosphere (Chimonobambusa szechuanensis, CS; Bashania fangiana, BF) in Daxiangling Nature Reserve (an important part of the Giant Panda National Park) were investigated respectively by amplicon sequencing of the whole 16S rRNA and ITS1-ITS2 genes on PacBio Sequel and whole-metagenome shotgun sequencing on Illumina NovaSeq 6000 platform. The results suggested that there were respectively 18 bacterial and 34 fungi biomarkers between the phyllosphere of the two species of bamboo. Beta diversity of bacteria and fungi communities exited between the two bamboos according to the (un)weighted UniFrac distance matrix. Moreover, the functional analysis showed that the largest relative abundance was found in the genes related to metabolism and global and overview maps. Glycoside hydrolases (GHs) and glycosyl transferases (GTs) have a higher abundance in two bamboo phyllospheres. Co-occurrence network modeling suggested that bacteria and fungi communities in CS phyllosphere employed a much more complex metabolic network than that in BF, and the abundance of multidrug, tetracycline, and glycopeptide resistance genes was higher and closely correlated with other ARGs. This study references the basis for protecting bamboo resources foraged by wild giant pandas and predicts the risk of antibiotic resistance in bamboo phyllosphere bacterial and fungal microbiota in the Giant Panda National Park, China.},
}

*Ursidae/microbiology
*Fungi/genetics/drug effects/classification/isolation & purification
*Bacteria/genetics/drug effects/classification/isolation & purification
Animals
RNA, Ribosomal, 16S/genetics
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics
*Poaceae/microbiology
Biodiversity
Gastrointestinal Microbiome

@article {pmid40210629,
year = {2025},
author = {Park, JW and Yun, YE and Cho, JA and Yoon, SI and In, SA and Park, EJ and Kim, MS},
title = {Characterization of the phyllosphere virome of fresh vegetables and potential transfer to the human gut.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3427},
pmid = {40210629},
issn = {2041-1723},
support = {2020R1A5A8017671//National Research Foundation of Korea (NRF)/ ; 2019R1C1C1009664//National Research Foundation of Korea (NRF)/ ; 2018R1D1A3B07050366//National Research Foundation of Korea (NRF)/ ; 2021R1F1A1064222//National Research Foundation of Korea (NRF)/ ; },
mesh = {Humans ; *Virome/genetics ; *Vegetables/virology ; *Gastrointestinal Microbiome/genetics ; Feces/virology ; *Plant Leaves/virology ; Metagenome ; Bacteriophages/genetics/classification/isolation & purification ; Phylogeny ; Metagenomics ; },
abstract = {Fresh vegetables harbor diverse microorganisms on leaf surfaces, yet their viral communities remain unexplored. We investigate the diversity and ecology of phyllosphere viromes of six leafy green vegetables using virus-like particle (VLP) enrichment and shotgun metagenome sequencing. On average, 9.2 × 10[7] viruses are present per gram of leaf tissue. The majority (93.1 ± 6.2%) of these viruses are taxonomically unclassified. Virome compositions are distinct among vegetable types and exhibit temporal variations. Virulent phages with replication-enhancing auxiliary metabolic genes (AMGs) are more dominant than temperate phages with host fitness-benefiting AMGs. Analysis of 1498 human fecal VLP metagenomes reveals that approximately 10% of vegetable viruses are present in the human gut virome, including viruses commonly observed in multiple studies. These gut-associated vegetable viruses are enriched with short-term vegetable intake, and depleted in individuals with metabolic and immunologic disorders. Overall, this study elucidates the ecological contribution of the fresh vegetable virome to human gut virome diversity.},
}

Humans
*Virome/genetics
*Vegetables/virology
*Gastrointestinal Microbiome/genetics
Feces/virology
*Plant Leaves/virology
Metagenome
Bacteriophages/genetics/classification/isolation & purification
Phylogeny
Metagenomics

@article {pmid40210403,
year = {2025},
author = {Africa, AJ and Setati, ME and Hitzeroth, AC and Blancquaert, EH},
title = {Exploring the evolution of microbial communities from the phyllosphere and carposphere to the grape must of Vitis vinifera L. cv's Chardonnay and Pinot noir.},
journal = {Food microbiology},
volume = {130},
number = {},
pages = {104780},
doi = {10.1016/j.fm.2025.104780},
pmid = {40210403},
issn = {1095-9998},
mesh = {*Vitis/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Fungi/classification/genetics/isolation & purification ; *Plant Leaves/microbiology ; *Fruit/microbiology ; Wine/microbiology/analysis ; South Africa ; },
abstract = {Microbial communities associated with the grapevine phyllosphere and carposhere are a fundamental determinant of grape and wine quality. High throughput amplicon sequencing was used to profile the fungal and bacterial communities on the associated phylloplane and carposphere of Vitis vinifera L. cv's Chardonnay and Pinot noir in the Elgin and Hemel-en-Aarde wine districts of South Africa in the 2021-2022 growing season. The subsequent grape must was analysed to determine the prevalent microbiome. The most abundant bacterial and fungal genera found in both the phylloplane and carposphere of Chardonnay and Pinot noir were Pseudomonas and Filobasidium. The LEfSe (Linear discriminant analysis Effect Size) revealed significant differences in fungal and bacterial biomarkers from leaf, berry and grape must samples; however, no biomarkers were identified for cultivar nor location. Fungal β-diversity was significantly similar at different phenological stages, whereas bacterial β-diversity was significantly similar regardless of the site of colonisation. However, skin integrity of the grapes was may have influenced the microbial diversity.},
}

*Vitis/microbiology
*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Fungi/classification/genetics/isolation & purification
*Plant Leaves/microbiology
*Fruit/microbiology
Wine/microbiology/analysis
South Africa

@article {pmid40209677,
year = {2025},
author = {Lin, Y and Lau, HC and Liu, C and Ding, X and Sun, Y and Rong, J and Zhang, X and Wang, L and Yuan, K and Miao, Y and Wu, WK and Wong, SH and Sung, JJ and Yu, J},
title = {Multi-cohort analysis reveals colorectal cancer tumor location-associated fecal microbiota and their clinical impact.},
journal = {Cell host & microbe},
volume = {33},
number = {4},
pages = {589-601.e3},
doi = {10.1016/j.chom.2025.03.012},
pmid = {40209677},
issn = {1934-6069},
mesh = {Humans ; *Feces/microbiology ; *Colorectal Neoplasms/microbiology/pathology/diagnosis ; *Gastrointestinal Microbiome ; Cohort Studies ; Metagenome ; Male ; Female ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Aged ; Fusobacterium nucleatum/isolation & purification ; Biomarkers, Tumor ; ROC Curve ; },
abstract = {Microbial alterations in different tumor locations of colorectal cancer (CRC) remain unclear. Here, 1,375 fecal metagenomes from six in-house and published datasets were analyzed, including 128 right-sided CRC (rCRC), 168 left-sided CRC (lCRC), 250 rectal cancer (RC), and 829 controls. Firmicutes progressively increase from rCRC, lCRC, to RC, in contrast to the gradual decrease of Bacteroidetes. Tumor location-associated fecal microbes are identified, including Veillonella parvula for rCRC, Streptococcus angionosus for lCRC, and Peptostreptococcus anaerobius for RC, while Fusobacterium nucleatum is enriched in all tumor locations. Tumor location-associated bacteria correlate with patient survival. Clinically, we establish a microbial biomarker panel for each tumor location that accurately diagnoses rCRC (area under the receiver operating characteristic curve [AUC] = 91.59%), lCRC (AUC = 91.69%), or RC (AUC = 90.53%) from controls. Tumor location-specific biomarkers also have higher diagnostic accuracy (AUC = 91.38%) than location-non-specific biomarkers (AUC = 82.92%). Overall, we characterize fecal microbes associated with different CRC tumor locations, highlighting that tumor location should be considered in non-invasive diagnosis.},
}

Humans
*Feces/microbiology
*Colorectal Neoplasms/microbiology/pathology/diagnosis
*Gastrointestinal Microbiome
Cohort Studies
Metagenome
Male
Female
*Bacteria/classification/genetics/isolation & purification
Middle Aged
Aged
Fusobacterium nucleatum/isolation & purification
Biomarkers, Tumor
ROC Curve

@article {pmid40207877,
year = {2025},
author = {Huang, L and Chen, C and Meng, J and Yan, Q and Luo, G and Sha, S and Xing, Y and Liu, C and Xu, M and Zhao, L and Guo, S and Wu, X and Chen, H and Ma, J and You, W and Zhang, Y and Guo, R and Li, S and Yao, X and Ma, W and Kong, X and Zhou, P and Sun, W},
title = {Metagenome-Based Characterization of the Gut Virome Signatures in Patients With Gout.},
journal = {Journal of medical virology},
volume = {97},
number = {4},
pages = {e70336},
doi = {10.1002/jmv.70336},
pmid = {40207877},
issn = {1096-9071},
support = {//This study was supported by 2024 High-quality Development Project of Shenzhen Bao'an Public Hospital (BAGZL2024138 and BAGZL2024130), National Natural Science Foundation of China (82370563), Dalian Medical University Interdisciplinary Research Cooperation Project Team Funding (JCH22023017), the Key Laboratory of Guizhou Provincial Education Department (Guizhou Education Technology [2023] No. 017), National and Provincial Science and Technology Innovation Talent Team Cultivation Program of Guizhou University of Traditional Chinese Medicine (GZUTCM-TD[2022]004)./ ; },
mesh = {Humans ; *Virome ; *Gastrointestinal Microbiome ; *Gout/virology ; Male ; Middle Aged ; Feces/virology ; Female ; *Metagenome ; Metagenomics ; *Viruses/classification/genetics/isolation & purification ; Adult ; Aged ; Longitudinal Studies ; },
abstract = {The gut microbiome has been implicated in the development of autoimmune diseases, including gout. However, the role of the gut virome in gout pathogenesis remains underexplored. We employed a reference-dependent virome approach to analyze fecal metagenomic data from 102 gout patients (77 in the discovery cohort and 25 in the validation cohort) and 86 healthy controls (HCs) (63 and 23 in each cohort). A subset of gout patients in the discovery cohort provided longitudinal samples at Weeks 2, 4, and 24. Our analysis revealed significant alterations in the gut virome of gout patients, including reduced viral richness and shifts in viral family composition. Notably, Siphoviridae, Myoviridae, and Podoviridae were depleted, while Quimbyviridae, Retroviridae, and Schitoviridae were enriched in gout patients. We identified 359 viral operational taxonomic units (vOTUs) associated with gout. Enriched vOTUs in gout patients predominantly consisted of Fusobacteriaceae, Bacteroidaceae, and Selenomonadaceae phages, while control-enriched vOTUs included Ruminococcaceae, Oscillospiraceae, and Enterobacteriaceae phages. Longitudinal analysis revealed that a substantial proportion of these virome signatures remained stable over 6 months. Functional profiling highlighted the enrichment of viral auxiliary metabolic genes, suggesting potential metabolic interactions between viruses and host bacteria. Notably, gut virome signatures effectively discriminated gout patients from HCs, with high classification performance in the validation cohort. This study provides the first comprehensive characterization of the gut virome in gout, revealing its potential role in disease pathogenesis and highlighting virome-based signatures as promising biomarkers for gout diagnosis and future therapeutic strategies.},
}

Humans
*Virome
*Gastrointestinal Microbiome
*Gout/virology
Male
Middle Aged
Feces/virology
Female
*Metagenome
Metagenomics
*Viruses/classification/genetics/isolation & purification
Adult
Aged
Longitudinal Studies

@article {pmid40207161,
year = {2025},
author = {Helmi, NR},
title = {Exploring the diversity and antimicrobial potential of actinomycetes isolated from different environments in Saudi Arabia: a systematic review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1568899},
pmid = {40207161},
issn = {1664-302X},
abstract = {The increasing prevalence of antimicrobial resistance (AMR) presents a significant global health challenge, underscoring the urgent need for novel antimicrobial agents. Actinomycetes, particularly Streptomyces species, are well known for synthesizing bioactive compounds with antibacterial, antifungal, and antiviral properties. This review explores the diversity and antimicrobial potential of actinomycetes from Saudi Arabia's unique ecosystems, including terrestrial (soil, rhizosphere), aquatic (marine, freshwater), extreme (deserts, caves, hot springs, mountains, and mangroves), and other unique environments. The adaptation of these microorganisms to harsh environmental conditions has driven the evolution of unique strains with enhanced biosynthetic capacities. Several studies have demonstrated their antimicrobial efficacy against multidrug-resistant pathogens, including methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, Pseudomonas aeruginosa, and Candida albicans. However, challenges in actinomycete research persist, including difficulties in culturing rare strains, limited genomic characterization, and high production costs. Recent advancements, such as genome mining, metagenomics, AI-driven bioinformatics, and CRISPR-based gene activation, offer promising avenues for unlocking novel antimicrobial compounds. Additionally, synthetic biology, advanced fermentation technologies, and nanotechnology-based drug delivery systems are enhancing the industrial scalability of actinomycete-derived antibiotics. Beyond antimicrobials, actinomycete-derived compounds show potential applications in oncology, immunotherapy, and agriculture. Alternative therapeutic strategies, including quorum sensing inhibitors, phage therapy, and combination therapies, are being explored to combat AMR. Cutting-edge analytical techniques, such as mass spectrometry, liquid chromatography, and nuclear magnetic resonance spectroscopy (NMR), are essential for structural elucidation and mechanism characterization of new bioactive compounds. To harness Saudi Arabia's microbial biodiversity effectively, interdisciplinary collaborations between microbiologists, biotechnologists, and pharmaceutical industries are crucial. Sustainable bioprospecting and advanced bioprocessing strategies will facilitate the translation of actinomycete-derived bioactive compounds into clinically viable therapeutics. Expanding research efforts into underexplored Saudi ecosystems can lead to groundbreaking discoveries in antibiotic development and beyond.},
}

@article {pmid40205678,
year = {2025},
author = {He, Y and Zhao, G and Ouyang, X and Wang, S and Chen, Y and Li, C and He, Y and Gao, J and Han, S and Zhao, J and Wang, J and Wang, C},
title = {Creatine-mediated ferroptosis inhibition is involved in the intestinal radioprotection of daytime-restricted feeding.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2489072},
doi = {10.1080/19490976.2025.2489072},
pmid = {40205678},
issn = {1949-0984},
mesh = {Animals ; Mice ; Gastrointestinal Microbiome/drug effects/radiation effects ; *Creatine/metabolism/pharmacology/administration & dosage ; *Ferroptosis/drug effects/radiation effects ; Mice, Inbred C57BL ; Male ; *Intestines/radiation effects/microbiology ; *Radiation-Protective Agents/metabolism/administration & dosage ; Radiation, Ionizing ; Feces/microbiology ; Enterocytes/radiation effects/metabolism ; },
abstract = {Ionizing radiation-induced intestinal injury (IRIII) is a catastrophic disease lack of sufficient medical countermeasures currently. Regulation of the gut microbiota through dietary adjustments is a potential strategy to mitigate IRIII. Time-restricted feeding (TRF) is an emerging behavioral nutrition intervention with pleiotropic health benefits. Whether this dietary pattern influences the pathogenesis of IRIII remains vague. We evaluated the impact of TRF on intestinal radiosensitivity in this study and discovered that only daytime TRF (DTRF), not nighttime TRF, could ameliorate intestinal damage in mice that received a high dose of IR. Faecal metagenomic and metabolomic studies revealed that the intestinal creatine level was increased by approximate 9 times by DTRF, to which the Bifidobacterium pseudolongum enrichment contribute. Further investigations showed that creatine could activate the energy sensor AMP-activated protein kinase in irradiated enterocytes and induce phosphorylation of acetyl-CoA carboxylase, resulting in reduced production of polyunsaturated fatty acids and reduced ferroptosis after IR. The administration of creatine mitigated IRIII and reduced bacteremia and proinflammatory responses. Blockade of creatine import compromised the ferroptosis inhibition and mitigation of DTRF on IRIII. Our study demonstrates a radioprotective dietary mode that can reshape the gut microbiota and increase intestinal creatine, which can suppress IR-induced ferroptosis, thereby providing effective countermeasures for IRIII prevention.},
}

Animals
Mice
Gastrointestinal Microbiome/drug effects/radiation effects
*Creatine/metabolism/pharmacology/administration & dosage
*Ferroptosis/drug effects/radiation effects
Mice, Inbred C57BL
Male
*Intestines/radiation effects/microbiology
*Radiation-Protective Agents/metabolism/administration & dosage
Radiation, Ionizing
Feces/microbiology
Enterocytes/radiation effects/metabolism

@article {pmid40205473,
year = {2025},
author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Eguiarte, LE and Souza, V},
title = {Running against the clock: Exploring microbial diversity in an extremely endangered microbial oasis in the Chihuahuan Desert.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf033},
pmid = {40205473},
issn = {1574-6941},
abstract = {The Cuatro Ciénegas Basin is a biodiversity hotspot known for its unique biodiversity. However, this ecosystem is facing severe anthropogenic threats that are drying its aquatic systems. We investigated microbial communities at three sites with different physicochemical and environmental characteristics (Pozas Rojas, Archean Domes, and the Churince system) within the basin to explore potential connections to deep aquifers and determine if the sites shared microorganisms. Utilizing 16S rRNA gene data, we identified a core microbiota between Pozas Rojas and Archean Domes. Sulfur reduction appears to shape the microbial connectivity among sites, since sulfur-reducing bacteria has the highest prevalence between samples from Pozas Rojas and Archean Domes: Halanaerobium sp. (88.46%) and Desulfovermiculus halophilus (65%); and between the Churince system and Archean Domes: Halanaerobium sp. (63%) and Desulfovermiculus halophilus (60%). Furthermore, metagenome assembled genomes from Ectothiorhodospira genus were found in both Archean Domes and Churince, suggesting microbial dispersal. An important finding is that microbial diversity in the Archean Domes system declined, from 2016 to 2023 the ecosystem lost 29 microbial phyla. If this trend continues, the basin will lose most of its water, resulting in the loss of various prokaryotic lineages and potential biotechnological solutions, such as enzymes or novel antibiotics. Our findings highlighting the need for water extraction regulations to preserve the basin's biodiversity.},
}

@article {pmid40057258,
year = {2025},
author = {Ragone, P and Parodi, C and Tomasini, N and Ramos, F and Uncos, A and Brandán, CP},
title = {The interplay between Trypanosoma cruzi and the microbiome of Triatoma infestans: Implications for the host's immune response.},
journal = {Acta tropica},
volume = {264},
number = {},
pages = {107577},
doi = {10.1016/j.actatropica.2025.107577},
pmid = {40057258},
issn = {1873-6254},
mesh = {Animals ; *Triatoma/microbiology/parasitology/immunology ; *Trypanosoma cruzi/immunology ; Feces/microbiology/parasitology ; Mice, Inbred C57BL ; Mice ; *Chagas Disease/immunology/parasitology ; RNA, Ribosomal, 16S/genetics ; Cytokines ; Female ; Disease Models, Animal ; *Microbiota ; Parasite Load ; Metagenomics ; Immunoglobulin G/blood ; },
abstract = {The infection dynamics of Trypanosoma cruzi is shaped by the parasite's genetics and interactions with host and vector factors. While most studies in the area use axenic parasite cultures devoid of insect fecal components, this study is focused on the immune response and the parasite loads generated after the interaction of T. cruzi with feces from Triatoma infestans in a murine model. First, using metagenomics, we analyzed the microbiota of infected and uninfected feces. Illumina sequencing of the 16S rRNA gene (V3-V4 region) revealed a predominance of the genus Arsenophonus in infected feces and of Enterococcus in uninfected ones. C57BL/6J mice inoculated with T. cruzi infected feces, displayed distinct immune responses compared to those inoculated with culture-derived metacyclic trypomastigotes alone, with lower levels of pro-inflammatory cytokines (IFN-ɣ, TNF-α) and higher amounts of IL-10, suggesting a regulatory response. Besides, total anti-T. cruzi IgG levels remained similar among groups, but IgG1 and IgG2c were reduced in the T. cruzi infected feces group, indicating a balanced Th1/Th2 response. Notably, mice inoculated with T. cruzi infected feces demonstrated significantly reduced blood and muscle parasite loads, potentially limiting inflammation and parasite dissemination. These findings highlight the possible role of vector fecal microbiota in shaping immune responses and influencing disease outcomes during natural T. cruzi infections.},
}

Animals
*Triatoma/microbiology/parasitology/immunology
*Trypanosoma cruzi/immunology
Feces/microbiology/parasitology
Mice, Inbred C57BL
Mice
*Chagas Disease/immunology/parasitology
RNA, Ribosomal, 16S/genetics
Cytokines
Female
Disease Models, Animal
*Microbiota
Parasite Load
Metagenomics
Immunoglobulin G/blood

@article {pmid40056781,
year = {2025},
author = {Chen, H and Li, J and Wu, Y and Li, Y and Zheng, S and Wu, Y and Xuan, R and Wu, L and Miao, J and Wang, Y and Tan, H and Zhou, J and Huang, J and Yan, X},
title = {Structural characteristics of intestinal microbiota of domestic ducks with different body sizes.},
journal = {Poultry science},
volume = {104},
number = {4},
pages = {104930},
pmid = {40056781},
issn = {1525-3171},
mesh = {Animals ; *Ducks/microbiology/anatomy & histology/physiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/analysis ; *Body Size ; *Bacteria/classification/isolation & purification/genetics ; Feces/microbiology ; Male ; },
abstract = {Domestic ducks are economically important agricultural animals, and their body size is a crucial economic trait. The intestinal flora plays a pivotal role in influencing body metabolism, growth, and development. Currently, no literature is available on the potential effect of the intestinal flora of domestic ducks on body size. This study used 16S rRNA sequencing technology to investigate the fecal microbiota of 229 individuals reared under identical feeding conditions. The findings revealed that partridge ducks with large body sizes (LBS) exhibited a higher level of intestinal microbial diversity than ducks with small body sizes (SBS). Notably, the gut microbiota composition of SBS displayed significantly elevated proportions of Streptococcus, Rothia, and Psychrobacter compared to their counterparts with LBS. Conversely, Lactobacillus was significantly more abundant in LBS. Jeotgalibaca and Psychrobacter were identified as key biomarkers of SBS, whereas Lactobacillus and Bacteroides were predominant biomarkers of LBS. Functional predictions based on intestinal microbiota indicated discernible differences among different body types, particularly evident in non- partridge ducks. The present study investigated the correlation between the intestinal microbiota and body size of domestic ducks, aiming to provide practical insights for the production management of domestic duck farming.},
}

Animals
*Ducks/microbiology/anatomy & histology/physiology
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/analysis
*Body Size
*Bacteria/classification/isolation & purification/genetics
Feces/microbiology
Male

@article {pmid40032028,
year = {2025},
author = {Ismaiah, MJ and Lo, EKK and Chen, C and Tsui, JS and Johnson-Hill, WA and Felicianna, and Zhang, F and Leung, HKM and Oger, C and Durand, T and Lee, JC and El-Nezami, H},
title = {Alpha-aminobutyric acid administration suppressed visceral obesity and modulated hepatic oxidized PUFA metabolism via gut microbiota modulation.},
journal = {Free radical biology & medicine},
volume = {232},
number = {},
pages = {86-96},
doi = {10.1016/j.freeradbiomed.2025.02.029},
pmid = {40032028},
issn = {1873-4596},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Fatty Acids, Unsaturated/metabolism ; Diet, High-Fat/adverse effects ; *Liver/metabolism/drug effects/pathology ; Male ; *Obesity, Abdominal/drug therapy/metabolism/microbiology/pathology ; Lipid Metabolism/drug effects ; Mice ; Oxidation-Reduction ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: High-fat diet (HFD) is associated with visceral obesity due to disruption in the lipid metabolism and gut dysbiosis. These symptoms may contribute to hepatic steatosis and the formation of oxidized polyunsaturated fatty acids (PUFAs). Alpha-aminobutyric acid (ABA) is an amino-acid derived metabolite, and its concentration has been correlated with several metabolic conditions and gut microbiome diversity while its direct effects on visceral obesity, lipid metabolism and the gut microbiota are not well understood. This study was designed to investigate the effect of physiological dose of ABA on diet-induced visceral obesity and lipid metabolism dysregulation by examining the fatty acids and oxidized PUFAs profile in the liver as well as the gut microbiota.

RESULTS: ABA administration reduced visceral obesity by 28 % and lessened adipocyte hypertrophy. The expression of liver Cd36 was lowered by more than 50 % as well as the saturated and monounsaturated FA concentration. Notably, the desaturation index for C16 and C18 FAs that are correlated with adiposity were reduced. The concentration of several DHA-derived oxidized PUFAs were also enhanced. Faecal metagenomics sequencing revealed enriched abundance of Leptogranulimonas caecicola and Bacteroides sp. ZJ-18 and were positively correlated with several DHA- and ALA-derived oxidized PUFAs in ABA group.

CONCLUSION: Our study revealed the modulatory effect of physiological dose of ABA on attenuating visceral obesity, reducing hepatic steatosis, and promoting the production of anti-inflammatory oxidized PUFAs that were potentially mediated by the gut microbiota.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Fatty Acids, Unsaturated/metabolism
Diet, High-Fat/adverse effects
*Liver/metabolism/drug effects/pathology
Male
*Obesity, Abdominal/drug therapy/metabolism/microbiology/pathology
Lipid Metabolism/drug effects
Mice
Oxidation-Reduction
Mice, Inbred C57BL

@article {pmid39628383,
year = {2025},
author = {Wang, H and Feng, L and Pei, Z and Zhao, J and Lu, S and Lu, W},
title = {Gut microbiota metabolism of branched-chain amino acids and their metabolites can improve the physiological function of aging mice.},
journal = {Aging cell},
volume = {24},
number = {4},
pages = {e14434},
doi = {10.1111/acel.14434},
pmid = {39628383},
issn = {1474-9726},
support = {2022YFF1100403//National Key Research and Development Program of China/ ; HB2023003//Top Talent Support Program for young and middle-aged people of Wuxi Health Committee/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Amino Acids, Branched-Chain/metabolism ; Mice ; *Aging/metabolism/drug effects ; Mice, Inbred C57BL ; Male ; },
abstract = {The metabolism of branched-chain amino acids by gut microbiota can improve overall health and may reverse aging. In this study, we investigated Parabacteroides merdae, a gut microbe that is known to catabolise branched-chain amino acids (BCAAs). Three metabolites of BCAAs isovalerate, 2-methylbutyrate, and isobutyrate were used to treat D-gal induced aging mice. The results showed that these treatments could delay aging in mice by providing health benefits in reducing oxidative stress and inflammation, improving muscle capacity, reversing brain acetylcholine levels, and regulating blood glucose. The mechanism was preliminarily explored by combining the gut microbiota metagenome and faecal serum metabolome. Parabacteroides merdae altered the species composition and structure of the gut microbiota in mice. Increasing the abundance of beneficial bacteria, such as Bifidobacterium pseudolongum. Three metabolites affects the gut microbiota and the body's pathways of protein and improves the overall health through a variety of signaling pathways. Overall, regulating the gut microbiota involved in branched-chain amino acid metabolism to bring health benefits may be a new way of reversing aging.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Amino Acids, Branched-Chain/metabolism
Mice
*Aging/metabolism/drug effects
Mice, Inbred C57BL
Male

@article {pmid40204761,
year = {2025},
author = {Li, F and Hooi, SL and Choo, YM and Teh, CSJ and Toh, KY and Lim, LWZ and Lee, YQ and Chong, CW and Ahmad Kamar, A},
title = {Progression of gut microbiome in preterm infants during the first three months.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12104},
pmid = {40204761},
issn = {2045-2322},
support = {IF047-2021//International Funding/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Infant, Premature ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Female ; Male ; Prospective Studies ; *Bacteria/genetics/classification ; Infant ; Gestational Age ; Bifidobacterium/genetics/isolation & purification ; Meconium/microbiology ; Metagenomics ; },
abstract = {The colonization and evolution of gut microbiota early in life play a vital role in shaping a healthy, robust immune system for infant health, whether in combating short-term illness or improving long-term health outcomes. Early-life clinical practices may interrupt or disrupt the normal colonization process of the infant gut microbiota, thereby increasing disease susceptibility. In this prospective cohort study, we analyzed the gut microbiota of 46 term and 23 preterm infants using 16S rRNA gene metagenomic sequencing. Fecal samples were collected at six timepoints during the first three months of life. Notably, gestational age was the main factor contributing to differences in the meconium microbial composition. Intriguingly, our study unveiled a more homogeneous microbial composition in preterm infants with more abundant Bifidobacterium from the postnatal age (PNA) of one month. Concurrently, the beneficial bacteria Bifidobacterium and Lactobacillus gradually increased, and the potentially pathogenic bacteria Clostridium, Enterobacter, Enterococcus, Klebsiella, and Pseudomonas gradually decreased. Furthermore, our study underscored a link between decreased microbial diversity of preterm infants and exclusive breastfeeding and antibiotic exposure. Moreover, preterm infants with patent ductus arteriosus (PDA) exhibited reduced microbial diversity but higher abundances of Streptococcus oralis and Streptococcus mitis.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Infant, Premature
Infant, Newborn
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Female
Male
Prospective Studies
*Bacteria/genetics/classification
Infant
Gestational Age
Bifidobacterium/genetics/isolation & purification
Meconium/microbiology
Metagenomics

@article {pmid40202375,
year = {2025},
author = {Pan, C and Xu, P and Yuan, M and Wei, S and Lu, Y and Lu, H and Zhang, W},
title = {Effects of Different Feeding Patterns on the Gut Virome of 6-Month-Old Infants.},
journal = {Journal of medical virology},
volume = {97},
number = {4},
pages = {e70344},
doi = {10.1002/jmv.70344},
pmid = {40202375},
issn = {1096-9071},
support = {//This study was supported by the Zhenjiang Science and Technology Innovation Funds-Clinical Medicine Key Laboratory and Scientific Research Project of Health Commission of Jiangsu Province./ ; },
mesh = {Humans ; Infant ; *Gastrointestinal Microbiome ; *Virome ; Feces/virology ; *Breast Feeding ; Female ; Male ; *Viruses/classification/genetics/isolation & purification ; Metagenomics ; *Feeding Behavior ; Bacteriophages/genetics/classification/isolation & purification ; Milk, Human/virology ; *Gastrointestinal Tract/virology ; },
abstract = {The gut microbiome is essential for infant health, and in recent years, the impact of enteroviruses on infant health and disease has received increasing attention. The transmission of breast milk phages to the infant gastrointestinal tract contributes to the shaping of the infant gut virome, while breastfeeding regulates the colonization of the infant gut virome. In this study, we collected fecal samples from healthy infants and analyzed the distribution characteristics of infant viral communities by viral metagenomic analysis, and analyzed the differences in infant viral communities under different feeding practices. Our results indicate that the infant intestinal virome consists of phages and eukaryotic viruses. Caudovirales and Microviridae dominated the phage composition, and except for Siphoviridae, which was more predominant in the intestines of formula-fed infants, there were no significant differences in the overall abundance of other Caudovirales and Microviridae in the intestines of infants with different feeding patterns. Breastfeeding can lead to a higher diversity of infant gut viruses through vertical transmission, and a highly diverse gut virome helps maintain the maturation of the gut microbiome. This study informs the shaping of gut virome in healthy infants by breastfeeding and contributes to further research on infant gut virome characteristics and formation processes.},
}

Humans
Infant
*Gastrointestinal Microbiome
*Virome
Feces/virology
*Breast Feeding
Female
Male
*Viruses/classification/genetics/isolation & purification
Metagenomics
*Feeding Behavior
Bacteriophages/genetics/classification/isolation & purification
Milk, Human/virology
*Gastrointestinal Tract/virology

@article {pmid40201423,
year = {2025},
author = {Boden, L and Bludau, D and Sieber, G and Deep, A and Baikova, D and David, GM and Hadžiomerović, U and Stach, TL and Boenigk, J},
title = {The impact of elevated temperature and salinity on microbial communities and food selectivity in heterotrophic nanoflagellates in the Boye River.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf049},
pmid = {40201423},
issn = {2730-6151},
abstract = {Microbial predator-prey interactions play a crucial role in aquatic food webs. Bacterivorous protists not only regulate the quantity and biomass of bacterial populations but also profoundly influence the structure of bacterial communities. Consequently, alterations in both the quantity and quality of protist bacterivory can influence the overall structure of aquatic food webs. While it is well-documented that changes in environmental conditions or the occurrence of abiotic stressors can lead to shifts in microbial community compositions, the impact of such disturbances on food selection remains unknown. Here, we investigated the effects of elevated temperature and salinization on food selectivity of heterotrophic nanoflagellates by monitoring the uptake of preselected target bacteria via catalyzed reporter deposition fluorescence in situ hybridization and fluorescence microscopy. Our results indicate that salinization, but not increased temperature, significantly increased the flagellates' selection against Microbacterium lacusdiani (Actinomycetota). However, the effect of the reduced grazing pressure was counterbalanced by the negative effect of increased salinity on the growth of Actinomycetota. Our results suggest that the effect of stressors on the feeding behavior of protistan predators may strongly affect the composition of their prey community, when bacterial taxa are concerned that are less sensitive to the particular stressor.},
}

@article {pmid40199830,
year = {2025},
author = {Singh, P and Haldhar, P and Das, T and Chaubey, G and Gupta, MK and Kumar, B},
title = {Thermal Stress and Its Effects on the Gut Microbiome of Parthenium Beetles.},
journal = {Archives of insect biochemistry and physiology},
volume = {118},
number = {4},
pages = {e70058},
doi = {10.1002/arch.70058},
pmid = {40199830},
issn = {1520-6327},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Animals ; *Coleoptera/microbiology/physiology ; *Gastrointestinal Microbiome ; *Stress, Physiological ; Bacteria/classification/isolation & purification/genetics ; Hot Temperature ; RNA, Ribosomal, 16S/analysis ; },
abstract = {The gut microbiota plays a vital role in nutrient and energy utilization, as well as in the host's ability to adapt its immune system to environmental changes. As a biological control agent for the invasive Parthenium weed, the Parthenium beetle Zygogramma bicolorata (Z. bicolorata) Pallister is often exposed to fluctuating temperatures, which may induce stress in its natural habitat. This study utilized 16S amplicon sequencing to explore the impact of temperature stress on the gut microbiome of Z. bicolorata under cold (15°C), control (27°C), and hot (35°C) conditions. A total of 11 bacterial phyla and 149 genera were identified, with Firmicutes, Proteobacteria, and Cyanobacteria being the most abundant. Temperature treatments significantly influenced the diversity of the gut microbiota, as evidenced by alpha diversity measures. Principal coordinate analysis further revealed substantial variations in microbiome composition across the different temperature conditions. Additionally, PICRUSt2 analysis suggested that the gut microbiota is linked to metagenomic functions related to amino acid and carbohydrate transport, inorganic ion metabolism, and cellular processes. Our findings suggest that thermal stress alters the gut microbiome of Parthenium beetles, offering new insights into how these beetles may have ecologically adapted to temperature fluctuations, while also highlighting the potential role of gut microbes in maintaining beetle health under environmental stress.},
}

Animals
*Coleoptera/microbiology/physiology
*Gastrointestinal Microbiome
*Stress, Physiological
Bacteria/classification/isolation & purification/genetics
Hot Temperature
RNA, Ribosomal, 16S/analysis

@article {pmid40197053,
year = {2025},
author = {Langsiri, N and Meyer, W and Irinyi, L and Worasilchai, N and Pombubpa, N and Wongsurawat, T and Jenjaroenpun, P and Luangsa-Ard, JJ and Chindamporn, A},
title = {Optimizing fungal DNA extraction and purification for Oxford Nanopore untargeted shotgun metagenomic sequencing from simulated hemoculture specimens.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0116624},
doi = {10.1128/msystems.01166-24},
pmid = {40197053},
issn = {2379-5077},
abstract = {UNLABELLED: Long-read metagenomics provides a promising alternative approach to fungal identification, circumventing methodological biases, associated with DNA amplification, which is a prerequisite for DNA barcoding/metabarcoding based on the primary fungal DNA barcode (Internal Transcribed Spacer (ITS) region). However, DNA extraction for long-read sequencing-based fungal identification poses a significant challenge, as obtaining long and intact fungal DNA is imperative. Comparing different lysis methods showed that chemical lysis with CTAB/SDS generated DNA from pure fungal cultures with high yields (ranging from 11.20 ± 0.17 µg to 22.99 ± 2.22 µg depending on the species) while preserving integrity. Evaluating the efficacy of human DNA depletion protocols demonstrated an 88.73% reduction in human reads and a 99.53% increase in fungal reads compared to the untreated yeast-spiked human blood control. Evaluation of the developed DNA extraction protocol on simulated clinical hemocultures revealed that the obtained DNA sequences exceed 10 kb in length, enabling a highly efficient sequencing run with over 80% active pores. The quality of the DNA, as indicated by the 260/280 and 260/230 ratios obtained from NanoDrop spectrophotometer readings, exceeded 1.8 and 2.0, respectively. This demonstrated the great potential of the herein optimized protocol to extract high-quality fungal DNA from clinical specimens enabling long-read metagenomics sequencing.

IMPORTANCE: A novel streamlined DNA extraction protocol was developed to efficiently isolate high molecular weight fungal DNA from hemoculture samples, which is crucial for long-read sequencing applications. By eliminating the need for labor-intensive and shear-force-inducing steps, such as liquid nitrogen grinding or bead beating, the protocol is more user-friendly and better suited for clinical laboratory settings. The automation of cleanup and extraction steps further shortens the overall turnaround time to under 6 hours. Although not specifically designed for ultra-long DNA extraction, this protocol effectively supports fungal identification through Oxford Nanopore Technology (ONT) sequencing. It yields high molecular weight DNA, resulting in longer sequence fragments that improve the number of fungal reads over human reads. Future improvements, including adaptive sampling technology, could further simplify the process by reducing the need for human DNA depletion, paving the way for more automated, bioinformatics-driven workflows.},
}

@article {pmid40196042,
year = {2025},
author = {Wang, H and Zhu, W and Lei, J and Liu, Z and Cai, Y and Wang, S and Li, A},
title = {Gut microbiome differences and disease risk in colorectal cancer relatives and healthy individuals.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1573216},
pmid = {40196042},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/epidemiology ; *Gastrointestinal Microbiome ; Feces/microbiology ; Male ; Female ; Middle Aged ; Risk Factors ; Aged ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Adult ; Cohort Studies ; Family ; Whole Genome Sequencing ; },
abstract = {Given the heightened focus on high-risk populations, this study aimed to provide insights into early susceptibility and preventive strategies for colorectal cancer (CRC) by focusing on high-risk populations. In this research, fecal samples from 1,647 individuals across three discovery cohorts and nine external validation cohorts were sequenced using whole-genome metagenomic sequencing. A prediction model based on random forest was constructed using the nine external cohorts and independently validated with the three discovery cohorts. A disease probability (POD) model based on microbial biomarkers was developed to assess CRC risk. We found that the gut microbiome composition of CRC relatives differed from that of controls, with enrichment of species such as Fusobacterium and Bacteroides and a reduction in beneficial genera like Coprococcus and Roseburia. Additionally, dietary red meat intake emerged as a risk factor. The POD model indicated an elevated risk of CRC in unaffected relatives. The findings suggest that the POD for CRC may be increased in unaffected relatives or individuals living in shared environments, although this difference did not reach statistical significance. Our study introduces a novel framework for assessing the risk of colorectal cancer in ostensibly healthy individuals.},
}

Humans
*Colorectal Neoplasms/microbiology/epidemiology
*Gastrointestinal Microbiome
Feces/microbiology
Male
Female
Middle Aged
Risk Factors
Aged
*Bacteria/classification/genetics/isolation & purification
Metagenomics
Adult
Cohort Studies
Family
Whole Genome Sequencing

@article {pmid40153355,
year = {2025},
author = {Klištincová, N and Koreňová, J and Rešková, Z and Čaplová, Z and Burdová, A and Farkas, Z and Polovka, M and Drahovská, H and Pangallo, D and Kuchta, T},
title = {Bacterial consortia of ewes' whey in the production of bryndza cheese in Slovakia.},
journal = {Letters in applied microbiology},
volume = {78},
number = {4},
pages = {},
doi = {10.1093/lambio/ovaf047},
pmid = {40153355},
issn = {1472-765X},
support = {APVV-20-0001//Slovak Research and Development Agency/ ; },
mesh = {Animals ; Slovakia ; *Cheese/microbiology ; *Whey/microbiology ; Sheep ; RNA, Ribosomal, 16S/genetics ; Fermentation ; *Bacteria/classification/genetics/isolation & purification ; *Microbial Consortia ; Female ; Food Microbiology ; DNA, Bacterial/genetics/chemistry ; Milk/microbiology ; },
abstract = {Whey from previous production is often used as a natural starter in the technology of traditional cheeses, including bryndza cheese in Slovakia. Therefore, studying its bacterial community and isolating new potential natural starters is important for improving the characteristics of the final product. Composition of bacterial consortia of fresh and fermented whey in the production of raw ewes' milk-based bryndza cheese from 8 small or medium-sized producers was analysed. Culture-based microbiological analysis and culture-independent analysis based on 16S rRNA gene sequencing by MiSeq and MinION were used. Results showed the dominance of lactococci or streptococci, with 3-8 log CFU ml-[1] of Lactobacillus sensu lato in all whey samples. Potential natural starters comprising Lacticaseibacillus paracasei/casei, Lactiplantibacillus plantarum, Lentilactobacillus parabuchneri, Lactobacillus helveticus, L. diolivorans, Levilactobacillus brevis, Limosilactobacillus fermentum, L. delbrueckii, L. gasseri and L. otakiensis were isolated. Coliforms were also present in all samples, with no consistently lower values in fermented whey samples. Some samples contained pseudomonads and/or acinetobacters. Coagulase-positive staphylococci were present at relevant levels in samples from 4 producers. The results revealed that whey is a source of natural starters due to the presence of lactobacilli.},
}

Animals
Slovakia
*Cheese/microbiology
*Whey/microbiology
Sheep
RNA, Ribosomal, 16S/genetics
Fermentation
*Bacteria/classification/genetics/isolation & purification
*Microbial Consortia
Female
Food Microbiology
DNA, Bacterial/genetics/chemistry
Milk/microbiology

@article {pmid40145240,
year = {2025},
author = {Zhou, Y and Oba, K and Xu, T and Kuroiwa, M and Hori, T and Terada, A},
title = {Actively N2O-Reducing Oxygen-Tolerant Microbial Consortium Attained by Using a High-Dilution-Rate Chemostat Fed with Methanol.},
journal = {Environmental science & technology},
volume = {59},
number = {13},
pages = {6673-6685},
doi = {10.1021/acs.est.4c12732},
pmid = {40145240},
issn = {1520-5851},
mesh = {Methanol/metabolism ; *Nitrous Oxide/metabolism ; Oxygen/metabolism ; *Microbial Consortia ; Bacteria/metabolism ; Oxidation-Reduction ; },
abstract = {Nitrous oxide-reducing bacteria (N2ORB) are generally considered the only biological sink for the potent greenhouse gas N2O. Although N2O consumption activities by diverse heterotrophic N2ORB have been detected, knowledge gaps remain about the phylogenies, physiologies, and activities of N2ORB. Here, we successfully enriched a methylotrophic N2ORB consortium under intermittent oxygen and N2O supplies. [15]N tracer analysis showed that the N2O consumption activity of the enriched consortium was higher than its N2O production activity in the presence of either a single or multiple electron acceptors (i.e., nitrogen oxides). The observed maximum N2O consumption was 80.7 μmol·g-biomass[-1]·h[-1]. Quantitative PCR results showed that clade I nosZ bacteria overwhelmed clade II nosZ bacteria at high (0.41 mmol·min[-1]) and low (0.08 mmol·min[-1]) N2O loading rates. The dilution rate and N2O loading rate affected the microbial community composition and activity. A higher N2O loading rate stimulated active and oxygen-tolerant N2ORB that boosted N2O consumption by approximately 50% in the presence of oxygen. Metagenomic analysis unraveled the predominance of a novel methylotrophic N2ORB, possessing entire denitrifying genes and high-affinity terminal oxidase genes, from the reactor with a high N2O loading rate. The unique physiological traits of the consortium enriched by methanol shed light on a novel function─aerobic N2O consumption by N2ORB─and pave the way for innovative N2O mitigation strategies applying powerful N2O sinks in engineered systems.},
}

Methanol/metabolism
*Nitrous Oxide/metabolism
Oxygen/metabolism
*Microbial Consortia
Bacteria/metabolism
Oxidation-Reduction

@article {pmid40138872,
year = {2025},
author = {Liang, T and Jiang, T and Liang, Z and Li, L and Chen, Y and Chen, T and Yang, L and Zhang, N and Dong, B and Xie, X and Gu, B and Wu, Q},
title = {Gut microbiota-driven BCAA biosynthesis via Staphylococcus aureus -expressed acetolactate synthase impairs glycemic control in type 2 diabetes in South China.},
journal = {Microbiological research},
volume = {296},
number = {},
pages = {128145},
doi = {10.1016/j.micres.2025.128145},
pmid = {40138872},
issn = {1618-0623},
mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; *Staphylococcus aureus/enzymology/genetics/metabolism ; *Amino Acids, Branched-Chain/biosynthesis ; *Acetolactate Synthase/metabolism/genetics ; Humans ; Animals ; Mice ; China ; Male ; Insulin Resistance ; Female ; Middle Aged ; *Glycemic Control ; Blood Glucose ; Feces/microbiology ; Staphylococcal Infections/microbiology ; Metagenomics ; Prediabetic State/microbiology ; Metabolomics ; Insulin ; },
abstract = {An increase in branched-chain amino acid (BCAA) levels can result in insulin resistance at different stages of type 2 diabetes (T2D), however, the causes of this increase are unclear. We performed metagenomics and metabolomics profiling in patients with prediabetes (PDM), newly diagnosed diabetes (NDDM), and post-medication type 2 diabetes (P2DM) to investigate whether altered gut microbes and metabolites could explain the specific clinical characteristics of different disease stages of T2D. Here we identify acetolactate synthase (ALS) a BCAA biosynthesis enzyme in Staphylococcus aureus as a cause of T2D insulin resistance. Compared with healthy peoples, patients with PDM, NDDM, and P2DM groups, especially in P2DM group, have increased faecal numbers of S. aureus. We also demonstrated that insulin administration may be a risk factor for S. aureus infection in T2D. The presence of ALS-positive S. aureus correlated with the levels of BCAAs and was associated with an increased fasting blood glucose (FBG) and insulin resistance. Humanized microbiota transplantation experiment indicated that ALS contributes to disordered insulin resistance mediated by S. aureus. We also found that S. aureus phage can reduced the FBG levels and insulin resistance in db/db mice. The ALS-positive S. aureus are associated with insulin resistance in T2D, opening a new therapeutic avenue for the prevention or treatment of diabetes.},
}

*Diabetes Mellitus, Type 2/microbiology/metabolism
*Gastrointestinal Microbiome/physiology
*Staphylococcus aureus/enzymology/genetics/metabolism
*Amino Acids, Branched-Chain/biosynthesis
*Acetolactate Synthase/metabolism/genetics
Humans
Animals
Mice
China
Male
Insulin Resistance
Female
Middle Aged
*Glycemic Control
Blood Glucose
Feces/microbiology
Staphylococcal Infections/microbiology
Metagenomics
Prediabetic State/microbiology
Metabolomics
Insulin

@article {pmid40096540,
year = {2025},
author = {Zhang, Q and Li, J and Tuo, J and Liu, S and Liu, Y and Liu, P and Ye, L and Zhang, XX},
title = {Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf051},
pmid = {40096540},
issn = {1751-7370},
support = {BE2022837//Jiangsu Province Key Research and Development Program/ ; 52200057//National Natural Science Foundation of China/ ; },
mesh = {*Sewage/microbiology ; *Bacteria/virology/genetics/classification ; *Bacteriophages/genetics ; Metagenomics ; *Metagenome ; *Microbiota ; },
abstract = {Bacteria have evolved various antiviral defense systems (DSs) to protect themselves, but how DSs respond to the variation of bacteriophages in complex bacterial communities and whether DSs function effectively in maintaining the stability of bacterial community structure and function remain unknown. Here, we conducted a long-term metagenomic investigation on the composition of bacterial and phage communities of monthly collected activated sludge (AS) samples from two full-scale wastewater treatment plants over 6 years and found that DSs were widespread in AS, with 91.1% of metagenome-assembled genomes (MAGs) having more than one complete DS. The stability of the bacterial community was maintained under the fluctuations of the phage community, and DS abundance and phage abundance were strongly positively correlated; there was a 0-3-month time lag in the responses of DSs to phage fluctuations. The rapid turnover of clustered regularly interspaced short palindromic repeat spacer repertoires further highlighted the dynamic nature of bacterial defense mechanisms. A pan-immunity phenomenon was also observed, with nearly identical MAGs showing significant differences in DS composition, which contributed to community stability at the species level. This study provides novel insights into the complexity of phage-bacteria interactions in complex bacterial communities and reveals the key roles of DSs in stabilizing bacterial community structure and function.},
}

*Sewage/microbiology
*Bacteria/virology/genetics/classification
*Bacteriophages/genetics
Metagenomics
*Metagenome
*Microbiota

@article {pmid40068342,
year = {2025},
author = {Song, R and Lv, B and He, Z and Li, H and Wang, H},
title = {Rhizosphere metabolite dynamics in continuous cropping of vineyards: Impact on microflora diversity and co-occurrence networks.},
journal = {Microbiological research},
volume = {296},
number = {},
pages = {128134},
doi = {10.1016/j.micres.2025.128134},
pmid = {40068342},
issn = {1618-0623},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Fungi/classification/metabolism/genetics/isolation & purification ; Biodiversity ; *Vitis/microbiology/growth & development ; Soil/chemistry ; Microbiota ; Crops, Agricultural/microbiology/growth & development ; Farms ; Metabolomics ; Metagenomics ; Metabolome ; },
abstract = {The metabolism of the crop rhizosphere affects microflora diversity and nutrient cycling. However, understanding rhizosphere metabolism in suitable crops within arid desert environments and its impact on microflora interactions remains limited. Through metagenomic and non-targeted metabolomic sequencing of rhizosphere soils from one uncultivated land and four vineyards with cropping years of 5, 10, 15 and 20 years, the critical importance of rhizosphere metabolites in maintaining bacterial and fungal diversity was elucidated. The results revealed that Nocardioides, Streptomyces, and Solirubrobacter were the relatively abundant bacterial genera in rhizosphere soils, while Rhizophagus, Glomus, and Pseudogymnoascus were the relatively abundant fungal genera. The composition of rhizosphere metabolic changed significantly during the continuous cropping of grapevines. Dimethylglycine, Formononetin, and Dehydroepiandrosterone were the most important metabolites. Enrichment analysis revealed significant involvement of metabolic pathways such as biosynthesis of amino acids, unsaturated fatty acids, and linoleic acid metabolism. Procrustes analysis highlighted stronger correlations between rhizosphere metabolites and bacterial community compared to those of fungal community. This suggests distinct responses of microflora to crop-released chemical elements across different soil habitats. Co-occurrence network analysis demonstrated complex associations between rhizosphere metabolites and soil microflora, the positive correlations between rhizosphere metabolites and microflora networks predominated over negative correlations. Partial least squares path model indicated that the effect of cropping years on rhizosphere metabolites was greater than that on bacterial microflora diversity. Futhermore, pH, total phosphorus, and alkali-hydrolyzed nitrogen were the key environmental factors affecting rhizosphere metabolites and microbial diversity. These results deepen our valuable insights into the complex biological processes that rhizosphere metabolites influence on microorganisms, and provide strong support for maintaining microbial diversity in farmland soils in arid regions.},
}

*Rhizosphere
*Soil Microbiology
*Bacteria/classification/metabolism/genetics/isolation & purification
*Fungi/classification/metabolism/genetics/isolation & purification
Biodiversity
*Vitis/microbiology/growth & development
Soil/chemistry
Microbiota
Crops, Agricultural/microbiology/growth & development
Farms
Metabolomics
Metagenomics
Metabolome

@article {pmid40062772,
year = {2025},
author = {Connolly, JP and Kelly, L},
title = {The physical biogeography of Fusobacterium nucleatum in health and disease.},
journal = {mBio},
volume = {16},
number = {4},
pages = {e0298924},
doi = {10.1128/mbio.02989-24},
pmid = {40062772},
issn = {2150-7511},
support = {5T32GM007491-46//HHS | National Institutes of Health (NIH)/ ; //Elsa U. Pardee Foundation (EUPF)/ ; },
mesh = {*Fusobacterium nucleatum/genetics/isolation & purification/classification/physiology ; Humans ; *Colorectal Neoplasms/microbiology ; Female ; Male ; *Fusobacterium Infections/microbiology ; Crohn Disease/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Metagenome ; Gingiva/microbiology ; Genome, Bacterial ; },
abstract = {UNLABELLED: Fusobacterium nucleatum (Fn) is an oral commensal inhabiting the human gingival plaque that is rarely found in the gut. However, in colorectal cancer (CRC), Fn can be isolated from stool samples and detected in metagenomes. We hypothesized that ecological characteristics of the gut are altered by disease, enabling Fn to colonize. Multiple genomically distinct populations of Fn exist, but their ecological preferences are unstudied. We identified six well-separated populations in 133 Fn genomes and used simulated metagenomes to demonstrate sensitive detection of populations in human oral and gut metagenomes. In 9,560 samples from 11 studies, Fn population C2 animalis is elevated in gut metagenomes from CRC and Crohn's disease patients and is observed more frequently in CRC stool samples than in the gingiva. Polymorphum, the most prevalent gingival Fn population, is significantly increased in Crohn's stool samples; this effect was significantly stronger in male hosts than in female. We find polymorphum genomes are enriched for biosynthetic gene clusters and fluoride exporters, while C2 animalis are high in iron transporters. Fn populations thus associate with specific clinical and demographic phenotypes and harbor distinct functional features. Ecological differences in closely related groups of bacteria inform microbiome impacts on human health.

IMPORTANCE: Fusobacterium nucleatum is a bacterium normally found in the gingiva. F. nucleatum generally does not colonize the healthy gut, but is observed in approximately a third of colorectal cancer (CRC) patient guts. F. nucleatum's presence in the gut during CRC has been linked to worse prognosis and increased tumor proliferation. Here, we describe the population structure of F. nucleatum in oral and gut microbiomes. We report substantial diversity in gene carriage among six distinct populations of F. nucleatum and identify population disease and body-site preferences. We find the C2 animalis population is more common in the CRC gut than in the gingiva and is enriched for iron transporters, which support gut colonization in known pathogens. We find that C2 animalis is also enriched in Crohn's disease and type 2 diabetes, suggesting ecological commonalities between the three diseases. Our work shows that closely related bacteria can have different associations with human physiology.},
}

*Fusobacterium nucleatum/genetics/isolation & purification/classification/physiology
Humans
*Colorectal Neoplasms/microbiology
Female
Male
*Fusobacterium Infections/microbiology
Crohn Disease/microbiology
Feces/microbiology
*Gastrointestinal Microbiome
Metagenome
Gingiva/microbiology
Genome, Bacterial

@article {pmid39998226,
year = {2025},
author = {Martino, C and Kellman, BP and Sandoval, DR and Clausen, TM and Cooper, R and Benjdia, A and Soualmia, F and Clark, AE and Garretson, AF and Marotz, CA and Song, SJ and Wandro, S and Zaramela, LS and Salido, RA and Zhu, Q and Armingol, E and Vázquez-Baeza, Y and McDonald, D and Sorrentino, JT and Taylor, B and Belda-Ferre, P and Das, P and Ali, F and Liang, C and Zhang, Y and Schifanella, L and Covizzi, A and Lai, A and Riva, A and Basting, C and Broedlow, CA and Havulinna, AS and Jousilahti, P and Estaki, M and Kosciolek, T and Kuplicki, R and Victor, TA and Paulus, MP and Savage, KE and Benbow, JL and Spielfogel, ES and Anderson, CAM and Martinez, ME and Lacey, JV and Huang, S and Haiminen, N and Parida, L and Kim, H-C and Gilbert, JA and Sweeney, DA and Allard, SM and Swafford, AD and Cheng, S and Inouye, M and Niiranen, T and Jain, M and Salomaa, V and Zengler, K and Klatt, NR and Hasty, J and Berteau, O and Carlin, AF and Esko, JD and Lewis, NE and Knight, R},
title = {SARS-CoV-2 infectivity can be modulated through bacterial grooming of the glycocalyx.},
journal = {mBio},
volume = {16},
number = {4},
pages = {e0401524},
doi = {10.1128/mbio.04015-24},
pmid = {39998226},
issn = {2150-7511},
support = {P01 HL131474/HL/NHLBI NIH HHS/United States ; AI Horizons Network//IBM | IBM Research/ ; P01 HL131474/HL/NHLBI NIH HHS/United States ; NNF20SA0066621//Novo Nordisk Foundation/ ; 2031989//National Science Foundation (NSF)/ ; //Alfred Benzon Foundation (The Alfred Benzon Foundation)/ ; 321351 and 354447//Academy of Finland/ ; //Emil Aaltosen Säätiö (Emil Aaltonen Foundation)/ ; //Sydäntutkimussäätiö (Finnish Foundation for Cardiovascular Research)/ ; R01ES027595//HHS | National Institutes of Health (NIH)/ ; 2018-72190270//ANID Becas Chile Doctorado/ ; 321356//Academy of Finland/ ; N/A//UC San Diego Center for Microbiome Innovation/ ; 335525//Academy of Finland/ ; 101046041//Union's Horizon Europe Research and Innovation 459 Actions/ ; ANR-17-CE11-0014//French National Research Agency/ ; ANR-20-CE44-0005//French National Research Agency/ ; R01GM069811//HHS | National Institutes of Health (NIH)/ ; //Munz Chair of Cardiovascular Prediction and Prevention/ ; //NIHR | NIHR Cambridge Biomedical Research Centre (NIHR Cambridge BRC)/ ; RG/13/13/30194//British Heart Foundation (BHF)/ ; RG/18/13/33946//British Heart Foundation (BHF)/ ; BRC-1215-20014//NIHR | NIHR Cambridge Biomedical Research Centre (NIHR Cambridge BRC)/ ; 1DP1AT010885//HHS | National Institutes of Health (NIH)/ ; //Health Data Research UK (HDR UK)/ ; U01-CA199277//HHS | National Institutes of Health (NIH)/ ; P30-CA033572//HHS | National Institutes of Health (NIH)/ ; P30-CA023100//HHS | National Institutes of Health (NIH)/ ; UM1-CA164917//HHS | National Institutes of Health (NIH)/ ; R01-CA077398//HHS | National Institutes of Health (NIH)/ ; 2038509//National Science Foundation (NSF)/ ; R00RG2503//UC | University of California, San Diego (UCSD)/ ; 3022//Emerald Foundation/ ; 1P30DK120515//HHS | National Institutes of Health (NIH)/ ; R35GM119850//HHS | National Institutes of Health (NIH)/ ; UH2AI153029//HHS | National Institutes of Health (NIH)/ ; },
mesh = {Humans ; *COVID-19/virology/microbiology/metabolism ; *Glycocalyx/metabolism/virology ; *SARS-CoV-2/pathogenicity/physiology ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Heparan Sulfate Proteoglycans/metabolism ; Middle Aged ; Gastrointestinal Tract/microbiology ; Adult ; *Bacteria/metabolism ; Spike Glycoprotein, Coronavirus/metabolism ; },
abstract = {The gastrointestinal (GI) tract is a site of replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and GI symptoms are often reported by patients. SARS-CoV-2 cell entry depends upon heparan sulfate (HS) proteoglycans, which commensal bacteria that bathe the human mucosa are known to modify. To explore human gut HS-modifying bacterial abundances and how their presence may impact SARS-CoV-2 infection, we developed a task-based analysis of proteoglycan degradation on large-scale shotgun metagenomic data. We observed that gut bacteria with high predicted catabolic capacity for HS differ by age and sex, factors associated with coronavirus disease 2019 (COVID-19) severity, and directly by disease severity during/after infection, but do not vary between subjects with COVID-19 comorbidities or by diet. Gut commensal bacterial HS-modifying enzymes reduce spike protein binding and infection of authentic SARS-CoV-2, suggesting that bacterial grooming of the GI mucosa may impact viral susceptibility.IMPORTANCESevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019, can infect the gastrointestinal (GI) tract, and individuals who exhibit GI symptoms often have more severe disease. The GI tract's glycocalyx, a component of the mucosa covering the large intestine, plays a key role in viral entry by binding SARS-CoV-2's spike protein via heparan sulfate (HS). Here, using metabolic task analysis of multiple large microbiome sequencing data sets of the human gut microbiome, we identify a key commensal human intestinal bacteria capable of grooming glycocalyx HS and modulating SARS-CoV-2 infectivity in vitro. Moreover, we engineered the common probiotic Escherichia coli Nissle 1917 (EcN) to effectively block SARS-CoV-2 binding and infection of human cell cultures. Understanding these microbial interactions could lead to better risk assessments and novel therapies targeting viral entry mechanisms.},
}

Humans
*COVID-19/virology/microbiology/metabolism
*Glycocalyx/metabolism/virology
*SARS-CoV-2/pathogenicity/physiology
*Gastrointestinal Microbiome/physiology
Male
Female
Heparan Sulfate Proteoglycans/metabolism
Middle Aged
Gastrointestinal Tract/microbiology
Adult
*Bacteria/metabolism
Spike Glycoprotein, Coronavirus/metabolism

@article {pmid40195460,
year = {2025},
author = {Bhagat, NR and Bharti, VK and Shukla, G and Rishi, P and Chaurasia, OP},
title = {Gut bacteriome dynamics in high altitude-adapted chicken lines: a key to future poultry therapeutics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11910},
pmid = {40195460},
issn = {2045-2322},
mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome ; *Altitude ; Metagenomics/methods ; *Bacteria/genetics/classification ; *Adaptation, Physiological ; Metagenome ; },
abstract = {High-altitude-adapted chickens harbor a unique gut bacteriome essential for their survival under extremely cold and hypoxic environment, however, little is known about their population and functional dynamics, limiting their application in poultry production. Hence, this study employed amplicon-based metagenomics to examine the gut bacterial diversity and their functional profile in two high-altitude-adapted chicken lines, e.g. LEHBRO-1 and LEHBRO-3. The results revealed significant variations in taxonomic abundance at the phylum level, with Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria predominating in LEHBRO-1, whereas Firmicutes, Proteobacteria, Bacteroidetes, Planctomycetes, and Actinobacteria predominated in LEHBRO-3. Genus-level diversity and Linear Discriminant Analysis Effect Size (LEfSe) biomarker analysis also substantiated the differences in the gut bacterial communities between the two chicken lines. Furthermore, functional profiling revealed enrichment of carbohydrate, nucleotide, lipid, amino acid, fatty acid, energy, and glycan metabolic pathways in the gut bacteriomes of these high-altitude chicken lines. The Statistical Analysis of Metagenomic Profiles (STAMP) for metabolic profiling identified a significant difference in purine and protein metabolism between these two chicken lines. These findings indicate the unique gut bacteriome and their functional diversity in high-altitude-adapted chickens, which would provide a foundation for future research on gut therapeutics to improve chicken health and productivity in high-altitude areas.},
}

Animals
*Chickens/microbiology
*Gastrointestinal Microbiome
*Altitude
Metagenomics/methods
*Bacteria/genetics/classification
*Adaptation, Physiological
Metagenome

@article {pmid40195156,
year = {2025},
author = {Sefrji, FO and Abulfaraj, AA and Alshehrei, FM and Al-Andal, A and Alnahari, AA and Tashkandi, M and Baz, L and Barqawi, AA and Almutrafy, AM and Alshareef, SA and Alkhatib, SN and Abuauf, HW and Jalal, RS and Aloufi, AS},
title = {Comprehensive analysis of orthologous genes reveals functional dynamics and energy metabolism in the rhizospheric microbiome of Moringa oleifera.},
journal = {Functional & integrative genomics},
volume = {25},
number = {1},
pages = {82},
pmid = {40195156},
issn = {1438-7948},
mesh = {*Moringa oleifera/microbiology/genetics/metabolism ; *Rhizosphere ; *Microbiota/genetics ; *Energy Metabolism/genetics ; Soil Microbiology ; Bacteria/genetics/classification ; Adenosine Triphosphate/metabolism ; Metagenome ; },
abstract = {Moringa oleifera, known for its nutritional and therapeutic properties, exhibits a complex relationship with its rhizospheric soil microbiome. This study aimed to elucidate the microbiome's structural composition, molecular functions, and its role in plant growth by integrating Clusters of Orthologous Genes (COG) analysis with enzymatic functions previously identified through KEGG, CAZy, and CARD databases. Metagenomic sequencing and bioinformatics analysis were performed from the rhizospheric soil microbiome of M. oleifera collected from the Mecca district in Saudi Arabia. The analysis revealed a role for the rhizospheric microbiome in energy production, storage, and regulation, with glucose serving as a crucial precursor for NADH synthesis and subsequent ATP production via oxidative phosphorylation. Key orthologous genes (OGs) implicated in this process include NuoD, NuoH, NuoM, NuoN, NuoL, atpA, QcrB/PetB, and AccC. Additionally, OGs involved in ATP hydrolysis, such as ClpP, EntF, YopO, and AtoC, were identified. Taxonomic analysis highlighted Actinobacteria and Proteobacteria as the predominant phyla, with enriched genera including Blastococcus, Nocardioides, Streptomyces, Microvirga, Sphingomonas, and Massilia, correlating with specific OGs involved in ATP hydrolysis. This study provides insights into the molecular mechanisms underpinning plant-microbe interactions and highlights the multifaceted roles of ATP-dependent processes in the rhizosphere. Further research is recommended to explore the potential applications of these findings in sustainable agriculture and ecosystem management.},
}

*Moringa oleifera/microbiology/genetics/metabolism
*Rhizosphere
*Microbiota/genetics
*Energy Metabolism/genetics
Soil Microbiology
Bacteria/genetics/classification
Adenosine Triphosphate/metabolism
Metagenome

@article {pmid40194944,
year = {2025},
author = {Wilson, I and Perry, T and Eisenhofer, R and Rismiller, P and Shaw, M and Grutzner, F},
title = {Microbiota changes in lactation in the short-beaked echidna (Tachyglossus aculeatus).},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf036},
pmid = {40194944},
issn = {1574-6941},
abstract = {Monotreme and marsupial development is characterised by a short gestation, with young exposed to the environment at an early developmental stage and supported by a long lactation in the pouch, pseudo-pouch, or burrow. The lack of a functional adaptive immune system in these altricial young raises questions about how they survive in a microbe-rich environment. Previous studies on marsupial pouches have revealed changes to pouch microbe composition during lactation, but no information is available in monotremes. We investigated changes in the echidna pseudo-pouch microbiota (n = 22) during different stages of the reproductive cycle and whether this differs between wild and zoo-managed animals. Metataxonomic profiling using 16S rRNA gene sequencing revealed that pseudo-pouch microbial communities undergo dramatic changes during lactation, with significant differences in taxonomic composition compared with samples taken outside of breeding season or during courtship and mating. This suggests that the echidna pseudo-pouch environment changes during lactation to accommodate young that lack a functional adaptive immune system. Furthermore, captivity was not found to have a significant effect on pseudo-pouch microbiota. This study pioneers pouch microbiota research in monotremes, provides new biological information on echidna reproduction, and may also provide information about the effects of captive management to inform breeding programs in the future.},
}

@article {pmid40193328,
year = {2025},
author = {Jagadesan, S and Guda, C},
title = {MetaDAVis: An R shiny application for metagenomic data analysis and visualization.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0319949},
doi = {10.1371/journal.pone.0319949},
pmid = {40193328},
issn = {1932-6203},
mesh = {*Metagenomics/methods ; Humans ; RNA, Ribosomal, 16S/genetics ; *Software ; *Metagenome ; Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {The human microbiome exerts tremendous influence on maintaining a balance between human health and disease. High-throughput sequencing has enabled the study of microbial communities at an unprecedented resolution. Generation of massive amounts of sequencing data has also presented novel challenges to analyzing and visualizing data to make biologically relevant interpretations. We have developed an interactive Metagenome Data Analysis and Visualization (MetaDAVis) tool for 16S rRNA as well as the whole genome sequencing data analysis and visualization to address these challenges using an R Shiny application. MetaDAVis can perform six different types of analyses that include: i) Taxonomic abundance distribution; ii) Alpha and beta diversity analyses; iii) Dimension reduction tasks using PCA, t-SNE, and UMAP; iv) Correlation analysis using taxa- or sample-based data; v) Heatmap generation; and vi) Differential abundance analysis. MetaDAVis creates interactive and dynamic figures and tables from multiple methods enabling users to easily understand their data using different variables. Our program is user-friendly and easily customizable allowing those without any programming background to perform comprehensive data analyses using a standalone or web-based interface.},
}

*Metagenomics/methods
Humans
RNA, Ribosomal, 16S/genetics
*Software
*Metagenome
Microbiota/genetics
High-Throughput Nucleotide Sequencing

@article {pmid40192235,
year = {2025},
author = {Jiao, Y and Ren, J and Xie, S and Yuan, N and Shen, J and Yin, H and Wang, J and Guo, H and Cao, J and Wang, X and Wu, D and Zhou, Z and Qi, X},
title = {Raffinose-metabolizing bacteria impair radiation-associated hematopoietic recovery via the bile acid/FXR/NF-κB signaling pathway.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2488105},
doi = {10.1080/19490976.2025.2488105},
pmid = {40192235},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/radiation effects ; *Bile Acids and Salts/metabolism ; Mice ; *NF-kappa B/metabolism/genetics ; Signal Transduction/radiation effects ; *Raffinose/metabolism ; Mice, Inbred C57BL ; Whole-Body Irradiation/adverse effects ; *Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Fecal Microbiota Transplantation ; Male ; *Acute Radiation Syndrome/microbiology/metabolism ; *Hematopoiesis/radiation effects ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Dysbiosis/microbiology ; },
abstract = {Radiation-associated hematopoietic recovery (RAHR) is critical for mitigating lethal complications of acute radiation syndrome (ARS), yet therapeutic strategies remain limited. Through integrated multi-omics analysis of a total body irradiation (TBI) mouse model, we identify Bacteroides acidifaciens-dominated gut microbiota as key mediators of RAHR impairment. 16S ribosomal rRNA sequencing revealed TBI-induced dysbiosis characterized by Bacteroidaceae enrichment, while functional metagenomics identified raffinose metabolism as the most significantly perturbed pathway. Notably, raffinose supplementation (10% w/v) recapitulated radiation-induced microbiota shifts and delayed bone marrow recovery. Fecal microbiota transplantation (FMT) revealed a causative role for raffinose-metabolizing microbiota, particularly Bacteroides acidifaciens, in delaying RAHR progression. Mechanistically, B. acidifaciens-mediated bile acid deconjugation activated FXR, subsequently suppressing NF-κB-dependent hematopoietic recovery. Therapeutic FXR inhibition via ursodeoxycholic acid (UDCA) had been shown to be a viable method for rescuing RAHR. Our results delineated a microbiome-bile acid-FXR axis as a master regulator of post-irradiation hematopoiesis. Targeting B. acidifaciens or its metabolic derivatives could represent a translatable strategy to mitigate radiation-induced hematopoietic injury.},
}

Animals
*Gastrointestinal Microbiome/radiation effects
*Bile Acids and Salts/metabolism
Mice
*NF-kappa B/metabolism/genetics
Signal Transduction/radiation effects
*Raffinose/metabolism
Mice, Inbred C57BL
Whole-Body Irradiation/adverse effects
*Receptors, Cytoplasmic and Nuclear/metabolism/genetics
Fecal Microbiota Transplantation
Male
*Acute Radiation Syndrome/microbiology/metabolism
*Hematopoiesis/radiation effects
*Bacteria/metabolism/genetics/classification/isolation & purification
Dysbiosis/microbiology

@article {pmid40190795,
year = {2025},
author = {Zhang, Y and Dai, Y and Li, J and Cong, W and Zhang, Y and Nie, X and Wu, Q and Xue, Y},
title = {Climate Change and Human Pressure: Assessing the Vulnerability of Snow Leopard (Panthera uncia) Habitat Integrated With Prey Distribution on the Qinghai-Tibet Plateau.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71232},
pmid = {40190795},
issn = {2045-7758},
abstract = {Climate change is significantly altering the distribution of large carnivores and their primary prey species, with particular emphasis on the changing prey distribution in high-altitude regions. The Qinghai-Tibet Plateau, known for its rich biodiversity, is highly sensitive to climate change, affecting the habitats of snow leopards (Panthera uncia) and blue sheep (Pseudois nayaur). Our study identified blue sheep as the primary prey of snow leopards through metagenomic analysis and used bioclimatic data and Land Use/Cover Change (LUCC) information to model habitat suitability under three climate scenarios (RCP 2.6, RCP 4.5, and RCP 8.5). Projections showed that under RCP 4.5 and RCP 8.5, snow leopard habitats will decrease by 13.0% and 23.4%, while blue sheep habitats will decrease by 38.3% and 49.7%, respectively. These habitats are expected to shift to higher altitudes, with snow leopards experiencing a more significant shift. Based on these findings, we recommend adjusting protected area boundaries for S1 (Ideal distribution range), establishing ecological corridors for S2 (stepping stone), and implementing targeted measures to mitigate human-wildlife conflicts in S3 (potential conflict area). To protect these species, international efforts to reduce carbon emissions, cross-administrative cooperation, and community-based conservation strategies are essential.},
}

@article {pmid40190120,
year = {2025},
author = {Aboulalazm, FA and Kazen, AB and deLeon, O and Müller, S and Saravia, FL and Lozada-Fernandez, V and Hadiono, MA and Keyes, RF and Smith, BC and Kellogg, SL and Grobe, JL and Kindel, TL and Kirby, JR},
title = {Reutericyclin, a specialized metabolite of Limosilactobacillus reuteri, mitigates risperidone-induced weight gain in mice.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2477819},
doi = {10.1080/19490976.2025.2477819},
pmid = {40190120},
issn = {1949-0984},
mesh = {Animals ; *Risperidone/adverse effects ; *Limosilactobacillus reuteri/metabolism ; *Weight Gain/drug effects ; Female ; Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred C57BL ; *Antipsychotic Agents/adverse effects ; Probiotics/administration & dosage ; Feces/microbiology ; Energy Metabolism/drug effects ; Bacteria/classification/genetics/isolation & purification/metabolism ; },
abstract = {The role of xenobiotic disruption of microbiota, corresponding dysbiosis, and potential links to host metabolic diseases are of critical importance. In this study, we used a widely prescribed antipsychotic drug, risperidone, known to influence weight gain in humans, to induce weight gain in C57BL/6J female mice. We hypothesized that microbes essential for maintaining gut homeostasis and energy balance would be depleted following treatment with risperidone, leading to enhanced weight gain relative to controls. Thus, we performed metagenomic analyses on stool samples to identify microbes that were excluded in risperidone-treated animals but remained present in controls. We identified multiple taxa including Limosilactobacillus reuteri as a candidate for further study. Oral supplementation with L. reuteri protected against risperidone-induced weight gain (RIWG) and was dependent on cellular production of a specialized metabolite, reutericyclin. Further, synthetic reutericyclin was sufficient to mitigate RIWG. Both synthetic reutericyclin and L. reuteri restored energy balance in the presence of risperidone to mitigate excess weight gain and induce shifts in the microbiome associated with leanness. In total, our results identify reutericyclin production by L. reuteri as a potential probiotic to restore energy balance induced by risperidone and to promote leanness.},
}

Animals
*Risperidone/adverse effects
*Limosilactobacillus reuteri/metabolism
*Weight Gain/drug effects
Female
Gastrointestinal Microbiome/drug effects
Mice
Mice, Inbred C57BL
*Antipsychotic Agents/adverse effects
Probiotics/administration & dosage
Feces/microbiology
Energy Metabolism/drug effects
Bacteria/classification/genetics/isolation & purification/metabolism

@article {pmid40189749,
year = {2025},
author = {Birebent, R and Drubay, D and Alves Costa Silva, C and Marmorino, F and Vitali, G and Piccinno, G and Hurtado, Y and Bonato, A and Belluomini, L and Messaoudene, M and Routy, B and Fidelle, M and Zalcman, G and Mazieres, J and Audigier-Valette, C and Moro-Sibilot, D and Goldwasser, F and Scherpereel, A and Pegliasco, H and Ghiringhelli, F and Reni, A and Barlesi, F and Albiges, L and Planchard, D and Martinez, S and Besse, B and Segata, N and Cremolini, C and Zitvogel, L and Iebba, V and Derosa, L},
title = {Surrogate markers of intestinal dysfunction associated with survival in advanced cancers.},
journal = {Oncoimmunology},
volume = {14},
number = {1},
pages = {2484880},
doi = {10.1080/2162402X.2025.2484880},
pmid = {40189749},
issn = {2162-402X},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Dysbiosis/microbiology ; Middle Aged ; *Colorectal Neoplasms/mortality/microbiology/pathology ; Aged ; Prognosis ; *Carcinoma, Non-Small-Cell Lung/mortality/microbiology/pathology ; *Lung Neoplasms/mortality/microbiology/pathology ; Akkermansia/isolation & purification ; *Urogenital Neoplasms/mortality/microbiology/pathology ; },
abstract = {Deviations in the diversity and composition of the gut microbiota are called "gut dysbiosis". They have been linked to various chronic diseases including cancers and resistance to immunotherapy. Stool shotgun based-metagenomics informs on the ecological composition of the gut microbiota and the prevalence of homeostatic bacteria such as Akkermansia muciniphila (Akk), while determination of the serum addressin MAdCAM-1 instructs on endothelial gut barrier dysfunction. Here we examined patient survival during chemo-immuno-therapy in 955 cancer patients across four independent cohorts of non-small cell lung (NSCLC), genitourinary (GU) and colorectal (CRC) cancers, according to hallmarks of gut dysbiosis. We show that Akk prevalence represents a stable and favorable phenotype in NSCLC and CRC cancer patients. Over-dominance of Akk above the healthy threshold was observed in dismal prognosis in NSCLC and GU and mirrored an immunosuppressive gut ecosystem and excessive intestinal epithelial exfoliation in NSCLC. In CRC, the combination of a lack of Akk and low sMAdCAM-1 levels identified a subset comprising 28% of patients with reduced survival, independent of the immunoscore. We conclude that gut dysbiosis hallmarks deserve integration within the diagnosis toolbox in oncological practice.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
*Dysbiosis/microbiology
Middle Aged
*Colorectal Neoplasms/mortality/microbiology/pathology
Aged
Prognosis
*Carcinoma, Non-Small-Cell Lung/mortality/microbiology/pathology
*Lung Neoplasms/mortality/microbiology/pathology
Akkermansia/isolation & purification
*Urogenital Neoplasms/mortality/microbiology/pathology

@article {pmid40189708,
year = {2025},
author = {Gen-Jiménez, A and Flores-Félix, JD and Rincón-Molina, CI and Manzano-Gómez, LA and Villalobos-Maldonado, JJ and Ruiz-Lau, N and Roca-Couso, R and Ruíz-Valdiviezo, VM and Rincón-Rosales, R},
title = {Native Rhizobium biofertilization enhances yield and quality in Solanum lycopersicum under field conditions.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {4},
pages = {126},
pmid = {40189708},
issn = {1573-0972},
support = {19337.24-P//Tecnológico Nacional de México/ ; },
mesh = {*Solanum lycopersicum/growth & development/microbiology ; *Rhizobium/physiology ; Soil Microbiology ; *Fertilizers ; Soil/chemistry ; Fruit/growth & development ; Nitrogen/analysis/metabolism ; Microbiota ; Agriculture/methods ; },
abstract = {In response to growing concerns about the environmental and economic impacts of chemical fertilizers, this study explores the potential of biofertilization using native Rhizobium strains to enhance the growth, yield, and quality of Solanum lycopersicum (tomato) under field conditions. The experiment assessed the effects of Rhizobium biofertilization on plant performance and soil microbial communities by applying R. calliandrae, R. jaguaris, R. mayense, and a bacterial consortium, in comparison to conventional chemical fertilization. Key parameters such as plant height, fruit yield, macronutrient and micronutrient content, and fruit quality (lycopene and β-carotene levels) were measured. Results showed that R. calliandrae and R. jaguaris significantly enhanced fruit yield, nitrogen, potassium, manganese, and boron levels, while also improving fruit quality compared to the control. The impact of strain inoculation on the structure of the microbial community was also examined. Metataxonomic analysis of rhizospheric soils revealed no significant changes in microbial diversity, indicating that biofertilization with Rhizobium strains promotes plant growth without disrupting the composition of the soil microbiome. These findings suggest that Rhizobium biofertilization is a viable and sustainable alternative to chemical fertilizers, providing benefits to both crop productivity and soil health while minimizing the environmental footprint associated with conventional agricultural practices. The study underscores the importance of carefully selecting bacterial species with complementary functions to maximize the effectiveness of biofertilization strategies.},
}

*Solanum lycopersicum/growth & development/microbiology
*Rhizobium/physiology
Soil Microbiology
*Fertilizers
Soil/chemistry
Fruit/growth & development
Nitrogen/analysis/metabolism
Microbiota
Agriculture/methods

@article {pmid40147232,
year = {2025},
author = {Wang, J and Ge, Y},
title = {Unveiling the latitudinal dependency of global patterns in soil prokaryotic gene content.},
journal = {The Science of the total environment},
volume = {974},
number = {},
pages = {179224},
doi = {10.1016/j.scitotenv.2025.179224},
pmid = {40147232},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Metagenome ; Soil/chemistry ; Bacteria/genetics ; Microbiota ; },
abstract = {Prokaryotic genomic traits offer insights into their functional roles, evolutionary processes, and ecological interactions, but global patterns in soil microbial genomes remain poorly understood. In this study, we examined 6436 metagenome-assembled genomes (MAGs) from global soil environments to explore the driving factors of prokaryotic gene content. Through random forest analysis, we found that, among numerous potential influencing factors such as climate, soil physicochemical properties, and human activities, geographic latitude was the primary factor affecting prokaryotic gene content. Our results showed a marked decrease in gene content from the tropics to the poles, with polar MAGs containing 10.4 % and 13.3 % fewer genes than those in tropical and temperate zones, respectively. This decline correlates with shifts in key metabolic processes, such as nitrogen fixation and energy conversion. Furthermore, we assessed interspecies metabolic interactions using Metabolic Resource Overlap (MRO) and Metabolic Interaction Potential (MIP) metrics. Our analysis revealed significantly lower MRO in high-latitude microbial communities, yet comparable MIP values to those in lower latitudes, indicating that reduced competition may contribute to genomic streamlining. These findings highlight the significant influence of latitude and interspecies interactions on microbial genomic characteristics, advancing our comprehension of microbial ecological adaptations.},
}

*Soil Microbiology
*Metagenome
Soil/chemistry
Bacteria/genetics
Microbiota

@article {pmid40132505,
year = {2025},
author = {Wang, L and Zhang, W and Yao, J and Qi, Z and Liu, Y and Li, Z and Qu, J and Ma, Y and Zhang, Y},
title = {Effect of freeze-thaw cycle aging on biochar application in DEHP contaminated Mollisols: Insights from soil properties and microbial community.},
journal = {Ecotoxicology and environmental safety},
volume = {294},
number = {},
pages = {118082},
doi = {10.1016/j.ecoenv.2025.118082},
pmid = {40132505},
issn = {1090-2414},
mesh = {*Charcoal/chemistry ; *Soil Microbiology ; *Soil Pollutants/analysis/metabolism ; *Diethylhexyl Phthalate/metabolism/analysis ; Soil/chemistry ; Biodegradation, Environmental ; Freezing ; China ; Microbiota ; *Environmental Restoration and Remediation/methods ; },
abstract = {Biochar holds significant promise for remediation of organic pollutants. However, the impact of biochar on di-(2-ethylhexyl) phthalate (DEHP)-contaminated Mollisols after freeze-thaw cycles is largely unknown, according to the seasonal traits observed at high latitudes. In this study, fresh biochar (BC) was produced from corn straw, and freeze-thaw aging biochar (FBC) was prepared by simulating winter temperatures in the Mollisol region of Northeast China using BC as a precursor. Pot experiments were conducted to evaluate the effects of freeze-thaw aging on the detoxification efficiency of biochar, the improvement of soil physical and chemical properties, and the regulation of soil microbial community structure and functional genes. The results indicated that biochar after freeze-thaw cycling significantly improved the physical and chemical properties of Mollisols compared with the control, reducing DEHP content by 99.08 % after 28 days. Metagenomic sequencing further revealed the presence of microorganisms and genetic elements potentially involved in DEHP degradation in the soil. The treatment group with freeze-thaw aging biochar exhibited higher microbial diversity and abundance, particularly in Proteobacteria, Bacteroides, and Firmicutes. Analysis of the DEHP degradation pathway via benzoic acid route revealed an increase in the abundance of degraded functional genes/enzymes (benC-xylZ, pacL, catB, pcaG, mhpE, and mhpF). The up-regulation of nitrogen fixation genes and nitrification genes (amoB, hao, narG, nifD, and vnfH) along with a 49.19 % increase in soil microbial biomass nitrogen suggested that freeze-thaw aging biochar benefited nitrogen cycling. Furthermore, the feasibility of applying biochar to high-latitude agricultural settings was validated using pakchoi (Brassica rapa L. ssp. chinensis) as a test crop. These findings suggest that the freeze-thaw aging process enhances the effectiveness of biochar in remediating DEHP-contaminated Mollisols. This study offers a novel perspective on the restoration and improvement of Mollisol productivity in high-latitude regions through biochar application.},
}

*Charcoal/chemistry
*Soil Microbiology
*Soil Pollutants/analysis/metabolism
*Diethylhexyl Phthalate/metabolism/analysis
Soil/chemistry
Biodegradation, Environmental
Freezing
China
Microbiota
*Environmental Restoration and Remediation/methods

@article {pmid40057978,
year = {2025},
author = {Jeevannavar, A and Florenza, J and Divne, AM and Tamminen, M and Bertilsson, S},
title = {Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf046},
pmid = {40057978},
issn = {1751-7370},
mesh = {*Microbiota ; Single-Cell Analysis ; Transcriptome ; Gene Expression Profiling ; Photosynthesis ; Bacteria/classification/genetics ; },
abstract = {Single-cell transcriptomics is a key tool for unravelling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with two distinct growth phases: a fast-growing phase and a slow-growing phase. Besides the two expected expression clusters, each corresponding to either growth phase, a third transcriptional state was identified across both growth phases. Metabolic mapping revealed a boost of photosynthetic activity in the fast growth over the slow growth stage, as well as downregulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism characteristic of the third transcriptional state. In addition, carry-over rRNA reads recapitulated the taxonomic identity of the target while revealing distinct bacterial communities, in co-culture with the eukaryote, each associated with distinct transcriptional states. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability to describe the ecological roles of environmental microeukaryotes, culture-free, and reference-free, surpassing alternative methods like metagenomics or metatranscriptomics.},
}

*Microbiota
Single-Cell Analysis
Transcriptome
Gene Expression Profiling
Photosynthesis
Bacteria/classification/genetics

@article {pmid39870396,
year = {2025},
author = {Rytter, H and Naimi, S and Wu, G and Lewis, J and Duquesnoy, M and Vigué, L and Tenaillon, O and Belda, E and Vazquez-Gomez, M and Touly, N and Arnone, D and Hao, F and Ley, RE and Clément, K and Peyrin-Biroulet, L and Patterson, AD and Gewirtz, AT and Chassaing, B},
title = {In vitro microbiota model recapitulates and predicts individualised sensitivity to dietary emulsifier.},
journal = {Gut},
volume = {74},
number = {5},
pages = {761-774},
doi = {10.1136/gutjnl-2024-333925},
pmid = {39870396},
issn = {1468-3288},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Emulsifying Agents/pharmacology/adverse effects ; *Carboxymethylcellulose Sodium/pharmacology/adverse effects ; Animals ; Mice ; Male ; Interleukin-10/genetics ; Female ; },
abstract = {BACKGROUND: Non-absorbed dietary emulsifiers, including carboxymethylcellulose (CMC), directly disturb intestinal microbiota, thereby promoting chronic intestinal inflammation in mice. A randomised controlled-feeding study (Functional Research on Emulsifiers in Humans, FRESH) found that CMC also detrimentally impacts intestinal microbiota in some, but not all, healthy individuals.

OBJECTIVES: This study aimed to establish an approach for predicting an individual's sensitivity to dietary emulsifiers via their baseline microbiota.

DESIGN: We evaluated the ability of an in vitro microbiota model (MiniBioReactor Arrray, MBRA) to reproduce and predict an individual donor's sensitivity to emulsifiers. Metagenomes were analysed to identify signatures of emulsifier sensitivity.

RESULTS: Exposure of human microbiotas, maintained in the MBRA, to CMC recapitulated the differential CMC sensitivity previously observed in FRESH subjects. Furthermore, select FRESH control subjects (ie, not fed CMC) had microbiotas that were highly perturbed by CMC exposure in the MBRA model. CMC-induced microbiota perturbability was associated with a baseline metagenomic signature, suggesting the possibility of using one's metagenome to predict sensitivity to dietary emulsifiers. Transplant of human microbiotas that the MBRA model deemed CMC-sensitive, but not those deemed insensitive, into IL-10[-/-] germfree mice resulted in overt colitis following CMC feeding.

CONCLUSION: These results suggest that an individual's sensitivity to emulsifier is a consequence of, and can thus be predicted by, examining their baseline microbiota, paving the way to microbiota-based personalised nutrition.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Emulsifying Agents/pharmacology/adverse effects
*Carboxymethylcellulose Sodium/pharmacology/adverse effects
Animals
Mice
Male
Interleukin-10/genetics
Female

@article {pmid39870395,
year = {2025},
author = {Nan, K and Zhong, Z and Yue, Y and Shen, Y and Zhang, H and Wang, Z and Zhuma, K and Yu, B and Fu, Y and Wang, L and Sun, X and Qu, M and Chen, Z and Guo, M and Zhang, J and Chu, Y and Liu, R and Miao, C},
title = {Fasting-mimicking diet-enriched Bifidobacterium pseudolongum suppresses colorectal cancer by inducing memory CD8[+] T cells.},
journal = {Gut},
volume = {74},
number = {5},
pages = {775-786},
doi = {10.1136/gutjnl-2024-333020},
pmid = {39870395},
issn = {1468-3288},
mesh = {Animals ; *Colorectal Neoplasms/immunology/diet therapy/microbiology ; Mice ; *CD8-Positive T-Lymphocytes/immunology ; *Gastrointestinal Microbiome/immunology ; *Probiotics ; *Fasting ; *Bifidobacterium ; Immunologic Memory ; Humans ; Disease Models, Animal ; Arginine/metabolism ; Male ; },
abstract = {BACKGROUND: Fasting-mimicking diet (FMD) boosts the antitumour immune response in patients with colorectal cancer (CRC). The gut microbiota is a key host immunity regulator, affecting physiological homeostasis and disease pathogenesis.

OBJECTIVE: We aimed to investigate how FMD protects against CRC via gut microbiota modulation.

DESIGN: We assessed probiotic species enrichment in FMD-treated CRC mice using faecal metagenomic sequencing. The candidate species were verified in antibiotic-treated conventional and germ-free mouse models. Immune landscape alterations were evaluated using single-cell RNA sequencing and multicolour flow cytometry. The microbiota-derived antitumour metabolites were identified using metabolomic profiling.

RESULTS: Faecal metagenomic profiling revealed Bifidobacterium pseudolongum enrichment in FMD-treated CRC mice. B. pseudolongum mediates the FMD antitumour effects by increasing the tissue-resident memory CD8[+] T-cell (TRM) population in CRC mice. The level of L-arginine, a B. pseudolongum functional metabolite, increased in FMD-treated CRC mice; furthermore, L-arginine induced the TRM phenotype in vivo and in vitro. Mechanistically, L-arginine is transported by the solute carrier family 7-member 1 (SLC7A1) receptor in CD8[+] T cells. Both FMD and B. pseudolongum improved anti-CTLA-4 efficacy in the orthotopic mouse CRC model. In FMD-treated patients with CRC, the CD8[+] TRM cell number increased as B. pseudolongum and L-arginine accumulated. The abundance of CD8[+] TRM cells and B. pseudolongum was associated with a better prognosis in patients with CRC.

CONCLUSION: B. pseudolongum contributes to the FMD antitumour effects in CRC by producing L-arginine. This promotes CD8[+] T-cell differentiation into memory cells. B. pseudolongum administration is a potential CRC therapeutic strategy.},
}

Animals
*Colorectal Neoplasms/immunology/diet therapy/microbiology
Mice
*CD8-Positive T-Lymphocytes/immunology
*Gastrointestinal Microbiome/immunology
*Probiotics
*Fasting
*Bifidobacterium
Immunologic Memory
Humans
Disease Models, Animal
Arginine/metabolism
Male

@article {pmid40189564,
year = {2025},
author = {He, Y and Zhuo, S and Li, M and Pan, J and Jiang, Y and Hu, Y and Sanford, RA and Lin, Q and Sun, W and Wei, N and Peng, S and Jiang, Z and Li, S and Li, Y and Dong, Y and Shi, L},
title = {Candidate Phyla Radiation (CPR) bacteria from hyperalkaline ecosystems provide novel insight into their symbiotic lifestyle and ecological implications.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {94},
pmid = {40189564},
issn = {2049-2618},
support = {42472366, 92051111 and 42272353//National Natural Science Foundation of China/ ; 122-G1323522144//Fundamental Research Funds for the Chinese Central Government via China University of Geosciences (Wuhan)/ ; },
mesh = {*Symbiosis ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics/methods ; Metagenome ; Folic Acid/biosynthesis ; Ecosystem ; Phylogeny ; Genome, Bacterial ; *Microbiota ; },
abstract = {BACKGROUND: Candidate Phyla Radiation (CPR) represents a unique superphylum characterized by ultra-small cell size and symbiotic lifestyle. Although CPR bacteria have been identified in varied environments, their broader distribution, associations with hosts, and ecological roles remain largely unexplored. To address these knowledge gaps, a serpentinite-like environment was selected as a simplified model system to investigate the CPR communities in hyperalkaline environments and their association with hosts in extreme conditions. Additionally, the enzymatic activity, global distribution, and evolution of the CPR-derived genes encoding essential metabolites (e.g., folate or vitamin B9) were analyzed and assessed.

RESULTS: In the highly alkaline serpentinite-like ecosystem (pH = 10.9-12.4), metagenomic analyses of the water and sediment samples revealed that CPR bacteria constituted 1.93-34.8% of the microbial communities. Metabolic reconstruction of 12 high-quality CPR metagenome-assembled genomes (MAGs) affiliated to the novel taxa from orders UBA6257, UBA9973, and Paceibacterales suggests that these bacteria lack the complete biosynthetic pathways for amino acids, lipids, and nucleotides. Notably, the CPR bacteria commonly harbored the genes associated with essential folate cofactor biosynthesis and metabolism, including dihydrofolate reductase (folA), serine hydroxymethyltransferase (glyA), and methylenetetrahydrofolate reductase (folD). Additionally, two presumed auxotrophic hosts, incapable of forming tetrahydrofolate (THF) due to the absence of folA, were identified as potential hosts for some CPR bacteria harboring folA genes. The functionality of these CPR-derived folA genes was experimentally verified by heterologous expression in the folA-deletion mutant Escherichia coli MG1655 ΔfolA. Further assessment of the available CPR genomes (n = 4,581) revealed that the genes encoding the proteins for the synthesis of bioactive folate derivatives (e.g., folA, glyA, and/or folD genes) were present in 90.8% of the genomes examined. It suggests potential widespread metabolic complementarity in folate biosynthesis between CPR and their hosts.

CONCLUSIONS: This finding deepens our understanding of the mechanisms of CPR-host symbiosis, providing novel insight into essential cofactor-dependent mutualistic CPR-host interactions. Our observations suggest that CPR bacteria may contribute to auxotrophic organisms and indirectly influence biogeochemical processes. Video Abstract.},
}

*Symbiosis
*Bacteria/genetics/classification/metabolism/isolation & purification
Metagenomics/methods
Metagenome
Folic Acid/biosynthesis
Ecosystem
Phylogeny
Genome, Bacterial
*Microbiota

@article {pmid40189545,
year = {2025},
author = {Serrana, JM and Nascimento, FJA and Dessirier, B and Broman, E and Posselt, M},
title = {Environmental drivers of the resistome across the Baltic Sea.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {92},
pmid = {40189545},
issn = {2049-2618},
mesh = {*Bacteria/genetics/drug effects/classification/isolation & purification ; *Microbiota/genetics ; *Seawater/microbiology ; Oceans and Seas ; *Geologic Sediments/microbiology ; Metagenome ; Salinity ; Anti-Bacterial Agents/pharmacology ; Temperature ; },
abstract = {BACKGROUND: Antimicrobial resistance is a major global health concern, with the environment playing a key role in its emergence and spread. Understanding the relationships between environmental factors, microbial communities, and resistance mechanisms is vital for elucidating environmental resistome dynamics. In this study, we characterized the environmental resistome of the Baltic Sea and evaluated how environmental gradients and spatial variability, alongside its microbial communities and associated functional genes, influence resistome diversity and composition across geographic regions.

RESULTS: We analyzed the metagenomes of benthic sediments from 59 monitoring stations across a 1,150 km distance of the Baltic Sea, revealing an environmental resistome comprised of predicted antimicrobial resistance genes (ARGs) associated with resistance against 26 antibiotic classes. We observed spatial variation in its resistance profile, with higher resistome diversity in the northern regions and a decline in the dead zones and the southern areas. The combined effects of salinity and temperature gradients, alongside nutrient availability, created a complex environmental landscape that shaped the diversity and distribution of the predicted ARGs. Salinity predominantly influenced microbial communities and predicted ARG composition, leading to clear distinctions between high-saline regions and those with lower to mid-level salinity. Furthermore, our analysis suggests that microbial community composition and mobile genetic elements might be crucial in shaping ARG diversity and composition.

CONCLUSIONS: We presented that salinity and temperature were identified as the primary environmental factors influencing resistome diversity and distribution across geographic regions, with nutrient availability further shaping these patterns in the Baltic Sea. Our study also highlighted the interplay between microbial communities, resistance, and associated functional genes in the benthic ecosystem, underscoring the potential role of microbial and mobile genetic element composition in ARG distribution. Understanding how environmental factors and microbial communities modulate environmental resistomes will help predict the impact of future environmental changes on resistance mechanisms in complex aquatic ecosystems. Video Abstract.},
}

*Bacteria/genetics/drug effects/classification/isolation & purification
*Microbiota/genetics
*Seawater/microbiology
Oceans and Seas
*Geologic Sediments/microbiology
Metagenome
Salinity
Anti-Bacterial Agents/pharmacology
Temperature

@article {pmid40187295,
year = {2025},
author = {Coskuner-Weber, O and Alpsoy, S and Yolcu, O and Teber, E and de Marco, A and Shumka, S},
title = {Metagenomics studies in aquaculture systems: Big data analysis, bioinformatics, machine learning and quantum computing.},
journal = {Computational biology and chemistry},
volume = {118},
number = {},
pages = {108444},
doi = {10.1016/j.compbiolchem.2025.108444},
pmid = {40187295},
issn = {1476-928X},
abstract = {The burgeoning field of aquaculture has become a pivotal contributor to global food security and economic growth, presently surpassing capture fisheries in aquatic animal production as evidenced by recent statistics. However, the dense fish populations inherent in aquaculture systems exacerbate abiotic stressors and promote pathogenic spread, posing a risk to sustainability and yield. This study delves into the transformative potential of metagenomics, a method that directly retrieves genetic material from environmental samples, in elucidating microbial dynamics within aquaculture ecosystems. Our findings affirm that metagenomics, bolstered by tools in big data analytics, bioinformatics, and machine learning, can significantly enhance the precision of microbial assessment and pathogen detection. Furthermore, we explore quantum computing's emergent role, which promises unparalleled efficiency in data processing and model construction, poised to address the limitations of conventional computational techniques. Distinct from metabarcoding, metagenomics offers an expansive, unbiased profile of microbial biodiversity, revolutionizing our capacity to monitor, predict, and manage aquaculture systems with high accuracy and adaptability. Despite the challenges of computational demands and variability in data standardization, this study advocates for continued technological integration, thereby fostering resilient and sustainable aquaculture practices in a climate of escalating global food requirements.},
}

@article {pmid40185819,
year = {2025},
author = {Manzoor, M and Leskelä, J and Pietiäinen, M and Martinez-Majander, N and Könönen, E and Sinisalo, J and Putaala, J and Pussinen, PJ and Paju, S},
title = {Oral microbiome dysbiosis in cryptogenic ischemic stroke patients with high-risk patent foramen ovale.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11535},
pmid = {40185819},
issn = {2045-2322},
support = {286246//Research Council of Finland/ ; 340750//Research Council of Finland/ ; 355532//Research Council of Finland/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; },
mesh = {Humans ; *Foramen Ovale, Patent/complications/microbiology ; Female ; Male ; *Ischemic Stroke/microbiology/etiology/complications ; *Dysbiosis/microbiology/complications ; *Microbiota ; Adult ; Middle Aged ; Saliva/microbiology ; Case-Control Studies ; *Mouth/microbiology ; Risk Factors ; },
abstract = {Patent foramen ovale (PFO) is the most common congenital heart abnormality of foetal origin and has been associated with cryptogenic ischemic stroke (CIS) through several mechanisms, with most theories supporting paradoxical embolism. Other possible but unknown contributing factors, such as the role of the microbiome in PFO-associated strokes, remain unclear. We analysed saliva metagenomes to study the differences in the oral microbiome between young-onset CIS patients with clinically relevant high-risk PFO (n = 52) and those without PFO (n = 52). Age- and sex-matched stroke-free controls (n = 16) with high-risk PFO were included for the comparison. Beta diversity was significantly different between patients and controls with high-risk PFO, but not between patients with and without high-risk PFO. The phylum Ascomycota and class Saccharomycetes were significantly more abundant in patients with high-risk PFO than in those without high-risk PFO. Additionally, the abundance of Lactococcus, including Lactococcus raffinolactis and L. cremoris, was higher in controls with high-risk PFO than in patients with high-risk PFO. These findings highlight that oral dysbiosis and high-risk PFO may form a critical but under-recognized combination in the aetiology of CIS. Future research should focus on elucidating the precise mechanisms of these interactions and developing targeted interventions.},
}

Humans
*Foramen Ovale, Patent/complications/microbiology
Female
Male
*Ischemic Stroke/microbiology/etiology/complications
*Dysbiosis/microbiology/complications
*Microbiota
Adult
Middle Aged
Saliva/microbiology
Case-Control Studies
*Mouth/microbiology
Risk Factors

@article {pmid40181255,
year = {2025},
author = {Mohammadzadeh, R and Mahnert, A and Shinde, T and Kumpitsch, C and Weinberger, V and Schmidt, H and Moissl-Eichinger, C},
title = {Age-related dynamics of predominant methanogenic archaea in the human gut microbiome.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {193},
pmid = {40181255},
issn = {1471-2180},
support = {P 32697//Austrian Science Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; Aged ; *Archaea/classification/genetics/metabolism/isolation & purification ; *Methane/metabolism ; Feces/microbiology ; Aged, 80 and over ; Young Adult ; Female ; Male ; *Aging ; Age Factors ; Methanobrevibacter/genetics ; Metagenomics ; Phylogeny ; Bacteria/classification/genetics/metabolism ; },
abstract = {BACKGROUND: The reciprocal relationship between aging and alterations in the gut microbiota is a subject of ongoing research. While the role of bacteria in the gut microbiome is well-documented, specific changes in the composition of methanogens during extreme aging and the impact of high methane production in general on health remain unclear. This study was designed to explore the association of predominant methanogenic archaea within the human gut and aging.

METHODS: Shotgun metagenomic data from the stool samples of young adults (n = 127, Age: 19-59 y), older adults (n = 86, Age: 60-99 y), and centenarians (n = 34, age: 100-109 years) were analyzed.

RESULTS: Our findings reveal a compelling link between age and the prevalence of high methanogen phenotype, while overall archaeal diversity diminishes. Surprisingly, the archaeal composition of methanogens in the microbiome of centenarians appears more akin to that of younger adults, showing an increase in Methanobrevibacter smithii, rather than Candidatus Methanobrevibacter intestini. Remarkably, Ca. M. intestini emerged as a central player in the stability of the archaea-bacteria network in adults, paving the way for M. smithii in older adults and centenarians. Notably, centenarians exhibit a highly complex and stable network of these two methanogens with other bacteria. The mutual exclusion between Lachnospiraceae and these methanogens throughout all age groups suggests that these archaeal communities may compensate for the age-related drop in Lachnospiraceae by co-occurring with Oscillospiraceae.

CONCLUSIONS: This study underscores the dynamics of archaeal microbiome in human physiology and aging. It highlights age-related shifts in methanogen composition, emphasizing the significance of both M. smithii and Ca. M. intestini and their partnership with butyrate-producing bacteria for potential enhanced health.},
}

Humans
*Gastrointestinal Microbiome
Middle Aged
Adult
Aged
*Archaea/classification/genetics/metabolism/isolation & purification
*Methane/metabolism
Feces/microbiology
Aged, 80 and over
Young Adult
Female
Male
*Aging
Age Factors
Methanobrevibacter/genetics
Metagenomics
Phylogeny
Bacteria/classification/genetics/metabolism

@article {pmid39956369,
year = {2025},
author = {Abe, M and Sekizuka, T and Miyazaki, Y},
title = {Gastrointestinal anaerobes and Enterococcus faecalis promote Candida glabrata gastrointestinal colonization and organ dissemination.},
journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy},
volume = {31},
number = {4},
pages = {102658},
doi = {10.1016/j.jiac.2025.102658},
pmid = {39956369},
issn = {1437-7780},
mesh = {*Candida glabrata/isolation & purification/pathogenicity ; Animals ; Mice ; *Candidiasis/microbiology/immunology ; *Gastrointestinal Microbiome ; *Enterococcus faecalis/isolation & purification ; *Gastrointestinal Tract/microbiology ; Coinfection/microbiology ; Disease Models, Animal ; Dysbiosis/microbiology ; *Bacteria, Anaerobic/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Female ; Metagenomics ; },
abstract = {BACKGROUND: Candida glabrata is a common causative pathogen of endogenous candidiasis. It is assumed that the gastrointestinal flora affects C. glabrata gastrointestinal colonization and organ dissemination in the gastrointestinal tract (GIT). However, no reports have yet described the relationships between C. glabrata and bacteria in the GIT. This study aimed to clarify these relationships using a mouse endogenous candidiasis model with cortisone acetate immunosuppression.

METHODS: Dysbiosis was induced in the GIT by several antibiotic combinations, and then C. glabrata gastrointestinal colonization and organ dissemination were evaluated. Next, metagenomic sequencing analysis of the gastrointestinal flora was performed to identify bacteria associated with C. glabrata organ dissemination. Finally, coinfection experiments were performed using bacteria isolated from the mouse GIT.

RESULTS: C. glabrata organ dissemination was significantly promoted using specific antibiotics regardless of the amount of colonization in the GIT. Metagenomic sequencing analysis of the gastrointestinal flora showed that Enterococcus species and anaerobes were significantly associated with enhanced organ dissemination, whereas Enterobacterales, such as Escherichia species and Klebsiella species, were associated with the suppression of organ dissemination. In coinfection experiments, Enterococcus faecalis and Faecalibaculum rodentium inoculation, but not either of them, increased C. glabrata organ dissemination without affecting gastrointestinal colonization.

CONCLUSIONS: Coinfection with gastrointestinal bacteria promoted C. glabrata organ dissemination, which would indicate that gastrointestinal flora could affect C. glabrata dissemination. Therefore, the gastrointestinal flora could be a target for intervention or treatment in clinical settings. Insights from this study would lead to better control of endogenous candidiasis focusing on the gastrointestinal flora.},
}

*Candida glabrata/isolation & purification/pathogenicity
Animals
Mice
*Candidiasis/microbiology/immunology
*Gastrointestinal Microbiome
*Enterococcus faecalis/isolation & purification
*Gastrointestinal Tract/microbiology
Coinfection/microbiology
Disease Models, Animal
Dysbiosis/microbiology
*Bacteria, Anaerobic/isolation & purification
Anti-Bacterial Agents/pharmacology
Female
Metagenomics

@article {pmid39798925,
year = {2025},
author = {Aleksandrova, RR and Nieuwenhuis, LM and Karmi, N and Zhang, S and Swarte, JC and Björk, JR and Gacesa, R and Blokzijl, H and Connelly, MA and Weersma, RK and Lisman, T and Festen, EAM and de Meijer, VE and , },
title = {Gut microbiome dysbiosis is not associated with portal vein thrombosis in patients with end-stage liver disease: a cross-sectional study.},
journal = {Journal of thrombosis and haemostasis : JTH},
volume = {23},
number = {4},
pages = {1407-1415},
doi = {10.1016/j.jtha.2024.12.036},
pmid = {39798925},
issn = {1538-7836},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis ; *Portal Vein ; Male ; Female ; Middle Aged ; Cross-Sectional Studies ; *Venous Thrombosis/microbiology/blood/diagnosis ; Methylamines/blood ; Feces/microbiology ; *End Stage Liver Disease/microbiology/complications/diagnosis/blood ; Case-Control Studies ; Aged ; Adult ; *Bacteria/classification/metabolism/genetics ; },
abstract = {BACKGROUND: Portal vein thrombosis (PVT) is a common complication in patients with end-stage liver disease (ESLD). The portal vein in patients with ESLD is proposedly an inflammatory vascular bed due to translocation of endotoxins and cytokines from the gut. We hypothesized that a proinflammatory gut microbiome and elevated trimethylamine N-oxide (TMAO), a driver of thrombosis, may contribute to PVT development.

OBJECTIVES: We investigated whether gut microbiome diversity, bacterial species, metabolic pathways, and TMAO levels are associated with PVT in patients with ESLD.

METHODS: Fecal samples, plasma samples, and data from patients with ESLD and healthy controls were collected through the TransplantLines Biobank and Cohort Study. PVT was defined as a thrombus in the portal vein within a year prior to or after fecal sample collection. Fecal samples were analyzed using Shotgun Metagenomic Sequencing, and TMAO levels were measured in plasma using a Vantera Clinical Analyzer.

RESULTS: One hundred two patients with ESLD, of which 23 with PVT, and 246 healthy controls were included. No significant difference in gut microbiome diversity was found between patients with PVT and without PVT (P = .18). Both ESLD groups had significantly lower alpha diversity than controls. Bacteroides fragilis and 3 Clostridiales species were increased in patients with PVT compared with without PVT. TMAO levels between the 3 groups were not significantly different.

CONCLUSION: We observed profound differences in gut microbiota between patients with ESLD and controls, but minimal differences between patients with ESLD with or without PVT. In our cohort, a gut-derived proinflammatory state was not associated with presence of PVT in patients with ESLD.},
}

Humans
*Gastrointestinal Microbiome
*Dysbiosis
*Portal Vein
Male
Female
Middle Aged
Cross-Sectional Studies
*Venous Thrombosis/microbiology/blood/diagnosis
Methylamines/blood
Feces/microbiology
*End Stage Liver Disease/microbiology/complications/diagnosis/blood
Case-Control Studies
Aged
Adult
*Bacteria/classification/metabolism/genetics

@article {pmid40180917,
year = {2025},
author = {Schmitz, MA and Dimonaco, NJ and Clavel, T and Hitch, TCA},
title = {Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3204},
pmid = {40180917},
issn = {2041-1723},
support = {460129525//Massachusetts Department of Fish and Game (DFG)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Metagenomics/methods ; *Bacterial Proteins/genetics/metabolism ; *Bacteria/genetics/classification/metabolism ; Phylogeny ; Computational Biology/methods ; },
abstract = {Microbes use a range of genetic codes and gene structures, yet these are often ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on the taxonomic assignment of genetic fragments, removes incomplete protein predictions, and optimises prediction of small proteins. Applied to 9634 metagenomes and 3594 genomes from the human gut, this approach increased the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimised small protein prediction captured 3,772,658 small protein clusters, which form an improved microbial protein catalogue of the human gut (MiProGut). To enable the ecological study of a protein's prevalence and association with host parameters, we developed InvestiGUT, a tool which integrates both the protein sequences and sample metadata. Accurate prediction of proteins is critical to providing a functional understanding of microbiomes, enhancing our ability to study interactions between microbes and hosts.},
}

Humans
*Gastrointestinal Microbiome/genetics
Metagenome/genetics
*Metagenomics/methods
*Bacterial Proteins/genetics/metabolism
*Bacteria/genetics/classification/metabolism
Phylogeny
Computational Biology/methods

@article {pmid39930907,
year = {2025},
author = {Doorenspleet, K and Jansen, L and Oosterbroek, S and Kamermans, P and Bos, O and Wurz, E and Murk, A and Nijland, R},
title = {The Long and the Short of It: Nanopore-Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species-Level Assignment Depend on Amplicon Lengths.},
journal = {Molecular ecology resources},
volume = {25},
number = {4},
pages = {e14079},
doi = {10.1111/1755-0998.14079},
pmid = {39930907},
issn = {1755-0998},
support = {//European Regional Development Fund Interreg North Sea region GEANS/ ; TEWZ118017//Rijksdienst voor Ondernemend Nederland/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; North Sea ; *Vertebrates/classification/genetics ; *Aquatic Organisms/classification/genetics ; DNA Primers/genetics ; Biodiversity ; *Nanopore Sequencing/methods ; *Metagenomics/methods ; *DNA, Environmental/genetics ; Fishes/genetics/classification ; Sequence Analysis, DNA ; DNA, Mitochondrial/genetics ; },
abstract = {To monitor the effect of nature restoration projects in North Sea ecosystems, accurate and intensive biodiversity assessments are vital. DNA-based techniques and especially environmental (e)DNA metabarcoding is becoming a powerful monitoring tool. However, current approaches rely on genetic target regions under 500 bp, offering limited taxonomic resolution. We developed a method for long-read eDNA metabarcoding, using Nanopore sequencing of a longer amplicon and present DECONA, a read processing pipeline to enable improved identification of marine vertebrate species. We designed a universal primer pair targeting a 2 kb region of fish mitochondrial DNA and compared it to the commonly used MiFish primer pair targeting a ~ 170 bp region. In silico testing showed that 2 kb fragments improved accurate identification of closely related species. Analysing eDNA from a North Sea aquarium showed that sequences from both primer pairs could be assigned to most species, and additional species level assignments could be made through the 2 kb primer pair. Interestingly, this difference was opposite in eDNA from the North Sea, where not the 2 kb but the MiFish primer pair detected more species. This study demonstrates the feasibility of using long-read metabarcoding for eDNA vertebrate biodiversity assessments. However, our findings suggests that longer fragments are less abundant in environmental settings, but not in aquarium settings, suggesting that longer fragments may provide a more recent snapshot of the community. Thus, long-read metabarcoding can expand the molecular toolbox for biodiversity assessments by improving species-level identification and may be especially useful when the temporal origin of the eDNA signal is better understood.},
}

Animals
*DNA Barcoding, Taxonomic/methods
North Sea
*Vertebrates/classification/genetics
*Aquatic Organisms/classification/genetics
DNA Primers/genetics
Biodiversity
*Nanopore Sequencing/methods
*Metagenomics/methods
*DNA, Environmental/genetics
Fishes/genetics/classification
Sequence Analysis, DNA
DNA, Mitochondrial/genetics

@article {pmid40180909,
year = {2025},
author = {Bedarf, JR and Romano, S and Heinzmann, SS and Duncan, A and Traka, MH and Ng, D and Segovia-Lizano, D and Simon, MC and Narbad, A and Wüllner, U and Hildebrand, F},
title = {A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson's Disease.},
journal = {NPJ Parkinson's disease},
volume = {11},
number = {1},
pages = {66},
pmid = {40180909},
issn = {2373-8057},
support = {BB/CCG2260/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
abstract = {Current treatment of Parkinson's Disease (PD) remains symptomatic, and disease-modifying approaches are urgently required. A promising approach is to modify intestinal microbiota and key metabolites of bacterial fermentation: short-chain fatty acids (SCFA), which are decreased in PD. A prospective, controlled pilot study (DRKS00034528) was conducted on 11 couples (PD patient plus healthy spouse as control (CO)). Participants followed a 4-week diet rich in dietary fibre, including intake of the prebiotic Lactulose. Gut metagenomes, faecal and urinary metabolites, and clinical characteristics were assessed. The dietary intervention significantly augmented faecal SCFA and increased Bifidobacteria spp., reducing PD-related gastrointestinal symptoms. The pre-existing bacterial dysbiosis in PD (depletion of Blautia, Dorea, Erysipelatoclostridium) persisted. Bacterial metabolite composition in faeces and urine positively changed with the intervention: Brain-relevant gut metabolic functions involved in neuroprotective and antioxidant pathways, including S-adenosyl methionine, glutathione, and inositol, improved in PD. These promising results warrant further investigation in larger cohorts.},
}

@article {pmid40178526,
year = {2025},
author = {Contreras-de la Rosa, PA and De la Torre-Zavala, S and O Connor-Sánchez, A and Prieto-Davó, A and Góngora-Castillo, EB},
title = {Exploring the microbial communities in coastal cenote and their hidden biotechnological potential.},
journal = {Microbial genomics},
volume = {11},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001382},
pmid = {40178526},
issn = {2057-5858},
mesh = {*Archaea/genetics/classification/metabolism/isolation & purification ; *Bacteria/genetics/classification/metabolism ; Biotechnology ; Secondary Metabolism/genetics ; Metagenomics/methods ; *Geologic Sediments/microbiology ; Multigene Family ; Polyketide Synthases/genetics ; *Microbiota/genetics ; Phylogeny ; },
abstract = {Bacterial secondary metabolites are crucial bioactive compounds with significant therapeutic potential, playing key roles in ecological processes and the discovery of novel antimicrobial agents and natural products. Cenotes, as extreme environments, harbour untapped microbial diversity and hold an interesting potential as sources of novel secondary metabolites. While research has focused on the fauna and flora of cenotes, the study of their microbial communities and their biosynthetic capabilities remains limited. Advances in metagenomics and genome sequencing have greatly improved the capacity to explore these communities and their metabolites. In this study, we analysed the microbial diversity and biotechnological potential of micro-organisms inhabiting sediments from a coastal cenote. Metagenomic analyses revealed a rich diversity of bacterial and archaeal communities, containing several novel biosynthetic gene clusters (BGCs) linked to secondary metabolite production. Notably, polyketide synthase BGCs, including those encoding ladderanes and aryl-polyenes, were identified. Bioinformatics analyses of these pathways suggest the presence of compounds with potential industrial and pharmaceutical applications. These findings highlight the biotechnological value of cenotes as reservoirs of secondary metabolites. The study and conservation of these ecosystems are essential to facilitate the discovery of new bioactive compounds that could benefit various industries.},
}

*Archaea/genetics/classification/metabolism/isolation & purification
*Bacteria/genetics/classification/metabolism
Biotechnology
Secondary Metabolism/genetics
Metagenomics/methods
*Geologic Sediments/microbiology
Multigene Family
Polyketide Synthases/genetics
*Microbiota/genetics
Phylogeny

@article {pmid40177264,
year = {2025},
author = {Kananen, K and Veseli, I and Quiles Pérez, CJ and Miller, SE and Eren, AM and Bradley, PH},
title = {Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf039},
doi = {10.1093/bioadv/vbaf039},
pmid = {40177264},
issn = {2635-0041},
abstract = {MOTIVATION: Gene function annotation in microbial genomes and metagenomes is a fundamental in silico first step toward understanding metabolic potential and determinants of fitness. The Kyoto Encyclopedia of Genes and Genomes publishes a curated list of profile hidden Markov models to identify orthologous gene families (KOfams) with roles in metabolism. However, the computational tools that rely upon KOfams yield different annotations for the same set of genomes, leading to different downstream biological inferences.

RESULTS: Here, we apply three open-source software tools that can annotate KOfams to genomes of phylogenetically diverse bacterial families from host-associated and free-living biomes. We use multiple computational approaches to benchmark these methods and investigate individual case studies where they differ. Our results show that despite their fundamental similarities, these methods have different annotation rates and quality. In particular, a method that adaptively tunes sequence similarity thresholds substantially improves sensitivity while maintaining high accuracy. We observe particularly large improvements for protein families with few reference sequences, or when annotating genomes from nonmodel organisms (such as gut-dwelling Lachnospiraceae). Our findings show that small improvements in annotation workflows can maximize the utility of existing databases and meaningfully improve in silico characterizations of microbial metabolism.

Anvi'o is available at https://anvio.org under the GNU GPL license. Scripts and workflow are available at https://github.com/pbradleylab/2023-anvio-comparison under the MIT license.},
}

@article {pmid40176190,
year = {2025},
author = {Xing, J and Niu, T and Yu, T and Zou, B and Shi, C and Wang, Y and Fan, S and Li, M and Bao, M and Sun, Y and Gao, K and Qiu, J and Zhang, D and Wang, N and Jiang, Y and Huang, H and Cao, X and Zeng, Y and Wang, J and Zhang, S and Hu, J and Zhang, D and Sun, W and Yang, G and Yang, W and Wang, C},
title = {Faecalibacterium prausnitzii-derived outer membrane vesicles reprogram gut microbiota metabolism to alleviate Porcine Epidemic Diarrhea Virus infection.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {90},
pmid = {40176190},
issn = {2049-2618},
support = {U21A20261//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Swine ; *Porcine epidemic diarrhea virus/physiology ; *Gastrointestinal Microbiome ; *Swine Diseases/virology/microbiology ; *Faecalibacterium prausnitzii/metabolism/physiology ; *Coronavirus Infections/veterinary/virology/microbiology ; Probiotics/administration & dosage ; Feces/microbiology ; *Bacterial Outer Membrane/metabolism ; },
abstract = {BACKGROUND: The Porcine Epidemic Diarrhea Virus (PEDV) is one of the major challenges facing the global pig farming industry, and vaccines and treatments have proven difficult in controlling its spread. Faecalibacterium prausnitzii (F.prausnitzii), a key commensal bacterium in the gut, has been recognized as a promising candidate for next-generation probiotics due to its potential wide-ranging health benefits. A decrease in F.prausnitzii abundance has been associated with certain viral infections, suggesting its potential application in preventing intestinal viral infections. In this study, we utilized a piglet model to examine the potential role of F.prausnitzii in PEDV infections.

RESULTS: A piglet model of PEDV infection was established and supplemented with F.prausnitzii, revealing that F.prausnitzii mitigated PEDV infection. Further studies found that outer membrane vesicles (OMVs) are the main functional components of F.prausnitzii, and proteomics, untargeted metabolomics, and small RNA-seq were used to analyze the composition of OMVs. Exhaustion of the gut microbiota demonstrated that the function of Fp. OMVs relies on the presence of the gut microbiota. Additionally, metagenomic analysis indicated that Fp. OMVs altered the gut microbiota composition, enhancing the abundance of Faecalibacterium prausnitzii, Prevotellamassilia timonensis, and Limosilactobacillus reuteri. Untargeted metabolomics analysis showed that Fp. OMVs increased phosphatidylcholine (PC) levels, with PC identified as a key metabolite in alleviating PEDV infection. Single-cell sequencing revealed that PC altered the relative abundance of intestinal cells, increased the number of intestinal epithelial cells, and reduced necroptosis in target cells. PC treatment in infected IPEC-J2 and Vero cells alleviated necroptosis and reduced the activation of the RIPK1-RIPK3-MLKL signaling axis, thereby improving PEDV infection.

CONCLUSION: F.prausnitzii and its OMVs play a critical role in mitigating PEDV infections. These findings provide a promising strategy to ameliorate PEDV infection in piglets. Video Abstract.},
}

Animals
Swine
*Porcine epidemic diarrhea virus/physiology
*Gastrointestinal Microbiome
*Swine Diseases/virology/microbiology
*Faecalibacterium prausnitzii/metabolism/physiology
*Coronavirus Infections/veterinary/virology/microbiology
Probiotics/administration & dosage
Feces/microbiology
*Bacterial Outer Membrane/metabolism

@article {pmid40176137,
year = {2025},
author = {Sommer, F and Bernardes, JP and Best, L and Sommer, N and Hamm, J and Messner, B and López-Agudelo, VA and Fazio, A and Marinos, G and Kadibalban, AS and Ito, G and Falk-Paulsen, M and Kaleta, C and Rosenstiel, P},
title = {Life-long microbiome rejuvenation improves intestinal barrier function and inflammaging in mice.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {91},
pmid = {40176137},
issn = {2049-2618},
support = {SO1141/10-1//Deutsche Forschungsgemeinschaft/ ; CRC1182//Deutsche Forschungsgemeinschaft/ ; miTARGET//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; RNA, Ribosomal, 16S/genetics ; *Fecal Microbiota Transplantation ; *Aging/physiology ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; *Intestinal Mucosa/microbiology/metabolism ; *Inflammation/microbiology ; Mice, Inbred C57BL ; *Rejuvenation ; Permeability ; *Intestines/microbiology ; Metagenomics ; Intestinal Barrier Function ; },
abstract = {BACKGROUND: Alterations in the composition and function of the intestinal microbiota have been observed in organismal aging across a broad spectrum of animal phyla. Recent findings, which have been derived mostly in simple animal models, have even established a causal relationship between age-related microbial shifts and lifespan, suggesting microbiota-directed interventions as a potential tool to decelerate aging processes. To test whether a life-long microbiome rejuvenation strategy could delay or even prevent aging in non-ruminant mammals, we performed recurrent fecal microbial transfer (FMT) in mice throughout life. Transfer material was either derived from 8-week-old mice (young microbiome, yMB) or from animals of the same age as the recipients (isochronic microbiome, iMB) as control. Motor coordination and strength were analyzed by rotarod and grip strength tests, intestinal barrier function by serum LAL assay, transcriptional responses by single-cell RNA sequencing, and fecal microbial community properties by 16S rRNA gene profiling and metagenomics.

RESULTS: Colonization with yMB improved coordination and intestinal permeability compared to iMB. yMB encoded fewer pro-inflammatory factors and altered metabolic pathways favoring oxidative phosphorylation. Ecological interactions among bacteria in yMB were more antagonistic than in iMB implying more stable microbiome communities. Single-cell RNA sequencing analysis of intestinal mucosa revealed a salient shift of cellular phenotypes in the yMB group with markedly increased ATP synthesis and mitochondrial pathways as well as a decrease of age-dependent mesenchymal hallmark transcripts in enterocytes and TA cells, but reduced inflammatory signaling in macrophages.

CONCLUSIONS: Taken together, we demonstrate that life-long and repeated transfer of microbiota material from young mice improved age-related processes including coordinative ability (rotarod), intestinal permeability, and both metabolic and inflammatory profiles mainly of macrophages but also of other immune cells. Video Abstract.},
}

Animals
*Gastrointestinal Microbiome/physiology
Mice
RNA, Ribosomal, 16S/genetics
*Fecal Microbiota Transplantation
*Aging/physiology
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Male
*Intestinal Mucosa/microbiology/metabolism
*Inflammation/microbiology
Mice, Inbred C57BL
*Rejuvenation
Permeability
*Intestines/microbiology
Metagenomics
Intestinal Barrier Function

@article {pmid40175903,
year = {2025},
author = {Cao, L and Sun, H and Xu, Z and Xu, X and Shi, G and Zhang, J and Liang, C and Li, T and Liu, C and Wang, M and Tian, S and Li, E},
title = {Metagenomic and physicochemical profiling reveal microbial functions in pit mud for Jiang-Nong Jianxiang Baijiu fermentation.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {190},
pmid = {40175903},
issn = {1471-2180},
mesh = {*Fermentation ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation & purification ; China ; Food Microbiology ; *Metagenome ; Microbiota ; *Alcoholic Beverages/microbiology ; },
abstract = {BACKGROUND: The unique flavour and quality of Baijiu, a treasure of traditional Chinese culture, has attracted increasing attention. The pit mud is a key component for forming the unique flavour styles of different Baijiu brands. Hence, conducting in-depth research on the microbial colonies present in pit mud is paramount for enhancing the intricate bouquets of Baijiu flavours.

RESULTS: This study conducts a comprehensive metagenomic examination of the microbial ecosystem within Chinese Jiang-Nong Jianxiang Baijiu fermentation pit mud. Within the pit mud walls, six prominent species, each accounting for more than 1% of the average relative abundance, emerged as key contributors: Lentilactobacillus buchneri, Secundilactobacillus silagincola, Clostridium tyrobutyricum, Lentilactobacillus parafarraginis, Ligilactobacillus acidipiscis, and Lactobacillus acetotolerans. Conversely, at the pit mud bases, four species surpassed this threshold: Petrimonas sp. IBARAKI, Methanosarcina barkeri, Methanofollis ethanolicus, and Proteiniphilum propionicum. Notably, the abundance of Clostridium in the pit mud walls impart superior saccharifying capabilities compared with those at the bases. The consistently high relative abundance of enzymes belonging to the glycoside hydrolases (GHs), glycosyltransferases (GTs), and carbohydrate-binding modules (CBMs) across both the pit mud walls and the bases highlight their importance in fermentation.

CONCLUSIONS: The microbial composition analysis results underscore the important role of pit mud microorganisms in facilitating starch saccharification, ethyl caproate and ethyl butyrate production, among other aromatic compounds. Microbes residing in the pit mud walls may be exhibited a heightened propensity for lactic acid generation, whereas those inhabiting the bases may be displayed a stronger inclination towards caproic acid production. This research serves as a valuable reference for future endeavours aimed at harnessing microbial resources to refine and optimize Baijiu fermentation methodologies.},
}

*Fermentation
*Metagenomics/methods
*Bacteria/genetics/classification/metabolism/isolation & purification
China
Food Microbiology
*Metagenome
Microbiota
*Alcoholic Beverages/microbiology

@article {pmid40175854,
year = {2025},
author = {Abuzahrah, SS},
title = {Exploring the microorganisms biodiversity associated with sponge species in the red sea through 18S ribosomal RNA gene sequencing.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {60},
pmid = {40175854},
issn = {2191-0855},
abstract = {Around the world, sponges play a significant role in marine ecosystems, and a wide variety of sponge species can be found in the coast of Red Sea of Saudi Arabia. The unique environmental conditions of the Red Sea, including warm, oligotrophic water and high salinity, have encouraged the growth of abundant sponge fauna. Our study aims to investigate the biodiversity, taxonomic composition, and phylogenetic relationships of eukaryotic organisms linked with sponges in the Red Sea off the coast of Saudi Arabia and infer the possible ecological roles and functional contributions of the identified eukaryotic taxa to sponge health and ecosystem functioning. The study investigated the microbial diversity, focusing on the genera Hyalosynedra sp., Navicula sp., Papiliocellulus sp., Psammodictyon sp., Pynococcus sp., Ostreococcus sp., Micromonas sp., and other unclassified species. Our metagenomic analysis and phylogenetic evaluation revealed a deep and diverse microbial community, with each genus performing significant ecological roles, including nutrient cycling, primary production, and contributing to marine food networks. Moreover, these genera display promising biotechnological prospects, including uses in bioremediation, biofuel production, and the synthesis of high-value biomolecules. Comparative analysis with other marine regions has focused on both the similarities and unique aspects of the Red Sea microbial community, which are influenced by its distinct environmental conditions. The gained findings contribute to a deeper understanding of the ecological dynamics in the Red Sea and open new avenues for biotechnological exploration in marine ecosystems.},
}

@article {pmid40175647,
year = {2025},
author = {Ahn, JS and Kim, S and Han, EJ and Hong, ST and Chung, HJ},
title = {Increasing spatial working memory in mice with Akkermansia muciniphila.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {546},
pmid = {40175647},
issn = {2399-3642},
support = {C512230//Korea Basic Science Institute (KBSI)/ ; RS-2023-00224099//National Research Foundation of Korea (NRF)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred C57BL ; *Fecal Microbiota Transplantation ; *Memory, Short-Term/physiology ; Male ; *Spatial Memory/physiology ; Akkermansia ; Humans ; Verrucomicrobia ; Feces/microbiology ; Brain-Derived Neurotrophic Factor/metabolism ; },
abstract = {Recent research has shown the gut microbiome's impact on memory, yet limitations hinder the identification of specific microbes linked to cognitive function. We measured spatial working memory in individual mice before and after fecal microbiota transplantation (FMT) to develop a targeted analysis that identifies memory-associated strains while minimizing host genetic effects. Transplantation of human fecal into C57BL/6 mice yielded varied outcomes: some mice showed significant improvements while others had negligible changes, indicating that these changes are due to differences in FMT colonization. Metagenomic analysis, stratified by memory performance, revealed a positive correlation between the abundance of Akkermansia muciniphila and improved memory. Moreover, administering two A. muciniphila strains, GMB 0476 and GMB 2066, to wild-type mice elevated spatial working memory via BDNF activation. Our findings indicate that specific gut microbes, particularly A. muciniphila, may modulate memory and represent potential targets for therapeutic intervention in cognitive enhancement.},
}