@article {pmid40640500,
year = {2025},
author = {Chen, C and Chen, C and Zheng, X and Wang, W and Shen, J and Jin, G and Lyu, J and Lin, L},
title = {Prediction model based on gut microbiota as a non-invasive tool for gastric cancer diagnosis.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {166},
pmid = {40640500},
issn = {1432-0614},
support = {U22A20342//Joint Funds of the National Natural Science Foundation of China/ ; U22A20342//Joint Funds of the National Natural Science Foundation of China/ ; U22A20342//Joint Funds of the National Natural Science Foundation of China/ ; U22A20342//Joint Funds of the National Natural Science Foundation of China/ ; U22A20342//Joint Funds of the National Natural Science Foundation of China/ ; U22A20342//Joint Funds of the National Natural Science Foundation of China/ ; U22A20342//Joint Funds of the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Stomach Neoplasms/diagnosis/microbiology ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Biomarkers, Tumor/analysis ; Female ; Middle Aged ; Male ; Aged ; Bacteria/classification/genetics/isolation & purification ; ROC Curve ; Adult ; },
abstract = {Gastric cancer (GC) is a malignant cancer of the digestive tract with high morbidity and mortality. Previous studies have shown that current diagnostic methods largely rely on invasive procedures. Moreover, there are no highly sensitive and accurate biomarkers available for early GC diagnosis. Recent studies using 16S rRNA technology show that gut microbiota can differentiate between diseased and healthy individuals. However, fewer studies emphasize the gut microbiome's value in GC diagnosis. In this study, we collected 455 fecal samples, including 100 from healthy individuals (healthy controls [HCs]), 153 from GC patients, 43 from patients with non-neoplastic diseases of the stomach, and 159 from verification individuals. Our analysis revealed a significantly increased microbial richness in the GC group (Chao1 index, P < 0.05) and distinct compositional differences (principal coordinates analysis). Linear discriminant analysis effect size analysis identified 19 HC-enriched genera (e.g., Bacteroides) and 31 GC-enriched genera (e.g., Streptococcus). The random forest model selected 20 key diagnostic genera, achieving an area under the receiver operating characteristic curve (AUC) of 0.81. By integrating 10 tumor biomarkers, the combined diagnostic model improved the AUC to 0.86 (validation set: 0.84). Tumor biomarker positivity (60.78%) did not directly correlate with microbiota, but the microbiota-biomarker model improved non-invasive diagnostic accuracy, providing a new approach for early GC screening. KEY POINTS: • Changchang Chen and Chen Chen contributed equally to this work • Gut microbiota changes significantly in gastric cancer • Microbiome shows promise as non-invasive diagnostic markers • The combined microbiota-tumor marker model improves diagnosis.},
}

Humans
*Gastrointestinal Microbiome
*Stomach Neoplasms/diagnosis/microbiology
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Biomarkers, Tumor/analysis
Female
Middle Aged
Male
Aged
Bacteria/classification/genetics/isolation & purification
ROC Curve
Adult

@article {pmid40640466,
year = {2025},
author = {Peng, K and Liu, L and Gao, S},
title = {Harnessing microbial nanobiotics: Lactobacillus extracellular vesicles as next-generation therapeutics across physiological systems.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {7},
pages = {261},
pmid = {40640466},
issn = {1573-0972},
mesh = {*Extracellular Vesicles/metabolism/chemistry ; Humans ; *Lactobacillus/metabolism/chemistry ; Animals ; },
abstract = {Lactobacillus-derived extracellular vesicles (LEVs) are emerging as pivotal mediators of interkingdom communication, carrying strain-specific bioactive cargo that influences diverse physiological systems, including the gut, nervous, respiratory, reproductive, and integumentary systems. These nanoscale structures demonstrate significant therapeutic potential, modulating host immunity, enhancing barrier integrity, combating pathogens, and contributing to tissue repair across numerous health contexts. However, realizing their full clinical and biotechnological promise faces substantial hurdles. Key challenges include variability in isolation and purification methods, inconsistencies in LEV yield and composition due to cultivation conditions and inherent strain differences, and the observation of context-dependent or even paradoxical effects in certain diseases. Furthermore, gaps persist in understanding their precise biogenesis, cargo sorting mechanisms, and long-term biodistribution. Future progress necessitates interdisciplinary efforts to standardize production and characterization, resolve mechanistic ambiguities, and develop robust bioengineering strategies for targeted delivery and enhanced functionality. Addressing these obstacles is crucial to harness LEVs effectively as versatile tools in precision medicine, microbiome engineering, and sustainable applications in health and industry.},
}

*Extracellular Vesicles/metabolism/chemistry
Humans
*Lactobacillus/metabolism/chemistry
Animals

@article {pmid40640325,
year = {2025},
author = {Sekiya, N and Mae, A and Murai, A and Peter, MA and Goto, M and Kato, H and Ichikawa, S and Watanabe, K},
title = {Soil microbes and organic fertilizer efficiency are associated with rice field topography.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24939},
pmid = {40640325},
issn = {2045-2322},
mesh = {*Oryza/growth & development/microbiology ; *Fertilizers/analysis ; *Soil Microbiology ; Nitrogen/metabolism ; Microbiota ; Soil/chemistry ; Agriculture/methods ; Biomass ; Japan ; Bacteria/genetics/metabolism/classification ; },
abstract = {Organic rice (Oryza sativa L.) cultivation represents a pathway toward sustainable agriculture. Soil microbial communities vary with topographic features, potentially affecting organic fertilizer efficiency and crop productivity, yet the relationship between topography, soil microbes, and fertilizer performance in rice farming remains largely unexplored. On-farm trials were conducted at two locations with contrasting topography (valley bottom vs. hillslope) in Yosano Town, Japan, comparing rice plant nitrogen uptake, biomass production, and grain yields under organic fertilizer management. Soil incubation experiments and microbiome analyses were performed to investigate differences in nitrogen mineralization rates and soil microbial community composition between locations. Valley bottom fields showed higher nitrogen uptake, biomass production, and grain yield with organic fertilizer application compared to hillslope fields. These differences are associated with higher nitrogen mineralization rates and lower abundance of genes involved in denitrification and bacterial ammonia assimilation in valley bottom soils, suggesting greater nitrogen retention and plant availability. These findings provide insights into site-specific management of organic fertilizers in rice production, highlighting the need for tailored strategies based on local topographic conditions and associated soil microbial communities.},
}

*Oryza/growth & development/microbiology
*Fertilizers/analysis
*Soil Microbiology
Nitrogen/metabolism
Microbiota
Soil/chemistry
Agriculture/methods
Biomass
Japan
Bacteria/genetics/metabolism/classification

@article {pmid40640255,
year = {2025},
author = {Nthebere, K and Tata, RP and Bhimireddy, P and Chandran, LP and Gudapati, J and Yadav, MBN and Sinha, NK and Admala, M},
title = {Cumulative impact of herbicides and tillage in conservation agriculture on soil microbiome, fungal diversity and crop productivity.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24992},
pmid = {40640255},
issn = {2045-2322},
mesh = {*Soil Microbiology ; *Herbicides/pharmacology ; *Microbiota/drug effects ; *Fungi/drug effects/classification ; Zea mays/growth & development/microbiology ; *Agriculture/methods ; *Crops, Agricultural/growth & development ; *Crop Production/methods ; Biodiversity ; Soil/chemistry ; },
abstract = {Conservation agriculture experiment was undertaken to investigate synergistic effects of tillage and weed management on soil microbiome, and fungal diversity at vegetative (30 DAS) and tasselling (60 DAS) of maize and monitor yield. Main-treatments included T1: Conventional tillage (CT) with Cotton- CT with maize- fallow, T2: CT with Cotton- Zero tillage (ZT) with Maize- ZT with Sesbania rostrata (Sr) and T3: ZT with Cotton + Sr residues- ZT with Maize + Cotton residues- ZT with Sr + Maize stubbles. Weed management (Sub-plots) were W1: Chemical weed control, W2: Herbicide rotation, W3: Integrated weed management (IWM) and W4: Single hand-weeded. Rhizo-sphere and plane samples were collected at 30 and 60 DAS for enzymatic, microbial analysis. The results demonstrated 25.90-44.72% and 20.31-50.72% decline on microbial and enzyme activities in T1 + W1, and in T2 + W2, respectively compared to T3 and W4 combinations at 30 DAS, due to herbicidal impact, which increased by 24.67-68.41% and 20.71-62.90% at tasseling. Metabolic quotient (qCO2) decreased with T3 and W4 combinations. Kernel and system yield were 39.42% and 51.60% higher under T3 + W1 and T3 + IWM combinations, respectively. Talaromyces flavus was identified under T3 + IWM. The qCO2 was exhibited with significant negative correlation with all biological attributes, while yield did not correlate. This suggest qCO2 as potential indicator to assess agro-ecosystem. The PCA selected variables (enzymes, organic carbon, and microbial parameters) are highly supported by zero-till + residues, and can indicate improved soil health and sustained productivity.},
}

*Soil Microbiology
*Herbicides/pharmacology
*Microbiota/drug effects
*Fungi/drug effects/classification
Zea mays/growth & development/microbiology
*Agriculture/methods
*Crops, Agricultural/growth & development
*Crop Production/methods
Biodiversity
Soil/chemistry

@article {pmid40640200,
year = {2025},
author = {King, OG and Yip, AYG and Horrocks, V and Miguéns Blanco, J and Marchesi, JR and Mullish, BH and Clarke, TB and McDonald, JAK},
title = {Vancomycin-resistant enterococci utilise antibiotic-enriched nutrients for intestinal colonisation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6376},
pmid = {40640200},
issn = {2041-1723},
support = {227795/Z/23/Z//Wellcome Trust (Wellcome)/ ; Start-up funds from the Department of Life Sciences//Imperial College London/ ; },
mesh = {*Vancomycin-Resistant Enterococci/drug effects/metabolism/growth & development ; *Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Enterococcus faecalis/drug effects/growth & development/metabolism ; Enterococcus faecium/drug effects/metabolism/growth & development ; Feces/microbiology ; *Nutrients/metabolism ; *Intestines/microbiology ; Fatty Acids, Volatile/metabolism/pharmacology ; Humans ; Animals ; Nitrogen/metabolism ; Carbon/metabolism ; Gram-Positive Bacterial Infections/microbiology ; },
abstract = {Antibiotic treatment significantly disrupts the gut microbiome and promotes vancomycin-resistant enterococci (VRE) intestinal colonisation. These disruptions cause the intestine to act as a reservoir for VRE that seed difficult-to-treat infections. Here we show that antibiotics that promote VRE intestinal colonisation increase the concentration of a wide range of nutrients and decrease the concentration of a wide range of microbial metabolites. We show significant but incomplete suppression of VRE growth by individual short chain fatty acids that were decreased in antibiotic-treated faecal microbiomes. However, mixtures of short chain fatty acids provide complete or near complete suppression of VRE growth. We show that VRE use most nutrients increased in antibiotic-treated faecal microbiomes as carbon or nitrogen sources to support their growth, where Enterococcus faecium and Enterococcus faecalis have some common and some distinct preferences for the use of these specific nutrients. Finally, we show that E. faecium and E. faecalis occupy overlapping but distinct nutrient-defined intestinal niches that promote high growth when cultured with each other and when cultured with carbapenem-resistant Enterobacteriaceae. Our results demonstrate that VRE occupy distinct intestinal niches in the antibiotic-treated intestine, defined by their abilities to utilise specific enriched nutrients and their abilities to grow with reduced concentrations of inhibitory microbial metabolites.},
}

*Vancomycin-Resistant Enterococci/drug effects/metabolism/growth & development
*Anti-Bacterial Agents/pharmacology
*Gastrointestinal Microbiome/drug effects
Enterococcus faecalis/drug effects/growth & development/metabolism
Enterococcus faecium/drug effects/metabolism/growth & development
Feces/microbiology
*Nutrients/metabolism
*Intestines/microbiology
Fatty Acids, Volatile/metabolism/pharmacology
Humans
Animals
Nitrogen/metabolism
Carbon/metabolism
Gram-Positive Bacterial Infections/microbiology

@article {pmid40640136,
year = {2025},
author = {Focardi, A and Bramucci, AR and Ajani, P and Khalil, A and Raina, JB and Seymour, JR},
title = {Defining the ecological strategies of phytoplankton associated bacteria.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6363},
pmid = {40640136},
issn = {2041-1723},
mesh = {*Phytoplankton/microbiology ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; Ecosystem ; },
abstract = {Ecological interactions between phytoplankton and bacteria govern the productivity and biogeochemistry of aquatic ecosystems. However, our understanding of these partnerships primarily comes from laboratory-based model systems, meaning that little is known about the establishment and dynamics of these interactions. Here, we tracked the development of the microbiome of 15 newly isolated phytoplankton species for 400 days. After only 20 days, each phytoplankton harboured a unique bacterial assemblage. Within these assemblages, we identify (i) specialist phytoplankton associates, which are bacteria that establish long-term interactions with 1-2 phytoplankton strains; (ii) generalists, which are associated with 3 or more phytoplankton strains; and (iii) transients, which do not develop sustained associations with any phytoplankton strains. Compared to transients, the generalists and specialists are enriched in genes involved in chemotaxis, vitamin synthesis, secondary metabolite production and the ability to uptake specific phytoplankton-derived compounds. Moreover, generalists display greater potential to move between hosts and release antimicrobials. Finally, examination of co-occurrence patterns in oceanographic time-series revealed that generalists and specialists mirror their phytoplankton partner's abundance in the environment. The divergent genomic characteristics of these discrete bacterial categories highlight different ecological strategies that likely shape phytoplankton microbiomes.},
}

*Phytoplankton/microbiology
*Bacteria/genetics/classification/isolation & purification/metabolism
*Microbiota/genetics
Ecosystem

@article {pmid40639850,
year = {2025},
author = {Feigenberg, SJ and Costabile, F and Tanes, C and Bittinger, K and O'Connor, R and Agarwal, D and Skoufos, G and Salaris, S and Hatzigeorgiou, A and Kostopoulos, N and Lloyd, S and Friedes, C and Chen, L and Yegya-Raman, N and Cengel, K and Levin, W and Valentić, B and Quarton, T and Shestov, AA and Berman, A and Bradley, J and Maity, A and Koumenis, C and Ben-Josef, E and Facciabene, A},
title = {Enhancing outcomes in medically inoperable early-stage NSCLC with gut-targeted antibiotics and stereotactic body radiotherapy: results from a randomized pilot study.},
journal = {Journal for immunotherapy of cancer},
volume = {13},
number = {7},
pages = {},
doi = {10.1136/jitc-2024-011356},
pmid = {40639850},
issn = {2051-1426},
mesh = {Humans ; Male ; *Carcinoma, Non-Small-Cell Lung/therapy/pathology/mortality ; Female ; Pilot Projects ; *Radiosurgery/methods ; Aged ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Middle Aged ; *Lung Neoplasms/therapy/pathology/mortality ; *Vancomycin/therapeutic use/pharmacology ; Treatment Outcome ; Neoplasm Staging ; Aged, 80 and over ; },
abstract = {BACKGROUND: Gut microbiota modulation is an emerging strategy to improve cancer therapy outcomes. This study evaluated the safety and therapeutic potential of combining oral vancomycin-a non-absorbed, gut-restricted antibiotic with primary activity against gram-positive bacteria-with stereotactic body radiotherapy (SBRT) in early-stage non-small cell lung cancer (NSCLC). The underlying hypothesis was that vancomycin-induced changes in gut microbiota could enhance the antitumor effects of SBRT.

METHODS: We conducted a randomized, open-label pilot study in patients with early-stage NSCLC. Patients received oral vancomycin (125 mg, four times daily for 5 weeks, starting 1 week prior to SBRT). Safety, progression-free survival (PFS), overall survival (OS), gut microbiota composition, gut metabolome, and immune responses were evaluated.

RESULTS: The combination of vancomycin and SBRT was well tolerated, with no grade 3 or 4 adverse events reported. Vancomycin treatment selectively depleted certain bacterial strains while enriching others, leading to significant restructuring of the gut microbiota and alterations in the gut metabolome, including reductions in short-chain fatty acids and shifts in other important immunomodulatory metabolites. These changes were associated with dendritic cell and T cell activation, suggesting enhanced systemic immune engagement. Patients receiving vancomycin showed improved outcomes, with a PFS HR of 0.42 (95% CI 0.18 to 0.96; p=0.049) and OS HR of 0.38 (95% CI 0.14 to 0.99; p=0.033), compared with controls.

CONCLUSIONS: This pilot study demonstrates that gut microbiome modulation using a gram-positive-targeting, gut-restricted antibiotic in combination with SBRT is safe and may improve clinical outcomes in early-stage NSCLC. These findings support further investigation of targeted microbiome modulation strategies as adjuvants to immunogenic therapies like radiation.

TRIAL REGISTRATION NUMBER: NCT03546829.},
}

Humans
Male
*Carcinoma, Non-Small-Cell Lung/therapy/pathology/mortality
Female
Pilot Projects
*Radiosurgery/methods
Aged
*Gastrointestinal Microbiome/drug effects
*Anti-Bacterial Agents/therapeutic use/pharmacology
Middle Aged
*Lung Neoplasms/therapy/pathology/mortality
*Vancomycin/therapeutic use/pharmacology
Treatment Outcome
Neoplasm Staging
Aged, 80 and over

@article {pmid40639690,
year = {2025},
author = {Newmei, K and Gorai, S and Mukherjee, S and Dey, P},
title = {Nrf2-dependent cytoprotective effects and depletion of gut microbial energy harvesting by chemically defined polyphenol-rich Clerodendrum infortunatum.},
journal = {Fitoterapia},
volume = {},
number = {},
pages = {106730},
doi = {10.1016/j.fitote.2025.106730},
pmid = {40639690},
issn = {1873-6971},
abstract = {Plants belonging to the genus Clerodendrum are consumed as functional foods to treat metabolic liver disease in the north-eastern sub-Himalayan region of India. The use of Clerodendrum spp. as hepatoprotective is mentioned in Ayurveda and Chinese traditional medicinal literatures. This study identifies a particular Clerodendrum spp. with the most superior bioactivity and evaluates the cellular mechanism behind its cytoprotective activities and its favorable impact on the gut microbiota. Twelve major Clerodendrum spp. were analyzed using GCMS, phytochemical enrichment, pathway analysis, and comparative antioxidant assays were performed. The superior most Clerodendrum sp. was chemically characterized using HPLC and tested against HepG2 and SH-SY5Y cells for cytoprotection using ML385, a pharmacological inhibitor of Nrf2, and its potential to modulate the gut microbiota using 16S rRNA sequencing. Clerodendrum infortunatum was identified as the most bioactive plant sp. with physiologically-relevant free radical scavenging capacities and containing stigmasterol, gallic acid, catechin, syringic acid, vanillic acid, rutin, p-coumaric acid and quercetin. C. infortunatum attenuated intracellular cytoprotective enzymes, lipid peroxidation and protected HepG2 and SH-SY5Y in a Nrf2-dependent manner which were otherwise affected by H2O[2]-induced cellular injury. C. infortunatum also improved gut microbial diversity, enriched the populations of gut commensals, reduced obesogenic microbes, and attenuated gut microbial metabolic functions associated with increased dietary energy harvesting capacity. In accordance to the traditional medicinal use, our data show that the hepatoprotective effects of C. infortunatum is associated with the enhancement of hepatocellular cytoprotection and a favorable modulation of the gut microbiome.},
}

@article {pmid40639662,
year = {2025},
author = {Secchi, G and Bisutti, V and Toscano, A and Pegolo, S and Giannuzzi, D and Cecchinato, A and Bittante, G and Franciosi, E},
title = {Changes in the milk and fecal microbiota in Holstein cows with subclinical intramammary infection.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26401},
pmid = {40639662},
issn = {1525-3198},
abstract = {Understanding the relationship between microbial community alterations and disease can provide valuable insights for improving diagnostics, prevention, and treatment strategies. This study used 16S rRNA amplicon sequencing to investigate and compare microbial diversity in the milk and feces of Holstein cows with subclinical mastitis caused by Streptococcus agalactiae and Prototheca spp. with that of healthy cows. A bacteriological screening identified 50 Holstein cows reared in a commercial dairy farm and classified into 3 experimental groups: i) animals negative at the bacteriological examination with no history of subclinical mastitis (HLTH; n = 16), ii) animals positive at the bacteriological examination for either Streptococcus agalactiae (STRP; n = 22) or Prototheca spp. (PRTH; n = 12). The milk microbiota showed significant pathogen-specific alterations, with increased Firmicutes in STRP cows (55.6%) and Cyanobacteria in PRTH cows (17.3%), compared with healthy cows (39.2% and 0.7%, respectively). Alpha diversity (Observed ASVs, Shannon, and Evenness indices) was significantly lower in infected cows (P < 0.05), confirming a microbial imbalance. Beta diversity analysis revealed significant differences in microbial composition between healthy and infected cows (P < 0.01, PERMANOVA), but no significant differences in fecal microbiota composition. Differential abundance analysis identified Streptococcus (log2FC = 7.3, P < 0.01) as the most enriched taxon in STRP cows and Cyanobacteria (log2FC = 8.9, P < 0.001) as the most enriched in PRTH cows in milk matrix, while Macrococcus caseolyticus was significantly reduced in both infected groups (log2FC = -4.5, P < 0.05). These findings suggest that subclinical mastitis leads to significant shifts in the milk microbiota but does not alter the fecal microbiome, supporting a localized rather than systemic microbial response. This study provides novel insights into the microbial dynamics of subclinical mastitis and potential biomarkers for disease monitoring.},
}

@article {pmid40639623,
year = {2025},
author = {Liao, K and Wen, J and Liu, Z and Zhang, B and Zhang, X and Fu, Y and Zhang, W and Hu, H and Ai, K and Zhu, W and Xia, M and Lai, Y and Qian, Y and Xu, Y and Sun, F and Zhang, L and Zhong, Q and Huang, B and Wang, X},
title = {The role of intratumoral microbiome in the occurrence, proliferation, metastasis of colorectal cancer and its underlying therapeutic strategies.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {102820},
doi = {10.1016/j.arr.2025.102820},
pmid = {40639623},
issn = {1872-9649},
abstract = {Colorectal cancer (CRC), a leading cause of cancer mortality globally, is shaped by dynamic interactions between intratumoral microbiota and the tumor microenvironment (TME). Emerging evidence highlights the critical role of intratumoral bacteria, fungi, and viruses, such as Fusobacterium nucleatum and genotoxic Escherichia coli, in driving carcinogenesis through DNA damage, immune evasion, and metabolic reprogramming. While their origins remain debated, hypotheses include mucosal barrier penetration, migration from adjacent tissues, hematogenous dissemination, and co-metastasis with tumor cells. Spatial profiling reveals non-randomized microbial distribution within immunosuppressive TME niches characterized by reduced T-cell infiltration and enriched immunosuppressive molecules. Mechanistically, microbiota-derived metabolites (e.g., butyrate) and genotoxins (e.g., colibactin) modulate host pathways, promote epithelial DNA damage, polarize immune cells (e.g., M2-like macrophages, Tregs), and collectively, these contribute to fostering tumor progression. Conversely, microbial peptides or STING pathway activation by commensals like Bifidobacterium may enhance antitumor immunity. Intratumoral microbiota significantly influences therapeutic outcomes: F. nucleatum induces chemoresistance via autophagy, while Gammaproteobacteria inactivate gemcitabine. Immunotherapy responses are similarly modulated, with microbiota either amplifying antitumor T-cell activity or suppressing immunity through cytokine-mediated pathways. Innovative strategies, including engineered probiotics, bacterial vectors for drug delivery, and nanotechnology-enabled microbial modulation (e.g., functionalized nanoparticles, biomaterial carriers), aim to exploit these interactions. However, challenges such as low microbial biomass, contamination risks, and interpatient heterogeneity complicate translational efforts. Multi-omics and spatial-profiling technologies offer promise in deciphering microbial-immune-metabolic networks, guiding personalized therapies. Future research must address the biocompatibility of microbial-nanotech hybrids and validate intratumoral microbiota as biomarkers or therapeutic targets. Bridging gut and tumor microbiome studies could unlock novel CRC management strategies, emphasizing the dual role of microbiota as oncogenic drivers and therapeutic allies in precision oncology.},
}

@article {pmid40639456,
year = {2025},
author = {Andrews, RAF and Lacey, A and Roach, H and Tomlinson, R and Kidd, EJ and Bache, K},
title = {Investigating the Effects of Probiotics during the Menopause Transition: A Systematic Review & Meta-Analysis.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnesp.2025.07.009},
pmid = {40639456},
issn = {2405-4577},
abstract = {This review investigated the impact of probiotics during the menopause transition and explored their potential to enhance the effectiveness of estrogenic substances in perimenopausal or recently postmenopausal women. A thorough literature search of EMBASE, MEDLINE, Cochrane Library, Scopus, and Web of Science was conducted, identifying 39 studies involving 3,187 women. Quality assessments were conducted using the relevant Cochrane Risk of Bias tools. The results demonstrated that probiotics had positive effects on menopausal symptoms, urogenital health, bone health, and the efficacy and safety of estriol and isoflavones. Meta analysis of 7 studies comparing probiotics versus placebo demonstrated large effects of probiotics on menopausal symptoms (total score) [standardized mean difference (SMD) = 0.82, 95% CI -0.52 to -1.09], vasomotor symptoms (SMD = -0.96, 95% CI -1.25 to -0.68), psychological symptoms (SMD = -0.51, 95% CI -0.95 to -0.08), vaginal dryness (SMD = 0.95, 95% CI -1.40 to -0.49), and vaginal microbiome health (Nugent score) (SMD = -0.91, 95% CI -1.32 to -0.49). Meta-analysis results were nonsignificant for reducing somatic and sexual symptoms. Probiotics hold promise in addressing symptoms related to low estrogen levels and may enhance the effects of estriol and isoflavones, offering potential benefits as part of the management of menopausal women. It's important to note that the included studies had a high risk of bias, emphasising the need for further rigorous research in this area. Should findings continue to show promise, clinicians should consider incorporating probiotics into their strategies for managing menopausal symptoms. Systematic Review Registration Number: CRD42019146270.},
}

@article {pmid40639442,
year = {2025},
author = {Zhan, Z and Chen, R and Deng, Z and Gao, J},
title = {Burgeoning momentum: the present and future of hyodeoxycholic acid in host microbiome dynamics.},
journal = {Biochemical pharmacology},
volume = {},
number = {},
pages = {117133},
doi = {10.1016/j.bcp.2025.117133},
pmid = {40639442},
issn = {1873-2968},
abstract = {This review critically examines the emerging role of hyodeoxycholic acid (HDCA) in metabolic and inflammatory disorders. We analyze the current understanding of HDCA biosynthesis, highlighting species-specific differences and challenges in identifying HDCA-producing bacteria. The study evaluated the signaling mechanism by which HDCA simultaneously activates intestinal G protein-coupled bile acid receptor 1 (TGR5) and farnesoid X receptor (FXR), challenging the traditional paradigm of bile acid （BA）signaling. We assess HDCA's immunomodulatory effects, particularly its Toll-like receptor 4 (TLR4) inhibition, and discuss potential therapeutic applications in metabolic diseases and sepsis. The review addresses challenges in translating rodent studies to human applications and explores future directions, including the development of HDCA derivatives and integration with microbiome modulation strategies. Ethical and regulatory considerations for microbiome-derived therapeutics are also discussed. We propose that HDCA research may catalyze paradigm shifts in understanding host-microbiome-BA interactions, calling for interdisciplinary approaches to harness its potential fully.},
}

@article {pmid40639331,
year = {2025},
author = {Xu, S and Wang, Z},
title = {Upper vs. lower airways: Microbes shape the local milieu.},
journal = {Cell host & microbe},
volume = {33},
number = {7},
pages = {1043-1045},
doi = {10.1016/j.chom.2025.06.007},
pmid = {40639331},
issn = {1934-6069},
mesh = {Humans ; *Microbiota ; *Respiratory System/microbiology/metabolism ; Inosine/metabolism ; Glutamic Acid/metabolism ; Prevotella/metabolism ; },
abstract = {In this issue of Cell Host & Microbe, Wong et al. investigate the contribution of the microbiome to airway metabolism, revealing differential microbial pathways and metabolites between the upper and lower airways. Oral commensals contribute to the metabolic milieu with Prevotella melaninogenica synthesizing inosine and glutamate in the lower airways.},
}

Humans
*Microbiota
*Respiratory System/microbiology/metabolism
Inosine/metabolism
Glutamic Acid/metabolism
Prevotella/metabolism

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

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

@article {pmid40638549,
year = {2025},
author = {Dasgupta, S},
title = {Unraveling the Microbiome-Asthma Axis: Metagenomic Insights from Airway and Gut Microbial Communities.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {},
doi = {10.1177/15578100251358958},
pmid = {40638549},
issn = {1557-8100},
abstract = {Asthma is a heterogeneous respiratory disease with complex pathogenesis involving immune dysregulation, environmental triggers, and increasingly recognized to have contributions from the human microbiome. Emerging evidence from longitudinal birth cohorts and multi-omics studies reveals that early-life microbial colonization patterns in both the gastrointestinal and respiratory tracts play a crucial role in shaping immune trajectories and influencing asthma susceptibility. This expert review highlights the findings from pivotal studies that associate dysbiosis in the gut and airway microbiota with asthma development and its diverse phenotypic manifestations. Reduced abundance of immunomodulatory genera such as Bifidobacterium, Faecalibacterium, and Lachnospira in the gut has been consistently associated with increased asthma risk. In the airways, increased colonization by potentially pathogenic taxa, including Moraxella, Haemophilus, and Streptococcus, correlates with viral respiratory infections and persistent wheezing. Microbiome diversity patterns also differ between asthma phenotypes: eosinophilic asthma typically features a community profile closer to healthy individuals, while neutrophilic asthma is marked by enrichment of pro-inflammatory bacterial species. Moreover, protective genera such as Dolosigranulum and Corynebacterium in the upper airways are associated with lower risk of asthma and reduced respiratory infections. Elucidating these microbiome-mediated mechanisms holds promise for the development of targeted microbiota-based strategies for asthma prevention and phenotype-specific therapeutic interventions. The present review unpacks these localized microbial patterns and their mechanistic implications for asthma development, severity, and endotypic variation. Finally, unraveling the microbiome-asthma axis from airway and gut microbial communities also has implications for new ways of thinking personalized medicine in the future.},
}

@article {pmid40638335,
year = {2025},
author = {Franco, EM and Alves, LA and Camargo, I and Salvatierra, GC and Garcia, MT and Chen, T and Junqueira, JC and Bastos, DC and Mattos-Graner, RO},
title = {Contribution of a LysM domain-containing protein regulated by VicRK to streptococcus sanguinis virulence.},
journal = {Virulence},
volume = {},
number = {},
pages = {2532036},
doi = {10.1080/21505594.2025.2532036},
pmid = {40638335},
issn = {2150-5608},
abstract = {Streptococcus sanguinis is a commensal member of the oral microbiome involved in opportunistic cardiovascular infections. In the present study, we investigated the contribution of ssa_0094, a gene strongly regulated by the two-component system VicRK, to functions associated with biofilm formation, immune evasion and cardiovascular virulence. In silico analysis showed that ssa_0094 encodes a protein with a LysM domain, which is highly conserved among S. sanguinis. Although not an ubiquitous gene, several commensal streptococcal species of the oronasopharynx and zoonotic strains of Streptococcus suis harbour ssa_0094 homologues. A ssa_0094 isogenic mutant (SK0094) showed defects in initiating biofilms on saliva-coated surfaces, reduced hydrophobicity and lower production of amyloid-like components when compared to the parent strain (SK36) or to the complemented mutant (SK0094+), although it showed mild changes in DNA release and production of H2O2. Deletion of ssa_0094 also impaired S. sanguinis binding to multiple human glycoproteins of plasma and/or extracellular matrix (ECM) (plasminogen, fibronectin, fibrinogen, fibrin, type I collagen and elastin), and promoted clear increases in C3b deposition, and in induction of NEtosis by neutrophils of peripheral blood. Moreover, SK0094 showed impaired invasiveness into HCAEC cells and reduced ex vivo persistence in human blood, but no clear change in virulence in a Galleria mellonella infection model. These findings indicate that ssa_0094 is highly conserved within S. sanguinis strains required for biofilm initiation as well as for multiple functions of immune evasion and cardiovascular virulence in S. sanguinis in a host-specific fashion.},
}

@article {pmid40638177,
year = {2025},
author = {Yoshimoto, Y and Ichinohe, N and Liu, H and Nagata, N and Inoue, R and Yamamoto, Y and Nagaoka, K},
title = {EFFECTS OF CLOSTRIDIUM BUTYRICUM SUPPLEMENTATION ON FECAL MICROBIOTA AND METABOLITES IN CAPTIVE RED KANGAROO (MACROPUS RUFUS).},
journal = {Journal of zoo and wildlife medicine : official publication of the American Association of Zoo Veterinarians},
volume = {56},
number = {2},
pages = {360-370},
doi = {10.1638/2024-0079},
pmid = {40638177},
issn = {1042-7260},
mesh = {Animals ; *Feces/microbiology ; *Clostridium butyricum ; *Macropodidae/microbiology ; *Probiotics/pharmacology/administration & dosage ; Male ; Female ; Animals, Zoo ; *Gastrointestinal Microbiome ; Dietary Supplements ; Animal Feed/analysis ; Diet/veterinary ; },
abstract = {The red kangaroo (Macropus rufus) is a prominent marsupial species native to Australia and is kept in zoos worldwide. Captive red kangaroos are often plagued with several diseases, such as lumpy jaw, incurring high treatment costs. Recent research suggests a significant link between the gut microbiota and various diseases in many species, indicating potential benefits of probiotics in maintaining health. The microbiota of the digestive tract of red kangaroos has been reported; however, the fecal microbiota and any compositional changes in this microbiota caused by probiotic intervention remain to be elucidated. Herein, the effects of the probiotic Clostridium butyricum, which produces the short-chain fatty acid butyrate, on fecal microbiota and metabolites in red kangaroos were investigated. Fecal samples were collected from six red kangaroos free from signs of diseases (three males and three females, aged 1-2 yr) during C. butyricum supplementation and suspension periods. Fecal C. butyricum levels decreased during the suspension period and increased upon resumption by quantitative PCR analysis. Despite changes in C. butyricum levels, fecal concentrations of measured short-chain fatty acids remained unchanged. Total microbiome analysis showed no significant differences by C. butyricum supplementation. Functional predictions indicated alterations in microbial community functions, such as activating penicillin and cephalosporin biosynthesis and inactivating the bacterial secretion system during C. butyricum supplementation. Metabolomic analyses identified significant changes in pathways related to amino acid degradation and metabolism, fatty acid biosynthesis, glycolysis and glycogenesis, and the citrate cycle (the tricarboxylic acid cycle), suggesting that C. butyricum supplementation affects metabolism independent of microbiota composition. These findings suggest that C. butyricum alters metabolism. However, this study's kangaroos were supplemented with C. butyricum prior to the study period, so its impact could not be verified. Further study is also required to determine how these changes might contribute to maintaining health in captive red kangaroos.},
}

Animals
*Feces/microbiology
*Clostridium butyricum
*Macropodidae/microbiology
*Probiotics/pharmacology/administration & dosage
Male
Female
Animals, Zoo
*Gastrointestinal Microbiome
Dietary Supplements
Animal Feed/analysis
Diet/veterinary

@article {pmid40638068,
year = {2025},
author = {Altendorf, S and Bertolini, M and Le Riche, A and Tosti, A and Paus, R},
title = {Frontiers in the physiology of male pattern androgenetic alopecia: Beyond the androgen horizon.},
journal = {Physiological reviews},
volume = {},
number = {},
pages = {},
doi = {10.1152/physrev.00005.2024},
pmid = {40638068},
issn = {1522-1210},
abstract = {Male pattern androgenetic alopecia (mpAGA), the most common form of hair loss in men, represents a heritable, androgen-dependent complex trait distinct from female pattern hair loss. Despite the psychosocial burden of mpAGA in some affected individuals and associations with other morbidities, we portray mpAGA as an essentially physiological phenomenon in which defined hair follicle (HF) populations in developmentally preprogrammed scalp skin regions undergo a dramatic, but reversible (mini-)organ transformation in genetically predisposed individuals. Histologically, mpAGA exhibits progressive HF miniaturization (terminal-to-vellus conversion) and anagen shortening. Clinically, this results in a characteristic balding pattern of frontotemporal and vertex scalp skin, associated with telogen effluvium. It remains unclear how exactly androgens induce this phenotype, since neither androgen receptor polymorphisms nor changes in androgen serum or local androgen skin levels persuasively explain it. It also is as yet unresolved if mpAGA-associated HF transformation and hair cycle changes are primarily driven by the HF mesenchyme, e.g. by excessive emigration and/or reduced inductive potential of dermal papilla fibroblasts, or by intraepithelial events such as prostaglandin D2-dependent reduced HF epithelial stem cell progenitor generation. While critically revisiting our limited current understanding of mpAGA physiology and the role of mpAGA-associated genes we discuss potential targets for future therapeutic intervention beyond androgens and highlight selected dysregulated signaling pathways in mpAGA. We underscore mpAGA as an instructive, accessible model for interrogating under-investigated physiological roles of immune cells, oxidative stress, aging/senescence, and the microbiome in human organ remodeling and hair cycle regulation, and define major open research questions beyond androgen receptor- mediated signaling.},
}

@article {pmid40638028,
year = {2025},
author = {Ali, SH and Fatima, M and Fatima, M and Shaikh, UA},
title = {Association of the gut microbiome with diabetic nephropathy and the mediated effect of metabolites: friend or enemy?.},
journal = {International urology and nephrology},
volume = {},
number = {},
pages = {},
pmid = {40638028},
issn = {1573-2584},
}

@article {pmid40638022,
year = {2025},
author = {Deng, Y and Xu, L and Yang, K and Lin, Z and Zang, S and Jiang, K and Li, W and Ibrahim, NA and Ma, H and Cheng, C and Feng, J},
title = {The Time Reliable Effect of Probiotic Clostridium butyricum on the Growth of Spotted Sea Bass (Lateolabrax maculatus).},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40638022},
issn = {1867-1314},
support = {2024A1515030244//the Natural Science Fund of Guangdong/ ; 2024RC01//the Central Public-interest Scientific Institution Basal Research Fund, South China Sea Fisheries Research Institute, CAFS/ ; 2025ZX04//the Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; 2023TD21//the Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; 2024YFD2401403//the National Key Research and Development Program of China/ ; 2024CXTD27//the Innovative Team Building Project of Guangdong Modern Agricultural Industrial Technology System/ ; },
abstract = {Probiotic Clostridium butyricum has been demonstrated to enhance the growth of spotted sea bass (Lateolabrax maculatus). However, the time reliable effect of C. butyricum application for L. maculatus growth promotion is poorly understood, limiting our ability to make informed decisions about when the C. butyricum should be added and why. To address this, we employed multidisciplinary approach to investigate the growth response (including growth performance, intestinal morphology, digestive enzyme activities, and gut microbiome) of L. maculatus to C. butyricum supplementation throughout the entire breeding cycle (from juvenile to marketable size). The C. butyricum supplementation significantly increased the weight of L. maculatus during its early life stages. Correspondingly, 16S rRNA sequence showed that C. butyricum addition increased probiotic bacteria (including Lactobacillales), decreased pathogenic bacteria (including Enterobacterales, Burkholderiales, and Fusobacteriales), and reduced bacterial virulence processes (including quorum sensing, biofilm formation, and bacterial secretion systems) of gut microbiota in L. maculatus. Concurrently, C. butyricum supplementation increased intestinal villus height (up to 32.1%), muscle thickness (up to 115.8%), and digestive enzyme activities (up to 77.8%). Nevertheless, during the later stages of incubation, treatment with C. butyricum did not result in further improvements or even showed similar outcomes to the non-supplemented treatment. These findings emphasize that C. butyricum supplementation during the early breeding stage can significantly benefit L. maculatus growth, rather than adding it during later stages. This study provides evidence on the appropriate timing for C. butyricum supplementation in L. maculatus culture, offering timely information and technical support for its culture management.},
}

@article {pmid40637840,
year = {2025},
author = {Tortelote, GG},
title = {Therapeutic strategies for hypertension: exploring the role of microbiota-derived short-chain fatty acids in kidney physiology and development.},
journal = {Pediatric nephrology (Berlin, Germany)},
volume = {},
number = {},
pages = {},
pmid = {40637840},
issn = {1432-198X},
abstract = {Gut microbiota have emerged as a key regulator of systemic health, influencing various physiological processes, including kidney development, function, and blood pressure regulation. This review highlights the role of microbiota-derived short-chain fatty acids (SCFAs), primarily acetate, propionate, and butyrate, in the gut-kidney axis, focusing on their signaling mechanisms, vascular effects, and developmental implications. Evidence suggests that SCFAs modulate kidney development and function and exert anti-inflammatory, antioxidant, and vasoregulatory effects through specific G protein-coupled receptors (GPR41, GPR43, GPR109A, OLFR78, and OLFR558). Human studies and research using genetically modified animals have demonstrated that gut dysbiosis disrupts SCFA metabolism, potentially contributing to hypertension, endothelial dysfunction, and chronic kidney disease (CKD). Germ-free microbiota-transplantation studies revealed that the presence of gut microbiota directly influences vascular tone and systemic blood pressure via SCFA-mediated mechanisms. Furthermore, acetate, a SCFA, is shown to impact fetal kidney development and nephron progenitor cell dynamics. Sex-specific effects of gut microbiota on vascular remodeling and immune responses further highlight the complexity of microbiome-host interactions. In pediatric patients, altered SCFA profiles are associated with CKD progression and relapse in nephrotic syndrome. Clinical data suggest that plasma SCFA levels may serve as biomarkers for hypertension risk and cardiovascular outcomes in children with kidney disease. Therapeutically, interventions targeting SCFA pathways, such as probiotics, prebiotics, dietary fiber diet, and receptor agonists, may help restore gut-kidney axis balance and improve kidney and cardiovascular outcomes. This review illustrates the critical role of SCFAs as mediators linking the gut microbiota to kidney and vascular health. Continued investigation into SCFA signaling may uncover novel strategies for preventing and managing hypertension, CKD, and developmental nephropathies.},
}

@article {pmid40637783,
year = {2025},
author = {Philippe, C and Denis, LA and Fonville, M and Devriendt, B and Dufrasne, FE and Obregon, D and Maître, A and Skičková, Š and Cox, E and Sprong, H and Cruz, AC and Mori, M},
title = {Diversity of the Ixodes ricinus Microbiome Across Belgian Ecoregions and Its Association with Pathogen and Symbiont Presence.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {73},
pmid = {40637783},
issn = {1432-184X},
mesh = {*Ixodes/microbiology ; Animals ; *Microbiota ; Belgium ; *Symbiosis ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Nymph/microbiology ; Anaplasma phagocytophilum/isolation & purification/genetics ; Biodiversity ; },
abstract = {Ticks are important vectors of zoonotic pathogens, and their presence can be influenced by the composition of the tick microbiome. In turn, this microbiome is shaped by environmental and ecological factors, as demonstrated in several studies conducted under controlled conditions. However, the extent of these influences under natural ecological conditions remains underexplored. In this study, we investigated the diversity of the microbiome and the prevalence of pathogens in Ixodes ricinus nymphs across three distinct Belgian ecoregions: Sandy Loam, Condroz, and Ardennes. Using real-time quantitative PCR (qPCR) and Oxford Nanopore 16S rRNA sequencing, we assessed how geography and pathogen presence influence tick-associated microbial communities. Our results revealed significant regional differences in microbiome composition and pathogen prevalence. Borrelia burgdorferi sensu lato (s.l.) was most prevalent in the Ardennes (9% (7.4-10.9) vs 3.8% (2.8-5.2) in the Condroz and 2.1% (1.4-3.2) in Sandy Loam) while Anaplasma phagocytophilum was more common in the Sandy Loam region (21.1% (18.7-23.8) vs 4% (3-5.4) in the Condroz and 3.2% (2.2-4.4) in the Ardennes). Endosymbionts such as Midichloria mitochondrii and Spiroplasma ixodetis also exhibited distinct geographic distributions. Network analysis identified potential pathogen-microbiota interactions, with certain bacterial taxa showing positive or negative associations with specific pathogens. Moreover, microbiome composition was influenced not only by ecoregion but also by microorganisms such as Rickettsia helvetica, suggesting that its colonization may actively shape microbial community structure, potentially through competition or facilitation mechanisms. Additionally, microbiome network robustness varied across ecoregions, highlighting the role of ecological context in shaping microbial interactions within ticks. These findings underscore the complex interplay between geography, pathogen presence, and microbial diversity in ticks, highlighting the importance of integrating these interactions to inform microbiome-based strategies for vector control and disease prevention.},
}

*Ixodes/microbiology
Animals
*Microbiota
Belgium
*Symbiosis
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Nymph/microbiology
Anaplasma phagocytophilum/isolation & purification/genetics
Biodiversity

@article {pmid40637409,
year = {2025},
author = {Imes, AM and Pavelsky, MN and Badal, K and Kamp, DL and Briseño, JL and Sakmar, T and Vogt, MA and Nyholm, SV and Heath-Heckman, EAC and Grasse, B and Septer, AN and Mandel, MJ},
title = {Euprymna berryi as a comparative model host for Vibrio fischeri light organ symbiosis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0000125},
doi = {10.1128/aem.00001-25},
pmid = {40637409},
issn = {1098-5336},
abstract = {Functional studies of host-microbe interactions benefit from natural model systems that enable the exploration of molecular mechanisms at the host-microbe interface. Bioluminescent Vibrio fischeri colonize the light organ of the Hawaiian bobtail squid, Euprymna scolopes, and this binary model has enabled advances in understanding host-microbe communication, colonization specificity, in vivo biofilms, intraspecific competition, and quorum sensing. The hummingbird bobtail squid, Euprymna berryi, can be generationally bred and maintained in lab settings and has had multiple genes deleted by CRISPR approaches. The prospect of expanding the utility of the light organ model system by producing multigenerational host lines led us to determine the extent to which the E. berryi light organ symbiosis parallels known processes in E. scolopes. However, the nature of the E. berryi light organ, including its microbial constituency and specificity for microbial partners, has not been examined. In this report, we isolated bacteria from E. berryi animals and tank water. Assays of bacterial behaviors required in the host, as well as host responses to bacterial colonization, illustrate largely parallel phenotypes in E. berryi and E. scolopes hatchlings. This study reveals E. berryi to be a valuable comparative model to complement studies in E. scolopes.IMPORTANCEMicrobiome studies have been substantially advanced by model systems that enable functional interrogation of the roles of the partners and the molecular communication between those partners. The Euprymna scolopes-Vibrio fischeri system has contributed foundational knowledge, revealing key roles for bacterial quorum sensing broadly and in animal hosts, for bacteria in stimulating animal development, for bacterial motility in accessing host sites, and for in vivo biofilm formation in development and specificity of an animal's microbiome. Euprymna berryi is a second bobtail squid host, and one that has recently been shown to be robust to laboratory husbandry and amenable to gene knockout. This study identifies E. berryi as a strong symbiosis model host due to features that are conserved with those of E. scolopes, which will enable the extension of functional studies in bobtail squid symbioses.},
}

@article {pmid40637405,
year = {2025},
author = {Hengoju, S and Abdissa, K and Boto, ST and Samimi, A and Martin, K and Jacobsen, ID and Rosenbaum, MA},
title = {A droplet microfluidic strategy for cultivation, investigation, and high-throughput isolation of mouse gut microbiome bacteria.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0069525},
doi = {10.1128/aem.00695-25},
pmid = {40637405},
issn = {1098-5336},
abstract = {Understanding the gut microbiome's intricate dynamics and its impact on host health necessitates the cultivation and isolation of its constituent microorganisms. Traditional culturing techniques often fall short in capturing the diversity of the gut microbiota, particularly for rare and slow-growing species. In this study, we present a droplet microfluidic platform as a high-throughput and efficient method for the cultivation and isolation of mouse gut microorganisms. Droplets, each encapsulating a single cell, were incubated under both aerobic and anaerobic conditions, thereby providing individual microenvironments without nutrient competition and facilitating the growth of a wide range of microorganisms. We validated the platform by successfully cultivating and isolating a diverse array of gut microorganisms, including strains with probiotic potential. A comparative analysis with traditional agar plating techniques revealed a higher number of unique isolates from the droplet cultivation method, demonstrating its enhanced capability to capture the cultivable fraction of the gut microbiome. Beyond isolation, 16S rDNA amplicon sequencing of the diverse microbial cultures in droplets demonstrated that our system reflects changes in microbial diversity induced by dietary interventions in mice. Droplet microfluidics offers a powerful and scalable tool for the high-throughput cultivation, evaluation, and isolation of gut microorganisms, paving the way for deeper insights into the gut microbiome's role in health and disease.IMPORTANCEThe gut microbiome plays a crucial role in health and disease, yet many of its microbial members remain difficult to cultivate using traditional methods. In this study, we present a droplet microfluidic platform that advances our ability to cultivate, isolate, and analyze mouse gut microorganisms. By providing individual microenvironments for single cells, this high-throughput method overcomes limitations of traditional culturing techniques, enhancing microbial diversity recovery compared to standard techniques. Furthermore, this platform can reflect changes in microbial diversity in response to dietary changes in mice, highlighting its potential for studying gut microbial dynamics.},
}

@article {pmid40637385,
year = {2025},
author = {Yang, L and Yang, J and Zhang, T and Xie, X and Wu, Q},
title = {Gut microbiota: a novel strategy affecting atherosclerosis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0048224},
doi = {10.1128/spectrum.00482-24},
pmid = {40637385},
issn = {2165-0497},
abstract = {Atherosclerosis is a common chronic inflammatory cardiovascular disease affecting both coronary and peripheral arteries, which is influenced by multiple factors. It is increasingly evident that gut microbes and their byproducts play a crucial role in the development of atherosclerosis. The most representative feature of microbial dysbiosis in coronary artery disease patients is the reduction of the abundance of the phylum Bacteroidetes and the increase of the abundance of the phylum Firmicutes, which may cause changes in functional genes and metabolites. The gut microbiota and its metabolites influence the early, intermediate, and late stages of atherosclerosis mainly by inhibiting or promoting inflammatory responses. In addition, the reshaping of gut microbiota through probiotics, prebiotics, and fecal microbiota transplantation (FMT) is discussed as an alternative to traditional therapeutic methods. By summarizing how gut microbiota and their metabolites affect the process of atherosclerosis, we can better understand the complex relationship between gut microbiota and atherosclerosis.IMPORTANCEAtherosclerosis is an inflammatory cardiovascular disease, making it crucial to understand its pathogenesis and develop effective treatments. This review thoroughly examines the literature, emphasizing the gut microbiome as a key factor influencing atherosclerosis. It also explores how the gut microbiota and its metabolites impact the primary, intermediate, and advanced stages of atherosclerosis and proposes that remodeling the gut microbiota is a promising strategy for improving atherosclerosis.},
}

@article {pmid40637292,
year = {2025},
author = {Ghosh, S and Goswami, A and Bandyopadhyay, A and Saha, RG and Mandal, P},
title = {Association of Vaginal Microbiota and Sociodemographic Factors With Cervical Human Papillomavirus in the Eastern Region of India.},
journal = {Journal of medical virology},
volume = {97},
number = {7},
pages = {e70472},
doi = {10.1002/jmv.70472},
pmid = {40637292},
issn = {1096-9071},
support = {//The study was funded by the Department of Biotechnology, Govt. Of India [Grant id: BT/PR18640/BIC/101/924/2016 Dated: 20.09.2017] and DST-SERB ECR, Govt. of India [Grant id: ECR/2017/000595, Dated: 16.07.2018]./ ; },
mesh = {Humans ; Female ; India/epidemiology ; *Papillomavirus Infections/epidemiology/virology/microbiology ; Adult ; *Microbiota ; *Vagina/microbiology/virology ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Young Adult ; *Bacteria/classification/genetics/isolation & purification ; Sociodemographic Factors ; Risk Factors ; *Papillomaviridae/isolation & purification/classification/genetics ; Socioeconomic Factors ; Cervix Uteri/virology ; Adolescent ; High-Throughput Nucleotide Sequencing ; Uterine Cervical Neoplasms/virology/epidemiology ; Human Papillomavirus Viruses ; },
abstract = {Prolonged exposure to the High-risk Human Papillomavirus (HPV) leads to the development of cervical carcinoma. Numerous factors aid in this virus's acquisition, persistence, and clearance. This study aims to determine the association of vaginal microbiota and socio-demographic factors with oncogenic HPV infections among women from Eastern region of India. Cervical scrapes and vaginal swab samples were collected from women (n = 300) having some gynecological complaints with informed consent. Cervical cytology and HPV types were screened among them. A subset of samples (n = 12) were subjected for next generation sequencing based 16S rRNA profiling to determine the vaginal bacterial diversity among the HPV-positive and HPV-negative women with normal cervical cytology. The taxonomic profiling, diversity and relative abundance of bacterial species were determined subsequently. With appropriate statistical tests, vaginal bacterial diversity along with socio-demographic risk factors was correlated with HPV infections. A PCR-based approach further detected the bacterial taxa that were exclusively present among the groups in the whole data set. HPV infection was identified among 11.60% of individuals, with the dominance of HPV18 (80%) among carcinogenic HPV. 16S rRNA profiling revealed that the HPV-positive group had lower abundance of Firmicutes phylum and higher abundance of Proteobacteria and Actinobacteria phyla than the HPV-negative group. A positive correlation between Genus Acinetobacter and HPV positivity was established, presenting higher susceptibility for oncogenic HPV16/18 (p = 0.016; relative mean abundance = 19.67). PCR-based detection of this genus in the whole data set (n = 300), a statistically significant association with oncogenic HPV16/18 infection (p ≤ 0.01, odds ratio (OR)= 22.48 [95% CI = 5.23-96.63]) was found. Among sociodemographic factors, Tobacco users (16.67%, 4/24; OR = 6.70 [95% CI: 1.86-24.18]; p = 0.001) and field-workers (15.79%, 3/19; OR = 5.67 [95% CI: 1.40-22.99]; p = 0.007) were associated with a higher risk of HPV18 infections. Assessment of geography-specific vaginal microbiota and other lifestyle induced risk factors might contribute to acquire chronic infection of oncogenic HPV and progression to cervical cancer.},
}

Humans
Female
India/epidemiology
*Papillomavirus Infections/epidemiology/virology/microbiology
Adult
*Microbiota
*Vagina/microbiology/virology
RNA, Ribosomal, 16S/genetics
Middle Aged
Young Adult
*Bacteria/classification/genetics/isolation & purification
Sociodemographic Factors
Risk Factors
*Papillomaviridae/isolation & purification/classification/genetics
Socioeconomic Factors
Cervix Uteri/virology
Adolescent
High-Throughput Nucleotide Sequencing
Uterine Cervical Neoplasms/virology/epidemiology
Human Papillomavirus Viruses

@article {pmid40637175,
year = {2025},
author = {Fahim, SM and Huey, SL and Palma Molina, XE and Agarwal, N and Ridwan, P and Ji, N and Kibbee, M and Kuriyan, R and Finkelstein, JL and Mehta, S},
title = {Gut microbiome-based interventions for the management of obesity in children and adolescents aged up to 19 years.},
journal = {The Cochrane database of systematic reviews},
volume = {7},
number = {7},
pages = {CD015875},
pmid = {40637175},
issn = {1469-493X},
mesh = {Humans ; Adolescent ; Child ; Randomized Controlled Trials as Topic ; *Pediatric Obesity/therapy/microbiology ; *Gastrointestinal Microbiome ; Probiotics/therapeutic use ; Child, Preschool ; Young Adult ; Prebiotics/administration & dosage ; Synbiotics/administration & dosage ; Infant ; Fecal Microbiota Transplantation ; Body Mass Index ; Overweight/therapy ; },
abstract = {BACKGROUND: The epidemic of overweight and obesity affects more than 390 million children and adolescents aged 5 to 19 years and 37 million children under five years of age. Overweight and obesity are associated with both short- and long-term consequences, including chronic inflammation, metabolic diseases, as well as alterations in the gut microbiome composition. Gut microbiome-based approaches may impact microbiome-related metrics such as diversity or the abundance of intestinal bacteria, which may be linked to obesity-related outcomes. However, evidence regarding the effect of gut microbiome-based interventions for the management of obesity is limited.

OBJECTIVES: To assess the effects of gut microbiome-based interventions in the management of overweight or obesity in children and adolescents in all their diversity aged 0 to 19 years.

SEARCH METHODS: We searched CENTRAL, MEDLINE, CINAHL, Web of Science Core Collection, BIOSIS Previews, Global Index Medicus (all regions), IBECS, SciELO, PAHO, PAHO IRIS, WHO IRIS, WHOLIS, Bibliomap, TRoPHI as well as ICTRP Search Portal and ClinicalTrials.gov. The date of the last search for all databases was 24 January 2025. We did not apply any language restrictions.

SELECTION CRITERIA: We included randomised controlled trials that evaluated gut microbiome-based interventions [i.e. prebiotics, probiotics, synbiotics, short-chain fatty acids (SCFAs), and faecal microbiota transplantation (FMT)] compared to standard-of-care, placebo, or control interventions in children and adolescents aged 0 to 19 years with overweight or obesity.

DATA COLLECTION AND ANALYSIS: Two review authors independently screened titles and abstracts and full texts, extracted data, and assessed the risk of bias using the Cochrane Risk of Bias 2 tool and certainty of the evidence using Grading of Recommendations Assessment, Development and Evaluation (GRADE), a framework for assessing the certainty of evidence and making recommendations in systematic reviews. Random-effects meta-analyses were performed unless only one study per outcome was available, for which fixed-effect analyses were performed.

MAIN RESULTS: We found 17 studies (838 participants) from various countries, evaluating the effects of prebiotics, probiotics, synbiotics, SCFAs, and FMT on body mass index (BMI), body weight, waist circumference, total body fat percentage (%TBF), systolic and diastolic blood pressure, and adverse events. Of the 17 studies included, five studies were in adolescents aged 10 to 19 years, and 12 studies were in children and adolescents spanning both age groups, 0 to 19 years. Upon contacting authors for data grouped by age of the participants, no studies provided separate outcomes data for children and adolescents. The included studies were funded by either academic funding sources or grants from the public and private sectors. Additionally, 15 studies were classified as currently being conducted ('ongoing'). The certainty of evidence throughout was very low. In adolescents 10 to 19 years of age, probiotics compared to placebo or no intervention may have little to no effect on BMI, body weight, waist circumference, %TBF, blood pressure, and adverse events. Similarly, FMT compared to placebo may have little to no effect on waist circumference, %TBF, blood pressure, and adverse events in this age group. According to one study with 41 participants and in children and adolescents 0 to 19 years of age, intervention with prebiotics compared to placebo may result in a small reduction in BMI (mean difference = -0.70, 95% CI = -1.25 to -0.15) and body weight (mean difference = -1.5, 95% CI = -2.61 to -0.39). Prebiotics compared to placebo may have little to no effect on waist circumference, %TBF, systolic blood pressure, and adverse events. No data were available on the effect of prebiotics on diastolic blood pressure. Probiotics compared to placebo may have little to no effect on BMI, body weight, waist circumference, %TBF, blood pressure, and adverse events in children and adolescents (0 to 19 years). Synbiotics compared to placebo may result in a reduction in systolic blood pressure (mean difference = -40.00, 95% CI = -50.63 to -29.37) in children and adolescents (0 to 19 years); according to one study with 56 participants. The evidence is very uncertain about the effects of synbiotics compared to a placebo on BMI, body weight, waist circumference, blood pressure, and adverse events. No data were available on the effect of synbiotics compared to placebo on %TBF. Synbiotics, compared to probiotics, may have little to no effect on waist circumference, %TBF, and adverse events. No data were available on the effect of synbiotics compared to probiotics on BMI, body weight, and blood pressure. According to one study with 48 participants and very low-certainty of evidence, SCFAs compared to placebo may result in a reduction in waist circumference (mean difference = -5.08, 95% CI = -7.40 to -2.76) and BMI (mean difference = -2.26, 95% CI = -3.24 to -1.28) in children and adolescents (0-19 years). SCFAs compared to placebo may have little to no effect on adverse events. No data were available on the effect of SCFAs on body weight, %TBF, and blood pressure. Adverse events, i.e. abdominal cramps, abdominal discomfort, abdominal pain, diarrhoea, vomiting, and migraine, were reported in the prebiotics group but with very low incidence. Additionally, adverse events such as nausea and headache were reported in the SCFAs group, but with low incidence.

AUTHORS' CONCLUSIONS: In adolescents aged 10 to 19 years, gut microbiome-based interventions may result in little to no difference in obesity-related outcomes. In children and adolescents aged 0 to 19 years, prebiotics may result in a small reduction in BMI and body weight; synbiotics may result in a reduction in systolic blood pressure, and SCFAs may result in a reduction in BMI and waist circumference, albeit the certainty of evidence was very low. The evidence was of very low certainty due to few studies per comparison, small sample sizes, short intervention durations, and insufficient reporting of adverse events. More rigorous research examining different types of gut microbiome-based interventions for the management of obesity is required in children and adolescents, both in clinical and community settings. Future trials should also report methods related to randomisation, blinding, and compliance, as well as include prespecified analysis plans.},
}

Humans
Adolescent
Child
Randomized Controlled Trials as Topic
*Pediatric Obesity/therapy/microbiology
*Gastrointestinal Microbiome
Probiotics/therapeutic use
Child, Preschool
Young Adult
Prebiotics/administration & dosage
Synbiotics/administration & dosage
Infant
Fecal Microbiota Transplantation
Body Mass Index
Overweight/therapy

@article {pmid40637165,
year = {2025},
author = {Blok, NB and Bozadjieva-Kramer, N},
title = {Unlocking the Gut: Microbiome's Role in Energy Metabolism Editorial Focus on "Reutericyclin mitigates risperidone-induced suppression of anaerobic energy expenditure".},
journal = {American journal of physiology. Regulatory, integrative and comparative physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpregu.00158.2025},
pmid = {40637165},
issn = {1522-1490},
}

@article {pmid40637070,
year = {2025},
author = {Chivu, RF and Melesteu, C and Bobirca, A and Dumitrescu, DA and Melesteu, I and Mustatea, P and Bobirca, F and Patrascu, T},
title = {Advances in Gastric Carcinogenesis Related to Helicobacter Pylori.},
journal = {Chirurgia (Bucharest, Romania : 1990)},
volume = {120},
number = {3},
pages = {322-344},
doi = {10.21614/chirurgia.3147},
pmid = {40637070},
issn = {1221-9118},
mesh = {Humans ; *Stomach Neoplasms/microbiology/genetics/immunology ; *Helicobacter pylori/pathogenicity/genetics ; *Helicobacter Infections/complications/microbiology/immunology ; Risk Factors ; Epigenesis, Genetic ; Cell Transformation, Neoplastic ; Carcinogenesis ; },
abstract = {Helicobacter pylori (H. pylori), a Gram-negative bacterium, has been classified as a Group I carcinogen by the World Health Organization. It represents the most significant modifiable risk factor for gastric cancer (GC), particularly the intestinal subtype. Although global infection rates are on the decline, its role in gastric oncogenesis remains prominent, especially in areas with elevated incidence rates. This review consolidates current insights into the molecular and immunological pathways through which H. pylori contributes to gastric tumorigenesis, with a focus on epigenetic modulation, host-microbe interactions, and the influence of the gastric microbiota. Chronic inflammation, instigated by H. pylori infection, advances through the Correa cascade, culminating in neoplastic transformation. Principal virulence determinants, including CagA and VacA, compromise epithelial barriers and initiate oncogenic signaling networks such as NF-úB, STAT3, Wnt/ÃÂ[2]-catenin, and Hippo/YAP. The infection is also associated with extensive epigenetic remodeling, notably promoter hypermethylation of tumor suppressor genes like CDH1, and regulation of non-coding RNAs (including miRNAs, lncRNAs, and circRNAs). Sustained colonization drives immune polarization toward Th1 and Th17 responses, promotes immune escape mechanisms such as PD-L1 overexpression, and alters the composition of the gastric microbiome. Recent findings highlight the potential role of non-H. pylori microbial species in supporting tumor progression. While eradication of H. pylori lowers the risk of gastric cancer, it does not confer complete protection, particularly in individuals with pre-existing mucosal alterations or microbial dysbiosis. The development of H. pylori-associated gastric cancer is a multifactorial process, shaped by microbial virulence, host genetics, epigenetic shifts, and immune dynamics. A deeper understanding of these interrelated mechanisms is crucial for refining preventive measures, diagnostic accuracy, and therapeutic approaches.},
}

Humans
*Stomach Neoplasms/microbiology/genetics/immunology
*Helicobacter pylori/pathogenicity/genetics
*Helicobacter Infections/complications/microbiology/immunology
Risk Factors
Epigenesis, Genetic
Cell Transformation, Neoplastic
Carcinogenesis

@article {pmid40637059,
year = {2025},
author = {Bachmann, KF and Cotoia, A and Reintam Blaser, A},
title = {Gastrointestinal function and nutritional interventions in septic shock.},
journal = {Current opinion in critical care},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCC.0000000000001302},
pmid = {40637059},
issn = {1531-7072},
abstract = {PURPOSE OF THE REVIEW: Gastrointestinal (GI) dysfunction significantly impacts patient outcomes in septic shock, complicating clinical management due to its central role in systemic inflammation, barrier integrity, and nutrient assimilation. This review summarizes the evolving understanding of GI dysfunction during septic shock and provides an updated framework for clinical management.

RECENT FINDINGS: New insights from recent studies focus on individualized nutritional strategies over standardized calorie-driven targets, highlighting risks associated with aggressive enteral nutrition, such as exacerbation of gut ischemia and bowel distension, and microbial dysbiosis. Maintaining splanchnic perfusion, monitoring GI dysfunction with standardized tools, and advancing nutritional support progressively based on patient-specific gastrointestinal tolerance are current strategies. Novel adjunctive therapies targeting gut permeability and microbiome restoration have been proposed, yet robust clinical data remain limited.

SUMMARY: Clinical management should prioritize hemodynamic stabilization and organ support rather than immediately targeting any nutritional goals. Monitoring GI function systematically and tailoring nutritional interventions may prevent complications and support recovery. Future research should validate monitoring tools, refine individual patient assessment, and evaluate novel therapeutic interventions to improve patient-centered outcomes in septic shock.},
}

@article {pmid40636558,
year = {2025},
author = {Dabritz, HA and Panditrao, MV and Pandey, S and Dover, N and Barash, JR and Khouri, JM and Read, JS},
title = {Infant Botulism and Carbohydrate Blood Group Antigens: Preliminary Results from a Discordant Twin Study.},
journal = {Journal of pediatrics. Clinical practice},
volume = {17},
number = {},
pages = {200152},
pmid = {40636558},
issn = {2950-5410},
abstract = {OBJECTIVE: We investigated if specific carbohydrate blood group antigens were associated with infant botulism (IB) among discordant twins and triplets.

STUDY DESIGN: Infants in the US and Canada from 2015 to 2022 who had laboratory-confirmed IB; were members of a multiple gestation birth; and had unaffected sibling(s), were eligible to participate. Blood specimens were tested for ABO, Lewis, H, and P1 carbohydrate blood antigens. FUT2 and FUT3 genes were sequenced to determine secretor and Lewis antigen status, respectively. In addition, characteristics of IB cases in the study were compared to the singleton US-Canadian IB cases from 2015 to 2022.

RESULTS: Parents of 14 of 26 IB cases who were twins or triplets with unaffected siblings consented to participate. No statistically significant associations between blood group antigens (ABO, Lewis, H, and P1) and IB were demonstrated. Twin cases in this study were significantly younger at onset of illness (median age 8.6 vs 17.3 weeks for the singleton US-Canadian IB cases, t test P < .001); and less likely to be fed exclusively breastmilk (14% for twin vs 63% for the US-Canadian IB cases) and more likely to be mixed-fed breast milk and formula (86% for twin vs 23% for the US-Canadian IB cases, Fisher exact test P < .001).

CONCLUSIONS: In this first-of-its-kind small study of IB twin or triplet cases and their unaffected siblings, no carbohydrate blood group antigens were associated with IB. Future studies could compare the microbial composition of the gut microbiome of IB cases and uninfected twin siblings or the prevalence of ABO blood groups in IB cases vs population norms.},
}

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

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

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

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

@article {pmid40636492,
year = {2025},
author = {van Essen, RRT and Kaur, J and Li, T and Mann, RC and Sawbridge, TI},
title = {The diversity, dynamics, and culturability of bacterial and fungal communities present in warm-season pasture grass seeds.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1621463},
pmid = {40636492},
issn = {1664-302X},
abstract = {A rapidly changing climate has resulted in increasing challenges for farmers. This has led to an increase in demand for beneficial microbes to help fight these challenges faced by farmers, improving crop production under harsh conditions. Increasing temperatures caused by the changing climate will also affect the dairy industry in temperate climates around the world. This has resulted in an increasing importance of warm-season pasture grasses to fill the feed gaps left by the affected temperate grasses. In this study, we assessed the microbial communities present in commercially available warm-season pasture grass seeds. We utilised amplicon metagenomics to profile and compare the bacterial and fungal communities of seeds from three different genera of warm-season pasture grasses. Microbial isolations have also been performed to assess the culturability of the seed microbiome. Significant differences in drivers of bacterial and fungal communities within warm-season pasture grass seeds were observed. In addition, most of the bacteria present in high abundance were found to be culturable, while a relatively lower percentage of abundant fungi were culturable. Analysis of the bacterial communities showed considerable variation between different distributors, possibly driven by differing seed processing methods. This variation indicates that the bacterial communities could be manipulated by providing different bacteria to the seed to promote plant growth under different conditions. In contrast, the fungal communities were more strongly driven by the genetics of the respective host genera. This suggests that differences in fungal strain levels could be exploited for modification of fungal microbiome effects.},
}

@article {pmid40636483,
year = {2025},
author = {Xing, J and Jia, M and Zhang, G and Li, L and Liu, S and Li, G and Liu, G},
title = {The composition and predictive function of the fecal microbiota in female donkeys across different reproductive cycles.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1565360},
pmid = {40636483},
issn = {1664-302X},
abstract = {The microorganisms residing in the gastrointestinal tract of monogastric herbivores play a vital role in nutrient absorption and maintaining the host's health. However, the quantitative and functional establishment of these microorganisms in female donkeys across different reproductive cycles has not yet been examined. Knowledge regarding the composition and function of gut microbiota in female donkeys during different reproductive cycles remains limited. By applying high-throughput sequencing technology and functional prediction applied to fecal samples from female donkeys across different reproductive cycles, we characterized their gut microbial composition and predicted their functional profiles. The fecal microbiota diversity in female donkeys showed no significant differences across different reproductive cycles through alpha diversity. However, the relative abundance of Firmicutes was higher during lactation, whereas Bacteroidetes were significantly higher during pregnancy. Principal coordinate analysis (PCoA) revealed the gut microbiota composition of pregnant female donkeys differed significantly from that in lactating and non-pregnant female donkeys. Bacteroidetes and Alloprevotella dominated during pregnancy in donkeys, while Firmicutes and unidentified Clostridiales were more prevalent during lactation. For functional prediction, there were significant differences in the relative abundance of pathways in the feces of female donkeys across different reproductive cycles, such as immune system processes, metabolism, glycan biosynthesis and metabolism, environmental adaptation and cell motility (p < 0.05 or p < 0.01). By correlating metabolic functions with microbial phyla, we suggest that metabolic and immune functions associated with the gut microbiota in lactating donkeys may be reduced compared to pregnant donkeys. Principal component analysis (PCA) revealed that the functional KEGG Orthologs (KOs) in the fecal microbiota of pregnant donkeys were distinctly separated from the lactation and non-pregnant female donkeys. Microbial community composition and structure exhibit distinct characteristics across different reproductive cycle, which are closely related to the functions of the microbiome. Our findings provide a foundation for understanding the compositional and functional differences in the microbial communities of mares' feces across different reproductive cycles, offering valuable insights for the precise feeding of mares throughout different reproductive cycles.},
}

@article {pmid40636353,
year = {2025},
author = {Tan, L and Jia, F and Liu, Y},
title = {Advances in research on the role of gut microbiota in the pathogenesis and precision management of gallstone disease.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1535355},
pmid = {40636353},
issn = {2296-858X},
abstract = {Gallstone disease remains a prevalent global gastrointestinal condition with a rising incidence, posing substantial challenges to healthcare systems and public health initiatives. Advances in multi-omics and sequencing technologies have illuminated the pivotal role of gut microbiota in its pathogenesis, progression, and management. This article reviews the disrupted microbiota profiles observed in patients with gallstone disease and their connection to the metabolic pathways involved in gallstone formation, particularly focusing on cholesterol metabolism, bile acid dynamics, and inflammatory pathways. It also discusses the enduring impacts of cholecystectomy on gut microbial functions and their metabolic implications. Novel strategies targeting gut microbiota, including probiotics, microbial metabolite supplementation, dietary adjustments, integrative medicine, and emerging microbial therapies, present promising avenues for precise treatment. Furthermore, this review underscores the value of future research into multi-omics integration, microbiome engineering, and global collaborations, advocating for interdisciplinary and personalized approaches to gallstone management. However, unresolved challenges, such as ensuring stable colonization of functional microbiota, refining tailored therapeutic strategies, and assessing long-term outcomes, warrant further investigation. This work aims to provide a comprehensive resource for understanding gallstone disease within a microecological framework, supporting the development of precision medicine-based prevention and treatment paradigms.},
}

@article {pmid40636324,
year = {2025},
author = {Liu, S and Zhang, Z},
title = {Distinct Lung Adenocarcinoma-Associated Microbiota Are Associated with Inflammatory Immune Landscapes and Tumor Cell Proliferation via LCIIAR-ISG15 Regulatory Networks.},
journal = {Cancer management and research},
volume = {17},
number = {},
pages = {1315-1328},
pmid = {40636324},
issn = {1179-1322},
abstract = {INTRODUCTION: Emerging research emphasizes the critical role of local microbiota in shaping the tumor microenvironment (TME) and influencing cancer progression. Lung adenocarcinoma (LUAD) is distinguished by unique bacterial communities that appear to regulate immune responses, gene expression, and patient outcomes.

METHODS: We compiled microbiome profiles from several cancer types-including LUAD, lung squamous cell carcinoma (LUSC), breast carcinoma (BRCA), and thyroid carcinoma (THCA)-using public databases. Non-negative matrix factorization (NMF) was employed to categorize LUAD cases based on TME features, while DESeq2 was used to pinpoint bacterial taxa with differing abundance. Multi-omics networks were developed to integrate microbial, transcriptomic, and clinical data. For in vitro verification, we conducted siRNA-mediated knockdown of the long non-coding RNA LCIIAR and ISG15 in Lewis lung carcinoma cells, followed by proliferation assays.

RESULTS: In contrast to LUSC, BRCA, and THCA, LUAD exhibited distinct microbial populations, with notable enrichment of Cylindrospermopsis, Cyanothece, and Sulfolobus. NMF clustering identified two LUAD subtypes with differing prognoses. One longer survival cluster, marked by reduced bacterial presence and stronger antitumor immunity-reflected in stronger immune response, increased effector T cells activity, and greater immune cell infiltration. A competing endogenous RNA (ceRNA) network analysis established a link between LCIIAR and ISG15, both overexpressed in LUAD and associated with worse survival outcomes. Knockdown LCIIAR or ISG15 through siRNA significantly inhibited lung cancer cell proliferation, pointing to their roles in tumor growth and ceRNA-mediated regulation.

CONCLUSION: LUAD features a distinctive microbiota that engages with inflammatory and ceRNA regulatory pathways. These observations underscore the value of targeting microbiome-influenced mechanisms, such as the LCIIAR-ISG15 axis, as a promising approach to enhance treatment outcomes in lung adenocarcinoma.},
}

@article {pmid40636281,
year = {2025},
author = {Magliano, G and Morello, E and Farina, M and Radici, V and Galli, M and Brambilla, G and Malagola, M and Russo, D and Avenoso, D},
title = {A case of Severe Gastrointestinal Toxicity after Allogeneic Hematopoietic Stem Cell Transplantation: Can We Improve the Evaluation of the "Gut Fitness"?.},
journal = {Mediterranean journal of hematology and infectious diseases},
volume = {17},
number = {1},
pages = {e2025054},
pmid = {40636281},
issn = {2035-3006},
}

@article {pmid40636258,
year = {2025},
author = {Lederer, AK and Chikhladze, S and Badr, MT},
title = {Editorial: The microbiome in surgery - friend or foe?.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1629822},
doi = {10.3389/fcimb.2025.1629822},
pmid = {40636258},
issn = {2235-2988},
}

@article {pmid40636116,
year = {2025},
author = {Garcia-Gonzalez, N and Wallaeys, C and Toussaint, W and Hochepied, T and Dewaele, S and De Beul, S and Van Loke, R and Vandewalle, J and Timmermans, S and Libert, C},
title = {Generation of a new Paneth cell-specific Cre-recombinase transgenic mouse line.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1576995},
pmid = {40636116},
issn = {1664-3224},
mesh = {Animals ; *Paneth Cells/metabolism/immunology ; Mice ; Mice, Transgenic ; *Integrases/genetics/metabolism ; Mice, Inbred C57BL ; *alpha-Defensins/genetics ; Intestine, Small/metabolism ; Muramidase/metabolism ; },
abstract = {Paneth cells are located in the crypts of Lieberkühn in mammalian small intestines and are producing antimicrobial peptides to keep the microbiome under control. The genetic manipulation of Paneth cells and their tracking and depletion depend on a solid Paneth cell-specific Cre-transgenic line. Here, we describe bulk RNA sequencing (RNA-seq)-based expression data from pure, sorted Paneth cells of C57BL/6J mice and identify several strongly expressed Paneth cell-specific genes, the expression of which is stable under pathophysiological conditions, as well as in the duodenum, jejunum, and ileum. We selected the Defa24 gene regulatory sequences and generated a new Defa24iCre transgenic line using BAC technology, Tg(Defa24-icre)Cli. The resulting transgenic line provides robust expression and allows for the complete depletion of Paneth cells by cell ablation, yielding mice without any detectable lysozyme biological activity in the small intestines.},
}

Animals
*Paneth Cells/metabolism/immunology
Mice
Mice, Transgenic
*Integrases/genetics/metabolism
Mice, Inbred C57BL
*alpha-Defensins/genetics
Intestine, Small/metabolism
Muramidase/metabolism

@article {pmid40636107,
year = {2025},
author = {Liang, B and Tan, J and Li, J and Wang, X and Li, G and Li, H and Li, T and Gao, H},
title = {Epidemiology, molecular typing, microbiome-immune interactions and treatment strategies of endometrial cancer: a review.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1595638},
pmid = {40636107},
issn = {1664-3224},
mesh = {Humans ; *Endometrial Neoplasms/epidemiology/therapy/immunology/microbiology/etiology ; Female ; *Microbiota/immunology ; Risk Factors ; },
abstract = {This review focuses on the field of endometrial cancer. Since 2020, there have been 417,367 new cases of endometrial cancer diagnosed globally and 97,370 deaths reported. Endometrial cancer ranks second in terms of incidence among female genital malignancies and third in terms of mortality among gynecological cancers. The stage, grade, and histological subtype of endometrial cancer were closely correlated with the risk of recurrence and prognosis for survival. Meanwhile, endometrial cancer exhibits significant biological heterogeneity. The complex interactions among the reproductive tract, host cells, and the microbial environment may harbor novel disease mechanisms. In this review, we provide an overview of the epidemiological characteristics, major risk factors, histological and molecular subtypes of endometrial cancer, as well as explore the associations between the female reproductive tract microbiome, immunity, and cancer progression. We also identify the specific roles of different cytokines in the pathophysiology of endometrial cancer. By integrating findings from diverse research fields, this comprehensive review offers an in-depth understanding of the multidimensional nature of endometrial cancer and highlights the significant potential and promising avenues that microbiological factors present for advancing future cancer research and guiding the development of innovative therapeutic strategies.},
}

Humans
*Endometrial Neoplasms/epidemiology/therapy/immunology/microbiology/etiology
Female
*Microbiota/immunology
Risk Factors

@article {pmid40636105,
year = {2025},
author = {Rijks, V and Zuurveld, M and Garssen, J and Kostadinova, AI and Willemsen, LEM},
title = {The potential immunomodulatory role of human milk oligosaccharides in prevention of viral infections and development of asthma in early life.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1572787},
pmid = {40636105},
issn = {1664-3224},
mesh = {Humans ; *Asthma/prevention & control/immunology ; *Oligosaccharides/immunology ; *Milk, Human/immunology/chemistry ; *Respiratory Syncytial Virus Infections/immunology/prevention & control ; Infant ; *Virus Diseases/prevention & control/immunology ; Gastrointestinal Microbiome/immunology ; Animals ; Immunomodulation ; *Picornaviridae Infections/immunology/prevention & control ; },
abstract = {Around 10% of the Western population is diagnosed with asthma, and this percentage is only expected to increase in the coming years. Allergic asthma often develops during early infancy and is characterized by chronic pulmonary type 2 inflammation and airway hyperresponsiveness. Severe viral infections in early life are thought to be a risk factor for allergic asthma. The most common causes of severe viral infections in early life are respiratory syncytial virus (RSV) and rhinovirus (RV). How viral infections in early life are related to the later development of asthma is not yet known, but the pathophysiology of RSV/RV infection and asthma overlap in several areas. RSV and RV are both able to induce type 2 immunity which may contribute to the development of allergic asthma which is driven by type 2 responses against airborne allergens such as house dust mites. In early life, infants' intestines, microbiome and immune function need to mature, and breastfeeding helps to facilitate these major steps in development. Human milk oligosaccharides (HMOs) are the third largest component of human milk and have been shown to promote the development and function of the infant microbiome and may have a beneficial effect on immune maturation by promoting type 1 and regulatory immune responses. In addition, they can stimulate epithelial barrier integrity and directly interact with glycan receptors. Certain bacteria in the gut can metabolize HMOs into short-chain fatty acids (SCFA), which can exert beneficial anti-inflammatory effects locally in the gut or systemically and help maintain barrier properties and immune homeostasis. HMOs and SCFA could have protective effects on both the immune pathways in allergic asthma and viral infections. This review describes the molecular and immunomodulatory mechanisms by which different HMOs and SCFA may help defend against viral infections and also protect against allergic asthma.},
}

Humans
*Asthma/prevention & control/immunology
*Oligosaccharides/immunology
*Milk, Human/immunology/chemistry
*Respiratory Syncytial Virus Infections/immunology/prevention & control
Infant
*Virus Diseases/prevention & control/immunology
Gastrointestinal Microbiome/immunology
Animals
Immunomodulation
*Picornaviridae Infections/immunology/prevention & control

@article {pmid40636093,
year = {2025},
author = {Espinosa, MA and Rivera Gutierrez, RJ and Villamarin, J and Acosta, A},
title = {Precision Medicine for Obesity Treatment.},
journal = {Journal of the Endocrine Society},
volume = {9},
number = {9},
pages = {bvaf102},
pmid = {40636093},
issn = {2472-1972},
abstract = {Obesity is a chronic, heterogeneous, and complex disease associated with increased morbidity, mortality, and health-care costs. By 2030, 1 in 2 people in the United States will have obesity. Lifestyle interventions are the cornerstone of obesity management. However, they often fail to achieve clinically significant weight loss, necessitating additional treatments involving pharmacotherapy or procedures. Advancements in obesity pharmacotherapy have improved weight-loss outcomes and reduced associated comorbidities. Despite these advances, variability in response to treatment between individuals is still considerable. This variability reflects limitations in the current "one-size-fits-all" approach to obesity management. A precision medicine approach aims to address this gap by incorporating genetic, physiological, and behavioral characteristics to guide treatment selection and improve outcomes. Advances in multi-omics technologies, such as genomics, proteomics, metabolomics, and microbiome profiling, offer new opportunities to refine patient stratification and identify novel therapeutic targets. These tools may help move obesity care toward a more individualized and mechanism-based approach.},
}

@article {pmid40635890,
year = {2025},
author = {Li, X and Liu, Y and Shen, C and Shao, C and Jiang, H},
title = {Association of dietary index for gut microbiota with frailty in middle-aged and older Americans: a cross-sectional study and mediation analysis.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1615386},
pmid = {40635890},
issn = {2296-861X},
abstract = {BACKGROUND: While frailty poses significant challenges in aging populations, evidence regarding gut microbiome-targeted nutritional strategies remains limited. The novel Dietary Index for Gut Microbiota (DI-GM), quantifying microbial-pertinent dietary patterns, provides a framework for personalized frailty mitigation.

METHODS: This cross-sectional study analyzed 12,914 middle-aged and older Americans (≥45 years) from National Health and Nutrition Examination Survey 2005-2018. Frailty status was assessed using a validated 49-item index (non-frail ≤0.21; frail >0.21). The DI-GM (range 0-10) was derived from 14 microbiota-linked dietary components through two 24-h recall interviews. Multivariable logistic regression with sensitivity analyses, restricted cubic splines (RCS), stratified analyses, and mediation effect were implemented to systematically evaluate DI-GM-frailty associations.

RESULTS: Adjusted analyses revealed a dose-dependent inverse association between DI-GM and frailty (OR = 0.86, 95%CI: 0.84-0.88 per unit increase). RCS identified a nonlinear inflection at DI-GM = 4.082 (p for nonlinearity = 0.031), beyond which each unit elevation corresponded to 12.6% reduced frailty probability (OR = 0.874, 95%CI: 0.806-0.947). Stratified analyses demonstrated enhanced protective effects in women (OR = 0.84 vs. male 0.90; p for interaction = 0.011) and college-educated individuals (OR = 0.85 vs. 0.93; p for interaction = 0.031). Mediation analysis indicated BMI mediated 38.28% (95%CI: 26.62-62.6, p < 0.001) of the DI-GM effect on frailty progression.

CONCLUSION: Higher DI-GM scores associate with lower frailty prevalence, particularly among women and highly-educated populations, partially mediated through BMI modulation. These findings establish DI-GM as a microbiota-targeted nutritional guideline for age-related frailty interventions, bridging dietary patterns with microbial homeostasis in geriatric care.},
}

@article {pmid40635758,
year = {2025},
author = {Pan, J and Lin, S and Qian, Q and Fu, S and Liu, X},
title = {Gut-brain axis in post-traumatic stress disorder: microbial - mediated mechanisms and new therapeutic approaches - A narrative review.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1621678},
pmid = {40635758},
issn = {1663-9812},
abstract = {Post-traumatic stress disorder (PTSD) is a severe mental disorder that occurs after experiencing or witnessing a traumatic event. Not only does this disorder severely impair the quality of life and emotional wellbeing of patients, but in recent years the global rate of PTSD diagnoses has increased to 1.5-2 times, and the prevalence of PTSD associated with COVID-19 events in particular has surged to 10%-25%, underscoring the urgency of developing effective treatments. The lifetime prevalence of PTSD in the general population is estimated to be approximately 3.9%, while in high-risk populations, such as war veterans, it can be as high as 30%. As a key pathway connecting the central nervous system to peripheral organs, the gut-brain axis has received increasing attention for its role in PTSD. Although the gut-brain axis has been shown to be associated with several psychiatric disorders, especially depression, its specific role in PTSD remains undercharacterized. Existing studies suggest that specific strains of Lactobacillus (e.g., Lactobacillus reuteri) may alleviate inflammatory responses and improve PTSD-like behaviors by down-regulating the expression of pro-inflammatory factors (IL-6 and TNF-α). In this study, we used a narrative review approach to sort out the research progress of gut microbiota alteration in PTSD, and compared the characteristics of changes in specific microbial taxa (e.g., Bacteroides, Lactobacillus, etc.), the index of microbiota diversity (α/β diversity), and the levels of inflammatory markers (e.g., IL-6, TNF-α) between the animal model and the human patients, respectively, in order to We further explored the potential pathogenic mechanisms mediated by microorganisms, such as influencing the vagal pathway, hypothalamic-pituitary-adrenal (HPA) axis function, immune system and other processes involved in the pathology of PTSD, and summarized the intervention strategies targeting gut microecology, such as probiotic supplementation, dietary interventions and fecal bacteria transplantation.},
}

@article {pmid40635484,
year = {2025},
author = {You, HS and Park, JY and Seo, H and Kim, BJ and Kim, JG},
title = {Distinct microbial signatures of liquid biopsy samples during gastric carcinogenesis and insights from extracellular vesicle analysis.},
journal = {The Korean journal of internal medicine},
volume = {40},
number = {4},
pages = {571-583},
doi = {10.3904/kjim.2024.339},
pmid = {40635484},
issn = {2005-6648},
support = {2022R1F1A1069321//National Research Foundation of Korea/ ; //Ministry of Science and ICT/ ; //Chung-Ang University/ ; },
mesh = {Humans ; *Stomach Neoplasms/microbiology/pathology/diagnosis ; *Extracellular Vesicles/microbiology ; Liquid Biopsy ; Male ; Female ; Middle Aged ; Aged ; Case-Control Studies ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification ; Gastric Juice/microbiology ; *Biomarkers, Tumor ; DNA, Bacterial/genetics ; Saliva/microbiology ; Adult ; },
abstract = {BACKGROUND/AIMS: The early detection of gastric cancer is crucial for improving patient outcomes. However, its pathogenesis is not fully understood. The microbiome and extracellular vesicles (EVs) might play a role in gastric carcinogenesis. We aimed to identify gastric-carcinogenesis-associated microbial signatures and evaluate whether these features vary across disease stages.

METHODS: We enrolled 141 participants (132 patients with gastric cancer or dysplasia and 9 healthy controls). Microbial-derived EVs were isolated from gastric juice, saliva, serum, and urine. Next-generation sequencing of EV-derived bacterial DNA was performed.

RESULTS: This sequencing revealed the alpha and beta diversities and microbial composition across different disease stages. The alpha diversity was significantly increased in the gastric juice and serum of disease groups. The beta diversity showed significant differences among patient groups. Distinct microbial signatures were observed across different disease stages in all four sample types. Specific bacterial species--Cutibacterium acnes, Streptococcus oralis, Pseudomonas antarctica, Ralstonia insidiosa, and Pseudomonas yamanorum--exhibited unique abundance patterns associated with disease progression, suggesting their potential as noninvasive biomarkers.

CONCLUSION: Changes in microbial diversity and distinct microbial signatures were observed during gastric carcinogenesis in both gastric juice and extragastric samples, indicating the potential of microbial-derived EVs from liquid biopsy samples as biomarkers for gastric cancer.},
}

Humans
*Stomach Neoplasms/microbiology/pathology/diagnosis
*Extracellular Vesicles/microbiology
Liquid Biopsy
Male
Female
Middle Aged
Aged
Case-Control Studies
*Gastrointestinal Microbiome
*Bacteria/genetics/classification
Gastric Juice/microbiology
*Biomarkers, Tumor
DNA, Bacterial/genetics
Saliva/microbiology
Adult

@article {pmid40635331,
year = {2025},
author = {Colagiero, M and Pocasangre, L and Ciancio, A and Pentimone, I and Rosso, LC},
title = {Farming System and Nematodes Affect the Rhizosphere Microbiome of Tropical Banana Plants.},
journal = {Environmental microbiology reports},
volume = {17},
number = {4},
pages = {e70155},
doi = {10.1111/1758-2229.70155},
pmid = {40635331},
issn = {1758-2229},
support = {727624//European Union Programme H2020/ ; },
mesh = {*Musa/microbiology/parasitology/growth & development ; *Rhizosphere ; Animals ; *Nematoda/physiology/classification ; *Microbiota ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; Costa Rica ; *Agriculture/methods ; Fungi/genetics/classification/isolation & purification ; Soil/chemistry/parasitology ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; },
abstract = {We studied the effects of farming systems and soil nematodes on the rhizosphere microbial profiles in three banana farming systems (conventional, barbecho and organic) compared with non-cultivated controls. Bacterial 16S Amplicon Sequence Variants (ASV) and fungal ITS1-2 OTUs were obtained by NGS from experimental fields in Costa Rica, each with a given farming system. Plant-parasitic nematodes included Meloidogyne, Helicotylenchus, Radopholus, and other species. The banana cultivation and, to a minor extent, the field management type influenced the rhizosphere ASV and OTUs abundances, with a higher diversity found in organic versus conventional crops, with the organic control as the most biodiverse. Diversity indices showed differences for the total number of individuals (lowest in conventional banana) and rare species (highest in organic controls). Fungi differed for the highest species richness in the organic controls. Soil variables affecting microbial abundance included low Fe content and acidic pH. Nematodes were associated with microbial taxa that were specific to each herbivore species or feeding group, with omnivores/predators influencing microbial profiles mostly in the organic crop and controls. The organic management had the lowest impact on the diversity of belowground nematodes and rhizosphere microbiome, highlighting its beneficial potential in sustainable banana production and agroecosystem resilience.},
}

*Musa/microbiology/parasitology/growth & development
*Rhizosphere
Animals
*Nematoda/physiology/classification
*Microbiota
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
Costa Rica
*Agriculture/methods
Fungi/genetics/classification/isolation & purification
Soil/chemistry/parasitology
Biodiversity
RNA, Ribosomal, 16S/genetics

@article {pmid40635009,
year = {2025},
author = {Schulz, C and Vilchez-Vargas, R and Öcal, E and Koch, N and Puhr-Westerheide, D and Burnell, LF and Hirner-Eppeneder, H and Benckert, J and Pech, M and Reimer, P and Verslype, C and Kuhl, C and Tran, A and Ricke, J and Malfertheiner, P and Alunni-Fabbroni, M},
title = {Profiling of the tumor-associated microbiome in patients with hepatocellular carcinoma.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {53},
pmid = {40635009},
issn = {1757-4749},
abstract = {BACKGROUND: Tumor tissues have been shown to host a diverse array of bacteria, suggesting a link between the intratumoral microbiota and the development and progression of cancer. The aim of this explorative study was to perform microbiome analysis in liver tumor and to evaluate its relationship with cancer stage and survival outcome.

RESULTS: We conducted an exploratory study on a cohort of 20 hepatocellular cancer patients from the SORAMIC trial. Patients were divided into curative and palliative groups according to treatment type (local ablation, alone or combined with systemic therapy). The V1-V2 regions of 16 S rRNA were sequenced starting from archival tissues. Amplicon Sequence Variants (ASVs) were taxonomically assigned to the upper (UGI) or lower (LGI) gastrointestinal tract. Bacteria were identified in both tumoral and non-tumoral tissues, showing higher diversity and correlation between diversity and shorter survival in the palliative group (S. aureus p < 0.05; B. parvula p < 0.01; A. chinensis p < 0.01). Both therapy groups were enriched with the genus Bacilli, including Streptococcus spp., Gemella haemolysans and Helicobacter pylori, commonly found in UGI. The results suggested that among palliative patients and those with shorter survival, G. haemolysans was more prevalent, while H. pylori was more often found in curative patients with longer survival. However none of the results were significantly different (p > 0.05). A higher microbiome biodiversity was associated with an increased number of lesions (Hoylesella, Agathobacter, Sphingobium, Cardiobacterium, Photobacterium and Serratia, all with p < 0.01).

CONCLUSIONS: The presence of bacteria, predominantly from communities of the UGI, suggests their translocation into liver tissue due to impaired barrier function of the upper gut or the ascending pathway along the biliary duct system. The intratumoral prevalence of bacteria with proinflammatory and oncogenic potential suggests their potential role in HCC pathomechanisms.},
}

@article {pmid40634894,
year = {2025},
author = {Liu, H and Xu, X and Wang, R and Kang, J and Shen, Y and Liu, W},
title = {Gender-specific protective effects of dietary index for gut microbiota on cardiovascular disease: insights from NHANES 2007-2020.},
journal = {BMC cardiovascular disorders},
volume = {25},
number = {1},
pages = {500},
pmid = {40634894},
issn = {1471-2261},
support = {XYJG2024003//the Teaching Reform Research Project of Postgraduate Education in 2024/ ; TDSK2024001//the Project of Provincial Colleges and Universities' Basic Scientific Research Operating Expenses Project in 2024/ ; YZSY2024005//the Yanzhao Medical Research Project of Hebei University of Traditional Chinese Medicine/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; *Cardiovascular Diseases/epidemiology/prevention & control/microbiology/diagnosis ; Middle Aged ; Nutrition Surveys ; Sex Factors ; United States/epidemiology ; Adult ; Protective Factors ; Risk Assessment ; Prevalence ; Cross-Sectional Studies ; *Diet, Healthy ; Aged ; },
abstract = {BACKGROUND: Cardiovascular disease (CVD) represents a significant global health burden. The gut microbiome, as a potential regulatory factor, and its synergistic interaction with dietary patterns remains underexplored. The dietary index for gut microbiota (DI-GM), which quantifies the impact of diet on gut microbiota, has limited evidence of DI-GM's association with CVD, particularly regarding gender-specific effects and dose-response patterns.

METHODS: This study utilized data from the National Health and Nutrition Examination Survey (NHANES) 2007-2020, which included 24,111 adult participants. We employed multivariable logistic regression models to assess the relationship between DI-GM and CVD. To explore possible nonlinear associations, we carried out a restricted cubic spline (RCS) analysis. Furthermore, we conducted subgroup analysis, gender stratification analysis, and sensitivity analysis.

RESULTS: A 1-unit increase in DI-GM score was associated with a 4% reduction in CVD prevalence (adjusted OR = 0.96, 95% CI: 0.93-0.98, p = 0.002). Compared to the lowest quartile (Q1), the highest quartile (Q4) showed a 17% lower CVD prevalence (OR = 0.83, 95% CI: 0.72-0.95, p = 0.008). Subgroup analysis revealed a more pronounced association in women (OR = 0.95, 95% CI: 0.92-0.99, p = 0.026). Gender-stratified logistic regression and RCS confirmed a significant inverse linear relationship between DI-GM and CVD in women. Sensitivity analyses further validated the robustness of these findings.

CONCLUSION: Dietary patterns with higher DI-GM scores were found to be linked to a lower prevalence of CVD, especially among women. These findings highlight DI-GM as a microbiota-targeted dietary strategy for CVD prevention. Prospective studies integrating multi-omics data are warranted to validate causality and elucidate sex-specific microbiota-mediated pathways.},
}

Humans
*Gastrointestinal Microbiome
Female
Male
*Cardiovascular Diseases/epidemiology/prevention & control/microbiology/diagnosis
Middle Aged
Nutrition Surveys
Sex Factors
United States/epidemiology
Adult
Protective Factors
Risk Assessment
Prevalence
Cross-Sectional Studies
*Diet, Healthy
Aged

@article {pmid40629270,
year = {2025},
author = {Sun, B and Yu, X and Qi, H and Xu, F and Jiao, W and Fang, M and Duan, L and Zeng, X and Yang, X and Wang, X and Zhu, Y and Mi, K and Shen, A and Sun, L},
title = {The gut dysbiosis and plasma lipid metabolisms signatures in children with active tuberculosis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {425},
pmid = {40629270},
issn = {1471-2180},
support = {82100010//Youth Fund of the National Natural Science Foundation of China/ ; 202201010925//Guangzhou Municipal Science and Technology Bureau/ ; 7222055//Beijing Natural Science Foundation/ ; 82170007//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The human gut microbiota is an important modulator of host immune responses and has a crucial role in the development of tuberculosis (TB). Evidences suggest that metabolites may function as a bridge between gut microbiome and TB progression in children. However, the underlying interactive mechanisms are not well explored. The results may provide useful insight into the role played by the gut microbiome in pulmonary TB in children.

METHODS: To explore the gut bacterial features and its interaction with plasma lipid metabolisms in children with TB. We enrolled children aged younger than 14 years old from Beijing Children’s Hospital and West China Second Hospital between January 2020 and June 2021. We investigated the gut bacterial community using 16S rRNA sequencing of 98 children with active TB, 37 other infectious diseases, and 80 healthy children. The plasma lipids were further analyzed using ultra-high-performance liquid chromatography coupled with mass spectrometry.

RESULTS: Children with TB showed decreased diversity and species richness indices compared to healthy children. Significant increases in the abundance of Firmicutes and Actinobacteriota combined with a decrease in the abundance of Bacteroidetes and Proteobacteria were also observed in TB children when compared with healthy controls. Among children with TB, gut bacterial composition differed in subgroups with pulmonary and extrapulmonary TB, or subgroups with different Mycobacterium tuberculosis (MTB) load. Children with TB had a higher risk of fever (OR = 3.02, P = 0.005) and poor appetite (OR = 2.96, P = 0.02) than the controls. Several bacterial genera were associated with severe illness and clinical indices, such as aspartate aminotransferase levels and fever. The plasma lipids showedc difference between TB patients and the children with other infectious diseases. Eight genera with the highest relative abundance strongly correlated with the plasma lipids.

CONCLUSIONS: The gut microbiome is compromised in TB children, with a correlation with the plasma lipid metabolites and clinical presentations. Integrating analysis of microbiome and metabolism may help improve precise diagnosis, treatment, and mechanism study for TB in children.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04141-x.},
}

@article {pmid40211819,
year = {2025},
author = {Abdullahi, IN and Trabelsi, I},
title = {Guts of healthy humans, livestock, and pets harbor critical-priority and high-risk Escherichia coli clones.},
journal = {Epidemiology and health},
volume = {47},
number = {},
pages = {e2025013},
doi = {10.4178/epih.e2025013},
pmid = {40211819},
issn = {2092-7193},
mesh = {Humans ; Animals ; *Livestock/microbiology ; *Escherichia coli/genetics/drug effects/isolation & purification ; *Pets/microbiology ; Anti-Bacterial Agents/pharmacology ; *Escherichia coli Infections/epidemiology/microbiology ; Drug Resistance, Bacterial ; *Gastrointestinal Microbiome ; },
abstract = {OBJECTIVES: In May 2024, the World Health Organization classified carbapenem (CARB)- and third-generation cephalosporin (3GC) resistance (R) in Escherichia coli as a critical priority, whereas colistin (COL) is a "last resort" antibiotic for their treatment. This meta-analysis evaluated the pooled prevalence, high-risk lineages, genetic relatedness, and mechanisms of CARBR, COLR, and 3GCR in E. coli from healthy humans and animals.

METHODS: We conducted a systematic review and meta-analyses following the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) criteria on all eligible studies that reported the analysis of E. coli, and antimicrobial susceptibility to CARB, COL and 3GC in E. coli from gut samples of clinically healthy humans, livestock, and pets from June 2014 to June 2024. Random-effect models and conserved signature indels phylogeny 1.4 were used to determine pooled prevalence rates (PPs) and the relatedness of publicly available E. coli genomes, respectively.

RESULTS: Of the 5,034 identified articles, 64 studies were deemed eligible. The overall PPs of 3GCR, CARBR, and COLR E. coli were 22.5% (95% confidence interval [CI], 17.5 to 28.3), 2.2% (95% CI, 1.0 to 4.7), and 15.5% (95% CI, 10.8 to 21.8), respectively. The PPs of 3GCR-, COLR- and CARBR E. coli significantly varied by hosts, continent, and year of studies (p<0.05). Diverse E. coli lineages were found, including 13 high-risk E. coli sequence types (STs), within which ST10 predominated. Phylogenomic analyses produced 4 clusters of related CARBR- and COLR E. coli strains (<25 single nucleotide polymorphism): ST940-blaOXA-181 from humans in Lebanon, ST617-mcr-1 from pigs in China, ST46-mcr-1 from poultry in Tanzania, and ST1720-mcr-1 from goats in France.

CONCLUSIONS: COLR and 3GCR are more frequent than CARBR in gut E. coli. These 10-year epidemiological data highlight the persistence and transmission of critical priority and high-risk E. coli strains in healthy humans and animals, raising significant One Health concerns.},
}

Humans
Animals
*Livestock/microbiology
*Escherichia coli/genetics/drug effects/isolation & purification
*Pets/microbiology
Anti-Bacterial Agents/pharmacology
*Escherichia coli Infections/epidemiology/microbiology
Drug Resistance, Bacterial
*Gastrointestinal Microbiome

@article {pmid40634580,
year = {2025},
author = {},
title = {Workouts can help gut microbes to quell cancer.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40634580},
issn = {1476-4687},
}

@article {pmid40634535,
year = {2025},
author = {Ondee, T and Pongpirul, K and Wongsaroj, L and Senaprom, S and Wattanaphansak, S and Leelahavanichkul, A},
title = {Lactiplantibacillus plantarum dfa1 reduces obesity caused by a high carbohydrate diet by modulating inflammation and gut microbiota.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24801},
pmid = {40634535},
issn = {2045-2322},
support = {FOODF67300006//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; FOODF67300006//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; N/A//Second Century Fund (C2F)/ ; N/A//Second Century Fund (C2F)/ ; N/A//Second Century Fund (C2F)/ ; N/A//Second Century Fund (C2F)/ ; },
mesh = {Animals ; *Obesity/etiology/microbiology/therapy ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Probiotics/pharmacology/administration & dosage ; *Inflammation ; Male ; *Dietary Carbohydrates/adverse effects ; Mice, Inbred C57BL ; *Lactobacillaceae ; },
abstract = {Given the potential of probiotics to counteract obesity induced by high glucose diets (HGD) and the beneficial effects of high-fiber diets, this study explored the impact of Lactiplantibacillus plantarum dfa1 (Lp dfa1) in mice consuming modified diets, including a unique high-carbohydrate biscuit diet (HBD) featuring Prachuap Khiri Khan's Pineapple Cheese Cake Biscuit for its rich fiber content. Notably, the fruit-derived soluble fiber HBD might have a synbiotic effect (the enhanced beneficial bacteria in the gut) different from HGD. in The standard mouse diet (RD) with a carbohydrate: protein: fat (C: P:F) ratio of 56:13:31 served as the base, which was then modified with either glucose to form the HGD (C: P:F at 60:25:15) or blended with the high-fiber dessert to create the HBD (C: P:F at 70:9:21). Over 12 weeks, mice were fed HGD or HBD with and without daily oral administration of Lp dfa1 at 1 × 10[9] CFU. This study aimed to assess the effects on obesity indicators (weight gain, lipid profiles, fat deposition), prediabetes markers (fasting glucose, insulin, oral glucose tolerance test, and Homeostatic Model Assessment for Insulin Resistance (HOMA-IR)), intestinal health (FITC-dextran assay for enterocyte injury, serum cytokines TNF-α, IL-10, and IL-6), and liver health (enzymes, weight, histology, carbohydrate and fat components, and oxidative stress). Both HGD and HBD induced similar obesity metrics, prediabetic conditions, enterocyte injury, altered serum cytokines, and liver damage. Remarkably, Lp dfa1 administration mitigated these adverse effects with an elevation in fecal short-chain fatty acids. Microbiome analysis revealed diet-induced dysbiosis, with a notable difference between HGD and HBD impacts, particularly in the Fermicutes/Bacteroides ratio and Akkermansia spp. abundance, which was significantly elevated in the HBD + Lp group. Actinomycota with a lower Proteobacteria in HBD compared with HGD group indicate the possible different impacts between the mixed sugar with fruit-derived soluble fiber versus pure glucose. Interestingly, Lp dfa1 elevated Akkermansia spp. (a well-known beneficial probiotic against obesity) only in mice with HBD but not HGD, despite an obesity attenuation by Lp dfa1 in both HGD and HBD groups, implying the different anti-obesity mechanisms. In vitro experiments revealed Lp dfa1's supernatant reduced inflammation in Caco-2 and HepG2 cell lines, evidenced by improved transepithelial electrical resistance (TEER), expression of occludin-1 (a tight junction molecule), decreased inflammatory mediators (NF-κB, TNF-α, IL-8, IL-6, and IL-10), and elevated mucin gene. Conclusively, Lp dfa1 demonstrates a dual mechanism in preventing sugar-induced intestinal injury and supporting metabolic health: direct cellular protection and microbiome modulation. These findings highlight the additive effects of Lp dfa1 and high-fiber diets, particularly emphasizing the Pineapple Cheese Cake Biscuit-based diet's role in enhancing gut microbiota and addressing diet-induced health issues.},
}

Animals
*Obesity/etiology/microbiology/therapy
*Gastrointestinal Microbiome/drug effects
Mice
*Probiotics/pharmacology/administration & dosage
*Inflammation
Male
*Dietary Carbohydrates/adverse effects
Mice, Inbred C57BL
*Lactobacillaceae

@article {pmid40634526,
year = {2025},
author = {Tarriño, M and Gutiérrez-Bautista, JF and Durán, MJO and Garcia-Diaz, A and Cabrera-Serrano, AJ and Sainz, J and Cobo, F and Rodriguez, T and Reguera, JA and Bernal, M and López-Nevot, MÁ and Sampedro, A},
title = {The role of intestinal microbiota in the humoral response to SARS-CoV-2 after mRNA-1273 vaccination.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24731},
pmid = {40634526},
issn = {2045-2322},
support = {PI21/01708//Instituto de Salud Carlos III/ ; PI21/01708//Instituto de Salud Carlos III/ ; PI21/01708//Instituto de Salud Carlos III/ ; PI21/01708//Instituto de Salud Carlos III/ ; PI21/01708//Instituto de Salud Carlos III/ ; PI21/01708//Instituto de Salud Carlos III/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Female ; Male ; *SARS-CoV-2/immunology ; *COVID-19/prevention & control/immunology/microbiology ; *Immunity, Humoral ; Adult ; 2019-nCoV Vaccine mRNA-1273/immunology ; Immunoglobulin G/immunology/blood ; Middle Aged ; Antibodies, Viral/immunology/blood ; *COVID-19 Vaccines/immunology ; Vaccination ; Feces/microbiology ; },
abstract = {The gut microbiota plays a key role in shaping immune responses, including those induced by vaccination. Its impact on the humoral response to mRNA-based SARS-CoV-2 vaccines, however, remains underexplored. We analyzed gut microbiota composition and anti-Spike (S) IgG levels in 50 healthcare workers vaccinated with the mRNA-1273 SARS-CoV-2 vaccine. Participants were stratified into low, medium, and high responders based on IgG titers 30 days post-vaccination. Stool samples were collected at baseline, and 16 S rRNA sequencing was used to assess microbiota diversity and taxonomic profiles. Alpha diversity indices showed no significant differences across response groups. However, specific microbial signatures were associated with vaccine response. Higher relative abundance of Clostridia, Clostridiales, Ruminococcaceae, and Odoribacter splanchnicus correlated with stronger IgG responses. Functional microbiome analysis revealed enrichment of acetate-producing pathways in high responders (p = 0.012), suggesting a role for short-chain fatty acids in enhancing vaccine-induced immunity. Logistic regression and Random Forest models identified these taxa as predictors of strong antibody responses. The area under the ROC curve (AUC) for individual taxa ranged from 0.70 to 0.76, indicating moderate predictive performance. Conversely, taxa such as Hallella and Sutterella wadsworthensis were linked to lower responses. These findings support a modulatory role of the gut microbiota in mRNA vaccine immunogenicity and highlight microbial metabolic functions as potential targets to boost vaccine efficacy in personalized immunization strategies.},
}

Humans
*Gastrointestinal Microbiome/immunology
Female
Male
*SARS-CoV-2/immunology
*COVID-19/prevention & control/immunology/microbiology
*Immunity, Humoral
Adult
2019-nCoV Vaccine mRNA-1273/immunology
Immunoglobulin G/immunology/blood
Middle Aged
Antibodies, Viral/immunology/blood
*COVID-19 Vaccines/immunology
Vaccination
Feces/microbiology

@article {pmid40634502,
year = {2025},
author = {},
title = {Tracking microbiome-derived cell-free RNA modifications detects colorectal cancer.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40634502},
issn = {1546-1696},
}

@article {pmid40634391,
year = {2025},
author = {Cullen, JT and Lawlor, PG and Cormican, P and Crispie, F and Slattery, H and Gardiner, GE},
title = {Bacteriome and mycobiome profiling of liquid feed for finisher pigs on commercial pig farms.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24718},
pmid = {40634391},
issn = {2045-2322},
support = {GOIPG/2021/331//Irish Research Council/ ; },
mesh = {Animals ; *Animal Feed/microbiology/analysis ; Swine/microbiology ; *Mycobiome ; Biogenic Amines/analysis/metabolism ; Farms ; *Bacteria/genetics/classification/isolation & purification ; Fermentation ; *Fungi/genetics/classification/isolation & purification ; },
abstract = {The aim was to assess the quality of liquid feed for grow-finisher pigs across commercial pig farms by profiling the bacteriome and mycobiome of samples and determining biogenic amine concentrations. Amplicon sequencing of liquid feed samples revealed that bacterial and fungal community structures were influenced by the farm of origin and sampling location (mixing tank/trough) on a given farm. Decreases in alpha-diversity of liquid feed between the mixing tank and the troughs corresponded with increased relative abundances of bacteria, particularly Lactobacillus, Weissella and Leuconostoc, as well as yeasts, including Kazachstania and Dipodascus, indicative of spontaneous fermentation. The concentration of biogenic amines, resulting from amino acid loss from the feed, which likely plays a role in poorer feed efficiency, also increased between the mixing tank and the troughs. The highest biogenic amine concentrations in the feed were found on the farm that had the highest lactic acid bacteria (LAB) and yeast counts. Both Lactobacillus and Kazachstania were correlated with biogenic amine concentrations in liquid feed, highlighting the unexplored role that LAB and yeast may play in amino acid decarboxylation and biogenic amine formation in liquid feed. Factors including the use of liquid co-products in diets also impacted the liquid feed microbiome.},
}

Animals
*Animal Feed/microbiology/analysis
Swine/microbiology
*Mycobiome
Biogenic Amines/analysis/metabolism
Farms
*Bacteria/genetics/classification/isolation & purification
Fermentation
*Fungi/genetics/classification/isolation & purification

@article {pmid40634281,
year = {2025},
author = {Bagaev, A and Sur, D and Agranyoni, O and Pe'er, N and Savita, BK and Rocha, BGS and Thanos, PK and Navon-Venezia, S and Pinhasov, A},
title = {Maternal oral sodium propionate supplementation restores gut integrity and mitigates stress-induced metabolic and behavioral outcomes in offspring.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {235},
pmid = {40634281},
issn = {2158-3188},
support = {2069/17//Israel Science Foundation (ISF)/ ; },
mesh = {Animals ; *Propionates/administration & dosage/pharmacology ; Female ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; *Behavior, Animal/drug effects ; *Stress, Psychological/metabolism ; Dietary Supplements ; *Maternal Behavior/drug effects ; Pregnancy ; Mice, Inbred C57BL ; Receptors, G-Protein-Coupled/metabolism ; Administration, Oral ; Feces/chemistry/microbiology ; },
abstract = {Maternal attachment is a critical determinant of offspring's postnatal development, significantly influencing their later-life metabolic and behavioral patterns. We previously showed that stress-vulnerable, socially submissive (Sub) mice exhibit significant disruptions in gut physiology including distorted microbiome composition, lower colonic propionate levels, and increased gut permeability. These alterations exacerbated chronic inflammation, caused metabolic imbalances and reduced maternal care. In this study, we revealed a significant reduction in bacterial diversity and fecal propionate levels in Sub dams. To investigate whether maternal gut integrity could mitigate adverse offspring outcomes, we provided oral sodium propionate (SP) supplementation to Sub dams via drinking water from postpartum day (PD) 0, until weaning (PD21). SP supplementation notably improved maternal care, reflected by faster pup retrieval times and better nesting. Beneficial effects were particularly pronounced in two-month-old male offspring, demonstrating decreased anxiety-like behavior, improved sociability and enhanced short-term memory accompanied by increased abundance of specific gut bacteria (Roseburia, and Shuttleworthia genus). Additionally, male offspring exhibited significant metabolic improvements, including reduced epididymal white adipose tissue (eWAT) mass, decreased adipocyte diameter accompanied by increased eWAT mRNA expression of GPR43 and PPAR-γ. Moreover, SP supplementation increased colon length linked with increased colonic mRNA expression of GPR43, PPAR-γ and Claudin-7, highlighting the importance of propionate in tight junction regulation and inflammation. Importantly, these positive outcomes exhibited notable sex-dependent differences, with male offspring responding robustly, whereas females showed minimal behavioral or metabolic improvements following maternal SP supplementation. Overall, our findings emphasize that innate stress vulnerability-related metabolic and behavioral alterations in offspring can be mitigated by restoring the dams' gut epithelial barrier integrity, highlighting the critical role of the maternal gut environment and demonstrating clear sex-specific responses to gut microbiota-targeted interventions.},
}

Animals
*Propionates/administration & dosage/pharmacology
Female
*Gastrointestinal Microbiome/drug effects
Male
Mice
*Behavior, Animal/drug effects
*Stress, Psychological/metabolism
Dietary Supplements
*Maternal Behavior/drug effects
Pregnancy
Mice, Inbred C57BL
Receptors, G-Protein-Coupled/metabolism
Administration, Oral
Feces/chemistry/microbiology

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

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

@article {pmid40634132,
year = {2025},
author = {Nijat, D and Zhao, Q and Abdurixit, G and He, J and Liu, H and Li, J},
title = {An Up-to-Date Review of Traditional Chinese Medicine in the Treatment of Atherosclerosis: Components, Mechanisms, and Therapeutic Potentials.},
journal = {Phytotherapy research : PTR},
volume = {},
number = {},
pages = {},
doi = {10.1002/ptr.70037},
pmid = {40634132},
issn = {1099-1573},
support = {2023B02030//Key Research and Development Program in Xinjiang Uygur Autonomous Region/ ; 2024B02005//Key Research and Development Program in Xinjiang Uygur Autonomous Region/ ; 2023TSYCLJ0043//Tianshan Talent Training Program/ ; },
abstract = {Atherosclerosis is a chronic inflammatory disease and a major global health concern. In recent years, traditional Chinese medicines (TCMs) have demonstrated multi-target therapeutic potential against atherosclerosis by modulating inflammatory responses, oxidative stress, lipid metabolism, and gut microbiota interactions. This review systematically evaluates (1) the anti-atherogenic mechanisms of key TCM herbs (e.g., Panax ginseng, Salvia miltiorrhiza) and bioactive compounds (e.g., ginsenosides, tanshinones), (2) their synergistic effects in proprietary formulations, and (3) clinical evidence for cardiovascular protection. Notably, we highlight how TCM compounds like berberine and resveratrol target the gut-vascular axis by regulating microbiota-derived metabolites (e.g., TMAO) and improving endothelial function. While preclinical studies show promising results through Nrf2/HO-1 activation, NF-κB inhibition, and plaque stabilization, translational challenges persist, including the lack of standardization and microbiome-dependent efficacy variations. We conclude that integrating TCM's multi-component advantages with cutting-edge technologies such as bioinformatics, nanotechnology, and patient-specific multiomics including microbiome profiling could revolutionize atherosclerosis management, though rigorous clinical validation and standardization remain imperative.},
}

@article {pmid40633803,
year = {2025},
author = {Xie, D and Wang, Y and Li, J and Yang, T and Zhang, Y and Zhang, W and Doherty, M and Zhu, Y and Yang, Z and Wang, Y and Wei, J and Lei, G and Zeng, C},
title = {Correlation between Gut Dysbiosis, Metabolite Alterations and Erosive Hand Osteoarthritis - an observational study within the community-based Xiangya Osteoarthritis (XO) cohort.},
journal = {Osteoarthritis and cartilage},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joca.2025.07.004},
pmid = {40633803},
issn = {1522-9653},
abstract = {OBJECTIVES: Erosive hand osteoarthritis (EHOA) is an aggressive subtype of hand osteoarthritis (HOA) with unclear pathogenesis. Since gut dysbiosis and related metabolite alterations may exacerbate inflammation and accelerate bone destruction, we investigated whether these abnormalities were involved in EHOA.

METHODS: Participants were drawn from the Xiangya Osteoarthritis Study. We compared gut microbial α-diversity and β-diversity between EHOA and controls (neither EHOA nor non-erosive HOA), and analyzed associations between microbial species abundance, functions, and EHOA. Targeted blood metabolomics were performed to identify microbiome-associated metabolites in EHOA. The associations between EHOA-related microbial species and blood metabolites were examine through multi-omics analyses.

RESULTS: Among 1,324 participants, significant differences in α-diversity (EHOA: median=4.53, non-HOA control: median=4.16; median difference=0.37 [95%CI: 0.09-0.57], P=0.016) and β-diversity (R²=0.002 [95%CI: 0.0018-0.006], P=0.015) were observed at the species level between EHOA and controls. Participants with EHOA had a higher relative abundance of Alistipes senegalensis (β coefficient:0.17 [95%CI:0.07-0.26]) and Fournierella massiliensis (β coefficient:0.39 [95%CI:0.28-0.49]). Tryptophan metabolism was the main altered metabolic pathway. Targeted blood metabolomics showed higher levels of L-5-hydroxytryptophan (β coefficient:0.38 [95%CI:0.15-0.61]), 3-indoleglyoxylic acid (β coefficient:0.35 [95%CI:0.01-0.69]), 5-hydroxyindoleacetic acid (β coefficient:0.27 [95%CI:0.09-0.45]), indoleacrylic acid (IA) (β coefficient:0.23 [95%CI:0.001-0.46]), and serotonin (β coefficient: 0.20 [95%CI: 0.004-0.40]), alongside lower levels of L-tryptophan (β coefficient:-0.41 [95%CI:-0.75 to -0.06]) and indole-3-acetyl-aspartate (β coefficient:-1.05 [95%CI:-1.79 to -0.32]) in EHOA. IA was positively correlated with EHOA-related microbial species, particularly Alistipes senegalensis (β coefficient:0.20 [95%CI:0.14-0.27]).

CONCLUSIONS: A higher relative abundance of Alistipes senegalensis and alterations in tryptophan metabolites, particularly higher levels of IA, are associated with EHOA.},
}

@article {pmid40633656,
year = {2025},
author = {Chakraborty, S and Banerjee, S and Kumar, S and Ghosh, S and Mukherjee, P and Das, S and Bhattacharyya, P},
title = {Biofortified Vermicompost: Exploring Bacterial Community Dynamics and Enzymatic Pathways through Bacteriome Analysis for Arsenic Bioremediation in Mine Waste.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126795},
doi = {10.1016/j.envpol.2025.126795},
pmid = {40633656},
issn = {1873-6424},
abstract = {The extraction of mica from open-cast mines generates substantial waste, often laden with arsenic, posing severe environmental risks. Addressing this waste is essential to mitigate co-contamination. Vermitechnology offers a promising solution by converting toxic waste into nutrient-enriched, sanitized compost suitable for agriculture. This study explored bioremediation of toxic mine tailings (MT) through aerobic composting, vermicomposting and enriched vermicomposting (with Bacillus subtilis K5BGRD). Earthworm fecundity was impaired in dense MT settings but improved in MT+CD (1:1) treatments. Vermicomposting stabilized pH, enhanced nutrient mineralization and increased potassium bioavailability compared to aerobic composting. Enriched vermicompost reduced bioavailable arsenic by 58-88% post-maturity, alongside increased microbial diversity and enzymatic activity. Earthworms bioaccumulated arsenic, contributing to a total reduction of 14.25%. Pearson correlation and PLS-SEM analyses highlighted reduced arsenic-induced stress upon compost maturity. Metataxonomic analysis revealed microbial similarities between V1 (MT+CD [1:1]) and EV1 (MT+CD+B [1:1:1]) composts, with enrichment of stress-resistant, bioremediating and plant growth-promoting taxa. Upon crop trial it was deduced that microbe-mediated vermicomposting, particularly when combined with recommended fertilizer doses (as in T2), not only minimized arsenic accumulation in tomato plants but also significantly enhanced yield, highlighting its potential as a sustainable and effective strategy for safe crop production in contaminated soils. The study demonstrated the symbiotic relationship between earthworms and microbes in waste-treated settings, establishing a novel feedstock combination to remediate hazardous mine waste. Ultimately, this approach has the potential to replace chemical fertilizers, improve crop yields and reduce arsenic exposure - offering a cost-effective and eco-friendly solution to mining waste management.},
}

@article {pmid40633607,
year = {2025},
author = {Linh, NV and Khang, LTP and Dinh-Hung, N and Wisetkaew, S and Therdtatha, P and Sangsawad, P and Wannavijit, S and Jitjumnong, J and Permpoonpattana, P and Van Doan, H},
title = {Effects of dietary corn silk (Zea mays L.) on growth, immune and antioxidant pathways, histological morphology, gut microbiome, and sensitivity to acute ammonia exposure in the koi carp (Cyprinus carpio var. koi).},
journal = {Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology},
volume = {},
number = {},
pages = {111127},
doi = {10.1016/j.cbpb.2025.111127},
pmid = {40633607},
issn = {1879-1107},
abstract = {Corn silk is a promising aquafeed additive due to its antioxidant, antibacterial, and anti-inflammatory properties. This study evaluated the impact of graded dietary levels of powdered corn silk (PCS) on growth, immunity, antioxidant enzyme activities, histology, gut microbiota composition, gene expression profiles, and sensitivity to acute ammonia exposure in koi carp (Cyprinus carpio var. koi). A total of 300 fish were assigned to five dietary treatments (0, 5, 10, 20, and 30 g/kg PCS) for eight weeks. Fish fed the PCS-30 diet showed significant improvements in growth parameters, including weight gain (WG) and specific growth rate (SGR) (p < 0.05). Antioxidant capacity (2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid); ABTS) and superoxide dismutase (SOD) activity, increased dose-dependently, while malondialdehyde (MDA) levels remained unchanged (p > 0.05). Expression of the immune and antioxidant genes interleukin 8 (il-8), lysozyme (lyz), catalase (cat), nuclear factor-κB (Nf-κB), and toll-like receptor 4 (tlr4) was significantly upregulated in the PCS-20 and PCS-30 groups (p < 0.05). Histological analysis revealed progressive improvements in anterior intestinal morphology, with the PCS-30 group exhibiting the greatest villus height and width. Gut microbiota analysis showed increased relative abundance of beneficial taxa (Gammaproteobacteria, Lactobacillales, Prevotella), which positively correlated with growth and antioxidant markers, and negatively with MDA levels. Survival under acute ammonia exposure was highest in the PCS-20 and PCS-30 groups. These findings demonstrate the efficacy of PCS, particularly at 30 g/kg, in enhancing growth, immunity, and stress resilience.},
}

@article {pmid40633493,
year = {2025},
author = {Sibinga, NA and Werner, E and Tegtmeier, D and De Smet, J},
title = {Animal board invited review: The need for, and the path towards, a functional understanding of the farmed insect microbiome.},
journal = {Animal : an international journal of animal bioscience},
volume = {19},
number = {8},
pages = {101575},
doi = {10.1016/j.animal.2025.101575},
pmid = {40633493},
issn = {1751-732X},
abstract = {The rapid growth of research on industrially produced insect species over the past two decades has coincided with breakthroughs in the speed and affordability of DNA sequencing. This has allowed researchers to rapidly generate data on the microbial communities associated with farmed insects, especially the gut-residing bacteria of the two cornerstone production species: black soldier fly (BSF, Hermetia illucens) and yellow mealworm (Tenebrio molitor). A picture of the most prevalent and abundant microbes associated with these species has rapidly come into focus. Specific microbial functions have been suggested under extreme or challenging rearing settings, but less is known about the contributions of the microbiome to insect rearing under realistic production conditions. There is limited understanding of how microbial communities of farmed insects arise, are maintained, and change in response to stimuli. Likewise for seemingly basic questions: what functions do insect-associated microbes perform for the host? Which (if any) taxa are essential for healthy insects? This is not intended as a criticism of existing research; indeed, these questions turn out not to be simple. Answering them requires targeted research approaches testing specific hypotheses about farmed insect microbiome function. This review aims to recalibrate the state of knowledge by critically assessing common and emerging strategies to study these microbiomes and existing knowledge gaps about the functional role of the microbiome for BSF and mealworm. Overall, it is clear that microbes are an intrinsic part of the ecology of these two farmed insects. Reciprocal interactions between microbes and insects are extensive, though microbiome community composition depends to a large extent on environmental conditions. To date, it remains unclear how taxonomical shifts correspond to functional shifts and to what extent such changes impact insect physiology. For example, when mealworms are fed plastics, their microbiomes undergo significant changes in microbial composition. These changes are presumed to increase the ability of mealworms and their microbiota to degrade plastic, but this change in function is hard to conclusively demonstrate with current tools. Furthermore, analysis of the literature shows that taxonomically disparate microbial communities may provide similar functional benefits, e.g. lignocellulose breakdown in BSF larvae. This review therefore aims to critically assess the state of the art with regard to functional analysis of the farmed insect microbiome and how available experimental methods can be best applied to identify links between microbial functions and insect physiology and improve the efficiency and sustainability of the farmed insect industry.},
}

@article {pmid40633399,
year = {2025},
author = {Criscuolo, A and Czepiel, A and Schwartze, M and Kotz, SA},
title = {A body-brain (dis)equilibrium regulating transitions from health to pathology.},
journal = {Physics of life reviews},
volume = {54},
number = {},
pages = {94-111},
doi = {10.1016/j.plrev.2025.07.003},
pmid = {40633399},
issn = {1873-1457},
abstract = {Recent empirical evidence and theoretical propositions motivate a paradigm shift in how we investigate neurocognitive functions. Rather than looking at the brain-behaviour relationship in isolation, research shows that cognition is shaped by reciprocal, dynamical interactions between the brain and the body across multiple timescales: from ultra-slow circadian rhythm to gastrointestinal and cardiorespiratory activity. This interest in body-brain-behaviour dynamics has raised new questions about if and how autonomic functioning, the coordination of intero- and exteroception, lifestyle and dietary choices, gut microbiome composition, hormonal cycles, and inflammation can impact behaviour, general health and well-being. We carefully reviewed existing theoretical accounts and empirical evidence on the body-brain-behaviour interface and delineated new emerging avenues for multimodal, functional, ecologically valid, and personalized research that also integrates smart sensing technologies. In a synopsis, we propose the concept of a body-brain (dis)equilibrium regulating transitions from health to pathology.},
}

@article {pmid40633350,
year = {2025},
author = {Huang, C and Wang, T and Chen, W and Wang, J and Cui, M and Zheng, C and Qiu, M and Shan, M and Li, B and Zhang, L and Yu, Y and Xu, L and Fang, H},
title = {Sheep and rapeseed cake manure promote antibiotic resistome in agricultural soil.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139157},
doi = {10.1016/j.jhazmat.2025.139157},
pmid = {40633350},
issn = {1873-3336},
abstract = {The application of manure in agriculture caused the emergence and spread of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil environments. However, the co-occurrence pattern and host diversity of ARGs and MGEs in soils amended with animal and green manures remains unclear. In this study, metagenomic assembly and binning techniques were employed to comprehensively explore the effects of sheep manure and green manure on soil microbiome, antibiotic resistomes, and ARG hosts. Both rapeseed cake manure and sheep manure increased the abundance and diversity of ARGs, with sheep manure particularly enhancing the abundance of ARGs conferring resistant to multidrug, quinolone, rifampicin, and macrolide-lincosamide-streptogramin (MLSB). Mobile genetic elements (MGEs), such as plasmids, transposases, and integrases, preferentially enhanced the potential mobility of some ARGs subtypes (i.e. sul2, aadA, qacH, and folp), facilitating the spread of ARGs. Additionally, sheep manure reshaped the bacterial community structure and composition as well as ARG hosts, some opportunistic pathogens (i.e. Staphylococcus, Streptococcus, and Pantoea) acquired antibiotic resistance and remained recalcitrant. It is concluded that rapeseed cake manure and sheep manure increased the co-occurrence of ARGs and MGEs, enriched the potential ARG hosts, and promoted the dissemination of ARGs in agricultural soils.},
}

@article {pmid40633153,
year = {2025},
author = {Missawi, O and Vaccari, F and Zhang, L and Miras-Moreno, B and Boughattas, I and Bandini, F and Lucini, L and Puglisi, E and Banni, M},
title = {Unleashing multi-omic approaches to address environmental microplastic hazards in marine polychaetes.},
journal = {Marine pollution bulletin},
volume = {220},
number = {},
pages = {118345},
doi = {10.1016/j.marpolbul.2025.118345},
pmid = {40633153},
issn = {1879-3363},
abstract = {The impact of an environmental microplastic mixture (< 100 μm) on marine polychaete was explored to simulate the plastic exposure patterns in the natural habitat. In this study, Hediste diversicolor was used to mimic a real scenario exposure model of five common types of widely distributed microplastics sampled from the southern Mediterranean Sea. Sediment and polychaete gut were collected for microbiome and metabolomic analysis. Interestingly, high-throughput sequencing revealed a shift in bacterial diversity depending on microplastic concentration (10, 100 and 1000 μg kg[-1]). Noteworthy, sediment revealed similar diversity with respect to the polychaete gut microbiome. Specific bacterial taxa, particularly Mesoflavibacter zeaxanthinifaciens and Vibrio cortegadensis, were notably affected, indicating adaptive responses to altered environments. The identification of different clusters of markedly altered metabolites, including indoles, benzene derivatives, coumarins, pyrones, flavonoids, cinnamates, diterpenes and sesquiterpenes, offered an insight into the physiological and pathological changes observed within the polychaete following microplastics exposure. These novel findings enhance our understanding of the intestinal hazards of environmental microplastics and underscore the potency of multi-omics investigations in unraveling the intricate mechanisms underlying microplastic toxicity.},
}

@article {pmid40632920,
year = {2025},
author = {Olsson, A and Steel, K and Cooper, R and Jones, AP and Chan, KR and Ogg, G and Irvine, AD and Flohr, C and Taams, LS},
title = {Methotrexate and ciclosporin both reduce levels of circulating IL-4 and IL-13 expressing CD4+ memory T-cells in childhood atopic dermatitis.},
journal = {Clinical and experimental dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/ced/llaf301},
pmid = {40632920},
issn = {1365-2230},
abstract = {Atopic dermatitis (AD) is a chronic dermatosis characterised by type-2 inflammatory responses, skin barrier anomalies, and microbiome dysregulation. The variation of AD presentation necessitates a better understanding of the underlying disease mechanisms and the modulation of immune markers over a treatment course. Globally the most used systemic therapies for moderate-to-severe AD are methotrexate (MTX) and ciclosporin (CyA). The TReatment of severe Atopic Eczema in children Trial (TREAT) was a randomised controlled trial assessing the efficacy and safety of methotrexate and ciclosporin. Peripheral blood samples from n=18 TREAT participants were analysed in a longitudinal immunological study with a focus on cytokine-expressing CD4+ T-cells. The analysis showed that both MTX and CyA were associated with a decreased percentage of IL-4 and IL-13 expressing CD4+ memory T-cells, corresponding to improved disease severity. Patients receiving MTX experienced a more sustained decrease in IL-4 expressing T-cells, which corresponds to the longer-term improved disease control observed in the MTX arm.},
}

@article {pmid40632657,
year = {2025},
author = {Bajaj, JS and Reddy, KR and Tandon, P and Lai, JC and O'Leary, JG and Wong, F and Garcia-Tsao, G and Vargas, HE and Kamath, PS and Biggins, SW and Vutien, P and Shaw, J and Limon Miro, AT and Bera, C and McGinley, JP and Sikaroodi, M and Bush, BJ and Thacker, LR and Gillevet, PM},
title = {Salivary microbiome and serum metabolomics add to clinical biomarkers to predict 6-month hospitalizations in a multi-center cirrhosis outpatient cohort.},
journal = {Hepatology (Baltimore, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/HEP.0000000000001462},
pmid = {40632657},
issn = {1527-3350},
abstract = {BACKGROUND AIMS: Prognosticating outcomes such as hospitalizations in cirrhosis outpatients is challenging, especially with changing etiologies and demographics. Aim: Determine impact of multi-omic strategies on outcome prediction.

APPROACH RESULTS: NACSELD3 enrolls cirrhosis outpatients with controlled/eradicated etiologies from 10 centers and follows them systematically. At baseline, clinical/demographic and cirrhosis details were recorded and saliva and serum samples were collected for microbiome and metabolome analysis respectively. Multi-omic bioinformatic studies to determine interaction of microbiota and metabolites with clinical prediction of 6-month hospitalizations were performed. 565 patients (60.2 years, 68% men, 35% alcohol, 33% MASH, 21%, eradicated HCV with MELD3.0 12) were enrolled. 163 (29%) required 6-month hospitalizations; most (75%) were liver-related. Those hospitalized had worse cirrhosis severity, co-morbidity indices, but similar demographics and oral health variables. Salivary microbiome alpha-diversity was lower (1.96±0.48 vs. 2.09±0.45, p=0.018) with greater pathobionts (Streptococcus, Treponema, Enterococcaceae) and lower commensal genera (Veillonella, Prevotella, Haemophilus, Lachnospiraceae spp) at baseline. Serum metabolomics showed significant separation at baseline between hospitalized/not patients using supervised analyses with microbial-origin (phenyllactate, secondary bile acids, indoles), choline moieties, and polyamine/GABA (3-ureidopropionate/spermidine) metabolites being most prominent. Area-under-the curve using random forest for clinical, microbial, and metabolomic variables were higher than that of these individually. Latent factor analysis showed clinical variables (MELD3.0, hemoglobin and albumin) with the greatest impact followed by salivary microbiota and then serum microbiome for hospitalization prediction.

CONCLUSION: In a multi-center North American outpatient cirrhosis cohort with controlled etiologies, serum metabolomics and salivary microbiome add to clinical variables to prognosticate 6-month hospitalization.},
}

@article {pmid40632459,
year = {2025},
author = {Ding, Y and Hou, Y and Lao, X},
title = {The Role of Akkermansia muciniphila in Disease Regulation.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40632459},
issn = {1867-1314},
abstract = {In recent years, Akkermansia muciniphila (A. muciniphila), as a representative of the core gut commensal bacteria, has shown outstanding therapeutic potential in the field of microecological interventions due to its unique mucin degrading ability and host-interaction mechanism. A. muciniphila is first isolated from human feces in 2004. It colonizes the intestinal mucus layer, utilizing mucin secreted by goblet cells as its primary carbon and nitrogen source. In 2013, researchers found that supplementation with A. muciniphila could improve obesity, demonstrating the potential of A. muciniphila in the treatment of disease. Recent studies show that A. muciniphila strengthens intestinal barrier integrity, improves metabolic diseases, and mitigates inflammation through multiple mechanisms, including adenosine monophosphate-activated protein kinase (AMPK) pathway activation via Toll-like receptor (TLR) 2 stimulation and NOD-like receptor family, pyrin domain containing 3 (NLRP3) activation. A. muciniphila and its derivatives also exhibit potent anti-tumor effects. They induce tumor-necrosis-factor-related apoptosis-inducing ligand (TRAIL) upregulation, triggering extrinsic (death receptor-mediated) and intrinsic (mitochondrial) apoptosis pathways in tumor cells. Additionally, A. muciniphila promotes M1-like tumor-associated macrophages (TAMs) through NLRP3 activation and remodels the tumor microenvironment via metabolic crosstalk with intratumoral microbiota. Notably, A. muciniphila combined with programmed death-1 (PD-1) antibody boost CD8[+] T cell infiltration, thereby overcoming host resistance to PD-1 blockade. Moreover, A. muciniphila contributes to the growth of butyric acid-producing bacteria and suppresses the growth of specific bacterial populations, playing an important role in the gut microbiome network. This review evaluates recent discoveries regarding A. muciniphila's multifaceted roles in maintaining intestinal barrier integrity, ameliorating metabolic and inflammatory disorders, and enhancing anti-tumor immune responses. We also discuss its ecological effect on the gut microbiota flora and point out the therapeutic limitations and prospect which provides theoretical references to promote the development of Akkermansia muciniphila in clinical diseases, especially in tumor therapy.},
}

@article {pmid40632357,
year = {2025},
author = {Arif, TB and Damianos, JA and Rahman, AU and Hasnain, N},
title = {Fecal Microbiota Transplantation for Disorders of Gut-Brain Interaction: Current Insights, Effectiveness, and Future Perspectives.},
journal = {Current gastroenterology reports},
volume = {27},
number = {1},
pages = {50},
pmid = {40632357},
issn = {1534-312X},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Dysbiosis/therapy/complications/microbiology ; *Gastrointestinal Microbiome ; *Brain-Gut Axis ; *Gastrointestinal Diseases/therapy/microbiology ; },
abstract = {PURPOSE OF REVIEW: Dysbiosis can disrupt intestinal barrier integrity and impact the immune and nervous systems, playing a significant role in developing disorders of gut-brain interaction (DGBI). This review aims to provide a comprehensive understanding of dysbiosis and its role in DGBI while examining the latest advancements in fecal microbiota transplantation (FMT). It also highlights key challenges in the field and outlines critical directions for future research to optimize FMT strategies, ultimately improving patient outcomes in this evolving treatment area.

RECENT FINDINGS: In DGBI, dysbiosis triggers immune responses, increases gut permeability, and disrupts nervous system signaling, with contributing factors including diet, antibiotics, stress, and infections. Individuals with DGBI exhibit distinct microbial imbalances, such as an increased Firmicutes-to-Bacteroidetes ratio and reduced beneficial bacteria. FMT has shown mixed results, with factors like patient selection, treatment protocols, and microbiome diversity influencing outcomes. While FMT can improve symptoms in refractory irritable bowel syndrome (IBS), effects may fade over time, requiring repeat treatments. Future FMT approaches should focus on targeted microbial interventions, considering the role of archaea, fungi, and microbial metabolites, while prioritizing optimal donor selection and large-scale trials for long-term efficacy. Despite the promising findings, FMT has not yet been widely endorsed in clinical guidelines due to the variability and heterogeneity of the data available. While much of the research has focused on IBS, studies have also explored the impact of FMT on other conditions such as functional diarrhea, functional constipation, and functional dyspepsia, which all exhibit altered microbial profiles.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Dysbiosis/therapy/complications/microbiology
*Gastrointestinal Microbiome
*Brain-Gut Axis
*Gastrointestinal Diseases/therapy/microbiology

@article {pmid40631920,
year = {2025},
author = {Wang, X and Jun, F and Lin, C and Wang, X},
title = {Psychedelics and the Gut Microbiome: Unraveling the Interplay and Therapeutic Implications.},
journal = {ACS chemical neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschemneuro.5c00418},
pmid = {40631920},
issn = {1948-7193},
abstract = {Classic psychedelics and the gut microbiome interact bidirectionally through mechanisms involving 5-HT2A receptor signaling, neuroplasticity, and microbial metabolism. This viewpoint highlights how psychedelics may reshape microbiota and how microbes influence psychedelic efficacy, proposing microbiome-informed strategies─such as probiotics or dietary interventions─to personalize and enhance psychedelic-based mental health therapies.},
}

@article {pmid40631910,
year = {2025},
author = {Deng, Y and Leib, N and Schnautz, S and Benfadal, S and Oldenburg, J and Bieber, T and Herrmann, N},
title = {Langerhans Cell Modulation in Atopic Dermatitis Is TLR2/SOCS1-Dependent and JAK Inhibitor-Sensitive.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16641},
pmid = {40631910},
issn = {1398-9995},
support = {//Christine Kühne - Center for Allergy Research and Education/ ; EXC2151-390873048//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Langerhans cells (LC) are epidermal dendritic cells building the skin's outermost immunological barrier and bridging innate and adaptive immune responses. Their sensing property of the microbiome via Toll-like receptors (TLR) is impaired in atopic dermatitis (AD). We hypothesize a desensitization of LC because of persistent Staphylococcus aureus exposure in AD and underlying mechanisms being TLR2-related.

METHODS: Human LC generated from hematopoetic stem cells were desensitized via repetitive exposure to TLR2-ligands (priming) and compared to unprimed cells for their TLR-responsiveness. JAK inhibitors impact was evaluated. Maturation marker, migration marker and behavior, cytokine release, and downstream molecule regulation were addressed by flow cytometry, qPCR, and transwell and multiplex assays.

RESULTS: Primed LC mimicked the LC behavior in AD skin, exhibiting desensitization toward TLR2-mediated activation monitored by impaired CD83/CD80/CD86 and MHCII expression as well as impaired regulation of chemokines CCR6 and CCR7, migration competence, and Th17-driving cytokines. IL-18 and IL-1β were elevated under these conditions. Negative regulators of the TLR2 pathway, specifically SOCS1 and IRAKM, were significantly upregulated, whereas activating molecules were hardly affected. JAK inhibitors reduced SOCS1 expression in primed cells and restored activation markers CD83/80/86 and MHCII upon TLR2 engagement, but had no effect on IRAKM expression.

CONCLUSION: Primed LC mimic the impaired LC-responsiveness toward TLR2 in AD skin. Our findings unravel a new direct contribution of LC to AD-associated IL-1β and IL-18 under these conditions and shed light on the mechanistical role of SOCS1 and the mode of action of JAK inhibitors.},
}

@article {pmid40631899,
year = {2025},
author = {Zhao, N and Geng, P and Perez, AG and Maya, AC and Yadav, B and Du, Y and Ge, Y},
title = {Genomic and functional characterization of a Butyricicoccus porcorum strain isolated from human gut microbiota.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0079025},
doi = {10.1128/msystems.00790-25},
pmid = {40631899},
issn = {2379-5077},
abstract = {The gut is the most complex microbial ecosystem in the body that greatly influences human immune and metabolic health. However, the functional understanding of gut microbiome is hampered by our limited ability to obtain bacterial cultures for experimental validation, particularly low-abundant species that may carry specific functions but are often overlooked by population-based analyses. Here, we isolated and characterized a novel strain of Butyricicoccus porcorum (named Bp 531D) from human gut microbiota, representing the first butyrate-producing human isolate within a phylogenetic clade of Butyricicoccus complex. Comparative whole-genome analysis revealed a unique capability of Bp 531D for one-carbon metabolism and a high abundance of mobile genetic elements, including six prophages and plentiful transposons, reflecting its evolutionary flexibility. Oral administration of the bacterium profoundly altered gut microbiome composition in C57BL/6 mice, leading to controlled microbial oxidative signaling and calibrated carbohydrate metabolic function in the gut. RNA sequencing (RNA-seq) analysis demonstrated notable functional programming of colonic ECs, whereupon Bp 531D primarily restricted the biosynthesis of cholesterols and activated the pathway of antigen processing and presentation. Furthermore, the expression of MHC class II was correlatively heightened in colonic dendritic cells (DCs), and the frequencies of interleukin-10- (IL-10) and IL-22-producing T helper 17 (Th17) cells were significantly elevated in mice treated with Bp 531D compared to controls. Our findings uncover the crucial roles of B. porcorum in supporting intestinal homeostasis and provide a novel functional modulator to potentially optimize microbial strategies for improving intestinal health.IMPORTANCEReduced abundance of the Butyricicoccus genus has been associated with human intestinal disorders, including inflammatory bowel diseases. While supplementation of B. pullicaecorum mitigates intestinal inflammation, it is unclear whether other Butyricicoccus species critically contribute to intestinal microbial and immune homeostasis. We identified a novel Butyricicoccus species within human gut microbiota and characterized its detailed intestinal functions using the C57BL/6 mouse model. Our findings may further highlight the genetic and functional diversities of the gut microbiome.},
}

@article {pmid40631880,
year = {2025},
author = {Stanojević, M and Kociszewska-Najman, B and Grünebaum, A and Chervenak, F and Kurjak, A},
title = {Quo vadis neonatologia? Where is neonatology heading in the 21st century?.},
journal = {Journal of perinatal medicine},
volume = {},
number = {},
pages = {},
pmid = {40631880},
issn = {1619-3997},
abstract = {INTRODUCTION: This comprehensive narrative review examines current paradigms, emerging trends, and future directions in neonatology through systematic analysis of contemporary literature, clinical practice patterns, and expert consensus. We synthesized evidence from recent publications, international guidelines, and clinical innovations to identify key transformation areas.

CONTENT: Several critical areas are reshaping neonatology. Gestational age has emerged as a lifelong health determinant with implications extending far beyond the neonatal period, affecting cardiovascular, metabolic, and neurodevelopmental outcomes throughout life. Global disparities in neonatal care remain unconscionably large, with survival rates for 28-week infants exceeding 90 % in high-income countries while similar infants in low-resource settings often die from preventable causes. Artificial intelligence applications are revolutionizing predictive analytics, real-time monitoring, and decision support systems, though implementation requires careful attention to bias, transparency, and human oversight. The neonatal microbiome's crucial role in immune development and long-term health has prompted interventions targeting healthy colonization. Salutogenic approaches emphasizing health promotion rather than disease treatment are gaining recognition. Most significantly, the systematic marginalization of mothers in neonatal care is being challenged, with growing recognition of the mother-infant dyad as the fundamental unit of care.

SUMMARY AND OUTLOOK: Future neonatal care must balance technological advancement with humanistic values, addressing global disparities while maintaining scientific rigor. Success requires committing to global health equity, embracing ethical complexity at viability margins, recognizing maternal centrality, thoughtfully integrating emerging technologies, implementing salutogenic principles, and adopting lifelong health perspectives. The field's future depends on interdisciplinary collaboration, ethical reflection, and unwavering commitment to ensuring every newborn receives compassionate, high-quality care.},
}

@article {pmid40631858,
year = {2025},
author = {Qu, S and Gu, Y and Hou, X and Wei, M and Wang, M and Su, Y and Miao, Y and Yang, J and Sun, Y and Zeng, Z},
title = {Dual associations of gut and oral microbial networks with kidney transplantation.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0025225},
doi = {10.1128/msystems.00252-25},
pmid = {40631858},
issn = {2379-5077},
abstract = {UNLABELLED: Gut and oral microbiomes play an essential role in the occurrence and development of kidney disease, but their changes after kidney transplantation in patients with end-stage renal disease and their relationships with host health remain unclear. Through shotgun metagenomic sequencing of fecal and saliva samples, we found that for both gut and oral microbiome, the initial loss of species diversity after kidney transplantation led to a reduction in network nodes and interactions, but strengthened the connections among the remaining species, which started to get a recovery approximately 7-14 days later. Different network modules tended to exhibit unique functions and showed different responses to transplantation. These network changes were significantly correlated with clinical indicators, especially with estimated glomerular filtration rate, suggesting that microbial networks contributed to regulating kidney function and host health from dual dimensions. Our study provides novel insights into associating microbiomes with patient recovery after kidney transplantation and offers new diagnostic strategies.

IMPORTANCE: Understanding the dynamics of gut and oral microbiomes after kidney transplantation is crucial for improving post-transplant outcomes and managing potential complications. Through shotgun metagenomic sequencing of fecal and saliva samples from patients following kidney transplantation, our study emphasizes that, in addition to focusing on the various microbial species themselves, the topological properties of gut and oral microbial networks are also critically important for kidney function. We aim to explore the relationship between host health and the oral and gut microbiomes following kidney transplantation from an ecological perspective and extend to other diseases to advance the study of the microbiome and its clinical impact.},
}

@article {pmid40631371,
year = {2025},
author = {Billet, LS and Hernández-Gómez, O and Skelly, DK},
title = {Ranavirus Epizootics and Gut Bacteriome Dysbiosis in Tadpoles: Evidence for the Anna Karenina Principle?.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70022},
doi = {10.1111/mec.70022},
pmid = {40631371},
issn = {1365-294X},
support = {//Yale University/ ; //Sigma Xia/ ; //American Museum of Natural History/ ; },
abstract = {The microbiome plays a critical role in animal health, yet its responses to pathogens under natural conditions remain poorly understood. We investigated gut bacterial community (bacteriome) dynamics in wood frog (Rana sylvatica [Lithobates sylvaticus]) tadpoles during natural ranavirus outbreaks to understand how pathogen-induced disturbances shape the bacteriome. Using 16S rRNA sequencing, we compared the bacteriomes of tadpoles in ponds experiencing ranavirus die-offs with those from unaffected ponds before, during and after die-offs. Ranavirus infection significantly altered gut bacteriome composition and increased variability (dispersion), consistent with the Anna Karenina principle. Tadpoles with high infection intensities exhibited reduced bacterial diversity and shifts in community structure, including enrichment of some genera that have been linked previously to antiviral immunity. The predicted functional pathway analyses revealed shifts toward carbohydrate metabolism pathways during die-offs, suggesting microbial adaptation to altered host physiology under infection stress. Some bacteriome changes were detectable even before die-offs occurred, highlighting potential early indicators of infection in the gut bacteriome. In a pond that recovered after an epizootic, we observed partial recovery of some of the bacteria that shifted in relative abundance during the die-off, a pattern that may reflect microbial resilience within hosts, selective survival of tadpoles that never developed severe infections, or a combination of both mechanisms. Our findings demonstrate that ranavirus epizootics disrupt gut bacteriomes in amphibians while simultaneously eliciting potentially adaptive microbial responses. These insights underscore the complex interplay between immunity, microbiome dynamics, and environmental conditions during disease outbreaks, highlighting opportunities for microbiome-based interventions to support amphibian conservation.},
}

@article {pmid40631329,
year = {2025},
author = {Magossi, G and Amat, S},
title = {Optimizing bacteriophage screening and isolation methods for microbial samples derived from different body sites of cattle.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.04.663187},
pmid = {40631329},
issn = {2692-8205},
abstract = {Bacteriophages are gaining increased research attention as alternatives to antibiotics and microbiome manipulation tools to enhance feed efficiency and animal health in cattle. However, challenges associated with phage specificity, microbial ecosystem variations, and the absence of effective screening methods have hindered harnessing the power of phage application in cattle. The objectives of this study were to (i) optimize phage screening method for microbial samples obtained from different cattle body sites, (ii) isolate lytic phages against key bovine pathogens and commensal bacteria, and (iii) characterize the isolated phages and their bacterial hosts. A total of 1,214 samples from different cattle body sites (n = 1194) and environmental sources were screened using 13 phage detection methods, including one high-throughput approach. Eighty-three phages were isolated, primarily from ruminal fluid (59), feces (15), vaginal (7) and nasopharyngeal swabs (1), and fetal ruminal fluid (1). The bacterial hosts inhibited by these phages were from 29 genera, with Bacillus (34), Escherichia/Shigella (8), Shouchella (5), Corynebacterium (4), and Lysinibacillus (4) being the most common. No phages were identified against bovine pathogens including Trueperella pyogenes, Mannheimia haemolytica, Pasteurella multocida, or Moraxella bovis. Method 12 demonstrated the highest efficiency in phage recovery, particularly from ruminal samples. The isolation of phages against commensal bacteria from the gastrointestinal, reproductive, and respiratory tracts, and fetal gut highlights their potential for microbiome modulation to improve cattle health and feed efficiency. These findings underscore the need for further research into pathogen-targeting phage isolation in cattle.},
}

@article {pmid40631287,
year = {2025},
author = {Zuffa, S and Thomas, SP and Mohanty, I and El Abiead, Y and Deleray, V and Kvitne, KE and Kousha, A and Suzuki, E and Tsai, CM and Nguyen, G and Ho, B and Liu, GY and Nizet, V and Dorrestein, PC and Askarian, F and Tsunoda, SM},
title = {Influence of perinatal ampicillin exposure on maternal fecal microbial and metabolic profiles.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.30.662372},
pmid = {40631287},
issn = {2692-8205},
abstract = {UNLABELLED: Indirect exposure to antibiotics during early life, via maternal intrapartum antibiotic prophylaxis (IAP) or postpartum maternal antibiotic usage, is increasingly common and has been epidemiologically linked to altered growth and immune developmental trajectories in offspring. Nevertheless, the underlying mechanisms remain poorly understood. Here, we explored the effects of antepartum and postpartum maternal ampicillin administration on the dams' fecal microbiome and metabolic profiles in vivo . Ampicillin caused a reproducible depletion of beneficial bacterial species belonging to the Muribaculaceae family, including Muribaculum intestinale and Duncaniella dubosii , and led to cohort-dependent enrichments of Enterococcus and Prevotella species. These microbial alterations were accompanied by substantial metabolic remodeling, characterized by elevated fecal acylcarnitines and dysregulation of the bile acids profile. Intriguingly, we identified two previously uncharacterized trihydroxylated bile acids conjugated to a hexose moiety, which appeared to be associated with antibiotic exposure across public metabolomics repositories. These alterations in the fecal maternal microbiome and metabolome coincided with increased weight gain in offspring, suggesting a possible role for maternal antibiotic exposure in shaping early developmental trajectories. Further studies are warranted to elucidate the long-term implications of these changes in infant health.

IMPORTANCE: Perinatal antibiotic administration is a critical intervention to reduce maternal and neonatal infections, including early-onset group B Streptococcus (GBS) disease, a major cause of neonatal mortality. Nevertheless, mounting evidence suggests that the use of broad-spectrum antibiotics during the perinatal period in mothers can affect infant gut microbiome development, with potential consequences for immune maturation and early development. Understanding how maternal antibiotic exposure affects the gut microbiome and metabolome is essential for uncovering the potential pathways by which maternal intervention may influence offspring outcomes and for guiding strategies that balance infection control with long-term infant health.},
}

@article {pmid40631266,
year = {2025},
author = {Villa Soto, VS and Degraeve, AL and Heath, CM and Orellana, DA and Reilly, ER and Mukherjee, M and Brockert, JG and Dumlao, DS and Blank, RB and Perlmutter, N and Yu, S and Ashouri, J and Scher, JU and Patterson, AD and Turnbaugh, PJ and Nayak, RR},
title = {The gut microbiome shapes pharmacology and treatment outcomes for a key anti-inflammatory therapy.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.26.661733},
pmid = {40631266},
issn = {2692-8205},
abstract = {UNLABELLED: The human gut microbiome encodes a formidable metabolic repertoire that harvests nutrients from the diet, but these same pathways may also metabolize medications. Indeed, large screens have revealed extensive microbial metabolism of drugs in vitro , but the pharmacologic and clinical repercussions of microbiota-mediated metabolism in vivo remain to be discerned. As a proof-of-concept, we investigate how human gut microbes contribute to in vivo pharmacology and efficacy of a key anti-inflammatory drug, methotrexate (MTX). Specifically, we demonstrate that the gut microbiome shapes drug pharmacology in vivo in mice, both by directly metabolizing the drug and by inducing host pathways that promote drug metabolism. Moreover, interindividual variation in the human gut microbiome contributes to variation in pharmacokinetic (PK) profiles. When we quantified metabolites produced by microbes, we unexpectedly identified novel MTX metabolites, one of which, p-methylaminobenzoyl-L-glutamic acid (pMABG), was a major byproduct of microbial metabolism both in vitro and in vivo . Further, we find that a large proportion of patient-associated microbes are capable of metabolizing MTX. Finally, we show that microbial metabolism of MTX is linked to PK profiles and disease outcomes in a mouse model of inflammatory arthritis. Taken together, these findings provide evidence that the human gut microbiome causally contributes to drug pharmacology in vivo for a key anti-inflammatory drug through known and novel mechanisms. Our studies provide a framework for elucidating the clinical relevance of drug microbial metabolism in the context of treatment response. These results are a first step towards understanding and manipulating the human gut microbiome in the treatment of autoimmunity and the advancement of precision medicine for millions of patients taking MTX for immune or inflammatory conditions.

HIGHLIGHTS: The gut microbiome impacts methotrexate (MTX) pharmacology in miceThe human gut microbiome contributes to interindividual variation in MTX pharmacologyHuman gut microbes produce novel MTX metabolites, pMABG and 6-MPDAMicrobial metabolism of MTX is linked to treatment outcomes.},
}

@article {pmid40631202,
year = {2025},
author = {Palmer, SN and Mishra, A and Gan, S and Liu, D and Koh, AY and Zhan, X},
title = {Identifying Optimal Machine Learning Approaches for Microbiome-Metabolomics Integration with Stable Feature Selection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.21.660858},
pmid = {40631202},
issn = {2692-8205},
abstract = {Microbiome research has been limited by methodological inconsistencies. Taxonomy-based profiling presents challenges such as data sparsity, variable taxonomic resolution, and the reliance on DNA-based profiling, which provides limited functional insight. Multi-omics integration has emerged as a promising approach to link microbiome composition with function. However, the lack of standardized methodologies and inconsistencies in machine learning strategies has hindered reproducibility. Additionally, while machine learning can be used to identify key microbial and metabolic features, the stability of feature selection across models and data types remains underexplored, despite its importance for downstream experimental validation and biomarker discovery. Here, we systematically compare Elastic Net, Random Forest, and XGBoost across five multi-omics integration strategies: Concatenation, Averaged Stacking, Weighted Non-negative Least Squares (NNLS), Lasso Stacking, and Partial Least Squares (PLS), as well as individual 'omics models. We evaluate performance across 588 binary and 735 continuous models using microbiome-derived metabolomics and taxonomic data. Additionally, we assess the impact of feature reduction on model performance and feature selection stability. Among the approaches tested, Random Forest combined with NNLS yielded the highest overall performance across diverse datasets. Tree-based methods also demonstrated consistent feature selection across data types and dimensionalities. These results demonstrate how integration strategies, algorithm selection, data dimensionality, and response type impact both predictive performance and the stability of selected features in multi-omics microbiome modeling.},
}

@article {pmid40631189,
year = {2025},
author = {Shahmohamadloo, RS and Gabidulin, AR and Andrews, ER and Rudman, SM},
title = {Microbiome evolution plays a secondary role in host rapid adaptation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.27.661976},
pmid = {40631189},
issn = {2692-8205},
abstract = {UNLABELLED: Understanding how populations adapt to environmental change is a central goal in evolutionary biology. Microbiomes have been proposed as a source of heritable variation that is central to rapid adaptation in hosts, yet empirical evidence supporting this remains limited, particularly in naturalistic settings. We combined a field evolution experiment in Drosophila melanogaster exposed to an insecticide with microbiome manipulations to disentangle the contributions of host standing genetic variation and microbiome evolution to adaptation. Within three generations, independent populations rapidly and repeatedly evolved increased survivorship, a defining feature of resistance evolution. Adaptive changes in sub-lethal traits such as reproductive output, stress tolerance, and body size occurred with a delayed response following the evolution of resistance. Core microbiome taxa declined following insecticide exposure, and resistant populations evolved to house lower microbial abundances. Axenic rearing and microbiome transplant experiments demonstrated that adaptation via host standing genetic variation was the mechanism for resistance evolution. Microbiome evolution played a secondary and cryptic role in host adaptation by masking slowed development rates that evolved in resistant populations. Together, these results reinforce the primacy of adaptation occurring through selection on host standing genetic variation while also demonstrating the contributions of microbiome evolution in host adaptation.

SIGNIFICANCE: Identifying the mechanisms that allow organisms to adapt to environmental stress is a foundational goal in biology. Using field experimental evolution and microbiome manipulations in Drosophila melanogaster , we directly tested the relative contributions of host genomic evolution and microbiome evolution to adaptation. We found that adaptation to environmental stress occurred rapidly and repeatedly, driven primarily by selection on host standing genetic variation, with microbiome evolution acting as a secondary contributor. These findings reinforce the importance of host genetic variation in rapid adaptation and demonstrate that microbiome evolution can contribute to host evolutionary trajectories in a cryptic manner.},
}

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

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

@article {pmid40630297,
year = {2025},
author = {Hellman, T and Yeo, LF and Palmu, J and Havulinna, A and Jousilahti, P and Laitinen, V and Pärnänen, K and Salomaa, V and Lahti, L and Knight, R and Niiranen, T},
title = {Gut Microbiome as a Risk Factor for Future CKD.},
journal = {Kidney international reports},
volume = {10},
number = {6},
pages = {1673-1682},
pmid = {40630297},
issn = {2468-0249},
abstract = {INTRODUCTION: Gut microbiome has been linked with chronic kidney disease (CKD) in several small cross-sectional studies. However, the relationship between baseline gut microbiome and long-term incident CKD remains unknown.

METHODS: We performed fecal sampling and measured serum creatinine (SCR) (N = 6699) and urine albumin-to-creatinine ratio (UACR) (N = 797) in a population-based cohort examined in the year 2002. We assessed the multivariable-adjusted associations of gut metagenome with baseline SCR, baseline UACR, and register-based incident CKD.

RESULTS: The mean age of the participants was 49.5 ± 12.9 years and 45.8% were men. During a median follow-up of 18.6 years, 108 participants developed incident CKD. In prospective analyses, increased baseline gut microbiome alpha diversity was associated with lower risk of incident CKD (hazard ratio per 1 SD: 0.84; 95% confidence interval [CI]: 0.71-0.99; P = 0.04). Gut microbial beta diversity and taxa were not related to incident CKD (P ≥ 0.09 for all). In cross-sectional analyses, alpha diversity (beta per 1 SD: 1.28; 95% CI: 0.64-1.98; P < 0.001) and beta diversity (P = 0.002; R[2] = 0.12%) were associated with SCR, whereas no associations were observed for UACR. In total, 43 significant species-level associations with SCR were observed and 16 negative associations (37.2%) for species belonging to the Lachnospiraceae family.

CONCLUSION: Our results suggest that decreased gut microbial diversity may be related to risk of future CKD and that a potential link between the Lachnospiraceae family and desirable kidney health exists. Our results extend previous cross-sectional studies and help to establish the basis for examining gut microbiome as a CKD risk factor.},
}

@article {pmid40630283,
year = {2025},
author = {Ness, C and Svistounov, D and Solbu, MD and Petrenya, N and Boardman, N and Ytrehus, K and Jenssen, TG and Holmes, A and Simpson, SJ and Zykova, SN},
title = {Gut Microbiome Diversity and Uric Acid in Serum and Urine.},
journal = {Kidney international reports},
volume = {10},
number = {6},
pages = {1683-1693},
pmid = {40630283},
issn = {2468-0249},
abstract = {INTRODUCTION: An increasing body of evidence has shown the importance of the gut microbiota in modulating serum uric acid (SUA) levels. In this study, we aimed to determine the association between gut microbiome diversity, diet, SUA, and fractional excretion of uric acid (FEUA) in the kidney.

METHODS: A cross-sectional study was conducted in 53 adults with normal or elevated SUA and estimated glomerular filtration rate (eGFR) range from 37 to 124 ml/min per 1.73 m[2]. Fecal microbiome composition was analyzed using 16S ribosomal RNA sequencing; and alpha diversity was expressed as reverse Simpson, Shannon, and Richness indices. Dietary data were collected, and dietary patterns were identified using principal component analysis. Unadjusted linear regression and models adjusted for sex, waist-hip ratio (WHR), and eGFR were used to study the association between gut microbial diversity, dietary pattern scores, and SUA/FEUA.

RESULTS: Shannon index was negatively associated with SUA after multiple adjustment (β -36.4, 95% CI [-66.2 to -6.7], P = 0.017; adjusted R[2] = 0.62, P < 0.001). Sex (standardized β = 0.52) and WHR (standardized β = 0.35) had the highest effect on SUA, followed by Shannon diversity index (standardized β = -0.22). We found that Shannon index (standardized β = 0.49, P < 0.001) was positively associated with FEUA after adjustment for sex and "sweet" dietary pattern. This model explained 40% of the variability in FEUA (P < 0.001). None of the dietary patterns were associated with SUA or FEUA.

CONCLUSION: A higher gut microbial diversity was associated with lower SUA and more efficient elimination of uric acid by the kidneys. There is a need for studies assessing efficacy and safety of interventions on the gut microbiome as a treatment of hyperuricemia.},
}

@article {pmid40630189,
year = {2025},
author = {Zhang, YF and Qin, YT and Liu, ZY and Zheng, HR and Hu, XD and Wang, XL},
title = {Diversity of endophytic bacteria in mulberry (Morus spp.) scions with different genetic resources.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1618773},
pmid = {40630189},
issn = {1664-302X},
abstract = {Endophytic bacteria in plants play crucial roles in promoting plant growth, facilitating nutrient acquisition, and enhancing stress tolerance. Although many studies have recently investigated endophytic bacteria in plants, the characteristics of endophytic bacterial communities in germplasm resource populations have rarely been reported. In this study, we investigated the endophytic bacterial communities of 21 mulberry scions, representing both wild and cultivated resources, all grafted onto a common rootstock and grown under identical cultivation conditions. High-throughput sequencing of 16S rRNA amplicons was performed using the Illumina MiSeq platform. The results revealed a total of 10 phyla, 31 classes, 50 orders, 50 families, and 113 genera of endophytic bacteria in the mulberry scions. The dominant phylum was Proteobacteria (89.07%), followed by Firmicutes (5.20%) and Actinobacteria (3.10%). At the genus level, Sphingomonas (32.84%), Methylobacterium-Methylorubrum (18.64%), and Aureimonas (8.76%) were the predominant genera enriched in the scion. Wild scions exhibited more complex endophytic bacterial communities compared to cultivated scions. Among the wild germplasm, XZBS and XZMK, originating from Tibet, China, displayed distinctive Actinobacteria signatures, suggesting a potential legacy of primitive geographic adaptation. Co-occurrence network analysis indicated that Sphingomonas and Methylobacterium-Methylorubrum acted as keystone taxa, forming critical bridges within the endophytic bacterial community network in the scions. Functional predictions further indicated that endophytic bacteria from wild species showed a greater metabolic capacity for aromatic compounds, amino acids, and carbohydrates compared with those from cultivated species. Moreover, analyses of the mulberry genetic population structure and endophytic bacterial community composition suggested that differentiation between wild and cultivated resources was associated with differences in endophytic bacterial communities. This study provides new insights into the diversity of endophytic bacteria among different mulberry germplasm resources and highlights geographically unique taxa, advancing our understanding of microbiome-driven adaptation in perennial grafted plants. It also offers a valuable reference for the future utilization of functional endophytic bacteria in mulberry improvement.},
}

@article {pmid40629992,
year = {2025},
author = {Saidu, MB and Moreira, IS and Amorim, CL and Wu, R and Ho, YW and Fang, JK and Castro, PML and Gonçalves, D},
title = {Exploring the biodegradation of PET in mangrove soil and its intermediates by enriched bacterial consortia.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-23},
doi = {10.1080/09593330.2025.2521762},
pmid = {40629992},
issn = {1479-487X},
abstract = {The biodegradation of Polyethylene terephthalate (PET) is important due to the environmental impact of plastic waste. This study investigates the degradation of PET films in soil microcosms, with and without mangrove plants, and with mangrove plants bioaugmented with a bacterial consortium (Bacillus sp.- GPB12 and Enterococcus sp.- WTP31B-5) while following the evolution of soil microcosm microbiome. The ability of bacterial consortia retrieved from soil microcosms of each tested condition to degrade PET intermediates - bis(2-hydroxyethyl) terephthalate (BHET), terephthalic acid (TPA), and monoethylene glycol (MEG) was also assessed. In the microcosms' assays with mangrove plants, variations in functional groups and surface morphology detected by FTIR and SEM analysis indicated PET degradation. Soil microcosms microbiome evolved differently according to the conditions imposed, with dominance of phylum Proteobacteria in all final microcosms. After 270 days, bacterial consortia retrieved from all soil microcosms revealed to be able to completely degrade TPA within three days. MEG degradation reached ca. 84% using the consortium retrieved from the microcosm with bioaugmented mangrove plants. BHETdegradation was ca. 96% with the consortium obtained from the microcosm with non-bioaugmented mangrove plants. These intermediates are key molecules in PET degradation pathways; thus, their degradation is an indicator of biodegradation potential. To the best of authors' knowledge, this is the first report on biodegradation of PET, BHET, TPA, and MEG by microbial community from mangrove soil, providing insights into key taxa involved in PET degradation. These findings can pave a way to develop bioremediation strategies and more efficient waste management solutions.},
}

@article {pmid40629974,
year = {2025},
author = {Haenel, A and Grzybowski, T and Skonieczna, K},
title = {Oral microbiome dynamics in Postmortem Interval estimation: research standards and guidelines.},
journal = {Archiwum medycyny sadowej i kryminologii},
volume = {75},
number = {1},
pages = {48-55},
doi = {10.4467/16891716AMSIK.25.004.21539},
pmid = {40629974},
issn = {1689-1716},
mesh = {Humans ; *Postmortem Changes ; *Mouth/microbiology ; *Microbiota ; Forensic Medicine ; },
abstract = {Determination of the postmortem interval (PMI) is a crucial aspect of forensic investigations as it verifies an alibi or narrows down suspects. Nevertheless, PMI estimation remains one of the most challenging problems in forensic science. Currently used methods are influenced by various biotic and abiotic factors affecting decomposition. Thus, determining the time of death largely depends on the skills and experience of the forensic experts. Consequently, currently used procedures are prone to inaccuracies. Lately, gut microbiome analysis has proven useful in determining the time of death. Furthermore, emerging evidence indicates that profiling the oral microbiome may also provide valuable insights into PMI estimation. In this review, we examine published reports on oral microbiome and highlight the methodological limitations that diminish their scientific value. Therefore, we summarize the research standards and guidelines for oral microbiome studies to enhance the accuracy and reproducibility of PMI studies. Consequently, standardization of this type of research could lead to the development of innovative approaches that may be implemented into routine forensic genetics practice.},
}

Humans
*Postmortem Changes
*Mouth/microbiology
*Microbiota
Forensic Medicine

@article {pmid40629894,
year = {2025},
author = {Dong, Y and Yan, G and Zhang, Y and Zhou, Y and Shang, J},
title = {Gut microbiota as a predictive tool for outcomes in IgA nephropathy.},
journal = {Renal failure},
volume = {47},
number = {1},
pages = {2514184},
doi = {10.1080/0886022X.2025.2514184},
pmid = {40629894},
issn = {1525-6049},
mesh = {Humans ; *Glomerulonephritis, IGA/microbiology/drug therapy/therapy/pathology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Adult ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Middle Aged ; *Dysbiosis/microbiology ; Treatment Outcome ; Disease Progression ; },
abstract = {Immunoglobulin A nephropathy (IgAN) is characterized by the deposition of glycosylation-deficient IgA1 in the glomeruli and has been linked to the gut-kidney axis. This study aimed to determine if baseline differences in gut microbiota could predict therapeutic responses in IgAN patients. We analyzed fecal microbiomes of 55 biopsy-confirmed IgAN patients and followed them for over 6 months. Patients were classified as responders (n = 39) or nonresponders (n = 16) based on remission status. Fecal microbiomes were profiled using 16S rRNA sequencing, revealing significant microbiota differences. Nonresponders had increased Proteobacteria and Firmicutes, with notable enrichment of opportunistic bacteria like Escherichia-Shigella and Pseudomonas. A predictive classifier based on 24 amplicon sequence variants, with Escherichia-Shigella and Pseudomonas as key contributors, showed high accuracy in identifying nonresponders (AUC 0.9103, p < 0.0001). These findings highlight the role of microbial dysbiosis in IgAN progression and treatment response, suggesting that gut microbiota analysis could guide personalized therapy for IgAN. Future studies with larger cohorts are needed to validate these results and explore microbiome-based treatments.},
}

Humans
*Glomerulonephritis, IGA/microbiology/drug therapy/therapy/pathology
*Gastrointestinal Microbiome/genetics
Male
Female
Adult
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Middle Aged
*Dysbiosis/microbiology
Treatment Outcome
Disease Progression

@article {pmid40629699,
year = {2025},
author = {Yuan, Y and Qian, XC and Chen, SM and Zhang, LL and Chen, TM and Ding, C and Liu, WZ and Chen, F and Wang, AJ},
title = {Alternating Current-Driven Bioredox Cycling Achieves in Situ Deep Mineralization of Nitroaromatic Pollutants in Sediments.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c11329},
pmid = {40629699},
issn = {1520-5851},
abstract = {Nitroaromatic compound (NAC)-contaminated sediments pose threats to aquatic ecosystems. The challenges of low mass transfer in sediments and the recalcitrance of NACs to degradation limit the effectiveness of conventional bioremediation techniques. This study demonstrates the potential of alternating current (AC)-driven bioredox cycling to overcome these barriers by coupling in situ reduction-oxidation processes. We report the successful application of AC stimulation in achieving the mineralization of nitrobenzene (NB) while elucidating its role in modulating bioredox dynamics, electron transfer, and electromicrobiome function. Sine-wave AC stimulation achieved an 87.7% reduction of NB and 90.3% mineralization of its intermediates. The AC stimulation promoted robust biofilm formation, enhanced bidirectional electrocatalytic activity, and increased microbial biomass. It also enriched a diverse microbial consortium capable of reducing NB, oxidizing aromatic intermediates, and facilitating electron transfer, as indicated by the upregulation of key enzymatic genes through multiomics analyses. Carbon metabolites from catechol meta-cleavage further supported nitro-reduction and sustained microbial viability. Compared to DC processes, AC-driven bioredox cycling reduced energy consumption by 16.8% in the remediation of NB-contaminated sediments. This approach offers a sustainable, low-carbon solution for efficient in situ biomineralization of NACs in sediments.},
}

@article {pmid40629635,
year = {2025},
author = {Zeng, B and Ren, X and Cheng, Y and Wang, C and Li, J and Jiang, L and Zhang, S and Chen, S and Yu, D and Lin, J},
title = {Correlation analysis between vaginal microecology and high-risk human papillomavirus (HR-HPV)-positive cervical squamous intraepithelial lesions (SIL).},
journal = {Medicine},
volume = {104},
number = {27},
pages = {e42914},
doi = {10.1097/MD.0000000000042914},
pmid = {40629635},
issn = {1536-5964},
mesh = {Humans ; Female ; Adult ; *Papillomavirus Infections/virology/complications/epidemiology ; *Vagina/microbiology/virology ; Middle Aged ; Risk Factors ; *Squamous Intraepithelial Lesions of the Cervix/virology/microbiology/pathology ; *Squamous Intraepithelial Lesions/virology/pathology/microbiology ; *Uterine Cervical Neoplasms/virology/pathology ; Papillomaviridae/isolation & purification ; *Uterine Cervical Dysplasia/virology ; Human Papillomavirus Viruses ; },
abstract = {This study is aimed to investigate the correlation between vaginal microecology and high-risk human papillomavirus (HR-HPV)-positive cervical squamous intraepithelial lesions (SIL) using the regression analysis. Patients (n = 372) with HR-HPV-positive from January 2020 to June 2022 were recruited after preliminary confirmation by colposcopy, HPV test, and typing, as well as loop electrosurgical excision procedure. Based on the pathological results, the recruited subjects were divided into 3 groups, that is, negative for intraepithelial lesion or malignancy, low-grade SIL, and high-grade SIL (HSIL). Finally, the clinical factors, virological data, and vaginal microecological changes of the 3 experimental groups were analyzed. Age was identified as a significant risk factor for HSIL, with an OR of 1.048 (95% CI: 1.006-1.094 and P = .026). Various HR-HPV types (HPV16, HPV18, and HPV52) were closely associated with HSIL, with multiple infections significantly increasing the risk (odds ratio, OR: 5.810, P = .04). The changes in the vaginal microecology were strongly associated with HSIL, including elevated pH (>4.5), reduced hydrogen peroxide levels, and increased bacterial vaginosis (BV) prevalence. BV demonstrated a sensitivity of 66.10% and a specificity of 70.31% for predicting HSIL. Furthermore, decreased Lactobacillus levels (OR: 3.20, P < .001) showed their protective role, while elevated sialidase activity (OR: 5.610, P = .002) emerged as a significant risk factor. Accordingly, the key independent predictors for low-grade SIL and HSIL included age, infection type, pH, microbiome density, BV, and sialidase activity. The mixed infection of HPV16, HPV18, HPV52, and HPV resulting in cervical SILs could be closely related to the vaginal microecology.},
}

Humans
Female
Adult
*Papillomavirus Infections/virology/complications/epidemiology
*Vagina/microbiology/virology
Middle Aged
Risk Factors
*Squamous Intraepithelial Lesions of the Cervix/virology/microbiology/pathology
*Squamous Intraepithelial Lesions/virology/pathology/microbiology
*Uterine Cervical Neoplasms/virology/pathology
Papillomaviridae/isolation & purification
*Uterine Cervical Dysplasia/virology
Human Papillomavirus Viruses

@article {pmid40629482,
year = {2025},
author = {Tretiak, S and Mendes Maia, T and Ducatelle, R and Cherlet, M and Rijsselaere, T and Van Immerseel, F and Impens, F and Antonissen, G},
title = {Proteomic profiling of dysbiosis-challenged broilers reveals potential blood biomarkers for intestinal health.},
journal = {Veterinary research},
volume = {56},
number = {1},
pages = {143},
pmid = {40629482},
issn = {1297-9716},
support = {Baekeland Mandate HBC.2020.2274//VLAIO/ ; BOF/STA/202209/011//Ghent University Concerted Research Action grant/ ; BOF21/GOA/033//Ghent University Concerted Research Action grant/ ; },
mesh = {Animals ; *Chickens/blood ; Biomarkers/blood ; *Dysbiosis/veterinary/microbiology/blood ; Proteomics ; *Gastrointestinal Microbiome ; *Poultry Diseases/microbiology/blood ; *Intestines/microbiology ; *Proteome ; },
abstract = {The intestinal microbiome forms a dynamic ecosystem whose balanced composition and functioning are essential for maintaining overall gut health and well-being in living organisms. In broilers, dysbiosis disrupts the microbiota-host balance, often without obvious clinical symptoms but with intestinal inflammation, and leads to impaired animal performance. This study aimed to identify host blood-based protein biomarkers that indicate intestinal inflammation and intestinal barrier dysfunction. Using mass spectrometry-based proteomics, blood plasma samples from broilers derived from an in vivo dysbiosis model were analyzed and compared to healthy controls. Microscopic histologic changes in the gut (shortened villi, increased crypt depth) were observed in the duodenal and jejunal tissue of 25-days old challenged birds. Elevated levels of permeability markers faecal ovotransferrin and serum iohexol additionally indicated increased intestinal leakage in the challenged group. The blood plasma proteome analysis enabled quantification of 388 proteins, 25 of which were significantly different between the tested groups. The challenge was marked by activation of immune and signaling pathways, and response to bacteria, while proteins related to cellular physiology, cell-cell communication, and extracellular matrix (ECM) processes were suppressed. Protein-protein interaction analysis revealed two clusters of downregulated proteins involved in ECM organization and cell adhesion. Intestinal dysbiosis in broilers demonstrated that the host prioritizes immune defense over structural maintenance. The activation of immune processes and suppression of ECM pathways highlight potential biomarkers and therapeutic targets. Data are available via ProteomeXchange with identifier PXD056546.},
}

Animals
*Chickens/blood
Biomarkers/blood
*Dysbiosis/veterinary/microbiology/blood
Proteomics
*Gastrointestinal Microbiome
*Poultry Diseases/microbiology/blood
*Intestines/microbiology
*Proteome

@article {pmid40629442,
year = {2025},
author = {Matson, AP and Unterhauser, K and Rezaul, K and Lesmes, S and Zhou, Y and Michelow, IC and Hussain, N and Driscoll, MD},
title = {Source-tracking Klebsiella outbreaks in premature infants using a novel amplicon fingerprinting method.},
journal = {Antimicrobial resistance and infection control},
volume = {14},
number = {1},
pages = {83},
pmid = {40629442},
issn = {2047-2994},
mesh = {Humans ; Infant, Premature ; *Klebsiella Infections/epidemiology/microbiology ; Infant, Newborn ; Intensive Care Units, Neonatal ; *Klebsiella/genetics/classification/isolation & purification ; *Disease Outbreaks ; Feces/microbiology ; Female ; *Cross Infection/microbiology/epidemiology ; Male ; Milk, Human/microbiology ; Sepsis/microbiology/epidemiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Even with state-of-the-art infection control practices, premature infants can develop life-threatening infections in the neonatal intensive care unit (NICU). The precise sources of most NICU-associated infections frequently remain unknown and, therefore, are difficult to address. In this study, we used a novel microbiome sequencing approach to source-track lethal sepsis-causing Klebsiella, opportunistic pathogens, and commensal bacterial strains colonizing the gut of hospitalized premature infants.

METHODS: An exploratory-methods, case series was at performed Connecticut Children's Medical Center NICU in 2021. Long-read 16-23 S rRNA gene sequencing was used to analyze fecal samples, mother's milk, and clinical bacterial isolates derived from a cluster of Klebsiella-infected, and concurrently hospitalized non-infected, premature infants who were simultaneously enrolled in a neonatal microbiome study. Distinct groups of amplicons comprising a unique fingerprint pattern for a given strain were compared among the samples to ascertain relatedness.

RESULTS: We confirmed 100% amplicon identity between lethal Klebsiella quasipneumoniae from milk, gut, blood and trachea during sepsis in twins, while differentiating other infecting and colonizing Klebsiella strains in concurrently hospitalized premature infants. The method also successfully discriminated between multiple Klebsiella strains within the gut microbiota of a non-infected infant. Additionally, we showed that human milk is the source of many early intestinal colonizers, including Klebsiella, Enterococcus, Veillonella, and Bifidobacterium strains.

CONCLUSIONS: Amplicon fingerprinting can be utilized as a high-throughput high-resolution test to assist in the investigation of nosocomial outbreaks. Additional applications such as routine monitoring of various reservoirs for potential pathogens could inform infection prevention and control strategies in the NICU.},
}

Humans
Infant, Premature
*Klebsiella Infections/epidemiology/microbiology
Infant, Newborn
Intensive Care Units, Neonatal
*Klebsiella/genetics/classification/isolation & purification
*Disease Outbreaks
Feces/microbiology
Female
*Cross Infection/microbiology/epidemiology
Male
Milk, Human/microbiology
Sepsis/microbiology/epidemiology
RNA, Ribosomal, 16S/genetics

@article {pmid40629427,
year = {2025},
author = {Bell, AG and Vaughan, ER and Kasprzyk-Hordern, B and Cable, J and Temperton, B and Tyler, CR},
title = {Impacts of environmentally relevant concentrations of antibiotic cocktails on the skin microbiome of Eurasian carp (Cyprinus carpio).},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {73},
pmid = {40629427},
issn = {2524-4671},
support = {NE/R011524/1//Natural Environment Research Council/ ; NE/R011524/1//Natural Environment Research Council/ ; CGR/SD6387//NERC Environmental Bioinformatics Centre/ ; },
abstract = {BACKGROUND: The skin surfaces of fish harbour diverse assemblages of microbes (microbiomes) that play critical roles in host health and disruption of these microbiomes can lead to disease conditions. Antibiotics, widely used in medicine for human and animal health treatments, are increasingly found in waterways and this is a growing concern due to their potential to alter the balance of microbial ecosystems and drive antimicrobial resistance (AMR). The effects of antibiotics on skin microbiomes in fish, however, have been little explored. This study examines how exposure to environmental levels of antibiotics affects the skin microbiomes of Eurasian carp (Cyprinus carpio).

RESULTS: A 2-week exposure of Eurasian carp to cocktails of five antibiotics (ciprofloxacin, clarithromycin, sulfamethoxazole, trimethoprim, and tetracycline) at concentrations found in the environment resulted in significant skin bacterial community compositional shifts. Applying 16S rRNA amplicon sequencing, we found enrichment of the genus Arcicella (Proteobacteria) and depletion of Sphaerotilus (Bacteroidetes) with limited recovery even after maintaining the fish for a further two weeks in clean (antibiotic-free) water. In the low-antibiotic concentration exposure group, the tank water microbiome assemblages resembled those of the fish skin suggesting similar responses to the antibiotic treatments. Metagenomic analysis observed no increase in antibiotic resistance genes or changes in metabolic pathway abundance, possibly due to the relatively short duration of antibiotic exposure.

CONCLUSION: This study highlights that even low-level exposure to chemical mixtures can alter fish skin microbiome compositions, with limited recovery observed after cessation of exposure. These findings warrant further assessments of the long-term effects and functional consequences of these altered microbiomes on fish health, particularly in environments increasingly affected by anthropogenic chemical pollution.},
}

@article {pmid40611897,
year = {2025},
author = {Fletcher, JR and Hunter, RC},
title = {Cross-feeding interactions between Fusobacterium nucleatum and the glycan forager Segatella oris.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40611897},
issn = {2692-8205},
abstract = {Fusobacterium nucleatum is a common member of the oral microbiota frequently associated with extraoral infections and diverse polymicrobial environments, including chronic airway diseases and colorectal tumors. Yet, its interactions with co-colonizing microbiota remain poorly defined. Here, we investigate cross-feeding interspecies dynamics between F. nucleatum and Segatella oris, a glycan-foraging anaerobe enriched in airways and gastrointestinal tumors. Using broth cultures, cell-free supernatants, and co-culture on primary human airway epithelial cells, we identify bidirectional interactions that shape nutrient acquisition, biofilm formation, gene expression, and host responses. While mucin or S. oris supernatants modestly enhanced F. nucleatum growth, both conditions triggered transcriptional remodeling, including induction of the nan operon for sialic acid catabolism, suggesting reliance on glycan degradation by S. oris. Conversely, S. oris exhibited differential expression of multiple polysaccharide utilization loci (PULs) when exposed to F. nucleatum or its metabolites. Biofilm formation by F. nucleatum was strongly inhibited by S. oris, indicative of antagonistic interactions. Dual and triple RNA-seq revealed that epithelial responses were predominately shaped by F. nucleatum, with enrichment of inflammatory and cancer-associated pathways; however, co-colonization with S. oris modulated the magnitude and specificity of host gene expression. These findings demonstrate that glycan-mediated cross-feeding and microbial interactions shape the physiology and pathogenic potential of F. nucleatum in mucosal environments. This work underscores the importance of modeling polymicrobial communities under host-relevant conditions to better understand pathobiont behavior at the epithelial interface.},
}

@article {pmid40451181,
year = {2025},
author = {Okumura, T and Hiraiwa, H and Yanagisawa, S and Murohara, T},
title = {The Gut-Heart Axis in Heart Failure: Emerging Evidence and Therapeutic Implications.},
journal = {Cardiology},
volume = {},
number = {},
pages = {1-3},
doi = {10.1159/000546542},
pmid = {40451181},
issn = {1421-9751},
}

@article {pmid40629403,
year = {2025},
author = {Somodi, C and Dora, D and Horváth, M and Szegvari, G and Lohinai, Z},
title = {Gut microbiome changes and cancer immunotherapy outcomes associated with dietary interventions: a systematic review of preclinical and clinical evidence.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {756},
pmid = {40629403},
issn = {1479-5876},
support = {#146775//Nemzeti Kutatási, Fejlesztési és Innovaciós Alap/ ; #142287//Nemzeti Kutatási, Fejlesztési és Innovaciós Alap/ ; Bolyai Research Scholarship//Magyar Tudományos Akadémia/ ; },
abstract = {INTRODUCTION: Cancer patient's survival has gradually improved due to immune checkpoint inhibitors (ICIs). Several studies showed a possible association between the intestinal microbiome and ICI efficacy. Strategies for modifying the composition of the gut microbiome encompass various dietary interventions, which may have distinct impacts on the outcomes of ICI-treated patients. In our systematic review, we explored how dietary habits correlate with therapeutic responses in cancer patients and cancer mouse models undergoing immunotherapy.

METHODS: A systematic review was conducted using search terms: "cancer", "immunotherapy", "diet", and "microbiome", from Medline, Web of Science, Scopus, and Cochrane Library databases. The outcomes in the clinical studies were overall response rate (ORR), overall survival (OS), or progression-free survival (PFS) in human studies. In mouse studies, change in tumor size was the endpoint. The comparator attributions were questionnaire-based dietary interventions.

RESULTS: Nineteen articles met the inclusion criteria and were included in the review (6 prospective cohort studies, 1 cross-sectional observational study, and 12 mouse studies). A consistent association was observed between high (vs. low) fiber consumption and improved therapeutic response with a pooled odds ratio of 5.79 when including all human prospective cohort studies. In mice, limited availability of methionine, cysteine, and low intake of leucine and glutamine was linked to reduced tumor progression. Combining ICIs with intermittent fasting or a fasting-mimicking diet significantly decreased tumor volume in mouse melanoma models. In humans, a higher relative abundance of short-chain fatty acid (SCFA) and lactic acid-producing bacteria-particularly Faecalibacterium prausnitzii and Akkermansia muciniphila-correlated with objective response rates (ORR). Similar microbiome alterations were observed in mouse models. Increased fiber intake enhanced ICI efficacy in mice by modulating the gut microbiome, primarily via elevated SCFA production-an effect also reflected in human studies.

CONCLUSION: Intermittent fasting, high fiber, and low sugar consumption are significantly associated with better ICI outcomes. The studies revealed alterations in microbiota composition linked to diet, and these findings were confirmed in animal models, regarding the production of SCFAs and lactic acid, as well as an increase in Bacteroidota/Bacillota ratio and microbial diversity.},
}

@article {pmid40629382,
year = {2025},
author = {Song, JX and Scales, BS and Nguyen, M and Westberg, E and Witalis, B and Urban-Malinga, B and Oberbeckmann, S},
title = {Close encounters on a micro scale: microplastic sorption of polycyclic aromatic hydrocarbons and their potential effects on associated biofilm communities.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {84},
pmid = {40629382},
issn = {2524-6372},
support = {BONUS (Art 185), 03F0775A//European Union and the German Federal Ministry of Education and Research/ ; BONUS (Art 185), 03F0775A//European Union and the German Federal Ministry of Education and Research/ ; BONUS (Art 185), 03F0775A//European Union and the German Federal Ministry of Education and Research/ ; Vinnova, 2017-00001//Swedish Governmental Agency for Innovation Systems/ ; Vinnova, 2017-00001//Swedish Governmental Agency for Innovation Systems/ ; BONUS-BB/MICROPOLL/06/2017//National Centre for Research and Development, Poland (NCBR)/ ; BONUS-BB/MICROPOLL/06/2017//National Centre for Research and Development, Poland (NCBR)/ ; },
abstract = {BACKGROUND: Within systems as dynamic as the aquatic environment, it is crucial to address the impacts of an ever-growing network of emerging pollutants at their intersection. With previous research having demonstrated the capacity of microplastics (MPs) to sorb persistent organic pollutants, we ask in our study how different plastic polymers that are found throughout aquatic systems interact with polycyclic aromatic hydrocarbons (PAHs) and how this intersection of pollutants might impact the bacterial communities that form on MP surfaces. We performed an in situ incubation experiment at different sites along the Baltic Sea coast and through a PAH and 16S amplicon analysis, we investigated the sorption patterns of different substrates and their potential impacts on associated biofilm communities.

RESULTS: PAH sorption patterns of polyethylene (PE), polystyrene (PS), and aquaria stone were found to be dictated predominantly by substrate type and secondly by incubation site. While PE showed a general positive trend of sorption, stone rather leached PAHs into the environment, whereas the PAH levels of PS remained relatively unchanged following incubation. These sorption patterns correlated significantly with the composition of biofilm communities observed on all three substrate types after a 6-week incubation period. Strong correlations between specific PAHs and bacterial taxa indicate a direct relationship between these factors. Elevated levels of specific 3- and 4-ring PAHs on PE and PS coincided with higher proportions of specific taxa reportedly capable of hydrocarbon utilisation as well as a reduced diversity among biofilm communities.

CONCLUSION: The findings in our study highlight the importance of investigating contaminants such as MPs holistically, including any associated substances, to fully understand how they impact surrounding ecological systems as they traverse the different compartments of the aquatic ecosystem.},
}

@article {pmid40629225,
year = {2025},
author = {Florek, K and Komorowska, K and Ptak, J and Jarocki, M and Gontarczyk, J and Mania, R and Boluk, A and Żurawska-Płaksej, E and Łaczmański, Ł and Sokolski, M},
title = {Gut microbiota's role in heart failure.},
journal = {Heart failure reviews},
volume = {},
number = {},
pages = {},
pmid = {40629225},
issn = {1573-7322},
abstract = {The pathogenesis of heart failure (HF) is complex, and from an immunological perspective, the "gut-heart axis" plays a pivotal role in its development. The composition of gut microbiota differs significantly between HF patients and healthy individuals, with variations observed across different nations, HF etiologies, and stages defined by the New York Heart Association (NYHA) classification. Moreover, gut-derived metabolites such as short-chain fatty acids (SCFAs), trimethylamine N-oxide (TMAO), bile acids, and lipopolysaccharides (LPS) influence HF progression through specific mechanisms and signaling pathways. Notably, medications recommended in cardiovascular diseases and advanced interventions applied in HF, such as heart transplantation requiring immunosuppressive therapy or the implantation of mechanical circulatory support devices, are associated with significant alterations in gut microbiota composition. However, these mechanisms are still not well-established. This review aims to summarize current data on the impact of the gut microbiome on HF progression and treatment, encompassing both standard medical treatment and advanced therapies of HF.},
}

@article {pmid40629040,
year = {2025},
author = {Ju, CW and Lyu, R and Li, H and Wei, J and Parra Vitela, AJ and Dougherty, U and Kwesi, A and Luna, A and Zhu, X and Shen, S and Liu, Y and Wang, L and Cui, X and Xu, Y and Jiang, B and Ji, Y and Xia, P and West-Szymanski, DC and Sun, C and Zhong, Y and Ye, C and Moran, A and Lehmann, C and Pamer, E and Zhang, W and Bissonnette, M and Zhang, LS and He, C},
title = {Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40629040},
issn = {1546-1696},
abstract = {Circulating cell-free RNA (cfRNA) in plasma represents a promising avenue for cancer detection. We report low-input multiple methylation sequencing, a method for profiling modification patterns in cfRNA, enabling the detection of diverse transfer RNAs and small noncoding RNAs derived from both the human genome and the microbiome. RNA modification patterns in microbiome-derived cfRNA accurately reflect host microbiota activity and hold potential for the early detection of colorectal cancer.},
}

@article {pmid40629022,
year = {2025},
author = {Teo, JJY and Ho, EXP and Ng, AHQ and How, SHC and Chng, KR and Ateş, YC and Fau'di, MT and Aung, KT and Nagarajan, N},
title = {Citywide metagenomic surveillance of food centres reveals local microbial signatures and antibiotic resistance gene enrichment.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {63},
pmid = {40629022},
issn = {2731-8745},
abstract = {The distribution of microorganisms in built environments with high human traffic, such as food centres, can potentially have a significant impact on public health, particularly in the context of increasing worldwide incidence of food and fomite-related outbreaks. In many major Asian cities, public food centres are central to daily food consumption, yet there is a lack of baseline knowledge about their environmental microbiomes. We performed a city-wide metagenomic survey of food-centre microbiomes in Singapore, covering 16 centres and 240 samples, to map the abundances of microbial (bacteria, archaea, fungi, viruses) and non-microbial DNA across two timepoints. Food-centre microbiomes were found to be enriched in food-related DNA signatures compared to other environments, such as hospitals and offices, with specific food-microbe associations (e.g., Enterobacteriaceae and fish) and food DNA providing a partial explanation for the microbial profiles observed (44% of variation explained). Machine learning analysis identified a small set of microbial species (n = 22) that serve as highly accurate (>80%) location-specific signatures for various food centres, some of which persist even after 3 years. Profiling of antibiotic resistance genes (ARGs) and pathogens identified a surprising enrichment of ARGs in food centres relative to other non-healthcare environments (>2.5×), and an order of magnitude enrichment of key pathogenic species (e.g., Klebsiella pneumoniae, Enterobacter spp) even compared to hospital environments. These results highlight the contribution of diverse biotic and abiotic factors in shaping the unique microbiome profiles of different food-centre environments, and the potential for using metagenomic surveillance to understand the risk for infections and antibiotic resistance gene transmission.},
}

@article {pmid40628921,
year = {2025},
author = {Maskawa, R and Takayasu, L and Takayasu, H and Watanabe, K and Takemine, S and Kakimoto, T and Takeshita, K and Narushima, S and Suda, W and Takayasu, M},
title = {High-resolution fecal pharmacokinetic modeling in mice with orally administered antibiotics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24441},
pmid = {40628921},
issn = {2045-2322},
support = {24KJ1073//Japan Society for the Promotion of Science/ ; JPMJCR22N3//Japan Science and Technology Agency/ ; JPMJCR22N3//Japan Science and Technology Agency/ ; JPMJCR22N3//Japan Science and Technology Agency/ ; 23ae0121046//Japan Agency for Medical Research and Development/ ; },
mesh = {Animals ; *Anti-Bacterial Agents/pharmacokinetics/administration & dosage ; *Feces/chemistry ; Administration, Oral ; Mice ; *Vancomycin/pharmacokinetics/administration & dosage ; Mice, Inbred C57BL ; *Models, Biological ; Male ; Gastrointestinal Motility/drug effects ; Gastrointestinal Microbiome/drug effects ; },
abstract = {High-resolution fecal pharmacokinetics are crucial for optimizing therapeutic design and evaluating gastrointestinal motility. However, empirical studies with detailed fecal concentration over time data remain limited. This study aims to characterize fecal pharmacokinetics through high-frequency sampling and parallelized fecal concentration quantification, establishing a simple pharmacokinetics model with physiologically interpretable parameters. We quantified vancomycin concentrations in fecal samples collected at a minimum interval of 4 hours from C57BL/6N mice following a single oral administration of either a low (1 mg/mL) or high (20 mg/mL) dose. Fecal concentrations gradually increased and exhibited an exponential decay, leading to the development of a compartmental model with an absorption phase. This simple model accurately fit the experimental data and provided physiological explanations for intra- and inter-individual pharmacokinetics variability. The results suggest that inter-individual differences in pharmacokinetics are attributable to fecal elimination capacity, which may be influenced by drug dosage via changes in gastrointestinal motility. Since the model predicts antibiotic concentrations within the gastrointestinal tract, it can be applied to fundamental studies investigating the effects of antibiotics on the gut microbiome and gastrointestinal motility.},
}

Animals
*Anti-Bacterial Agents/pharmacokinetics/administration & dosage
*Feces/chemistry
Administration, Oral
Mice
*Vancomycin/pharmacokinetics/administration & dosage
Mice, Inbred C57BL
*Models, Biological
Male
Gastrointestinal Motility/drug effects
Gastrointestinal Microbiome/drug effects