@article {pmid41473682,
year = {2025},
author = {Fu, X and Wu, F and Liu, X},
title = {Bio-Archive of Cultural Heritage Microbiomes for Sustainable Conservation in the Multi-Omics Era.},
journal = {Advanced genetics (Hoboken, N.J.)},
volume = {6},
number = {4},
pages = {e00046},
pmid = {41473682},
issn = {2641-6573},
abstract = {Cultural heritage sites are commonly exposed to outdoor environments, resulting in severe damage to heritage objects from biotic and abiotic processes. Control of outdoor environments is impossible for heritage conservation, and we cannot prevent the abiotic processes. However, a variety of mitigation management can be developed for biotic damage, such as microbial colonization and biodeterioration. Over the past few decades, both conventional cultivation-dependent and modern cultivation-independent techniques have been employed to elucidate the microbiomes associated with the biodeterioration of cultural heritage. However, many studies are limited to segmentary analyses or simply stop at examining the community composition of the microbiomes, lacking solid evidence of microbial metabolism and biochemical reactions between microorganisms and heritage materials to support the core microbiomes associated with the biodeterioration. Here, we recommend thoroughly exploring the benefits of more advanced multi-omics techniques for analyzing cultural heritage microbiomes. We propose establishing a professional open-access database to standardize analytical procedures, integrating both culture-dependent and culture-independent approaches, and bio-archive valuable information on the core microbiomes, including their biodeterioration mechanisms, timelines, causes, and environmental conditions. This bio-archive of cultural heritage microbiomes will empower conservators and researchers worldwide to develop evidence-based, sustainable approaches for cultural heritage conservation under environmental change.},
}

@article {pmid41473651,
year = {2025},
author = {Damoulaki, E and Sioutis, D and Sarli, V and Trakakis, E and Mastorakos, G and Katoulis, A and Kastrinakis, K and Koratzanis, C and Machairiotis, N and Panagopoulos, P and Christodoulaki, C},
title = {Polycystic Ovary Syndrome-Associated Acne: The Interplay of Hyperandrogenism, Insulin Resistance, and Therapeutic Strategies.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e98103},
pmid = {41473651},
issn = {2168-8184},
abstract = {Acne vulgaris is one of the most prevalent dermatologic disorders in adolescent and adult women. Beyond classic pathogenic factors, such as sebaceous hypersecretion, follicular hyperkeratinization, Cutibacterium acnes overgrowth, and inflammation, endocrine drivers are pivotal. Polycystic ovary syndrome (PCOS) is common across reproductive ages and frequently presents with dermatologic manifestations, notably acne, through mechanisms dominated by hyperandrogenism and compounded by insulin resistance (IR). This narrative review synthesizes current evidence linking PCOS with acne, explains the interrelated roles of hyperandrogenism and IR, and outlines evidence-based management strategies tailored to women with PCOS. The Rotterdam diagnostic framework remains the globally favored standard for PCOS, emphasizing combinations of oligo-/anovulation, clinical/biochemical hyperandrogenism, and polycystic ovarian morphology. PCOS pathophysiology involves dysregulation of the hypothalamic-pituitary-ovarian axis with increased gonadotropin-releasing hormone pulsatility, elevated luteinizing hormone, and suppression of follicle-stimulating hormone, promoting thecal androgen excess and impaired folliculogenesis. IR, prevalent in PCOS, augments ovarian/adrenal androgen synthesis and lowers sex hormone-binding globulin levels, increasing free testosterone and sebum production; IGF-1 signaling further amplifies sebogenesis and follicular hyperkeratinization. Emerging data implicate genetic/epigenetic determinants, endocrine-disrupting chemicals, gut microbiome dysbiosis, and endoplasmic reticulum stress as modulators of the PCOS-acne phenotype. Epidemiologic studies and meta-analyses report higher acne prevalence and severity in PCOS, particularly among adolescents. First-line therapy includes combined oral contraceptive pills with antiandrogenic progestins; spironolactone is an effective adjunct. Where indicated, metformin addresses IR and may improve acne and ovulatory function. Judicious use of standard acne modalities such as topical retinoids, benzoyl peroxide, and oral/topical antibiotics remains essential; oral isotretinoin is reserved for refractory disease with careful risk management. PCOS-associated acne reflects converging endocrine and metabolic disturbances. Integrating androgen-targeted therapy, IR mitigation, and guideline-based acne care provides the most durable control. Future research should refine phenotype-directed treatment and clarify the contributions of microbiome, environmental exposures, and cellular stress pathways.},
}

@article {pmid41473600,
year = {2025},
author = {Zhang, Z and Chang, C and Xiao, L and Su, H and Lyu, Y and Zhao, J and Chen, J and Gou, K and Zhou, J and Wang, C and Zhu, X and Fu, S and Lu, M and Shi, L},
title = {The Neuroimmune Axis in Atopic Dermatitis: From Pathogenic Mechanisms to Targeted Neuroimmunotherapy.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {18079-18113},
pmid = {41473600},
issn = {1178-7031},
abstract = {Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disease in which intense pruritus and eczematous lesions arise from tightly coupled disturbances of the nervous and immune systems. Emerging evidence indicates that a dysregulated neuroimmune axis-as reflected by peripheral neuronal sensitization, epidermal barrier dysfunction, and central itch processing-plays a central role in disease onset, persistence, and clinical heterogeneity. In this review, we synthesize current knowledge on the neuroimmune mechanisms that drive AD, focusing on how cytokines such as IL-31, IL-4/IL-13, TSLP and IL-33, together with neuropeptides including substance P, CGRP and VIP, establish self-reinforcing itch-scratch and inflammation loops at the level of the skin and the central nervous system. We then highlight recent multi-omics and systems biology approaches, including single-cell and spatial transcriptomics, neuroimaging, and microbiome profiling, that have reshaped the understanding of neuroimmune "neighbourhoods" and the gut-skin-brain axis in AD. Building on these mechanistic insights, we summarize key neuroimmune biomarkers-such as NGF, IL-31, TARC/CCL17, S100 proteins, barrier-related lipids, neurofunctional readouts from fMRI, and microbial signatures-and discuss their potential for improving diagnosis, patient stratification, and treatment monitoring within a precision medicine framework. Finally, we review established and emerging neuroimmune-targeted therapies, including IL-4/IL-13 and IL-31 pathway inhibitors, JAK inhibitors, OX40/OX40L-directed biologics, TRP and NK1R antagonists, phototherapy, and microbiome-based interventions, with a particular emphasis on biomarker-guided sequencing and combination strategies. Overall, we propose that positioning the neuroimmune axis at the core of AD pathogenesis provides a conceptual basis for developing stratified, durable, and patient-centred neuroimmunotherapy, while also outlining the remaining challenges regarding clinical validation of biomarkers, long-term safety, accessibility, and implementation across diverse patient populations.},
}

@article {pmid41473328,
year = {2025},
author = {Primov, K and Scott, C and Huzar, A and Peterson, C and Kirkpatrick, M and Matz, M},
title = {Acropora millepora 's microbiome is predicted by algal symbionts, host genetics, and environment.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.15.694400},
pmid = {41473328},
issn = {2692-8205},
abstract = {The coral microbiome is a critical component of coral health and resilience, yet it is unclear what factors drive coral microbiome composition, especially within the context of coral bleaching. Here, we use whole genome sequencing data combined with a machine learning approach (RDAforest) to assess predictors of the microbiome in 208 colonies of Acropora millepora from 12 reef sites in the Central Great Barrier Reef during a 2016 bleaching event. We characterized microbiome variation using k-mers. While some environmental variables, such as chlorophyll seasonal range and maximum degree heating weeks, were associated with microbiome composition, we find that host genetics and dominant photosymbionts were more powerful predictors. In contrast, bleaching score had negligible predictive power. The coral's microbiome therefore correlates with dominant photosymbiont identity even during a bleaching event. The association of the microbiome with the environment suggests that the coral microbiome can serve as a proxy for environmental variation when environment cannot be measured directly, which may be especially useful in ancient DNA studies.},
}

@article {pmid41473293,
year = {2025},
author = {Estrada, KB and Azamar, KMM and Wang, C and Sudi, SD and Friday-Saunders, K and Márquez, V and Quintanilla-Carvajal, MX and Acosta-González, A and Conde-Martinez, N and Porras, AM and Alviña, K},
title = {Supplementation with a Limosilactobacillus fermentum K73 synbiotic modulates gut microbiota function and behavior in gnotobiotic mice transplanted with microbiota from children diagnosed with autism spectrum disorder.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.16.694732},
pmid = {41473293},
issn = {2692-8205},
abstract = {BACKGROUND: Gut dysbiosis has been implicated in numerous pathological conditions, including neurodevelopmental and neurodegenerative disorders. Recently, dietary interventions targeted at restoring microbial balance have therefore gained attention as potential therapeutic strategies. We recently demonstrated that an encapsulated synbiotic containing high-oleic palm oil and Limosilactobacillus fermentum K73 can modulate the metabolic activity and composition of human-derived gut microbiota in an in vitro batch bioreactor. Here, we extended this work through an in vivo supplementation pilot study using gnotobiotic mice colonized with gut microbiota from Colombian pediatric patients diagnosed with autism spectrum disorder (ASD) or age-matched neurotypical (NT) donors. Behavioral assessments and analyses of gut microbiota composition and function were performed before and after synbiotic supplementation.

RESULTS: First, we found that the gut microbiota from Colombian ASD patients exhibited significantly reduced richness relative to NT donors, consistent with reports from other geographical regions, and displayed distinct compositional features unique to this population. Humanization of the gnotobiotic mice with this donor microbiota was successful, with murine gut communities reflecting features of their corresponding donor microbiota. Notably, synbiotic supplementation induced significant increases in the abundance of beneficial taxa and the production of short chain fatty acids that were more pronounced in mice colonized with ASD-derived microbiota, with concurrent behavioral changes associated with beneficial modulation of gut microbiota.

CONCLUSIONS: Overall, we provide evidence that supports synbiotic supplementation as a viable strategy to positively modulate gut microbiome in conditions of dysbiosis. Our study also expands the body of knowledge of gut microbiome to understudied populations such as Latin America.},
}

@article {pmid41473253,
year = {2025},
author = {Wagner, ES and Oliphant, K and D'Souza, M and Cruz-Ayala, W and Azzam, RK and Andrews, B and Claud, EC},
title = {Fecal Microbiome and Bile Acid Profiles Differ in Preterm Infants with Parenteral Nutrition-associated Cholestasis.},
journal = {Journal of clinical and translational hepatology},
volume = {13},
number = {12},
pages = {1036-1045},
pmid = {41473253},
issn = {2310-8819},
abstract = {BACKGROUND AND AIMS: Parenteral nutrition (PN)-associated cholestasis (PNAC) is frequently diagnosed in premature infants; however, not all PN-exposed infants develop PNAC. We propose that, in premature infants receiving PN and varying amounts of enteral feeds, differences in the gut microbiome and fecal bile acid content are associated with PNAC development. This study aimed to examine the fecal microbiome and bile acid content of premature infants on PN to determine if there is a relationship with the development of PNAC.

METHODS: Twenty-two preterm infants had serial bilirubin measurements and fecal samples collected during their neonatal intensive care unit admission. Fecal samples underwent 16S rRNA gene sequencing and bile acid analysis. Binomial regression, adjusting for postmenstrual age with feed amount as a moderator, was used to assess the impact of the fecal microbiome and bile acids on PNAC development.

RESULTS: Cholestatic patients (n = 11) had greater PN and antibiotic exposure (p = 0.020; p = 0.010) and longer neonatal intensive care unit stays (p = 0.0038) than non-cholestatic patients. Microbiome richness was higher in non-cholestatic infants (p < 2E-16), with no difference in β diversity (p = 1.0). Cholestatic infants had a significantly higher abundance of Proteobacteria and Fusobacteriota and a lower abundance of Bacteroidota (p < 2E-16). Akkermansia was abundant in all infants on low feeds; as feed volume increased, Akkermansia abundance significantly increased in non-cholestatic infants (p < 2E-16). Bile acid analysis demonstrated significantly lower deoxycholic acid concentrations in cholestatic infants (p < 2E-16). Metagenomic analysis revealed an increase in Proteobacteria requiring augmented stress responses in non-cholestatic infants.

CONCLUSIONS: This is the first study to directly explore the relationship between PNAC susceptibility, the microbiome, and fecal bile acids in preterm infants. The microbiome and bile acid patterns identified here may inform the development of targeted therapeutics for this vulnerable population.},
}

@article {pmid41473248,
year = {2025},
author = {Zhang, Y and Cao, J and Wang, Y and Fan, X and Deng, R and Mi, J},
title = {Effects of fecal microbiota transplantation on glycemic and lipid profiles in overweight or obese patients with metabolic disorders: a systematic review and meta-analysis.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1737543},
pmid = {41473248},
issn = {1664-2392},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Obesity/therapy/blood/complications ; *Metabolic Diseases/therapy/blood ; *Overweight/therapy/blood ; *Lipids/blood ; *Blood Glucose/metabolism ; Gastrointestinal Microbiome ; Randomized Controlled Trials as Topic ; Lipid Metabolism ; },
abstract = {UNLABELLED: Obesity and its associated metabolic disorders (such as type 2 diabetes, metabolic syndrome, and NAFLD/MASLD) represent a global health challenge. Fecal microbiota transplantation (FMT), as a therapy regulating the gut microbiome, has demonstrated inconsistent clinical efficacy. This systematic review aims to evaluate the impact of FMT on key indicators of glucose and lipid metabolism in overweight/obese adults with metabolic diseases. We systematically searched PubMed, Embase, Cochrane, and Web of Science databases up to September 28, 2025, to identify randomized controlled trials evaluating FMT for obesity and metabolic disorders. Data were pooled using a random-effects model, with primary outcomes being changes in BMI, HOMA-IR, and HbA1c relative to baseline. A total of 11 RCTs (320 participants) were included. The primary analysis showed that FMT intervention demonstrated a trend toward improvement in the primary outcome measures, BMI (MD: -0.65, p = 0.070) and HOMA-IR (MD: -0.64, p = 0.062), but these trends did not reach statistical significance. There was no significant effect on HbA1c (MD: 0.06, p = 0.742). However, this negative conclusion based on the conventional assumption (Corr = 0.5) exhibited high instability: sensitivity analysis revealed that FMT's improvement effects on BMI became statistically significant (p = 0.010) when the correlation coefficient (Corr) used to estimate the standard deviation of change was adjusted to 0.75. Furthermore, meta-regression analysis revealed that treatment regimen, follow-up duration, and patient baseline characteristics were significantly associated with HbA1c efficacy. Based on the current "low" certainty evidence, the overall improvement of metabolic parameters in overweight or obese patients with metabolic diseases following FMT did not reach statistical significance in the primary analysis. However, the robustness of this negative finding is limited, exhibiting high sensitivity to statistical hypotheses and likely being significantly confounded by methodological factors (e.g., administration protocols) and donor variability. Consequently, the true efficacy of FMT for treating systemic metabolic disorders remains uncertain. Future trials should shift toward precision medicine, prioritizing the standardization of donor selection and optimization of administration protocols.

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD420251172011, identifier CRD420251172011.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Obesity/therapy/blood/complications
*Metabolic Diseases/therapy/blood
*Overweight/therapy/blood
*Lipids/blood
*Blood Glucose/metabolism
Gastrointestinal Microbiome
Randomized Controlled Trials as Topic
Lipid Metabolism

@article {pmid41473189,
year = {2025},
author = {Duysburgh, C and Verstrepen, L and Van Meulebroek, L and Marzorati, M},
title = {Tributyrin (CoreBiome[®]) enhances butyrate levels and modulates the gut microbiota, barrier function, and immune response in vitro.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1712993},
pmid = {41473189},
issn = {2296-861X},
abstract = {BACKGROUND/OBJECTIVES: Oral butyrate is unstable during upper gastrointestinal tract (GIT) transit and very little reaches the colon. Tributyrin, a butyrate precursor, resists gastric acid and is converted to butyrate by pancreatic lipases. This study aimed to quantify tributyrin stability during upper GIT passage and to uncover the effects of tributyrin supplementation on the human gut microbiome and cellular responses.

METHODS: In vitro upper GIT simulations were used to evaluate the stability of a capsule and softgel formulation of tributyrin (CoreBiome[®]). The effects of tributyrin supplementation on the human gut microbiome and cellular responses were evaluated using the Simulator of the Human Intestinal Microbial Environment (SHIME[®]) model and Caco-2/THP1 co-cultures.

RESULTS: The upper GIT simulations showed that 40.9 and 48.7% of the tributyrin dose administered via the capsule or softgel, respectively, was hydrolyzed to butyrate in the small intestine; 59.1 and 51.3% remained stable and was available to enter the colon. Using the SHIME[®] model, it was shown that 3 weeks of daily tributyrin supplementation increased butyrate levels and enhanced the abundance of several bacterial species, including Bifidobacterium spp. and Akkermansia mucinophila. Metabolic impacts on the gut microbiome were also observed. Assessment of cellular responses revealed that tributyrin fermentation had a protective effect on the intestinal barrier and exerted immunomodulatory properties.

CONCLUSION: Enhanced butyrate concentrations and beneficial impacts on the gut microbial community composition were observed in an in vitro simulation of the human intestinal environment, suggesting that tributyrin could be considered as a solid alternative to butyrate supplementation.},
}

@article {pmid41472866,
year = {2025},
author = {Namasivayam, S and Romero-Soto, HN and Bacorn, M and Perez-Chaparro, PJ and Burns, AS and Mistry, S and Brandes, N and Chong, A and Cooper, G and LaCroix, IS and LaPoint, P and Banks, K and Chen, Q and Patel, A and Mueller, NT and Dominguez-Bello, MG and Maxwell, GL and Levy, S and Schwarz, B and Belkaid, Y and Hourigan, SK},
title = {The pioneering gut microbiome acquired via different delivery modes in neonates shapes distinct immune and metabolic environments.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.30.25337005},
pmid = {41472866},
abstract = {BACKGROUND: Cesarean section (CS) delivery is associated with an increased risk of inflammatory diseases, hypothesized to be driven by differences in the microbiome acquired at birth compared to vaginally delivered (VD) infants. How delivery mode associated differences in initial colonizers directly modulate early life immune education and metabolic development is poorly understood.

OBJECTIVE: First, to investigate how differences in pioneering colonizers associated with delivery mode directly modulate early life immune education and metabolic programming. Second, to examine the effect of vaginal seeding, an intervention aimed to restore the microbiome of CS infants to a VD state.

DESIGN: Germ-free mice were colonized with transitional stool from VD, CS or CS-delivered and vaginally seeded neonates. Immune cell populations, serum immunoglobulin levels, and fecal microbiome and metabolome profiles were analyzed.

RESULTS: Mice colonized with stool from VD neonates displayed increased numbers of myeloid cells at barrier tissues, whereas CS microbiome colonized mice exhibited decreased Th1/Th2 ratios and increased serum IgE levels. Key amino-acid pathways including tryptophan metabolism, riboflavin co-enzymes and carbohydrate metabolites were significantly enriched in the murine VD fecal metabolome and correlate with the increased abundance of Escherichia typically observed in the VD microbiome. Mice colonized with stool from CS neonates who received vaginal seeding, resulted in increased regulatory T cells and serum IgA in mice, suggesting potential benefits of vaginal seeding.

CONCLUSION: Collectively, our studies demonstrate the ability of pioneering colonizers to set the immune and metabolic tone that could have long-lasting effects and provide avenues for microbiome-mediated interventions.},
}

@article {pmid41472856,
year = {2025},
author = {Qi, C and Zhang, Y and Qing, W and Chen, R and Zhou, Z and Liu, Y and Chen, E and Chen, W and , and Zhou, H and Chen, M},
title = {Nationwide profiling of vaginal microbiota in Chinese women reveals age-dependent shifts and predictive biomarkers for reproductive health.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70088},
pmid = {41472856},
issn = {2770-596X},
abstract = {The vaginal microbiome is central to reproductive health, yet large-scale studies in East Asian populations remain scarce. Here, we characterized the vaginal microbiota of 6423 Chinese women of reproductive age across 18 provinces and assessed associations with 33 host factors. We observed a striking compositional transition around age 40, marked by declining Lactobacillus crispatus and enrichment of dysbiosis-associated taxa including Gardnerella vaginalis, independent of lifestyle or sociodemographic influences. Sexual behavior, contraceptive use, and educational attainment emerged as key determinants of community structure, differentially shaping Lactobacillus crispatus and Lactobacillus iners. Despite these associations, host factors explained less than 2% of overall variation, highlighting the resilience and individuality of the vaginal microbiome. To quantify vaginal health, we derived a microbiome balance score, validated it in external cohorts, and demonstrated its predictive power for incident bacterial vaginosis and sexually transmitted infections. Our findings establish a national-scale reference for the vaginal microbiome in Chinese women, reveal a midlife inflection point in microbial composition, and introduce a clinically actionable metric for risk stratification. These insights advance mechanistic understanding of host-microbiome interactions and inform strategies for precision interventions to preserve vaginal health.},
}

@article {pmid41472855,
year = {2025},
author = {Wu, D and Wang, AJ and Bu, DC and Sun, YY and Li, CH and Hong, YM and Zhang, S and Chen, SY and Zhou, JA and Zhang, TY and Yu, MH and Ma, YJ and Wang, XL and Xu, J and He, W and Heeschen, C and Chen, JF and Mao, WJ and Ding, H and Wu, WJ and Zhao, Y and Wang, H and Liu, NN},
title = {The interplay between tissue-resident microbiome and host proteins by integrated multi-omics during progression of colorectal adenoma to carcinoma.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70090},
pmid = {41472855},
issn = {2770-596X},
abstract = {The intratumoral microbiome is an emerging hallmark of cancer, yet its multi-kingdom host-microbiome ecosystem in colorectal cancer (CRC) remains poorly characterized. Here, we conducted an integrated analysis using deep shotgun metagenomics and proteomics on 185 tissue samples, including adenoma (A), paired tumor (T), and para-tumor (P). We identified 4057 bacterial, 61 fungal, 108 archaeal, and 374 viral species in tissues and revealed distinct intratumor microbiota dysbiosis, indicating a CRC-specific multi-kingdom microbial ecosystem. Proteomic profiling uncovered four CRC subtypes (C1-C4), each with unique clinical prognoses and molecular signatures. We further discovered that host-microbiome interactions are dynamically reorganized during carcinogenesis, where different microbial taxa converge on common host pathways through distinct proteins. Leveraging this interplay, we identified 14 multi-kingdom microbial and 8 protein markers that strongly distinguished A from T samples (area under the receiver operating characteristic curve (AUROC) = 0.962), with external validation in two independent datasets (AUROC = 0.920 and 0.735). Moreover, we constructed an early- versus advanced-stage classifier using 8 microbial and 4 protein markers, which demonstrated high diagnostic accuracy (AUROC = 0.926) and was validated externally (AUROC = 0.659-0.744). Functional validation in patient-derived organoids and murine allograft models confirmed that enterotoxigenic Bacteroides fragilis and Fusobacterium nucleatum promoted tumor growth by activating Wnt/β-catenin and NF-κB signaling pathways, corroborating the functional potential of these biomarkers. Together, these findings reveal dynamic host-microbiome interactions at the protein level, tracing the transition from adenoma to carcinoma and offering potential diagnostic and therapeutic targets for CRC.},
}

@article {pmid41472853,
year = {2025},
author = {Xu, J and Hu, P and Liu, M and Zhang, W and Xie, K},
title = {Cultivar-specific preference of bacterial communities and host immune receptor kinase modulate the outcomes of rice-microbiota interactions.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70098},
pmid = {41472853},
issn = {2770-596X},
abstract = {Deciphering how plant-microbiota interactions achieve beneficial outcomes for crops will provide innovative strategies for sustainable agriculture. Here, we dissected rice-microbiota dynamics using a tailored gnotobiotic cultivation system that models the semiaquatic environment in a paddy field. Inoculation with native soil microbiota resulted in root-growth-promotion (RGP) and root-growth-inhibition (RGI) phenomena in different cultivars. This preference persisted in a simplified synthetic community and individual bacterial strains, indicating that cultivar-specific growth promotion is an intrinsic property of microbial inocula. Though stochastic process dominated the assembly of root microbiome in gnotobiotic cultivation, absolute quantification revealed that imbalance of detrimental and beneficial bacterial loads in roots correlated with RGP or RGI outcomes in different rice cultivars. From the host perspective, genetic screening identified that receptor-like kinase mutants, including OsFLS2 (FLAGELLIN-SENSITIVE 2), inverted microbiota functionality, converting RGP to RGI. In particular, over 4534 rice genes responded to microbiota inoculation and 46.1% of them were reprogrammed in osfls2 mutants, demonstrating the prominent regulatory role of OsFLS2 in rice-microbiota signaling. On the basis of these results, we propose that the rice-microbiota relationships are gated by cultivar-specific preferences of the bacterial microbiota and host immune receptor kinase, which provides a useful framework for crop microbiome engineering in the future.},
}

@article {pmid41472849,
year = {2025},
author = {Xiao, Z and Ding, K and Guo, X and Zhao, Y and Li, X and Jiang, D and Zhu, D and Chen, Q and Jong, MC and Graham, DW and Li, G and Zhu, YG},
title = {Soil-borne legacy facilitates the dissemination of antibiotic resistance genes in soil-plant continua.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70094},
pmid = {41472849},
issn = {2770-596X},
abstract = {Antimicrobial resistance (AMR) disseminates throughout the soil-plant continuum via complex microbial interactions. Plants shape root- and leaf-associated microbiomes that sustain plant health; however, soil-borne legacies-enriched with antibiotic-producing microbes and resistance genes-govern AMR dynamics across agroecosystems. Using 16S rRNA gene sequencing, shotgun metagenomics, and high-throughput quantitative PCR, we profiled antibiotic resistance genes (ARGs), mobile genetic elements, and virulence factor genes across bulk soil, rhizosphere, phyllosphere, and root endosphere within soil-tomato and soil-strawberry continua. Recurrent bacterial wilt amplified the resistome, particularly polypeptide resistance genes, thereby establishing the rhizosphere as a major hotspot of ARG accumulation. Multidrug-resistant Ralstonia solanacearum (R. solanacearum) strains acted as major ARG reservoirs, harboring resistance determinants on both chromosomes and megaplasmids. Collectively, these findings demonstrate that pathogen-driven restructuring of the plant microbiome accelerates ARG dissemination, establishing soil-borne diseases as critical amplifiers of AMR across agricultural ecosystems.},
}

@article {pmid41472817,
year = {2025},
author = {Zhao, Z and Mao, Z and He, D and Wang, H and Wu, Q},
title = {Host specificity and uniqueness of shell microbiome in freshwater mollusks.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1702047},
pmid = {41472817},
issn = {1664-302X},
abstract = {INTRODUCTION: Mollusk shells represent a major substrate for the colonization of microbial communities and the functioning of aquatic ecosystems. However, our knowledge of the shell microbiome is very limited.

METHODS: Here, we selected Bellamya aeruginosa and Corbicula fluminea as two types of snails and clams, respectively, to explore their shell epiphytic bacteria by 16S amplicon sequencing.

RESULTS: We found different shell bacterial communities between snails and clams, which were also distinct from those in the surrounding environment. Source tracking analysis indicated that snail-shell bacteria were mostly derived from sediments, whereas clamshells originated from tissues. There was a site-specific difference in the shell bacteria within the habitat. Temporal variation in clamshell bacteria was observed, but not in snail shells, which corresponds to their source dynamics in the water column and stable surface sediment bacterial communities, respectively. The genus Nitrospira is mostly enriched in shell bacteria, particularly in eutrophic lakes. Taxa related to carbon, nitrogen, and sulfur cycling were recognized as the keystone species in the co-occurrence network associated with the shell surface. Our results demonstrate that mollusk shells represent a unique ecological niche for microbiomes in aquatic ecosystems and may serve as hotspots for biogeochemical cycling.},
}

@article {pmid41472812,
year = {2025},
author = {Xie, X and Tao, H and Li, Y and Feng, X and Li, K and Zhang, Z and Yan, J and Wang, X},
title = {Microbial fertilizer for improving maize yield, straw decomposition and soil microbiome structure.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1670118},
pmid = {41472812},
issn = {1664-302X},
abstract = {Microbial fertilizers represent a promising strategy to sustainably produce crops by enhancing the biological function of soil and availability of nutrients. However, there is a lack of study on their performance across diverse agroecological zones. In this study, we conducted a 3-year, two-site field experiment to assess the effects of a composite microbial fertilizer (Bacillus subtilis and Trichoderma harzianum) on the yield of maize (Zea mays), soil properties, straw degradation, and composition of the microbial community. The results showed that the microbial fertilizer treatment (MF) increased the yield of maize by 11.4 and 6.9% in Qingfeng Country (QF) and Xun Country (Xun), China, respectively, compared to normal chemical fertilizer (CF). These gains coincided with an enhanced straw degradation rate (SDR; +8.4-8.6%) and a tendency toward higher available phosphorus (AP; +15.4-19.7%), alongside shifts in bacterial and fungal composition. High-throughput sequencing revealed that Proteobacteria, Actinobacteriota, Acidobacteriota, and Chloroflexi dominated the bacterial communities at both sites, whereas the fungal communities were mainly composed of Sordariomycetes, Dothideomycetes, and Eurotiomycetes-taxa whose abundances displayed pronounced site specificity. Application of the microbial fertilizer was associated with higher relative abundance of Acidobacteriota by 22.7% (QF) and 60.8% (Xun) and that of Sordariomycetes by 13.7% (QF) and 30.9% (Xun), underscoring its strong, selective impact on the dominant bacterial and fungal assemblages. These regional differences underscore the influence of site-specific microbial assemblages on the performance of fertilizer. Partial least squares path modeling supported a plausible pathway in which changes in community structure and straw decomposition are linked to improved soil nutrient status, which in turn predicted yield (β = 0.846, R [2] = 0.715). Together, the field data indicate that microbial fertilizers may act through multi-step, microbiome-associated pathways, with success depending on compatibility with native microbial assemblages and environmental context.},
}

@article {pmid41472811,
year = {2025},
author = {Liao, J and Duan, L and Wang, G and Yu, S and Shen, X and Jiang, M and Shen, K and Singla, RK and Shen, B and Zhou, Y},
title = {Gut microbiome associated with melanin deposition by supporting energy metabolism in Sichuan mountainous black-bone chickens.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1682376},
pmid = {41472811},
issn = {1664-302X},
abstract = {INTRODUCTION: Variation in melanin deposition profoundly influences the economic value of Sichuan mountainous black-boned chickens; however, the contribution of the gut microbiome in modulating this process remains poorly understood. This study aimed to characterize the gut microbiome in Sichuan mountainous black-boned chickens with distinct skin color brightness (quantified by colorimeter) and to explore its association with melanin deposition.

METHODS: Cecal microbiota composition was profiled using 16S rRNA sequencing in dark-skinned (BlackD) and light-skinned (BlackL) groups. Serum metabolic profiles were determined via untargeted metabolomics. Differential abundance of bacterial genera was assessed, followed by pathway enrichment analysis (KEGG and MetaCyc). Associations between microbiome, metabolites, and melanin-related pathways were evaluated.

RESULTS: The BlackD group exhibited higher alpha diversity and significant alterations in 10 bacterial genera (primarily linked to short-chain fatty acid metabolism and melanin-related metabolites) compared to the BlackL group. Pathway enrichment showed upregulation of energy metabolism-related KEGG pathways (AMPK signaling, insulin signaling, thyroid hormone signaling) and MetaCyc pathways in BlackD. Untargeted serum metabolomics revealed elevated melanin-related metabolites in BlackD, including L-Tyrosine, L-DOPA, and Dopaquinone. Gut microbiome and serum metabolite profiles in BlackD were strongly correlated with enhanced energy metabolism.

DISCUSSION: The gut microbiome may influence melanin deposition by modulating host metabolic activity, with microbiome-derived metabolites supporting the high energy demands of melanocyte activity. These findings uncover a potential mechanism linking microbial composition to phenotypic variation in melanin deposition.},
}

@article {pmid41472810,
year = {2025},
author = {Lan, B and Liang, Y and Zhou, Z and Liu, J},
title = {Gut microbiome dysbiosis implicates the gut-bone axis in Modic changes: a metagenomic case-control study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1702357},
pmid = {41472810},
issn = {1664-302X},
abstract = {INTRODUCTION: Modic changes (MCs) are vertebral endplate lesions strongly associated with discogenic low back pain (LBP), though their pathogenesis remains poorly understood. Emerging evidence implicates gut microbial dysbiosis in systemic inflammation and musculoskeletal disorders, yet its potential role in MCs has not been investigated. This study aimed to characterize the gut microbiome in patients with MCs and identify microbial and metabolic features linked to disease severity.

METHODS: In a case-control study, shotgun metagenomic sequencing was performed on fecal samples from 31 patients with MCs (16 Type 1, 15 Type 2) and 25 age- and sex-matched healthy controls. Microbial community structure was assessed via alpha and beta diversity analyses. Differential taxa and predictive biomarkers were identified using linear discriminant analysis effect size (LEfSe) and Random Forest modeling. Functional potential was evaluated via Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Associations between microbial features and clinical markers (C-reactive protein [CRP], Pfirrmann grade) were also examined.

RESULTS: Patients with MCs showed significantly reduced gut microbial alpha diversity compared to controls (Chao1 index: p = 0.005; Shannon index: p = 0.034; Simpson index: p = 0.042), with the most pronounced reduction in Type 1 MCs. Beta diversity analysis revealed distinct microbial communities between groups (PERMANOVA, p = 0.001). Key discriminative taxa included unclassified_Parabacteroides (AUC = 0.895) and Bacteroides uniformis (AUC = 0.889). Metabolic pathway analysis identified 52 differentially abundant pathways, with significant enrichment of quorum sensing (p < 0.001) and glycerolipid metabolism (p < 0.001) in MC patients, both strongly correlated with elevated CRP and higher Pfirrmann grade (p < 0.001).

DISCUSSION: Gut microbial dysbiosis is associated with MCs, marked by reduced diversity, specific bacterial biomarkers, and altered metabolic pathways related to inflammation and tissue degeneration. These results suggest a potential role of the gut-bone axis in MC pathogenesis and highlight novel targets for diagnostic and therapeutic strategies in LBP.},
}

@article {pmid41472807,
year = {2025},
author = {Zhang, Q and Ding, L and Xie, X and Ru, L and Li, Q and Yao, C and Solkner, J and Jiang, R},
title = {Third-generation sequencing reveals the spatial variation of microbial composition of airborne bacteria in an intensive dairy farm.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1688472},
pmid = {41472807},
issn = {1664-302X},
abstract = {INTRODUCTION: The intensification of livestock farming has led to increased bacterial bioaerosol emissions, posing potential health risks to both animals and humans. This study aimed to investigate the bacterial community composition, abundance, diversity, and variation in different functional zones of cattle farms to assess their impact on public health and environmental quality.

METHODS: We employed third-generation sequencing on the PacBio platform to analyze 16S ribosomal RNA (rRNA) sequences from air samples, identifying a diverse range of bacterial phyla, including Proteobacteria, Firmicutes, Verrucomicrobia, Bacteroidetes, Fusobacteria, Actinobacteria, Deinococcus-Thermus, Cyanobacteria, and Acidobacteria. The phylogenetic tree was built using the microbiome abundance of these samples.

RESULTS: Notably, Firmicutes and Proteobacteria were predominantly enriched in the samples, with genera such as Staphylococcus, Acinetobacter, Enterococcus, and Bacillus, and the family Enterobacteriaceae, which was unknown, being particularly abundant. These bacteria are known to be associated with various infections and chronic diseases. Correlation and canonical correspondence analysis (CCA) revealed that environmental factors, particularly ultraviolet (UV) radiation and global horizontal irradiance (GHI), significantly influence microbial species distribution, with R [2] values of 0.774 (p < 0.05) and 0.769 (p < 0.05), respectively. We further calculated the alpha and beta diversity of microbiome in these samples and observed that fermenting manure (F1), fresh manure (X2), and piled-up manure after fermentation (D3) samples have the highest alpha diversity, while PC1 from beta diversity, that is, weighted principal coordinates analysis (PCoA), explained 32.66% of the variance in the data. Interestingly, the relative abundance of the Kocuria genus was significantly different between the waste management area (FW) and the milking parlor (NT) (t-test, p < 0.013).

DISCUSSION: Our findings underscore the importance of understanding the complex microbial ecosystems in livestock farming environments and highlight the need for targeted interventions to mitigate public health risks associated with bacterial bioaerosols.},
}

@article {pmid41472804,
year = {2025},
author = {Zhao, R and Liu, P and Wu, Y and Bi, H and He, J and Zhang, J and Qu, Y and Chen, X and Chen, Z},
title = {Triclocarban exposure at environmentally relevant concentrations perturbs the gut microbiota and metabolic profile in Rana taihangensis (Anura, Ranidae) tadpoles.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1740880},
pmid = {41472804},
issn = {1664-302X},
abstract = {INTRODUCTION: The antibacterial agent triclocarban (TCC) poses a significant threat to aquatic ecosystems and its impact on amphibians remain poorly understood.

METHODS: Here, we investigated its acute and chronic effects on Rana taihangensis tadpoles at environmentally relevant concentrations (i.e., 5, 15 and 45 μg/L) using an integrated approach combining morphology, gut microbiome, and non-targeted metabolomic analyses.

RESULTS AND DISCUSSION: The acute toxicity tests for 96 h revealed that TCC had a lethal concentration (LC50) value of 169.863 μg/L for R. taihangensis tadpoles. Chronic exposure resulted in reduced body condition score across all the three TCC-treated groups compared to the control. Gut microbiome analysis revealed that TCC exposure significantly altered the community composition at both phylum (e.g., Pseudomonadota and Fusobacteriota) and genus (e.g., Cetobacterium and Citrobacter) levels. In addition, several metabolites (e.g., 20-carboxy-leukotriene B4, 11b-PGF2a, and leukotriene E4) associated with immune response and neural signaling were significantly perturbed in TCC-exposed tadpoles. Interestingly, correlation analysis indicated a significant relationship between specific metabolite changes and shifts in gut microbiota. Overall, our findings demonstrated that TCC exposure adversely affects the growth indexes, gut microbial composition and metabolites in R. taihangensis tadpoles, and the present study will provide new insights into the ecotoxicological risks of TCC and enhance the understanding of its mechanisms of toxicity in aquatic organisms.},
}

@article {pmid41472773,
year = {2025},
author = {Charoenwai, O and Tanpichai, P and Sukkarun, P and Jeon, HJ and Kim, B and Han, JE and Piamsomboon, P},
title = {Emergence of decapod hepanhamaparvovirus genotype V and its co-infection with Enterocytozoon hepatopenaei in cultured Penaeus vannamei in Thailand: Evidence from epidemiological, pathogenicity, and microbiome analyses.},
journal = {Veterinary world},
volume = {18},
number = {11},
pages = {3496-3508},
pmid = {41472773},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Growth retardation syndrome in cultured Penaeus vannamei has been associated with Enterocytozoon hepatopenaei (EHP) and a recently identified decapod hepanhamaparvovirus (DHPV) genotype V. However, data on its prevalence, pathogenicity, and interaction with the shrimp hepatopancreatic microbiome in Thailand remain limited. This study aimed to determine the incidence and co-infection rate of DHPV genotype V with EHP, evaluate its pathogenic potential, and explore microbiome alterations associated with infection.

MATERIALS AND METHODS: Between 2022 and 2023, 1,270 shrimp from 127 grow-out ponds across 46 farms in eastern Thailand and post-larvae 12 from five hatcheries in the south were screened for DHPV and EHP by polymerase chain reaction. Six representative isolates underwent phylogenetic analysis based on non-structural protein 1 (NS1) and NS2 genes. Pathogenicity was evaluated by immersion challenge bioassays in specific pathogen-free P. vannamei. Hepatopancreatic microbiomes of naturally infected and healthy shrimp were compared using 16S ribosomal RNA gene sequencing and Quantitative Insights Into Microbial Ecology 2-based analysis.

RESULTS: DHPV was detected in 54.33% (69/127) of ponds and 4% (1/25) of hatchery tanks. Co-infection with EHP occurred in 40.16% of ponds. Phylogenetic analysis showed 97.99%-98.82% similarity with DHPV genotype V from South Korea, confirming transboundary genetic relatedness. Experimental infection caused low mortality (20%) but resulted in viral replication (10[1]-10[3] copies/μL) and characteristic intranuclear inclusion bodies in hepatopancreatic cells. DHPV-infected shrimp exhibited distinct microbiome profiles with elevated Firmicutes, Planctomycetota, and Actinobacteriota abundances, supporting a pathobiome shift during infection.

CONCLUSION: This is the first report of DHPV genotype V in P. vannamei from Thailand and its frequent co-infection with EHP. Despite its low experimental virulence, the widespread occurrence and microbiome dysbiosis suggest that it may have subclinical impacts that could exacerbate growth retardation. Routine molecular screening in hatcheries and farms, coupled with integrated viral-microbiome surveillance, is essential for sustainable aquaculture biosecurity and aligns with the United Nations Sustainable Development Goal 14 (Life Below Water) by promoting resilient aquatic food systems.},
}

@article {pmid41472726,
year = {2025},
author = {Jani, CT and Edwards, K and Bhanushali, C and Zheng, X and Salazar, AS and Lopes, G and Watson, DC},
title = {Leveraging beneficial microbiome-immune interactions via probiotic use in cancer immunotherapy.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1713382},
pmid = {41472726},
issn = {1664-3224},
mesh = {*Probiotics/therapeutic use ; Humans ; *Neoplasms/therapy/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Animals ; *Immunotherapy/methods ; Immune Checkpoint Inhibitors/therapeutic use ; },
abstract = {The gut microbiome is a critical regulator of systemic immunity and a major modulator of response to cancer immunotherapy with immune checkpoint inhibitors (ICIs). However, the clinical implementation of microbiome-inspired therapies that leverage these associations have proven challenging. Probiotics-live microorganisms thought to confer health benefits as part of food or food supplements-have gained increasing attention as readily testable, low-toxicity agents with potential of favorably influencing host-microbiome-immune interactions in the context of cancer immunotherapy. In this review, we critically evaluate the growing body of evidence supporting the role of probiotics in enhancing ICI efficacy and summarize published and ongoing clinical trials formally testing their role as adjuncts to cancer immunotherapy. Probiotics have been shown in preclinical murine models to exert immunomodulatory effects, including activation and maturation of dendritic cells, enhancement of MHC-I-mediated antigen presentation, modulation of cytokine profiles, and promotion of pro-inflammatory macrophage polarization. Probiotics also regulate adaptive immunity via microbial metabolites such as short-chain fatty acids (SCFAs), inosine, and tryptophan derivatives that support effector T cell activation and reduce T cell exhaustion. Cross-reactivity between microbial and tumor-associated antigens (molecular mimicry) further underscores the potential of probiotic strains to stimulate antitumor responses. In these models, supplementation with specific bacterial strains such as Bifidobacterium spp., Lactobacillus spp., Clostridium butyricum, and Akkermansia muciniphila enhanced ICI responses across tumor types including melanoma, lung cancer, and colorectal cancer. These findings are in part supported by early-phase clinical studies and retrospective cohorts, particularly in lung and renal cancers, where probiotic use has been associated with improved progression-free and overall survival. However, most clinical data are observational, and the field lacks standardized probiotic formulations and dosing protocols. To transition probiotics from food supplements to clinically validated immunotherapy adjuncts, rigorous mechanistic, translational, and clinical studies are necessary. These approaches have the potential to define mechanism-of-action, identify immunologically active strains, and inform rational clinical trial design. With careful development, probiotics hold promise as cost-effective, scalable, and personalized tools to optimize the efficacy and safety of cancer immunotherapy.},
}

*Probiotics/therapeutic use
Humans
*Neoplasms/therapy/immunology/microbiology
*Gastrointestinal Microbiome/immunology
Animals
*Immunotherapy/methods
Immune Checkpoint Inhibitors/therapeutic use

@article {pmid41472687,
year = {2025},
author = {Loke, P and Smith, A and Kiwanuka, K and Pessenda, G and Rahmberg, A and Flynn, J and Herbert, R and Brenchley, J},
title = {Hematological Consequences of Environmental Change During Dewilding of Rhesus Macaques.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7767375/v1},
pmid = {41472687},
issn = {2693-5015},
abstract = {The environment shapes immune system development and the regulation of inflammatory responses, which may affect the prevalence of immune mediated inflammatory diseases. However, the hematological consequences of a major environmental change, such as those experienced during migration, remain poorly understood. Here, we used cellular and molecular approaches to assess the immunological consequences in rhesus macaques as they transitioned from an outdoor provisioned environment to an indoor laboratory facility in a process we term 'dewilding.' Dewilding led to a sharp decrease in neutrophils and increased lymphocytes in the peripheral blood, a skewing toward a proinflammatory TH1 response, and increased T cell activation. Concurrently, we observed changes in the microbiome, with fungal abundance decreasing while bacterial abundance increased during dewilding. In the bone marrow, we observed increased granulopoiesis, reduced lymphocytes, and reduced hematopoietic stem cells and progenitors, with their shift toward less committed progenitor states. Single-cell nuclear RNA sequencing of the bone marrow revealed increased erythrocyte progenitors in the bone marrow during dewilding, with upregulation of genes involved in hemoglobin control and erythropoiesis. Notably, the vaccination response against measles varied based on vaccination period during the dewilding process. Together, our findings illustrate how dewilding alters immune homeostasis, with implications for understanding immune adaptation in migrants from rural to urban environments and for optimizing immunization strategies during environmental change.},
}

@article {pmid41472620,
year = {2025},
author = {Zhang, D and Xu, X and Zhang, Z},
title = {Effect of Social Rank on Gut Microbes and Their Metabolites of Greater Long-Tailed Hamsters (Tscherskia triton).},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70049},
pmid = {41472620},
issn = {1749-4877},
support = {RZ2300002832//Hainan University research start-up fund project/ ; },
abstract = {Although the effects of social rank on behavior and physiology are well established, their relationship with gut microbiota is not yet fully understood. We investigated how social rank affects physiological responses, gut microbiota, and metabolites in the greater long-tailed hamster (Tscherskia triton), a naturally solitary rodent. Dominant male hamsters displayed a "high-vigilance, metabolically activated" phenotype, characterized by increased aggression, elevated serum corticosterone (CORT) and serotonin (5-HT) levels, and activation of the paraventricular nucleus, a key regulator of the hypothalamic-pituitary-adrenal axis. In contrast, subordinates exhibited lower CORT and 5-HT levels, with increased activation of the arcuate nucleus (ARC), suggesting a more energy-conserving and stress-resilient phenotype. Social rank strongly shaped gut microbiota and metabolic output: dominants were enriched in energy-harvesting taxa (e.g., Limosilactobacillus and Alistipes) and had higher fecal queuine levels, a metabolite derived from gut microbiota. Conversely, subordinates were enriched in immunomodulatory taxa (e.g., Faecalibacterium and Butyrivibrio). These findings suggest that dominance in solitary species may be supported by coordinated host-microbiome interactions, which meet high energetic demands while maintaining stress resilience. This provides a novel framework for understanding the gut-brain-microbiome axis in social dominance.},
}

@article {pmid41472585,
year = {2025},
author = {Orhan, F and Bektaş, M and Bariş, Ö},
title = {Elucidating environmental reservoir of antimicrobial resistance - a phenotypic characterization of gut microbiota from aquatic coleoptera in a low-anthropogenic impact zone.},
journal = {Annals of agricultural and environmental medicine : AAEM},
volume = {32},
number = {4},
pages = {504-510},
doi = {10.26444/aaem/210421},
pmid = {41472585},
issn = {1898-2263},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Gastrointestinal Microbiome/drug effects ; *Coleoptera/microbiology ; *Bacteria/drug effects/isolation & purification/genetics/classification ; *Drug Resistance, Bacterial ; Turkey ; *Gram-Negative Bacteria/drug effects/isolation & purification/genetics ; Drug Resistance, Multiple, Bacterial ; },
abstract = {INTRODUCTION AND OBJECTIVE: This study investigated the antibiotic resistance of bacterial isolates obtained from the gut microbiota of certain insects (Coleoptera: Hydrophilidae and Helophoridae), which were collected from aquatic areas in Erzurum Province, Türkiye. This area is characterised by a low level of human impact, thereby providing a unique opportunity to investigate the baseline microbial diversity and ecological roles within relatively pristine aquatic environments.

MATERIAL AND METHODS: The antimicrobial susceptibility of the isolates was assessed using disc diffusion and minimum inhibitory concentration (MIC) methods. The analysis encompassed 30 Gram-negative bacteria belonging to the genera Aeromonas, Acinetobacter, Vibrio, Pseudomonas, Escherichia and Yersinia.

RESULTS: The results indicated that the most resistant bacteria were Aeromonas, Pseudomonas and Acinetobacter, while enteric bacteria demonstrated greater sensitivity. It is noteworthy that nitrofurantoin, a commonly used antibiotic for treating urinary tract infections, exhibited the highest level of resistance among the antibiotics tested by disc diffusion, followed by cephalosporins and penicillins.

CONCLUSIONS: The MIC testing with DKGM and NF kits demonstrated high resistance to cephalosporins, sulfonamides, polymyxins and monobactams. Furthermore, two multidrug-resistant (MDR) isolates exhibited resistance to at least two antibiotic classes. These findings underscore the necessity for expanded antimicrobial resistance surveillance beyond clinical settings, extending into environmental samples, and contributing to ongoing research on resistance mechanisms.},
}

Animals
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
*Gastrointestinal Microbiome/drug effects
*Coleoptera/microbiology
*Bacteria/drug effects/isolation & purification/genetics/classification
*Drug Resistance, Bacterial
Turkey
*Gram-Negative Bacteria/drug effects/isolation & purification/genetics
Drug Resistance, Multiple, Bacterial

@article {pmid41472545,
year = {2026},
author = {Chen, W and Lai, X and Tang, X and Ye, Q and Zhang, C and Yang, Y and Wang, Z and Li, M and Wang, Z and Li, Z and Yuan, C and Zhang, X and Li, L and Wang, B and Wang, R and Yan, Y},
title = {Dysbiosis in Acne Vulgaris and Hidradenitis Suppurativa: A Comparative Microbiome Analysis.},
journal = {Experimental dermatology},
volume = {35},
number = {1},
pages = {e70198},
doi = {10.1111/exd.70198},
pmid = {41472545},
issn = {1600-0625},
support = {82073471//National Natural Science Foundation of China/ ; CFH-2022-2-4043//Capital's Funds for Health Improvement and Research/ ; },
mesh = {Humans ; *Hidradenitis Suppurativa/microbiology ; *Acne Vulgaris/microbiology ; *Dysbiosis/microbiology ; Male ; Female ; Adult ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Skin/microbiology ; Young Adult ; Mouth Mucosa/microbiology ; Case-Control Studies ; Feces/microbiology ; Gastrointestinal Microbiome ; Adolescent ; },
abstract = {Acne and hidradenitis suppurativa (HS) are inflammatory disorders of the pilosebaceous unit that exhibit distinct clinical manifestations, indicating that they likely differ in their underlying pathophysiology. Microbial dysbiosis is implicated in both diseases, yet direct comparisons using unified methods and analyses incorporating the oral microbiome are lacking. In this study, we collected lesional and nonlesional skin, buccal mucosa and faecal samples from 28 HS patients, 29 acne patients and 40 healthy controls, and profiled microbial communities using 16S rRNA V3-V4 sequencing with qPCR validation. HS lesions showed a pronounced enrichment of anaerobic Gram-negative taxa, including Prevotella, Porphyromonas and Fusobacterium, whereas acne lesions were dominated by Cutibacterium and Pseudomonas. Oral microbiome diversity was increased in both diseases, with HS showing distinct enrichment of Prevotella and Veillonella. HS patients also exhibited reduced gut microbial diversity. Correlation analyses revealed coordinated microbial alterations across the oral-gut-skin axis, and qPCR confirmed elevated concentrations of key anaerobes in HS. By directly comparing acne and HS across multiple anatomical sites, our study helps differentiate general inflammatory microbiome changes from those more specific to HS. The findings also suggest a potential oral-gut-skin microbial axis that may contribute to the chronic and destructive phenotype of HS, providing insights that could inform future microbiome-targeted therapeutic approaches.},
}

Humans
*Hidradenitis Suppurativa/microbiology
*Acne Vulgaris/microbiology
*Dysbiosis/microbiology
Male
Female
Adult
RNA, Ribosomal, 16S/genetics
*Microbiota
Skin/microbiology
Young Adult
Mouth Mucosa/microbiology
Case-Control Studies
Feces/microbiology
Gastrointestinal Microbiome
Adolescent

@article {pmid41472301,
year = {2025},
author = {Yagi, K and Ethridge, AD and Asai, N and Malinczak, CA and Arzola Martinez, L and Rasky, AJ and Morris, SB and Falkowski, NR and Fonseca, W and Huffnagle, GB and Lukacs, NW},
title = {Changes in Microbiome Correspond with Diminished Lung Pathophysiology Following Early-Life Respiratory Syncytial Virus Infection or Antibiotic Treatment: Microbiome Following RSV Infection.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
pmid = {41472301},
issn = {1999-4915},
mesh = {*Respiratory Syncytial Virus Infections/microbiology/physiopathology/drug therapy/virology ; Animals ; *Lung/physiopathology/microbiology/virology/drug effects ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Mice ; Mice, Inbred BALB C ; Dysbiosis ; *Microbiota/drug effects ; Gastrointestinal Microbiome/drug effects ; Animals, Newborn ; Disease Models, Animal ; Ampicillin/pharmacology ; Respiratory Syncytial Viruses ; Humans ; Female ; },
abstract = {Early-life respiratory syncytial virus (EL-RSV) infection has been implicated in long-term pulmonary disease in children. In these studies, neonatal BALB/c mice were infected at day 7 of life, leading to >35% losses in critical lung function, airway mucus metaplasia, and transcriptional hallmarks of mucus hypersecretion four weeks after RSV infection. While EL-RSV minimally reshaped the resident lung microbiota, it led to significant gut dysbiosis, including a long-term reduction of Proteobacteria that can be a source of protective metabolites related to barrier and immune function. Subsequent studies assessing whether a common infant antibiotic (ampicillin) could mitigate EL-RSV-induced lung alterations revealed further severe gut microbiome alterations and, on its own, later in life, recapitulated the full spectrum of RSV-associated alterations in lung function. Metagenomic inference showed that both RSV and ampicillin administered during early life reduced biosynthetic pathways for microbiome-derived metabolites, which are known to reinforce tight junctions, regulate inflammation, and preserve extracellular matrix elasticity. The shared loss of these metabolic programs provides a mechanistic bridge linking distinct early-life exposures to the microbiome changes and airway mechanical deficits later in life. Collectively, the data suggest that RSV and/or antibiotic-triggered gut dysbiosis is the primary insult that likely promotes improper lung maturation/repair through a metabolite-mediated mechanism and may suggest metabolite restoration as a strategy to promote proper developmental lung function.},
}

*Respiratory Syncytial Virus Infections/microbiology/physiopathology/drug therapy/virology
Animals
*Lung/physiopathology/microbiology/virology/drug effects
*Anti-Bacterial Agents/pharmacology/therapeutic use
Mice
Mice, Inbred BALB C
Dysbiosis
*Microbiota/drug effects
Gastrointestinal Microbiome/drug effects
Animals, Newborn
Disease Models, Animal
Ampicillin/pharmacology
Respiratory Syncytial Viruses
Humans
Female

@article {pmid41472294,
year = {2025},
author = {Mandal, E and Noirungsee, N and Disayathanoowat, T and Kil, EJ},
title = {TSWV Infection Differentially Reshapes the Symbiotic Microbiome of Two Frankliniella Thrips Species.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
pmid = {41472294},
issn = {1999-4915},
support = {0//Gyeongkuk National University/ ; },
mesh = {*Thysanoptera/microbiology/virology ; Animals ; *Symbiosis ; *Microbiota ; *Tospovirus/physiology ; Serratia/genetics ; Bacteria/classification/genetics/isolation & purification ; Insect Vectors/virology/microbiology ; Metagenomics ; Plant Diseases/virology ; Wolbachia/genetics ; },
abstract = {Vectoring tomato spotted wilt virus (TSWV) by two well-known thrips species, Frankliniella occidentalis Pergande and F. intonsa Trybom (Thysanoptera: Thripidae), is facilitated in different ways. Symbiotic bacteria positively influence thrips fitness, but the interaction between these bacteria and tospovirus inside the thrips' body remains unknown. Metagenomic profiling of symbionts in nonviruliferous and viruliferous Frankliniella thrips was performed to elucidate the interactions between symbiotic bacteria and the virus. A total of 97 operational taxonomic units (OTUs) were identified by profiling the microbes, where Proteobacteria was the most abundant phylum, with a high richness in Serratia spp. F. occidentalis showed lower variation in bacterial diversity between nonviruliferous and viruliferous treatments than F. intonsa. RT-qPCR validation for Serratia and Escherichia revealed opposite abundance patterns between the two thrips species. In contrast, Enterobacteriaceae and Pantoea showed similar patterns with higher abundance in nonviruliferous conditions. Wolbachia was detected exclusively in F. intonsa, with a higher bacterial titer in the viruliferous sample. Our findings suggest that TSWV association may influence the abundance of different bacterial symbionts within the thrips' body, potentially via induction of antimicrobial peptides in response to viral invasion, and to our knowledge this is the first report addressing this tripartite interaction. These findings improve our understanding of how virus-symbiont association contributes to thrips vector competence.},
}

*Thysanoptera/microbiology/virology
Animals
*Symbiosis
*Microbiota
*Tospovirus/physiology
Serratia/genetics
Bacteria/classification/genetics/isolation & purification
Insect Vectors/virology/microbiology
Metagenomics
Plant Diseases/virology
Wolbachia/genetics

@article {pmid41472213,
year = {2025},
author = {Abdelbary, ER and Ramadan, M and Amin, IA and Abd-Elsamea, FS and Elsaghier, AM and Abd-Alrahman, EA and Ozbak, HA and Hemeg, HA and Almutawif, YA and Zakai, SA and Abdelrahman, AA and Salah, M},
title = {Early-Life Demographic Factors Shape Gut Microbiome Patterns Associated with Rotavirus Gastroenteritis Severity.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/v17121542},
pmid = {41472213},
issn = {1999-4915},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Gastroenteritis/microbiology/virology/epidemiology ; *Rotavirus Infections/microbiology/epidemiology/virology ; Infant ; Female ; Male ; Case-Control Studies ; Infant, Newborn ; Severity of Illness Index ; RNA, Ribosomal, 16S/genetics ; Rotavirus ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; Sociodemographic Factors ; },
abstract = {BACKGROUND: Rotavirus gastroenteritis (RVGE) remains a leading cause of severe infant diarrhea worldwide, with growing evidence supporting the role of the gut microbiome in modulating the disease. However, the interplay between early-life demographic factors, the gut microbiome, and their combined impact on RVGE clinical severity remains inadequately characterized, particularly in specific geographic populations.

AIM: We aimed to investigate how demographic determinants shape gut microbiome composition and function in RVGE and how these features relate to clinical severity.

METHODS: In our comprehensive case-control study of 165 infants (120 RVGE cases and 45 healthy controls, aged 0-12 months), we utilized 16S rRNA sequencing combined with advanced statistical modeling and machine learning to investigate how demographic factors influence microbiome composition and clinical outcomes.

RESULTS: RVGE cases exhibited significantly reduced bacterial diversity (Kruskal-Wallis, Static = 14.85, p < 0.001) and distinct patterns, with community structure most strongly associated with dehydration severity (PERMANOVA; R[2] = 0.15, p < 0.001). Substantial taxonomic alterations were identified characterized by depletion of beneficial commensals including Akkermansia (LDA score = 3.8, p < 0.001), Faecalibacterium (Random Forest AUC = 0.82, p < 0.001), and Bifidobacterium (r = -0.42 with breastfeeding, p < 0.001), alongside enrichment of inflammation-associated taxa such as Escherichia-Shigella (WBC; r = 0.49, p < 0.001, and CRP; r = 0.56, p < 0.001), Streptococcus (LDA score = 4.2, p < 0.001), and Staphylococcus. Proteobacteria was the top potential biomarker of severe outcomes (Random Forest AUC = 0.85), with abundance positively correlated with systemic inflammation (CRP: r = 0.51, p = 0.003). Functional predictions revealed increased lipopolysaccharide biosynthesis (ko00540) and reduced butanoate metabolism (ko00650, p < 0.001) in severe disease. Importantly, demographic factors significantly modulated clinical outcomes: cesarean-delivered, formula-fed infants presented the most dysbiotic profiles and experienced 3.2-fold longer hospitalization (95% CI: 1.8-5.6, p < 0.001) than vaginally delivered, breastfed infants did.

CONCLUSIONS: Collectively, these findings demonstrate that early-life demographic factors potentially shape the gut microbiome composition and function, may influence RVGE severity and recovery trajectories, thus providing candidate biomarkers for risk stratification and identifying targets for microbiota-based interventions.},
}

Humans
*Gastrointestinal Microbiome
*Gastroenteritis/microbiology/virology/epidemiology
*Rotavirus Infections/microbiology/epidemiology/virology
Infant
Female
Male
Case-Control Studies
Infant, Newborn
Severity of Illness Index
RNA, Ribosomal, 16S/genetics
Rotavirus
Bacteria/classification/genetics/isolation & purification
Feces/microbiology
Sociodemographic Factors

@article {pmid41472186,
year = {2025},
author = {Lu, Y and Li, Z and Yang, Z and Zhu, R and Yan, M and Liu, Z and Liu, M and Wang, Y and Wang, J and Wang, Q and Liu, J and Zhang, C and Wang, X and Cui, H},
title = {Effects of Combined Oregano Essential Oil and Macleaya cordata Extract on Growth, Antioxidant Capacity, Immune Function, and Fecal Microbiota in Broilers.},
journal = {Veterinary sciences},
volume = {12},
number = {12},
pages = {},
pmid = {41472186},
issn = {2306-7381},
support = {YJ2023038；246Z6604G；HBCT2024270204；CARS-41-13；KY2024006//This research was funded by the special project of introducing talents for scientific research in Hebei Agricultural University；Central government guided local science and technology development fund projects；Hebei Agriculture Research System；China Agricu/ ; },
abstract = {With the growing demand for antibiotic-free and sustainable poultry production, plant-derived antimicrobials have emerged as promising alternatives. However, a systematic understanding of the combined effects of oregano essential oil (OEO) and Macleaya cordata extract (MCE) on the broiler gut microbiome remains lacking. This study employed an integrated "structure-function-phenotype" framework to investigate the individual and combined (OMS) effects of OEO and MCE on gut microecological remodeling and its coupling with host growth, metabolic, and immune phenotypes. A total of 960 one-day-old broiler chicks were individually weighed and then randomly allocated to four treatments using body-weight-stratified randomization, with 6 replicate pens per treatment and 40 birds per pen, to ensure similar initial body weight across groups. Over a 42-day trial, we evaluated growth performance, serum biochemistry, antioxidant status, and immune parameters. Compared to the control, the OMS treatment significantly enhanced average daily feed intake (ADFI) and average daily gain (ADG), increased serum total protein (TP), and decreased blood urea nitrogen (BUN), triglycerides (TG), total cholesterol (TC), and alkaline phosphatase (ALP). However, the feed-to-gain ratio (F/G) was also higher in the OMS group, indicating that the improvement in growth rate did not translate into enhanced feed efficiency but was primarily driven by increased feed consumption. OMS also improved overall antioxidant capacity and key enzyme activities, elevated immunoglobulin levels, and reduced pro-inflammatory cytokines. Notably, OMS maintained Lactobacillus dominance, enriched Bacteroides, Enterococcus, and Butyricicoccus, and reduced Escherichia-Shigella. Functional predictions via PICRUSt2 suggested enhanced metabolic pathways related to antioxidant and immune functions; however, these results represent inference-based predictions and should be interpreted cautiously. Overall, the combination of OEO and MCE exerted synergistic benefits on growth, physiological health, and gut microbiota, supporting its potential as a phytogenic strategy for antibiotic-free broiler production.},
}

@article {pmid41472081,
year = {2025},
author = {Urga, and Wang, X and Wei, H and Zhao, G},
title = {Mechanisms and Applications of Gastrointestinal Microbiota-Metabolite Interactions in Ruminants: A Review.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472081},
issn = {2076-2607},
support = {2025YJRC077//Research Foundation for Advanced Talents of InnerMongolia Normal University/ ; },
abstract = {The gastrointestinal microbiota of ruminants constitutes a complex invisible organ, which converts plant fibers into volatile fatty acids (VFAs) and microbial protein through fermentation, serving as the primary energy and protein sources for the host. While substantial progress has been made in characterizing this system, critical gaps remain in understanding causal mechanisms and translating knowledge into scalable interventions. This review systematically synthesizes current knowledge on the composition, function, and metabolite profiles of gastrointestinal microbial communities in ruminants, with emphasis on interaction mechanisms, methodological advances, and intervention strategies. We highlight persistent challenges, including the uncultured majority of microbes, causal inference limitations, and translational bottlenecks. The review further evaluates strategies for targeted microbiome modulation aimed at improving production performance and reducing environmental emissions. Finally, we propose integrated research priorities for developing efficient, low-carbon, and sustainable ruminant production systems.},
}

@article {pmid41472077,
year = {2025},
author = {Xu, L and Long, K and Zhang, Y and Zhou, G and Liu, J},
title = {Responses of Soil Microbial Communities and Anthracnose Dynamics to Different Planting Patterns in Dalbergia odorifera.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472077},
issn = {2076-2607},
abstract = {Anthracnose is one of the major diseases affecting Dalbergia odorifera T. Chen. However, the soil microbial mechanisms underlying D. odorifera responses to anthracnose remain largely unexplored. This study investigated three planting systems: a Dalbergia odorifera monoculture (J); a mixed plantation of D. odorifera and Pterocarpus macrocarpus (JD); and a composite mixed plantation of D. odorifera, P. macrocarpus, and Clinacanthus nutans (JDY). Using amplicon sequencing technology for soil microbial analysis and combining soil physical and chemical properties with disease severity, we comprehensively analyzed changes in soil microbial community structure and function across different planting modes. The results showed that the diverse mixed mode (JD, JDY) significantly improved soil physicochemical properties and promoted soil nutrient cycling. Redundancy analysis (RDA) indicated that soil organic matter (SOM) and disease severity, quantified by the area under the disease progress curve (AUDPC), were the primary environmental drivers of microbial community variation. Genera positively correlated with SOM and negatively correlated with AUDPC were significantly enriched in JDY and JD, whereas genera showing opposite relationships were predominantly enriched in J. Functional predictions revealed enhanced nutrient-cycling capacities in JD and JDY, with JDY uniquely harboring functional groups such as Arbuscular Mycorrhizal, Epiphyte, and Lichenized taxa. In contrast, microbial functions in the J plantation were mainly limited to environmental amelioration. Co-occurrence network analysis further showed that as planting patterns shifted from J to JDY, microbial communities evolved from competition-dominated networks to cooperative defensive networks, integrating efficient decomposition with strong pathogen suppression potential. The study demonstrates that complex mixed planting systems regulate soil properties, enhance the enrichment of key functional microbial taxa, reshape community structure and function, and ultimately enable ecological control of anthracnose disease. This study provides new perspectives and theoretical foundations for ecological disease management in plantations of rare tree species and for microbiome-based ecological immunization strategies.},
}

@article {pmid41472044,
year = {2025},
author = {Hu, C and Wu, Y and Li, Z and Wang, Z and Huang, F and Fan, Z and Peng, M},
title = {Ecological Modulation of Soil Microbial Communities by Fertilization Regimes: Insights from Castor Bean Cake, Chemical Fertilizers, and Organic Fertilizer.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472044},
issn = {2076-2607},
support = {S202510517029//Student Innovation and Entrepreneurship Training Program of Hubei Minzu University/ ; KYPT012305//Open Fund of Hubei Key Laboratory of Biological Resources Protection and Utilization (Hubei Minzu University)/ ; },
abstract = {Fertilization plays a vital role in replenishing soil nutrients, shaping microbial community composition, and enhancing agricultural productivity. Castor bean cake (CBC) is a nitrogen- and carbon-rich by-product increasingly used as an organic amendment, yet its effects on soil microbiomes remain unclear. Here, we compared CBC with a compound chemical fertilizer (CF) and a manure-based organic fertilizer (OF) across dose gradients using 16S rRNA sequencing and multi-level ecology analyses (α/β diversity, co-occurrence networks, and community assembly models). The results revealed that CBC increased bacterial richness and phylogenetic breadth relative to the unfertilized cultivated control, whereas OF showed dose-dependent declines in richness and CF maintained relatively stable richness with slight reductions in evenness at higher doses. Phylum-level composition shifted strongly with fertilizer identity: Bacillota decreased, whereas Pseudomonadota and Acidobacteriota increased under fertilization, with the largest compositional changes under CBC. CBC strengthened nutrient-enzyme-microbe coupling and generated increasingly complex, highly connected, and robust co-occurrence networks along the dose gradient, outperforming high-dose OF in network complexity and robustness, while OF maintained higher modularity. Null-model partitions (βNTI/RC_bray, NST, NCM, iCAMP) indicated that stochastic processes dominated community assembly across treatments; along the CBC gradient, dispersal limitation decreased from CBC1 to CBC2 and drift remained dominant, indicating increasing stochastic stabilization at moderate-high doses. Together, CBC promoted microbiome recovery and ecological resilience and represents a promising amendment for soil health.},
}

@article {pmid41472041,
year = {2025},
author = {Sharma, SB and Raverkar, KP and Wani, SP and Bagyaraj, DJ and Kannepalli, A and Kandula, DRW and Mikaelyan, A and Ansari, MA and Stock, SP and Davies, KG and Sharma, R},
title = {Role of the Plant-Microbiome Partnership in Environmentally Harmonious 21st Century Agriculture.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472041},
issn = {2076-2607},
abstract = {The 21st century calls for a paradigm shift in agricultural practices to address the pressing issues of regeneration of soil health, climate change, environmental degradation, sustainability under growing population pressures, and food security challenges. This article reviews the potential of the plant-microbiome approach as a key driver for eco-conscious green farming. The focus is on the diverse roles of microbial communities in close association with plants in improving plant health, crop productivity, and soil ecosystem functions, and in enhancing environmental sustainability, with focus on four key areas: (1) Soil health and fertility through microbial partnerships; (2) Ecosystem sustainability through microbial functions; (3) Plant health, productivity and food security through microbial innovations emphasising the potential of microbial applications (biofertilisers, bioprotectants, and biostimulants) in sustainable agriculture; (4) Standardisation and stewardship in microbial agriculture highlighting the need for standardisation and quality control in microbial product development and use, and the concept of microbial stewardship and its importance in long-term agricultural sustainability. By synthesising current knowledge and identifying future challenges, this review underscores the transformative potential of the plant-associated microbiome approach in creating resilient, productive, and environmentally harmonious agricultural systems. We highlight current research gaps and future directions, arguing that embracing microbial solutions is not just an option but a necessity for ensuring food security and environmentally benign sustainability in the face of global challenges.},
}

@article {pmid41472037,
year = {2025},
author = {Aschalew, ND and Liu, J and Liu, Y and Sun, W and Yin, G and Cheng, L and Wang, H and Zhao, W and Zhang, L and Wang, Z and Jiang, H and Wang, T and Qin, G and Zhen, Y and Sun, Z},
title = {Enhancing Sheep Rumen Function, and Growth Performance Through Yeast Culture and Oxalic Acid Supplementation in a Hemicellulose-Based Diet.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472037},
issn = {2076-2607},
support = {20230202075NC//the Scientific and Technological Development Scheme of Jilin Province/ ; 20230202075NC//the Scientific and Technological Development Scheme of Jilin Province/ ; },
abstract = {Yeast culture (YC) is a microbial product that enhances ruminal fiber breakdown and improves nutrient digestion and utilization. Our previous research showed that oxalic acid (OA) is a crucial metabolite in YC that enhances rumen function. This study aimed to investigate the effects of YC, OA, and their combination (YO) on rumen function, growth, and fattening in sheep. Twenty lambs were divided into 4 groups (ctrl, YC, OA, and YO; n = 5 each) and fed a diet supplemented with 2 levels of YC and 2 doses of OA for 60 days in a 2 × 2 factorial design. Growth and fattening performance, rumen microbiome analysis, serum indices and anti-oxidant levels, and metabolomic profiling were performed. Individual supplementation with YC and OA significantly increased the digestibility of dry matter (DM), organic matter (OM), and crude protein (CP) (p < 0.001); neutral detergent fiber (NDF) (p < 0.05); and acid detergent fiber (ADF) (p < 0.001) and their interaction significantly increased dry matter intake (DMI) (p = 0.05). Serum IgA and IgM levels were higher in the supplemented groups (p < 0.05). Serum calcium levels were higher in the OA and YO groups (p < 0.001). The supplemented groups showed significantly higher growth hormone and superoxide dismutase levels (p < 0.05). The longissimus dorsi muscle had higher levels of iron in the OA and YO groups; zinc in the OA, YO, and YC groups (p < 0.01); and selenium in the YC group (p < 0.05). The OA group had a higher total antioxidant capacity. All supplemented groups showed higher bacterial richness and diversity. Ruminococcus, Succinivibrio, and Fibrobacter were positively correlated with the fermentation and digestibility parameters. The supplementation also altered metabolite levels and types in key physiological pathways. In conclusion, this supplementation improved bacterial composition, nutrient digestibility, weight gain, carcass weight and quality, serum indices, antioxidant levels and metabolomic profiles. This suggests potential for the development of dietary supplements for ruminants.},
}

@article {pmid41472035,
year = {2025},
author = {Mntambo, N and Arumugam, T and Pramchand, A and Pillay, K and Ramsuran, V},
title = {A Review of Global Patterns in Gut Microbiota Composition, Health and Disease: Locating South Africa in the Conversation.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472035},
issn = {2076-2607},
abstract = {The gut microbiota plays an essential role in human health through its contributions to immune regulation, metabolism, pathogen defence and disease susceptibility. Despite this significance, most gut microbiome research remains disproportionately focused on high-income countries, resulting in a limited and underrepresented view of global microbial diversity. This bias is evident in Africa, where populations, including those in South Africa, show unique combinations of genetic variation, dietary patterns and environmental exposures that are insufficiently captured in current datasets but offer opportunities to uncover novel insights into microbial evolution and its influences on health across diverse settings. In response to this gap, this review synthesises global patterns in gut microbiota composition and diversity while situating South African findings within this broader context. We examine evidence across microbial domains, including bacteria, fungi, viruses, archaea, protozoa and helminths, and highlight the impact of dietary transitions and environmental exposures on microbial community structure. Although still emerging, research on the gut microbiome of South African populations consistently reports contrasts between rural and urban populations, with rural groups enriched in fibre-fermenting and anti-inflammatory taxa, whereas urban communities often exhibit reduced diversity and features of dysbiosis linked to Westernisation. However, limited sample sizes, heterogeneous methodologies and absence of multi-omic approaches constrain robust interpretation. These lacunae in current knowledge emphasise the urgent need for large-scale, longitudinal studies that reflect South Africa's demographic and geographic diversity. Strengthening this evidence will not only help identify microbial signatures linked to modifiable lifestyle factors but will also guide nutrition, prevention and screening programmes to improve health in African populations.},
}

@article {pmid41472032,
year = {2025},
author = {Li, M and Chen, P and Liu, C and Wang, S and Zhang, H and Li, J and Karrow, NA and Mao, Y and Yang, Z},
title = {Gut Microbiome and Metabolome Signatures Associated with Heat Tolerance in Dairy Cows.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472032},
issn = {2076-2607},
support = {2022YFF1001200//National Key Research and Development Program of China/ ; BK20241934//Natural Science Foundation of Jiangsu Province/ ; 32172686//National Natural Science Foundation of China/ ; },
abstract = {Heat stress significantly impairs dairy cow health and productivity, highlighting the need to understand the gut microbiome-metabolite interactions that contribute to heat tolerance. Here, we integrated metagenomic sequencing and untargeted metabolomics in twelve holstein cows selected from a previously phenotyped herd of 120 individuals, including six heat-tolerant (HT) and six heat-sensitive (HS) cows identified using entropy-weighted TOPSIS scoring. HT cows were enriched in genera such as Faecalimonas and UBA737, which were functionally linked to pathways of energy and lipid metabolism, whereas, HS cows harbored taxa associated with bacterial lipopolysaccharide and glycosphingolipid biosynthesis. A total of 135 metabolites were differentially abundant between groups. Among them, glycerol 2-phosphate and 24(28)-dehydroergosterol showed perfect classification performance (AUC = 1.000), and were mainly involved in membrane lipid remodeling and redox regulation. Integrated analysis revealed coordinated microbial-metabolite networks, exemplified by the Faecalimonas-LysoPS (16:0/0:0) and UBA737-Glycerol 2-phosphate axes, suggesting functional coupling between microbial composition and metabolic adaptation. Together, these findings demonstrate that HT cows harbor gut microbiota and metabolites favoring energy balance, membrane remodeling, and oxidative stress resilience, while HS cows display stress-related metabolic patterns. This study elucidates the microbial-metabolic mechanisms underlying thermal resilience and highlights potential biomarkers and metabolic pathways that could be applied in heat-tolerance breeding and precision management of dairy cattle.},
}

@article {pmid41472025,
year = {2025},
author = {Yun, Y and Ying, Y and Sun, J and Zhao, J and Wang, W and Kang, B},
title = {Effects of Adding Astragali Radix and Inulae Radix on Fermentation Quality, Nutrient Preservation, and Microbial Community in Barley Silage.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472025},
issn = {2076-2607},
support = {Science and Technology Project from Inner Mongolia//2021GG0068/ ; Ordos Science and Technology Program//2022EEDSKJXM002/ ; },
abstract = {Chinese herbal medicine (CHM) residues represent a promising and sustainable category of silage additives, with the potential to modulate fermentation and enhance nutrient preservation. This study investigated the effects of two CHMs, Astragalus membranaceus L. (Astragali Radix, AR) and Inula helenium L. (Inulae Radix, IR), on the fermentation profile, nutritional composition, and bacterial community structure in barley silage. The forage was ensiled without additive (control, CK), or with 1% or 2% (w/w) of AR or IR for 75 days. The results showed that all additive treatments significantly improved fermentation quality, as evidenced by lower pH and reduced ammonia-nitrogen (NH3-N) content compared to CK. The 2% IR treatment was most effective in promoting homolactic fermentation, yielding the highest lactic acid content and lactic acid-to-acetic acid ratio. Nutritionally, additives significantly increased dry matter, starch, and water-soluble carbohydrates, while decreasing neutral and acid detergent fiber contents. High-throughput sequencing of the 16S rRNA gene revealed that both herbal additives profoundly reshaped the microbial community. They suppressed undesirable bacteria and significantly enriched beneficial Lactobacillus species. Principal component analysis confirmed a distinct separation in microbial community structure between control and treated silages. These findings underscore the potential of these herbal residues as natural modulators of the silage microbiome for improved forage conservation.},
}

@article {pmid41471992,
year = {2025},
author = {Wang, J and Li, D and Lu, D and Chen, C and Zhang, Q and Fu, R and Huang, F},
title = {Differential Assembly of Rhizosphere Microbiome and Metabolome in Rice with Contrasting Resistance to Blast Disease.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471992},
issn = {2076-2607},
support = {SCCXTD-2024-SD-4 & SCCXTD-2024-SD-8//Sichuan Rice Innovation Team Project/ ; 2021YFYZ0021//Sichuan Provincial Science and Technology Planning Project/ ; 5+1QYGG002//Sichuan Academy of Agricultural Sciences Financial Guidance Fund Project/ ; },
abstract = {Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases threatening global rice production. Although host resistance represents a sustainable control strategy, the underlying mechanisms mediated by the rhizosphere microbiome remain poorly understood. In this study, we selected four rice varieties with varying resistance to blast and demonstrated, through an integrated approach of 16S rRNA/ITS amplicon sequencing, untargeted metabolomics, and soil physicochemical analysis, that the rice genotype reprograms the genotype-root exudate-rhizosphere microbiome system. Results showed that the resistant variety P104 significantly decreased the soil pH while increasing the contents of total nitrogen, ammonium nitrogen, and nitrate nitrogen. On the other hand, the susceptible variety P302 exhibited higher pH and available phosphorus content. Furthermore, the rhizosphere of P104 was enriched with specific beneficial microbes such as Desulfobacterota, Ascomycota, and Pseudeurotium, and activated defense-related metabolic pathways including cysteine and methionine metabolism and phenylpropanoid biosynthesis. In contrast, susceptible varieties showed reduced bacterial diversity and fostered a microecological environment more conducive to pathogen proliferation. Our findings indicate that blast-resistant rice genotypes are associated with a protective rhizosphere microbiome, potentially mediated by alterations in root metabolism, thereby suppressing pathogen establishment. These insights elucidate the underground mechanisms of blast resistance and highlight the potential of microbiome-assisted breeding for sustainable crop protection.},
}

@article {pmid41471991,
year = {2025},
author = {Qiao, S and Wang, Z and Zhang, R and Wang, Y and Wang, C and Gao, G and Pan, J},
title = {Microbial Community Analysis and Environmental Association in Cave 6 of the Yungang Grottoes.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471991},
issn = {2076-2607},
abstract = {The Yungang Grottoes, a World Heritage Site, face biodeterioration risks. This study analyzed microbial communities in five microenvironments within Cave 6 using high-throughput sequencing (16S/18S rRNA). Communities showed high microenvironment specificity. Ascomycota and Proteobacteria dominated fungi and bacteria, respectively. Areas near the lighting window, with high external interaction, showed the highest diversity, while red pigment areas, likely under heavy metal stress, had the lowest diversity. Human-associated microbes (e.g., Escherichia-Shigella, Malassezia) indicated anthropogenic pollution on statue surfaces. Core microbiome and functional prediction (PICRUSt2) suggested high biodegradation risk in dust accumulation and inter-statue areas, enriched with organic-degrading and acid-producing taxa (e.g., Rubrobacter, Cladosporium). Microbial distribution and function were driven by openness, substrate, and human impact. This study identifies key risk zones and informs targeted conservation strategies for the Yungang Grottoes.},
}

@article {pmid41471974,
year = {2025},
author = {Tu, Y and Chen, B and Wei, Q and Xu, Y and Peng, Y and Li, Z and Liang, J and Zhuo, L and Zhong, W and Huang, J},
title = {Biochar-Urea Peroxide Composite Particles Alleviate Phenolic Acid Stress in Pogostemon cablin Through Soil Microenvironment Modification.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471974},
issn = {2076-2607},
support = {2023B0202010027//Key-Area Research and Development Program of Guangdong Province/ ; 42177337//National Natural Science Foundation of China/ ; 2022A1515020753//Natural Science Foundation of Guangdong Province/ ; },
abstract = {The continuous-cropping obstacles of Pogostemon cablin (patchouli) is severely constrained by autotoxic phenolic acids accumulated in the rhizosphere soil. Biochar adsorption and chemical oxidation are common remediation strategies; they often fail to simultaneously and efficiently remove phenolic allelochemicals while improving the soil micro-ecological environment. To address this issue, this study developed a novel biochar-urea peroxide composite particle (BC-UP). Batch degradation experiments and electron paramagnetic resonance (EPR) analysis confirmed the synergistic adsorption-oxidation function of BC-UP. A pot experiment demonstrated that application of BC-UP (5.0 g/kg) significantly alleviated phenolic acid stress. Specifically, BC-UP application significantly enhanced shoot biomass by 28.8% and root surface area by 49.3% compared to the phenolic acid-stressed treatment and concurrently reduced the total phenolic acid content in the rhizosphere soil by 37.3%. This growth promotion was accompanied by the enhanced accumulation of key bioactive compounds (volatile oils, pogostone, and patchouli alcohol). BC-UP amendment also improved key soil physicochemical properties (e.g., pH, and organic matter) and enhanced the activities of critical enzymes. Furthermore, BC-UP reshaped the microbial community, notably reducing the fungi-to-bacteria OTU ratio by 49.7% and enriching the relative abundance of Firmicutes and Nitrospirota but suppressing the Ascomycota phylum abundance. Redundancy analysis identified soil sucrase and catalase activity, total phenolic acid content, and Ascomycota abundance as key factors influencing patchouli biomass. In conclusion, BC-UP effectively mitigates phenolic acid stress through combined adsorption and radical oxidation, subsequently improving soil properties and restructuring the rhizosphere microbiome, offering a promising soil remediation strategy for patchouli and other medicinal crops.},
}

@article {pmid41471968,
year = {2025},
author = {Huang, X and Huang, J and Zhong, CC and Wong, MCS},
title = {Cell-to-Cell and Patient-to-Patient Variability in Antimicrobial Resistance.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471968},
issn = {2076-2607},
abstract = {Antimicrobial resistance (AMR) remains a global health crisis, yet treatment outcomes cannot be explained by resistance genes alone. Increasing evidence highlights the importance of variability at two levels: within bacterial populations and across patients. At the microbial level, cell-to-cell variability including genetic mutations, stochastic gene expression, persister cell formation, heteroresistance, and spatial heterogeneity within biofilms creates phenotypic diversity that allows subsets of bacteria to survive antimicrobial stress. At the host level, patient-to-patient variability including differences in genetic background, immune competence, comorbidities, gut microbiome composition, and pharmacokinetics shapes both susceptibility to resistant infections and the likelihood of treatment success. Together, these dimensions explain why infections with the same pathogen can lead to divergent clinical outcomes. Understanding and integrating both microbial and host variability offers a path toward more precise diagnostics, personalized therapy, and novel strategies to counter AMR.},
}

@article {pmid41471964,
year = {2025},
author = {Jotic, A and Cirkovic, I and Jovicic, N and Bukurov, B and Krca, N and Savic Vujovic, K},
title = {Biofilm Formation and Its Relationship with the Microbiome in Pediatric Otitis Media.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471964},
issn = {2076-2607},
support = {451-03-65/2025-03/200110//Ministry of Science, Technological Development and Innovation, Republic of Serbia/ ; },
abstract = {Otitis media is among the most common pediatric illnesses globally, constituting a leading cause of antimicrobial prescriptions, recurrent medical consultations, and preventable hearing loss in early childhood. Traditionally regarded as a sterile cavity intermittently invaded by pathogens, the middle ear is now recognized as a dynamic ecological niche influenced by anatomical immaturity of the Eustachian tube, host immune development, and the composition of resident microbial communities. Increasing evidence demonstrates that microbial dysbiosis and the establishment of biofilms are central to the persistence and recurrence of disease. This review synthesizes current knowledge of the pediatric middle ear microbiome, highlighting how commensal organisms contribute to mucosal resilience and colonization resistance, whereas pathogenic bacteria exploit ecological disruption to establish biofilm communities. Biofilm formation provides bacteria with enhanced survival through immune evasion, altered microenvironments, and antibiotic tolerance, thereby transforming acute otitis media into recurrent or chronic states. Furthermore, studies demonstrate how adenoids act as reservoirs of biofilm-forming organisms, seeding the middle ear and perpetuating infection. The emerging ecological perspective emphasizes the limitations of conventional antibiotic-centered management and directs attention toward innovative strategies, including microbiome-preserving interventions, probiotic or live biotherapeutic approaches, and antibiofilm agents. By defining pediatric otitis media as a disorder of disrupted host-microbe equilibrium, future research may pave the way for precision-based preventive and therapeutic strategies aimed at reducing the global burden of this pervasive disease.},
}

@article {pmid41471956,
year = {2025},
author = {Xue, N and Liu, D and Feng, Q and Zhu, Y and Cheng, C and Wang, F and Su, S and Xu, J and Tao, J},
title = {Comparison of Gut Microbiome Profile of Chickens Infected with Three Eimeria Species Reveals New Insights on Pathogenicity of Avian Coccidia.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471956},
issn = {2076-2607},
support = {No. 31972698 to JT//National Natural Science Foundation of China/ ; },
abstract = {Avian coccidiosis is an intestinal disease caused by Eimeria spp. infection. A deeper understanding of the interaction between host gut microbiota and the Eimeria parasite is crucial for developing alternative therapies to control avian coccidiosis. Here, we used full-length sequencing of 16S ribosomal RNA amplicons to compare changes in the gut microbiota of chickens infected with Eimeria tenella, Eimeria maxima, and Eimeria necatrix, aiming to identify both species-specific and common alterations in gut microbiota at 4 and 10 days post-infection. The result revealed that infection with all three Eimeria species led to a decrease in the abundance of the microbial genera Limosilactobacillus, Streptococcus, Alistipes, Lactobacillus and Phocaeicola, while the abundance of Bacteroides, Escherichia and Ligilactobacillus increased. Escherichia and Enterococcus were most abundant in the jejunum of the E. necatrix-infected group and in the cecum of the E. tenella-infected group, whereas Megamonas abundance was highest in the E. maxima-infected group. LEfSe analysis showed that infection with all three Eimeria species significantly reduced the abundance of 13 bacterial species, including Acetilactobacillus jinshanensis, Bacteroides ndongoniae, Barnesiella viscericola, Christensenella minuta, Enterocloster clostridioformis, Gemella haemolysans_A, Granulicatella adiacens, Lawsonibacter sp000177015, Limosilactobacillus reuteri, Limosilactobacillus reuteri_D, Limosilactobacillus vaginalis_A, Limosilactobacillus caviae, Limosilactobacillus vaginalis. Infection with E. tenella significantly increased the abundance of five bacterial species, including Bacteroides fragilis, Enterococcus cecorum, Helicobacter pylori, Methylovirgula ligni, and Phocaeicola sp900066445. Infection with E. maxima significantly increased the abundance of seven bacterial species, including Clostridioides difficile, Faecalibacterium prausnitzii, Mediterraneibacter torques, Muribaculum intestinale, Mediterraneibacter massiliensis, Phascolarctobacterium faecium, and Phocaeicola plebeius. Infection with E. necatrix significantly increased the abundance of seven bacterial species, including Alistipes sp900290115, Anaerotignum faecicola, Bacteroides fragilis_A, Escherichia coli, Harryflintia acetispora, Pseudoclostridium thermosuccinogenes, and Tidjanibacter inops_A. The results showed that Eimeria infection causes significant species- and time-dependent changes in the gut microbiota of chickens. These findings enhance our understanding of coccidiosis pathogenesis and offer potential targets for developing probiotics.},
}

@article {pmid41471952,
year = {2025},
author = {Li, TP and Li, HX and Bao, JS and Wang, CH and Wang, KL and Hao, BR and Wang, ZH and Hu, JH and Zhao, LQ},
title = {Geographical Variation in Bacterial Community Diversity and Composition of Corythucha ciliata.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471952},
issn = {2076-2607},
support = {32301594//National Natural Science Foundation of China/ ; 32171803//National Natural Science Foundation of China/ ; },
abstract = {The sycamore lace bug, Corythucha ciliata, a globally invasive pest that damages Platanus spp., harbors a bacterial microbiome that may help it adapt to different geographical environments. However, the geographical differentiation patterns of its bacterial community and the underlying driving mechanisms remain unclear. In this study, we standardized rearing of three C. ciliata populations (collected from Beijing, Lianyungang, and Nanjing) for three generations to reduce immediate environmental interference, then analyzed their bacterial communities via 16S rRNA gene amplicon sequencing. The principal coordinate analysis revealed a significant separation of the bacterial community in the Nanjing population, while the Beijing and Lianyungang populations were more similar. Bacterial alpha diversity followed the gradient of "Nanjing > Lianyungang > Beijing", with the Nanjing population exhibiting significantly higher species richness and evenness than the Beijing population. All three populations shared core bacterial taxa (e.g., phyla Proteobacteria, Bacteroidota; genera Cardinium, Serratia), but their relative abundances differed significantly: Cardinium dominated the Beijing population (50.1%), Serratia dominated the Lianyungang population (45.86%), and the Nanjing population harbored unique dominant genera such as Sphingomonas. For the three target populations, monthly average temperature and wind speed were positively correlated with bacterial diversity, while latitude was negatively correlated (Pearson correlation coefficient: 0.6564 < |r| < 0.7010, p < 0.05). Core bacterial functions (e.g., substance transport) were conserved across populations, whereas differential functions (e.g., detoxification, lipid metabolism) were linked to geographical adaptation. This study confirms the climate-driven geographical differentiation of the C. ciliata bacterial community provides insights into the "insect-microbiome" interactive invasion mechanism that is present here.},
}

@article {pmid41471933,
year = {2025},
author = {Frizon, L and Rocchetti, TT and Frizon, A and de Alcântara, RJA and de Paiva, CS and Gomes, JÁP},
title = {The Gut Microbiome in Stevens-Johnson Syndrome and Sjögren's Disease: Correlations with Dry Eye.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471933},
issn = {2076-2607},
abstract = {Changes in gut microbial composition may influence mucosal immune responses and contribute to systemic autoimmune manifestations. In this pilot exploratory study, we investigated and compared the gut microbiome in patients with Stevens-Johnson syndrome (SJS), patients with Sjögren's disease (SjD), and healthy controls, using next-generation sequencing (NGS), and assessed correlations with dry eye parameters. The study included 10 patients with SJS matched by age and sex to 10 healthy controls, and 10 patients with SjD matched to an additional set of 10 healthy controls. Dry eye parameters were employed to evaluate dry eye disease (DED). Microbiome profiles were determined using next-generation sequencing of the 16S V3-V4 region and analyzed using the Silva database. The gut microbiome exhibited significant differences in the SJS group, including a reduced Chao1 index (p = 0.01) that was progressively correlated with increased ocular severity and a decrease in Faecalibacterium (p = 0.048) compared to the healthy control group. In the SJS group, strong correlations were observed between increased Christensenellaceae with decreased DED DEWS (Dry Eye Workshop score) (p = 0.04), increased Subdoligranulum with decreased NEI (National Eye Institute) score (p = 0.04), and increased Clostridia and longer TBUT (tear break-up time) (p = 0.009). In contrast, the gut microbiome of SjD patients was similar to that of healthy controls. Patients with SJS exhibited distinct alterations in gut microbial composition, characterized by reduced microbial richness and depletion of Faecalibacterium. Furthermore, a significant association was found between specific bacterial taxa and milder dry eye severity, suggesting a possible link between changes in the gut microbiome and inflammation of the ocular surface.},
}

@article {pmid41471929,
year = {2025},
author = {Han, D and Zhao, R and Yang, X and Wang, T and Li, Z and Zhu, M and Yang, Q and Qu, Y and Chen, X and Chen, Z},
title = {Comparative Analysis of Environmental and Host-Associated Microbiome in Odorrana schmackeri (Auran: Ranidae): Insights into Tissue-Specific Colonization and Microbial Adaptation.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471929},
issn = {2076-2607},
support = {ZC (Grant no. 32270440), XHC (Grant no. U21A20192) and YFQ (32171498)//National Natural Science Foundation of China/ ; },
abstract = {Amphibian microbial communities are known to be shaped by host physiology and environmental factors, yet the relative roles of sexual dimorphism and tissue specialization remain poorly understood. Using 16S rRNA gene sequencing, we compared the gastrointestinal and integumentary microbiomes of a monomorphic Chinese frog population, Odorrana schmackeri, inhabiting identical montane streams. Our results showed distinct phylogenetic stratification between niches: Proteobacteria dominated both environmental microbiota and O. schmackeri gut and skin microbiotas but with differential sub-phylum specialization. The soil microbiota was dominated by unclassified_Vicinamibacteraceae, the water microbiota was Limnohabitans-dominated, the skin microbiota was dominated by Bordetella, and the gut microbiota was led by Acinetobacter. Alpha diversity analysis revealed significant tissue- and environmental-based divergences but no sexual differentiation, a pattern confirmed by beta diversity assessments showing stronger microbial community separation by tissue and environmental compartmentalization than by sex. Functional metagenomic prediction indicated convergent enrichment of metabolic pathways across host-associated and environmental communities. These results suggest that microbial community structure in O. schmackeri is principally governed by tissue-specific ecological selection pressures rather than host sexual characteristics. Our findings enhance understanding of microbiome assembly rules in vertebrate ectotherms and identify potential connections between microbiota in different ecological niches.},
}

@article {pmid41471926,
year = {2025},
author = {Presutti, L and Gueningsman, MC and Fredericksen, B and Smith, A and Taylor, R and Tuckett, A and Folsom, C and Wainwright, R and Klena, C and Ericsson, AC and Zapata, I and Brooks, AE},
title = {Exploring the Interplay Between Fatigue and the Oral Microbiome: A Longitudinal Approach.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471926},
issn = {2076-2607},
abstract = {Fatigue is a pervasive burden for emerging medical professionals, often impacted by stress and lifestyle factors, yet insufficiently explained by these aspects alone. Considering the profound immediate and long-term consequences for physician well-being and patient care, exploring the interplay between biological factors, such as the oral microbiome and fatigue, emerges as a critical area of investigation. This exploratory longitudinal study investigates the relationship between oral microbiome diversity and fatigue in first-year medical students across four timepoints, where they provided buccal swabs and completed lifestyle and standardized stress, sleep, and fatigue assessments (PSQI, FAS, PSS). Microbiome analysis was performed using 16S rRNA sequencing and QIIME2-based bioinformatics to identify genus-level profiles and core microbiome composition. Forty-five healthy participants were assessed. Significant increases in fatigue and fluctuations in oral microbiome diversity were observed, with alpha diversity peaking mid-year before declining. Illness frequency and antibiotic use also rose, potentially influencing microbial shifts. These fluctuations may be indicative of an adaptation process where oral microbial diversity adjusts to changes in the subject's environment, which in this case is entering medical school. Despite no clear clustering in biodiversity metrics, associations between fatigue and microbiome richness were noted, suggesting that physiologic fatigue and environmental stressors may contribute to microbial variability. Limitations of the study include a small sample size, attrition, and representativeness of the study population. This study presents a longitudinal baseline that may serve as a reference for future investigations. These findings may support the development of targeted interventions designed to modulate microbial composition as a novel approach to alleviating fatigue.},
}

@article {pmid41471906,
year = {2025},
author = {Yang, Z and Duan, Y and Wei, R and Yuan, Y and Yan, H and Tang, T and Shang, H},
title = {Rhizosphere Microbiome and Nutrient Fluxes Reveal Subtle Biosafety Signals in Transgenic Cotton.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471906},
issn = {2076-2607},
support = {2023ZD04062//Biological Breeding-Major Projects/ ; 32201828//National Natural Science Foundation of China/ ; 241111114200//Key R&D Program of Henan Province/ ; 2022M722899//China Postdoctoral Science Foundation/ ; 1610162019010101, 1610162023002//Central Public-interest Scientific Institution Basal Research Fund/ ; CB2025C12, CB2024C05//Independent Fund of State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/ ; CAASASTIP-2016-ICR//National Agricultural Science and Technology Innovation Project for CAAS/ ; },
abstract = {Genetically modified crops have transformed agriculture, but their long-term ecological impacts remain incompletely understood. Here we investigate how herbicide-tolerant transgenic cotton affects rhizosphere microbial communities and nutrient cycling over a 28-day growth period using 16S rRNA amplicon sequencing and multivariate analyses. We sampled rhizosphere soil from greenhouse-grown transgenic and wild-type cotton plants at five time points, analyzing microbial diversity, community structure, and nutrient dynamics. Despite initial concerns about transgenic modifications disrupting soil ecosystems, we found no significant differences in microbial α-diversity or β-diversity between genotypes. Only minor, transient changes occurred at the genus level, including <5% shifts in Flavobacterium and Ramlibacter abundance on day 14, alongside brief nutrient flux variations that normalized by day 28. Notably, transgenic plants showed enhanced above-ground biomass accumulation without compromising rhizosphere stability or soil moisture content. These results demonstrate that herbicide-tolerant cotton maintains rhizosphere homeostasis while improving agronomic performance, supporting the environmental safety of this biotechnology for sustainable agricultural intensification.},
}

@article {pmid41471878,
year = {2025},
author = {Qi, X and Han, Z and Meng, J and Zhao, H and Zhou, M and Wang, M and Kang, S and Shi, Q and Li, H and Lu, F and Zhao, H},
title = {Integrated Metagenomic and Lipidomic Profiling Reveals Dysregulation of Facial Skin Microbiome in Moderate Acne Vulgaris.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471878},
issn = {2076-2607},
support = {32402248//the National Natural Science Foundation of China/ ; No. 24JCQNJC00880//the Natural Science Foundation of Tianjin/ ; },
abstract = {Acne vulgaris is a prevalent chronic inflammatory dermatosis primarily affecting the pilosebaceous units. Current therapeutic approaches often exhibit limited efficacy and high recurrence rates. To investigate the microbiome-related mechanisms of acne vulgaris, facial skin samples from 19 patients with moderate acne and 20 healthy individuals were analyzed using an integrated metagenomic and lipidomic profiling strategy. Metagenomic analysis revealed a significant reduction in microbial diversity (Chao index) in acne-affected skin compared to healthy controls (p < 0.001). The relative abundance of Staphylococcus, particularly Staphylococcus epidermidis, was significantly elevated in acne group (p < 0.05), while Cutibacterium acnes levels remained unchanged. Carbon metabolism pathways were enriched in the acne group (p < 0.05), predominantly driven by Cutibacterium, whereas other enriched metabolic pathways, such as ABC transporters and glycine, serine, and threonine metabolism (p < 0.05), showed a greater contribution from Staphylococcus. Virulence factors enriched in acne samples were primarily offensive in nature and largely attributed to Staphylococcus. Moreover, acne-associated microbiome exhibited a significantly higher prevalence of resistance genes against fluoroquinolones, fosfomycin, and triclosan (p < 0.05). Untargeted lipidomic analysis demonstrated significantly elevated total serum and triglyceride levels, along with a reduction in fatty acid chain length and a higher degree of saturation compared to the healthy group (p < 0.01). Specific triglycerides significantly enriched in the acne group, such as TG (15:0_14:0_16:0) + NH4, exhibited a significant positive correlation with Staphylococcus. This correlation is associated with elevated clinical erythema and melanin indices, suggesting that Staphylococcus is implicated in the development of acne-related inflammation. Additionally, Thermus exhibits negative correlations with acne-associated lipids and inflammatory parameters, potentially exerting a protective role. These findings suggest that Cutibacterium and Staphylococcus play differential yet synergistic roles in acne pathogenesis. The observed skin microbiome dysbiosis and lipid metabolic alterations provide novel insights into the pathophysiology of acne vulgaris, which may inform the development of targeted therapeutic strategies.},
}

@article {pmid41471876,
year = {2025},
author = {Wang, Y and Gong, L and Gao, Z and Dong, D and Li, X},
title = {Comparative Analysis of Sponge-Associated, Seawater, and Sediment Microbial Communities from Site F Cold Seep in the South China Sea.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471876},
issn = {2076-2607},
support = {42176114//National Natural Science Foundation of China/ ; ZR2023MD100//the Shandong Provincial Natural Science Foundation/ ; CAS-TAX-24-30//Biological Resources Programme, Chinese Academy of Sciences/ ; },
abstract = {Microbial communities at Site F cold seep, ubiquitous in both the environment and the associated fauna, demonstrate clear habitat-specific partitioning. Metagenomic sequencing and binning demonstrated a striking partitioning of microbial taxa at the cold seep: whereas the sponge-associated microbiome was distinctly enriched with specialized sulfur- and methane-oxidizing bacteria that were rare in the environment, it simultaneously exhibited a significantly reduced archaeal content, lower α-diversity, and a simpler overall community structure compared to the sediment and seawater communities. Distinct evolutionary lineages and varying abundances were observed among the microbiomes from seawater, sediment, and sponges. Furthermore, their Metagenome-Assembled Genomes (MAGs) exhibited significant differences in genomic features, including genome size and GC content. The sponge-associated microbiome exhibits lower diversity but maintains a high abundance of key functional genes, particularly those involved in sulfur cycling (e.g., apr, dsr, metZ), indicating enhanced metabolic efficiency in energy conservation and nutrient acquisition. This study reveals that the seawater, sediment, and sponge-associated microbiomes exhibit genome simplification and functional specialization in the cold seep environment, with varying lifestyles driving structural optimization and functional remodeling of the symbiotic microbiomes.},
}

@article {pmid41471874,
year = {2025},
author = {Song, S and Iino, K and Nakamura, M and Sato, M and Oishi, M and Ito, A and Yokoyama, Y},
title = {Comparative Characterization of Vaginal and Gut Microbiota in Late-Pregnancy Women with or Without Group B Streptococcus Colonization.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471874},
issn = {2076-2607},
support = {JMWH Bayer Grant, 2022//JMWH Bayer Grant/ ; },
abstract = {Group B Streptococcus (GBS) colonization during pregnancy is a major cause of neonatal infection, yet its microbial determinants remain unclear. This pilot study compared the vaginal and gut microbiota of late-pregnancy women with and without GBS colonization to explore potential microbial cues for peripartum risk stratification. Forty-three Japanese pregnant women (GBS-Negative = 34; GBS-Positive = 9) were enrolled at 35-37 weeks of gestation. Vaginal secretions and stool were analyzed by 16S rRNA (V3-V4) sequencing using QIIME 2 with SILVA annotation and community state type (CST) classification. Vaginal communities were mainly Lactobacillus-dominant. GBS-Positive women showed a non-significant tendency toward more L. iners-dominant CST III and fewer L. crispatus-dominant CST I compared with GBS-Negative women. Prevotella, Atopobium, and Gardnerella were significantly enriched in the GBS-Positive group (false discovery rate < 0.05), whereas gut microbial diversity and composition showed no significant differences between groups. Cross-site gut-vagina genus-level correlations were generally weak and non-significant. These findings suggest that, in late pregnancy, GBS colonization is linked to subtle shifts within Lactobacillus-dominant vaginal communities, with more L. iners and bacterial vaginosis-associated genera, rather than global microbiota disruption. The apparent shift from L. crispatus- to L. iners-dominant communities is hypothesis-generating and should be confirmed in larger cohorts.},
}

@article {pmid41471873,
year = {2025},
author = {Zang, B and Xu, L and Huang, H and Liu, Q and Yao, Y and Li, J and Yang, Y and Zhao, C and Liu, B and Liu, B},
title = {Decoding the Gut Microbiome in Primary Sjögren's Syndrome and Primary Biliary Cholangitis: Shared Dysbiosis, Distinct Patterns, and Associations with Clinical Features.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471873},
issn = {2076-2607},
support = {81671600//National Natural Science Foundation of China/ ; 81241094//National Natural Science Foundation of China/ ; ZR2016HM13 /ZR2023MH066//Natural Science Foundation of Shandong Province/ ; 2024-WJKY160//Qingdao Medical and health scientific research project/ ; },
abstract = {This study aimed to analyze gut microbiome similarities and differences between primary biliary cholangitis (PBC) and primary Sjögren's syndrome (pSS), exploring potential associations with disease pathogenesis. High-throughput sequencing of the 16S rRNA gene was performed on fecal samples from 100 subjects (PBC: 38; pSS: 42; HC: 20) to compare the composition, diversity, and key microbial markers, examining associations with clinical indicators. The gut microbiome of PBC and pSS patients exhibited reduced alpha diversity (p < 0.05) and decreased abundance of the Bacteroides genus (both p < 0.001). While the majority of differentially abundant species were similar in PBC and pSS, unique imbalances were noted: Actinobacteria was elevated in pSS, whereas Proteobacteria was higher in PBC (p < 0.05). At the species level, a higher relative abundance of Ruminococcus torques, Clostridium celatum, and Lactobacillus vaginalis was identified in PBC patients, with positive correlations observed with key clinical indicators such as liver enzymes and TBA. In pSS patients, Faecalibacterium prausnitzii showed a negative correlation with GGT and ALT. Although PBC and pSS shared many similarities in their gut microbiome's composition and diversity, indicating common mechanistic microbial influences on their pathogenicity, distinct microbial profiles correlated with clinical indicators in each disease, highlighting specific microbiome-disease interactions that may underlie their differential pathogenesis.},
}

@article {pmid41471872,
year = {2025},
author = {Yang, B and Zhong, S and Wang, J and Yu, W},
title = {Dietary Modulation of the Gut Microbiota in Dogs and Cats and Its Role in Disease Management.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471872},
issn = {2076-2607},
support = {No. 20242BAB20315//Natural Science Foundation for Youth of Jiangxi Province/ ; GJJ2200410//The Science and Technology Program of Jiangxi Provincial Department of Education/ ; },
abstract = {Food has a massive influence on the gut microbiota and is one of the most useful therapeutic levers in disease. Recent developments have highlighted how macronutrient balance, food format, and functional ingredients can regulate microbial diversity, metabolism, and host physiology in companion animals such as dogs and cats. This narrative review condenses evidence on the bidirectional gut microbiota-diet connection and on nutritional therapy for gastrointestinal, metabolic, renal, hepatic, and immune-mediated disorders. Protein-based diets including high or hydrolyzed protein, omega-3 acids, fermentative fiber, and probiotics can positively affect microbial composition, stimulate short-chain fatty acid synthesis, and enhance intestinal barrier functions. Conversely, excess fats or refined carbohydrates may cause dysbiosis, inflammation, and metabolic imbalances. Numerous studies have shown that therapeutic nutrition-e.g., low-protein renoprotective, hepatoprotective antioxidants, and allergen-elimination diets-holds enormous potential for treatment. In addition, fecal microbiota transplantation (FMT) can be used as an additive therapy for resistant gastrointestinal illnesses. Despite these developments, constraints remain in terms of standardization, study duration, and species-specific data, especially for cats. This review underscores dietary modification as a clinically actionable tool for microbiota-targeted therapy and calls for integrative, multi-omics research to translate microbiome modulation into precision nutrition for companion animals.},
}

@article {pmid41471858,
year = {2025},
author = {Long, N and Zuo, Y and Li, J and Yao, R and Yang, Q and Deng, H},
title = {Thuja sutchuenensis Franch. Essential Oil Ameliorates Atopic Dermatitis Symptoms in Mice by Modulating Skin Microbiota Composition and Reducing Inflammation.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471858},
issn = {2076-2607},
support = {zlg2021-cq20211210, zlg2022-cq20220907//National Key Wildlife Conservation Project of Central Forestry Reform and Development Funds/ ; CSTB2024NSCQ-MSX1297//the Chongqing Natural Science Foundation/ ; 25MSZX555//the Sichuan Provincial Administration of Traditional Chinese Medicine/ ; CYZYB24-08//the Chengdu Medical College Natural Science Foundation/ ; },
abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disorder characterized by dysregulated immunity, skin barrier dysfunction, and cutaneous microbiome dysbiosis. While current therapies face limitations, Thuja sutchuenensis essential oil (TEO) shows promise due to its multi-target potential. We sought to explore the beneficial effects of TEO and delve into its mechanistic actions in a mouse model of AD. We combined network pharmacology with in vivo validation to evaluate the therapeutic efficacy and mechanisms of TEO in an AD model, and confirmed network-predicted targets in an in vitro inflammatory cell model. In AD mice, TEO alleviated pruritus and epidermal hyperplasia, suppressed systemic IL-4/TNF-α and IgE, and partially normalized serum ALB, LDL-C, and HDL-C. Microbial diversity increased after treatment, although potentially pathogenic taxa (Arthrobacter sp. and Corynebacterium mastitidis) remained enriched. Machine-learning analysis indicated the highest predicted metabolic activity in CK controls, whereas the AD and TEO groups showed elevated pathogenic phenotype scores. Network pharmacology prioritized active compounds [(E)-ligustilide, senkyunolide A, 3-butylisobenzofuran-1(3H)-one, butylated hydroxytoluene, Z-buthlidenephthalide, and β-Myrcene] and core targets (TNF, PTPRC, CCR5, JAK1), implicating T-cell receptor signaling, Staphylococcus aureus infection, and STAT3 pathways. Docking and molecular dynamics supported strong, stable binding of major constituents to JAK1, and Western blotting confirmed TEO-mediated inhibition of the JAK1/STAT3 axis. TEO effectively alleviates atopic dermatitis symptoms by modulating immune responses and enhancing microbial diversity. It targets key signaling pathways, such as JAK1/STAT3, highlighting its potential as a therapeutic option for AD.},
}

@article {pmid41471710,
year = {2025},
author = {Oliveira, MB and Maurício, AC and Barros, AN and Botelho, C},
title = {Rebalancing the Skin: The Microbiome, Acne Pathogenesis, and the Future of Natural and Synthetic Therapies.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {24},
pages = {},
pmid = {41471710},
issn = {1420-3049},
support = {LA/P/0059/2020//Fundação para a Ciência e Tecnologia/ ; UIDB/00211/2020//Fundação para a Ciência e Tecnologia/ ; UID/04033/2025//Fundação para a Ciência e Tecnologia/ ; },
mesh = {Humans ; *Acne Vulgaris/microbiology/drug therapy/pathology/etiology ; *Microbiota/drug effects ; *Skin/microbiology/drug effects/pathology ; *Biological Products/therapeutic use/pharmacology ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Dysbiosis ; Animals ; },
abstract = {The skin serves as a primary interface between the human body and the external environment, functioning both as a protective barrier and as a habitat for a complex and diverse microbiome. These microbial communities contribute to immune regulation, barrier integrity, and defence against pathogens. Disruptions in this equilibrium can precipitate dermatological disorders such as acne vulgaris, which affects millions of adolescents and adults worldwide. This chronic inflammatory disorder of the pilosebaceous unit is driven by microbial dysbiosis, hyperkeratinisation, sebum overproduction, and inflammation. This review synthesizes data from over 100 sources to examine the interplay between the skin microbiome and acne pathogenesis, and to compare synthetic treatments, including retinoids, antibiotics, and hormonal therapies, with natural approaches such as polyphenols, minerals, and resveratrol. The analysis highlights the therapeutic convergence of traditional pharmacology and bioactive natural compounds, proposing microbiome-conscious and sustainable strategies for future acne management.},
}

Humans
*Acne Vulgaris/microbiology/drug therapy/pathology/etiology
*Microbiota/drug effects
*Skin/microbiology/drug effects/pathology
*Biological Products/therapeutic use/pharmacology
Anti-Bacterial Agents/therapeutic use/pharmacology
Dysbiosis
Animals

@article {pmid41471248,
year = {2025},
author = {Shi, X and Bi, N and Liu, W and Ma, L and Liu, M and Xu, T and Shu, X and Gao, L and Wang, R and Chen, Y and Li, L and Zhu, Y and Li, D},
title = {Identification of Oral Microbiome Biomarkers Associated with Lung Cancer Diagnosis and Radiotherapy Response Prediction.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/pathogens14121294},
pmid = {41471248},
issn = {2076-0817},
support = {NCC202416006//National High Level Hospital Clinical Research Funding and National Cancer Center Climbing Fund/ ; 2023ZD0502100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Lung Neoplasms/radiotherapy/diagnosis/microbiology ; Male ; Female ; Middle Aged ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Aged ; Biomarkers ; *Bacteria/classification/genetics/isolation & purification ; Prognosis ; Biomarkers, Tumor ; },
abstract = {The oral cavity acts as the anatomical gateway to the respiratory tract, sharing both microbiological and pathophysiological links with the lower airways. Although radiotherapy is a cornerstone treatment for lung cancer, reliable oral microbiome biomarkers for predicting patient outcomes remain lacking. We analyzed the oral microbiome of 136 lung cancer patients and 199 healthy controls across discovery and two validation cohorts via 16S rRNA sequencing. Healthy controls exhibited a significantly higher abundance of Streptococcus compared to patients (p = 0.049, p < 0.001, p < 0.001, respectively). The structure of the microbial community exhibited substantial dynamic changes during treatment. Responders showed enrichment of Rothia aeria (p = 0.027) and Prevotella salivae (p = 0.043), associated with prolonged overall survival (OS) and progression-free survival (PFS), whereas non-responders exhibited elevated Porphyromonas endodontalis (p = 0.037) correlating with shorter OS and PFS. According to Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2) analysis, Akkermansia and Alistipes were nearly absent in non-responders, while Desulfovibrio and Moraxella were virtually absent in responders. A diagnostic model based on Streptococcus achieved area under the curve (AUC) values of 0.85 (95% CI: 0.78-0.91) and 0.99 (95% CI: 0.98-1) in the validation cohorts, and a response prediction model incorporating Prevotella salivae and Neisseria oralis yielded an AUC of 0.74 (95% CI: 0.58-0.90). Furthermore, in small cell lung cancer, microbiota richness and diversity were inversely correlated with Eastern Cooperative Oncology Group (ECOG) performance status (p = 0.008, p < 0.001, respectively) and pro-gastrin-releasing peptide (ProGRP) levels (p = 0.065, p = 0.084, respectively). These results demonstrate that lung cancer-associated oral microbiota signatures dynamically reflect therapeutic response and survival outcomes, supporting their potential role as non-invasive biomarkers for diagnosis and prognosis.},
}

Humans
*Microbiota/genetics
*Lung Neoplasms/radiotherapy/diagnosis/microbiology
Male
Female
Middle Aged
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics
Aged
Biomarkers
*Bacteria/classification/genetics/isolation & purification
Prognosis
Biomarkers, Tumor

@article {pmid41471188,
year = {2025},
author = {Nikolić, N and Pucar, A and Tomić, U and Petrović, S and Mihailović, Đ and Jovanović, A and Radunović, M},
title = {Oral Microbiota and Carcinogenesis: Exploring the Systemic Impact of Oral Pathogens.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/pathogens14121233},
pmid = {41471188},
issn = {2076-0817},
support = {2019-191//eklund foundation/ ; 451-03-137/2025-03/200129//Ministry of Science, Technological Development and Innovations of the Republic of Serbia/ ; 03-136/2025-03/200129//Ministry of Science, Technological Development and Innovations of the Republic of Serbia/ ; },
mesh = {Humans ; *Mouth/microbiology ; *Microbiota ; *Carcinogenesis ; *Neoplasms/microbiology/etiology ; *Dysbiosis/microbiology/complications ; Fusobacterium nucleatum/pathogenicity ; Animals ; },
abstract = {For decades, cancer risk has been explained mainly by local factors. However, emerging evidence shows that the oral microbiome acts as a systemic modifier of oncogenesis well beyond the head and neck. This review synthesizes clinical and mechanistic data linking dysbiotic oral communities, especially Porphyromonas gingivalis, Fusobacterium nucleatum, and Treponema denticola, to malignancies across gastrointestinal, respiratory, hepatobiliary, pancreatic, breast, and urogenital systems. We summarize organ-specific associations from saliva, tissue, and stool studies, noting the recurrent enrichment of oral taxa in tumor and peri-tumoral niches of oral, esophageal, gastric, colorectal, lung, pancreatic, liver, bladder, cervical, and breast cancers. Convergent mechanisms include the following: (i) persistent inflammation (lypopolysacharide, gingipains, cytolysins, and collagenases); (ii) direct genotoxicity (acetaldehyde, nitrosation, and CDT); (iii) immune evasion/suppression (TLR/NLR signaling, MDSC recruitment, TAN/TAM polarization, and TIGIT/CEACAM1 checkpoints); and (iv) epigenetic/signaling rewiring (NF-κB, MAPK/ERK, PI3K/AKT, JAK/STAT, WNT/β-catenin, Notch, COX-2, and CpG hypermethylation). Plausible dissemination along an oral-gut-systemic axis, hematogenous, lymphatic, microaspiration, and direct mucosal transfer enables distal effects. While causality is not yet definitive, cumulative data support oral dysbiosis as a clinically relevant cofactor, motivating biomarker-based risk stratification, saliva/stool assays for early detection, and microbiome-targeted interventions (periodontal care, antimicrobials, probiotics, and microbiota modulation) alongside conventional cancer control.},
}

Humans
*Mouth/microbiology
*Microbiota
*Carcinogenesis
*Neoplasms/microbiology/etiology
*Dysbiosis/microbiology/complications
Fusobacterium nucleatum/pathogenicity
Animals

@article {pmid41471163,
year = {2025},
author = {Ziaka, M},
title = {Targeting Gut-Lung Crosstalk in Acute Respiratory Distress Syndrome: Exploring the Therapeutic Potential of Fecal Microbiota Transplantation.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/pathogens14121206},
pmid = {41471163},
issn = {2076-0817},
mesh = {*Respiratory Distress Syndrome/therapy/microbiology ; Humans ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; *Lung/microbiology/immunology ; Animals ; *Gastrointestinal Tract/microbiology ; },
abstract = {The gastrointestinal (GI) tract contributes significantly to the pathogenesis of acute respiratory distress syndrome (ARDS) by influencing systemic inflammation and sepsis, which are key factors in the development of multiple organ dysfunction syndrome (MODS), while the significant impact of gut microbiota in critically ill patients, including those with sepsis and ARDS, further underscores its importance. The intestinal microbiota is vital to immune system function, responsible for triggering around 80% of immune responses. Therefore, it may be hypothesized that modifying fecal microbiota, such as through fecal microbiota transplantation (FMT), could serve as a valuable therapeutic approach for managing inflammatory diseases like lung injury (LI)/ARDS. Indeed, emerging experimental research suggests that FMT may have beneficial effects in ARDS models by improving inflammation, oxidative stress, LI, and oxygenation. However, well-designed randomized clinical trials in patients with ARDS are still lacking. Our study seeks to examine how therapeutic interventions such as FMT might benefit LI/ARDS patients by exploring the interactions between the gut and lungs in this context.},
}

*Respiratory Distress Syndrome/therapy/microbiology
Humans
*Fecal Microbiota Transplantation/methods
*Gastrointestinal Microbiome
*Lung/microbiology/immunology
Animals
*Gastrointestinal Tract/microbiology

@article {pmid41471117,
year = {2025},
author = {Shuvo, MSH and Kim, S and Jo, S and Rahim, MA and Barman, I and Hossain, MS and Yoon, Y and Tajdozian, H and Ahmed, I and Atashi, A and Jeong, G and Suh, HS and You, J and Sung, C and Kim, M and Seo, H and Song, HY},
title = {Flavonifractor plautii as a Next-Generation Probiotic Enhancing the NGP F/P Index in a Simulated Human Gut Microbiome Ecosystem.},
journal = {Pharmaceutics},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/pharmaceutics17121603},
pmid = {41471117},
issn = {1999-4923},
support = {No. RS-2023-00219563//Ministry of Science and ICT/ ; Bio Workforce Training Program//Ministry of Trade, Industry, and Energy/ ; Soonchunhyang University Research Fund//Soonchunhyang University/ ; },
abstract = {Background/Objectives: Traditionally consumed fermented foods and lactic acid bacteria (LAB)-based products have primarily been investigated for their nutritional and health-promoting benefits as dietary supplements. More recently, research has advanced toward exploring their therapeutic potential in pharmaceutical development. However, reliance on conventional LAB strains despite their established safety and efficacy has led to saturation at the strain level, underscoring the need for next-generation probiotics (NGPs) with novel therapeutic potential. In this context, we identified Flavonifractor plautii from human feces as a candidate NGP and investigated its effects on the human gut microbiota. Methods: Whole-genome sequencing revealed distinct genetic features that supported its uniqueness, and the strain was designated PMC93. A human gut microbial ecosystem simulator was used to administer F. plautii daily for one week, after which microbial community changes were evaluated using 16S rRNA gene-based metagenomic sequencing. Results: The administration did not induce significant changes in alpha or beta diversity, suggesting that F. plautii does not disrupt overall bacterial community structure, thereby supporting its microbial community safety. Taxonomic analysis demonstrated a significant increase in the Firmicutes-to-Proteobacteria ratio (NGP F/P index). The improvement surpassed that of conventional LAB treatments and was consistently maintained under supplementation with commonly encountered pharmaceutical compounds and nutrients. The shift was associated with an increase in short-chain fatty acid (SCFA)-producing beneficial taxa and a decrease in pro-inflammatory and potentially pathogenic groups. Functional outcomes, including elevated SCFA levels and downregulation of inflammation-related gene expression, further corroborated these compositional changes. The strain also demonstrated safety in in vivo models. Conclusions: Collectively, these findings suggest that strain PMC93 is a promising NGP candidate with substantial therapeutic potential for microbiota-associated health and disease modulation, particularly due to its ability to enhance the NGP F/P index.},
}

@article {pmid41471111,
year = {2025},
author = {Holler, N and Ruseska, I and Schachner-Nedherer, AL and Zimmer, A and Petschacher, C},
title = {Oral Treatment of Obesity by GLP-1 and Its Analogs.},
journal = {Pharmaceutics},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/pharmaceutics17121596},
pmid = {41471111},
issn = {1999-4923},
abstract = {Obesity is a multifaceted disease that significantly increases the risk of various chronic conditions. GLP-1R (co)-agonists first emerged as therapeutics for treatment of type 2 diabetes mellitus and have since become an established drug class for improving glycemic control. The interest in GLP-1 for obesity treatment has surged in 2015 after the approval of Saxenda[®] (liraglutide). To date, GLP-1 analogs are primarily administered by s.c. injection, which poses a significant burden on patient compliance. To address this challenge, research has focused on oral delivery. This review provides a concise overview of the techniques explored to enhance the oral delivery of GLP-1 analogs for the treatment of obesity. Relevant strategies include the following: (1) the use of permeation enhancers to increase gastrointestinal absorption of peptides; (2) micro- and nanocarriers loaded with GLP-1, including targeted delivery systems and general techniques for active drug targeting; (3) GLP-1 gene delivery; and (4) advanced microbiome systems for GLP-1 delivery. The potential for misuse and side-effects of GLP-1 analogs are also discussed.},
}

@article {pmid41471101,
year = {2025},
author = {Tauser, RG and Vasincu, IM and Iacob, AT and Apotrosoaei, M and Profire, BȘ and Lupascu, FG and Chirliu, OM and Profire, L},
title = {A State-of-the-Art Overview on (Epi)Genomics and Personalized Skin Rejuvenating Strategies.},
journal = {Pharmaceutics},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/pharmaceutics17121585},
pmid = {41471101},
issn = {1999-4923},
abstract = {This article aims to point out new perspectives opened by genomics and epigenomics in skin rejuvenation strategies which target the main hallmarks of the ageing. In this respect, this article presents a concise overview on: the clinical relevance of the most important clocks and biomarkers used in skin anti-ageing strategy evaluation, the fundamentals, the main illustrating examples preclinically and clinically tested, the critical insights on knowledge gaps and future research perspectives concerning the most relevant skin anti-ageing and rejuvenation strategies based on novel epigenomic and genomic acquisitions. Thus the review dedicates distinct sections to: senolytics and senomorphics targeting senescent skin cells and their senescent-associated phenotype; strategies targeting genomic instability and telomere attrition by stimulation of the deoxyribonucleic acid (DNA) repair enzymes and proteins essential for telomeres' recovery and stability; regenerative medicine based on mesenchymal stem cells or cell-free products in order to restore skin-resided stem cells; genetically and chemically induced skin epigenetic partial reprogramming by using transcription factors or epigenetic small molecule agents, respectively; small molecule modulators of DNA methylases, histone deacetylases, telomerases, DNA repair enzymes or of sirtuins; modulators of micro ribonucleic acid (miRNA) and long-non-coding ribonucleic acid (HOTAIR's modulators) assisted or not by CRISPR-gene editing technology (CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats); modulators of the most relevant altered nutrient-sensing pathways in skin ageing; as well as antioxidants and nanozymes to address mitochondrial dysfunctions and oxidative stress. In addition, some approaches targeting skin inflammageing, altered skin proteostasis, (macro)autophagy and intercellular connections, or skin microbiome, are very briefly discussed. The review also offers a comparative analysis among the newer genomic/epigenomic-based skin anti-ageing strategies vs. classical skin rejuvenation treatments from various perspectives: efficacy, safety, mechanism of action, evidence level in preclinical and clinical data and regulatory status, price range, current limitations. In these regards, a concise overview on senolytic/senomorphic agents, topical nutrigenomic pathways' modulators and DNA repair enzymes, epigenetic small molecules agents, microRNAs and HOTAIRS's modulators, is illustrated in comparison to classical approaches such as tretinoin and peptide-based cosmeceuticals, topical serum with growth factors, intense pulsed light, laser and microneedling combinations, chemical peels, botulinum toxin injections, dermal fillers. Finally, the review emphasizes the future research directions in order to accelerate the clinical translation of the (epi)genomic-advanced knowledge towards personalization of the skin anti-ageing strategies by integration of individual genomic and epigenomic profiles to customize/tailor skin rejuvenation therapies.},
}

@article {pmid41470907,
year = {2025},
author = {Sekikawa, A and Weaver, A and Mroz, K and Heilmann, NZ and Madrid Fuentes, DA and Koltun, KJ and Carlson, LJ and Cattell, KL and Li, M and Li, J and Hughes, TM and Strotmeyer, E and Nindl, B and Cauley, JA},
title = {S-Equol as a Gut-Derived Phytoestrogen Targeting Estrogen Receptor β: A Promising Bioactive Nutrient for Bone Health in Aging Women and Men: A Narrative Review.},
journal = {Nutrients},
volume = {17},
number = {24},
pages = {},
doi = {10.3390/nu17243962},
pmid = {41470907},
issn = {2072-6643},
support = {R01 AG074971/AG/NIA NIH HHS/United States ; P30 AG021332/AG/NIA NIH HHS/United States ; P30 AG024827/AG/NIA NIH HHS/United States ; 1S10AG030295-01A1/NH/NIH HHS/United States ; 5UM1TR004929-02/NH/NIH HHS/United States ; },
mesh = {Humans ; *Equol/pharmacology/metabolism ; *Phytoestrogens/pharmacology ; *Estrogen Receptor beta/metabolism/agonists ; Male ; Female ; *Osteoporosis/prevention & control/drug therapy ; Animals ; *Bone and Bones/drug effects/metabolism ; Gastrointestinal Microbiome ; Isoflavones/metabolism ; Bone Density/drug effects ; *Aging ; Aged ; },
abstract = {Background/Objectives: Osteoporosis is highly prevalent and contributes substantially to morbidity and mortality, yet long-term concerns about pharmacologic therapies leave a major treatment gap. Soy isoflavones have been investigated as safer alternatives, but results across trials are inconsistent. A key unresolved issue is the equol-producer phenotype, the gut microbial ability to convert daidzein to S-equol, the most bioactive isoflavone metabolite, which may explain much of this variability. This narrative review synthesizes mechanistic, translational, and clinical evidence to clarify the potential skeletal relevance of S-equol. Methods: Literature was identified through PubMed and Scopus searches (January 2000-October 2025) for experimental, mechanistic, and clinical studies examining S-equol, estrogen receptor β (ERβ), and bone metabolism, with emphasis on equol-producing status, bone strength and bone microarchitecture. Results: S-equol acts as a high-affinity ERβ agonist with antioxidant and anti-inflammatory properties but lacks the carcinogenic or thrombotic risks linked to ERα activation. In estrogen-deficient rodent models, S-equol improves trabecular bone volume by 10-20%, increases trabecular number, and enhances biomechanical strength. These findings align with preclinical evidence demonstrating that S-equol preserves trabecular microarchitecture, enhances bone strength, and reduces bone turnover. A limited number of human trials show reductions in bone resorption by 20% at a daily dose of 10 mg S-equol. In contrast, trials of soy isoflavones in humans have produced inconsistent findings, partly because of substantial variability in equol-producer phenotype among participants and the reliance on dual-energy X-ray absorptiometry, which cannot distinguish trabecular from cortical compartments. Advanced bone imaging and microbiome-informed approaches enable the precise evaluation of S-equol's skeletal effects on trabecular bone and cortical bone, separately. Conclusions: S-equol represents a promising model for "precision nutrition," where microbiome, hormonal, and host factors converge with potential to prevent age-related bone fragility. Rigorous trials that integrate microbiome phenotyping and advanced imaging are needed to validate this approach, translate mechanistic promise into clinical benefit, and better define safety.},
}

Humans
*Equol/pharmacology/metabolism
*Phytoestrogens/pharmacology
*Estrogen Receptor beta/metabolism/agonists
Male
Female
*Osteoporosis/prevention & control/drug therapy
Animals
*Bone and Bones/drug effects/metabolism
Gastrointestinal Microbiome
Isoflavones/metabolism
Bone Density/drug effects
*Aging
Aged

@article {pmid41470885,
year = {2025},
author = {Jung, SH and Hwang, S and Seo, KH and Park, Y and Kim, MJ and Kim, H},
title = {Bioconversion-Based Postbiotics Enhance Muscle Strength and Modulate Gut Microbiota in Healthy Individuals: A Randomized, Double-Blind, Placebo-Controlled Trial.},
journal = {Nutrients},
volume = {17},
number = {24},
pages = {},
doi = {10.3390/nu17243937},
pmid = {41470885},
issn = {2072-6643},
support = {Otoki Ham Taiho Foundation//Otoki Ham Taiho Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Double-Blind Method ; Male ; Adult ; Female ; *Muscle Strength/drug effects ; *Whey Proteins/administration & dosage ; Young Adult ; Feces/microbiology ; Hand Strength ; Healthy Volunteers ; Dietary Supplements ; Biomarkers/blood ; },
abstract = {BACKGROUND: Postbiotics produced by kefir lactic acid bacteria through bioconversion of polyphenol-rich extract and whey protein are emerging as promising modulators of gut microbiota and muscle health. This study investigated whether Lentilactobacillus kefiri DH5-derived postbiotics, prepared with Cucumis melo L. and whey protein (KP, Kefir lactic acid bacteria-derived postbiotics), improve muscle strength and gut microbiota composition in healthy adults.

METHODS: In this 12-week, randomized, double-blind, placebo-controlled trial, participants consumed either KP (6 g/day) or placebo. Handgrip strength, circulating biomarkers, and fecal microbiota profiling (using 16S rRNA sequencing) were analyzed. Correlations between microbial taxa and muscle-related biomarkers were assessed.

RESULTS: KP supplementation significantly increased dominant-hand grip strength and plasma irisin and reduced IL-1β concentrations after 12 weeks, whereas IGF-1, lean mass, and non-dominant grip strength showed no significant changes. Gut microbiota profiling revealed enrichment of Bifidobacterium adolescentis, Latilactobacillus sakei, Lentihominibacter hominis, Mediterraneibacter gnavus, Streptococcus anginosus and Phocaeicola plebeius, with concomitant reductions in Lachnospira eligens, Roseburia inulinivorans, Ruthenibacterium lactatiformans and Vescimonas fastidiosa. Notably, relative abundance of Faecalibacterium prausnitzii was positively correlated with plasma irisin concentration.

CONCLUSIONS: KP supplementation produced a modest within-group improvement in grip strength, potentially through gut-muscle axis modulation involving irisin and anti-inflammation pathways. These preliminary findings suggest that kefir-derived postbiotics may have potential relevance for muscle health.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Double-Blind Method
Male
Adult
Female
*Muscle Strength/drug effects
*Whey Proteins/administration & dosage
Young Adult
Feces/microbiology
Hand Strength
Healthy Volunteers
Dietary Supplements
Biomarkers/blood

@article {pmid41470864,
year = {2025},
author = {Torres-Mejías, J and Arriaza, K and Mena, F and Rivarola, E and Paredes, P and Ahmad, H and López, I and Soza, D and Pino-Villalón, JL and López-Espinoza, MÁ and Duran-Agüero, S and Merellano-Navarro, E},
title = {Body Composition, Microbiome and Physical Activity in Workers Under Intermittent Hypobaric Hypoxia.},
journal = {Nutrients},
volume = {17},
number = {24},
pages = {},
doi = {10.3390/nu17243919},
pmid = {41470864},
issn = {2072-6643},
mesh = {Humans ; *Body Composition/physiology ; *Exercise/physiology ; Adult ; Male ; *Gastrointestinal Microbiome/physiology ; *Hypoxia/physiopathology/microbiology ; Nutritional Status ; Energy Metabolism ; Female ; Electric Impedance ; Body Mass Index ; Middle Aged ; Feces/microbiology ; },
abstract = {Background/Objectives: Intermittent hypobaric hypoxia (IHH) induces various physiological and metabolic adaptations. This study aimed to investigate the effects of a seven-day IHH exposure on nutritional status, body composition, gut microbiota, movement intensity, and energy expenditure in 10 workers. Methods: A pre-post comparative design was employed, with measurements taken at the beginning and end of the exposure period. Nutritional status, body composition, and phase angle (PhA) were assessed via bioelectrical impedance analysis (BIA). Gut microbiota composition was analyzed through fecal DNA extraction and qPCR for specific bacterial families. Movement intensity and energy expenditure were monitored using accelerometry. An initial statistical analysis was performed, which included paired t-tests and Wilcoxon signed-rank tests. Results: A significant increase in PhA (mean difference: 0.40; p = 0.0053 for t-test, p = 0.0136 for Wilcoxon) and a significant decrease in BMI (mean difference: -0.38; p = 0.0311 for t-test, p = 0.0546 for Wilcoxon). Conclusions: While the original paper reported no significant changes in nutritional status or body composition, our re-analysis suggests a significant change in BMI. The original paper also reported significant changes in specific gut bacterial families (butyrate-producing bacteria, p = 0.037; Lactobacillus species, p = 0.006). Physical activity levels remained consistently low.},
}

Humans
*Body Composition/physiology
*Exercise/physiology
Adult
Male
*Gastrointestinal Microbiome/physiology
*Hypoxia/physiopathology/microbiology
Nutritional Status
Energy Metabolism
Female
Electric Impedance
Body Mass Index
Middle Aged
Feces/microbiology

@article {pmid41470852,
year = {2025},
author = {Stumpf, KA and Green, M and Niu, X and Lu, D and Gan, S and Zhan, X and Maxey, MN and Boren, M and Nayak, SP and Jaleel, S and Brown, LS and Foster, JA and Mirpuri, J},
title = {Gut Microbiome Composition and Variance Are Modified by Degree of Growth Failure in Preterm Infants: A Prospective Study.},
journal = {Nutrients},
volume = {17},
number = {24},
pages = {},
doi = {10.3390/nu17243907},
pmid = {41470852},
issn = {2072-6643},
support = {R01 DK121975/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Prospective Studies ; Infant, Newborn ; *Infant, Premature/growth & development ; Feces/microbiology ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Infant ; Clostridium/isolation & purification ; Gestational Age ; Bifidobacterium/isolation & purification ; *Growth Disorders/microbiology ; Intensive Care Units, Neonatal ; },
abstract = {Background/Objectives: Preterm infants often require increased caloric intake to maintain appropriate growth while in the neonatal intensive care unit (NICU). Emerging evidence suggests that alterations of the gut microbiome may play a role in infant and childhood growth patterns. The fecal microbiome patterns in infants with normal and poor growth patterns were classified in this study. Methods: We conducted a prospective trial of infants of less than 29 weeks' gestation with an embedded case-control analysis of infants with normal or poor growth patterns. Fecal samples were collected weekly from infants on full enteral feeds and analyzed blindly using 16s rRNA next-generation sequencing. The relationship between gut microbial diversity and composition and growth pattern and trajectory were assessed. Results: A total of 115 infants were enrolled in the trial with 263 fecal samples selected from 87 enrolled infants for analysis. In total, 37 samples were available from the normal growth cohort, 56 samples from the poor growth cohort, and 170 samples were available for analysis from the very poor growth cohort. Analysis of relative abundance revealed increased representation of Veillonella, Bifidobacterium, and Clostridium in very poor growth infants compared to normal growth infants. Variation in specific taxa was also found to vary significantly across post-menstrual age depending on the degree of growth failure. Conclusions: Gut microbiome composition and variance was modified by the degree of growth failure in our cohort of preterm infants. Our study adds to the growing body of evidence that alteration of the microbiome is associated with poor growth in preterm infants. This may ultimately represent a therapeutic target for growth failure in preterm infants.},
}

Humans
*Gastrointestinal Microbiome
Prospective Studies
Infant, Newborn
*Infant, Premature/growth & development
Feces/microbiology
Male
Female
RNA, Ribosomal, 16S/genetics
Case-Control Studies
Infant
Clostridium/isolation & purification
Gestational Age
Bifidobacterium/isolation & purification
*Growth Disorders/microbiology
Intensive Care Units, Neonatal

@article {pmid41470806,
year = {2025},
author = {Black, EG and Bugarcic, A and Lauche, R and El-Omar, E and El-Assaad, F},
title = {The Effects of Kefir on the Human Oral and Gut Microbiome.},
journal = {Nutrients},
volume = {17},
number = {24},
pages = {},
doi = {10.3390/nu17243861},
pmid = {41470806},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Kefir/microbiology ; *Mouth/microbiology ; Probiotics ; Functional Food ; },
abstract = {Kefir, a fermented probiotic drink made from milk, water, or plant-based ingredients, has gained significant attention as a dietary supplement. Originating from the Caucasus Mountains over three thousand years ago, kefir is believed to harbor a range of health benefits through its ability to alter the composition of microbial niches within the human body. These microbial niches are called microbiomes and encompass the collective community of microbial organisms, their genomes and environment. The modern commercialization of kefir has driven the need for high-quality research into its impact on the human microbiome and associated health outcomes; however, there is currently very limited scientific evidence supporting effects of kefir consumption on the human oral and gut microbiome. High-quality human clinical trials are essential to establish the safety and effectiveness of kefir before it can be advised for use in treating conditions linked to the oral and gut microbiota or metabolic health. This literature review aims to critically analyze recent studies investigating the effect of kefir consumption on the oral and gut microbiome, as well as its potential implications for human health. By examining kefir's effects on these interconnected microbial ecosystems, we can better understand its potential and limitations as a functional food for promoting systemic health.},
}

Humans
*Gastrointestinal Microbiome
*Kefir/microbiology
*Mouth/microbiology
Probiotics
Functional Food

@article {pmid41470796,
year = {2025},
author = {Zhu, W and Edirisuriya, P and Ai, Q and Yang, F and Tang, J and Nie, K and Ji, X and Soltanieh, S and Musarrat, M and Alim, MA and Liao, Z and Zhou, K},
title = {C. cochlearium 2316 Ameliorates High-Fat Diet-Induced Obesity and Metabolic Syndrome Risk Factors via Enhanced Energy Expenditure and Glucose Homeostasis.},
journal = {Nutrients},
volume = {17},
number = {24},
pages = {},
doi = {10.3390/nu17243848},
pmid = {41470796},
issn = {2072-6643},
mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Obesity/etiology/metabolism ; *Energy Metabolism/drug effects ; Mice, Inbred C57BL ; *Metabolic Syndrome/etiology/prevention & control ; *Probiotics/pharmacology/administration & dosage ; Mice ; Male ; Homeostasis ; *Blood Glucose/metabolism ; Risk Factors ; Insulin/blood ; Insulin Resistance ; },
abstract = {OBJECTIVES: This study investigated the potential beneficial effects of a probiotic candidate, Clostridium cochlearium 2316, in modulating physiological and metabolic markers in mice with high-fat diet-induced obesity (DIO).

METHODS: C57BL/6 DIO mice were assigned to three groups (ad libitum): standard low-fat control (LF, 10% fat), high-fat diet (HF, 60% fat), and high-fat diet supplemented with approximately one billion CFU/day of CC2316 via daily oral gavage for 16 weeks.

RESULTS: After 16 weeks, the CC group exhibited 17.3% lower body weight gain (p < 0.001) and significant fat mass decrease (p < 0.0001) compared to HF mice. Serum biochemistry showed that CC2316 supplementation resulted in a 27.7% reduction in fasting blood glucose (p < 0.05), a 58.4% reduction in fasting insulin (p < 0.01), and an 89.4% improvement in HOMA-IR score (p < 0.05). Furthermore, serum total cholesterol level decreased dramatically by 40.2% in the CC group (p < 0.001). Despite a higher caloric absorption rate (p < 0.001), CC mice demonstrated a significant beneficial shift in energy expenditure, characterized by an increased basal metabolic rate (p < 0.05), higher energy expenditure (p < 0.05), and an elevated respiratory quotient (RER) (p < 0.05), alongside increased physical activity (p < 0.05).

CONCLUSIONS: This investigation strongly suggests that CC2316 supplementation mitigates the adverse effects of HFD-induced obesity by modulating whole-body energy metabolism, positioning it as a potential aid to lower risk factors associated with metabolic syndrome. The precise mechanisms linking the gut microbiome to altered energy substrate utilization are discussed and suggested for further investigation.},
}

Animals
*Diet, High-Fat/adverse effects
*Obesity/etiology/metabolism
*Energy Metabolism/drug effects
Mice, Inbred C57BL
*Metabolic Syndrome/etiology/prevention & control
*Probiotics/pharmacology/administration & dosage
Mice
Male
Homeostasis
*Blood Glucose/metabolism
Risk Factors
Insulin/blood
Insulin Resistance

@article {pmid41470771,
year = {2025},
author = {Polyzou, M and Goules, AV and Tzioufas, AG},
title = {The Role of Nutrition in the Development, Management, and Prevention of Rheumatoid Arthritis: A Comprehensive Review.},
journal = {Nutrients},
volume = {17},
number = {24},
pages = {},
doi = {10.3390/nu17243826},
pmid = {41470771},
issn = {2072-6643},
mesh = {Humans ; *Arthritis, Rheumatoid/prevention & control/etiology ; Diet, Mediterranean ; *Diet/adverse effects ; *Nutritional Status ; Risk Factors ; Fatty Acids, Omega-3/administration & dosage ; },
abstract = {Background: Rheumatoid arthritis (RA) is a chronic autoimmune disease, with key features being synovial hyperplasia, autoantibody production, and ultimately cartilage and bone destruction. The pathogenesis of rheumatoid arthritis (RA) is not fully understood, but it is estimated that genetic factors account for 50-60% of the risk, with the remainder attributed to environmental factors, including infectious agents, smoking, gut microbiota, and diet. Given that most current clinical trials on RA and nutrition are limited in sample size and duration, there is an unmet need for higher-quality studies in the future, a need that EULAR has already recognized. Objective: This article aims to investigate the impact of diet and nutritional factors on the development, progression, and potential prevention of RA. Specifically, it provides a comprehensive review of certain foods, such as alcohol, gluten, red meat, and saturated and trans fats, and their contribution to the onset and progression of rheumatoid arthritis (RA). In addition, it examines the effect of key anti-inflammatory nutrients in reducing the risk of RA, including olive oil, fatty fish, juices, and certain fruits. Finally, it discusses the potential protective effects of certain dietary patterns, such as the Mediterranean diet (MD) and diets rich in omega-3 polyunsaturated fatty acids (PUFAs). Methods: A comprehensive literature search was conducted in the PubMed/Medline, Science Direct, and Scopus databases (1990-2025). English-language observational studies, clinical trials, and systematic reviews addressing the relationship between diet and dietary patterns and RA were included. Results: High consumption of red and processed meat, saturated and trans fats, sugary drinks, and gluten (in vulnerable individuals) is associated with increased RA risk and greater disease activity, partly through pro-inflammatory pathways and gut dysbiosis. In contrast, regular intake of olive oil, fatty fish rich in omega-3 polyunsaturated fatty acids, fruit juices, cocoa, certain fruits, and vitamin D appears protective and may reduce disease activity and symptom severity. Adherence to anti-inflammatory dietary patterns, particularly the Mediterranean diet and diets rich in omega-3 fatty acids, is consistently associated with a lower incidence of RA, reduced inflammatory markers, and improved clinical outcomes. However, most available studies are limited by small sample sizes, short duration, heterogeneous methodologies, and potential confounding by other lifestyle factors (e.g., smoking, obesity). Conclusions: Although an appropriate diet and dietary habits cannot replace pharmacological therapy, current knowledge supports the inclusion of an anti-inflammatory diet as an adjunct strategy in the prevention and management of RA. The relatively limited studies that have been conducted suggest that high-quality, large-scale, prospective studies are needed to prevent and treat RA. These studies should incorporate genetic, microbiome, and long-term clinical endpoints, so as to establish definitive dietary recommendations and allow for personalized nutritional interventions for patients with RA.},
}

Humans
*Arthritis, Rheumatoid/prevention & control/etiology
Diet, Mediterranean
*Diet/adverse effects
*Nutritional Status
Risk Factors
Fatty Acids, Omega-3/administration & dosage

@article {pmid41470606,
year = {2025},
author = {Karpova, D and Belkina, D and Porotikova, E and Yurchenko, E and Vinogradova, S},
title = {Metagenomic Study of the Grapevine Decline Detected a Cocktail of Fungi Associated with Grapevine Trunk Diseases.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {24},
pages = {},
pmid = {41470606},
issn = {2223-7747},
support = {23-16-00232//Russian Science Foundation/ ; 00000//Ministry of Education and Science of Russian Federation/ ; },
abstract = {This study analyzed the microbiome of three varieties differing in genotype and technical purpose: Cristal, Riesling, and Avgustin, all exhibiting decline symptoms of unknown etiology. A total of 92 symptomatic and asymptomatic grapevines were analyzed using ITS and 16S rRNA amplicon sequencing and molecular genetic methods. Phytoplasmas and the pathogenic bacteria Xylella fastidiosa and Xylophilus ampelinus were not present in the samples. The decline symptoms were associated with a cocktail of fungal pathogens that cause grapevine trunk diseases. In particular, the analysis revealed the causative agents of Botryosphaeria dieback (Sphaeropsis spp. and Botryosphaeria spp.), fungi associated with the Esca complex (Phaeomoniella spp., Phaeoacremonium spp., Inonotus spp., Seimatosporium spp., Stereum spp., and Cadophora spp.), and the causative agents of Phomopsis dieback (Diaporthe spp.). The symptoms of decline may be increased by several facultative grapevine pathogens that have been identified in microbiome (genera Stemphylium, Alternaria, Aspergillus, Penicillium, Talaromyces, and Fusarium). The metagenomic data of the grapevine microbiome provides opportunities for developing disease control strategies, which is important for the sustainable management of vineyards.},
}

@article {pmid41470243,
year = {2025},
author = {Kayer, A and Özen, A and Dinleyici, EÇ},
title = {Urinary Microbiota Composition in Treatment-Naïve Bladder Cancer: A Case-Control Study with Tumor Invasiveness Stratification.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {12},
pages = {},
pmid = {41470243},
issn = {1648-9144},
support = {2599//Eskişehir Osmangazi University/ ; },
mesh = {Humans ; *Urinary Bladder Neoplasms/microbiology/urine/pathology ; Male ; Female ; Case-Control Studies ; Middle Aged ; Aged ; *Microbiota/physiology ; RNA, Ribosomal, 16S/analysis ; *Urine/microbiology ; Neoplasm Invasiveness ; },
abstract = {Background and Objectives: Emerging evidence suggests that the genitourinary microbiota may influence the development and progression of urological malignancies, including bladder cancer. This study aimed to characterize the urinary microbiota at diagnosis in patients with bladder cancer and compare findings with healthy controls. Materials and Methods: Urine samples were collected from 30 patients with treatment-naïve bladder cancer and 20 age- and sex-matched healthy individuals. Microbiota composition was analyzed using 16S rRNA sequencing, and subgroup comparisons were made between muscle-invasive bladder cancer (MIBC) and non-muscle-invasive bladder cancer (NMIBC). Differentially abundant taxa were identified using linear discriminant analysis effect size (LEfSe) with an LDA threshold > 2 and p < 0.05. Results: No significant differences were observed in alpha or beta diversity between patients and controls or between MIBC and NMIBC. At the phylum level, Firmicutes was dominant in both groups but relatively more abundant in bladder cancer cases. Enterococcus was the most abundant genus in the cancer group (35.0%) and especially in MIBC (58.0%), while Lactobacillus was more prevalent in healthy controls (19.8% vs. 9.5%). At the species level, Veillonella dispar was notably enriched in MIBC cases (70.9%) compared to NMIBC (3.9%). LEfSe analysis revealed significant enrichment of Ralstonia, Microbacterium, and Facklamia in patients with bladder cancer, while Parvimonas, Sneathia, Gemella, and Acinetobacter guillouiae were more abundant in controls. Conclusions: These findings highlight preliminary microbiota differences associated with bladder cancer and tumor invasiveness; however, the results are exploratory and larger studies are required to evaluate their diagnostic or clinical relevance.},
}

Humans
*Urinary Bladder Neoplasms/microbiology/urine/pathology
Male
Female
Case-Control Studies
Middle Aged
Aged
*Microbiota/physiology
RNA, Ribosomal, 16S/analysis
*Urine/microbiology
Neoplasm Invasiveness

@article {pmid41470224,
year = {2025},
author = {Tatarciuc, D and Ghica, DC and Darnea, M and Esanu, IM and Vasluianu, RI and Stamatin, O and Indrei, L and Antohe, M and Lupu, IC and Bobu, L and Dima, AM},
title = {Beyond H. pylori: Re-Examining the Oral Microbiome's Role in Gastric Health and Disease, a Narrative Review.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {12},
pages = {},
pmid = {41470224},
issn = {1648-9144},
mesh = {Humans ; Helicobacter pylori/pathogenicity ; *Helicobacter Infections/complications/microbiology ; *Microbiota/physiology ; Dysbiosis/microbiology/complications ; Oral Health/standards ; Gastritis/microbiology ; Periodontitis/microbiology/complications ; *Mouth/microbiology ; Risk Factors ; },
abstract = {Background: The separation between oral and systemic health is increasingly challenged. Globally prevalent inflammatory diseases such as gastritis, often caused by Helicobacter pylori (H. pylori), and oral pathologies like periodontitis may be interconnected through microbial and inflammatory pathways. Objective: This review synthesizes evidence on the dental-gastric link, examining mechanistic pathways and clinical implications. Methods: A structured literature search identified key studies from 2000 to 2025, prioritizing systematic reviews and high-quality human research. Findings: Three key mechanistic pathways link oral dysbiosis with gastric pathology: (1) the direct translocation of oral pathogens to the stomach, including H. pylori and the broader dysbiotic oral microbiome; (2) the systemic inflammatory spillover from the periodontium, which primes the host immune system and exacerbates gastric inflammation; and (3) ancillary mechanisms such as the disruption of beneficial nitrate-nitrite-nitric oxide metabolism. Epidemiological studies show strong associations, and initial interventional trials indicate periodontal therapy may improve H. pylori eradication rates and reduce recurrence. However, the evidence is tempered by methodological limitations, including profound confounding by shared risk factors (e.g., smoking, socioeconomic status), the challenge of reverse causality, and inconsistent results from interventional studies. Conclusion: While confounding factors require consideration, oral health is a promising modifiable risk factor for gastritis. Interdisciplinary collaboration between dentistry and gastroenterology is essential to advance research and integrate oral care into gastrointestinal disease management.},
}

Humans
Helicobacter pylori/pathogenicity
*Helicobacter Infections/complications/microbiology
*Microbiota/physiology
Dysbiosis/microbiology/complications
Oral Health/standards
Gastritis/microbiology
Periodontitis/microbiology/complications
*Mouth/microbiology
Risk Factors

@article {pmid41470214,
year = {2025},
author = {Kahraman, T and Ayaz, A},
title = {Dietary Phytonutrients in Fibromyalgia: Integrating Mechanisms, Biomarkers, and Clinical Evidence-A Narrative Review.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {12},
pages = {},
pmid = {41470214},
issn = {1648-9144},
mesh = {Humans ; *Fibromyalgia/diet therapy/physiopathology ; Biomarkers/analysis/blood ; *Phytochemicals/therapeutic use/pharmacology ; Oxidative Stress/drug effects ; },
abstract = {Background and Objectives: Fibromyalgia (FM) is associated with chronic pain, oxidative stress, low-grade inflammation, and disturbances in signalling along the gut-brain axis. These pathways may be modulated by plant-derived phytonutrients. This narrative review summarises mechanistic and clinical evidence on phytonutrient-based strategies in FM. Materials and Methods: Following SANRA guidelines, we searched PubMed, Web of Science, Scopus and ScienceDirect for human and relevant preclinical studies published between 2005 and October 2025 that evaluated phytonutrient-rich dietary patterns or isolated bioactives in relation to FM symptoms or underlying mechanisms. Results: There is a consistent association between FM and increased oxidative damage and reduced antioxidant defences. Adopting plant-based diets, particularly Mediterranean-type and low-FODMAP diets, has been linked to improvements in pain, fatigue, sleep, and gastrointestinal symptoms, as well as modest gains in quality of life. However, the effects on inflammatory markers are conflicting. Trials of selected bioactive compounds, such as coenzyme Q10, curcumin-based formulations, L-carnitine and certain probiotics, suggest beneficial effects on symptoms, whereas others show little or no effect. Studies of the microbiome indicate a loss of butyrate-producing bacteria and altered microbial metabolites. Early dietary or probiotic interventions may partially mitigate these changes to some extent. Preclinical studies have identified SIRT1 as a potential mediator, but there is a lack of human data. Reporting on safety, dosage and formulation is often inadequate. Conclusions: Given the narrative design of this review and the methodological heterogeneity of the included studies, the overall certainty of the evidence cannot be formally graded and should be regarded as limited and heterogeneous. Nevertheless, current data supports phytonutrient-rich, food-based approaches as adjuncts rather than alternatives to standard FM care. Well-designed randomised trials with standardised outcomes and reporting of dose, formulation and relevant biomarkers are needed to identify the most effective strategies and the patient subgroups most likely to benefit.},
}

Humans
*Fibromyalgia/diet therapy/physiopathology
Biomarkers/analysis/blood
*Phytochemicals/therapeutic use/pharmacology
Oxidative Stress/drug effects

@article {pmid41470154,
year = {2025},
author = {Tjiu, JW and Lu, CF},
title = {Oral Probiotics in Acne vulgaris: A Systematic Review and Meta-Analysis of Double-Blind Randomized Clinical Trials.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {12},
pages = {},
pmid = {41470154},
issn = {1648-9144},
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; *Acne Vulgaris/therapy/drug therapy ; Randomized Controlled Trials as Topic ; Double-Blind Method ; Administration, Oral ; Adolescent ; },
abstract = {Background and Objectives: Acne vulgaris is a prevalent chronic inflammatory skin condition affecting adolescents and young adults worldwide. Increasing concern regarding antimicrobial resistance has renewed interest in microbiome-modulating therapies, including oral probiotics. This systematic review and meta-analysis evaluated the efficacy and safety of oral probiotic supplementation for acne vulgaris using contemporary random-effects methods. Materials and Methods: Following PRISMA 2020 guidelines, we searched PubMed, Embase, Web of Science, and ClinicalTrials.gov through November 2025 without language restrictions. Eligible studies were double-blind randomized controlled trials (RCTs) comparing oral probiotics with placebo or standard therapy for ≥4 weeks and reporting quantitative acne severity outcomes. Risk of bias was assessed using RoB 2.0. Standardized mean differences (SMDs) were pooled using restricted maximum likelihood (REML) with Hartung-Knapp adjustment. Heterogeneity was summarized using I[2], τ[2] (95% CI), and 95% prediction intervals. Adverse events were extracted. Results: Three RCTs (n = 231) met eligibility criteria. Pooled analysis suggested a modest reduction in inflammatory lesion counts favoring probiotics (SMD -0.57; 95% CI -0.94 to -0.21), although heterogeneity was substantial (I[2] = 72%; τ[2] = 0.11). The 95% prediction interval (-1.25 to 0.11) indicated that future studies may plausibly observe no meaningful effect. Sensitivity analyses using the DerSimonian-Laird estimator produced comparable results. All trials reported good short-term tolerability with no serious adverse events. Risk of bias was low in two trials and of some concern in one. Certainty of evidence was rated low to moderate. Conclusions: Oral probiotics may modestly reduce acne severity as a generally safe, antibiotic-sparing adjunct; however, the current evidence base is small and heterogeneous, and the certainty of effect remains low-to-moderate. Larger, standardized RCTs are required before firm clinical recommendations can be made. Registration: PROSPERO CRD420251181388. Funding: This research received no external funding.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
*Acne Vulgaris/therapy/drug therapy
Randomized Controlled Trials as Topic
Double-Blind Method
Administration, Oral
Adolescent

@article {pmid41469665,
year = {2025},
author = {Zheng, SH and Li, KZ and Feng, G and Wang, YT and Wang, JN and Li, SQ and Sun, YD},
title = {Gut microbiota reshaping the pancreatic cancer immune microenvironment: new avenues for immunotherapy.},
journal = {Molecular cancer},
volume = {24},
number = {1},
pages = {313},
pmid = {41469665},
issn = {1476-4598},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Gastrointestinal Microbiome/immunology ; *Pancreatic Neoplasms/therapy/immunology/etiology/pathology/microbiology/metabolism ; *Immunotherapy/methods ; Animals ; Fecal Microbiota Transplantation ; },
abstract = {Pancreatic cancer remains one of the deadliest malignancies, primarily due to its highly immunosuppressive tumor microenvironment (TME) and poor response to conventional therapies. Increasing evidence highlights the gut microbiota as a pivotal regulator of antitumor immunity, modulating T cell activation, macrophage polarization, and dendritic cell function. Microbial communities and their metabolites can either inhibit or enhance immune surveillance, thereby influencing the efficacy of immunotherapies such as immune checkpoint inhibitors (ICIs) and CAR-T cell therapy. Approaches including dietary modulation, probiotics, fecal microbiota transplantation (FMT), and microbial metabolite supplementation show promise in restoring immune homeostasis and improving treatment outcomes. Additionally, gut microbiome profiling has emerged as a potential source of biomarkers for predicting therapeutic response and immune-related adverse events. This review summarizes current insights into microbiota-immune interactions in pancreatic cancer, emphasizes microbiome-targeted therapeutic strategies, and explores future opportunities for precision immunotherapy guided by microbial modulation.},
}

Humans
*Tumor Microenvironment/immunology
*Gastrointestinal Microbiome/immunology
*Pancreatic Neoplasms/therapy/immunology/etiology/pathology/microbiology/metabolism
*Immunotherapy/methods
Animals
Fecal Microbiota Transplantation

@article {pmid41469598,
year = {2025},
author = {Mbabazi, M and Kateete, DP and Nakazzi, F and Wandera, JN and Mutesi, N and Ocan, M and Biraro, IA and Abaasa, A and Johnson, WE and Wee, B and Muwonge, A},
title = {The impact of tuberculosis and its treatment on the lung and gut microbiota: a global systematic review, meta-analysis, and amplicon-based metagenomic meta-analysis.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-025-12369-1},
pmid = {41469598},
issn = {1471-2334},
}

@article {pmid41469399,
year = {2025},
author = {Fang, J and Wang, G and Zhang, C and Liu, G and Xu, J and Gao, Y and Guo, Y and Wang, X and Qiu, T},
title = {Conserved genotype-independent rhizobacteria promote maize growth.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00895-4},
pmid = {41469399},
issn = {2055-5008},
support = {TSXM202525//Exploratory Research Project of Beijing Academy of Agriculture and Forestry Sciences/ ; KJCX20251102//Special Program for Creative Ability of Beijing Academy of Agriculture and Forestry Sciences/ ; KJCX20230113//Special Program for Creative Ability of Beijing Academy of Agriculture and Forestry Sciences/ ; },
abstract = {Rhizosphere microbiomes play an essential role in promoting plant growth and health. Although host genotype is known to shape rhizosphere microbial communities, it remains unclear whether core microbial taxa can persist across genetically diverse hosts and contribute to plant performance. Here, we conducted a large-scale analysis of 1005 rhizosphere samples from 335 maize populations to investigate the effects of host genetic variation on rhizosphere microbiota. We observed significant genotype-dependent variation in both bacterial and fungal community diversity and composition. However, community assembly was predominantly governed by stochastic processes, suggesting an evolutionary conservation of rhizosphere microbiota across genotypes. Based on the hypothesis that core microbes may consistently associate with maize independent of genotypes, we identified a core bacterial taxon, ASV245 (Pseudomonas sp.), which was consistently enriched across all maize genotypes. The corresponding strain, designated as WY16, was isolated from maize roots and significantly promoted both stem and root growth by activating maize hormone signaling pathways. These findings highlight the persistence and functional roles of genotype-independent core microbes, deepening our understanding of plant-microbiome interactions and providing new insights for microbiome-based strategies in sustainable agriculture.},
}

@article {pmid41469282,
year = {2025},
author = {Grover, BT and Docimo, S and Shin, TH and Shope, T and Albaugh, VL and Byers, R and Passerini, H and Northup, CJ and Vosburg, RW},
title = {American Society of Metabolic and Bariatric Surgery review of gut microbiome and alterations related to weight loss treatment, by the Clinical Issues Committee.},
journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.soard.2025.11.021},
pmid = {41469282},
issn = {1878-7533},
abstract = {The gut microbiome is a critical mediator of metabolic health including obesity and type 2 diabetes. Microbial composition variation - driven by diet, genetics, environment, and host physiology - can influence insulin sensitivity, energy absorption, fat storage, and systemic inflammation. Metabolic and bariatric surgery (MBS) is associated with distinct shifts in gut microbiota that may contribute to weight loss and metabolic improvements. Changes in microbial diversity, bile acid metabolism, and enrichment of beneficial taxa have all been linked to favorable metabolic outcomes. Furthermore, the gut microbiome may interact with molecular signaling pathways including glucagon-like peptide-1 signaling. Despite probiotics and prebiotics showing potential modulation of the gut microbiota, their clinical impact on obesity management remains inconsistent. Understanding the complex interplay between MBS, the gut microbiome, and host metabolism may offer novel insights into future therapeutic targets. As the field advances, microbiome-based strategies may enhance procedure selection, improve patient outcomes after MBS, and contribute to more personalized, durable treatment approaches for obesity and its related diseases.},
}

@article {pmid41469211,
year = {2025},
author = {Munteanu, C and Dhanasekaran, DN},
title = {Obesity as a Systems-Level Driver of Cancer: Mechanisms and Nutritional Reprogramming.},
journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
volume = {},
number = {},
pages = {e70075},
doi = {10.1111/obr.70075},
pmid = {41469211},
issn = {1467-789X},
support = {W81XWH-22-1-0415//Department of Defense Ovarian Cancer Research Program Award/ ; P30CA225520//National Cancer Institute of the National Institutes of Health/ ; P30GM154635//National Institutes of General Medical Sciences of the National Institutes of Health/ ; },
abstract = {Obesity has emerged as a global health crisis and a potent driver of cancer incidence and mortality, yet its mechanistic impact on tumor biology remains underappreciated. Far from being a passive risk factor, obesity acts as a systems-level oncogenic stressor, reshaping hormonal signaling, immunometabolism, and epigenetic stability across the body. This review synthesizes current knowledge on the physiological, cellular, and molecular cascades linking obesity to carcinogenesis, with emphasis on chronic inflammation, metabolic reprogramming, tumor microenvironment remodeling, and microbiome dysbiosis. We also examine how dietary patterns modulate these cancer-associated processes, positioning nutrition not merely as a preventive tool but as a programmable interphase with cancer biology through soft epigenetic reprogramming. Emerging frameworks in precision nutritional oncology, driven by nutrigenomics, metabolomics, and patient-specific molecular profiling, offer promising avenues for personalized cancer prevention and metabolic targeting. By integrating epidemiological trends, mechanistic insights, and translational strategies, we propose a paradigm shift: treating obesity not just as a comorbid risk factor but also as a modifiable oncogenic ecosystem-one that can be reprogrammed through informed, individualized precision dietary interventions.},
}

@article {pmid41469026,
year = {2025},
author = {Yao, L and Solania, A and Luissint, AC and Balana, AT and Zhang, H and Sangaraju, D and Lai, Z and Kuo, J and Storek, KM and Wolan, DW},
title = {The Secreted Metabolite Isopentenyladenine from Faecalibacterium prausnitzii Is Anti-inflammatory with Barrier-Protective Properties.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00771},
pmid = {41469026},
issn = {2373-8227},
abstract = {Colonic microbiome dysbiosis is correlated with inflammatory bowel disease (IBD), and depletion of the commensal bacterium Faecalibacterium prausnitzii (F. prausnitzii) is routinely observed in the metagenomic analyses of IBD patient microbiome samples. F. prausnitzii is likely beneficial to hosts, as oral administration of F. prausnitzii strain A2-165 has anti-inflammatory properties in murine models of colitis. Previous studies attribute the anti-inflammatory effects of F. prausnitzii A2-165 to production of the short-chain fatty acid butyrate, as well as a secreted protein known as microbial anti-inflammatory molecule (MAM). Here, we verified that oral dosing of strain A2-165 protects against DSS-induced murine colitis and further showed that the aqueous-soluble secreted fraction of overnight cultures from a collection of F. prausnitzii strains inhibits inflammatory signatures, including the activation of the host's NF-κB pathway, production of IL-8, and differentiation of naïve T cells into the TH17 lineage. Our findings against a panel of in vitro assays suggested that the anti-inflammatory responses were attributable to secreted small-molecule or peptide metabolites, as both heat-inactivated and proteinase K-treated F. prausnitzii culture supernatants retained activity. Untargeted and targeted mass spectrometry metabolomics analyses on the soluble anti-inflammatory secretome yielded several unique F. prausnitzii metabolites, including isopentenyladenine. We demonstrated that isopentenyladenine independently modulates host cellular signaling and immune responses and suggest that this newly identified metabolite with human immunomodulatory properties may be useful toward the discovery of IBD-focused therapeutics.},
}

@article {pmid41468854,
year = {2025},
author = {Chatterjee, S and Basak, C and Basak, G and Karjee, A and Mukherjee, S and Barman, P and Khan, NB and Sarkar, P and Majumdar, S and Chakraborty, R and Barman, C},
title = {Mitigating cadmium-induced stress in Capsicum annuum L. by Pseudomonas aeruginosa strain CD3: Impacts on morpho-physiology, reproductive traits, capsaicin content and soil microbiome.},
journal = {The Science of the total environment},
volume = {1013},
number = {},
pages = {181229},
doi = {10.1016/j.scitotenv.2025.181229},
pmid = {41468854},
issn = {1879-1026},
abstract = {Cadmium (Cd[2+]) contamination poses a major challenge to agricultural productivity and food safety by impairing plant physiology, inducing oxidative stress, and facilitating toxic metal accumulation in plants. Capsicum annuum, a widely cultivated crop, is highly susceptible to heavy metal toxicity, which hampers its growth, reproduction, and physiochemical balance. Although several studies have documented Cd[2+]-induced phytotoxicity in chili, mitigation strategies, particularly involving beneficial microbes, remain underexplored. This study investigates the role of Pseudomonas aeruginosa strain CD3 to alleviate cadmium stress in chili plants under controlled conditions. Morphological, physiological, biochemical, and reproductive traits were analyzed along with rhizospheric microbiome profiling in monsoon and winter seasons. CD3 inoculation significantly enhanced plant height (74.51 %), shoot biomass (73.08 %), relative water content (21.31 %), and antioxidant enzyme activity at 100 ppm Cd[2+] stress in both the season. Reactive oxygen species accumulation was reduced, while photosynthetic pigment content was restored. Our results verify that Cd[2+] severely disrupts chili reproductive biology, while strain CD3 markedly mitigates these effects by improving pollen viability, fruit yield, and seed production. Importantly, this study demonstrates the novel role of CD3 in regulating capsaicin accumulation under Cd[2+] stress, where microbial application alleviated stress-induced capsaicin enrichment. Cd[2+] accumulation was found to be below detectable levels in fruits of CD3-treated plants. Metataxonomic analysis demonstrated that CD3 successfully persisted in the soil, and its central role in the microbial network with strengthened interactions indicated a stabilizing and resilience-enhancing effect under cadmium stress. This research emphasizes the potential of P. aeruginosa strain CD3 as a green, sustainable bioremediation agent to improve crop yield, minimize metal translocation to edible tissues, and stabilize soil integrity in contaminated agricultural soils.},
}

@article {pmid41468691,
year = {2025},
author = {Leduc, F and Barko, PC and de Souza, CP and Reinhart, JM},
title = {Oral itraconazole may alter the gastrointestinal microbiome in healthy cats.},
journal = {American journal of veterinary research},
volume = {},
number = {},
pages = {1-13},
doi = {10.2460/ajvr.25.09.0338},
pmid = {41468691},
issn = {1943-5681},
abstract = {OBJECTIVE: To determine if and how oral itraconazole alters the gastrointestinal microbiome of cats.

METHODS: This was a single-arm, longitudinal exploratory study performed in a university setting. Healthy cats were administered 5 mg/kg/day of itraconazole solution orally with food during alternating weeks over a 5-week time period. Rectal swabs were collected at 2 time points before treatment and serially during and after treatment over 31 weeks. Bacterial and fungal populations were quantified by 16S and internal transcribed spacer 3 and 4 sequencing, respectively. Changes in α diversity, β diversity, and differential abundance were evaluated over time.

RESULTS: There were no significant changes in bacterial α diversity, β diversity (R2 = 0.0077; P = .550), or relative abundance between the 2 pretreatment time points indicating stable microbial populations before itraconazole exposure in 16 cats. Time was a significant determinant of β diversity during and after itraconazole treatment (R2 = 0.0181; P = .002), and several α-diversity indices significantly decreased in the posttreatment timeframe. Ruminococcus torques (-1.916; 95% CI, -2.971 to -0.861), Acidaminococcus spp (-1.291; 95%, CI -1.866 to -0.716), and Blautia hansenii (-1.475, 95% CI, -2.295 to -0.691) relative abundances were significantly decreased at weeks 1, 5, and 9, respectively. The final fungal internal transcribed spacer dataset only included 5 taxa limiting analysis and interpretation.

CONCLUSIONS: These findings provide preliminary evidence for possible dysbiosis in the feline gastrointestinal tract during itraconazole treatment. However, many changes in differential abundance were small and no longer significant posttreatment.

CLINICAL RELEVANCE: Itraconazole administration might induce gastrointestinal bacterial dysbiosis in cats. Alternate methods for fungal microbiome assessment should be used in future feline studies.},
}

@article {pmid41468674,
year = {2025},
author = {Feng, W and Ma, R and Guo, Y and Zhang, B and Lan, J and Liu, J and Chen, S},
title = {Rhizosphere metagenomics and metabolomes provide new insights into the relationship between rhizosphere microecology and early bolting of Angelica dahurica.},
journal = {Microbiological research},
volume = {305},
number = {},
pages = {128435},
doi = {10.1016/j.micres.2025.128435},
pmid = {41468674},
issn = {1618-0623},
abstract = {Angelica dahurica is a medicinal and edible plant with a wide range of pharmaceutical and food applications. However, the early bolting, which leads to reduced yield and loss of bioactive constituents, has become a major obstacle to the industrial development of A. dahurica. Rhizosphere microecology affects plant growth and secondary metabolite accumulation, but the association of rhizosphere microecology with the early bolting of A. dahurica is not fully understood. This study integrated metagenomic and metabolomic analyses to systematically characterize the differences in rhizosphere microecology of non-bolting and early bolting A. dahurica plants. Results revealed significant disparities in soil physicochemical properties, root exudate profiles, and microbial community composition between two groups, all of which exhibited correlations with the coumarin compounds content, the primary pharmacologically active constituents of A. dahurica. Integrated analysis suggested that root-derived acyl-homoserine lactone (AHL) quorum-sensing signals, as the primary chemical signals of the prevalent Gram-negative bacteria, may participate in regulating the microbial community structure and soil properties, thereby influencing the bolting and flowering process. This study proposes a potential complex regulatory network of "rhizosphere microbiome - quorum-sensing signals - soil nitrogen cycle - bolting and flowering" linking the rhizosphere microecology to early bolting in A. dahurica, thereby addressing a key knowledge gap in this area. The findings offer a scientific foundation and innovative strategy for the simultaneous prevention of early bolting and quality improvement in A. dahurica through soil microecological management, which is of significant importance for promoting the sustainable commercial development of the A. dahurica industry.},
}

@article {pmid41468549,
year = {2025},
author = {Ye, L and Wu, Y and Guo, J and Wang, H and Cai, J and Chen, K and Dong, N and Yu, J and Chao, S and Zhou, H and Chen, G and Chen, S and Zhang, R},
title = {Elucidation of population-based bacterial adaptation to antimicrobial treatment by single-cell sequencing analysis of the gut microbiome of a hospital patient.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0163124},
doi = {10.1128/msystems.01631-24},
pmid = {41468549},
issn = {2379-5077},
abstract = {In this study, we used single-cell sequencing to analyze the gut microbiome of an adult male patient with acute cerebral hemorrhage undergoing antibiotic treatment. We identified 92 bacterial species, including 23 Firmicutes and one archaeon from Methanobacteriota, along with 69 unclassified strains. Single-cell sequencing effectively detected bacteria carrying antibiotic resistance genes (ARGs), particularly in unclassified species, and traced the evolution of these genes across diverse bacterial taxa. Notably, the cfr(C) gene was detected in 11 bacterial species following antimicrobial treatment, with mutation patterns characterized in Enterococcus faecalis, Klebsiella pneumoniae, Ruthenibacterium UN-1, and four unclassified species. In total, 29 ARG subtypes across eight types were identified in 13 known, five unknown, and 18 unclassified species, allowing us to trace their evolution routes. In addition, we detected a total of 309 horizontal gene transfer (HGT) events, in which several genes like folE and queE were frequently involved. The products of these genes are known to enhance the ability of the recipient bacterial strains to repair DNA damage and maintain genomic stability, especially following prolonged antibiotic treatment. Comparison between isolated strain genomes (IS-KP1) and single-cell analysis confirmed the presence of at least two K. pneumoniae strains in the patient, with one exhibiting a larger extent of involvement in ARG co-evolution. This strain was found to contain the cfr(C) and fosXCC genes, which were absent in IS-KP1. Klebsiella strains were also found to participate actively in HGT events. In conclusion, the study identified a wide range of ARGs and HGT events within the microbiome. The detection of K. pneumoniae strains with distinct ARG evolution patterns underscores the gut microbiome's adaptability to environmental changes. These findings facilitate the development of novel antimicrobial strategies by fine-tuning the gut microbiome composition.IMPORTANCEThis study highlights the power of single-cell sequencing to unravel the diversity and dynamics of the gut microbiome during antibiotic treatment in a patient with acute cerebral hemorrhage. By identifying antibiotic resistance genes (ARGs) in both known and unclassified bacterial species, we reveal the intricate evolution and horizontal transfer of resistance traits across taxa. The discovery of distinct ARG patterns, including the emergence of the cfr(C) gene in multiple species and its co-evolution in K. pneumoniae, underscores the gut microbiome's adaptability to antimicrobial pressures. These findings provide critical insights into the mechanisms driving resistance dissemination and offer potential pathways for developing precision microbiome-based therapies to combat antibiotic resistance.},
}

@article {pmid41468410,
year = {2025},
author = {Molina, MA},
title = {From dysbiosis to mechanisms: Why cervicovaginal microbiome-HPV studies must catch up with biology.},
journal = {PLoS pathogens},
volume = {21},
number = {12},
pages = {e1013830},
pmid = {41468410},
issn = {1553-7374},
}

@article {pmid41468125,
year = {2025},
author = {Kirschen, GW and Gerson, KD},
title = {Performance Characteristics of Current Biomarkers for the Prediction of Spontaneous Preterm Birth.},
journal = {Clinical chemistry},
volume = {72},
number = {1},
pages = {71-81},
doi = {10.1093/clinchem/hvaf141},
pmid = {41468125},
issn = {1530-8561},
mesh = {Humans ; *Premature Birth/diagnosis/metabolism ; *Biomarkers/analysis/blood ; Female ; Pregnancy ; },
abstract = {BACKGROUND: Preterm birth (PTB), or birth occurring before 37 weeks' gestation, remains a significant public health burden, accounting for 10% of live births annually in the United States and incurring substantial healthcare expenditures. Our understanding of the molecular mechanisms underlying spontaneous preterm birth (sPTB) has advanced across the previous 4 decades, yet precise prediction tools and prevention strategies are lacking.

CONTENT: Numerous studies have identified potential anatomical and molecular risk factors for sPTB, including sonographic characteristics of the cervix; maternal serum circulating RNA and proteins; maternal urine metabolic byproducts; cervicovaginal cytokine, microbiome, and metabolome composition; amniotic fluid cytokines; umbilical cord blood leukocyte DNA methylation status; and placental transcriptome profiles. This review focuses on recent developments in sPTB biomarker determination among singleton gestations.

SUMMARY: Herein, we synthesize and evaluate the test characteristics of candidate biomarkers of sPTB, concluding that no single biomarker can accurately predict sPTB. However, several individual or combined panels of biomolecules, including some commercially available, carry clinically significant predictive information. These biomarkers include cervical ultrasonography, the ratio of insulin-like growth factor-binding protein 4 to sex-hormone binding globulin, panels of urinary metabolites and amniotic fluid proteins, and maternal circulating cell-free RNA. Future integration of select biomarkers drawn from prospective validation cohorts into existing risk stratification strategies may enhance sPTB prediction, thereby identifying patients at greatest risk.},
}

Humans
*Premature Birth/diagnosis/metabolism
*Biomarkers/analysis/blood
Female
Pregnancy

@article {pmid41468056,
year = {2025},
author = {Karikis, I and Arda, Y and Sanyal, R and DeWane, MP and Luckhurst, CM and Kaafarani, HM and Hwabejire, JO and Velmahos, GC and Paranjape, CN},
title = {Acute Appendicitis and the Microbiome: A Review of Microbial Signatures.},
journal = {Surgical infections},
volume = {},
number = {},
pages = {},
doi = {10.1177/10962964251408687},
pmid = {41468056},
issn = {1557-8674},
abstract = {Introduction: Acute appendicitis remains one of the most common surgical emergencies, yet its pathogenesis is incompletely understood. Although mechanical luminal obstruction has traditionally been considered the initiating factor, emerging evidence suggests that the appendix hosts a unique microbial community that may influence disease onset and severity. Methods: We conducted a narrative review that summarizes current data on the role of microbiota in appendicitis, while focusing on differences between complicated and uncomplicated presentations. Results: High-throughput sequencing studies have identified key taxa associated with inflamed appendices, including Fusobacterium, Prevotella, and oral cavity genera such as Gemella and Parvimonas. On the contrary, protective commensals such as Faecalibacterium prausnitzii and Akkermansia muciniphila appear depleted. Studies suggest that there is significant variation regarding the microbial composition of complicated and uncomplicated cases. We also examine the role of the appendix as a microbial reservoir and the potential health consequences of its removal. Finally, we discuss how microbiome-based approaches may improve treatment, particularly antibiotic agent selection both in operative and non-operative management. Conclusion: Current evidence supports that appendicitis may represent a disease spectrum carrying multiple rather than a single microbial signature that dictates different pathophysiologic processes.},
}

@article {pmid41467904,
year = {2026},
author = {Maruyama, D and Tian, X and Doan, TNM and Liao, WI and Chaki, T and Taenaka, H and Maishan, M and Matthay, MA and Prakash, A},
title = {Gut microbiome-derived propionate reprograms alveolar macrophages metabolically and regulates lung injury responses in mice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2606486},
doi = {10.1080/19490976.2025.2606486},
pmid = {41467904},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Macrophages, Alveolar/metabolism/immunology ; Mice ; *Lung Injury/microbiology/metabolism/immunology ; Dietary Fiber/metabolism/administration & dosage ; Fatty Acids, Volatile/metabolism ; *Propionates/metabolism ; Mice, Inbred C57BL ; Male ; Bacteria/metabolism/classification/genetics/isolation & purification ; Lung/metabolism/immunology ; },
abstract = {Responses to lung injury can vary between individuals with the diet and gut microbiome representing two underappreciated sources for this variability. The gut microbiome can influence lung injury outcomes through the gut‒lung axis, but exactly how diet and its effects on the microbiota are involved remains unclear. We hypothesized that dietary fiber interventions would favor the presence of short-chain fatty acid (SCFA)-producing fermentative bacteria presence in the gut microbiome, thereby influencing the resting lung immunometabolic tone as well as influencing downstream responses to lung injury and infection. To test this hypothesis, we fed mice fiber-rich (FR) and fiber-free (FF) diets, and observed changes in the steady-state transcriptional programming of alveolar macrophages (AM). Next, we examined the effects of the FR and FF diets on murine responses to sterile and infectious lung injury in vivo while simultaneously profiling the gut microbiota and SCFA levels transmitted along the gut‒lung axis. Finally, we validated our in vivo observations with mechanistic studies of the metabolic, signaling, and chromatin-modifying effects of specific SCFAs on lung AM ex vivo and in vitro. Overall, our fiber-rich diet reprogrammed AMs and attenuated lung inflammation after sterile injury while exacerbating lung infection. This effect of FR diets could be transferred to germ-free (GF) mice by fecal microbiome transplantation (FMT) and depended on the ability of the microbiota to produce propionate. Mechanistically, SCFAs altered the metabolic programming of AMs and lung tissue ex vivo without a clear role for free fatty acid receptors (FFAR) or chromatin remodeling. These findings demonstrate that the gut‒lung axis can regulate resting lung metabolic tone through dietary fiber intake and the enrichment of SCFA-producing gut bacteria, as well as influence sterile and non-sterile lung injury responses. These results provide evidence to support the development of therapeutic dietary interventions to preserve or enhance specific aspects of host pulmonary immunity.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Macrophages, Alveolar/metabolism/immunology
Mice
*Lung Injury/microbiology/metabolism/immunology
Dietary Fiber/metabolism/administration & dosage
Fatty Acids, Volatile/metabolism
*Propionates/metabolism
Mice, Inbred C57BL
Male
Bacteria/metabolism/classification/genetics/isolation & purification
Lung/metabolism/immunology

@article {pmid41467862,
year = {2025},
author = {van Straalen, KR and Gudjonsson, JE},
title = {Hidradenitis suppurativa: Why dose escalation often fails and what biology tells us about next steps.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2025.11.012},
pmid = {41467862},
issn = {1097-6825},
}

@article {pmid41467811,
year = {2025},
author = {Ha, LH and On, YY and Pohan, C and Lee, J and How, SHC and Teo, Y-Y and Seedorf, H and Gounot, J-S and Nagarajan, N},
title = {High-throughput single-cell isolation of Bifidobacterium strains from the human gut microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0303325},
doi = {10.1128/spectrum.03033-25},
pmid = {41467811},
issn = {2165-0497},
abstract = {UNLABELLED: Bifidobacterium represents a diverse genus of commensal gut bacteria with key roles in human health, from metabolizing indigestible fibers to protecting against pathogens. While metagenomic studies have highlighted significant strain diversity for Bifidobacterium species within individuals, their systematic isolation and phenotypic characterization can be hampered by the significant effort and biases inherent in traditional culturomics. Here, we explored the utility of a high-throughput single-cell dispensing system (B.SIGHT)-based workflow for accelerating the process of isolating diverse Bifidobacterium strains from fecal samples. Systematic assessment of this workflow revealed a high single-cell dispensing frequency (>88%) and the ability to preserve species diversity when a pool of Bifidobacterium strains was dispensed. Culturing-related factors including the use of an effective selection medium, such as the Bifidus Selective Medium supplemented with mupirocin, and the length of pre-dispensing incubation were found to be critical in determining isolation success. Leveraging this workflow, we obtained a total of 622 viable isolates from five Singaporean fecal samples, of which >98% were found to be from Bifidobacterium species. Whole-genome sequencing of 96 isolates identified six different Bifidobacterium species with both inter- and intra-subject strain and lineage diversity, and the majority (>66%) were novel relative to large public genomic databases. Our findings highlight the ability of this high-throughput culturomics workflow to accelerate the recovery of diverse and novel Bifidobacterium strains, enabling further interrogation of their functional characteristics and advancing our understanding of important bacterial species in the gut microbiome.

IMPORTANCE: The field of high-throughput microbial culturomics is still in its early stages. Enhancing our ability to isolate and phenotypically test bacterial strains from complex communities is crucial for advancing microbiome research and healthcare development. Given the time and cost inefficiencies of traditional culturing methods, a more efficient, high-throughput approach to obtain isolates is needed. In the present study, we assessed a single-cell dispensing platform and developed a workflow to isolate diverse Bifidobacterium strains from fecal samples. We demonstrated here the capability of this novel technology to efficiently obtain hundreds of isolates of a targeted group, covering both species and strain diversities. This generalizable and scalable method can potentially allow for the high-throughput recovery of microbes from other taxonomic groups, providing a fundamental step in improving the culturomics framework to complement metagenomic approaches and enable isolate-level functional studies of important microbes.},
}

@article {pmid41467444,
year = {2025},
author = {Wang, R and Hatano, T and Hattori, N and Cossu, D},
title = {Interplay of GBA1 with lysosomal dysfunction and inflammation in Parkinson's disease.},
journal = {Neural regeneration research},
volume = {},
number = {},
pages = {},
doi = {10.4103/NRR.NRR-D-25-01082},
pmid = {41467444},
issn = {1673-5374},
abstract = {Mutations in the glucocerebrosidase (GBA1) gene, encoding the lysosomal enzyme glucocerebrosidase, represent the most significant genetic risk factor for Parkinson's disease. These variants define a distinct clinical subtype characterized by earlier onset, accelerated motor decline, and pronounced cognitive impairment. This review synthesizes current insights into the molecular mechanisms linking GBA1 dysfunction to lysosomal failure, α-synuclein aggregation, and neuroinflammation. Pathogenic alleles such as N370S and L444P disrupt sphingolipid metabolism, resulting in toxic accumulations of glucosylceramide and glucosylsphingosine, endoplasmic reticulum stress, and impaired clearance of misfolded proteins. This initiates a self-reinforcing cycle in which glucocerebrosidase deficiency promotes α-synuclein aggregation, which subsequently impairs glucocerebrosidase trafficking. We explore the convergence of GBA1 mutations on the lysosomal-mitochondrial-autophagy axis, where impaired autophagic flux and disrupted organelle crosstalk amplify oxidative stress and activate the NLR family pyrin domain containing 3 inflammasome. The contribution of microglia, astrocytes, and oligodendrocytes to the neuroinflammatory cascade is eamined, along with the emerging influence of the microbiome-gut-brain axis in disease progression. Finally, we evaluate emerging therapeutic strategies, including pharmacological chaperones, NLRP3 inhibitors, adeno-associated virus-based gene therapy, and microbiome modulation, highlighting both promises and translational challenges such as blood-brain barrier penetration and mutation-specific efficacy. We conclude by advocating for precision medicine approaches, supported by robust biomarker development and advanced disease models, to guide tailored interventions for this aggressive Parkinson's disease subtype.},
}

@article {pmid41467389,
year = {2025},
author = {Stahlke, S and Theiss, C},
title = {Sex hormones, the gut microbiome, and neurodegenerative diseases: Lifespan perspective.},
journal = {Neural regeneration research},
volume = {},
number = {},
pages = {},
doi = {10.4103/NRR.NRR-D-25-00932},
pmid = {41467389},
issn = {1673-5374},
abstract = {The gut-brain axis represents a highly integrated communication network, connecting the gastrointestinal tract and the central nervous system via neural, immune, endocrine, and metabolic pathways. Steroid hormones, such as estrogens, androgens, and glucocorticoids, play a pivotal role in modulating these interactions across the lifespan. These hormones influence the composition of microbiota, intestinal permeability, and neuroimmune responses, thereby shaping brain function and behavior. Emerging evidence suggests a correlation between disruptions in the gut-brain axis and the onset and progression of neurodegenerative diseases, including Parkinson's disease, Alzheimer's disease, and multiple sclerosis. The diseases exhibit distinct sex-specific patterns in terms of prevalence, symptomatology, and progression. These patterns are often the consequence of differences in steroid hormone levels, receptor distribution, and immune responses. Despite these differences, the role of sex as a biological variable remains underrepresented in experimental and clinical research. This review synthesizes current evidence on how steroid hormones modulate gut-brain axis interactions and how these mechanisms contribute to neurodegeneration in a sex-specific manner. We highlight recent findings on hormonal regulation of the gut microbiome and its impact on neuroinflammation and neuronal vulnerability. This overview focuses not only on Parkinson's disease, in which genetic variations in the gene for brain-derived neurotrophic factor have been observed among others as triggers for dopaminergic neurodegeneration. In addition, Alzheimer's disease and multiple sclerosis are also considered, in which the prevalence of intestinal dysbiosis and impaired intestinal barrier function have been identified as significant influencing factors. This review provides a comprehensive framework for understanding the gender-specific neurobiology of gut-brain axis by integrating perspectives from the fields of endocrinology, neuroimmunology, and microbiome research. It is argued that a targeted investigation of the interactions between hormones and gut-brain axis is essential for the development of sex-specific therapeutic strategies for neurodegenerative diseases.},
}

@article {pmid41467356,
year = {2025},
author = {Vadillo Gonzalez, S and Jongen, R and Thomas, T and Marzinelli, EM and Gribben, PE},
title = {Seagrass-microbe interactions: a systematic review of current research trends and mapping of the core microbiome.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {},
number = {},
pages = {},
doi = {10.1002/brv.70126},
pmid = {41467356},
issn = {1469-185X},
support = {LP200200220//Australian Research Council/ ; DP240100556//Australian Research Council/ ; },
abstract = {Seagrass-microbe interactions are crucial for seagrass performance and the coastal ecosystem services they support. However, significant variation in experimental and analytical approaches has hindered our broader understanding of seagrass-microbe interactions and the potential existence of a functional core microbiome, i.e. microbial taxa that are consistently present on hosts and likely exert a disproportionate impact on host function. Through a systematic review, we aimed first to understand current trends and knowledge gaps in seagrass-microbe research. Additionally, we conducted a systematic mapping of global 16S ribosomal RNA (rRNA) gene sequencing data to characterise core bacterial taxa in three plant microenvironments (leaves, roots and rhizosphere) across multiple species and within a highly studied seagrass species, Zostera marina. The results revealed a growing number of studies since the 2010s manipulating environmental variables and/or seagrass microbes to investigate their roles in seagrass performance and responses to stressors. Most studies have primarily focused on seagrass leaves, examined a limited number of species, and investigated only bacteria via 16S rRNA gene amplicon sequencing. A few studies attempted to characterise seagrass core microbiomes, often using highly variable approaches to define core taxa. Our systematic mapping based on global sequencing data allowed the identification of prevalent bacterial taxa belonging to the families Desulfocapsaceae and Sulfurovaceae in the seagrass rhizosphere, which may play an important role in the performance of Z. marina and other seagrass species. The results also showed that many other bacterial families were prevalent across different seagrass microenvironments, such as Rhodobacteraceae and Flavobacteriaceae, with substantial taxonomic variability and functional metabolic redundancy. We identified key challenges stemming from available data and variable methodologies and provided insights to guide future experimental work and deepen our understanding of seagrass-microbe interactions. We argue that such knowledge may improve seagrass management outcomes, especially by informing restoration strategies based on core microbial taxa.},
}

@article {pmid41467315,
year = {2025},
author = {Sun, Y and Li, P and Wang, X and Jiang, D and Shao, Y},
title = {Gut dysbiosis in early severe burns contributes to acute lung injury by impairing neutrophil chemotaxis.},
journal = {Journal of leukocyte biology},
volume = {118},
number = {1},
pages = {},
doi = {10.1093/jleuko/qiaf169},
pmid = {41467315},
issn = {1938-3673},
support = {82302800//National Natural Science Foundation of China/ ; 2024M751108//China Postdoctoral Science Foundation/ ; SDCX-ZG-202400032//Postdoctoral Innovation Program in Shandong Province/ ; },
mesh = {Animals ; *Dysbiosis/complications/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Acute Lung Injury/etiology/pathology/microbiology/immunology ; *Neutrophils/immunology/pathology ; Humans ; Mice ; *Burns/complications/microbiology/pathology/immunology ; *Chemotaxis, Leukocyte ; Male ; Female ; Mice, Inbred C57BL ; Butyrates/pharmacology ; Disease Models, Animal ; Neutrophil Infiltration ; Chemotaxis ; },
abstract = {Severe burns complicated by acute lung injury are critical causes of respiratory failure and multiple organ dysfunction syndrome. Neutrophils extensively infiltrate lung tissues early postburn to mediate pulmonary damage, but the underlying mechanisms remain unclear. We analyzed gut microbiota of severe burn patients via metagenomics and metabolomics, assessed neutrophil chemotaxis using a self-developed in vitro agarose model, and validated Faecalibacterium prausnitzii and butyrate's effects on restoring neutrophil chemotaxis in gut microbiota-depleted mice via oral gavage (plus in vivo validation with small animal imaging). Bronchoalveolar lavage fluid biomarkers and pulmonary function tests evaluated pulmonary injury from impaired neutrophil chemotaxis. Early postburn, F. prausnitzii and its metabolite butyrate were significantly depleted in patients, concurrent with impaired neutrophil chemotaxis-restored by butyrate supplementation. In murine burn models, F. prausnitzii or butyrate rescued neutrophil chemotaxis, reduced pulmonary neutrophil infiltration, and attenuated lung injury. Mechanistically, butyrate restored neutrophil function in a severe burn patient plasma-stimulated model by downregulating P2X1 receptor expression and suppressing myosin light chain phosphorylation. Our findings indicate postburn gut microbiota dysbiosis and metabolite alterations disrupt neutrophil chemotaxis, causing excessive pulmonary neutrophil infiltration/activation. This highlights gut microbiota-derived metabolites as potential therapeutics for mitigating neutrophil-driven lung injury early postsevere burns.},
}

Animals
*Dysbiosis/complications/immunology/microbiology
*Gastrointestinal Microbiome/immunology
*Acute Lung Injury/etiology/pathology/microbiology/immunology
*Neutrophils/immunology/pathology
Humans
Mice
*Burns/complications/microbiology/pathology/immunology
*Chemotaxis, Leukocyte
Male
Female
Mice, Inbred C57BL
Butyrates/pharmacology
Disease Models, Animal
Neutrophil Infiltration
Chemotaxis

@article {pmid41467213,
year = {2025},
author = {Wang, S and Carroll-Portillo, A},
title = {Editorial: Genetic modulation of gut microbiome: effects on neurological health and aging.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1760164},
pmid = {41467213},
issn = {1664-8021},
}

@article {pmid41466840,
year = {2025},
author = {Hendesi, H and Godfrey, DA and Ruble, AF and Tran, AM and Villani, DA and Landgrave, SH and Hasan, NA and Adams, DJ and Zuscik, MJ},
title = {Intermittent fasting alleviates obesity-associated impairments in bone fracture healing: Exploring the role of gut microbiome.},
journal = {Bone reports},
volume = {27},
number = {},
pages = {101876},
pmid = {41466840},
issn = {2352-1872},
abstract = {Intermittent Fasting (IF) is a dietary strategy with metabolic benefits that can reverse certain obesity-related pathologies. This study aimed to investigate whether IF can mitigate delayed bone fracture healing associated with obesity. Using cohorts of mice on high-fat or control diets, we applied either an ad libitum feeding or an alternate-day fasting regimen to animals from both diet groups. We assessed bone healing outcomes by evaluating callus mineralization and adipocyte accumulation within the callus through micro computed tomography (micro-CT), histology, and immunohistochemical analyses. Since IF is known to modulate gut microbiome composition, often associated with improvement in various metabolic and inflammatory processes, particularly in high-fat-fed mice, we also explored the microbial community changes in IF mice through 16S rRNA sequencing of cecal samples. Metabolically, IF led to reduced body weight and improved glucose tolerance in obese mice. Regarding fracture healing outcomes, reduced/delayed mineralization and adipocyte accumulation in fracture callus tissue in the high-fat-fed cohort were significantly attenuated when the high-fat-fed mice were subjected to alternate-day fasting. These benefits of IF were not observed in lean mice fed a control diet. Furthermore, IF significantly altered the gut microbiota of mice on a high-fat diet, including an increased abundance of short-chain fatty acid producing bacteria, known for their positive effect on bone density, and a reduction in various pro-inflammatory taxa. While the mechanistic role remains unknown, these findings suggest that the improved fracture healing observed in obese mice following IF may be associated with alterations in gut microbiome composition and function.},
}

@article {pmid41466681,
year = {2025},
author = {Gupta, PS and Padmakumar, VM and Usmani, OI},
title = {Cross-sectional analysis of gut microbiome diversity with progression of Alzheimer's disease.},
journal = {Bioinformation},
volume = {21},
number = {9},
pages = {3329-3332},
pmid = {41466681},
issn = {0973-2063},
abstract = {The relationship between gut microbiome diversity and stages of Alzheimer's disease (AD) progression is of interest. Hence, a total of 124 participants, including cognitively normal controls and patients with mild, moderate, and severe AD, were assessed for microbiome composition using 16S rRNA sequencing. Results revealed significantly reduced microbial diversity and altered bacterial profiles, notably lower levels of Bifidobacterium and Faecalibacterium and increased Proteobacteria, in advanced AD stages. Correlations were observed between cognitive declines and reduced alpha diversity. Thus, we show gut dysbiosis may play a contributory role in Alzheimer's pathology.},
}

@article {pmid41466653,
year = {2025},
author = {Arvindssinh, RN and Patel, TG and Karthik Raj, MRM},
title = {Cross-sectional study on ethnic variations in gut microbiome diversity and hypertension severity.},
journal = {Bioinformation},
volume = {21},
number = {9},
pages = {3043-3046},
pmid = {41466653},
issn = {0973-2063},
abstract = {Stool samples were analyzed using 16S rRNA sequencing and blood pressure measurements were categorized per AHA guidelines. Hence, 130 adults from three ethnic groups to assess differences in gut microbiome diversity and their association with hypertension severity were studied. Significant ethnic variations were observed in microbial composition, particularly in Firmicutes-to-Bacteroidetes ratios. Greater microbial diversity was associated with lower hypertension severity in certain ethnicities. Thus, we show ethnic-specific microbiome patterns may influence hypertension outcomes.},
}

@article {pmid41466512,
year = {2025},
author = {Merz, E and Hale, RJ and Saberski, E and Kenitz, KM and Carter, ML and Bowman, JS and Barton, AD},
title = {Temperature alters interactions and keystone taxa in the marine microbiome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf287},
pmid = {41466512},
issn = {1751-7370},
abstract = {Marine microbes shape global biogeochemical cycles and marine food webs. Although biotic interactions underpin microbial community dynamics, most interactions between wild marine microbes are unknown. Here, we used empirical dynamic modeling to examine a six-year record of coastal microbial community composition to quantify microbial interactions and their changes through time. We found that, on average, marine microbes interact with 20% of other taxa in the community, most interactions are weak (80%), and that positive interactions are more common than negative interactions. Keystone taxa, defined as having disproportionally strong and frequent interactions, were not generally the most abundant taxa. The strength and sign of interactions, as well as the identity of the keystone taxa, varied through time and with changes in water temperature. An increase of 13°C, the dynamic range in water temperature at this location during the observational period, led to a 33% less interactive microbial community and an 11% shift towards more positive interactions. Only a few of the keystone taxa are the most interactive in the community at all times, and we found a temporal succession of keystone taxa. These results reveal that interactions in the marine microbiome are common, more facilitative than previously thought, and highly variable through time.},
}

@article {pmid41466423,
year = {2025},
author = {Chen, L and Tang, C and Hu, D and Yu, S and Liao, P},
title = {Brevilin a reverses colitis of inflammatory bowel disease via modulation of TNF-α signaling and microbiome dysregulation.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-025-00792-3},
pmid = {41466423},
issn = {1757-4749},
support = {2024000003-09//Middle-aged Backbone Talents in the Province/ ; },
abstract = {BACKGROUND: Brevilin A (Br) has shown potential in modulating inflammatory bowel disease (IBD). Our study aims to explore its mechanism of anti-inflammatory action.

METHODS: Colitis was induced in C57BL/6 mice with dextran sulfate sodium (DSS), followed by treatment with or without Br(20 mg/kg). Fecal microbiota and metabolites were profiled by metagenomic sequencing and liquid chromatography-mass spectrometry (LC-MS), respectively. Furthermore, to delineate the essential role of the gut microbiota, we employed antibiotic-treated (microbiota-depleted) mice in our investigation of Br's mechanism of action.

RESULTS: Br significantly alleviated DSS-induced colitis and modulated the gut microbiota profile. Specifically, Br enriched beneficial bacteria such as Lactobacillus, while suppressing pathogenic bacteria including Escherichia coli and Clostridium perfringens. Metabolomic analysis revealed that Br significantly altered bacterial metabolites, including 7-Oxolithocholic Acid, Kudinoside A, Veratrine, and Soyasaponin. These metabolites were linked to key pathways such as GPCR signaling, DNA damage response, aminoacyl-tRNA biosynthesis, riboflavin metabolism, and central carbon metabolism in cancer. Transcriptomic profiling indicated that Br inhibited the TNF-α signaling pathway, and this inhibition was confirmed as TNF-α overexpression reversed its anti-inflammatory effects. Furthermore, the therapeutic effects of Br were partially recapitulated in microbiota-depleted mice through fecal microbiota transplantation from Br-treated donors.

CONCLUSION: Br's ability to regulate gut microbiota and metabolites, improve gut barrier function, and eliminate inflammation by inhibiting TNF-α highlights its potential as a novel therapeutic medicine for IBD. Future research should focus on further exploring its mechanisms and clinical applications.},
}

@article {pmid41466331,
year = {2025},
author = {Li, J and Zhang, X and Zhao, X and Gong, G and Li, J and Dalai, B and Mo, Z and Xu, X and Jia, X and Li, Y and Lai, J and Wang, P and Sun, L and Liu, Y and Luo, X},
title = {Characterising gut microbiome dysbiosis in diarrhoea calves from multiple farms in Inner Mongolia using 16S and metagenomics.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {259},
pmid = {41466331},
issn = {2049-2618},
support = {2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; },
mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome/genetics ; *Diarrhea/microbiology/veterinary/epidemiology ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; China/epidemiology ; *Dysbiosis/microbiology/veterinary ; *Cattle Diseases/microbiology/epidemiology ; Feces/microbiology ; Escherichia coli/genetics/isolation & purification/pathogenicity ; *Bacteria/classification/genetics/isolation & purification ; Farms ; },
abstract = {BACKGROUND: The pathogenesis of neonatal calf diarrhoea (NCD), a critical disease that contributes to neonatal mortality in calves, remains nebulous.

RESULTS: Inner Mongolia, a key region for cattle farming in China, was selected as a study area to provide a comprehensive overview of the epidemiology and treatment of calf diarrhoea. No significant correlation was found between the incidence of diarrhoea and sampling points or medications. The severity of diarrhoea cases was stratified into five levels based on faecal characteristics. To elucidate the pathogenesis of NCD, 16S rRNA gene and metagenomic sequencing analyses were performed across severity levels. Microbial diversity analyses revealed distinct variations in microbial communities at different severity levels. Employing binning and LEfSe methodologies, two potential bacterial pathogens were identified: Escherichia coli (bin.216), leveraging non-canonical virulence mechanisms; and Streptococcus ruminantium (bin.338), an uncharacterised diarrhoeagenic bacterium. Furthermore, the viral agent Escherichia phage VpaE1_ev108 was significantly associated with disease progression. Gene function enrichment analysis revealed a broad spectrum of antibiotic resistance genes even in farms without direct antibiotic treatment, underscoring the pervasive prevalence of drug resistance.

CONCLUSIONS: The findings of this study revealed significant gut microbial dysbiosis in calves with severe diarrhoea, through which two putative NCD-associated pathogens were identified: E. coli (bin.216) and S. ruminantium (bin.338). Marked enrichment of Bacteroides spp. and Methanobrevibacter_A sp. 900313645 was observed in healthy cohorts, suggesting their potential protective roles. Therapeutic strategies employing phage-mediated pathogen targeting combined with probiotic transplantation have demonstrated dual benefits, potentially reducing antimicrobial dependency and preserving microbial homeostasis through ecological network reconstruction. Video Abstract.},
}

Animals
Cattle
*Gastrointestinal Microbiome/genetics
*Diarrhea/microbiology/veterinary/epidemiology
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
China/epidemiology
*Dysbiosis/microbiology/veterinary
*Cattle Diseases/microbiology/epidemiology
Feces/microbiology
Escherichia coli/genetics/isolation & purification/pathogenicity
*Bacteria/classification/genetics/isolation & purification
Farms