@article {pmid40903688,
year = {2025},
author = {Ahmed, T and Lemberg, DA and Day, AS and Leach, ST},
title = {The Interplay Between Immunological Status and Gut Microbial Dysbiosis in the Development of the Symptoms of Irritable Bowel Syndrome: A Systematic Review with Meta-Analysis.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {40903688},
issn = {1573-2568},
abstract = {PURPOSE: Irritable bowel syndrome (IBS) is a chronic disorder of gut-brain interaction (DGBI) characterized by recurrent abdominal pain and altered bowel habits. Treatment typically focuses on symptom management without addressing underlying causes. This systematic review and meta-analysis aimed to explore the association between inflammatory markers and gut microbiome changes in individuals with IBS.

METHODS: A systematic search of PubMed, Scopus, EMBASE, and CINAHL databases was conducted in June 2024, identifying 41 studies that compared inflammatory markers and gut microbial composition in patients with IBS versus healthy controls. Meta-analysis was performed using a random-effects model, reporting standard mean differences (SMD) for inflammatory markers and mean differences (MD) for microbiome data, with 95% confidence intervals (CI).

RESULTS: The results showed significantly elevated pro-inflammatory markers in individuals with IBS, including Interleukin (IL)-6 (SMD =  - 2.64), Tumor Necrosis Factor (TNF)-α (SMD =  - 1.97), platelet-to-lymphocyte ratio (PLR, SMD =  - 0.98), and fecal calprotectin (FC, SMD =  - 0.42), while IL-10 was lower (SMD = 2.00). Microbiome analysis revealed increased Bacteroidetes (MD =  - 15.92) and decreased Firmicutes (MD = 16.85) in people with IBS.

CONCLUSION: These findings suggest that inflammation and gut microbial imbalance contribute to IBS, warranting further studies on their interplay and impact on the typical symptoms seen in IBS.},
}

@article {pmid40903589,
year = {2025},
author = {Yang, C and Snelson, M and El-Osta, A and Marques, FZ},
title = {Parental diet and offspring health: a role for the gut microbiome via epigenetics.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {40903589},
issn = {1759-5053},
abstract = {The effects of diet and nutrition extend beyond individual health: food intake before conception or during pregnancy and lactation can affect the health of offspring. Diet is one of the most powerful modulators of the gut microbiome, influencing gene-environment interactions, with several emerging mechanisms pointing to the microbiome-metabolite-epigenome axis. In this Review, we discuss the effect of dietary changes on the gametes ('gut-germline axis') or in utero ('gut-neonatal axis') that may change the predisposition of offspring to several non-communicable diseases. Examples of diets discussed are those that detrimentally modulate the parental microbiota and lead to epigenetic changes in the progeny, including Western diets characterized by high saturated fat and low protein or fibre intake. We summarize studies using animal models, which suggest that these diets can have long-lasting effects on the offspring microbiome, epigenome and phenotype, particularly across the cardiometabolic and immune systems, and discuss the limitations of current studies as well as future directions for the field. Translational research investigating the benefits of parental dietary interventions before and during pregnancy, mainly using personalized approaches, is needed. This would, in turn, reduce rates of non-communicable diseases in generations to come.},
}

@article {pmid40903424,
year = {2025},
author = {Droby, S and Wisniewski, M and Zhimo, VY and Kumar-Sharma, V and Freilich, S},
title = {Biological Control of Postharvest Diseases: The Evolution of New Concepts and Perspectives.},
journal = {Annual review of phytopathology},
volume = {63},
number = {1},
pages = {501-528},
doi = {10.1146/annurev-phyto-121823-025820},
pmid = {40903424},
issn = {1545-2107},
mesh = {*Plant Diseases/prevention & control/microbiology ; *Fruit/microbiology ; *Vegetables/microbiology ; *Pest Control, Biological/methods ; Microbiota ; Biological Control Agents ; },
abstract = {Postharvest biological control based on the use of microbial antagonists has been the subject of research and development for more than three decades. Several formulated products have been developed; however, their widespread use has not been realized, which has led to the development of new concepts and paradigms to better describe, understand, and employ biocontrol systems under commercial conditions. In the first part of this review, the evolution of postharvest biocontrol and its current status are briefly discussed. This is followed by a discussion of new concepts of postharvest disease and biocontrol systems based on studies of the microbiome of fruits and vegetables during development, harvest, and storage. A deeper understanding of the assembly, composition, interactive dynamics, and functional impact of microbial communities will enable the development of strategies to manipulate/engineer beneficial microbial assemblages that effectively suppress infection and disease development in harvested fresh fruit and vegetables.},
}

*Plant Diseases/prevention & control/microbiology
*Fruit/microbiology
*Vegetables/microbiology
*Pest Control, Biological/methods
Microbiota
Biological Control Agents

@article {pmid40903035,
year = {2025},
author = {Hou, Y and Wu, H and Zhang, Z and Wang, J and Chen, Q and Lian, C and He, D and Li, Z and Wei, W and Lin, X and Sun, D and Cao, B and Xu, T and Cai, M and Wang, G and Zhang, X and Duan, L and Hao, H and Zheng, X},
title = {Bacteroides intestinalis mediates the sensitivity to irinotecan toxicity via tryptophan catabolites.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-334699},
pmid = {40903035},
issn = {1468-3288},
abstract = {BACKGROUND: Late-onset diarrhoea remains a poorly managed concern for clinical irinotecan therapy. Although bacterial β-glucuronidases (β-GUS) mediated SN-38 production is prevailingly thought to mediate intestinal toxicity, β-GUS inhibitors confer limited benefits in the clinic.

OBJECTIVE: This study aimed to explore the role and mechanism of endogenous bacterial metabolites in susceptibility to irinotecan toxicity.

DESIGN: Gut microbiota profiles and metabolites in patients with colorectal cancer (CRC) with or without diarrhoea were investigated via 16S rRNA sequencing, shotgun metagenomics and metabolomics. The role of microbial metabolites was investigated in mice by metabolic bioengineering and intestinal organoid culture. The mechanism of microbial metabolites on intestinal stem cells was investigated by transcriptional profiling and chemical intervention.

RESULTS: Gut microbial configuration was differentially remodelled in diarrhoea and non-diarrhoea patients with irinotecan therapy, and the susceptibility was transmissible to recipient mice via transplantation of baseline faecal microbiome. Bacteroides intestinalis (B. intestinalis) was notably expanded in the diarrhoea-prone cohorts as well as in irinotecan-treated mice. B. intestinalis colonisation sensitised intestinal epithelia to irinotecan-induced chemical injury, partially via tryptophan metabolite indole-3-acetate (IAA). Both B. intestinalis and bioengineered bacteria that produce IAA exacerbated irinotecan-induced intestinal epithelial injury in mice. Mechanistically, IAA suppressed PI3K-Akt signalling, thereby impairing the renewal of intestinal epithelia under the insult of irinotecan. In clinical patients receiving irinotecan therapy, faecal IAA level was closely associated with the diarrhoea severity.

CONCLUSION: Our study uncovers the mechanism of endogenous bacterial metabolite in shaping the individual susceptibility to irinotecan toxicity and suggests IAA as a potential predictive biomarker.},
}

@article {pmid40902902,
year = {2025},
author = {Li, X and Ding, K and Ma, Y and Xiao, H and Liu, Y and Wu, G and Chen, D},
title = {Gut microbial signatures in type 2 diabetes are highly associated with geographic region, diet habits and common comorbidities: Insights from a bioinformatics analysis of Chinese population.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {112438},
doi = {10.1016/j.diabres.2025.112438},
pmid = {40902902},
issn = {1872-8227},
abstract = {AIMS: Emerging evidence implicates the gut microbiota in type 2 diabetes (T2D) development and their association with multiple host factors. This study aimed to explore the differences in gut microbiota between T2D patients and non-diabetic controls, and to estimate the relationship between host factors and specific microbial signatures in T2D.

METHODS: 16S rRNA gene sequencing was performed on fecal samples from 508 T2D patients and 1,538 controls in a Chinese population.

RESULTS: We observed significant differences in microbial composition and diversity between T2D and controls, with 20 microbial signatures associated with T2D. Microbial co-occurrence networks revealed that T2D patients exhibited a distinct microbiome signatures pattern. Random forest models incorporating these microbial signatures and covariates improved accuracy of T2D classification. Furthermore, geographic region, diet habits of different staple food sources and coffee drinking habit, and common comorbidities, such as hypertension, were associated with specific microbial signatures.

CONCLUSIONS: Our study highlights the potential role of gut microbiota in T2D pathogenesis and provides clues that specific microbial signatures may serve as biomarkers for T2D diagnosis and personalized management in Chinese populations. The findings indicate that modifiable factors including dietary factors, living regions and common comorbidities may influence the gut microbiota, thereby affecting T2D development.},
}

@article {pmid40902888,
year = {2025},
author = {Wei, Y and Huang, Q and Fu, Z and Wang, R and Zhou, R and Le, J and Hu, L and Lei, X},
title = {Improvement of Spermogenesis Impairment Induced by High-Fat Diet in Obese Mice through Pyrroloquinoline Quinone Regulation of Glycolysis Pathway.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110066},
doi = {10.1016/j.jnutbio.2025.110066},
pmid = {40902888},
issn = {1873-4847},
abstract = {This research utilized obese mouse models to investigate the impact of PQQ intervention on both reproductive system function and the glycolytic pathway in mice. The findings demonstrated that PQQ notably boosted glycolytic pathway activity in obese mice, enhancing glucose breakdown and metabolism, which in turn improved energy supply efficiency. These changes not only enhanced the overall metabolic status of the mice but also significantly supported the function of their reproductive system. Additional mechanistic analyses suggested that PQQ may influence mitochondrial activity, mitigate mitochondrial dysfunction, and reduce inflammation associated with obesity, thus supporting the balance between fatty acid degradation and the glycolysis-cholesterol metabolism pathway. In conclusion, this study presents the first evidence of PQQ's potential role and molecular mechanisms in promoting glycolysis and alleviating infertility in obese males.},
}

@article {pmid40902774,
year = {2025},
author = {Azeem, M and Han, R and Liu, S and Jacques, KJ and Abdelrahman, H and Kazmi, SSH and Kareem, A and Khan, ZH and Rafiq, N and Li, H and Kuzyakov, Y and Qin, K},
title = {Biochar-derived dissolved organic matter induced changes in the bacterial communities structure and metabolic functions in As and Cd contaminated soil.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122749},
doi = {10.1016/j.envres.2025.122749},
pmid = {40902774},
issn = {1096-0953},
abstract = {This study investigates the effects of pyrolytic temperature and feedstock type on the release of biochar-derived dissolved organic matter (BDOM) and its impact on the soil bacterial community and the composition of soil dissolved organic matter (SDOM). The BDOM was extracted from biochars produced from sheep bones, rice husk, and rabbit manure, prepared at low (400 °C, LPT) or high (700 °C, HPT) pyrolytic temperatures. The BDOM was then applied at a concentration of 2.5% (w/w). LPT-BDOM produced higher contents of BDOM (up to 1440±43 mg kg[-1]), resulting in higher SDOM (up to 78%, compared with control soil) after application and higher availability of nutrients (Ca, Mg, and P) and toxic metalloids (TMs; As and Cd) in soil. The addition of BDOM altered the bacterial community composition, with increased bacterial richness and diversity observed in the HPT-BDOM compared to the control. The community shift was linked with higher levels of volatile organic compounds and increased nutrient availability compared with HPT. The increase in fluorescence (up to 54%), freshness (up to 29%), biological (up to 112%), and humification (up to 52%) indices was associated with LPT-derived BDOM, particularly with sheep bone-BDOM. Manure-LPT and sheep bone-HPT enhanced hydrocarbon degradation, while rice husk-LPT enriched taxa related to nitrogen fixation and nitrate reduction. LPT treatments favored cellulolysis and fermentation, whereas HPT treatments promoted methylotrophy, aligning with their contrasting carbon lability. These findings highlight the dual role of biochar's labile fraction in shaping carbon availability, influencing SDOM dynamics, nutrient and total metals (TMs) bioavailability, and microbial ecology, underscoring the need for feedstock- and temperature-specific selection in environmental applications.},
}

@article {pmid40902732,
year = {2025},
author = {Blecksmith, SE and Oliver, A and Alkan, Z and Lemay, DG},
title = {Gut microbiome genes involved in plant and mucin breakdown correlate with diet and gastrointestinal inflammation in healthy US adults.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.08.027},
pmid = {40902732},
issn = {1541-6100},
abstract = {BACKGROUND: Dietary carbohydrates shape the composition and function of gut microbes which may potentially influence human health. It is not known if these diet-microbiome relationships are relevant to healthy American adults.

OBJECTIVE: We hypothesized that intake of dietary fiber by healthy adults would be associated with the carbohydrate active enzyme (CAZyme) capacity of their gut microbiome and that this capacity would be negatively correlated with gastrointestinal (GI) inflammation.

METHODS: We analyzed dietary data, GI inflammation and CAZyme profiles from shotgun metagenomes of fecal samples in the USDA Nutritional Phenotyping Study cohort of healthy US adults (n=330).

RESULTS: CAZyme diversity varied across participants. Plant CAZyme diversity and abundance correlated significantly with fecal pH (Shannon: adjusted R[2] = 0.053, p < 0.001; Chao1: adjusted R[2] = 0.056, p < 0.001; abundance: adjusted R[2] = 0.036, p < 0.001) and habitual energy-adjusted total fiber (Shannon: adjusted R[2] = 0.015, p = 0.029; abundance: adjusted R[2] = 0.015, p = 0.010) and soluble fiber intake (Shannon: adjusted R[2] = 0.017, p = 0.019; abundance: adjusted R[2] = 0.015, p = 0.0010). The ratio of mucin-degrading CAZymes to plant-degrading enzymes, coined here as the metric Muc2Plant, varied across participants and differed by sex (Wilcoxon, p = 0.035) and BMI (adjusted R[2] = 0.028, p = 0.017). Muc2Plant positively correlated with GI inflammation (calprotectin: adjusted R[2] = 0.038, p = 0.001; neopterin: adjusted R[2] = 0.071, p < 0.001). ML classification models were used to identify specific foods (e.g. potatoes) and microbes (e.g. Lachnospiraceae) as predictors of low Muc2Plant.

CONCLUSION: These results support the relevance of diet-microbiome relationships even in healthy adults, and that reduction of Muc2Plant, via dietary and/or microbial interventions, would be a beneficial health target to potentially prevent dysbiosis and reduce GI inflammation.

CLINICAL TRIALS REGISTRY: NCT02367287, ClinicalTrials.gov.},
}

@article {pmid40902672,
year = {2025},
author = {Sharma, S and Bashir, B and Kolekar, KA and Acharya, A and Gupta, M and Jena, R and Vishwas, S and Kaur, J and Gupta, G and Kumbhar, PS and Patle, D and Chaitanya, M and Gulati, M and Singh, SK},
title = {Tailoring the biomarkers of Alzheimer's disease using a gut microbiome-centric approach: Preclinical, clinical, and regulatory perspectives.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {102888},
doi = {10.1016/j.arr.2025.102888},
pmid = {40902672},
issn = {1872-9649},
abstract = {Alzheimer's disease (AD), a progressive neurodegenerative disorder, poses significant therapeutic challenges due to its complex etiology and limited treatment options. Traditional pharmacotherapies targeting amyloid-β (Aβ) and cholinergic pathways offer modest benefits and are often associated with adverse effects. Emerging evidence implicates gut dysbiosis and the gut-brain axis in the pathogenesis and progression of AD. This review explores the multifactorial pathophysiology of AD and evaluates the therapeutic potential of gut-based interventions such as probiotics, prebiotics, synbiotics, metabiotics, postbiotics, and fecal microbiota transplantation (FMT) in mitigating disease pathology. Emphasis has also been given on role of miRNA released from FMT in management of AD. Preclinical and clinical studies demonstrate that these strategies can restore microbial homeostasis, reduce neuroinflammation, enhance gut barrier integrity, and improve cognitive outcomes. The regulatory aspects with use of probiotics based products and FMT is also highlighted. The modulation of neuroimmune, neuroendocrine, and neural pathways through microbiota-derived metabolites offers a promising avenue for AD management. Despite encouraging findings, further research is needed to address interindividual microbiome variability, delivery challenges, and the requirement for large-scale, randomized trials. Personalized gut-targeted approaches may open new horizons for the prevention and treatment of AD.},
}

@article {pmid40902671,
year = {2025},
author = {Srour, L and Bejaoui, Y and She, J and Alam, T and El Hajj, N},
title = {Deep Aging Clocks: AI-powered Strategies for Biological Age Estimation.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {102889},
doi = {10.1016/j.arr.2025.102889},
pmid = {40902671},
issn = {1872-9649},
abstract = {Several strategies have emerged lately in response to the rapid increase in the aging population to enhance health and life span and manage aging challenges. Developing such strategies is imperative and requires an assessment of biological aging. Several aging clocks have recently been developed to measure biological aging and to assess the efficacy of longevity interventions. Biological age better reflects a person's actual age and is closely associated with health outcomes and time to mortality. Traditionally, most aging clocks assume that biological changes occur linearly over time. However, age-related changes do not necessarily follow a linear trajectory. Thus, "Deep Aging Clocks" have been developed to overcome previous clocks' limitations and better capture subtle changes that occur during aging. Here, we summarize the current deep aging clocks, including epigenetics, transcriptomics, metabolomics, microbiome, and imaging based clocks for age prediction. Recent advances in artificial intelligence (AI), utilizing deep learning techniques, have significantly enhanced the prediction of biological aging, and this would help improve aging clocks and accelerate efforts to reach longer and healthier lives.},
}

@article {pmid40902632,
year = {2025},
author = {Poulain, C and Bouras, M and Roquilly, A},
title = {Glucocorticoid Treatment in Hospital-Acquired and Ventilator-Associated Pneumonia.},
journal = {Seminars in respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2694-4781},
pmid = {40902632},
issn = {1098-9048},
support = {HAP2 - agreement number 847782//HORIZON EUROPE European Innovation Council/ ; },
abstract = {Hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP) remain among the most frequent complications in critically ill patients. Despite the implementation of modern preventive strategies and the widespread use of broad-spectrum antibiotics, both the incidence and treatment failure rates remain high. However, no adjunctive therapy is currently recommended. Glucocorticoids have recently attracted renewed interest as potential immunomodulatory agents in this setting. By reducing excessive inflammation and promoting the resolution of the immune response, they may help limit lung injury and improve clinical outcomes. This hypothesis is supported by findings from related conditions such as community-acquired pneumonia, acute respiratory distress syndrome, and severe COVID-19, where corticosteroids have demonstrated benefits in selected populations. However, evidence specific to HAP and VAP remains limited. A few randomised trials have evaluated corticosteroids for prevention, particularly in trauma patients, where findings suggest a potential benefit and highlight the relevance of this strategy in select populations. More recently, individualised approaches based on inflammatory biomarkers have shown promise in identifying patients who are more likely to benefit from corticosteroid therapy. Two randomised controlled trials, currently ongoing to evaluate their role as adjunctive treatment in established HAP and VAP, will help define the efficacy and tolerance of steroids. Given the heterogeneity of immune responses in critically ill patients, a "one-size-fits-all" approach is unlikely to be effective. Identifying inflammatory sub-phenotypes using clinical and biological markers (such as C-reactive protein or interleukin-6) may help guide a more personalized use of immunomodulatory therapies. Alterations in the lung microbiome could also influence host response and treatment efficacy. Altogether, corticosteroids represent a promising but still understudied adjunctive strategy for HAP and VAP. Future research should aim to refine patient selection and optimize treatment strategies within a precision medicine framework.},
}

@article {pmid40902606,
year = {2025},
author = {Zhang, D and Zou, Y and Shi, Y and Zhang, J and Liu, J and Wu, G and Zhang, J and Gao, Y and Chen, M and Li, YX},
title = {Systematically investigating and identifying bacteriocins in the human gut microbiome.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100983},
doi = {10.1016/j.xgen.2025.100983},
pmid = {40902606},
issn = {2666-979X},
abstract = {Human gut microbiota produces unmodified bacteriocins, natural antimicrobial peptides that protect against pathogens and regulate host physiology. However, current bioinformatic tools limit the comprehensive investigation of bacteriocins' biosynthesis, obstructing research into their biological functions. Here, we introduce IIBacFinder, a superior analysis pipeline for identifying unmodified class II bacteriocins. Through large-scale bioinformatic analysis and experimental validation, we demonstrate their widespread distribution across the bacterial kingdom, with most being habitat specific. Analyzing over 280,000 bacterial genomes, we reveal the diverse potential of human gut bacteria to produce these bacteriocins. Guided by meta-omics analysis, we synthesized 26 hypothetical bacteriocins from gut commensal species, with 16 showing antibacterial activities. Further ex vivo tests show minimal impact of narrow-spectrum bacteriocins on human fecal microbiota. Our study highlights the huge biosynthetic potential of unmodified bacteriocins in the human gut, paving the way for understanding their biological functions and health implications.},
}

@article {pmid40902416,
year = {2025},
author = {Gao, Y and Wu, Y and Wang, M and Liu, S and Liu, Z},
title = {Therapeutic effects of Panax ginseng polysaccharides on qi deficiency diabetes: Insights from microbiomics and metabolomics.},
journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences},
volume = {1267},
number = {},
pages = {124781},
doi = {10.1016/j.jchromb.2025.124781},
pmid = {40902416},
issn = {1873-376X},
abstract = {Panax ginseng, a traditional medicinal and edible plant valued for its tonifying properties, exhibits diverse pharmacological activities, including anti-fatigue, anti-oxidation and anti-diabetes. Polysaccharides represent a key active ingredient of Panax ginseng, known for their immunomodulatory properties and potential for development as health foods. However, the effect and mechanism of Panax ginseng polysaccharides (GP) on improving qi deficiency diabetes (QDD) is still unclear. In this study, a multi-omics approach integrating microbiomics, untargeted and targeted metabolomics was used to elucidate the protective effect and mechanisms of GP based on the QDD rat model. Furthermore, the prebiotic effects of GP were explored through microbiome and metabolome profiling. GP demonstrated significant therapeutic efficacy in QDD rats, manifested by the amelioration of hyperlipidemia and insulin resistance, reduction of oxidative stress, enhancement of immune responses, and restoration of intestinal injury. Untargeted fecal metabolomics and 16S rRNA gene sequencing revealed that GP significantly altered the abundance of 31 metabolites and corrected gut microbiota dysbiosis in QDD rats. Additionally, GP ameliorated bile acid metabolism disorders, significantly increased short-chain fatty acids (SCFAs) levels, and reduced branched-chain amino acids (BCAAs) concentrations. Spearman correlation analysis further confirmed significant associations between gut microbes and metabolites. Thus, GP exerts its therapeutic effect on QDD by ameliorating intestinal flora imbalance and associated metabolic disorders involving bile acids, branched-chain amino acids, and short-chain fatty acids. Together, these findings provide a foundation for the further development of GP-based functional foods.},
}

@article {pmid40902409,
year = {2025},
author = {Shukla, A and Tangney, M},
title = {Bacterial exopolysaccharides and live biotherapeutics: Orchestrating immune modulation and therapeutic potential in the gut microbiome era.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {191},
number = {},
pages = {118510},
doi = {10.1016/j.biopha.2025.118510},
pmid = {40902409},
issn = {1950-6007},
abstract = {Microbial exopolysaccharides (EPS) are emerging as critical effector molecules orchestrating host immunity. Their remarkable structural diversity, driven by variations in monosaccharide composition, charge, and glycosidic linkages, dictates potent immunomodulatory functions through specific interactions with host pattern recognition receptors (CLRs, TLRs), triggering defined cellular responses and cytokine profiles, often with minimal toxicity. Beyond direct immune effects, EPS shape the gut environment by fortifying barrier integrity and acting as prebiotics. This therapeutic potential can be harnessed via Live Biotherapeutics (LBs) as natural producers, or through purified or rationally engineered EPS for targeted intervention. Cutting-edge synthetic biology and production strategies aim to unlock this potential, though significant structure-function knowledge gaps and scalability challenges in linking specific structural motifs to predictable immune outcomes and in developing scalable, reproducible production methods remain. This review synthesizes and critically evaluates current understanding, focusing specifically on the immunomodulatory EPS produced by gut-commensal and probiotic bacteria. We highlight the promise of these molecules as therapeutics and provide a roadmap for the rational design of next-generation immunotherapies, including engineered LBs that produce tailored EPS in situ to target the gut ecosystem.},
}

@article {pmid40902289,
year = {2025},
author = {Grammatikopoulou, MG and Gkouskou, KK and Gkouvi, A and Bogdanos, DP and Lambrinoudaki, I and Goulis, DG},
title = {Vegetarian diets for longevity: friend or foe?.},
journal = {Maturitas},
volume = {202},
number = {},
pages = {108711},
doi = {10.1016/j.maturitas.2025.108711},
pmid = {40902289},
issn = {1873-4111},
abstract = {Vegetarianism is a healthy dietary pattern that is postulated to increase longevity. Vegetarianism is adopted for animal ethics, environmental reasons, or religious beliefs. Vegetarian diets are believed to improve the gut microbiome, body weight, cardiovascular health and inflammation; however, a synthesis of the up-to-date evidence does not seem to support these effects. When objective measures are sought, it becomes apparent that there is a lack of high-quality evidence regarding the effect of vegetarian diets on telomere length. Moreover, studies indicating lower mortality rates for vegetarians than for meat eaters appear to be highly biased. Among the geographical areas with higher-than-expected numbers of centenarians ('blue zones'), only one site is largely inhabited by vegetarians, whereas the rest have populations largely of flexitarians. Overall, available research does not indicate the superiority of vegetarian diets over flexitarian ones. The issue merits further research to help us understand vegetarianism's effects on longevity.},
}

@article {pmid40902203,
year = {2025},
author = {Emery, HL and Kerby, RL and Rey, FE},
title = {The Central Role of Gut Microbes in Host Purine Homeostasis.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-041522-100126},
pmid = {40902203},
issn = {1545-3251},
abstract = {Purines are ubiquitous metabolites that play evolutionarily conserved roles, including as precursors to molecules central to life. Purine synthesis is metabolically and energetically expensive; thus, under physiological conditions, intermediates of purine degradation are efficiently reused through salvage pathways. Excess purines are oxidized and eliminated via the kidneys and intestine. The efficient elimination of excess purines in humans is critical because the primary waste product of purine metabolism, uric acid, is proinflammatory and has been linked to multiple health conditions. Recent studies suggest that gut bacteria influence the purine pool locally and systemically. Bacteria can break down uric acid and other purines aerobically and anaerobically and may regulate their homeostasis. In this article, we provide an overview of purines and their metabolism, and we discuss our current understanding of the complex purine-dependent cross talk and cross-feeding between the host and the gut microbiome.},
}

@article {pmid40901870,
year = {2025},
author = {Jacobsen, Á and Mortensen, AM and Eliasen, K and Egholm, E and Nolsøe, M and Johannesen, Á},
title = {Effect of plastic and seaweed shelters on the skin microbiome of lumpfish Cyclopterus lumpus used as cleaner fish in aquaculture pens.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0322261},
doi = {10.1371/journal.pone.0322261},
pmid = {40901870},
issn = {1932-6203},
mesh = {Animals ; *Skin/microbiology ; *Aquaculture/methods ; *Microbiota ; *Seaweed ; *Plastics ; Copepoda ; *Perciformes/microbiology ; Salmo salar ; Gills/microbiology ; Skin Microbiome ; },
abstract = {Atlantic salmon (Salmo salar) aquaculture is a major industry in several countries worldwide and a growing enterprise in others. One of the main challenges the industry faces is infestations with the parasitic copepod Lepeoptheirus salmonis, or salmon lice. Several different chemical and mechanical methods are available for alleviating the problem, but often at cost to salmon welfare and/or the environment. In some regions cleaner fish have been introduced to farming facilities as an environmentally and salmon welfare friendly option for reducing sea lice infestations. In some North Atlantic countries, lumpfish (Cyclopterus lumpus) are being used as cleaner fish. However, poor welfare and high mortality rates of lumpfish in salmon farming are frequent issues, and the need to improve lumpfish welfare is great. One adaptation for salmon farms is to provide the lumpfish with shelters to meet their need to rest and hide. Plastic shelters are the most widely used form, but seaweed shelters have more recently also been applied as a more natural solution. This project investigated the potential effect of seaweed and plastic shelters on the skin and gill microbiome of lumpfish and any potential correlation to their welfare. In an experimental setup in a commercial salmon farming facility, lumpfish from pens with either plastic or seaweed shelters were sampled over a period of approximately three months. The results showed that the bacterial communities on the two shelter types were significantly different and fewer potentially pathogenic bacteria dominated the skin microbiome of lumpfish living with seaweed shelters than of those living with plastic shelters. No differences were detected in the welfare of the lumpfish and further investigations are needed to clarify any potential implications of the differences detected in the skin microbiome of lumpfish including responses to stressful conditions.},
}

Animals
*Skin/microbiology
*Aquaculture/methods
*Microbiota
*Seaweed
*Plastics
Copepoda
*Perciformes/microbiology
Salmo salar
Gills/microbiology
Skin Microbiome

@article {pmid40901853,
year = {2025},
author = {Gómez-Palacio, A and Junca, H and Vivero-Gomez, RJ and Suaza, J and Moreno-Herrera, CX and Cadavid-Restrepo, G and Pieper, DH and Uribe, S},
title = {Metagenomic profiling of the insect-specific virome in non-urban mosquitoes (Culicidae: Culicinae) from Colombia's Northern inter-Andean valleys.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331552},
doi = {10.1371/journal.pone.0331552},
pmid = {40901853},
issn = {1932-6203},
mesh = {Animals ; Colombia ; *Virome/genetics ; *Culicidae/virology ; *Metagenomics/methods ; *Metagenome ; Phylogeny ; *Insect Viruses/genetics/classification ; },
abstract = {Hematophagous mosquitoes are major vectors of diverse pathogens and serve as bioindicators in tropical ecosystems, yet their virome in non-urban Neotropical regions remains poorly characterized. We analyzed the virome of 147 mosquitoes from two natural ecosystems in Colombia using a hybrid viral identification approach, combining high-confidence and less stringent methods. Most high-confidence viral contigs remained unclassified or unknown, as expected for metagenomic surveys in novel ecosystems. However, members for the Magrovirales and Ortervirales, and other six orders were detected at lower abundance. Using a complementary, less stringent approach, we identified 168 viral species from 68 genera and 22 families across four mosquito tribes (Aedini, Culicini, Orthopodomyiini, Sabethini), with dominance of Metaviridae, Retroviridae, Iridoviridae, and Poxviridae, though many sequences could not be taxonomically assigned. Insect-specific viruses predominated, while no medically relevant arboviruses were detected. Both methods consistently identified Trichoplusia ni TED virus, Cladosporium fulvum T-1 virus, Lymphocystis disease viruses, and Oryctes rhinoceros nudivirus among the most abundant and frequently detected taxa across samples. Alpha diversity indices revealed the highest virome diversity in Sabethini, followed by Orthopodmyiini, and substantially lower richness and diversity in Aedini and Culicini. These results provide a baseline for virome characterization in sylvatic mosquitoes from Colombia and highlight the need for further research on the ecological roles of the mosquito virome in pathogen transmission and microbiome evolution.},
}

Animals
Colombia
*Virome/genetics
*Culicidae/virology
*Metagenomics/methods
*Metagenome
Phylogeny
*Insect Viruses/genetics/classification

@article {pmid40901658,
year = {2025},
author = {Zhang, X and Fan, G},
title = {The Anti-Lupus Plate: Mapping Nutritional Interventions to Inflammatory Pathways in Systemic Lupus Erythematosus.},
journal = {Food science & nutrition},
volume = {13},
number = {9},
pages = {e70890},
doi = {10.1002/fsn3.70890},
pmid = {40901658},
issn = {2048-7177},
abstract = {A complicated autoimmune illness known as systemic lupus erythematosus (SLE) is typified by multi-organ dysfunction and ongoing inflammatory processes. Although medication is still the mainstay of managing SLE, tailored nutrition provides a mechanistically sound way to reduce inflammation and promote immunological balance. The present article links certain nutritional factors to pathways controlling cytokine equilibrium, oxidative damage, endothelium integrity, and regulatory T cell activity. These elements include unsaturated fats, vitamins, polyphenols, probiotics, and fiber-derived short-chain fatty acids (SCFAs). Additionally, it assesses microbiome-based therapies and looks at nutritional habits that may have anti-inflammatory properties, such as the Mediterranean style of eating. Based on these findings, we suggest an evidence-based "anti-lupus plate" approach that takes into consideration renal function, concurrent medical conditions, and drug-nutrient relationships while matching dietary habits to pathophysiological goals. Research limitations are highlighted as major obstacles, especially the lack of broad, biomarker-driven research. These shortfalls must be filled in order to integrate food into a research-based SLE treatment. Regulated procedures, extended follow-up, and multimodal dietary treatments are necessary to achieve this.},
}

@article {pmid40901606,
year = {2025},
author = {Al-Busafi, SA and Alwassief, A and Madian, A and Atalla, H and Alboraie, M and Elbahrawy, A and Eslam, M},
title = {Exploring the interplay between metabolic dysfunction-associated fatty liver disease and gut dysbiosis: Pathophysiology, clinical implications, and emerging therapies.},
journal = {World journal of hepatology},
volume = {17},
number = {8},
pages = {108730},
doi = {10.4254/wjh.v17.i8.108730},
pmid = {40901606},
issn = {1948-5182},
abstract = {Metabolic dysfunction-associated fatty liver disease (MAFLD) now affects roughly one-quarter of the world's population, reflecting the global spread of obesity and insulin resistance. Reframing non-alcoholic fatty liver disease as MAFLD emphasizes its metabolic roots and spotlights the gut-liver axis, where intestinal dysbiosis acts as a key driver of hepatic injury. Altered microbial communities disrupt epithelial integrity, promote bacterial translocation, and trigger endotoxin-mediated inflammation that accelerates steatosis, lipotoxicity, and fibrogenesis. Concurrent shifts in bile acid signaling and short-chain fatty acid profiles further impair glucose and lipid homeostasis, amplifying cardiometabolic risk. Epidemiological studies reveal pervasive dysbiosis in MAFLD cohorts, linked to diet quality, sedentary behavior, adiposity, and host genetics. Newly developed microbiome-derived biomarkers, advanced elastography, and integrated multi-omics panels hold promise for non-invasive diagnosis and stratification, although external validation remains limited. In early trials, interventions that re-engineer the microbiota including tailored pre-/pro-/synbiotics, rational diet patterns, next-generation fecal microbiota transplantation, and bile-acid-modulating drugs show encouraging histological and metabolic gains. Optimal care will likely couple these tools with weight-centered lifestyle programmes in a precision-medicine framework. Key challenges include inter-ethnic variability in microbiome signatures, the absence of consensus treatment algorithms, and regulatory barriers to live biotherapeutics. Rigorous longitudinal studies are required to translate mechanistic insight into durable clinical benefit and improve patient-centered outcome measures.},
}

@article {pmid40901604,
year = {2025},
author = {Sharma, T and Kaushal, N and Garla, R},
title = {Toxins to treatments: Impact of environmental pollutants, gut microbiota, and natural compounds on non-alcoholic fatty liver disease progression.},
journal = {World journal of hepatology},
volume = {17},
number = {8},
pages = {108772},
doi = {10.4254/wjh.v17.i8.108772},
pmid = {40901604},
issn = {1948-5182},
abstract = {Non-alcoholic fatty liver disease (NAFLD) is the fastest-growing global contributor to the disease burden associated with the consequences of chronic liver disease, including cirrhosis and liver cancer. It is projected that more than fifty percent of the adult population, including women, smokers, and individuals without metabolic syndrome, will have NAFLD by 2040. Various mechanisms linking the gut microbiome to NAFLD and the consequent fibrosis have been discerned, which suggest the dysbiosis-induced impairment of gut endothelial barrier function, leading to hepatic inflammation through the translocation of bacterial components. NAFLD is progressively associated with environmental variables, especially exposure to heavy metals that impair liver metabolism, produce oxidative stress, and exacerbate inflammation, hence accelerating its progression. These toxicants also modify the composition of gut microbiota, hence intensifying liver damage. Comprehending the processes by which heavy metals contribute to NAFLD is essential for formulating tailored therapies. This review examines strategies to alleviate liver toxicity caused by heavy metals, including chelation therapy, dietary modifications (antioxidants and hepatoprotective nutrients), gut microbiome modulation via probiotics and postbiotics like short-chain fatty acids to restore intestinal barrier function and use of essential minerals like selenium, with potent antioxidant characteristics. Employing these measures may offer an integrated approach for addressing NAFLD in individuals subjected to heavy metal poisoning.},
}

@article {pmid40901398,
year = {2025},
author = {Sato, Y and Kanayama, M and Nakajima, S and Komatsu, Y and Kokubo, T},
title = {Comparative Analysis of Fucosyllactose-Induced Changes in Adult Gut Microbiota and Short-Chain Fatty Acid Production Using the Simulator of Human Intestinal Microbial Ecosystem Model.},
journal = {Preventive nutrition and food science},
volume = {30},
number = {4},
pages = {331-339},
doi = {10.3746/pnf.2025.30.4.331},
pmid = {40901398},
issn = {2287-1098},
abstract = {As the third most abundant solid component of human milk, human milk oligosaccharides (HMOs) exert well-known effects on the infant gastrointestinal tract, including promoting Bifidobacterium growth and preventing pathogen infection. However, the effects of HMOs on the adult gut microbiome remain unknown. In this study, we examined the effects of 2'-fucosyllactose (2'-FL) and 3-fucosyllactose (3-FL), the most abundant HMOs, on the adult gut microbiome using the Simulator of Human Intestinal Microbial Ecosystem (SHIME[Ⓡ]), which can simulate human gastrointestinal conditions. Healthy adult feces were subjected to SHIME[Ⓡ] and incubated with either 2'-FL or 3-FL. The changes in the short-chain fatty acid concentration in feces and the gut microbiota composition were investigated using high-performance liquid chromatography and 16S rRNA gene sequencing, respectively. The addition of 2'-FL or 3-FL altered the microbial composition and increased acetate, propionate, and butyrate concentrations in the adult SHIME[Ⓡ] culture. Remarkably, a difference was observed in the timing of butyrate production because of the addition of 2'-FL and 3-FL. The present findings can help clarify how FLs affect the gut microbiome of Japanese adults and support the development of targeted products.},
}

@article {pmid40901290,
year = {2025},
author = {White, I and Cunningham, J and Georgopoulou, S and Tilt, L and Rawson, R and Thilaganathan, E and Brown, MRD},
title = {Evaluation of a 12-week Mediterranean diet-based nutritional and educational programme for breast cancer survivors: impact on BMI, fatigue, dietary adherence, and menopausal symptoms.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1629806},
doi = {10.3389/fnut.2025.1629806},
pmid = {40901290},
issn = {2296-861X},
abstract = {INTRODUCTION: Breast cancer survivors commonly experience persistent symptoms after treatment. These include weight gain, fatigue, and menopausal symptoms, alongside an increased risk of long-term morbidity, including cardiovascular disease, bone loss and gut microbiome alterations. Maintaining a healthy diet is challenging due to treatment-related metabolic changes, fatigue, and dietary confusion. This research assessed the impact of a 12-week Mediterranean diet-based intervention, incorporating structured frozen meal provision and an online educational programme in breast cancer survivors. Outcomes evaluated included BMI, dietary adherence, fatigue, and menopausal symptoms. Additionally, bone, gut, and cardiovascular health within the context of survivorship was considered.

METHODS: A pre-post intervention evaluation design was employed. Seventy-two participants were enrolled, with 46 completing the full intervention and post-programme evaluation. The intervention comprised weekly delivery of Mediterranean diet-based frozen meals providing key nutrients. A concurrent online educational programme covered topics related to a bio-psycho-social approach to cancer rehabilitation. Primary and secondary outcomes were assessed pre-and post-intervention, educational programme engagement and adherence to meal provision were also evaluated.

RESULTS: Following the intervention, BMI decreased from 26.9 to 26.3 kg/m[2] (p < 0.001). Participants classified as having a healthy BMI increased from 50% at baseline to 52.2%, while the proportion classified as overweight or obese decreased from 50% to 47.8%. Mediterranean diet adherence significantly improved, with mean MEDAS scores increasing from 6.7 at baseline to 7.9 (p < 0.001). The proportion of participants with high adherence to the Mediterranean diet doubled from 8.7% to 17.4%. Menopausal symptoms significantly improved, mean scores decreasing from 23.5 at baseline to 17.5 (p < 0.001), and the prevalence of moderate symptoms reduced from 82.6% to 63%. Fatigue levels did not change significantly (p = 0.37). Subjective feedback from 28% of participants indicated perceived improvements in energy levels, citing increased consumption of fiber, omega-3 fats, and fermented foods as contributing factors. Educational programme engagement varied; 89% of participants accessed at least one module, while 40% completed all modules. Adherence to the meal provision component was high, with 79% of participants consuming at least 75% of the provided meals.

DISCUSSION: The findings highlight the potential for dietary interventions to address key survivorship concerns.},
}

@article {pmid40901273,
year = {2025},
author = {Worsley, SF and Lee, CZ and Versteegh, MA and Burke, T and Komdeur, J and Dugdale, HL and Richardson, DS},
title = {Gut microbiome communities demonstrate fine-scale spatial variation in a closed, island bird population.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf138},
doi = {10.1093/ismeco/ycaf138},
pmid = {40901273},
issn = {2730-6151},
abstract = {Environmental variation is a key factor shaping microbial communities in wild animals. However, most studies have focussed on separate populations distributed over large spatial scales. How ecological factors shape inter-individual microbiome variation within a single landscape and host population remains poorly understood. Here, we use dense sampling of individuals in a natural, closed population of Seychelles warblers (Acrocephalus sechellensis) on Cousin Island (<0.7 km diameter, 0.34 km[2] total area) to determine whether gut microbiome communities exhibit high-resolution spatial variation over fine scales (average territory area is 0.0023 km[2]). We identified a small but highly significant quadratic relationship between geographic distance and gut microbiome beta diversity across the island. Microbiome composition initially diverged with increasing geographic distance between territories. However, after ca. >300 m, microbiome composition became increasingly similar amongst individuals situated on different sides of the island. This relationship was robust to the effects of host relatedness, age, and sex. Further analysis showed that microbiome composition differed between individuals inhabiting coastal and inland territories. Warblers in coastal territories harboured greater abundances of marine bacteria and lower abundances of anaerobic taxa commonly linked to host metabolic health, suggesting that exposure to different environmental microbes and variation in host condition (which is lower in coastal territories) could drive spatial patterns of gut microbiome variation across the island. This work demonstrates that host-microbe interactions can be labile even at very fine spatial scales. Such variability may have implications for how species respond to anthropogenic disturbance in wild habitats.},
}

@article {pmid40901177,
year = {2025},
author = {Singh, A and Verma, A and Ashraf, S and Sarfraz Sheikh, D and Irfan, H and Riaz, R and Venjhraj, F and Meghwar, S and Kumar, R and Tariq, MD and Hamza, HM and Ahsan, A and Satapathy, P},
title = {Role of gut microbiota in the pathogenesis of metabolic syndrome: an updated comprehensive review from mechanisms to clinical implications.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {9},
pages = {5851-5861},
doi = {10.1097/MS9.0000000000003656},
pmid = {40901177},
issn = {2049-0801},
abstract = {Modern studies have linked gut microbiota to metabolic syndrome - a condition linked to obesity, characterized by insulin resistance, dyslipidemia, hyperglycemia, and hyperlipidemia. The gut microbiota, influenced by diet, plays a pivotal role in metabolic syndrome, affecting energy absorption, metabolism, and immune responses. Dysbiosis disrupts energy metabolism and immune responses contributing to metabolic endotoxemia, leading to insulin resistance and systemic inflammation. Key metabolites like short-chain fatty acids and bile acids, modulate insulin sensitivity and metabolic pathways. Therapeutic strategies involving probiotics and prebiotics show potential in managing diabetes and cardiovascular diseases by targeting lipid metabolism, inflammation, and atherosclerosis. However, challenges in therapy standardization and regulatory approval remain. Continued research on gut microbiota's role in metabolic syndrome could lead to innovative, personalized treatment and prevention strategies based on individual metabolic profiles. The review aims to elucidate the underlying mechanisms that influence metabolic health and cardiovascular function. It seeks to synthesize current research findings, highlighting the role of microbial composition, diversity, and metabolic byproducts in the modulation of host metabolism and cardiovascular outcomes.},
}

@article {pmid40901166,
year = {2025},
author = {Mohan, A and Ghaffar, U and Basharat, A and Nawaz, G and Khenhrani, RR and Rimsha, and Vera, GJA and Lal, PM and Tanush, D and Khan, MK and Duseja, N and Sherazi, SL and Vikash, and Kumar, V and Nanavaty, D},
title = {IgG4 unveiled: navigating the interplay with Crohn's disease - from immunology insights to machine learning.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {9},
pages = {5798-5806},
doi = {10.1097/MS9.0000000000003633},
pmid = {40901166},
issn = {2049-0801},
abstract = {Crohn's disease (CD) is a chronic inflammatory bowel disease characterized by relapsing-remitting episodes and a progressive course that often leads to bowel damage and disability. While the etiology of CD is multifactorial, involving genetic, environmental, and immunological factors, recent studies have highlighted the role of food antigens and the gut microbiome in its pathogenesis. This paper explores the immunological underpinnings of CD, with a focus on the elevated levels of serum immunoglobulin G4 (IgG4) and their correlation with disease severity and therapeutic response. We review clinical trials and case studies that demonstrate the potential of IgG4-guided exclusion diets and intravenous immunoglobulin (IVIG) therapy in ameliorating CD symptoms and inflammation. Additionally, we delve into advancements in machine learning (ML) models that utilize fecal microbiome data, offering promising diagnostic tools for distinguishing CD from ulcerative colitis and non-IBD conditions. The integration of ML in endoscopy and predictive models for therapy complications signifies a leap toward precision medicine in IBD management. This paper underscores the necessity for a nuanced understanding of CD's immunological aspects and the innovative application of ML in its diagnosis and treatment, paving the way for personalized therapeutic strategies and improved patient outcomes.},
}

@article {pmid40901066,
year = {2025},
author = {Raidal, SL and Freccero, F and Carstens, A and Weaver, S and Padalino, B},
title = {Road transportation is associated with decreased intestinal motility in horses.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1647236},
doi = {10.3389/fvets.2025.1647236},
pmid = {40901066},
issn = {2297-1769},
abstract = {BACKGROUND: Transportation of horses has been associated with colic and changes to the gastrointestinal microbiome. Percutaneous abdominal ultrasonography using wireless, point-of-care transducers can be used to assess gastrointestinal motility in field settings.

OBJECTIVES: Characterization of intestinal motility and salivary cortisol responses of horses completing commercial transportation of 10-12h.

STUDY DESIGN: Prospective observational study of 30 horses with diverse signalment and transport histories. Clinical parameters, sonographic assessment of intestinal motility and saliva samples, were collected before departure (Tpre or T0), after off-loading (T1) and 2h after arrival (T2).

RESULTS: After transportation, intestinal motility grades were reduced [Tpre median (IQR) composite motility grade: 8 (7-10), T1: 6 (4-7), T2: 7 (6-7); p < 0.001] and qualitative changes were observed in small intestinal sonographic appearance. High ambient temperatures during transport were associated with reduced intestinal motility at T1 (composite motility grade vs arrival temperature r s -0.45, p = 0.017) and T2 (cecal motility grade vs arrival temperature r s -0.74, p < 0.001). Horses with high heart rates, high sweat scores or abnormal demeanour on arrival demonstrated decreased intestinal motility. Salivary cortisol concentrations increased after transportation (mean difference, 95% CI, for T0 vs T1 was 1.66, 1.09-2.53 nmol/L) and were inversely associated with intestinal motility. Signalment and past travel history were not predictive of intestinal motility, but horses with unknown or no prior travel history (mean 12.8, 95%CI 8.2-17.4 nmol/L) had higher cortisol concentrations prior to departure than horses known to have travelled previously (7.9, 5.8-9.9 nmol/L, p = 0.023).

CONCLUSIONS: These findings suggest that transportation is associated with transient reductions in intestinal motility, particularly during hot ambient conditions and in horses with increased cortisol response. Possible effects of provision of water and food during transport warrant further investigation.},
}

@article {pmid40901024,
year = {2025},
author = {Chen, N and Li, L and Han, Y and Chen, Z},
title = {The Role of Gut Microbiota in the Modulation of Pulmonary Immune Response to Viral Infection Through the Gut-Lung Axis.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {11755-11781},
doi = {10.2147/JIR.S525880},
pmid = {40901024},
issn = {1178-7031},
abstract = {Viral respiratory infections, including influenza, respiratory syncytial virus (RSV), and SARS-CoV-2, remain major global health challenges due to their high morbidity and mortality. Emerging evidence highlights the pivotal role of the gut-lung axis in regulating pulmonary immunity. The gut microbiota communicates with the lungs via endocrine, immune, and neuroimmune pathways-particularly through metabolites such as short-chain fatty acids (SCFAs) and vagus nerve-mediated signaling-which modulate immune cells including alveolar macrophages and dendritic cells. Disruption of gut microbial balance has been linked to impaired pulmonary immune responses and increased susceptibility to infection. This review synthesizes findings from animal models and clinical studies, demonstrating that interventions such as probiotics (eg, Lactobacillus gasseri), prebiotics (eg, galacto-oligosaccharides), fecal microbiota transplantation (FMT), and Traditional Chinese Medicine (eg, Astragalus, curcumin) can enhance antiviral cytokine production, restore gut-lung homeostasis, and reduce lung inflammation. For example, FMT from H7N9-survivor mice improved influenza resistance in recipients, and oral probiotics reduced respiratory failure risk in COVID-19 patients. These findings suggest that gut-lung axis modulation is a promising adjunctive approach for treating viral respiratory infections. Future research should prioritize personalized microbiome-based therapies and large-scale clinical trials to validate efficacy and safety.},
}

@article {pmid40901000,
year = {2025},
author = {Huang, F and Li, J and Liu, D and Li, Y and Tang, J},
title = {Neonatal microbiome dysbiosis decoded by mNGS: from mechanistic insights to precision interventions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1642072},
doi = {10.3389/fcimb.2025.1642072},
pmid = {40901000},
issn = {2235-2988},
mesh = {Humans ; Infant, Newborn ; *Dysbiosis/microbiology/diagnosis/therapy ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Infant, Newborn, Diseases/microbiology/diagnosis/therapy ; Precision Medicine/methods ; *Microbiota/genetics ; },
abstract = {The neonatal period is a critical stage for microbial colonization and immune system development, with dynamic changes in the microbiome closely linked to the pathogenesis of various diseases. Traditional microbiological testing methods have low sensitivity and time-consuming limitations compared to metagenomic next-generation sequencing (mNGS), which makes it difficult to meet the diagnostic and therapeutic needs of critically ill neonates. mNGS analyzes the total DNA in a sample without bias, allowing comprehensive identification of bacteria, viruses, fungi, and parasites, and resolution of functional genes, providing new avenues for precision diagnosis and treatment of diseases such as neonatal sepsis, necrotizing enterocolitis, neonatal pneumonia, neonatal meningitis, neonatal jaundice, and other diseases. However, challenges remain, including the need to optimize sample processing workflows and develop portable devices to enhance clinical conversion potential. In this review, we summarize the application, efficacy, and limitations of mNGS in neonatal diseases. This approach paves the way for novel avenues in mechanistic research, early diagnosis, and personalized therapy for these conditions.},
}

Humans
Infant, Newborn
*Dysbiosis/microbiology/diagnosis/therapy
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Infant, Newborn, Diseases/microbiology/diagnosis/therapy
Precision Medicine/methods
*Microbiota/genetics

@article {pmid40900873,
year = {2025},
author = {Hafez, MM and Bahcecioglu, IH and Yalniz, M and Kouta, KA and Tawheed, A},
title = {Future of inflammatory bowel disease treatment: A review of novel treatments beyond guidelines.},
journal = {World journal of methodology},
volume = {15},
number = {4},
pages = {107643},
doi = {10.5662/wjm.v15.i4.107643},
pmid = {40900873},
issn = {2222-0682},
abstract = {Inflammatory bowel disease (IBD) is a chronic condition consisting of two main types: Crohn's disease and ulcerative colitis. Conventional treatments for these diseases include aminosalicylates, corticosteroids, immunomodulators, and biologics. However, these treatments have several drawbacks, including high costs for patients and numerous side effects. Recently, advanced treatments have been developed, such as small-molecule therapies, targeted biologics, innovative drug delivery systems, and microbiome-based interventions. Emerging therapies like anti-interleukin-23 monoclonal antibody inhibitors, sphingosine-1-phosphate receptor modulators, and Janus kinase inhibitors are more specialized in reducing immune activity. They enhance bioavailability, reduce side effects, and specifically target the gastrointestinal tract without affecting other systems. Innovative drug delivery systems for IBD, such as nanoparticles, hydrogels, and microgrippers, improve bioavailability and prolong drug release. The combination of conventional and advanced therapies may benefit from the synergistic effects of both. Furthermore, fecal microbiota transplantation and probiotics can help restore the balance of gastrointestinal microbiota, reducing disease flare-ups. Advances in artificial intelligence, endoscopic techniques, and stem cell therapies have shown great potential in treating IBD, although several significant challenges remain. Treating this disease requires multidisciplinary integration and the application of technology and telemedicine.},
}

@article {pmid40900872,
year = {2025},
author = {Singh, JP and Aleissa, M and Chitragari, G and Drelichman, ER and Mittal, VK and Bhullar, JS},
title = {Uncovering the role of microbiota and fecal microbiota transplantation in Crohn's disease: Current advances and future hurdles.},
journal = {World journal of methodology},
volume = {15},
number = {4},
pages = {106148},
doi = {10.5662/wjm.v15.i4.106148},
pmid = {40900872},
issn = {2222-0682},
abstract = {Crohn's disease (CD) is an idiopathic, chronic, and recurrent inflammatory condition of the gastrointestinal tract. Recent studies suggest a potential role of gut microbiota in CD, particularly dysbiosis-an imbalance in gut bacteria. While dysbiosis is consistently observed in CD, it remains uncertain whether it is a cause or a consequence of the disease. Given its association with CD, the therapeutic potential of fecal microbiota transplantation (FMT) has been explored. This review examines the role of gut microbiota in CD, evaluates the therapeutic potential of probiotics and FMT, and highlights current research findings and limitations. Key studies on the relationship between gut dysbiosis, probiotics, and FMT in CD were analyzed, with a focus on randomized trials, meta-analyses, and clinical observations. Dysbiosis is a consistent feature of CD, but its causative role remains unclear. Probiotics, prebiotics, and synbiotics have shown no efficacy in inducing or maintaining remission in CD. FMT shows potential as a therapeutic option for CD, but its efficacy remains inconsistent and inconclusive. The variability in outcomes, including diminished effects over time despite repeated FMT, underscores the need for larger, well-controlled trials. Only one randomized controlled trial (RCT) has compared FMT with sham transplantation, but the sample size was very small. Other studies are limited by factors such as small sample sizes, lack of control groups, short follow-up periods, and inconsistent methodologies, making it challenging to draw definitive conclusions. While gut dysbiosis likely plays a role in CD pathogenesis, its causative role remains uncertain. Current evidence does not support FMT as a reliable treatment for inducing or maintaining remission in CD, though it appears generally safe. Larger, standardized, RCTs are necessary to clarify the therapeutic role of FMT in CD management.},
}

@article {pmid40900844,
year = {2025},
author = {Nagamine, T},
title = {Current state of nutritional psychiatry: A scoping review of randomized controlled trials.},
journal = {World journal of methodology},
volume = {15},
number = {4},
pages = {104664},
doi = {10.5662/wjm.v15.i4.104664},
pmid = {40900844},
issn = {2222-0682},
abstract = {BACKGROUND: Nutritional psychiatry is a rapidly expanding field of research, with mounting evidence suggesting that nutritional factors may play a role in the development of psychiatric disorders.

AIM: To examine the level of evidence for nutritional psychiatry.

METHODS: A scoping review was conducted to assess the current state of nutritional psychiatry, including a search for randomized controlled trials (RCTs).

RESULTS: The review identified a total of seven papers, with many concentrating on the relationship between depression and the gut microbiome. A salient issue that emerged from this review was the paucity of sample size in many studies. The inherent complexity of nutritional studies, characterized by a multitude of potential factors and exposures that often act as confounders, poses significant challenges to the development of effective RCT designs. The analysis revealed that probiotics, though demonstrating efficacy, exhibited a modest effect size.

CONCLUSION: Conducting RCTs with effective markers is imperative from these studies. The implementation of Mendelian randomization and the investigation of mechanisms in basic research are essential complementary approaches.},
}

@article {pmid40900748,
year = {2025},
author = {Chen, L and He, H and Li, C and Nie, S and Liu, D and Shi, Q},
title = {A mini-review of the relationship between intestinal microecology and acute respiratory distress syndrome.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19995},
pmid = {40900748},
issn = {2167-8359},
mesh = {Humans ; *Respiratory Distress Syndrome/microbiology/immunology ; *Gastrointestinal Microbiome/physiology/immunology ; Dysbiosis ; },
abstract = {Acute respiratory distress syndrome (ARDS), a critical condition with high mortality, arises from dysregulated inflammation and lung injury. While evidence-based supportive care remains foundational, the lack of effective targeted therapies underscores the need for novel approaches. This review focuses on the emerging role of intestinal microecology in ARDS pathogenesis via the gut-lung axis. We discuss how ARDS disrupts gut barrier integrity, promotes dysbiosis and bacterial translocation, and highlight the significance of some gut microbiota-derived metabolites in modulating pulmonary immunity and inflammation. Furthermore, we explore how intestinal microecology influences ARDS progression through mechanisms like oxidative stress, apoptosis, autophagy, and pyroptosis. The review also examines the potential of microecology-based interventions and draws insights from failed immunomodulatory trials, emphasizing the critical interplay between the microbiome and host immunity. By synthesizing these links, this review identifies the gut microbiota as a source of potential early-warning biomarkers and novel therapeutic targets, aiming to inform future strategies for managing ARDS in the intensive care unit (ICU).},
}

Humans
*Respiratory Distress Syndrome/microbiology/immunology
*Gastrointestinal Microbiome/physiology/immunology
Dysbiosis

@article {pmid40900729,
year = {2025},
author = {Lee, W and He, T and Kurihara, Y and Shiroishi, I and Ushida, K and Tsuchida, S and Hanya, G},
title = {Seasonal Adaptation of the Gut Microbiome in Japanese Macaques: Linking Gut Microbiome Shifts With Fermentative Function.},
journal = {Ecology and evolution},
volume = {15},
number = {9},
pages = {e72076},
pmid = {40900729},
issn = {2045-7758},
abstract = {Seasonal fluctuations in food availability strongly influence the ecology of wild mammals, yet the role of the gut microbiome in mediating these challenges remains insufficiently explored. In this study, we examined how seasonal dietary shifts influence gut microbial composition and fermentative function in wild Japanese macaques (Macaca fuscata). Integrating meta-16S rRNA sequencing and in vitro fermentation assays, we investigated how the gut microbiome and the associated fermentative ability of Japanese macaques vary with seasonal dietary shifts. Although alpha diversity remained relatively stable throughout the year, significant changes in microbial composition revealed a flexible, seasonally responsive microbiome. Importantly, in vitro fermentation assays indicated that fermentative ability was stable across seasons for leaf fermentation but flexible for fermenting easily fermentable monkey chow. This dual strategy may represent an essential adaptive feature of the macaque gut microbiome, balancing metabolic stability and plasticity to effectively cope with seasonal dietary fluctuations. By linking microbial dynamics with dietary variation, this study provides new insights into the feeding ecology of Japanese macaques and highlights the essential role of gut microbiomes in supporting the ecological success of temperate primates.},
}

@article {pmid40900098,
year = {2025},
author = {Husain, MI and Giacobbe, P},
title = {Innovations in the Treatment of Mood Disorders: Exploring Microbiome, Digital and Culturally Adapted Approaches.},
journal = {Canadian journal of psychiatry. Revue canadienne de psychiatrie},
volume = {},
number = {},
pages = {7067437251374600},
doi = {10.1177/07067437251374600},
pmid = {40900098},
issn = {1497-0015},
}

@article {pmid40900031,
year = {2025},
author = {Wang, S and Yuan, P and Zhou, S and Li, L and Peng, W and Qu, S},
title = {Inulin-Based Prebiotic Delivery System Enhances Gut Microbiota Modulation to Alleviate Enteric Infections.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c05576},
pmid = {40900031},
issn = {1520-5118},
abstract = {Current antibiotic-based treatments for bacterial enteric infections often disrupt gut microbiota and face reduced efficacy due to gastrointestinal complexity and mucosal barriers. Here, we developed a genistein-loaded nanoparticle using whey protein isolate and prebiotic inulin (Gen_Wi) to improve the gut microbiome health. Gen_Wi nanoparticles mitigated oxidative stress and inflammation in intestinal epithelial cells by activating Nrf2 and suppressing NF-κB pathways, reducing TNF-α and IL-1β levels by nearly 39 and 55.6%, respectively. Remarkably, oral administration of Gen_Wi significantly mitigated Salmonella-induced intestinal damage, reducing bacterial colonization by 1000-fold, restoring goblet cell counts, and enhancing tight junction proteins. Mechanistic analysis revealed that Gen_Wi reshaped gut microbiota composition by promoting beneficial bacteria and increasing production of gut barrier-strengthening short-chain fatty acids, including acetate, propionate, and butyrate. These results highlight Gen_Wi as a prebiotic system that integrates prebiotic functionality with anti-inflammation to combat enteric infections through modulation of host-microbe interactions.},
}

@article {pmid40899832,
year = {2025},
author = {Cunningham, P and Vesey, R and Chaudry-Phipps, H and Fayle, TM and Diara, U and Chomicki, G and Lestina, D and Tuma, J and Templer, PH and Klimes, P and Henry, LM},
title = {Dietary niche shapes bacterial community in Indo-Pacific ants.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0196525},
doi = {10.1128/spectrum.01965-25},
pmid = {40899832},
issn = {2165-0497},
abstract = {Ants are among the most ecologically diverse insects, especially in tropical forest ecosystems, yet what shapes their microbial associates remains poorly understood. Most research has focused on Neotropical ants, where strong microbial associations have been linked to shifts in diet-such as herbivory-and nesting ecology. In contrast, Indo-Pacific ants, which have independently evolved similar specialized lifestyles, remain largely unstudied for their microbial associations. Here, we integrate deep-coverage 16S rRNA sequencing with stable isotope (δ[15]N) analyses to characterize the microbiomes of 239 ants from 36 species across 24 genera from the Indo-Pacific region. These ants span a broad ecological range, from ground-dwelling predators to strict arboreal herbivores, allowing us to ask: which ecological traits shape bacterial diversity in tropical ants? Our results reveal that dietary niche (δ[15]N)-rather than nesting habitat-is the primary explanatory variable of microbial diversity and composition. Ants consuming protein-rich diets (predators and omnivores) exhibit significantly higher bacterial alpha diversity and distinct community composition profiles compared to their plant-based (herbivorous) counterparts, with Rickettsiales, Rhizobiales, and Enterobacterales as major contributors to these differences. Notably, herbivorous ants tend to harbor simpler, Enterobacterales-dominated microbiomes, whereas predators support more complex communities, frequently containing Rhizobiales bacteria. Phylogenetic comparative analyses suggest that the acquisition of specific bacteria, particularly Enterobacterales, is strongly correlated with evolutionary transitions toward herbivory. Our findings expand on previously documented trends in ant-microbe interactions while also offering new insights into how symbioses drive the evolution of dietary strategies in tropical ecosystems.IMPORTANCEHost-microbe interactions have played an integral role in the evolution of specialized lifestyles in insects. Ants, with their ecological diversity and broad microbial associations, offer a powerful model for studying these dynamics. However, most research has focused on Neotropical ant lineages, limiting our broader understanding of how microbes influence ant evolution. Our study addresses this gap by examining Indo-Pacific ants-an underexplored but ecologically rich group-and reveals that diet, rather than nesting habitat, is the primary driver of microbial diversity. Notably, our findings challenge established patterns: Rhizobiales are more frequently associated with predatory ants than herbivores, contrasting with trends in Neotropical taxa. Furthermore, phylogenetic analyses suggest Enterobacterales may have played a key role in the evolution of herbivory. These results underscore the value of expanding research beyond taxa in well-studied regions and show how microbial partnerships can both reinforce and reshape our understanding of lifestyle evolution in ants.},
}

@article {pmid40899776,
year = {2025},
author = {Deng, W and Zhu, M and Lloyd, I and Nedunuri, M and Zhou, C and Liu, W and Li, Y and Li, Q and Wang, X and Zhang, Q and Jhuma, TA and Li, J and Yang, T},
title = {Beyond the Microbiome: The Gut's Role in Hypertension.},
journal = {Function (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/function/zqaf037},
pmid = {40899776},
issn = {2633-8823},
abstract = {This review emphasizes the importance of investigating the gut itself-beyond microbiota-centered studies in the context of hypertension. Since the initial discovery of the connection between gut microbiota and blood pressure regulation, research has increasingly focused on understanding the role of gut microbiota and exploring strategies to modify it for better blood pressure management. The intestine as an organ has received comparatively less attention. Yet, hypertension-associated intestinal pathological changes are well documented in both rodent models and human patients. Research to restore the intestinal function may serve as a valuable but unexplored therapeutic target. This underscores the need for a summary of our understanding of the gut's intrinsic physiological and pathological roles in hypertension. To address this, we structured our review to (1) revisit the physiological functions of the intestine; (2) describe the pathological changes that are associated with hypertension; (3) summarize available current studies targeting to restore intestinal function for blood pressure control; (4) discuss knowledge gaps and future opportunities.},
}

@article {pmid40899772,
year = {2025},
author = {Barton, X and Fontaine, JB and Tobe, SS and Oskam, CL},
title = {Harnessing 50 years of tick population genetics: Choosing the right molecular tool for contemporary research.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.70127},
pmid = {40899772},
issn = {1365-2656},
support = {19384//2021-2022 Murdoch University Research Seed Funding Scheme/ ; 12CIFS-RD2021//Cattle Industry Funding Scheme Biosecurity R&D Grant/ ; //Australian Government Research Training Program (RTP) Scholarship awarded by Murdoch University/ ; },
abstract = {Ticks are ectoparasites of major medical, veterinary and ecological importance, transmitting a wide range of pathogens to humans, companion animals and livestock. Understanding the population structure of ticks is essential for uncovering patterns of pathogen transmission, and population genetics provides a powerful method for this purpose. Tick population studies are uniquely challenging as their biology is shaped by complex interactions between hosts, microbiome and environmental factors. The choice of population genetic tools is crucial, as different methods offer varying levels of cost, throughput, resolution and accessibility, which can significantly influence the quality and scope of results. This review traces the evolution of molecular tools in tick population genetics, from early allozyme electrophoresis in the 1970s to advanced whole genome sequencing (WGS) technologies. It critically evaluates key methodologies, including allozyme electrophoresis, random amplified polymorphic DNA (RAPD), microsatellites (STRs), amplified fragment length polymorphisms (AFLP), sequence typing, restriction-site associated DNA sequencing (RADseq) and WGS, highlighting their strengths, limitations and applications. By offering a practical guide to these tools, this review helps researchers select the most appropriate methods for their studies and allows interpretation of results from older tools in the context of modern research. Sequence typing and RADseq currently provide the best balance of cost and practicality, while WGS has great potential once sequencing costs decline. This resource empowers researchers to make informed decisions, maximise the impact of their work and gain deeper insights into disease vector population structure.},
}

@article {pmid40899597,
year = {2025},
author = {Kolli, D and Rout, SK and Riek, R and Chapman, MR},
title = {The Evolution of Functional Amyloids and Their Impact on Host-Microbe Interactions.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e10109},
doi = {10.1002/advs.202510109},
pmid = {40899597},
issn = {2198-3844},
support = {R01 GM118651/NH/NIH HHS/United States ; NIH T32 AI007528/NH/NIH HHS/United States ; /SNSF_/Swiss National Science Foundation/Switzerland ; //ETH Zurich/ ; },
abstract = {Amyloids are highly ordered β-sheet-rich structures that are well conserved across the domains of life. Amyloids have a unique repetitive structure that enables autocatalytic self-replication. This property is most well-known in the context of neurodegeneration, in which proteins misfold into amyloid and begin an amyloid cascade resulting in the deposition of large amyloid aggregates characteristic of various diseases such as Alzheimer's disease and Parkinson's disease. The amyloid fold, however, can be pathological or functional. The repetitive nature of amyloids positions self-replicating amyloids as a potential key player in the origin of life. This may explain why, despite the pathogenic potential of amyloids, the amyloid fold is readily found. Many amyloids are not pathogenic and instead they contribute positively to the overall fitness of the cell. Bacteria, for example, use functional amyloids to facilitate biofilm formation, dissemination, storage, adhesion to cells or surfaces, and virulence. Interestingly, the high conservation of the amyloid fold and its ability to self-replicate enables bacterial functional amyloids to accelerate amyloid-associated disease in a human host. Here, the structure, conservation, and biology of the bacterial functional amyloids, as well as their impact on human health, are discussed.},
}

@article {pmid40899487,
year = {2025},
author = {Gu, T and Zerry, Y and Zhang, B and Tan, J and Taft, DH},
title = {Influence of Resistant Starch-Added Meat Analogs on the Resistome of Fecal Fermentations Using Human Gut Microbiota.},
journal = {Journal of food science},
volume = {90},
number = {9},
pages = {e70430},
doi = {10.1111/1750-3841.70430},
pmid = {40899487},
issn = {1750-3841},
support = {//University of Florida/ ; //U.S. Department of Agriculture/ ; },
mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Fermentation ; *Starch/metabolism ; Bacteria/genetics/classification/isolation & purification/drug effects/metabolism ; *Meat/analysis ; Adult ; Male ; Female ; *Resistant Starch ; Drug Resistance, Bacterial/genetics ; Middle Aged ; Drug Resistance, Microbial ; Meat Substitutes ; },
abstract = {Meat analogs are emerging as a sustainable alternative to meat products, and novel meat analog products could potentially offer additional health benefits. Antimicrobial resistance (AMR) poses a serious threat to global human health. Dietary choices affect the composition of bacteria in the human gut microbiome and can influence the carriage of antimicrobial resistance genes (ARGs). Individuals with lower ARG carriage tend to consume more fiber, suggesting that novel fiber-rich meat analogs may help tackle the growing AMR crisis. We therefore hypothesized that adding resistant starch to meat analogs would reduce the number and abundance of ARGs in human gut microbial communities and tested this using in vitro fecal fermentation. Fecal samples were collected from three human donors. Meat analogs formulated from raw ingredients (pea, soy, and resistant starch)-including 100% pea, 90% pea and 10% resistant starch, 100% soy, and 90% soy and 10% resistant starch-served as the carbohydrate source for fecal fermentations. Whole metagenomic sequencing was performed on DNA from the fermentations. ANOVA showed significant differences in normalized ARG abundance by carbohydrate source (p = 0.021), though not in total ARG counts. Meat analogs with resistant starch resulted in a lower median normalized abundance of drug-resistant ARGs than meat analogs without resistant starch, but post-hoc testing could not determine which groups differed from each other due to limited sample size. Adding resistant starch to meat analogs is associated with reduced ARGs in human gut microbial communities, but more research is needed. PRACTICAL APPLICATIONS: Lowering the prevalence of antimicrobial resistance genes (ARGs) is an important public health goal, and emerging work suggests that diet may contribute to controlling the spread of ARGs. One association with diet and the resistome is a lower carriage of ARGs in individuals who consume more dietary fiber. This research therefore sought to pilot if adding resistant starch to meat analogs has the potential to reduce resistance gene carriage. The results found that adding resistant starch to plant-based meat products may help lower the abundance of antimicrobial resistance genes in the human gut microbiome. This provides the justification for larger scale studies and suggests that food manufacturers may be able to develop foods, including healthier meat alternatives, to assist in preserving the function of antibiotics for future generations.},
}

Humans
*Feces/microbiology
*Gastrointestinal Microbiome
Fermentation
*Starch/metabolism
Bacteria/genetics/classification/isolation & purification/drug effects/metabolism
*Meat/analysis
Adult
Male
Female
*Resistant Starch
Drug Resistance, Bacterial/genetics
Middle Aged
Drug Resistance, Microbial
Meat Substitutes

@article {pmid40899391,
year = {2025},
author = {Zhao, D and Niu, H and Xu, L and Zhang, Z and Xu, H and Guo, H},
title = {Fungicides compatible with entomopathogenic fungi eliminate beneficial symbionts of the brown planthopper, Nilaparvata lugens.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70198},
pmid = {40899391},
issn = {1526-4998},
support = {//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: In agricultural pests, both microbial pathogens and partners, that threaten their life and benefit them, respectively, face challenges from fungicides that are ubiquitous to control crop pathogens. However, an integrated understanding of the fungicide-impacts on pest microbial pathogens and partners, which in turn influence pest management outcomes, remains largely unexplored.

RESULTS: We investigated the impacts of the most commonly used rice fungicides on an entomopathogenic fungus Cordyceps javanica, a biocontrol agent of rice pest Nilaparvata lugens, as well as the communities of bacteria and fungi within this pest. We found that while traditional fungicides were incompatible with C. javanica, the new generation fungicides Fenoxanil and Thifluzamide did not significantly inhibit its growth. Furthermore, no significant difference was observed in C. javanica infection densities and survival curves of N. lugens individuals exposed to C. javanica spores alone versus in mixtures with Fenoxanil and Thifluzamide, respectively. Subsequently, density measurements of C. javanica on rice seedlings revealed that both Fenoxanil and Thifluzamide did not reduce its habitation, ensuring the sustainable control of N. lugens feeding on rice. Additionally, while Fenoxanil and Thifluzamide did not change the fungal community of N. lugens, they remarkably reshape its bacterial community by eliminating the symbiont Arsenophonus that conferred higher fecundity on N. lugens.

CONCLUSION: Overall, the new generation fungicides may act as 'double enemies' for the pest by being compatible with entomopathogenic fungi and eliminating beneficial symbionts. Our study provides a new avenue for broadening the understanding of the functional effects of fungicides on pest management and highlights their potential to enhance biocontrol effect. © 2025 Society of Chemical Industry.},
}

@article {pmid40899389,
year = {2025},
author = {Ananda, N and Ariawan, D and Juniantito, V and Julia, V and Yunial, A and Januarti, RD and Irfan, I and Bachtiar, EW},
title = {Effects of the probiotics on the proliferation phase in oral wound healing: In vivo study.},
journal = {Dental and medical problems},
volume = {62},
number = {4},
pages = {681-690},
doi = {10.17219/dmp/195282},
pmid = {40899389},
issn = {2300-9020},
mesh = {*Probiotics/pharmacology/therapeutic use ; Animals ; Rats, Sprague-Dawley ; *Wound Healing/drug effects ; Male ; Rats ; Limosilactobacillus reuteri ; Cell Proliferation/drug effects ; Collagen ; Neovascularization, Physiologic/drug effects ; Streptococcus salivarius ; Palate/injuries ; Re-Epithelialization/drug effects ; },
abstract = {BACKGROUND: Probiotics, known for their anti-inflammatory properties and ability to balance the oral microbiome, show promise in enhancing wound healing, particularly through topical application, in oral healthcare.

OBJECTIVES: The main objective of the present study was to investigate the topical application of probiotics to accelerate oral wound healing, focusing on key indicators, like collagen density, angiogenesis, the reepithelization rate, the wound area, and the wound length.

MATERIAL AND METHODS: Palatal wounds were induced in 60 male Sprague-Dawley® rats, which were divided into 4 groups. Probiotics, including Streptococcus salivarius K12 (BLIS K12®) and Lactobacillus reuteri (Interlac® Pro-D and Interlac®), were topically administered. The rates were sacrificed on days 3, 7 and 14 to evaluate the early, middle and late proliferation phases. Histopathological examinations assessed collagen density, angiogenesis, the re-epithelialization rate, the wound area, and the wound length.

RESULTS: Probiotics showed beneficial effects on the oral wound healing indicators examined in this study. This study demonstrates the significant benefits of applying probiotics in enhancing wound healing throughout various proliferation stages. Our findings consistently highlight their positive impact across key indicators. With 3 different probiotic types, we observed improvement in all aspects of wound healing, from early to late stages.

CONCLUSIONS: The study underscores the potential of probiotics as effective agents in promoting wound repair and regeneration, offering promising avenues for enhanced clinical outcomes.},
}

*Probiotics/pharmacology/therapeutic use
Animals
Rats, Sprague-Dawley
*Wound Healing/drug effects
Male
Rats
Limosilactobacillus reuteri
Cell Proliferation/drug effects
Collagen
Neovascularization, Physiologic/drug effects
Streptococcus salivarius
Palate/injuries
Re-Epithelialization/drug effects

@article {pmid40899311,
year = {2025},
author = {Lee, JY and Park, SS and Cho, IK and Moon, KS and Cho, Y},
title = {Bacillus subtilis pb2441 Ameliorates Hepatic Steatosis by Decoupling Liver and Fat Tissue Lipid Accumulation in a High-Fat Diet-Fed Mouse Model.},
journal = {Journal of medicinal food},
volume = {},
number = {},
pages = {},
doi = {10.1177/1096620X251372435},
pmid = {40899311},
issn = {1557-7600},
abstract = {Nonalcoholic fatty liver disease (NAFLD) is a global health issue, often associated with gut dysbiosis. In recent years, probiotics have gained attention as potential therapeutic agents for NAFLD. This study explored the effects of a single strain, Bacillus subtilis with high surfactin secretion, on C57BL/6 mice fed a high-fat diet (HFD), a model for NAFLD, for 13 weeks. We conducted efficacy assays over 13 weeks on liver fat accumulation and gut microbiome modulation. Bacillus supplementation reduced body weight gain and fat accumulation in the liver, but not in adipose tissues. This indicates a decoupling of hepatic and adipose lipid accumulation-meaning that lipid reduction occurred selectively in the liver, independent of changes in peripheral fat storage. Hepatic steatosis and liver enzyme levels were significantly improved. The supplementation largely maintained or amplified the bacterial abundance shifts caused by the HFD. Only seven-including Lactobacillus, Akkermansia, and Romboutsia-out of 53 bacterial genera which were significantly changed by HFD were restored to normal levels by the supplementation. These three genera are commonly regarded as beneficial for human health due to their roles in gut barrier integrity, immune modulation, and metabolic regulation. In contrast, despite these limited changes in bacterial composition, bacterial enzyme analysis suggested significant metabolic modulation by Bacillus supplementation. A single strain of Bacillus subtilis, instead of a mixture of multiple bacterial strains, can prevent hepatic steatosis without affecting fat tissue weight, underscoring its potential as a targeted therapeutic option through microbiome modulation of a few beneficial bacteria. [Figure: see text].},
}

@article {pmid40899134,
year = {2025},
author = {van Smoorenburg, MY and Nerwinska, JL and van Hamme, JL and Remmerswaal, EBM and Segui-Perez, C and Strijbis, K and Geijtenbeek, TBH},
title = {Bacterial Vaginosis-Associated Prevotella timonensis Enhances Dendritic Cell-T Cell Clustering and Subsequent T Cell Proliferation.},
journal = {European journal of immunology},
volume = {55},
number = {9},
pages = {e70051},
pmid = {40899134},
issn = {1521-4141},
support = {91218017/NWO_/Dutch Research Council/Netherlands ; 670424/ERC_/European Research Council/International ; },
mesh = {*Vaginosis, Bacterial/immunology/microbiology ; *Dendritic Cells/immunology ; Female ; Humans ; *CD4-Positive T-Lymphocytes/immunology ; *Prevotella/immunology ; Cell Proliferation ; Lymphocyte Activation/immunology ; Monocytes/immunology ; Vagina/microbiology/immunology ; },
abstract = {Dysbiosis of the vaginal microbiome is associated with increased inflammation in the female genital tract. Microbiota associated with bacterial vaginosis (BV), such as Gardnerella vaginalis, Megasphaera elsdenii, and Prevotella timonensis, replace the health-associated bacterium Lactobacillus crispatus and cause inflammation affecting mucosal integrity and immunity. However, it remains unclear how these BV-associated bacteria modulate immune cells and enhance inflammation. Here, we investigated whether BV-associated bacteria directly affected dendritic cell (DC) function. Notably, P. timonensis but not M. elsdenii induced cell-cell clustering between monocytic cell lines and, importantly, between primary DCs and primary CD4 T cells. Our data indicate that this increased clustering is independent of LFA-1. Moreover, P. timonensis enhanced DC-mediated CD4 T cell proliferation. Altogether, these results suggest that P. timonensis-induced cell-cell clustering contributes to the elevated mucosal inflammation observed during bacterial vaginosis.},
}

*Vaginosis, Bacterial/immunology/microbiology
*Dendritic Cells/immunology
Female
Humans
*CD4-Positive T-Lymphocytes/immunology
*Prevotella/immunology
Cell Proliferation
Lymphocyte Activation/immunology
Monocytes/immunology
Vagina/microbiology/immunology

@article {pmid40899103,
year = {2025},
author = {Stamper, CE and Cominski, TP and Hoisington, AJ and Yoe, CW and Agbolou, XM and Stiritz, VA and Interian, A and Goodman, M and Hazlett, EA and Myers, CE and Beck, KD and Brenner, LA},
title = {Longitudinal Effects of Mild Traumatic Brain Injury on the Gut Microbiome and Acoustic Startle Response in Male and Female Rats.},
journal = {Journal of neurotrauma},
volume = {},
number = {},
pages = {},
doi = {10.1177/08977151251372118},
pmid = {40899103},
issn = {1557-9042},
abstract = {Traumatic brain injuries (TBI) frequently occur and can lead to lasting negative cognitive, physical, and mental health outcomes. The biological response to even mild TBIs (mTBI) includes well-characterized inflammatory sequelae that start immediately post-injury, remain for weeks, and can develop into long-term systemic inflammation. Studies have shown that TBI influences multiple physiological systems, including the gastrointestinal tract, through bidirectional communication modulated, in part, by the gut microbiome. Brainstem functioning post-TBI, as measured by acoustic startle sensorimotor processing, might play a role in this feedback loop. The current study investigated pre- to post-TBI (lateral fluid percussion injury model) changes in microbial communities and acoustic startle response in male and female rats. That is, the influence of mTBI on gut microbiome and sensorimotor processing was explored to examine: 1) overall and sex-specific differences in the gut microbiome and taxa in response to mTBI; 2) overall and sex-specific differences in sensorimotor processing following mTBI; and 3) associations between the gut microbiome and sensorimotor processing. Results showed mTBI had a limited effect on microbial diversity overall, and the same was observed in males and females independently. Yet, mTBI was associated with differences in 13 genus-level taxa. Further evaluation highlighted that 11 of the 13 genus-level taxa were sex-specific, with several being known to have short-chain fatty acid-producing capabilities. Alterations in sensorimotor processing were identified following mTBI; however, no sex-specific differences were evident. In addition, no associations were observed between sensorimotor processing and the gut microbiome. This study contributes longitudinal and sex-specific findings to the growing body of research examining the diverse effects of mTBI on the brain and gut microbial communities.},
}

@article {pmid40899073,
year = {2024},
author = {Balajewicz-Nowak, M and Kabzinska-Turek, M and Kosiawa, V},
title = {Association between cervical intraepithelial neoplasia progression and cervicovaginal microbiota status - narrative review.},
journal = {Folia medica Cracoviensia},
volume = {64},
number = {4},
pages = {15-21},
doi = {10.24425/fmc.2024.152178},
pmid = {40899073},
issn = {0015-5616},
mesh = {Humans ; Female ; *Uterine Cervical Dysplasia/microbiology/virology/pathology ; *Papillomavirus Infections/complications/microbiology ; *Microbiota ; *Vagina/microbiology ; *Uterine Cervical Neoplasms/microbiology/virology/pathology ; Disease Progression ; *Cervix Uteri/microbiology ; },
abstract = {In 2022, an estimated 660 000 women were diagnosed with cervical cancer worldwide and about 350 000 women died from the disease. Human papillomavirus (HPV) infection is one of the most common sexually transmitted infections. However, only a small percentage of high-risk (HR) HPV infections progress to cervical precancer and cancer. In this study, we presented the role of the cervicovaginal microbiome(CVM) in the natural history of HPV infection. Non-viral factors associated with the outcomes of HR-HPV infections have not been fully elucidated. While smoking, hormonal contraceptive use, and parity are associated with developing precancer and cancer, systemic and local immune responses are thought to be important for clearance and control of infection. In addition, specific host immune regulatory alleles are associated with risk of cervical cancer development. There is a strong association between changes in vaginal microbiota and persistent HPV infection, and improving vaginal microbial environment would reduce the risk of developing cervical cancer.},
}

Humans
Female
*Uterine Cervical Dysplasia/microbiology/virology/pathology
*Papillomavirus Infections/complications/microbiology
*Microbiota
*Vagina/microbiology
*Uterine Cervical Neoplasms/microbiology/virology/pathology
Disease Progression
*Cervix Uteri/microbiology

@article {pmid40898827,
year = {2025},
author = {Lu, L and Li, Y and Zhou, Y and Chen, J and Fu, T and Zhuang, J and Peng, H and Liu, F and Sun, L and Lu, J and Xiong, G},
title = {Triptolide improves microbial dysbiosis and metabolite disorder in db/db mice.},
journal = {Renal failure},
volume = {47},
number = {1},
pages = {2552913},
doi = {10.1080/0886022X.2025.2552913},
pmid = {40898827},
issn = {1525-6049},
mesh = {Animals ; *Diterpenes/pharmacology/therapeutic use ; *Phenanthrenes/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Epoxy Compounds/pharmacology/therapeutic use ; Mice ; *Dysbiosis/drug therapy/microbiology ; Male ; Disease Models, Animal ; *Diabetic Nephropathies/drug therapy/microbiology/metabolism ; Metabolome/drug effects ; Metabolomics ; Kidney/pathology/drug effects ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Diabetic kidney disease (DKD) is an increasing global public health problem. Triptolide (TP) has a good therapeutic effect on DKD and is widely used in China. However, the mechanism of TP is still unclear.

METHODS: Db/db mice models were subjected to TP for 12 weeks. UHPLC-QE-MS and 16S rRNA amplicon sequencing were used to investigate the correlations between the metabolome, microbiome, and DKD-related indicators under DKD condition.

RESULTS: TP demonstrated significant nephroprotective effects in db/db mice, ameliorated renal functional impairment and structural damage while attenuated inflammatory responses associated with DKD. Notably, TP administration effectively restored gut microbiota dysbiosis in db/db mice. Comparative analysis identified ten altered microbial taxa across groups, including Bifidobacterium, Erysipelotrichaceae_U-CG003, Herminiimonas, Domibacillus, Methylobacterium-Methylorubrum, Phascolarctobacterium, Dorea, Ralstonia, UCG-002, and Dubosiella, suggesting their potential utility as discriminative biomarkers for DKD progression and therapeutic response. Metabolomic profiling revealed 11 significantly perturbed metabolites, with small molecule pathway database (SMPDB) enrichment analysis highlighting three critical metabolic pathways: vitamin K metabolism, propionate metabolism, and steroid biosynthesis. Mechanistic investigations suggest that TP may reduce the inflammatory response through the JNK/STAT/P53 pathway, regulate the changes of intestinal flora, and correct renal metabolic disorders to exert renal protection.

CONCLUSION: TP may play a renal protective role by regulating the changes of intestinal microflora and correcting renal metabolic disorders, which may be related to the JNK/STAT/P53 pathway involved in reducing the inflammatory response. In addition, Vitamin K2 has a synergistic anti-inflammatory effect with TP.},
}

Animals
*Diterpenes/pharmacology/therapeutic use
*Phenanthrenes/pharmacology/therapeutic use
*Gastrointestinal Microbiome/drug effects
Epoxy Compounds/pharmacology/therapeutic use
Mice
*Dysbiosis/drug therapy/microbiology
Male
Disease Models, Animal
*Diabetic Nephropathies/drug therapy/microbiology/metabolism
Metabolome/drug effects
Metabolomics
Kidney/pathology/drug effects
Mice, Inbred C57BL

@article {pmid40898817,
year = {2025},
author = {Yan, H and Li, Z and Cai, J and Wang, L},
title = {Helicobacter pylori eradication: developing antibiotic-independent antimicrobial moieties.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/1040841X.2025.2554619},
pmid = {40898817},
issn = {1549-7828},
abstract = {Helicobacter pylori (H. pylori) infection is a common and serious infectious disease that requires eradication as it is the primary cause of gastric adenocarcinoma. However, the growing prevalence of antibiotic resistance, severe side effects, and the inability of current treatments to effectively address biofilm-embedded, intracellular, and dormant H. pylori strains, alongside their long-term gut microbiome disruptions, have rendered standard therapies increasingly ineffective. This predicament underscores the pressing need to explore antibiotic-independent antimicrobial moieties. This pursuit involves a multifaceted approach, encompassing innovative strategies that target critical regulatory points in H. pylori infection. These include the development of urease inhibitors, anti-adhesion therapies, treatments for intracellular H. pylori, strategies for eradicating dormant forms, interventions against biofilm formation, among others. Additionally, various antibiotic-independent antimicrobial moieties that can target multiple bacterial mechanisms and forms are being explored, such as intraluminal photoacoustic therapy, the use of nanoparticles, antimicrobial peptides (AMPs), vaccines, phage therapy, and other cutting-edge treatments. These strategies offer promising prospects for non-antibiotic treatments to overcome this persistent and often debilitating infection.},
}

@article {pmid40898716,
year = {2025},
author = {Romagnuolo, M and Calabrese, L and D'Onghia, M and Cioppa, V and Rubegni, P and Marzano, AV and Moltrasio, C},
title = {The Role of Cutaneous B-Cells in Hidradenitis Suppurativa: From Preclinical Evidence to Novel Targeted Therapies.},
journal = {Experimental dermatology},
volume = {34},
number = {9},
pages = {e70163},
doi = {10.1111/exd.70163},
pmid = {40898716},
issn = {1600-0625},
mesh = {*Hidradenitis Suppurativa/immunology/drug therapy/therapy ; Humans ; *B-Lymphocytes/immunology ; *Skin/immunology ; Animals ; Molecular Targeted Therapy ; },
abstract = {Hidradenitis Suppurativa (HS) is a chronic autoinflammatory skin disease of the terminal hair follicle, whose pathogenesis is complex and multifactorial. Alongside a predisposing genetic background, environmental/epigenetic factors, alterations in the skin microbiome, and dysregulation of both innate and adaptive immune responses contribute to the persistent inflammatory network. Despite advancing knowledge, the exact molecular and cellular mechanisms underlying HS have yet to be untangled. Moreover, the lack of experimental disease models that closely mimic disease phenotypes or pathophysiological processes has hindered the development of effective therapeutic strategies. Recent advances in immunology highlighted the important role of B cells in HS pathogenesis, not only in the chronic but also in the early stages of the disease, implying great potential for the development of novel therapeutic targets. This study gathers the preclinical and clinical scientific evidence that supports the role of cutaneous B-cells in HS pathogenesis and the therapeutic potential of their targeting.},
}

*Hidradenitis Suppurativa/immunology/drug therapy/therapy
Humans
*B-Lymphocytes/immunology
*Skin/immunology
Animals
Molecular Targeted Therapy

@article {pmid40898692,
year = {2025},
author = {Pickett, AT and Cooke, RF and Mackey, SJ and do Prado, MB and Gouvêa, VN},
title = {Effects of intravenous lipopolysaccharide administration on physiological and ruminal responses that modulate feed intake in beef cattle.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf311},
pmid = {40898692},
issn = {1525-3163},
abstract = {This experiment evaluated feed intake, physiological reactions, and ruminal parameters in beef cattle receiving or not a lipopolysaccharide (LPS) challenge. Ten ruminally-cannulated Angus steers [590 ± 16 kg of body weight (BW)] were housed in individual pens on d -7, ranked by BW, and allocated to 1 of 2 treatments administered intravenously on d 0: 1) 0.5 μg/kg of BW of bacterial LPS (Escherichia coli 0111:B4) diluted in 5 mL of 0.9% sterile saline, or 2) 5 mL of 0.9% physiological saline (CON). Steers had free-choice access to wheat hay, water, and a commercial vitamin + mineral mix (d -7 to 7). Hay DMI was evaluated daily from d -5 to 7. Prior to treatment administration on d 0 (h 0), polyester bags containing 4 g of ground dietary hay (DM basis) were immersed into the rumen of each steer, and incubated for 0, 4, 8, 12, 24, 36, 48, 60, and 72 h for dry matter (DM) and neutral detergent fiber (NDF) degradability evaluation. Steers were also intra-ruminally pulse-dosed with 5 g of Co-EDTA and with Cr-EDTA (0.1 g/kg of BW) prior to treatment administration. Rumen fluid samples were collected at 0, 2, 4, 6, 8, 12, 16, 24, 36, and 48 h, and blood samples were collected at -2, 0, 2, 4, 6, 8, 12, 18, 24, 36, 48, 60, 72, 96, 120, and 144 h relative treatment administration. Values obtained before treatment administration were used as covariate within each respective analysis. Steers receiving LPS had less (P ≤ 0.05) hay DMI on d 0 and 1, less (P < 0.01) rumen liquid volume and dilution rate, and less (P < 0.01) ruminal effective degradability of DM and NDF compared with CON. Steers receiving LPS had greater (P ≤ 0.05) plasma haptoglobin concentration from 18 to 144 h, greater (P ≤ 0.04) plasma cortisol concentration from 2 to 12 h, and less (P ≤ 0.04) total plasma total Cr concentration from 2 to 18 h compared with CON. Steers receiving LPS had less (P ≤ 0.03) mean concentrations of acetate, butyrate, valerate, and total VFA in the rumen fluid compared with CON. Steers receiving LPS had less (P ≤ 0.05) mean total bacterial load in the ruminal fluid, and less mean prevalence of the phyla Spirochaetes and Fibrobacteres and the genera Treponema compared with CON. Results from this experiment suggest that LPS administration elicited host-microbiome endocrine interactions that impaired feed degradability and VFA production in the rumen, particularly a reduction in total bacterial load, which may have contributed to a 48-h decrease in hay DMI.},
}

@article {pmid40898564,
year = {2025},
author = {Zhang, D and He, F and Zhao, Z and Zheng, Y and Shi, B},
title = {Effect of the gut microbiota-blood metabolite axis on anti-influenza IgG levels after vaccination: A Mendelian randomization study.},
journal = {Medicine},
volume = {104},
number = {35},
pages = {e44100},
doi = {10.1097/MD.0000000000044100},
pmid = {40898564},
issn = {1536-5964},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Influenza Vaccines/immunology ; Mendelian Randomization Analysis ; *Immunoglobulin G/blood/immunology ; Genome-Wide Association Study ; *Influenza, Human/prevention & control/immunology ; Influenza A Virus, H1N1 Subtype/immunology ; Male ; Female ; *Antibodies, Viral/blood ; Vaccination ; Longitudinal Studies ; },
abstract = {While antibody responses to influenza viruses have been extensively studied, the immunogenicity of influenza vaccines remains highly variable among individuals. Growing evidence suggests that the gut microbiota (GM) and associated metabolites play a critical yet understudied role in shaping host immunity, including responses to vaccines. However, the mechanistic pathways linking microbial communities, blood metabolites, and influenza vaccine-induced antibody production remain poorly understood. This study investigates the GM-blood metabolite-antibody level axis to identify potential modulators of vaccine immunogenicity. In this study, 2-sample Mendelian randomization (MR) were conducted to identify causality. We performed 2-sample MR using genome-wide association study data from MiBioGen (GM, N = 14,306), Avon Longitudinal Study of Parents and Children (anti-influenza immunoglobulin G (IgG), N = 4735), and metabolite genome-wide association study (N = 7824). Instrumental variables (P < 5 × 10-[5], r[2] < 0.01, F > 10) were analyzed via inverse-variance-weighted (IVW) regression with sensitivity analyses (MR-Egger, weighted median). Two-step MR assessed metabolite mediation effects. Our analysis revealed positive correlations between influenza virus subtype influenza A H1N1 virus IgG levels and the Escherichia Shigella genus, Ruminococcaceae UCG002, and Ruminococcaceae UCG003 genera. Conversely, negative correlations were observed with the Erysipelotrichaceae family, Rhodospirillaceae family, Barnesiella genus, and Eubacterium fissicatena group. For influenza virus subtype influenza A H3N2 virus IgG antibodies, positive associations were identified with the Bacteroidales S24-7*group, Defluviitaleaceae family, Adlercreutzia, Desulfovibrio, Eubacterium eligens group, Eubacterium rectale group, and Ruminococcaceae UCG014 genus, while negative associations were noted for the Negativicutes class and Selenomonadales order. Two-step MR analysis suggested mediation effects: the association between the Erysipelotrichaceae family and influenza A H1N1 virus IgG levels was partially mediated by bradykinin, des-Arg(9) (proportion mediated: 27.16%, P = .006). The link between Ruminococcaceae UCG014 and influenza A H3N2 virus IgG levels was partially mediated by alanine (proportion mediated: 26.86%, P = .002). This study demonstrates the potential role of blood metabolites as mediators in modulating the impact of the GM on immunity to influenza.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Influenza Vaccines/immunology
Mendelian Randomization Analysis
*Immunoglobulin G/blood/immunology
Genome-Wide Association Study
*Influenza, Human/prevention & control/immunology
Influenza A Virus, H1N1 Subtype/immunology
Male
Female
*Antibodies, Viral/blood
Vaccination
Longitudinal Studies

@article {pmid40890568,
year = {2025},
author = {Gong, X and Lai, Z and Li, L and Fan, L and Ren, Y and Zhong, Q and Mao, Q},
title = {Esketamine alleviates depressive-like behavior in mice via modulation of the microbiota-gut-brain axis and amino acid metabolism.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {570},
pmid = {40890568},
issn = {1471-2180},
support = {CSTB2022NSCQ-BHX0010//The Chongqing Postdoctoral Foundation/ ; 2023MD734117//the China Postdoctoral Science Foundation/ ; CSTB2022NSCQ-MSX1165//the Natural Science Foundation Project of Chongqing, Chongqing Science and Technology Commission/ ; },
abstract = {BACKGROUND: The microbiota‒gut‒brain axis is increasingly recognized as a critical pathway in the pathogenesis of depression and the response to antidepressant treatments. Esketamine(S-Ket), a noncompetitive glutamatergic N-methyl-D-aspartate receptor (NMDAR) antagonist, has shown a rapid and long-lasting antidepressant effects. However, the precise mechanisms underlying the antidepressant actions of S-Ket remain unclear.

METHODS: In this study, we explore the role of gut microbiota and metabolites in the antidepressant effects of esketamine in lipopolysaccharide (LPS)-induced mouse model of depression. Behavioral tests, including the open-field test, forced swimming test, tail suspension test, and sucrose preference test, were conducted to evaluate the antidepressant efficacy of S-Ket. Additionally,16S rRNA sequencing and untargeted metabolomics were performed to characterize the gut microbiota and metabolome profiles in fecal and hippocampal tissues of LPS-induced mice treated with S-Ket. Bioinformatics analysis was employed to identify key changes. Spearman's rank correlation analyses were used to explore associations between depression-like behaviors (DLBs), differential gut microbes, and metabolites.

RESULTS: S-Ket significantly alleviated DLBs in LPS-induced mice, partially restored the disrupted gut microbiota composition (β-diversity), and improved metabolic dysfunction. Pathway analysis revealed that four key amino acid metabolism pathways were significantly altered in both fecal and hippocampal samples, including ‘Glutathione metabolism’. ‘Alanine, aspartate, and glutamate metabolism’, ‘Arginine biosynthesis’, and ‘Arginine and proline metabolism’. Further analysis indicated that the genus Rikenella was significantly correlated with DLBs and host amino acids (e.g., glutamic acid and pyro glutamic acid).

CONCLUSIONS: This study demonstrates that a single dose of S-Ket rapidly alleviates depression-like behaviors in LPS-induced mice, and its mechanisms are associated with regulating both the composition of gut microbiota and associated metabolites in fecal and hippocampal tissues, particularly the alteration of host amino acid metabolism. These results highlight the potential role of the gut–microbiome–amino acid metabolism axis in esketamine’s antidepressant effects and suggest that targeting this axis may offer therapeutic benefits for depression. Further research is needed to fully elucidate these mechanisms.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04181-3.},
}

@article {pmid40898384,
year = {2025},
author = {Nieto, PA and Nakama, C and Trachsel, J and Goad, D and Soderborg, TK and Tan, DS and Orlandi, A and Yuan, Q and Song, E and Mueller, NT and Mars, RA and Hoy, CS and Sukhum, KV},
title = {Improving immune-related health outcomes post-cesarean birth with a gut microbiome-based program: A randomized controlled trial.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {36},
number = {9},
pages = {e70182},
doi = {10.1111/pai.70182},
pmid = {40898384},
issn = {1399-3038},
support = {//Seeding Inc. DBA Tiny Health/ ; },
abstract = {BACKGROUND: Infants born via Cesarean section (C-section) often have a distinct gut microbiome and higher risks of atopic and immune-related conditions than vaginally delivered infants. We evaluated whether a microbiome-based program could shift gut microbiome composition and improve microbiome-associated health outcomes in C-section born infants.

METHODS: This open-label, randomized, controlled trial included full-term C-section-born infants aged 0-3 months, randomized to an intervention (n = 25) or control arm (n = 29). Over 6 months, the intervention arm received two microbiome reports, personalized recommendations based on their microbiome, educational materials, and coaching calls focused on microbiome health. Parents reported health conditions via surveys.

PRIMARY OUTCOME: Difference between study arms in relative abundance of key gut microbiome taxa and functional genes. Other outcomes: Changes in a C-section index-a taxonomy-based metric comparing C-section-associated taxa to vaginally-associated taxa-and prevalence of atopic conditions.

RESULTS: Compared to controls, the intervention arm had higher Bifidobacterium (p = .025, q = .121) and higher abundance of genes associated with human milk oligosaccharide degradation (e.g., α-L-fucosidase, p = .019, q = .046) at timepoint 2. In the intervention arm, the C-section index decreased to a level similar to vaginally born infants (p = .807, q = .807). At the end of the intervention, atopic dermatitis prevalence was lower in the intervention arm than in controls (odds ratio, 0.17 [95% CI, 0.023-0.723], p = .031).

CONCLUSION: A personalized microbiome-based program can modulate the gut microbiome of C-section-born infants and may reduce the risk of atopic conditions (ClinicalTrials.gov: NCT06424691).},
}

@article {pmid40897914,
year = {2025},
author = {Kavanagh, K},
title = {A mammoth toothache: bacterial community discovered in mouth of ancient mammal.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40897914},
issn = {1476-4687},
}

@article {pmid40897718,
year = {2025},
author = {Huang, L and Li, Y and Zhang, C and Jiang, A and Zhu, L and Mou, W and Li, K and Zhang, J and Cui, C and Cui, X and Lin, A and Luo, P and Wei, T},
title = {Microbiome meets immunotherapy: unlocking the hidden predictors of immune checkpoint inhibitors.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {180},
pmid = {40897718},
issn = {2055-5008},
support = {B2023341//Guangdong Provincial Medical Science and Technology Research/ ; 82172750//National Natural Science Foundation of China/ ; },
abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized cancer immunotherapy, with the microbiome significantly influencing treatment outcomes. Analysis of 4663 studies (2014.01-2024.10) identified 71 eligible randomized controlled trials (RCTs) and cohort studies (41 viral, 30 bacterial). Analyses included subgroup assessments by cancer type, microbial taxa, and ICI regimens. Among 4663 identified studies, 71 met inclusion criteria (41 viral, 30 bacterial). Viral status, particularly hepatitis B virus (HBV) and human papillomavirus (HPV), significantly associated with ORR and DCR. Bacterial enrichment correlated with improved survival in hepatobiliary (OS: HR = 4.33, 95%CI: 2.20-8.50) and lung cancers (PFS: HR = 1.70, 95%CI: 1.04-2.78). Multi-microbiome models demonstrated superior outcome prediction, with microbial diversity correlating with improved PFS (HR = 0.64, 95%CI: 0.42-0.98). Viral status showed cancer-specific associations with SAEs. The microbiome serves as a valuable predictor of ICI outcomes. Future studies should emphasize large-scale RCTs, standardized assessment methods, and host-microbiome interactions.},
}

@article {pmid40897518,
year = {2025},
author = {Salihoglu, R},
title = {The Microbiome Shaping Cancer Development, Progression, and Therapeutic Response.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00091.2025},
pmid = {40897518},
issn = {1531-2267},
abstract = {The human microbiome is emerging as a key regulator of cancer biology, modulating tumor development, immune dynamics, and therapeutic responses across diverse malignancies. In this review, recent insights are synthesized regarding how microbial communities (bacterial, fungal, and viral) shape oncogenic signaling, immune checkpoint blockade (ICB) efficacy, and metabolic reprogramming in lung, pancreatic, colorectal, breast, cervical, melanoma, and gastric cancers. Mechanistic links between microbial metabolites, intratumoral colonization, and host immune phenotypes are highlighted proposing that the microbiome constitutes a programmable axis within the tumor immune-metabolic ecosystem. Drawing on multi-omics integration and translational studies, a shift from associative profiling toward causal, spatially resolved, and intervention-ready frameworks is proposed. This perspective positions the microbiome not as a passive bystander, but as a co-evolving participant in tumor progression and treatment response, with the potential to reshape diagnostics, prognostics, and therapeutic strategies in precision oncology.},
}

@article {pmid40897178,
year = {2025},
author = {Xu, T and Jiao, X and Liu, G and Chen, X and Luo, Q and Zhang, G and Li, B and Zhang, Y and Li, X and Cheung, Y and Chai, X and Huang, Y and Wu, H and Deng, F and Chen, F and Liang, G},
title = {Oral virome metagenomic catalog links Porphyromonas gingivalis phages to obesity and type 2 diabetes.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102325},
doi = {10.1016/j.xcrm.2025.102325},
pmid = {40897178},
issn = {2666-3791},
abstract = {The human microbiota has a critical role in maintaining human microbiome homeostasis and health, yet the viral component of the oral microbiome remains largely unidentified. We establish the Human Oral Virome Database (HOVD) catalog, a freely accessible online resource cataloging 24,440 bacteriophage viral operational taxonomic units and 83 eukaryotic viral genomes. Utilizing HOVD, we investigate oral virome variation and its correlation with oral bacteria and gut virome in 220 obese individuals with or without type 2 diabetes mellitus (T2D). Obese individuals with T2D exhibit reduced oral viral diversity, lower correlations with clinical features, disrupted viral-bacterial correlations, and enhanced oral-gut virome transmission. Furthermore, we computationally identify bacteriophages that infect Porphyromonas gingivalis and screen six putative endolysins. Experimental validation reveals that a mixture of three endolysins significantly inhibits Porphyromonas gingivalis growth. These findings highlight the potential of phage-derived endolysins for periodontitis with T2D, offering a path toward oral and systemic disease intervention.},
}

@article {pmid40897151,
year = {2025},
author = {Wei, W and Qiu, Z and Xiao, L and Huang, Y and Chen, M},
title = {Genetic evidence for a causal relationship between oral bacterial taxa and asthma in east Asian population.},
journal = {Cytokine},
volume = {195},
number = {},
pages = {157021},
doi = {10.1016/j.cyto.2025.157021},
pmid = {40897151},
issn = {1096-0023},
abstract = {BACKGROUND: Emerging evidence highlights the significant role of microbiota (lung and gut) in the development of asthma. However, the potential effect between oral microbiota and asthma remains poorly understood.

METHODS: This study performed a bidirectional Mendelian randomization (MR) study using summary statistics from the genome-wide association studies of oral microbiota, immune cell traits and asthma. Various MR analysis methods were employed, including inverse variance weighted (IVW), constrained maximum likelihood model averaging-based method (cML-MA-BIC), maximum likelihood (ML), weighted mode, weighted median, and MR-robust adjusted profile score (MR-RAPS). Additionally, mediation analyses were performed to identify the immune cell traits that mediate these effects.

RESULTS: This study identified 12 oral bacterial taxa and 36 inflammatory cytokines associated with asthma. After identifying the oral microbiota and immune cell characteristics associated with asthma, we applied a mediation MR framework to investigate whether immune cell traits mediate the effect of microbiota on asthma. Finally, we identified eight immune cell traits that mediate asthma caused by bacteria.

CONCLUSIONS: Our results highlight the causal associations between oral bacterial taxa, immune cell traits, and asthma, providing evidence that various immune cell traits serve as critical mediators between the oral microbiota and asthma. The link between the oral microbiome and asthma has important implications for clinical practice.},
}

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

@article {pmid40897048,
year = {2025},
author = {Egea, LG and Jiménez-Ramos, R and Rodríguez-Arias, L and Infantes, E},
title = {Microplastics threaten seagrass carbon sinks through microbial changes.},
journal = {Marine pollution bulletin},
volume = {222},
number = {Pt 1},
pages = {118638},
doi = {10.1016/j.marpolbul.2025.118638},
pmid = {40897048},
issn = {1879-3363},
abstract = {Seagrass beds are key blue carbon ecosystems but their capacity to sequester carbon is threatened by microplastic (MP) pollution in the marine environment. A 28-day mesocosm experiment examined the effect of microplastics and nutrient enrichment (NE) on eelgrass (Zostera marina). We tested concentrations of 320 mg MPs per 100 g DW sediment[-1] and 70 mg of total nitrogen per 100 g DW sediment[-1] to evaluate impacts on plant performance, microbiome composition and detritus decomposition (after 60-days assay). MPs reduced leaf growth rate (-39 %), net production (-57 %) and rhizome elongation (-35 %), while NE shifted microbial assemblages, increasing phyllosphere and rhizosphere by 1.6-fold. MPs favored the growth of microbial taxa related with the consumption of plant-derived polysaccharides and lignin compounds (1.7-fold higher), accelerating detritus decomposition by 1.5-fold. Critically, MPs produced a notable decrease of bacteria involved in sulfur-cycle (0.45-fold lower under combined MPs + NE vs. NE alone), disrupting REDOX processes essential for seagrass survival in reducing sediments. By reducing plant growth, altering microbial communities and accelerating organic matter turnover, MPs compromise the carbon sequestration capacity of eelgrass meadows. These findings evidence the need for policies addressing plastic pollution to safeguard seagrass ecosystem services while prompt further research on mechanisms of interaction between MPs and biota.},
}

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

@article {pmid40896863,
year = {2025},
author = {Zhang, X and Chen, X and Ruan, S and Wang, H and Xu, Y and Fu, H and Lin, S and Efferth, T and Tian, Y and Li, C and Shi, S and Hong, C},
title = {Gut microbiome and glial cell dialog: Role of TCM in the treatment of depression.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {147},
number = {},
pages = {157196},
doi = {10.1016/j.phymed.2025.157196},
pmid = {40896863},
issn = {1618-095X},
abstract = {BACKGROUND: Depression is characterized by low mood, cognitive slowing and a tendency to self-harm, and has a complex etiology involving abnormalities in neuromodulation (e.g., monoamine transmitter imbalance and reduced neuroplasticity). Gut-brain axis studies have shown that dysregulation of gut flora can trigger neuroinflammation and impair glial cell function, leading to depression. Modulation of flora-glial cell interactions and their pharmacological mechanisms is key to treatment.

PURPOSE: This review discusses the new discovery of the interaction mechanism between glial cells and gut microflora in depression models, providing new targets and directions for the treatment of TCM in depression. Further bridging the gap in current research on the gut-brain axis in depression.

METHOD: Literature was searched, analyzed, and collected using PubMed, Web of Science, and China National Knowledge Infrastructure. The search terms used were " gut-brain axis ", " neuroinflammation ", " depression ", " glial cells ", " Gut microbiota "," TCM ", etc. Several combinations of these keywords were used. Studies using models of depression were used.

RESULTS: During the literature screening process, a total of 1685 records were initially retrieved from databases. After removing duplicates (1068) and other ineligible records (200), 417 articles underwent title and abstract screening, with 134 excluded. Further full-text assessment of 283 articles led to the inclusion of 149 new studies. Reasons for exclusion included mismatched outcomes (8), ineligible experimental models (12), among others. Combined with 14 previously included studies, the final review comprised 163 articles (See Figure 1). The dialog mechanism between gut microflora and glial cells plays an important role in the pathogenesis of depression. In addition, there are a variety of herbal active ingredients and herbal formulas that can significantly affect the composition of the gut flora and glial cell activation in depression models, and consequently, there is significant antidepressant potential.

CONCLUSION: Intestinal flora metabolites modulate glial cell activation, and the release of inflammatory factors by glial cells alters intestinal flora composition, both phenomena are contributory to depressive pathogenesis. In addition, we found that a variety of TCMs can improve depression based on this mechanism, providing new perspectives for clinical diagnosis and treatment of depression.},
}

@article {pmid40896847,
year = {2025},
author = {Muir, RQ and Xu, J and Medcalf, AD and Pluznick, JL},
title = {Novel Advances in Our Understanding of Sex-Dependent Control of Blood Pressure.},
journal = {Annual review of physiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-physiol-050724-022450},
pmid = {40896847},
issn = {1545-1585},
abstract = {Sex differences in blood pressure are evident from puberty through menopause, with premenopausal females exhibiting lower blood pressure than males. This review discusses key factors contributing to sex differences in blood pressure, focusing on the normotensive state. Key contributions from a number of systems are discussed, including cardiovascular and renal function, oxidative stress, immune cell involvement, the microbiome, and the roles of the nervous system and renin-angiotensin-aldosterone system. Additionally, we highlight novel advances in the field, including findings related to the G protein-coupled estrogen receptor (GPER), Klotho, olfactory receptor 558 (OLFR558), and the four-core genotype (FCG) model. Insights from clinical data and their implications for hypertension management are also considered. In sum, this review aims to integrate current knowledge on sex differences in blood pressure regulation to inform future research and clinical care.},
}

@article {pmid40896761,
year = {2025},
author = {Shaheen, N and Iyer, P and Eluri, S},
title = {New Approaches to Screening for Barrett Esophagus.},
journal = {Gastroenterology & hepatology},
volume = {21},
number = {6},
pages = {353-361},
pmid = {40896761},
issn = {1554-7914},
abstract = {Current screening methods for Barrett esophagus (BE), the precursor to esophageal adenocarcinoma (EAC), are inadequate with less than one-third of screen-eligible patients currently undergoing screening. In addition to low screening rates, key issues include overemphasis on gastroesophageal reflux disease symptoms and lack of provider awareness, owing in part to heterogeneous guidelines. To address these challenges, several new approaches are being explored: swallowable cell collection devices, exhaled volatile organic compounds analysis, blood-based molecular biomarkers, microbiome analysis, and alternative visualization methods such as transnasal and capsule endos-copy. Proposed strategies to improve BE screening integrate enhanced risk stratification tools using machine learning and electronic health record data, noninvasive screening for low-risk patients, traditional endoscopy for high-risk patients, primary care education, and public health initiatives to increase awareness. This article highlights the latest developments in BE detection, including noninvasive screening methods and strategies to improve risk stratification, that have the potential to reduce EAC incidence and mortality.},
}

@article {pmid40896728,
year = {2025},
author = {Chalif, J and Morton, M and McLaughlin, E and Gonzalez, A and Fulton, J and Sciuva, J and Marcu, I and Bixel, KL and Cohn, DE and Cosgrove, CM and Copeland, LJ and Nagel, CI and Backes, F and O'Malley, DM and Spakowicz, DJ and Chambers, LM},
title = {Exploratory evaluation of immunotherapy response and medication use in endometrial and cervical carcinoma.},
journal = {Gynecologic oncology reports},
volume = {60},
number = {},
pages = {101782},
doi = {10.1016/j.gore.2025.101782},
pmid = {40896728},
issn = {2352-5789},
abstract = {OBJECTIVE: (s): To assess the effect of medication use during immune checkpoint inhibitor (ICI) therapy on treatment response and oncologic outcomes.

METHODS: An IRB-approved single-institution retrospective cohort study was performed in patients with endometrial cancer (EC) and cervical cancer (CC) who were treated with ICIs from January 1, 2017 to January 1, 2023. Concomitant medications used during the ICI course were recorded. The associations between medication use and ICI response, progression-free survival (PFS), and overall survival (OS) was assessed.

RESULTS: 217 CC and EC patients were treated with ICIs during this study period; 32 % (n = 71) had CC, and 67 % (n = 146) had EC. There was a significant difference in ICI complete response between CC patients who did and did not use oral steroids during treatment. Of CC patients who achieved a complete response, 28 % (n = 7) used steroids vs. 13.6 % (n = 6) of non-steroid users (Fisher's exact p = 0.045). In patients with EC, proton pump inhibitor (PPI) use was associated with ICI response, with 43.8 % (n = 21) of PPI users achieving a complete response vs. 16.3 % (n = 15) of non-PPI users (chi-squared p = 0.002). PPI use in the EC cohort was associated with improved progression-free survival and overall survival (log-rank p < 0.05). This was also demonstrated among mismatch repair-deficient EC patients where PPI use during ICI therapy significantly associated with both PFS (HR 0.26, 95 % CI 0.12-0.55; p < 0.001) and OS (HR 0.22, 95 % CI 0.08-0.59; p < 0.001).Conclusion(s)In this retrospective cohort study of EC and CC patients treated with ICI therapy, medication use, specifically PPIs and oral steroids, was seen to have a significant positive effect on ICI response, PFS, and OS.},
}

@article {pmid40896726,
year = {2025},
author = {Borgianni, L and Cardinali, G and Cassetti, C and Cavalieri, D and De Filippo, C and De Giuseppe, R and Di Leonardo, R and Druzhinina, IS and Duprex, WP and Egamberdieva, D and Gophna, U and Kurtböke, Dİ and Lanfranco, L and Mattanovich, D and Moore, ERB and Nguyen, NK and Overmann, J and Pizza, M and Ricci, A and Ron, EZ and Shurtleff, A and Stein, L and Theuretzbacher, U and Tonjum, T and Ventura, M and Yacoby, I and Young, P and Yurkov, A and Rappuoli, R},
title = {The power of microbial life for the transformation towards a sustainable planet: key messages from the 2024 IUMS Congress in Florence, the city of the Renaissance.},
journal = {microLife},
volume = {6},
number = {},
pages = {uqaf018},
doi = {10.1093/femsml/uqaf018},
pmid = {40896726},
issn = {2633-6693},
abstract = {The 2024 International Union of Microbiological Societies Congress was held in Florence, the city of Renaissance. The theme was to increase the awareness of the power of microbial life, recognizing that it can lead the transformation towards a sustainable planet. The meeting gathered over 1400 experts from more than 90 countries and focused on the transformative potential of microbiology in addressing global challenges and aligning microbial science with the Sustainable Development Goals. Six roundtable discussions explored the pivotal role of microbiology in mitigating climate change, preparing for pandemics, producing sustainable energy, promoting a One Health approach, understanding microbiome dynamics, and developing data infrastructure. The discussions revealed that microbes are still overlooked agents in sustainable solutions. Expert panellists at the roundtables discussed microbial innovations in hydrogen and biofuel production, conversion of greenhouse gases, biomanufacturing, and soil restoration, the role of microbiome in immune health, the importance of cross-kingdom interactions, and the integration of food, environmental, and microbiomes under the One Health framework. Panels stressed the need for equitable access to vaccines, diagnostics, and data sharing, especially in the face of antimicrobial resistance. The importance of global collaboration, data repositories, and regulatory alignment, was repeatedly emphasized. The congress invited calls for the formation of an international microbiology coalition, need for interdisciplinary partnerships, increased investment in microbial technologies, updating of regulatory frameworks, and integration of microbiome science into public health and environmental policy. Microorganisms are the oldest architects of nature, able to build a sustainable future for the planet.},
}

@article {pmid40896512,
year = {2025},
author = {Chi, YY and Xiang, JY and Li, HM and Shi, HY and Ning, K and Xiang, H and Xie, Q},
title = {Lignans-rich extract of Schisandra chinensis prevent alcohol-associated liver disease by regulating the gut microbiota and tryptophan metabolism.},
journal = {Current research in food science},
volume = {11},
number = {},
pages = {101172},
doi = {10.1016/j.crfs.2025.101172},
pmid = {40896512},
issn = {2665-9271},
abstract = {Alcohol-associated liver disease (ALD) has emerged as a global public health concern, and gut microbiota plays a decisive role in its pathogenesis. Schisandra chinensis, a functional edible berry, exhibits hepatoprotective properties. However, the preventive effects of its main active component lignans against ALD, as well as their connections with gut microbiota and intestinal metabolites remain unclear. This study employed a mouse model of ALD induced by chronic-binge ethanol feeding to evaluate the hepatoprotective effects of lignans-rich extract of S. chinensis (SCL) interventions at different doses. 16S rDNA sequencing and metabolomic analysis were used to investigate microbial and metabolite profiles in intestinal contents. The hepatoprotective activity of key metabolite responding to SCL was further verified by in vivo and in vitro experiments. The results demonstrated that SCL effectively restored intestinal barrier function and alleviated alcohol-induced hepatic injury. SCL modulated intestinal tryptophan (Trp) metabolism and restored indole-3-acetic acid (IAA) levels. Concurrently, SCL reshaped the gut microbiota composition, enriched L. reuteri. Further in vivo and in vitro investigations demonstrated that SCL-mediated enrichment of L. reuteri contributed to intestinal IAA restoration which reactivated the ethanol-suppressed AHR pathway, enhanced intestinal barrier integrity, reduced lipopolysaccharide translocation into circulation and ultimately attenuates liver injury. Collectively, SCL prevent ALD by regulating intestinal microbiota and Trp metabolism. This study provides a scientific foundation for the development of S. chinensis as a functional food for ALD prevention.},
}

@article {pmid40896489,
year = {2025},
author = {Zhang, J and Liang, W and Wang, J and Longshaw, M and Dong, X and Yang, Q and Liu, H and Deng, J and Tan, B and Chi, S},
title = {Methanotroph (Methylococcus capsulatus) bacteria meal, influences the intestinal microbiome, and improves intestinal barrier function and immunity in hybrid grouper (Epinephelus fuscointestinetatus ♀ × E. lanceolatus ♂).},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {22},
number = {},
pages = {321-336},
doi = {10.1016/j.aninu.2025.03.020},
pmid = {40896489},
issn = {2405-6383},
abstract = {The hybrid grouper (Epinephelus fuscointestinetatus ♀ × E. lanceolatus ♂) is an important aquaculture marine species in China. The current study was designed to test the effects of methanotroph (Methylococcus capsulatus) bacteria meal (MBM) on hybrid grouper growth and intestinal health outcomes. Five iso-nitrogenous and iso-lipidic diets were formulated, comprising a control diet (MBM0) with 400 g/kg fish meal (FM) as the main protein source, and four experimental diets, in which FM was replaced at 5% (MBM2), 10% (MBM4), 20% (MBM8) and 30% (MBM12) with 20, 40, 80 and 120 g/kg of MBM, respectively. The 450 healthy juvenile hybrid grouper (initial weight 28.84 ± 0.05 g) were randomly allocated into five groups, with three replicates in each group and 30 fish in each replicate. They were fed for eight weeks prior to being sampled for transcriptome and microbiome research. The final body weight (FBW, P < 0.001) and weight gain rate (WGR, P < 0.001) were obviously enhanced in MBM2 and MBM8 groups compared to MBM0 group, and the specific growth rate (SGR) in the MBM2 and MBM8 groups were significantly enhanced compared to MBM0 group (P < 0.001). The condition factor (CF) in MBM4 and MBM8 groups were considerably reduced than that in MBM0 group (P = 0.008). The hepatosomatic index (HSI) in MBM8 and MBM12 groups were obviously enhanced than that in the other groups (P < 0.001). In the intestinal microflora analysis, the number of operational taxonomic units (OTUs) exhibited a significant linear increase with increasing MBM replacement ratio (P = 0.015). Concurrently, the richness of bacterial families and genera showed significant linear enrichment (P = 0.023 and P = 0.028, respectively). There was a decrease in the relative abundance of the potentially pathogenic genera Photobacterium and Vibrio in the MBM-fed groups compared with the control group. The study has effectively shown that MBM may significantly enhance the health and growth of hybrid groupers by partially replacing FM in diets at the required amount of 3.70%, as determined by WGR regression analysis.},
}

@article {pmid40896484,
year = {2025},
author = {Liu, Y and Wang, X and Zhao, X and Ma, Y and Qu, L and Wang, Z and Ning, Z},
title = {The combination of dietary active dry yeast and Bacillus subtilis improves productive performance, egg quality, and immunity of aged breeder hens.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {22},
number = {},
pages = {442-458},
doi = {10.1016/j.aninu.2025.04.004},
pmid = {40896484},
issn = {2405-6383},
abstract = {This study aimed to investigate the effects of dietary supplementation with active dry yeast (ADY) alone or in combination with Bacillus subtilis (BS) on physiological parameters (laying performance, egg quality, blood indexes), reproductive traits, ileum microbiome, metabolome, and uterine gene expression in aged breeder hens. A total of 336 Hy-line brown layer hens aged 55 weeks were randomly assigned to three groups using a completely randomized design: control group (Con, basal diet), ADY group (1 g ADY/kg diet), and ADY-BS combination group ([1 g ADY + 0.1 g BS]/kg diet). Compared with the Con group, ADY-BS group significantly improved egg production (P = 0.024) and reduced feed conversion ratio (P = 0.034), while also significantly increasing feed intake compared to the ADY group (P = 0.020). Additionally, both ADY and ADY-BS significantly enhanced eggshell-breaking strength compared to untreated hens (P < 0.001), with ADY-BS further notably increasing lysozyme levels (P = 0.031), antibody titers against avian influenza H5 and H9 subtypes (P = 0.008 and P = 0.001, respectively), and calcium content in serum (P = 0.021). Analysis of the ileal microbiota revealed significant modifications, as evidenced by reduced richness (Chao1 index: P = 0.016 and P = 0.008 for the ADY and ADY-BS groups, respectively) and improved evenness (Simpson index: P = 0.032 for both groups). Relative to the untreated group hens, ADY enriched Streptococcus (P = 0.007), Enterococcus (P = 0.009), and Gallibacterium (P = 0.027), whereas ADY-BS remarkably enriched Lactobacillus (P = 0.028). Furthermore, Lactobacillus enriched in ADY-BS group hens was negatively correlated with ileum differential metabolites such as phenylalanyl-threonine and phenylalanyl-tryptophan. Correlation analysis based on RNA-seq data indicated that these differential metabolites were negatively associated with the expression of genes related to calcium ion transport and immune pathways in the uterus. In summary, the results suggest that ADY-BS combination significantly improved production performance, eggshell quality, gut microenvironment, and immune function compared to ADY alone in late-laying hens.},
}

@article {pmid40896480,
year = {2025},
author = {Yang, J and Li, Y and Sun, M and Guo, S and Lin, P and Wang, A and Jin, Y},
title = {Understanding the differences in rumen bacteria and their impact on dairy cows' production performance: A review.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {22},
number = {},
pages = {259-279},
doi = {10.1016/j.aninu.2025.04.006},
pmid = {40896480},
issn = {2405-6383},
abstract = {This review aimed to summarize the relationship between rumen bacteria and production performance in dairy cows. The composition and metabolic functions of rumen bacteria significantly influenced production performance. However, previous studies lacked a systematic review of how variations in rumen bacterial composition correlate with production performance. This review described the differences in rumen bacterial composition among dairy cows with varying production performance, focusing on milk yield and composition, feed efficiency (FE), average daily gain (ADG) and methane production. Additionally, we explored the differences in rumen bacteria across different parities and testing time points. Through this systematic summary, we discussed the impact of rumen bacterial composition on dairy cow production performance and provided new insights and guidelines for devising targeted microbiome adjustment strategies.},
}

@article {pmid40896477,
year = {2025},
author = {Kong, Y and Wang, Q and Wang, J and Qiu, X and Yang, Y and Liu, J and Yang, F and Qi, R},
title = {Indole-3-propionic acid enhances glycolytic myofiber formation in piglets through PI3K-mTOR activation and gut microbiota-driven tryptophan metabolic alteration.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {22},
number = {},
pages = {363-374},
doi = {10.1016/j.aninu.2025.02.013},
pmid = {40896477},
issn = {2405-6383},
abstract = {Indole-3-propionic acid (IPA) is a metabolite of tryptophan produced by gut bacterial catabolism that has a variety of functions, including anti-inflammatory, free radical scavenging, and regulation of glucose metabolism. The present study evaluated the effects of dietary IPA supplementation on early muscle development in piglets. Twelve healthy Landrace × Rongchang piglets at 30 d of age were randomly divided into control (CON group, 10.78 ± 0.040 kg) and 0.01% IPA (IPA group, 10.80 ± 0.062 kg) for 50 d. The results showed that IPA increased the proportion of glycolytic myofibers significantly in muscle (P = 0.002). Supplementation with IPA increased pyruvate kinase (PK) activity (P = 0.025) and gene expression of myosin heavy chain 4 (MYH4) in muscle (P < 0.001), and decreased the gene expression of MYH7 and MYH2 (P < 0.01) and mitochondrial respiratory chain complexes (P < 0.01). Supplementation with IPA enhanced insulin sensitivity and activated phosphatidylinositol 3-kinase (PI3K)-protein kinase B (Akt)-mammalian target of rapamycin (mTOR) pathway in vivo and accelerated differentiation of C2C12 cells in vitro. In addition, IPA affected gut microbiota by increasing the Firmicutes-to-Bacteroidetes ratio and significantly reduced the concentration of kynurenine and melatonin (P < 0.05). In conclusion, IPA increased glycolytic myofibers and promoted muscle growth by regulating the homeostasis of glucose metabolism mediated by PI3K-mTOR signaling and the gut microbiota in piglets.},
}

@article {pmid40896414,
year = {2025},
author = {Prandovszky, E and Liu, H and Severance, EG and Splan, VW and Dickerson, FB and Yolken, RH},
title = {Altered gut microbial diversity, composition, and metabolomic potential in patients with major depressive disorder and recent suicide attempt.},
journal = {Brain, behavior, & immunity - health},
volume = {48},
number = {},
pages = {101081},
doi = {10.1016/j.bbih.2025.101081},
pmid = {40896414},
issn = {2666-3546},
abstract = {This study investigates the role of the gut microbiome in suicidal behavior among individuals with major depressive disorder (MDD). Fecal samples from 50 hospitalized patients with MDD, including 35 with recent suicide attempts (60 % female) and 15 without a history of suicide (73 % female), were analyzed using 16S rRNA and shotgun sequencing to assess microbiome diversity and metabolic potential. Results revealed that suicide attempters exhibited significantly greater microbial richness and distinct beta-diversity patterns. Notably, they had higher levels of Fenollaria timonensis and lower levels of Corynebacterium aurimucosum. Additionally, 25 metabolic pathways differed between groups, with several linked to energy metabolism and amino acid processing-processes previously associated with MDD and suicidal behavior. These findings suggest that microbiome composition may influence suicide risk through gut-brain axis-mediated pathways, although due to the exploratory nature of this study further investigation is needed to validate our findings. Given the microbiome's modifiability, future research should explore microbial-targeted interventions as a potential strategy for suicide prevention in individuals with MDD.},
}

@article {pmid40896191,
year = {2025},
author = {Song, W and Liu, D and Xing, Z and Jiang, L and Tang, Y and Xu, Z and Li, L and Yan, S and Fu, X and Wang, Y and Wu, Q},
title = {Association of the newly proposed dietary index for gut microbiota and all-cause and cardiovascular mortality among individuals with diabetes and prediabetes.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1621277},
doi = {10.3389/fnut.2025.1621277},
pmid = {40896191},
issn = {2296-861X},
abstract = {BACKGROUND: The Gut Microbiota Dietary Index (DI-GM) is a newly developed assessment tool that quantitatively evaluates the nutritional modulation of intestinal microbial communities through systematic characterization of diet-microbiome interactions. The relationship between DI-GM and the risk of death has not been elucidated in patients with diabetes or prediabetes. The present cohort study examined the longitudinal relationship between DI-GM scores and both overall mortality and mortality from cardiovascular disease in this clinically vulnerable population.

METHOD: The investigation used data from the National Health and Nutrition Examination Survey (NHANES) 2007-2018. Analytical approaches, including multivariable-adjusted Cox proportional hazards regression, restricted cubic spline (RCS) modeling, stratified subgroup evaluations, and sensitivity assessments, were employed to examine the relationships linking DI-GM scores to mortality outcomes among individuals with diabetes or prediabetes.

RESULT: During an average monitoring duration of 77.39 months within the cohort of 8,409 participants, 1,430 fatalities from all causes were documented, including 381 cases attributed to cardiovascular events. Multivariable-adjusted Cox regression analyses showed a negative correlation, with a 1-unit increase in DI-GM corresponding to an 8% lower all-cause mortality risk (HR = 0.92, 95% CI: 0.89-0.95; p < 0.001) and an 11% reduction in cardiovascular-specific mortality (HR = 0.89, 95% CI: 0.83-0.95; p < 0.001). When comparing extreme quartiles of DI-GM distribution, participants in the highest quartile exhibited 26% lower all-cause mortality (HR = 0.74, 95% CI: 0.63-0.87; p < 0.001; trend p < 0.05) and 30% lower cardiovascular mortality (HR = 0.70, 95% CI: 0.52-0.96; p = 0.025; trend p < 0.05) than those in the lowest quartile. Subgroup analyses confirmed the consistency of the results in most categories. Restricted cubic splines demonstrated negative correlations between DI-GM and both mortality outcomes. The Beneficial Gut Microbiota Score (BGMS) exhibited inverse associations with mortality risks, while the Unfavorable Gut Microbiota Score (UGMS) showed no significant relationship. In the sensitive analysis, the robustness of multiple interpolation results was verified by deleting missing data.

CONCLUSION: Among patients with diabetes or prediabetes, elevated DI-GM levels were negatively correlated with all-cause mortality and cardiovascular mortality risks.},
}

@article {pmid40896188,
year = {2025},
author = {Pathak, AK and Kolesnikova, A and Sambreker, DU and Org, E and Kivisild, T},
title = {Precision nutrition across climates: decoding diet, tradition, and genomic adaptations from South Asia to the Arctic.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1638843},
doi = {10.3389/fnut.2025.1638843},
pmid = {40896188},
issn = {2296-861X},
abstract = {Human populations have developed distinct genetic adaptations to diet in response to changes in lifestyle and environments in which they live. Particularly contrasting patterns of dietary adaptations are expected in populations living in tropical versus extreme cold environments. This article explores the genetic, dietary, and microbiome-related adaptations in populations of South Asia and the Arctic. We review adaptations related to high-carbohydrate, plant-based diets in South Asians and compare these against adaptations in Arctic populations who have evolved to rely on fat- and protein-rich diets from marine and animal sources. We discuss how these genetic adaptations interact with traditional diets and microbiomes, and the implications for chronic disease risks as modern, westernized diets disrupt ancestral gene-diet-microbiome interactions. By comparing these regions, we highlight the need for genome-based nutrition created strategies that account for genetic diversity, local dietary traditions, and environmental context to promote precision health and prevent diet-related chronic diseases. This analysis offers new insights into how nutrition, culture, and genetics intersect in shaping population-specific health outcomes.},
}

@article {pmid40896133,
year = {2025},
author = {Kim, J and Nam, KH and Lee, JW and Chun, SJ},
title = {Bacterial and fungal microbiome dataset from holobionts of CP4-EPSPS-containing hybrids and wild-type Brassica juncea in South Korea.},
journal = {Data in brief},
volume = {62},
number = {},
pages = {111966},
doi = {10.1016/j.dib.2025.111966},
pmid = {40896133},
issn = {2352-3409},
abstract = {This dataset provides comprehensive profiles of bacterial and fungal communities associated with the holobionts of CP4-EPSPS-containing hybrids and wild-type B. juncea in a natural roadside habitat. The hybrids were genetically consistent with B. napus × B. juncea origin and possible backcrossing with B. juncea, though the site and mechanism of hybridization are unclear. A total of 120 holobiont samples, including flowers, leaves, dead leaves, roots, and surrounding soil, were collected from twelve wild-type and twelve hybrid individuals (60 samples per group), in a natural roadside environment. Bacterial 16S rRNA and fungal ITS genes obtained through the Illumina Miseq approach were employed to characterize the holobiont-associated microbiomes. Metadata and raw sequences collected in this study are available from the National Center for Biotechnology Information (BioProject ID: PRJNA1237916 and 1237917). Amplicon Sequence Variants (ASVs) of bacteria and fungi were processed using the DADA2 pipeline. After quality filtering, trimming, and eliminating the chimeric sequences, 15,131 bacterial and 5,353 fungal ASVs were identified in the holobiont. Proteobacteria in bacteria, and Ascomycota in fungi were the predominant groups in the holobiont. Given the reported unintended releases and hybridization of transgenic B. napus in South Korea, this dataset provides a comprehensive baseline of the microbial communities associated with wild-type and hybrids, offering novel insights into their holobiont structures.},
}

@article {pmid40896132,
year = {2025},
author = {Pant, A and Srinivasan, J and Venkadesan, S and Sarkar, S and Babu, SP and Mohanty, D and Das, B and Arimbasseri, GA},
title = {Comprehensive genomic insights into Mixta calida isolated from the faecal sample of a tuberculosis patient in India.},
journal = {Data in brief},
volume = {62},
number = {},
pages = {111983},
doi = {10.1016/j.dib.2025.111983},
pmid = {40896132},
issn = {2352-3409},
abstract = {Mixta calida, formerly known as Pantoea calida, is a motile Gram-negative, facultatively anaerobic bacterium with coccoid rod morphology. Although previously considered non-pathogenic, emerging case studies indicate its potential role in causing serious infections, including bacteraemia, meningitis, sepsis, and implant-associated infections. This study presents the first whole-genome sequence of M. calida of Indian origin, isolated from the stool sample of a tuberculosis patient undergoing treatment. Sequencing was performed using the Illumina NextSeq 2000 and Oxford Nanopore PromethION platforms. The genomic data provides valuable insights into the antimicrobial resistance traits and mobile genetic elements of the bacterium, contributing to a deeper understanding of its pathogenic potential.},
}

@article {pmid40895792,
year = {2025},
author = {Yu, HL and Hou, XW and Zhao, JX and Liu, GH and Meng, JX and Wei, YJ and Cai, Y and Liu, J and Shang, KM and Ni, HB and Liu, R and Ma, H and Nan, FL and Zhang, XX and Chen, BN and Yang, X},
title = {Insights from metagenomics on microbial biosynthesis of vitamins B and K2 in chicken gut microbiota.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1646825},
doi = {10.3389/fvets.2025.1646825},
pmid = {40895792},
issn = {2297-1769},
abstract = {INTRODUCTION: The chicken gut microbiome plays a pivotal role in nutrient absorption and overall health, contributing to the biosynthesis of essential vitamins. However, the biosynthesis of vitamins B and K2 by the whole gut microbiome, as well as their abundances across different gut regions, remains largely unknown.

METHODS: We employed both metagenomic sequencing and culture-based techniques, collecting a total of 25,825 genomes (25,764 metagenome-assembled genomes and 61 isolated genomes). After quality assessment and average nucleotide identity (ANI), 13,734 genomes were retained for downstream analysis.

RESULTS: Whole-genome clustering analysis identified 2,675 species-level genome bins (SGBs), predominantly from the phyla Bacillota, Bacteroidota, Pseudomonadota, and Actinomycetota. A gene catalog comprising 9.69 million genes revealed that 195,517 genes are involved in the biosynthesis of vitamins B and K2, exhibiting significant regional variation. The large intestine exhibited greater species richness and evenness compared to the small intestine. From the 13,734 genomes, we discovered 3,063 high-quality ones capable of synthesizing at least one vitamin. Genomic analysis revealed that a mere 8.2% of genomes were capable of producing five or more vitamins, while almost half were limited to synthesizing just one. Comparative genomics of cobalamin (B12) biosynthesis highlighted the predominance of the anaerobic pathway. Additionally, changes in microbial abundance were observed, such as increased abundance of the genera Phocaeicola and Faecalibacterium during bacterial infections, and Limisoma during parasitic infections.

DISCUSSION: This study provides detailed metagenomic insights into the capacity of chicken gut microbiome for vitamins B and K2 biosynthesis, revealing significant regional and taxonomic variations. These results suggest a collaborative microbial effort in vitamin biosynthesis, with potential implications for optimizing poultry health and nutrition through targeted microbial interventions.},
}

@article {pmid40895537,
year = {2025},
author = {Deng, Y and Li, Y and Liu, T and Wu, F},
title = {Interaction of vaginal microbiota and biomarkers in Premature rupture of membranes: from bench to beside.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1642942},
doi = {10.3389/fimmu.2025.1642942},
pmid = {40895537},
issn = {1664-3224},
abstract = {Preterm premature rupture of membranes (PROM) is a critical obstetric complication endangering maternal and neonatal health, with growing evidence linking vaginal microecology to its pathogenesis. This review synthesizes the relationship between vaginal microbiota and PROM risk, as well as microecology-targeted prevention and management strategies. A balanced vaginal microbiome, dominated by lactobacilli that maintain an acidic protective environment, is essential for reproductive health. Dysbiosis-marked by reduced lactobacilli and increased pathogens like Gardnerella and Atopobium-impairs local immunity, weakens fetal membranes, and elevates PROM risk, with bacterial vaginosis (BV) strongly associated with this condition. Pathogenic overgrowth activates inflammatory (via TLR-mediated IL-1β, TNF-α, IL-6 overproduction) and oxidative stress pathways: pro-inflammatory cytokines promote cervical ripening, induce matrix metalloproteinases (MMPs) to degrade fetal membrane collagen, while reactive oxygen species (ROS) directly damage structural proteins, compromising membrane integrity. Monitoring inflammatory/oxidative stress biomarkers (e.g., cytokine levels, ROS activity) enables early risk assessment. Potential interventions include probiotics to restore microbial balance, antioxidants/immunomodulators to counteract stress/inflammation, and MMP inhibitors to preserve membrane structure, all aiming to improve pregnancy outcomes. In conclusion, vaginal microecology plays a pivotal role in PROM development, underscoring the need for early microecological monitoring. Future research should dissect mechanistic complexities and develop precision tools for preterm labor management.},
}

@article {pmid40895532,
year = {2025},
author = {Omran, TA and Subirats Camacho, JL and Senthakumaran, T and Gundersen, G and Alte, AK and Randen, U and Tunsjø, HS and Sæther, PC and Bemanian, V},
title = {Fusobacterium-associated molecular and immunological alterations in colorectal cancer: Insights from a Norwegian cohort.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1601423},
doi = {10.3389/fimmu.2025.1601423},
pmid = {40895532},
issn = {1664-3224},
abstract = {BACKGROUND: The gut microbiome may significantly influence the development of colorectal cancer (CRC), with Fusobacterium species playing a key role. Recent research has identified Fusobacterium animalis as the predominant Fusobacterium species in CRC tumors. This pilot research explores the immunological and molecular interactions associated with F. animalis and other Fusobacterium species in Norwegian CRC patients.

METHODS: Tumor samples from 25 CRC patients were divided by Fusobacterium load and analyzed for molecular alterations, immunological gene expression, and macrophage polarization. Fusobacterium-high tumors were associated with microsatellite instability (MSI).

RESULTS: Analysis of differential immune gene expression, combined with correlation analyses, identified 25 genes, including C-X-C motif chemokine ligand 8 (CXCL8), interleukin-6 (IL6), indoleamine 2,3-dioxygenase 1 (IDO1), and secreted phosphoprotein 1 (SPP1), that exhibited significant associations with Fusobacterium abundance in this cohort. Analysis of Fusobacterium adhesion protein 2 (Fap2) revealed active transcription and constitutive expression across multiple colonic sites, including CRC tumor tissues, adjacent non-neoplastic tissues, the ascending colon, and the sigmoid colon. The analysis revealed a positive correlation between RNA levels of Fusobacterium-specific genes (fap2 and nusG) and immune genes (CXCL8, IL6, SPP1, and IDO1) across different colonic sites. This suggests that the abundance of active Fusobacterium cells is related to and possibly influences the pro-inflammatory response in the colonic microenvironment. Although arginase 1 (ARG1) expression was elevated in Fusobacterium-high tumors, no significant link was found between Fusobacterium abundance and M2 macrophage polarization, contradicting previous studies.

CONCLUSIONS: High Fusobacterium, dominated by F. animalis, was linked to increased immune gene expression and constitutive fap2 activity. M2 polarization was unaffected, possibly reflecting in vivo tumor complexity.},
}

@article {pmid40895484,
year = {2025},
author = {Liu, S and Chen, Y and Zhang, K and Tang, D and Zhang, J and Wang, Y and Zhao, J and Li, D and Wang, T},
title = {Exploring vaginal microbiome: from traditional methods to metagenomic next-generation sequencing-a systematic review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1578681},
doi = {10.3389/fmicb.2025.1578681},
pmid = {40895484},
issn = {1664-302X},
abstract = {Recent research has highlighted the vaginal microbiome as a crucial factor in women's health and fertility. The growing recognition of its significance has intensified the focus on studying the female reproductive tract's microbial ecosystem. While various analytical methods exist for examining the vaginal microbiome, metagenomic next-generation sequencing (mNGS) has emerged as an auspicious approach. This study examines how mNGS technology can be applied to analyze vaginal microbiota. We begin by exploring the relationship between vaginal bacterial communities and women's health, followed by a comparative analysis of metagenomics against other detection methods, highlighting their respective strengths and limitations. The paper systematically reviews different detection techniques, examining their fundamental principles, constraints, and advantages. Several factors can affect data quality, including sampling procedures, contamination issues, and PCR amplification errors. We suggest implementing third-generation sequencing (TGS) to address these challenges to enhance reproducibility and read length, utilizing single-molecule sequencing (SMS) to eliminate PCR amplification-related errors, and integrating multiple analytical approaches to provide comprehensive insights. In summary, mNGS technology allows us to collect valuable information at a lower cost, and it remains a leading method for detecting female reproductive tract microbes. The goal of this review is to describe the principle, benefits and drawbacks, and application areas of mNGS, as well as to serve as a reference for research into female reproductive tract microbial detection methods, promote the improvement of mNGS in the detection of female reproductive tract microbial technology, and ensure the health of the female reproductive tract.},
}

@article {pmid40895482,
year = {2025},
author = {Poonguzhali, S and Kim, K and Madhaiyan, M and Sa, T},
title = {The plant growth-promoting Burkholderia vietnamiensis produces acyl-homoserine lactones and modulates the quorum-sensing signaling in the rhizosphere.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1638793},
doi = {10.3389/fmicb.2025.1638793},
pmid = {40895482},
issn = {1664-302X},
abstract = {The genus Burkholderia, comprising over 60 species, represents a highly diverse group of bacteria known for their exceptional metabolic versatility. Quorum sensing (QS), a mechanism of cell-density-dependent gene regulation, plays a critical role in host colonization, environmental adaptation, and, in many cases, pathogenesis. Due to the established link between QS and virulence, most QS studies in Burkholderia cepacia complex (Bcc) species have focused on pathogenic strains. In contrast, comparatively little attention has been given to QS in plant growth-promoting (PGP) Burkholderia strains. In this study, we investigated the QS systems of Burkholderia vietnamiensis strains with plant growth-promoting potential. We identified two functional QS circuits, CepI/R and BviI/R, responsible for the synthesis of distinct AHL molecules with N-decanoyl homoserine lactone (C10-HSL) as the dominant molecule. In B. vietnamiensis CBMB40, both synthases contributed to the production of N-hexanoyl (C6-) and N-Octanoyl (C8-) homoserine lactones, while bviI synthase contributed to the production of C10-HSL and N-Dodecanoyl (C12-) homoserine lactones. The AHLs produced by CBMB40 could be detected in plant tissues, and they served as interpopulation signaling molecules within the rhizosphere. A random transposon mutagenesis approach was employed to generate an AHL-deficient mutant (ΔCBMB40). The mutant exhibited an extended log phase, reduced protease activity, and loss of antagonism against Erwinia carotovora subsp. carotovora, as well as diminished activity against multiple fungal pathogens. Notably, the addition of AHL extracts from the wild-type strain restored antagonistic activity in the mutant. Furthermore, in vitro potato tuber assays and pot culture experiments in red pepper confirmed that AHL-mediated QS is essential for the biocontrol potential of CBMB40. Together, these findings enhance our understanding of QS-regulated functions in PGP B. vietnamiensis CBMB40 and support its potential application as a sustainable biocontrol agent in agriculture. Importantly, this study underscores the potential of using PGP bacteria (PGPB) to prime plant defenses, offering a biologically meaningful and ecologically sustainable alternative to genetically modified plants engineered with AHL synthase genes. AHL-mediated cross-communication in the rhizosphere may further disrupt pathogenic signaling, opening new avenues for microbiome-based crop protection strategies.},
}

@article {pmid40895481,
year = {2025},
author = {Kemmerling, R and Dintilhac, LE and Zancarini, A and Mataigne, A and Mougel, C and Vannier, N},
title = {Carbon substrates utilization determine antagonistic fungal-fungal interactions among root-associated fungi.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1645107},
doi = {10.3389/fmicb.2025.1645107},
pmid = {40895481},
issn = {1664-302X},
abstract = {INTRODUCTION: The assembly of the plant microbiome results from a complex network of interactions. The role of microbial taxa in shaping the microbiome has recently gained attention, emphasizing the competitive dynamics and chemical warfare occurring within this dynamic environment. Within and around the roots, microbe-microbe interactions are piloted by nutritional constraints that can be modulated by the host. In this context, while nutrient blocking and antimicrobial production have largely been described as competitive traits in bacterial taxa, the importance of fungal metabolism in determining fungal-fungal interactions remains largely unexplored.

METHODS: In this work, we profiled the carbon substrate utilization of 91 root-associated fungal isolates from Brassica napus and Triticum aestivum and evaluated their antagonistic abilities against two agronomically relevant fungal competitors, Rhizoctonia solani and Fusarium graminearum.

RESULTS: Our results indicate that fungi arbor contrasted carbon utilization profiles and strategies that are independent from the two host plant species tested, the plant compartment and the geographic region. Strikingly, specific carbon utilization signatures were associated with antagonistic abilities with antifungal-mediated antagonism characterized by higher utilization rates of diverse carbon substrates while direct competitive abilities were associated with lower utilization rates of fewer carbon substrates.

DISCUSSION: Together with taxonomy-based predictions of antagonism-specific enzymatic reactions, these results suggest that carbon utilization profiles and enzymatic reactions prediction could be considered as markers of fungal antagonistic potential. From an ecological point of view, our results suggest that root-associated fungi have contrasted carbon usage strategies likely shaped by and determining fungal-fungal antagonistic interactions.},
}

@article {pmid40895473,
year = {2025},
author = {Batistel, F and Gonzalez, O and Sears, A and Khan, SU and de Souza, J},
title = {Palmitic acid alone or combined with stearic and oleic enhances ruminal fiber degradation and alters microbiome composition.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1624738},
doi = {10.3389/fmicb.2025.1624738},
pmid = {40895473},
issn = {1664-302X},
abstract = {INTRODUCTION: Improving ruminal fiber degradation is a key focus for enhancing animal performance and reducing the environmental impact of ruminant production systems. While dietary fat is typically recognized for impairing ruminal fiber degradation, recent research suggests that specific fatty acids, such as palmitic, stearic, and oleic, may have the potential to improve it. Since palmitic, stearic, and oleic are major components of the membranes of ruminal mixed bacteria, we hypothesize that supplying these fatty acids in proportions that mimic bacterial composition will promote microbial flow and, consequently, improve fiber degradation.

METHODS: Diets were randomly assigned to 8 single-flow continuous culture fermenters arranged in a replicated 4 × 4 Latin square with 6 days of adaptation and 4 days of sampling. Treatments were: (1) a basal diet without supplemental fatty acids (CON); (2) the basal diet plus 1.5% of palmitic acid (PA); (3) the basal diet plus 1.41% of stearic acid and 0.09% of oleic acid (SO); and (4) the basal diet plus 0.48% of palmitic acid, 0.95% of stearic acid, and 0.075% of oleic acid (PSO). Data were analyzed using a mixed model considering treatment as a fixed effect, and period and fermenter as random effects.

RESULTS AND DISCUSSION: Both PA and PSO diets improved fiber degradation, increased the flow of short-chain fatty acids, and tended to increase microbial flow compared to the other treatments. Although the supply of dietary fatty acids did not change the total lipid content, they did alter the membrane fatty acid profile. For example, PA and PSO increased the concentration of specific fatty acids, such as anteiso C15:0, in the bacterial cell membranes, while SO and PSO reduced unsaturated fatty acids compared to PA and CON. Additionally, PA and PSO diets influenced the bacterial community, increasing populations of Fibrobacter and Prevotella while reducing Ruminococcus and Butyrivibrio. Our results indicate that including palmitic acid or a combination of palmitic, stearic, and oleic acids in proportions resembling those found in ruminal mixed bacteria improved ruminal fiber degradation, likely by partially modulating the rumen bacterial community composition.},
}

@article {pmid40895468,
year = {2025},
author = {Yang, J and Chen, J and Li, D and Wu, Q and Zhang, Y and Li, Y and Deng, Y},
title = {Hyperuricemia and the gut microbiota: current research hotspots and future trends.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1620561},
doi = {10.3389/fmicb.2025.1620561},
pmid = {40895468},
issn = {1664-302X},
abstract = {BACKGROUND: Hyperuricemia (HUA), found widely in humans and birds, is a key physiological factor responsible for the development of gout. In recent years, the relationship between the gut microbiota and HUA has garnered significant attention from researchers. This study aims to explore the current research hotspots, knowledge gaps, and future research trends regarding the gut microbiota and HUA.

METHODS: We performed a thorough search of the literature on gut flora and HUA published between 2005 and 2024 using the Web of Science and PubMed databases. The resulting data were analyzed using VOSviewer, CiteSpace, and Bibliometrix.

RESULTS: Including 735 papers in total, the study found that the number of publications in the subject increased significantly between 2020 and 2024, with 2024 being the year with the highest number of publications. The primary research countries are highlighted as China and the United States, with institutions such as the University of California, San Diego, and Qingdao University making significant contributions. Sanjay K. Nigam and Chenyang Lu have made the most important contributions as authors. Keywords analysis highlighted high-frequency terms including "gastrointestinal microbiome," "uric acid," "hyperuricemia," "inflammation," "gout," and "probiotics." In the visualization map of the keyword timeline, emerging research hotspots include "diets," "dietary fiber," "fecal microbiota transplantation," and "gut-kidney axis."

CONCLUSION: This study is the first to conduct a quantitative literature analysis in the field of gut microbiota in HUA, revealing that the core research hotspots include disease-related microbiota characteristics, probiotic therapy, microecological intervention, and the gut-distal target organ axis. The emerging hotspots focus on dietary supplementation, fecal microbiota transplantation (FMT) treatment strategies, and in-depth research on the above organ axes. Provide valuable guidance for future research directions.},
}

@article {pmid40895303,
year = {2025},
author = {Yaprak Çolak, E and Duran, N},
title = {Synergistic antibacterial effects of postbiotics combined with linezolid and amikacin against nosocomial pathogens.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1616501},
doi = {10.3389/fcimb.2025.1616501},
pmid = {40895303},
issn = {2235-2988},
abstract = {BACKGROUND AND AIM: The global rise in antimicrobial resistance (AMR) has rendered many conventional antibiotics less effective, particularly against nosocomial pathogens such as Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Proteus mirabilis. This study investigated the antimicrobial and synergistic effects of postbiotics derived from Lacticaseibacillus casei, Lactobacillus bulgaricus, Enterococcus faecium, and Streptococcus thermophilus, administered alone or in combination with either linezolid (for S. aureus) or amikacin (for Gram-negative strains).

MATERIALS AND METHODS: Postbiotics were obtained through anaerobic fermentation, followed by centrifugation and filtration. Cytotoxicity was assessed via MTT assays on Vero cell lines. Infection models involving pathogen-specific adhesion and invasion assays were used, with CFU/mL quantification and statistical evaluation by one-way ANOVA and Tukey's post hoc test.

RESULTS: The postbiotics exhibited potent antimicrobial activity across all tested pathogens. Combined with linezolid, the dual and triple postbiotic formulations significantly enhanced antibacterial effects against S. aureus from the early hours of incubation. Similarly, combinations with amikacin produced potent synergistic effects against E. coli, P. aeruginosa, and P. mirabilis, particularly in triple combinations involving L. casei and L. bulgaricus. Postbiotics sometimes outperformed antibiotics, such as ST+LC postbiotics against P. mirabilis. These findings suggest that postbiotics can enhance antibiotic efficacy-possibly by modulating membrane permeability, disrupting biofilms, or altering bacterial communication systems. Their low cytotoxicity and pathogen-specific responses indicate that postbiotics are safe and may be tailored for targeted use.

CONCLUSIONS: In conclusion, postbiotic-antibiotic combinations, especially with linezolid and amikacin, present promising low-toxicity, synergistic therapeutic strategies. These results lay a strong foundation for advancing microbiome-based adjunct therapies to combat AMR in clinical settings.},
}

@article {pmid40895300,
year = {2025},
author = {Zhou, M and Li, X and Xiao, N and Tan, Z},
title = {One mechanism of Sishen Pill on diarrhea with kidney Yang deficiency syndrome: influencing metabolic function by intestinal microorganisms and enzyme activity mediates the gut-kidney axis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1620789},
doi = {10.3389/fcimb.2025.1620789},
pmid = {40895300},
issn = {2235-2988},
abstract = {INTRODUCTION: Sishen Pill (SSP), a classic TCM formula, warms the kidney and spleen, astringes the intestine, and stops diarrhea. Emerging evidence suggests that diarrhea with KYDS is linked to gut microbiota imbalance and altered intestinal enzyme activities. At the same time, SSP has been shown to regulate gut microbiota, improve metabolism, and alleviate intestinal disorders. This research investigates how SSP prevents and treats diarrhea by studying the interaction between SSP and intestinal microorganisms.

METHODS: In a murine model of diarrhea induced by adenine and Foliuem sennae co-administration, we collected various biospecimens, including intestinal mucosa (ileum and colon), luminal contents, serum, and major organs (kidney, spleen) for comprehensive mechanistic analyses. Techniques such as microbial culture, enzyme activity assays, and HE staining were employed to assess cultivable microbial colony counts, enzyme activity, relevant metabolic indicators, oxidative stress markers, and to observe kidney tissue sections.

RESULTS: The results indicated that SSP treatment significantly reduced uric acid levels, Escherichia coli (E. coli) count, and amylase activity compared to the spontaneous recovery (MC) group, while the spleen and thymus index, total bacterial count, sucrase activity in contents, protease activity and microbial activity in mucosa were significantly higher than the measurements in MC group. Significant differences were observed in alanine aminotransferase level, Lactobacillus count, Bifidobacterium count, sucrase activity, and microbial activity between the SSP and blank control groups. Serum uric acid levels showed a positive correlation with E. coli colony count and a negative correlation with Lactobacillus colony count. Additionally, total bacterial colony count was negatively correlated with aspartate aminotransferase levels.

CONCLUSIONS: The SSP may alleviate diarrhea with kidney Yang deficiency syndrome by reducing E. coli count, enhancing specific enzyme activities, and regulating organ indices and oxidative stress, with the regulatory effects on organ indices and oxidative stress potentially associated with its modulation of E. coli and enzyme activity. This cascade of microbial-enzymatic regulation likely contributes to the normalization of organ indices (e.g., spleen and thymus indices) and alleviation of oxidative stress, as reflected by enhanced superoxide dismutase activity. These findings highlight the multitarget therapeutic potential of SSP in addressing dysfunction in the intestinal-microbiome-enzymatic-organ axis in diarrhea with kidney Yang deficiency syndrome.},
}

@article {pmid40895298,
year = {2025},
author = {Jia, X and Sun, S and Ci, Z},
title = {Meta-analysis of probiotic metabolites in the prevention of gestational weight gain and postpartum weight retention.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1627206},
doi = {10.3389/fcimb.2025.1627206},
pmid = {40895298},
issn = {2235-2988},
abstract = {INTRODUCTION: Maternal weight gain and metabolic health during pregnancy significantly influence both short- and long-term outcomes for mother and child.

METHODS: This systematic review and meta-analysis included data from 46 randomized controlled trials (RCTs), comprising over 12,500 pregnant women across diverse populations.

RESULTS: Probiotic supplementation, especially multispecies formulations, initiated in the first trimester led to a mean reduction in gestational weight gain (GWG) of 1.25 kg (95% CI: -1.78 to -0.72 kg; p < 0.001) compared to controls. Furthermore, postpartum weight retention was reduced by an average of 1.05 kg (95% CI: -1.53 to -0.58 kg; p < 0.001) when probiotic use extended into the postpartum period. Significant improvements were also observed in metabolic markers: fasting glucose decreased by 0.22 mmol/L, Homeostatic Model Assessment for Insulin Resistance (HOMA-IR) scores decreased by 0.45 units, and total cholesterol and Low-density lipoprotein (LDL) were reduced by 0.28 and 0.17 mmol/L, respectively.

DISCUSSION: These effects were mediated by the modulation of gut microbiota, promoting the production of beneficial short-chain fatty acids (butyrate) and reducing systemic inflammation through increased levels of microbial-derived metabolites, including conjugated linoleic acids and indole-3-propionic acid, which enhance gut barrier integrity and metabolic resilience. The heterogeneity in strains, dosage, and duration and pooled analysis consistently favored probiotic intervention. These findings support the use of probiotics as a safe, non-pharmacological strategy to improve metabolic outcomes during pregnancy. Future studies should focus on personalized probiotic interventions and long-term maternal-child health effects.},
}

@article {pmid40895126,
year = {2025},
author = {Ngo, THV and Riche, M and Bruce, TJ and Davis, DA},
title = {Growth Performance, Blood Chemistry, and Intestinal Bacterial Community of Florida Pompano (Trachinotus carolinus) Fed Different Levels of Corn Fermented Protein and Yeast Diets.},
journal = {Aquaculture nutrition},
volume = {2025},
number = {},
pages = {8872997},
doi = {10.1155/anu/8872997},
pmid = {40895126},
issn = {1365-2095},
abstract = {Developing species-specific diets for Florida pompano (Trachinotus carolinus) requires understanding both nutritional needs and ingredient responses in practical formulations. Previous research has successfully reduced animal protein inclusion to ~15% by using solvent-extracted soybean meal (SBM) as the primary protein source. Further cost savings may be achieved by incorporating other low-cost alternatives, such as corn fermented protein (CFP), a new sustainable ingredient produced using Fluid Quip Technologies. A 12-week growth trial was conducted with juvenile Florida pompano (initial weight 6.08 ± 0.55 g) using a fishmeal-free basal diet. The basal diet contained poultry by-product meal (15% diet) and the SBM (52% diet) as primary protein sources. The SBM was then incrementally replaced with CFP (5%, 10%, and 20% diet) and Saccharomyces cerevisiae fermentation product (FSC) (2%) on an equal protein basis. All diets were formulated to be isonitrogenous (40% protein) and isolipidic (8% lipid), and fish were reared in a recirculating aquaculture system (RAS). Fish across all treatments exhibited similar growth metrics, including final weight (FW) (44.61-56.98 g), weight gain (WG) (557%-738%), and feed conversion ratio (FCR) (1.56-1.75), with no significant differences (p > 0.05). Blood parameters remained within healthy ranges, and microbiome analyses revealed stable gut bacterial diversity and composition among treatments. These results suggest that CFP can be used as a protein source in practice for Florida pompano without impairing growth, health status, or intestinal microbiota composition.},
}

@article {pmid40895066,
year = {2025},
author = {Mo, C and Zhou, S and Du, Z and Huang, X},
title = {Impact of fructooligosaccharides on gut microbiota composition and metabolite production: implications for childhood obesity.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19894},
doi = {10.7717/peerj.19894},
pmid = {40895066},
issn = {2167-8359},
abstract = {BACKGROUND: Contemporary dietary habits in children have been linked to various health issues, particularly the increasing prevalence of childhood obesity. However, the complex relationship between children's diets, gut microbiota, and health outcomes remains incompletely understood. This study investigates the effects of fructooligosaccharides (FOS) on gut microbiota composition and metabolic processes in children, and explores their potential impact on pediatric health outcomes such as obesity and metabolic disorders.

METHODS: Fecal samples from 39 children (19 boys, 20 girls) aged 6-15 were subjected to in vitro fermentation with or without FOS supplementation. Bacterial composition, short-chain fatty acid (SCFA) production, and gas generation were analyzed. Potential biomarkers and associations between gut microbiota, metabolites, and metabolic pathways were identified using Random Forest algorithms and the MetOrigin cloud platform.

RESULTS: FOS supplementation significantly altered the β-diversity of the gut microbiota, increasing the abundance of Bifidobacterium and Lactobacillus, while decreasing Escherichia-Shigella and Bacteroides. FOS also led to a significant increase in SCFA levels, particularly acetic acid, which correlated positively with Bifidobacterium and negatively with Streptococcus. Conversely, gas production (NH3, H2, and H2S) decreased significantly and showed a positive correlation with Escherichia-Shigella and a negative correlation with Bifidobacterium.

CONCLUSIONS: This study highlights changes in microbial structure, metabolite production, potential biomarkers, and altered metabolic pathways following FOS intervention. These findings provide valuable insights into the complex relationship between diet and gut microbiota in obese children and suggest that dietary interventions may influence pediatric health through modulation of the gut microbiome.},
}

@article {pmid40895054,
year = {2025},
author = {Cárdenas-Hernández, V and Lemos-Lucumi, C and Toro-Perea, N},
title = {Uncovering tissue-specific endophytic microbiota composition and activity in Rhizophora mangle L.: a metagenomic and metatranscriptomic approach.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19728},
doi = {10.7717/peerj.19728},
pmid = {40895054},
issn = {2167-8359},
abstract = {The interaction of mangrove trees with endophytic microorganisms contributes to the successful establishment of these plants in the challenging intertidal environment. The red mangrove, Rhizophora mangle L. (Rhizophoraceae), is one of the dominant species in mangrove ecosystems and is characterized by the provision of several ecologically relevant services. In this work, we integrated metagenomics and metatranscriptomics to perform a robust characterization of the community of endophytic microorganisms associated with R. mangle leaf and root tissues. The microbiota were characterized at taxonomic and functional levels, and abundance and gene expression profiles were compared between these two plant tissues. We found that the endophyte community consisted mainly of bacteria and eukaryotes, which were the most active groups at the transcriptional level, while archaea and viral groups were identified in lower abundance and expression. In addition, the results show that the community of endophytic microorganisms changes depending on the tissue type, with root-associated microorganisms being the most abundant at the metagenome level and active at the metatranscriptome level. It was also found that R. mangle endophytes actively contribute to key functions for adaptation to an intertidal ecosystem with high human intervention, such as salinity tolerance and degradation of heavy metals and xenobiotic compounds. Thus, according to the functions found and contributed by the endophyte community of red mangrove leaf and root tissues, it can be concluded that these microbial communities are crucial for the survival of R. mangle in the extreme environment of mangrove forests. This study provides a solid basis for future research aimed at understanding the role of plant-endophyte interactions.},
}

@article {pmid40894914,
year = {2025},
author = {Yu, J and Yang, YN and Chen, W and Hu, J and Jin, Z and Wu, C and Li, Y},
title = {Role of gut microbiota and derived metabolites in cardiovascular diseases.},
journal = {iScience},
volume = {28},
number = {9},
pages = {113247},
doi = {10.1016/j.isci.2025.113247},
pmid = {40894914},
issn = {2589-0042},
abstract = {Cardiovascular diseases (CVDs) remain one of the leading causes of death worldwide, imposing a significant societal burden and highlighting the urgent need for effective disease management strategies to reduce mortality and prevent disability. Recently, gut microbiota and its metabolites have been considered as an essential part of human physiology, emphasizing their contributions in CVD development and management. An increasing number of studies have shown that gut microbiota affects the process of CVDs either directly through changes in its composition and function or indirectly through its metabolites, and plays an important role in host physiology and disease development. This review provides a comprehensive overview of how gut microbes and their specific metabolites interact and contribute to the generation and development of CVDs. In addition, the therapeutic potential to treat CVDs by targeting the gut microbiota is also discussed, which may provide promising possibilities for the clinical treatment of CVDs in the future.},
}

@article {pmid40894811,
year = {2025},
author = {Ding, X and Le Clerc, S},
title = {Editorial: Interaction between genes and the environment in skin aging.},
journal = {Frontiers in aging},
volume = {6},
number = {},
pages = {1671721},
doi = {10.3389/fragi.2025.1671721},
pmid = {40894811},
issn = {2673-6217},
}

@article {pmid40894792,
year = {2025},
author = {Krout, IN and Matsuzaki, R and White, AC and Tsui, S and Blackmer-Raynolds, L and Kelly, SD and Chang, J and Braselton, M and D'Souza, PE and Mullins, CE and Panuwet, P and Yakimavets, V and Barr, DB and Walker, DI and Caudle, WM and Sampson, TR},
title = {The gut microbiome promotes detoxification responses to an environmental toxicant.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.14.670327},
pmid = {40894792},
issn = {2692-8205},
abstract = {UNLABELLED: At the host-environment interface, the indigenous microbiome is poised to facilitate interactions with exogenous components. Here, we show that the microbiome is necessary for metabolic and transcriptional detoxification responses to the neurotoxic pyrethroid insecticide, deltamethrin. While oral deltamethrin exposure shapes gut microbiome composition, it is not directly microbially metabolized. Instead, we observe microbiome-dependence on host hepatic and intestinal detoxification responses, with diminished activity in germ-free mice. Colonization with a complex microbiome in adulthood maintained limited hepatic responses, suggesting developmental contributions. However, mono-colonization with specific microbes increased colonic expression of a key detoxification enzyme, revealing a protective role for active microbial signaling in the colon. Overall, our data demonstrate that the microbiome is necessary to prime and activate a host response against a model environmental toxicant. Through both developmental and active signaling across organ compartments, these data support that the microbiome may contribute to risk and outcomes of toxicant-associated disease.

HIGHLIGHTS: The gut microbiome mediates the host response to environmental toxicants.Key xenobiotic metabolism genes are modulated by the microbiomeEarly life signaling is necessary to promote hepatic responsiveness to toxicants in adulthood.Specific and active microbial signaling promotes colonic detoxification gene expression.},
}

@article {pmid40894776,
year = {2025},
author = {Wang, Y and Tangpricha, V and Gewirtz, A},
title = {Comparison of iSeq and Miseq in 16S rRNA sequencing-based human gut microbiome analysis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.22.671784},
pmid = {40894776},
issn = {2692-8205},
abstract = {Illumina's MiSeq platform is a common approach in 16S-based microbiome analysis. Such usage is self-perpetuating in that many studies seek to employ widely used approaches to facilitate comparison of their results to existing literature. Yet, a range of factors, including cost and equipment availability can necessitate alternate approaches. For example, use of a Nano kit, lowers reagent costs by over 60% while others may only have access to entry-level sequencers such as Illumina's iSeq. The extent to which these approaches would impact results and subsequently conclusions is unknown. Attempting to address this question from the literature is complicated in that various studies not only use distinct cohorts but also differ in the reagents/methodologies to used to isolate DNA and generate sequencing libraries. Hence, we sequenced a single 16S rRNA gene amplicon library derived from 60 fecal samples, collected during a dietary supplement intervention study via MiSeq, MiseqNano, and iSeq. We evaluated platform performance by several key measurements: alpha diversity, beta diversity, taxonomic composition, and differential taxonomic abundance analysis. We found that iSeq outperformed MiSeq-Nano in alpha diversity and differential abundance detection, while MiSeq-Nano provided better taxonomic resolution than iSeq. Most importantly, all platforms showed similar core biological patterns in alpha and beta diversity and overall taxonomic composition. Thus, MiSeq, MiseqNano, and iSeq are likely to yield the same biological conclusions although specific questions and logistical consideration may favor one of these approaches.},
}

@article {pmid40894753,
year = {2025},
author = {Ndlovu, KS and Pavan, RR and Corry, J and Gregory, AC and Mahamed, S and Zotova, N and Tabala, M and Babakazo, P and Funderburg, NT and Yotebieng, M and Klatt, NR and Kwiek, JJ and Sullivan, MB},
title = {The cervicovaginal microbiome of pregnant people living with HIV on antiretroviral therapy in the Democratic Republic of Congo: A Pilot Study and Global Meta-analysis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.18.670785},
pmid = {40894753},
issn = {2692-8205},
abstract = {UNLABELLED: Recent studies are revealing that a suboptimal cervicovaginal microbiome (CVMB), including enrichment of anaerobic bacteria associated with multiple female genital disorders, and adverse pregnancy and birth outcomes in pregnant people. Problematically, however, the majority of the available data to date are biased towards highly developed, Global North countries, leaving underrepresented populations like the Democratic Republic of Congo (DRC) poorly characterised. Here, we investigate the CVMB from a cohort of 82 pregnant people living with HIV (PLWH) on antiretroviral therapy (ART) from the DRC. Specifically, we explore the associations between the CVMB via 16S rRNA gene sequencing and maternal peripheral immune factors. Additionally, we compare the CVMB of PLWH-ART from DRC to publicly available CVMB data (5 studies, 1861 samples) in a meta-analysis to elucidate the impact of HIV on the CVMB. Combined, these analyses revealed differences in community structure and predicted function of the microbiota between PLWH-ART and pregnant people without HIV (PWoH). Taxonomically, the CVMB of DRC PLWH-ART were enriched for Lactobacillus iners- dominated CVMBs (53%) or a diverse, polymicrobial CVMB, i.e., bacterial vaginosis (BV) (43%). Functional predictions made from these taxa suggested that protein-coupled receptors, amino sugar and nucleotide sugar metabolism, fatty acid metabolism, and polycyclic aromatic hydrocarbon degradation pathways were differentially abundant between communities. Correlation with host plasma immune factors revealed putative links between some CVMB metrics (e.g., alpha diversity and species abundance) that have been linked to adverse pregnancy and birth outcomes.

IMPORTANCE: HIV remains prevalent in sub-Saharan Africa, where it has been linked to adverse birth outcomes. . Suboptimal CVMBs have shown similar links. This pilot study fills critical gaps in understanding how HIV interacts with the pregnant CVMB in populations underrepresented in microbiome research, like the Democratic Republic of Congo. We identified maternal systemic immune factors associated with suboptimal CVMBs that have been linked to poor birth outcomes. In a global meta-analysis, we found significant taxonomic and functional difference in the CVMBs between pregnant people living with and without HIV, revealing potential biomarkers that for increased risks for adverse birth outcomes. These findings provide crucial insights into CVMB features that may influence pregnancy health in pregnant people living with HIV, guiding future research and tailored interventions to support safer pregnancies in the DRC and similar populations.},
}

@article {pmid40894719,
year = {2025},
author = {De Santiago, A and Barnes, S and Pereira, TJ and Marcellino-Barros, M and Durden, L and Han, MK and Thrash, JC and Bik, HM},
title = {Pseudoalteromonas is a novel symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.22.671635},
pmid = {40894719},
issn = {2692-8205},
abstract = {Despite growing insights into the composition of marine invertebrate microbiomes, our understanding of their ecological and evolutionary patterns remains poor, owing to limited sampling depth and low-resolution datasets. Previous studies have provided mixed results when evaluating patterns of phylosymbiosis between marine invertebrates and marine bacteria. Here, we investigated potential animal-microbe symbioses in Pseudoalteromonas, an overlooked bacterial genus consistently identified as a core microbiome taxon in diverse invertebrates. Using a pangenomic analysis of 236 free-living and invertebrate-associated bacterial strains (including two new nematode-associated isolates generated in this study), we confirm that Pseudoalteromonas is a novel symbiont with substantial evidence of phylosymbiosis across at least three marine invertebrate phyla (e.g., Nematoda, Mollusca, and Cnidaria). Patterns of symbiosis were consistent irrespective of geography (including in Antarctica), with FISH images from nematodes indicating that bacterial symbionts form biofilms in the mouth and esophagus. The evolutionary history of Pseudoalteromonas is marked by substantial host-switching and lifestyle transitions, and host-associated genomes suggest that these bacteria are facultative symbionts involved in nutritional mutualisms. In marine environments, we hypothesize that horizontally-acquired symbionts may have co-evolved with invertebrates, using host mucus as a physical niche and food source, while providing their animal hosts with Vitamin B, amino acids, and bioavailable carbon compounds in return.},
}

@article {pmid40894716,
year = {2025},
author = {Berardi, S and Beltz, JK and Rudman, SM and Grainger, TN and Levine, JM and Oken, H and Schmidt, P},
title = {Seasonal evolution of Drosophila melanogaster abdominal pigmentation is associated with a multifarious selective landscape.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.15.670575},
pmid = {40894716},
issn = {2692-8205},
abstract = {Pigmentation has been widely studied by evolutionary biologists due to both ease of measure and relationship to fitness. Drosophila melanogaster pigmentation has represented a particularly useful avenue of investigation, as extensive genetic tools have enabled the characterization of the trait's complex architecture. Drosophila pigmentation also varies predictably across space and time in wild populations, suggesting pigmentation is a component of adaptation to local environmental conditions. Despite this, the impact of D. melanogaster pigmentation on fitness, and the environmental factors that drive the evolution of pigmentation, are not well understood. To address this gap, we experimentally evolved replicated D. melanogaster populations in field mesocosms to determine whether and how pigmentation evolves in response to environmental variation. We found that pigmentation rapidly and predictably adapted to a direct manipulation of temperature, supportive of melanization playing a role in thermoregulation. However, we also determined that pigmentation responded adaptively to direct manipulations of numerous additional factors, including intraspecific competition, diet, and the microbiome. These findings suggest that the selective landscape acting on pigmentation is complex and multifaceted, and that patterns of melanization may be driven, at least in part, by indirect selection due to correlations with other fitness-related traits.},
}

@article {pmid40894707,
year = {2025},
author = {Sohail, S and Bushnell, D and Khemmani, M and Narla, S and Lamana, O and Sharma, B and Moreland, RB and Wolfe, AJ and Forster, CS},
title = {Evidence for an indigenous female mouse urobiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.20.671418},
pmid = {40894707},
issn = {2692-8205},
abstract = {Mice have been used as a valuable model of understanding pathophysiological mechanisms of urinary tract infection for almost six decades. Mice offer many advantages including genetic manipulation to test the role of genes and mechanisms, the availability of germ-free mice, and similarities to humans in innate immune defenses and the strain-dependent presence of vesicoureteral reflux. However, like with humans, the mouse bladder urine above the urinary sphincter has generally been assumed to be sterile. Yet, given the presence of urobiomes in other mammals and the emerging role of the human urobiome in the defense of the urinary bladder and upper urinary tract, the existence of a mouse urobiome should be critically examined as indigenous microbiota may influence experimental results. To determine if an indigenous murine urobiome exists, we obtained expressed urine from two sets of female C57BL/6J mice during three different intervals using two different extraction and sequencing methods and analyzed them simultaneously by a single method. For one set, we also obtained urine by suprapubic aspiration, which we compared to the paired expressed urine samples. We conclude that an indigenous murine urobiome exists and that expressed urine contains post-urethral microbes.},
}

@article {pmid40894694,
year = {2025},
author = {Regan, MD and Chiang, E and Grahn, M and Tonelli, M and Assadi-Porter, FM and Suen, G and Carey, HV},
title = {Host-microbiome mutualism drives urea carbon salvage and acetogenesis during hibernation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.13.638127},
pmid = {40894694},
issn = {2692-8205},
abstract = {UNLABELLED: Hibernation is a seasonal survival strategy employed by certain mammals that, through torpor use, reduces overall energy expenditure and permits long-term fasting. Although fasting solves the challenge of winter food scarcity, it also removes dietary carbon, a critical biomolecular building block. Here, we demonstrate a process of urea carbon salvage (UCS) in hibernating 13-lined ground squirrels, whereby urea carbon is reclaimed through gut microbial ureolysis and used in reductive acetogenesis to produce acetate, a short-chain fatty acid (SCFA) of major value to the host and its gut microbiota. We find that urea carbon incorporation into acetate is more efficient during hibernation than the summer active season, and that while both host and gut microbes oxidize acetate for energy supply throughout the year, the host's ability to absorb and oxidize acetate is highest during hibernation. Metagenomic analysis of the gut microbiome indicates that genes involved in the degradation of gut mucins, an abundant endogenous nutrient, are retained during hibernation. The hydrogen disposal associated with reductive acetogenesis from urea carbon helps facilitate this mucin degradation by providing a luminal environment that sustains fermentation, thereby generating SCFAs and other metabolites usable by both the host and its gut microbes. Our findings introduce UCS as a mechanism that enables hibernating squirrels and their gut microbes to exploit two key endogenous nutrient sources - urea and mucins - in the resource-limited hibernation season.

SIGNIFICANCE STATEMENT: 3. When food becomes scarce during winter, hibernating mammals induce torpor to minimize energy demands and enable monthslong fasting. However, fasting eliminates the intake of essential nutrients such as carbon. We identified a two-step microbial-host interaction in ground squirrels - urea carbon salvage (UCS) - which counters carbon limitation by salvaging carbon from waste urea. Through activities of ureolytic and acetogenic bacteria, urea-derived CO 2 is reduced by free hydrogen to form acetate, whose oxidation provides energy for gut microbes and the host. This process also helps maintain a permissive environment for fermentation of other host-derived, energy-dense compounds such as mucins. UCS broadens our understanding of host-microbe mutualism under extreme nutritional constraints and may represent a widespread adaptation among fasting mammals.},
}