@article {pmid40188731,
year = {2025},
author = {Li, Y and Huang, S and Jiang, S and Yang, L and Huang, J and Yang, Q and Jiang, Z and Shi, J and Ma, Z and Li, E and Zhou, F},
title = {Multi-omics insights into antioxidant and immune responses in Penaeus monodon under ammonia-N, low salinity, and combined stress.},
journal = {Ecotoxicology and environmental safety},
volume = {295},
number = {},
pages = {118156},
doi = {10.1016/j.ecoenv.2025.118156},
pmid = {40188731},
issn = {1090-2414},
abstract = {Ammonia nitrogen and salinity are critical environmental factors that significantly impact marine organisms and present substantial threats to Penaeus monodon species within aquaculture systems. This study utilized a comprehensive multi-omics approach, encompassing transcriptomics, metabolomics, and gut microbiome analysis, to systematically examine the biological responses of shrimp subjected to low salinity, ammonia nitrogen stress, and their combined conditions. Metabolomic analysis demonstrated that exposure to ammonia nitrogen stress markedly influenced the concentrations of antioxidant-related metabolites, such as glutathione, suggesting that shrimp mitigate oxidative stress by augmenting their antioxidant capacity. The transcriptomic analysis revealed an upregulation of genes linked to energy metabolism and immune responses and antioxidant enzymes. Concurrently, gut microbiome analysis demonstrated that ammonia nitrogen stress resulted in a marked increase in Vibrio populations and a significant decrease in Photobacterium, indicating that alterations in microbial community structure are intricately associated with the shrimp stress response. A comprehensive analysis further indicated that the combined stressors of ammonia nitrogen and salinity exert a synergistic effect on the immune function and physiological homeostasis of shrimp by modulating antioxidant metabolic pathways and gut microbial communities. These findings provide critical systematic data for elucidating the mechanisms through which ammonia nitrogen and salinity influence marine ecosystems, offering substantial implications for environmental protection and ecological management.},
}

@article {pmid40188549,
year = {2025},
author = {Sun, J and Yang, W and Li, M and Zhang, S and Sun, Y and Wang, F},
title = {Metagenomic analysis reveals soil microbiome responses to microplastics and ZnO nanoparticles in an agricultural soil.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138164},
doi = {10.1016/j.jhazmat.2025.138164},
pmid = {40188549},
issn = {1873-3336},
abstract = {Both microplastics (MPs) and engineered nanoparticles are pervasive emerging contaminants that can produce combined toxicity to terrestrial ecosystems, yet their effects on soil microbiomes remain inadequately understood. Here, metagenomic analysis was employed to investigate the impacts of three common MPs [i.e., polyethylene (PE), polystyrene (PS), and polylactic acid (PLA)] and zinc oxide nanoparticles (nZnO) on soil microbiomes. Both MPs and nZnO significantly altered the taxonomic, genetic, and functional diversity of soil microbes, with distinct effects depending on dosage or type. Archaea, fungi, and viruses exhibited more pronounced responses compared to bacteria. Higher doses of MPs and nZnO reduced gene abundance for nutrient cycles like C degradation and N cycling, but enhanced CO2 fixation and S metabolism. nZnO consistently decreased the complexity, connectivity, and modularity of microbial networks; however, these negative effects could be mitigated by co-existing MPs, particularly at elevated doses. Notably, PLA (10 %, w/w) exhibited greater harm to fungal communities and increased negative interactions between microbes and nutrient-cycling genes, posing unique risks compared to PE and PS. These findings demonstrate that MPs and nZnO interact synergistically, complicating ecological predictions and emphasizing the need to consider pollutant interactions in ecological risk assessments, particularly for biodegradable MPs.},
}

@article {pmid40188410,
year = {2025},
author = {Oyovwi, MO and Ben-Azu, B and Babawale, KH},
title = {Therapeutic potential of microbiome modulation in reproductive cancers.},
journal = {Medical oncology (Northwood, London, England)},
volume = {42},
number = {5},
pages = {152},
pmid = {40188410},
issn = {1559-131X},
mesh = {Humans ; *Microbiota ; Probiotics/therapeutic use ; Female ; Dysbiosis/microbiology/therapy ; *Genital Neoplasms, Female/microbiology/therapy ; Fecal Microbiota Transplantation/methods ; Animals ; Gastrointestinal Microbiome ; },
abstract = {The human microbiome, a complex ecosystem of microbial communities, plays a crucial role in physiological processes, and emerging research indicates a potential link between it and reproductive cancers. This connection highlights the significance of understanding the microbiome's influence on cancer development and treatment. A comprehensive review of current literature was conducted, focusing on studies that investigate the relationship between microbiome composition, reproductive cancer progression, and potential therapeutic approaches to modulate the microbiome. Evidence suggests that imbalances in the microbiome, known as dysbiosis, may contribute to the development and progression of reproductive cancers. Specific microbial populations have been associated with inflammatory responses, immune modulation, and even resistance to conventional therapies. Interventions such as probiotics, dietary modifications, and fecal microbiota transplantation have shown promise in restoring healthy microbiome function and improving cancer outcomes in pre-clinical models, with pilot studies in humans indicating potential benefits. This review explores the therapeutic potential of microbiome modulation in the management of reproductive cancers, discussing the mechanisms involved and the evidence supporting microbiome-targeted therapies. Future research is warranted to unravel the complex interactions between the microbiome and reproductive cancer pathophysiology, paving the way for innovative approaches.},
}

Humans
*Microbiota
Probiotics/therapeutic use
Female
Dysbiosis/microbiology/therapy
*Genital Neoplasms, Female/microbiology/therapy
Fecal Microbiota Transplantation/methods
Animals
Gastrointestinal Microbiome

@article {pmid40188058,
year = {2025},
author = {Zhang, L and Zhang, X and Leach, JM and Rahman, AKMF and Howell, CR and Yi, N},
title = {Bayesian compositional generalized linear mixed models for disease prediction using microbiome data.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {98},
pmid = {40188058},
issn = {1471-2105},
mesh = {Bayes Theorem ; Humans ; *Microbiota ; Linear Models ; Algorithms ; Inflammatory Bowel Diseases/microbiology ; Monte Carlo Method ; Computational Biology/methods ; Markov Chains ; },
abstract = {The primary goal of predictive modeling for compositional microbiome data is to better understand and predict disease susceptibility based on the relative abundance of microbial species. Current approaches in this area often assume a high-dimensional sparse setting, where only a small subset of microbiome features is considered relevant to the outcome. However, in real-world data, both large and small effects frequently coexist, and acknowledging the contribution of smaller effects can significantly enhance predictive performance. To address this challenge, we developed Bayesian Compositional Generalized Linear Mixed Models for Analyzing Microbiome Data (BCGLMM). BCGLMM is capable of identifying both moderate taxa effects and the cumulative impact of numerous minor taxa, which are often overlooked in conventional models. With a sparsity-inducing prior, the structured regularized horseshoe prior, BCGLMM effectively collaborates phylogenetically related moderate effects. The random effect term efficiently captures sample-related minor effects by incorporating sample similarities within its variance-covariance matrix. We fitted the proposed models using Markov Chain Monte Carlo (MCMC) algorithms with rstan. The performance of the proposed method was evaluated through extensive simulation studies, demonstrating its superiority with higher prediction accuracy compared to existing methods. We then applied the proposed method on American Gut Data to predict inflammatory bowel disease (IBD). To ensure reproducibility, the code and data used in this paper are available at https://github.com/Li-Zhang28/BCGLMM .},
}

Bayes Theorem
Humans
*Microbiota
Linear Models
Algorithms
Inflammatory Bowel Diseases/microbiology
Monte Carlo Method
Computational Biology/methods
Markov Chains

@article {pmid40188054,
year = {2025},
author = {Kritikos, A and Bernasconi, E and Choi, Y and Scherz, V and Pagani, JL and Greub, G and Bertelli, C and Guery, B},
title = {Lung and gut microbiota profiling in intensive care unit patients: a prospective pilot study.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {468},
pmid = {40188054},
issn = {1471-2334},
mesh = {Humans ; Pilot Projects ; Prospective Studies ; Intensive Care Units ; Male ; Female ; Middle Aged ; *Lung/microbiology ; *Gastrointestinal Microbiome ; Pneumonia, Ventilator-Associated/microbiology ; Aged ; RNA, Ribosomal, 16S/genetics ; Critical Illness ; *Bacteria/classification/genetics/isolation & purification ; Respiration, Artificial ; Adult ; },
abstract = {BACKGROUND: The gut and lung microbiomes play crucial roles in host defense and mayserve as predictive markersfor clinical outcomes in critically ill patients. Despite this, the simultaneous dynamics of lung and gut microbiomes during critical illness remain unclear. This study aims to assess the longitudinal changes in lung and gut microbiota among mechanically ventilated ICU patients with and without infection and to identify microbial features predictive of clinical outcomes, including the development of ventilator associated pneumonia (VAP).

METHODS: In this prospective observational study, we analyzed 73 endotracheal aspirates (ETA) and 93 rectal swabs collected from 38 ICU patients over multiple timepoints (intubation, infection onset, post-antibiotic, and extubation/discharge). Patients were categorized into three groups: (1) VAP, (2) other infections, and (3) uninfected controls. Lung and gut microbiota were characterized using 16S rRNA gene sequencing. Primary outcomes included microbial diversity and community composition; secondary outcomes included ICU length of stay and ventilator-free days.

RESULTS: Alpha diversity declined more significantly in infected patients than in controls during the ICU stay, with the most pronounced changes in lung microbiota. We found an enrichment of Enterobacteriaceae and other Proteobacteria in the lung microbiome of pneumonia patients, while the gut microbiota remained relatively stable. Relative abundances of key taxa such as Mogibacterium were associated with mechanical ventilation duration.

CONCLUSIONS: This study reveals that distinct microbial patterns in both lung and gut microbiota are associated with infection and clinical outcomes in critically ill patients. Understanding these dynamics is crucial for developing targeted microbiota interventions, potentially improving outcomes such as VAP prevention and management.

TRIAL REGISTRATION: Ethics Committee of Canton Vaud, Switzerland (2017-01820).},
}

Humans
Pilot Projects
Prospective Studies
Intensive Care Units
Male
Female
Middle Aged
*Lung/microbiology
*Gastrointestinal Microbiome
Pneumonia, Ventilator-Associated/microbiology
Aged
RNA, Ribosomal, 16S/genetics
Critical Illness
*Bacteria/classification/genetics/isolation & purification
Respiration, Artificial
Adult

@article {pmid40187923,
year = {2025},
author = {Fernández-Barat, L and López-Aladid, R and Alcaraz-Serrano, V and Vázquez, N and Bueno-Freire, L and Pastor-Ibañez, R and Lingren, L and Sanz-Fraile, H and Oscanoa, P and Motos, A and Cabrera, R and Vila, J and Martínez, D and Otero, J and Farré, R and Høiby, N and Torres, A},
title = {Clinical and Lung Microbiome Impact of Chronic Versus Intermittent Pseudomonas aeruginosa Infection in Bronchiectasis.},
journal = {Archivos de bronconeumologia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arbres.2025.03.003},
pmid = {40187923},
issn = {1579-2129},
abstract = {BACKGROUND: In patients with non-cystic fibrosis bronchiectasis (BE) Pseudomonas aeruginosa (PA) has been recently associated with low rather than high number of exacerbations without distinguishing chronic versus intermittent infection. The aim of our study was to determine whether the intermittent or chronic stage of P. aeruginosa (PA) infection is associated with the rate of exacerbations, quality of life and respiratory microbiome biodiversity after a one-year follow-up.

METHODS: We conducted a longitudinal study, with 1-year follow-up, in patients with BE intermittently or chronically infected by PA involving sequential (3-monthly) measurements of microbiological (cultures, PA load, phenotype and biofilms presence) immunological (Serum IgGs against P. aeruginosa were measured by ELISA immunoassay) and clinical variables (Quality-of-Life and the number exacerbations). Additionaly, 16S sequencing was performed on a MiSeq Platform and compared between chronically infected patients with the mucoid PA versus intermittently infected patients with the non-mucoid PA.

RESULTS: We collected 235 sputa and 262 serum samples from 80 BE patients, 61 with chronic and 19 with intermittent PA infection. Chronically compared to intermittently. Presented reduced quality of life but less hospitalized exacerbations after 1-year follow-up. Chronically infected patients presented reduced sputum biodiversity and higher systemic IgGs against P. aeruginosa levels that were associated to decreased number of hospitalized exacerbations.

CONCLUSIONS: The assessment of Chronic versus intermittent P. aeruginosa infection has clinical implications such as quality of life, rate of hospitalized exacerbations and lung microbiome biodiversity. The distinction of these two phenotypes is easy to perform in clinical practice.

TRIAL REGISTRATION: NCT04803695.},
}

@article {pmid40187732,
year = {2025},
author = {Yang, C and Na, X and Yang, H and Xi, M and Yang, Y and Yan, Y and Duan, S and Li, T and Szeto, IM and Zhao, A},
title = {Maternal sleep and psychological status in the postpartum period are associated with functional protein alterations in breast milk:a mother-infant cohort study.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnesp.2025.03.167},
pmid = {40187732},
issn = {2405-4577},
abstract = {BACKGROUND & AIMS: Postpartum sleep disorder and mental disorders are common unpleasant conditions faced by women after delivery, and they have many adverse effects on both mothers and infants. It is unclear whether breast milk composition is affected by maternal sleep, psychological state, diet and gut microbiome. This study aims to explore the effects of these key factors on the functional protein components of breast milk.

METHODS: With a prospective design, this pilot study included a total of 41 postpartum women. Breast milk and maternal faecal samples collected at 42 days and 3 months postpartum were tested by liquid chromatography-mass spectrometry and 16S RNA sequencing, respectively. Sleep state, psychological state and dietary intake data were also collected from the mothers with validated questionnaires.

RESULTS: In the early postpartum period, sleep disorders and depression were associated with a decrease in the functional proteins in breast milk. Disordered sleep was significantly negatively correlated with α-lactalbumin (cor = -0.578, p<0.001), osteopontin (cor = -0.522, p<0.01) and κ-casein (cor = -0.451, p<0.01). Depression was negatively correlated with αs1-casein (cor = -0.422, p<0.01), β-casein (cor = -0.317, p<0.05) and casein (cor = -0.318, p<0.05). In 3 months postpartum, most associations were disappeared. But a positive correlation was observed between β-casein (cor = 0.414, p<0.01), casein (cor = 0.372, p<0.05), total protein (cor = 0.376, p<0.05) and depression, while a positive correlation was found between total protein (cor = 0.357, p<0.05) and disordered sleep at 3 months postpartum. Faecal microbiome data illustrated that changes in the gut microbiome at early postpartum were associated with sleep disorders/depression, but not with the diet. Furthermore, functional pathway analysis revealed metabolic regulation in the amino acid synthesis and metabolic pathways associated with specific microbes was involved in the reduction of breast milk protein.

CONCLUSION: Sleep disorders/depression could lead to significant changes in breast milk profiles at 42 days postpartum. Maternal gut microbiome might affect breast milk protein composition through regulating amino acid synthesis and metabolic pathways.},
}

@article {pmid40187695,
year = {2025},
author = {Palumbo, S and Lucarelli, G and Lasorsa, F and Damiano, R and Autorino, R and Aveta, A and Spena, G and Perdonà, S and Russo, P and Giulioni, C and Cafarelli, A and Finati, M and Siracusano, S and Pandolfo, SD},
title = {Urobiome and Inflammation: A Systematic Review on Microbial Imbalances and Diagnostic Tools for Urinary Disorders.},
journal = {Urology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.urology.2025.03.050},
pmid = {40187695},
issn = {1527-9995},
abstract = {OBJECTIVE: To synthesize current knowledge on urobiome alterations, innovative diagnostic advancements, and emerging therapeutic strategies targeting urobiome dysbiosis in inflammatory urinary tract disorders, including urinary tract infections (UTIs), non-gonococcal urethritis (NGU), and interstitial cystitis.

METHODS: A systematic review was conducted by screening the most important scientific databases. The search included the keywords: (microbiome) OR (microbial) OR (bacteria) OR (bacterial profile) AND (urine) OR (urinary) AND (first-morning sample) OR (first void). Only original studies in English involving human specimens were considered.

RESULTS: Of the 760 articles initially identified, a final sample of 20 original studies met the inclusion criteria. Disruptions in the urobiome composition were associated with increased colonization by pathogens such as Escherichia coli and Mycoplasma genitalium, resulting in inflammation and recurrent urinary conditions. Advanced diagnostic techniques, including metaproteomics, metagenomics, and point-of-care assays like NG-LFA, demonstrated enhanced capabilities for rapid pathogen detection and differentiation of inflammatory conditions. Therapeutic interventions targeting urobiome dysbiosis, particularly probiotics (Lactobacillus rhamnosus, L. reuteri, L. crispatus), showed promising efficacy in reducing recurrence and inflammation in clinical trials.

CONCLUSIONS: Urobiome dysbiosis plays a critical role in inflammatory urinary tract disorders. Innovative diagnostic methods and targeted therapeutic approaches, especially probiotics, offer substantial potential to improve patient outcomes. Further research is warranted to refine these strategies and validate their clinical applicability.},
}

@article {pmid40187667,
year = {2025},
author = {Sim, M and Hong, S and Jung, MH and Choi, EY and Hwang, GS and Shin, DM and Kim, CS},
title = {Gut microbiota links vitamin C supplementation to enhanced mental vitality in healthy young adults with suboptimal vitamin C status: A randomized, double-blind, placebo-controlled trial.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2025.03.032},
pmid = {40187667},
issn = {1090-2139},
abstract = {The intricate relationship between nutrition, gut microbiome, and mental health has gained increasing attention. We aimed to determine how vitamin C supplementation improves mental vitality through the gut microbiome and associated neurological and immunological changes. We used 16S rRNA sequencing to analyze gut microbiota profiles of participants from our previous trial, in which healthy young adults (20-39 years) with inadequate serum vitamin C levels (<50 μM) received 500 mg vitamin C or a placebo twice daily for 4 weeks (vitamin C, n = 21; placebo, n = 19). We examined whether changes in gut microbiota correlated with previously determined mental vitality indices, including Stroop test performance, work engagement, and serum brain-derived neurotrophic factor (BDNF) levels. Serum concentrations of microbial-derived molecules, cytokines, and neurotransmitters were analyzed using enzyme-linked immunosorbent assay, electrochemiluminescence-based immunoassay, or ultra-high-performance liquid chromatography-mass spectrometry. Monocyte subpopulations in peripheral blood were quantified using fluorescence-activated cell sorting analysis. Vitamin C supplementation increased the relative abundance of Bacillaceae and Anaerotruncus, while decreasing Desulfovibrio, with the Desulfovibrio reduction correlating with Stroop test performance. Moreover, participants showing a substantial Desulfovibrio reduction ("responders") demonstrated greater BDNF increases and stronger correlations between serum L-DOPA levels and work engagement scores than did non-responders. In addition, vitamin C supplementation suppressed inflammatory responses with concurrent reduction in serum lipopolysaccharide levels, and responders showed greater decreases in IL-10 levels and classical monocyte frequencies than non-responders. In conclusion, vitamin C supplementation modulates gut microbiota composition, particularly by reducing Desulfovibrio abundance, with the extent of reduction correlating with mental vitality improvements and decreased inflammation. This study provides insights into vitamin C supplementation as a critical dietary intervention, as it may modulate mental health through its influence on the gut-brain-immune axis.},
}

@article {pmid40187613,
year = {2025},
author = {Stickley, SA and Fang, ZY and Ambalavanan, A and Zhang, Y and Zacharias, AM and Petersen, C and Dai, D and Azad, MB and Brook, JR and Mandhane, PJ and Simons, E and Moraes, TJ and Surette, MG and Turvey, SE and Subbarao, P and Duan, Q},
title = {Gene-by-environment interactions modulate the infant gut microbiota in asthma and atopy.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2025.03.018},
pmid = {40187613},
issn = {1097-6825},
abstract = {BACKGROUND: Gut microbiota has been associated with health and susceptibility to childhood diseases, including asthma and allergies. However, the genomic factors contributing to inter-individual variations in gut microbiota remain poorly understood.

OBJECTIVE: Our study integrates host genomics with early-life exposures to investigate main and interaction effects on gut microbiota during the first year of life. In addition, we identified gut microbes associated with childhood respiratory (asthma, wheeze) and atopic (atopic dermatitis, food/inhalant sensitization) outcomes.

METHODS: We leveraged microbiome data from infant stool at ages 3 months (N=779) and 1 year (N=770) from the CHILD Cohort Study. We identified microbial taxa and co-occurring network clusters associated with asthma and atopy by age 5 years. Genome-wide association studies and gene-by-environment interaction analyses determined main and interaction effects of host genomics and early-life environmental exposures (e.g., feeding practices, household pets, birth characteristics) on gut microbial features.

RESULTS: Shifts in microbial taxa and network clusters during the first year of life were associated with childhood respiratory and atopic outcomes (P<0.05), some of which were sex-specific. Additionally, some of these implicated microbes were associated with host genomics and early-life exposures. For example, Blautia obeum was associated with reduced food/inhalant sensitization and genetic variants near the MARCO gene (P=9.4E-11). Also, variants in the SMAD2 gene interact with breastfeeding to influence the green microbial network cluster (P=8.3E-10), associated with asthma.

CONCLUSION: Our study reports main and interaction effects of genomics and exposures on early-life gut microbiota, which may contribute to childhood asthma and atopy. Improved understanding of the factors contributing to gut dysbiosis will inform on early-life biomarkers and interventions.},
}

@article {pmid40187583,
year = {2025},
author = {Dong, Y and Ramzan, R and Zhang, Y and Tang, W and Li, S and Chen, A},
title = {Exploring the antagonistic mechanism of Bacillus atrophaeus CY1 for the biological control of potato common scab.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107528},
doi = {10.1016/j.micpath.2025.107528},
pmid = {40187583},
issn = {1096-1208},
abstract = {Streptomyces scabies is a pathogenic actinomycete that infects potato crops and commonly causes scab-like lesions on potato tubers. Screening of strains antagonistic towards S. scabies in the natural environment was performed in this study. This study focused on the extraction of antibacterial substances and changes in potato defense enzymes and the rhizosphere microbiota. Together, these factors constitute biological control mechanisms. Pot experiments showed that Bacillus atrophaeus CY1 reduced the infection of scabs caused by S. scabies from 92% to 60% and the disease index from 62% to 25%. Scanning electron microscopy analysis revealed that B. atrophaeus CY1 repressed the growth of S. scabies by disrupting the mycelium and affecting potato defense enzymes. Compared with the infected group, catalase, peroxidase, and polyphenol oxidase activities in potato tubers of the co-culture group increased by 21.98%, 71.49%, and 116.15%, respectively, and SOD activity decreased by 4.9%. Moreover, at different developmental stages, the microbiota counts in the CY1 cocultured groups were significantly higher, and the actinomycete count was considerably lower. At the budding stage, urease activity was 13.39 mg.g[-1] in the co-culture group, representing an increase of 37.37% and 20.62%, respectively, compared to the control group. Cellulase activity in the SC group was 0.675 mg[-1], which represented increases of 39.18% and 43.92%, respectively. These results demonstrate that B. atrophaeus CY1 is a potential candidate for the biological control of S. scabies.},
}

@article {pmid40187540,
year = {2025},
author = {Langeraert, J and Gasthuys, E and Vermeulen, A},
title = {Small molecule drug absorption in inflammatory bowel disease and current implementation in physiologically- based pharmacokinetic models.},
journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
volume = {},
number = {},
pages = {107095},
doi = {10.1016/j.ejps.2025.107095},
pmid = {40187540},
issn = {1879-0720},
abstract = {Inflammatory bowel disease (IBD) is characterized by a chronic inflammation of the intestinal mucosa, with predominant localization in the colon in ulcerative colitis (UC) or affecting the entire length of the gastrointestinal tract in Crohn's disease (CD). Recent advances in the drug development space have been marked by a return to orally administered small molecules with novel mechanisms of action such as Janus kinase inhibitors. Additionally, the prevalence of certain chronic conditions is higher in IBD patients, many of which are treated with orally administered drugs. Given the pathophysiology and localization of IBD, altered drug absorption from the gastrointestinal tract can be expected. This review discusses several physiological differences between the small and large intestine with the potential to influence drug absorption including pathophysiology related alterations associated with IBD. The main physiological parameters which are identified include luminal fluid volume, luminal pH, transit time, bile salt concentration, microbiome, absorptive surface area, permeability and metabolizing enzymes and transporters. Literature regarding these factors in IBD patients is marked with high heterogeneity in reporting of disease severity and location leading to difficulties in interpreting data across different studies. While the influence of most of these factors has been directly assessed in healthy volunteers, this is rarely the case for IBD patients. Furthermore, studies which used PBPK modelling to describe the PK of an orally administered drug in an IBD population and were able to verify their findings using clinical data are critically examined. These models were able to incorporate the pathophysiological changes associated with IBD and partly succeeded in adequately predicting drug absorption in this population. Given the limited amount of PBPK studies performed on a limited number of drugs, the developed models are most likely not suitable to be used as a general PBPK model for the IBD population.},
}

@article {pmid40187430,
year = {2025},
author = {Cai, M and Xue, SS and Zhou, CH and Feng, YC and Liu, JZ and Liu, R and Wang, P and Wang, HN and Peng, ZW},
title = {Effects of fecal microbiota transplantation from patients with generalized anxiety on anxiety-like behaviors: The role of the gut-microbiota-endocannabinoid-brain Axis.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jad.2025.04.018},
pmid = {40187430},
issn = {1573-2517},
abstract = {BACKGROUND: Intestinal dysbacteriosis is frequently implicated in generalized anxiety disorder (GAD). However, the molecular mechanisms and functional changes of the gut-brain axis in GAD remain largely unexplored.

METHODS: We investigated anxiety-like behaviors, gut microbiota changes, brain region-specific endocannabinoid (eCB) system alterations, including the expression of cannabinoid type 1 (CB1R), monoacylglycerol lipase (MAGL), and fatty acid amide hydrolase (FAAH) in the hippocampus (Hip), prefrontal cortex (PFC), and amygdala (Amy), as well as plasma medium- and long-chain fatty acids (MLCFAs) in a mouse model of chronic restraint stress (CRS) and antibiotic-treated mice receiving fecal microbiota transplantation from GAD patients (FMT-GAD). Additionally, we assessed the impact of FMT-GAD on anxiety-like behavior in systemic CB1R/FAAH/MAGL knockout mice.

RESULTS: CRS induced anxiety-like behaviors, suppressed eCB signaling in the brain, and altered the gut microbiota and plasma MLCFA composition in mice. FMT-GAD-treated mice exhibited anxiety-like behaviors, increased FAAH expression in the Hip and Amy, and MAGL expression in the Hip, while reducing CB1R expression in the Hip. FMT-GAD was associated with decreased plasma polyunsaturated fatty acids (PUFAs) and reduced microbiome function for fatty acid biosynthesis. Notably, FMT-GAD intensified anxiety-like behaviors in CB1R-KO mice but failed to induce anxiety-like behaviors in MAGL-KO and FAAH-KO mice.

CONCLUSIONS: This study demonstrates that the interplay between the gut microbiota and the eCB system modulates GAD-related anxiety-like behaviors.},
}

@article {pmid40187346,
year = {2025},
author = {Liu, M and Blattman, SB and Takahashi, M and Mandayam, N and Jiang, W and Oikonomou, P and Tavazoie, SF and Tavazoie, S},
title = {Conserved genetic basis for microbial colonization of the gut.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.03.010},
pmid = {40187346},
issn = {1097-4172},
abstract = {Despite the fundamental importance of gut microbes, the genetic basis of their colonization remains largely unexplored. Here, by applying cross-species genotype-habitat association at the tree-of-life scale, we identify conserved microbial gene modules associated with gut colonization. Across thousands of species, we discovered 79 taxonomically diverse putative colonization factors organized into operonic and non-operonic modules. They include previously characterized colonization pathways such as autoinducer-2 biosynthesis and novel processes including tRNA modification and translation. In vivo functional validation revealed YigZ (IMPACT family) and tRNA hydroxylation protein-P (TrhP) are required for E. coli intestinal colonization. Overexpressing YigZ alone is sufficient to enhance colonization of the poorly colonizing MG1655 E. coli by >100-fold. Moreover, natural allelic variations in YigZ impact inter-strain colonization efficiency. Our findings highlight the power of large-scale comparative genomics in revealing the genetic basis of microbial adaptations. These broadly conserved colonization factors may prove critical for understanding gastrointestinal (GI) dysbiosis and developing therapeutics.},
}

@article {pmid40187247,
year = {2025},
author = {Zhou, Q and Pu, Y and Deng, H and Gong, J and Guo, L and Ma, J and Liu, L and Yuan, S and Chen, Y and Su, Y},
title = {Rhodobacter sphaeroides reduces Pb accumulation by reshaping the intestinal microenvironment and improving liver oxidant resistance in common carp (Cyprinus carpio L.).},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138152},
doi = {10.1016/j.jhazmat.2025.138152},
pmid = {40187247},
issn = {1873-3336},
abstract = {In recent years, the application of probiotics to reduce lead (Pb) toxicity in organisms has gained attention. Our previous studies showed that Rhodobacter sphaeroides SC01 exhibits high Pb tolerance and efficient Pb removal from aqueous solution. In this study, the capacity and mechanisms in alleviating Pb toxicity was investigated using strain SC01 in common carp (Cyprinus carpio L.). Results showed strain SC01 successfully colonized the intestine of common carp under Pb exposure, thereby enhancing the abundance of Rhodobacter, heavy-metal-tolerant, and denitrifying bacteria, which ameliorated intestinal microenvironment and enhanced gut microbiota diversity. Strain SC01 supplementation promoted the increase in beneficial metabolites, enhanced the anti-stress capability, and facilitated damage repair in intestine. The Pb-induced alterations of gene expression in the tight junction proteins (Claudin-3c) and pro-inflammatory cytokines (IL-1β and IL-6) were obviously reversed by strain SC01. Dietary administration of strain SC01 offered direct protection against Pb-induced oxidative stress in liver, and had several beneficial effects on hematological responses and growth performance of carp. Pb accumulation in intestinal contents, intestine, liver, kidney, and blood were markedly decreased compared to the Pb group. Therefore, R. sphaeroides SC01 may be a novel dietary supplement that enhances fish growth performance and mitigates Pb-induced toxicity in aquaculture.},
}

@article {pmid40187224,
year = {2025},
author = {Chávez-Alfaro, L and Tenorio Jiménez, C and Silveira-Sanguino, V and Noguera Gómez, MJ and Fernández-Moreno, C and Rodríguez Cuesta, AM and Lebrón Arana, AF and Segura Calvo, Ó and Merino De Haro, I and Aguilera, CM and Gómez-Llorente, C and Rangel-Huerta, ÓD and Astbury, N and Pérez-Cornago, A and Guasch-Ferre, M and Piernas, C},
title = {Intervention design and adherence to Mediterranean diet in the Cardiovascular Risk Prevention with a Mediterranean Dietary Pattern Reduced in Saturated Fat (CADIMED) randomized trial.},
journal = {Nutrition research (New York, N.Y.)},
volume = {136},
number = {},
pages = {120-132},
doi = {10.1016/j.nutres.2025.03.001},
pmid = {40187224},
issn = {1879-0739},
abstract = {Effective interventions targeting modifiable cardiovascular disease (CVD) risk factors, such as diet, are urgently needed. The Cardiovascular Risk Prevention with a Mediterranean Dietary Pattern Reduced in Saturated Fat study hypothesizes that eliminating red and processed meat in the context of a Mediterranean diet (MD) will significantly modify circulating low-density lipoprotein cholesterol concentration and the fatty acid profile compared to general CVD prevention advice. Here we describe the intervention design and summarize baseline dietary intakes (mean ± standard deviation) related to MD adherence and red/processed meat intakes in a sample of 81 participants. The Cardiovascular Risk Prevention with a Mediterranean Dietary Pattern Reduced in Saturated Fat study is a two-arm, 8-week parallel randomized controlled intervention trial involving a final sample of 156 adults (≥18 years) with dyslipidemia (not undergoing pharmacological treatment) recruited from healthcare and community settings in Granada (Spain). The primary outcome will assess changes in circulating low-density lipoprotein cholesterol and the fatty acid profile, whilst secondary outcomes will measure changes in CVD-related metabolites/biomarkers, gut microbiome, diet/lifestyle, and intervention feasibility/acceptability. Preliminary findings indicate low MD adherence (Mediterranean Diet Adherence Screener score 7.6 ± 1.9), and high consumption of red and processed meat (1.04 ± 0.90) servings/d). These results underscore the need for targeted dietary interventions to address the growing burden of dyslipidemia and CVD. If successful, this intervention holds potential for scalability and significant impact on public health, dietary guidelines, and advancements in nutrition science by improving MD adherence and reducing CVD risk factors in adults with dyslipidemia.},
}

@article {pmid40187207,
year = {2025},
author = {Pourali, A and Aali, S and Kamrava, A},
title = {Confounders of the skin microbiome and wound healing in burn patients.},
journal = {Burns : journal of the International Society for Burn Injuries},
volume = {51},
number = {5},
pages = {107450},
doi = {10.1016/j.burns.2025.107450},
pmid = {40187207},
issn = {1879-1409},
}

@article {pmid40187200,
year = {2025},
author = {Alias, A and Amin, KAM and Heng, LS and Nor, SMM and Omar, WBW and Ibrahim, YS and Heděnec, P},
title = {Microplastic contamination alters microbial community in commercially important bivalves, Geloina expansa, Anadara cornea, and Meretrix meretrix from tropical waters.},
journal = {Marine pollution bulletin},
volume = {215},
number = {},
pages = {117931},
doi = {10.1016/j.marpolbul.2025.117931},
pmid = {40187200},
issn = {1879-3363},
abstract = {Microplastics pose serious risks for aquatic organisms such as fishes, shrimps and bivalves. Bivalves are particularly vulnerable due to their filter-feeding strategy and sedentary life. While the microplastic bioaccumulation in bivalves has been well documented, the effects of microplastics accumulation on bivalve's gut microbiome in tropical sea waters remains poorly understood. To fill this knowledge gap, a 10-day feeding experiment with 13 mg L[-1] polyethylene terephthalate particles was conducted using three commercially important bivalve species: Anadara cornea, Geloina expansa, and Meretrix meretrix taken from two contrasting locations (brackish water in protected Setiu Wetlands compared to open water in Kertih River) to investigate the effect of microplastic pollution on diversity and composition of gut prokaryotes using 16S rRNA amplicon sequencing. The results showed that alpha diversity of gut prokaryotes differed among species after microplastic exposure. For example, microplastic exposure increased operational taxonomic units (OTUs) richness of gut prokaryotes in G. expansa compared to A. cornea and M. meretrix during 10-day treatment. Community structure of prokaryotic community in bivalves gut showed strong divergence between Setiu Wetlands and Kertih River. Significant effects of microplastic exposure on relative abundance of prokaryotic phyla were also observed. Gut microbiome of G. expansa showed increase of relative abundance of Archaea and Firmicutes after microplastic exposure. The results suggest that microplastic treatment promotes dominance of certain bacterial species, likely those with plastic-metabolizing capabilities, potentially boosting bivalve resilience to microplastic contamination.},
}

@article {pmid40187012,
year = {2025},
author = {Khan, MM and Mushtaq, MA and Suleman, M and Ahmed, U and Ashraf, MF and Aslam, R and Mohsin, M and Rödiger, S and Sarwar, Y and Schierack, P and Ali, A},
title = {Fecal microbiota landscape of commercial poultry farms in Faisalabad, Pakistan: A 16S rRNA gene-based metagenomics study.},
journal = {Poultry science},
volume = {104},
number = {6},
pages = {105089},
doi = {10.1016/j.psj.2025.105089},
pmid = {40187012},
issn = {1525-3171},
abstract = {This study explores the microbiota of broiler and layer farms, aiming to understand how genetic breed, age, and farm type influence microbial communities in commercial settings. Fecal samples from 18 poultry farms (twelve layers and six broilers) in Faisalabad, Pakistan were analyzed using 16S rRNA gene sequencing of the V3-V4 region to evaluate bacterial composition. The dominant phylum, Firmicutes, accounted for 58.72 % of the microbial population, with Lactobacillus being the most abundant genus in both broilers and layers. The total abundance of potentially pathogenic genera was also assessed with Enterococcus and Corynebacterium being the most prevalent across all farms, regardless of bird type. Layers exhibited greater microbial richness and diversity than broilers, while the Karachi cage system (KCS) farm type showed higher richness than Floor system (FS). Although the breed significantly influenced microbial diversity, age was not a determining factor. Co-occurrence analyses revealed close interactions among phyla (Actinobacteriota, Proteobacteria, Firmicutes, Fusobacteriota, and Bacteroidota) and genera (Lactobacillus, Brevibacterium, Enterococcus), suggesting their pivotal roles within the microbial community. Additionally, functional analysis detected important metabolic pathways and traced microbial signatures of key pathogenic bacteria, enhancing our understanding of microbial contributions to poultry health. Despite limitations such as the need for broader geographic sampling and accounting for diet and medication, this study advances microbiome research in Pakistan's poultry sector, emphasizing consistent taxa and opening avenues for future investigations into microbiome manipulations for improved food safety and achieve better sustainable practices.},
}

@article {pmid40186969,
year = {2025},
author = {Mohan, H and Acharaya, S and Park, JH and Oh, BT},
title = {Doxycycline degradation by Enterobacter cloacae HS-08: A comparative analysis of biodegradation and bio-electrodegradation approaches with toxicity implications.},
journal = {Journal of environmental management},
volume = {381},
number = {},
pages = {125212},
doi = {10.1016/j.jenvman.2025.125212},
pmid = {40186969},
issn = {1095-8630},
abstract = {Doxycycline (DOX), a commonly prescribed antibiotic, poses a growing environmental concern due to its recalcitrant nature, insufficient removal by conventional treatment methods, and detrimental effects on ecosystems and living organisms. This study evaluates the comparative efficacy of biodegradation and bio-electrodegradation approaches for DOX removal using Enterobacter cloacae HS-08, focusing on degradation efficiency, intermediate toxicity, systemic impacts, and gut microbiome alterations. The results showed that biodegradation achieved 61% DOX removal (75 mg/L) within 8 days; however, HPLC-MS/MS analysis revealed the formation of toxic intermediates, resulting in residual toxicity. Interestingly, bio-electrodegradation demonstrated superior performance, achieving 99.19% degradation under optimized conditions with minimal toxic intermediates. In-vivo toxicity studies using mice revealed that untreated DOX effluent significantly reduced body weight, food intake, and organ health while disrupting gut microbiome composition, marked by reduced diversity and dysbiosis. Biodegradation effluent exhibited moderate toxicity, reflecting the lingering effects of intermediate by-products. Conversely, bio-electrodegradation effluent mitigated toxicity, preserved gut microbiome structure and diversity, and supported normal physiological function, with growth, appetite, and organ health comparable to the control group. These findings highlight the critical need to address doxycycline contamination and emphasize the superior efficacy of bio-electrodegradation as a sustainable solution for mitigating pharmaceutical pollutants and restoring ecological balance.},
}

@article {pmid40186955,
year = {2025},
author = {Sayed, Y and Hassan, M and Salem, HM and Al-Amry, K and Eid, G},
title = {Probiotics/prebiotics effect on chicken gut microbiota and immunity in relation to heat-stress and climate-change mitigation.},
journal = {Journal of thermal biology},
volume = {129},
number = {},
pages = {104097},
doi = {10.1016/j.jtherbio.2025.104097},
pmid = {40186955},
issn = {0306-4565},
abstract = {Heat stress is a serious hazard that threatens world poultry production. The avian gut microbiome plays a critical role in improving nutrient utilization, competing with pathogens, stimulating an immune response, and reducing inflammatory reactions. Hence, the gut microbiome has a positive impact on the host's health which appears in the shape of improved body weight, feed conversion rate, and increased birds' productivity (meat or eggs). Accordingly, this review shed light on the chicken gut microbiome, its correlation with the immunity of chicken, and how this affects the general health condition of the bird as well as, the role of prebiotics and probiotics in improving the gut health and increasing birds' productivity, especially under climate change and heat stress condition. The review aims to focus on the significance of maintaining healthy chickens in order to increase the production of poultry meat to satisfy human needs. A robust microbiota and a well-functioning immune system synergistically contribute to the optimal health and productivity of chickens.},
}

@article {pmid40186907,
year = {2025},
author = {Jiang, Y and Chen, J and Du, Y and Fan, M and Shen, L},
title = {Immune modulation for the patterns of epithelial cell death in inflammatory bowel disease.},
journal = {International immunopharmacology},
volume = {154},
number = {},
pages = {114462},
doi = {10.1016/j.intimp.2025.114462},
pmid = {40186907},
issn = {1878-1705},
abstract = {Inflammatory bowel disease (IBD) is an inflammatory disease of the intestine whose primary pathological presentation is the destruction of the intestinal epithelium. The intestinal epithelium, located between the lumen and lamina propria, transmits luminal microbial signals to the immune cells in the lamina propria, which also modulate the intestinal epithelium. In IBD patients, intestinal epithelial cells (IECs) die dysfunction and the mucosal barrier is disrupted, leading to the recruitment of immune cells and the release of cytokines. In this review, we describe the structure and functions of the intestinal epithelium and mucosal barrier in the physiological state and under IBD conditions, as well as the patterns of epithelial cell death and how immune cells modulate the intestinal epithelium providing a reference for clinical research and drug development of IBD. In addition, according to the targeting of epithelial apoptosis and necroptotic pathways and the regulation of immune cells, we summarized some new methods for the treatment of IBD, such as necroptosis inhibitors, microbiome regulation, which provide potential ideas for the treatment of IBD. This review also describes the potential for integrating AI-driven approaches into innovation in IBD treatments.},
}

@article {pmid40186906,
year = {2025},
author = {Lu, H and Zhang, M and Hu, Y and Sun, X and Zhang, R and Zhang, X and Zhang, M and Tang, C and Cui, Q and Zhang, Z and Wu, Z and Wang, W and Song, S and Cui, L and Zhu, J and Yang, X and Yang, Z},
title = {Short-chain fatty acids alleviate cholestatic liver injury by improving gut microbiota and bile acid metabolism.},
journal = {International immunopharmacology},
volume = {154},
number = {},
pages = {114564},
doi = {10.1016/j.intimp.2025.114564},
pmid = {40186906},
issn = {1878-1705},
abstract = {Cholestasis, characterized by the obstruction of bile flow and the accumulation of bile acids, can lead to severe liver damage. Current treatments, such as ursodeoxycholic acid (UDCA) and obeticholic acid (OCA), are limited in effectiveness and have significant side effects, underscoring the need for new therapies. In our study, we investigated the effects of short-chain fatty acids (SCFAs) as a treatment in a mouse model of cholestasis induced by α-naphthylisothiocyanate (ANIT). Our findings demonstrated that SCFAs improved liver function, as indicated by reductions in liver function markers, decreased necrosis, and reduced bile duct proliferation and inflammation. Furthermore, SCFAs enhanced intestinal barrier function and increased the abundance of beneficial gut bacteria, such as Akkermansia muciniphila (A. muciniphila). SCFAs also triggered the FXR-Fgf15-Cyp7a1 pathway, reducing bile acid synthesis and improving bile acid metabolism. These findings indicate that SCFAs could offer a viable new treatment strategy for cholestatic liver conditions by improving gut-liver interactions, stabilizing bile acid metabolism, and alleviating inflammation.},
}

@article {pmid40186782,
year = {2025},
author = {Neyrinck, AM and Rodriguez, J and Sánchez, CR and Autuori, M and Cani, PD and Bindels, LB and Bindelle, J and Delzenne, NM},
title = {Interest of inulin in obesity: comparison of the prebiotic effect of edible-food sources versus purified inulin from chicory root.},
journal = {European journal of nutrition},
volume = {64},
number = {4},
pages = {148},
pmid = {40186782},
issn = {1436-6215},
support = {1318148//SPW-EER/ ; PDR T.0085.24//Fonds De La Recherche Scientifique - FNRS/ ; },
mesh = {*Inulin/administration & dosage/pharmacology ; *Prebiotics/administration & dosage ; *Cichorium intybus/chemistry ; Animals ; *Obesity/microbiology/diet therapy ; Gastrointestinal Microbiome/drug effects ; Plant Roots/chemistry ; Mice ; Diet, High-Fat/adverse effects ; Male ; Mice, Inbred C57BL ; Dietary Fiber/administration & dosage ; },
abstract = {PURPOSE: Inulin-type fructans (ITF) are fermentable dietary fibres (DF) that can confer beneficial metabolic health effects through changes in the gut microbiota. Many papers suggest that complex food rich in DF could be more relevant than purified DF in terms of health effect. We compared the prebiotic effect of natural source of inulin (scorzonera) versus native inulin extracted from chicory root in a model of obesity.

METHODS: Mice were fed during 6 weeks a low-fat (LF), high-fat (HF) or high-fat diet enriched with either purified inulin from chicory root (Inu) or lyophilized scorzonera (Sco), with the same amount of ITF intake (10%) versus a non-fermentable fibre (cellulose). Metabolic parameters were correlated with the gut microbiome composition (16S rRNA gene sequencing).

RESULTS: Both inulin sources reduced food intake without significantly modifying body weight gain or adiposity compared to HF. Purified inulin and lyophilized scorzonera differentially modulate the gut physiology and microbiota. Both inulin and scorzonera shifted global gut microbial composition from HF group, decreased members of Desulfovibrionaceae and boosted bifidobacteria level. Some effects were specific to Sco group, such as the increase of Akkermansia and the decrease of Bacteroides, that correlated to biological outcomes. Inu improved hepatic steatosis whereas scorzonera boosted intestinal immunity markers and antimicrobial peptides expression, and increased intestinal crypt depth.

CONCLUSION: Differences occur between natural edible versus isolated sources of ITF. Both sources of inulin shifted the gut microbiota, but differently affected intestinal and lipid homeostasis. This study highlights the importance of food matrix and origins of fructans for their use in the context of metabolic disorders.},
}

*Inulin/administration & dosage/pharmacology
*Prebiotics/administration & dosage
*Cichorium intybus/chemistry
Animals
*Obesity/microbiology/diet therapy
Gastrointestinal Microbiome/drug effects
Plant Roots/chemistry
Mice
Diet, High-Fat/adverse effects
Male
Mice, Inbred C57BL
Dietary Fiber/administration & dosage

@article {pmid40186699,
year = {2025},
author = {Golden, A and Williams, C and Yadav, H and Masternak, MM and Labyak, C and Holland, PJ and Arikawa, AY and Jain, S},
title = {The selection of participants for interventional microbiota trials involving cognitively impaired older adults.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {40186699},
issn = {2509-2723},
abstract = {Gut microbiota plays a significant role in nutrient extraction, metabolism, and immune function. Thus, the growing number of microbiome studies seek to link the presence and prevalence of specific bacteria, fungi, and viruses with a variety of physiological and disease outcomes. However, recruiting a diverse group of patients has been a challenge. Poor hearing and vision, lack of transportation, cognitive impairment, and a non-English primary language may interfere with patient enrollment as well as adherence to the requirements of a Microbiome study. Much of what we do know about diseases in older adults comes from studies that exclude many of these patients commonly encountered in clinical practice. The purpose of this review article is to highlight recruitment and retention strategies for engaging people who typically do not participate in microbiome studies, and it seeks to develop and explicate inclusion and exclusion criteria to promote more robust study results.},
}

@article {pmid40186645,
year = {2025},
author = {Du, B and Yan, R and Hu, X and Lou, J and Zhu, Y and Shao, Y and Jiang, H and Hao, Y and Lv, L},
title = {Role of Bifidobacterium animalis subsp. lactis BB-12 in mice with acute pancreatitis.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {62},
pmid = {40186645},
issn = {2191-0855},
support = {2022YFC2304500, 2023YFC2506000, and 2021YFA1301104)//National Key Research and Development Program/ ; 2022ZFJH003//Fundamental Research Funds for the Central Universities/ ; 81570512//National Natural Science Foundation of China/ ; SYS202202//Shandong Provincial Laboratory Project/ ; 2024ZY01054//Central Guidance Fund for Local Science and Technology Development/ ; },
abstract = {Acute pancreatitis (AP) is a prevalent acute gastrointestinal disease, which may be prevented and alleviated by probiotics. Bifidobacterium animalis subsp. lactis BB-12 (BB-12) is a widely studied probiotic strain; however, its specific effects in this context remain unexplored. In this study, we aimed to investigate the prophylactic and therapeutic effects of BB-12 in AP. Our findings revealed that BB-12 administration via gavage significantly reduced pathological pancreatic damage and serum amylase activity. Microbiome analysis showed that BB-12 treatment significantly increased the relative abundance of Ligilactobacillus and decreased that of Bilophila in the gut microbiota of mice with AP. Transcriptome analysis revealed that BB-12 mitigated the AP-induced dysregulation of several pathways, specifically attenuating the upregulation of the pancreatic secretion and ascorbate and aldarate metabolism pathways while reversing the downregulation of the ribosome, oxidative phosphorylation, and thermogenesis pathways. Spearman's correlation analysis revealed a positive correlation between the abundances of Bilophila and ASF356 and serum amylase activity. Furthermore, the abundances of Bilophila and ASF356 were significantly correlated with BB-12-regulated pancreatic genes and were predominantly enriched in the ribosome pathway. In conclusion, BB-12 pretreatment alleviated AP, likely by regulating the abundance of intestinal Lactobacillus, Bilophila, and ASF356, as well as the pancreatic secretion, ascorbate and aldarate metabolism, oxidative phosphorylation, ribosome, and thermogenesis pathways.},
}

@article {pmid40186338,
year = {2025},
author = {Li, P and Li, M and Chen, WH},
title = {Best practices for developing microbiome-based disease diagnostic classifiers through machine learning.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2489074},
doi = {10.1080/19490976.2025.2489074},
pmid = {40186338},
issn = {1949-0984},
mesh = {*Machine Learning ; Humans ; *Gastrointestinal Microbiome ; Algorithms ; },
abstract = {The human gut microbiome, crucial in various diseases, can be utilized to develop diagnostic models through machine learning (ML). The specific tools and parameters used in model construction such as data preprocessing, batch effect removal and modeling algorithms can impact model performance and generalizability. To establish an generally applicable workflow, we divided the ML process into three above-mentioned steps and optimized each sequentially using 83 gut microbiome cohorts across 20 diseases. We tested a total of 156 tool-parameter-algorithm combinations and benchmarked them according to internal- and external- AUCs. At the data preprocessing step, we identified four data preprocessing methods that performed well for regression-type algorithms and one method that excelled for non-regression-type algorithms. At the batch effect removal step, we identified the "ComBat" function from the sva R package as an effective batch effect removal method and compared the performance of various algorithms. Finally, at the ML algorithm selection step, we found that Ridge and Random Forest ranked the best. Our optimized work flow performed similarly comparing with previous exhaustive methods for disease-specific optimizations, thus is generally applicable and can provide a comprehensive guideline for constructing diagnostic models for a range of diseases, potentially serving as a powerful tool for future medical diagnostics.},
}

*Machine Learning
Humans
*Gastrointestinal Microbiome
Algorithms

@article {pmid40186246,
year = {2025},
author = {Ge, Y and Tang, G and Fu, Y and Deng, P and Yao, R},
title = {The impact of environmental factors on respiratory tract microbiome and respiratory system diseases.},
journal = {European journal of medical research},
volume = {30},
number = {1},
pages = {236},
pmid = {40186246},
issn = {2047-783X},
support = {2022YFC2403603//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Microbiota ; *Respiratory System/microbiology ; *Respiratory Tract Diseases/microbiology/etiology ; *Environmental Exposure/adverse effects ; },
abstract = {The respiratory tract microbiome, a complex ecosystem of microorganisms colonizing the respiratory mucous layers and epithelial surfaces along with their associated microenvironment, plays a vital role in maintaining respiratory function and promoting the maturation of the respiratory immune system. Current research suggests that environmental changes can disrupt the respiratory microbiota, potentially leading to disease. This review summarizes existing research on the impact of environmental factors on the respiratory microbiome and associated diseases, aiming to offer new insights into the prevention and treatment of respiratory disease.},
}

Humans
*Microbiota
*Respiratory System/microbiology
*Respiratory Tract Diseases/microbiology/etiology
*Environmental Exposure/adverse effects

@article {pmid40186224,
year = {2025},
author = {Mahnic, A and Krivec, JL and Paro-Panjan, D and Valcl, A and Obermajer, T and Matijašić, BB and Benedik, E and Bratina, P and Rupnik, M},
title = {Clostridioides difficile concentration-dependant alterations in gut microbiota of asymptomatic infants.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {17},
pmid = {40186224},
issn = {1757-4749},
support = {P3-0387//The Slovenian Research and Innovation Agency/ ; P4-0097//The Slovenian Research and Innovation Agency/ ; P4-0097//The Slovenian Research and Innovation Agency/ ; P3-0395//The Slovenian Research and Innovation Agency/ ; P3-0387//The Slovenian Research and Innovation Agency/ ; ID-20150021//University Medical Centre Ljubljana/ ; ID-20150021//University Medical Centre Ljubljana/ ; },
abstract = {BACKGROUND: Asymptomatic carriage of Clostridioides difficile is highly prevalent in early infancy, affecting approximately 40% of infants. This phenomenon offers a unique opportunity to study its impact on the gut microbiota without the confounding effects of disease. In this study, we analysed C. difficile-associated gut microbiome alterations in 76 asymptomatic infants, one year after receiving antibiotic treatment during early infancy. The presence and concentration of C. difficile were assessed in relation to gut microbiota structure and an extensive set of metadata.

RESULTS: Bacterial gut community structure was characterized using 16 S rRNA amplicon sequencing, while C. difficile concentration and the presence of the tcdB gene were quantified via digital PCR. C. difficile was detected in 36.8% of infants, with 10.5% testing positive for the tcdB gene. Significant alterations in gut microbiota were observed in relation to C. difficile concentration. Specifically, higher C. difficile loads were associated with reduced microbial diversity, greater deviations from average community structure, and co-occurrence with the genus Escherichia. Conversely, C. difficile colonization alone or the presence of the tcdB gene did not result in significant gut microbiota alterations. Additionally, no host-specific factors were significantly linked to C. difficile prevalence or concentration.

CONCLUSIONS: Asymptomatic carriage of C. difficile in neonates is not associated with significant gut microbiota alterations unless pathogen concentration is considered. Our findings suggest that elevated C. difficile proliferation occurs in dysbiotic infant gut microbiota, characterized by reduced alpha diversity and an increase in Escherichia.},
}

@article {pmid40186181,
year = {2025},
author = {Tort-Miró, C and Lorenzo-Rebenaque, L and Montoro-Dasi, L and Vega, S and Rodríguez, JC and Ventero, MP and Pérez-Gracia, MT and Guitart-Matas, J and Giler-Baquerizo, N and Marco-Fuertes, A and D'Auria, G and Marin, C and Migura-Garcia, L},
title = {Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health status.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {246},
doi = {10.1186/s12917-025-04693-0},
pmid = {40186181},
issn = {1746-6148},
support = {PID2021-125641OB-C22 and PID2021-125641OB-C21//I+D+I National Program/ ; PID2021-125641OB-C22 and PID2021-125641OB-C21//I+D+I National Program/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; Female ; RNA, Ribosomal, 16S/genetics ; Swine Diseases/microbiology ; Nanopores ; Bacteria/classification/genetics ; Diarrhea/veterinary/microbiology ; Farms ; Health Status ; Animal Husbandry ; },
abstract = {BACKGROUND: Antibiotics are used in animal husbandry to control infectious diseases. Different stressors can compromise animal health, leaving piglets vulnerable to pathogens, especially enterotoxigenic Escherichia coli (ETEC), which causes post-weaning diarrhoea (PWD), the major source of mortality and morbidity in swine production. Furthermore, PWD is a recurrent disease for certain farms, suggesting a link between gut microbial composition and animal health. The aim of this study was to identify the intestinal microbiota of pigs on farms with high health status (HHS) and low health status (LHS) to determine the relationships between sanitary status and gut health. Therefore, three pig farms with LHS presenting recurrent problems of PWD and three farms with HHS were selected to characterise the intestinal microbiome of sows and their piglets. 16 S rRNA gene sequencing technology was used to determine the associations of the gut microbiome with health. With the aim of bringing the MinION Nanopore device to the field for its portability and taxonomic resolution, the results obtained with Illumina were compared to those obtained with Nanopore.

RESULTS: Overall, the results indicated remarkable differences in intestinal microbial communities between animals from LHS farms and those from HHS farms, suggesting that the microbiomes of LHS animals were enriched with potential pathogenic microorganisms, mainly from the Pseudomonadota phylum, such as the genus Escherichia-Shigella, and their associated related species. Moreover, animals from HHS were enriched with beneficial microorganisms, such as Lactobacillus spp., Christensenellaceae R7 group, Treponema, Acetitomaculum and Oscillospiraceae UCG-005.

CONCLUSIONS: This study identifies potential microorganisms that may contribute to health and disease in pig farms with HHS and LHS, suggesting that tracking their occurrence might provide insight into sanitary conditions. Moreover, this research highlights the compatibility between Illumina and Nanopore sequencing platforms, justifying the use of MinION Nanopore device in field applications for in situ studies of PWD. This application has the potential to enhance sustainable economic growth in swine farms by enabling more effective monitoring and management of animal health.},
}

Animals
*Gastrointestinal Microbiome/genetics
Swine/microbiology
Female
RNA, Ribosomal, 16S/genetics
Swine Diseases/microbiology
Nanopores
Bacteria/classification/genetics
Diarrhea/veterinary/microbiology
Farms
Health Status
Animal Husbandry

@article {pmid40186151,
year = {2025},
author = {Wei, K and Ma, Y and Xu, J and Zheng, H and Xue, L and Chu, Y and Shi, Y and Sun, Z and Sun, Q},
title = {Potential changes in microorganisms and metabolites associated with oral cancer: a preliminary study.},
journal = {BMC cancer},
volume = {25},
number = {1},
pages = {611},
pmid = {40186151},
issn = {1471-2407},
support = {20240349//Graduate Student Independent Innovation Project of Zhengzhou University/ ; 24A320056//Education Department of Henan Province/ ; JC23862075//Zhengzhou University/ ; HNSWJW-2022016//Health Commission of Henan Province/ ; 212102310592//Science and Technology Department of Henan Province,China/ ; GCC2025054//Talent Training Project in Henan Province/ ; },
mesh = {Humans ; *Mouth Neoplasms/microbiology/metabolism ; Male ; Female ; Middle Aged ; Saliva/microbiology ; *Metabolome ; *Microbiota ; Aged ; Case-Control Studies ; Metabolomics/methods ; Adult ; Chromatography, Liquid ; *Carcinoma, Squamous Cell/microbiology/metabolism ; *Bacteria/genetics/classification/metabolism/isolation & purification ; },
abstract = {BACKGROUND: Oral squamous cell carcinoma is a malignant tumor with high morbidity and mortality, and changes in microflora have a close relationship with tumor development. In this study, we tried to identify the changes in oral microbial characteristics and metabolite levels in OSCC patients.

METHODS: In this study, saliva samples were collected from 40 oral cancer cases and 39 healthy controls. The microbiome was analysed by 16 S rDNA gene sequencing, and the metabolome was detected by Liquid Chromatography-Mass Spectrometry (LC-MS) with metabolite traceability using the Metorigin platform. Correlations between the microbiome and metabolome were analysed using the Spearman correlation method.

RESULTS: The study found a significant difference in the β diversity of oral microbiota between the oral cancer group and healthy controls, while α diversity showed no significant difference. At the phylum level, Deferribacterota significantly increased, and Cyanobacteria significantly decreased in the oral cancer group. At the genus level, Vibrio and Lactococcus were significantly elevated, while Bifidobacterium and Faecalibacterium were significantly reduced. Metabolomic analysis identified 36 differentially abundant metabolites; 13(S)-HOTrE and 13-HODE were significantly downregulated, while docosanamide was significantly upregulated in the oral cancer group. Six bacteria-specific metabolites, including Indole, were also downregulated. Correlation analysis showed that N-Acetylneuraminic acid had a significant negative correlation with Pseudoalteromonas and Vibrio (r < -0.4).

CONCLUSION: This study found large differences in microbiome levels at the portal level, at the genus level, and significant differences in the levels of a variety of metabolites labeled by indoles, providing a new and potentially valuable direction for the diagnosis and treatment of oral squamous carcinoma.},
}

Humans
*Mouth Neoplasms/microbiology/metabolism
Male
Female
Middle Aged
Saliva/microbiology
*Metabolome
*Microbiota
Aged
Case-Control Studies
Metabolomics/methods
Adult
Chromatography, Liquid
*Carcinoma, Squamous Cell/microbiology/metabolism
*Bacteria/genetics/classification/metabolism/isolation & purification

@article {pmid40186137,
year = {2025},
author = {Fagnano, FM and Ventorino, V and Pasolli, E and Romano, I and Ambrosino, P and Pepe, O},
title = {From microbiome to biostimulants: unlocking the potential of tomato root endophytes.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {427},
pmid = {40186137},
issn = {1471-2229},
mesh = {*Solanum lycopersicum/microbiology/growth & development ; *Endophytes/physiology/genetics ; *Plant Roots/microbiology ; *Microbiota ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: Microbe-based biostimulants offer a sustainable and promising alternative to synthetic inputs, potentially reducing or replacing conventional inputs in crop management. Studying the native microbiota, particularly endophytic microbes, helps in selecting those that are naturally adapted to persist and to enhance plant growth under specific environmental conditions. This study aims to define the endophytic microbiota adapted to tomato crops by selecting discriminant amplicon sequence variant (ASVs) that are enriched during key plant growth stages and found in the core microbiota.

RESULTS: This study presents a large-scale analysis of tomato root endophytic prokaryotic microbiota using 16 S sequencing across the most common and widespread conditions used for tomato cultivation, offering comprehensive insight into its structure and dynamics. The results revealed a predominance of the Actinobacteriota and Proteobacteria phyla; less abundant groups included Bacteroidota, Verrucomicrobiota, Patescibacteria, and Firmicutes. Core microbiota analysis and discriminant ASV identification across different plant growth stages enabled the selection of the most abundant and persistent taxa adapted to the tomato endorhizosphere. Streptomyces, Shinella, Devosia, and Pseudoxanthomonas, as well as the lesser known genera Variovorax, Pseudarthrobacter, and Lechevalieria, represented the key genera identified, suggesting long-term host‒microbe associations.

CONCLUSIONS: The description of the representative framework of the tomato-associated microbiota and the identification of its most important components provide a basis for developing tailored microbial formulations that can increase crop resilience and reduce dependence on synthetic agricultural inputs, aimed at developing more sustainable environmental management strategies.},
}

*Solanum lycopersicum/microbiology/growth & development
*Endophytes/physiology/genetics
*Plant Roots/microbiology
*Microbiota
Bacteria/genetics/classification

@article {pmid40186063,
year = {2025},
author = {Saveetha, K and Somala, CS and Anand, T and Balamurugan, D and Vasudevan, V and Saravanan, KM and Senthil, R},
title = {Impact of Soil Microbiomes on Mung Bean Cultivation: Insights from 16S rRNA Metagenomics.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40186063},
issn = {1559-0305},
abstract = {Cyclic nutrient processes, soil health maintenance, and plant development are contingent upon soil microbiomes. The microbial makeup of the soil of Maruthupandiyar College, Thanjavur, is assessed using 16S rRNA gene sequencing. QIIME2, in conjunction with the SILVA database, analyzed the sequencing data to examine microbial diversity and composition. The experimental results revealed a diverse array of bacteria in soil physicochemical properties. The alpha and beta diversity assessment revealed significant microbial community complexity and distribution patterns disparities. The research revealed bacterial groups associated with biological nitrogen fixing, suggesting their potential to enhance mung bean growth. The current study illustrates the significance of microbial interactions in soil for sustaining soil fertility and enhancing crop output. Research findings provide essential insights into improving the sustainability of tropical agriculture through intentional microbial management to create sustainable soil health systems.},
}

@article {pmid40185904,
year = {2025},
author = {Wang, D and Gui, S and Pu, J and Zhong, X and Yan, L and Li, Z and Tao, X and Yang, D and Zhou, H and Qiao, R and Zhang, H and Cheng, X and Ren, Y and Chen, W and Chen, X and Tao, W and Chen, Y and Chen, X and Liu, Y and Xie, P},
title = {PsycGM: a comprehensive database for associations between gut microbiota and psychiatric disorders.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {40185904},
issn = {1476-5578},
support = {CSTB2024NSCQ-MSX1027//Natural Science Foundation of Chongqing (Natural Science Foundation of Chongqing Municipality)/ ; CSTB2024NSCQ-QCXMX0033//Natural Science Foundation of Chongqing (Natural Science Foundation of Chongqing Municipality)/ ; 82371526//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Psychiatric disorders pose substantial global burdens on public health, yet therapeutic options remain limited. Recently, gut microbiota is in the spotlight of new research on psychiatric disorders, as emerging discoveries have highlighted the importance of gut microbiome in the regulation of central nervous system via mediating the gut-brain-axis bidirectional communication. While metagenomics studies have accumulated for psychiatric disorders, few systematic efforts were dedicated to integrating these high-throughput data across diverse phenotypes, interventions, geographical regions, and biological species. To present a panoramic view of global data and provide a comprehensive resource for investigating the gut microbiota dysbiosis in psychiatric disorders, we developed the PsycGM, a manually curated and well-annotated database that provides the literature-supported associations between gut microbiota and psychiatric disorders or intervention measures. In total, PsycGM incorporated 559 studies from 31 countries worldwide, encompassing research involving humans, rats, mice, and non-human primates. PsycGM documented 8907 curated associations between 1514 gut microbial taxa and 11 psychiatric disorders, as well as 4050 associations between 869 taxa and 232 microbiota-based and non-microbiota-based interventions. Moreover, PsycGM provided a user-friendly web interface with comprehensive information, enabling browsing, retrieving and downloading of all entries. In the application of PsycGM, we panoramically depicted the intestinal microecological imbalance in depression. Additionally, we identified 9 microbial taxa consistently altered in patients with depression, with the most common dysregulations observed for Parabacteroides, Alistipes, and Faecalibacterium; in animal models of depression, consistent changes were observed in 21 microbial taxa, most frequently reported as Helicobacter, Lactobacillus, Roseburia, and the ratio of Firmicutes/Bacteroidetes. PsycGM is a comprehensive resource for future investigations on the role of gut microbiota in mental and brain health, and for therapeutic target innovations based on modifications of gut microbiota. PsycGM is freely accessed at http://psycgmomics.info .},
}

@article {pmid40185849,
year = {2025},
author = {Rajbhandari, RM and Forcina, G and Manandhar, P and Rajbhandari, PG and Napit, R and Raut, R and Shrestha, S and Sadaula, A and Gortázar, C and Alves, PC and de la Fuente, J and Queirós, J and Karmacharya, D},
title = {Gut microbiota diversity among humans, elephants, livestock and wild herbivores in Chitwan National Park bears implications for conservation medicine.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11596},
pmid = {40185849},
issn = {2045-2322},
support = {PTDC/BAA-360 AGR/28866/2017//Fundação para a Ciência e a Tecnologia/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Elephants/microbiology ; Humans ; *Livestock/microbiology ; *Herbivory ; Animals, Wild/microbiology ; Parks, Recreational ; Conservation of Natural Resources ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Gut microbiome influences host health and well-being. Co-occurring hosts may exchange disease-causing bacteria belonging to these microbial communities. Therefore, monitoring gut microbiota composition in wildlife and humans is paramount to prevent zoonotic diseases, thus protecting and strengthening public health. We characterized diversity and abundance of the gut microbiome bacterial component across mahouts (captive elephant trainers and handlers), their pachyderms, livestock and wild herbivores in and around Chitwan National Park (Nepal). Firmicutes and Bacteroidota were invariably the dominant phyla. In humans, the relative abundance of Firmicutes was higher, the alpha diversity lower and beta diversity different compared to other host categories. Livestock and wild herbivores displayed similar alpha and beta diversity due to the presence of Proteobacteria, Actinobacteriota and Verrucomicrobiota. Elephants had a higher alpha diversity, and a significant beta diversity compared to other mammals. Our results suggest that taxonomic affiliation and diet niche are the main drivers of gut microbiota composition. Nevertheless, Mycobacterium and other potentially pathogenic bacteria genera were detected in elephants and livestock other than wild herbivores. These findings shed light on microbiota sharing and interlinking in each environment, thereby highlighting the importance of conservation medicine to better our understanding of health in co-occurring host species.},
}

Animals
*Gastrointestinal Microbiome
*Elephants/microbiology
Humans
*Livestock/microbiology
*Herbivory
Animals, Wild/microbiology
Parks, Recreational
Conservation of Natural Resources
Bacteria/classification/genetics/isolation & purification
Biodiversity
RNA, Ribosomal, 16S/genetics

@article {pmid40185839,
year = {2025},
author = {Yincharoen, P and Mordmuang, A and Techarang, T and Tangngamsakul, P and Kaewubon, P and Atipairin, P and Janwanitchasthaporn, S and Goodla, L and Karnjana, K},
title = {Microbiome and biofilm insights from normal vs tumor tissues in Thai colorectal cancer patients.},
journal = {NPJ precision oncology},
volume = {9},
number = {1},
pages = {98},
pmid = {40185839},
issn = {2397-768X},
abstract = {Colorectal cancer (CRC) is a prevalent global malignancy with complex etiologies, including microbiota alterations. This study investigates gut microbiota and biofilm-producing bacteria in 35 Thai CRC patients, analyzing paired normal and tumor biopsy samples. Bacterial DNA from the V3-V4 region of 16S rRNA was sequenced, and biofilms were visualized via scanning electron microscopy and fluorescence in situ hybridization (FISH). Results revealed Firmicutes as the dominant phylum, followed by Bacteroidota, Proteobacteria, and Fusobacteriota, with Fusobacteriota and Bacteroidota notably enriched in left-sided CRC. Key biofilm producers-Bacteroides fragilis, Fusobacterium nucleatum, and Pasteurella stomatis-showed significantly higher gene expression in tumor tissues. Dense biofilms and higher Fusobacterium abundance, localized within the crypts of Lieberkuhn, were observed in CRC tissues. These findings highlight CRC-associated microbiota alterations and pathogenic biofilm production, emphasizing a spatial relationship between tumor location and microbial distribution, with potential implications for understanding CRC pathogenesis and therapeutic targeting.},
}

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

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

@article {pmid40185726,
year = {2025},
author = {Song, H and Zou, J and Sun, Z and Pu, Y and Qi, W and Sun, L and Li, Q and Yuan, C and Wang, X and Gao, X and Zheng, Y},
title = {Nasal microbiome in relation to olfactory dysfunction and cognitive decline in older adults.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {122},
pmid = {40185726},
issn = {2158-3188},
support = {2023SHZDZX02//Science and Technology Commission of Shanghai Municipality (Shanghai Municipal Science and Technology Commission)/ ; },
mesh = {Humans ; Aged ; Female ; Male ; *Cognitive Dysfunction/microbiology/physiopathology ; *Microbiota ; Aged, 80 and over ; *Olfaction Disorders/microbiology ; *Nose/microbiology ; Smell ; },
abstract = {Emerging evidence has highlighted that olfactory dysfunction, a common feature of aging, is increasingly linked to cognitive decline in older adults. However, research on the underlying mechanism, particularly the role of nasal microbiome, remains limited. In this study, we investigated the associations between olfactory function, the nasal microbiome, and cognition among 510 older adults with an average age of 77.9 years. Olfactory function was assessed using the brief Chinese Smell Identification Test, and cognitive assessments were conducted via the Mini-Mental State Examination and the Revised Hasegawa Dementia Scale. Nasal microbiome profiles were generated through 16S RNA gene sequencing. We observed that olfactory dysfunction (i.e., hyposmia) was associated with a higher richness of nasal bacteria, and such observation was replicated in an external dataset. A total of 18 nasal bacterial genera were identified to be associated with olfactory function, with eight genera such as Acidovorax and Morganella being enriched in the hyposmic group. A composite microbial index of nasal olfactory function significantly improved the reclassification accuracy of traditional risk model in distinguishing hyposmic from normosmic participants (P = 0.008). Furthermore, participants with a nasal biotype dominated by Corynebacterium had a lower prevalence of mild cognitive impairment compared to those dominated by Dolosigranulum or Moraxella. Our findings suggested that the nasal microbiome may play a role in the association of olfactory function with cognition in older adults, providing new insights into the microbial mechanisms underlying hyposmia and cognitive decline.},
}

Humans
Aged
Female
Male
*Cognitive Dysfunction/microbiology/physiopathology
*Microbiota
Aged, 80 and over
*Olfaction Disorders/microbiology
*Nose/microbiology
Smell

@article {pmid40185172,
year = {2025},
author = {Liu, C and Fan, P and Dai, J and Ding, Z and Yi, Y and Zhan, X and Wang, CC and Liang, R},
title = {Integrated microbiome and metabolome analysis reveals that Zishen Qingre Lishi Huayu recipe regulates gut microbiota and butyrate metabolism to ameliorate polycystic ovary syndrome.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107533},
doi = {10.1016/j.micpath.2025.107533},
pmid = {40185172},
issn = {1096-1208},
abstract = {BACKGROUND: s: Polycystic ovary syndrome (PCOS) is a metabolic disorder disease strongly associated with gut microbiota (GM). Zishen Qingre Lishi Huayu recipe (ZQLHR), a traditional Chinese medicinal compound, has patented and shown therapeutic effects in treating PCOS in clinical trials without clear pharmacological mechanisms. This study aimed to disclose the potential therapeutic mechanism of ZQLHR on PCOS.

METHODS: We firstly confirmed the therapeutic effects of ZQLHR treatment in PCOS patients. 16S rRNA sequencing, untargeted metabolomics, fecal microbiota transplantation (FMT), high performance liquid chromatography (HPLC) and Person's correlation analysis were conducted to elucidate the potential therapeutic mechanism.

RESULTS: These results showed that PCOS symptoms in ZQLHR patients were significantly ameliorated. ZQLHR could increase the levels of butyrate-producing Lachnospira and Faecalibacterium and decrease the abundance of Escherichia-Shigella. Untargeted metabolomics showed that ZQLHR significantly improved host metabolic function, particularly butyrate metabolism and citrate cycle (TCA cycle) metabolism. The combined Faecalibacterium and butyrate metabolism datasets were correlated. Stool samples from ZQLHR patients could ameliorate ovarian architecture, significantly reduce testosterone (T), estradiol (E2) and luteinizing hormone (LH) levels and increased follicle-stimulating hormone (FSH) levels and increase the content of butyric acid in PCOS mice (P < 0.01). Moreover, the correlation analysis showed that some biochemical parameters (T, E2, LH levels and FSH) and butyric acid were correlated.

CONCLUSION: We firstly depicted that ZQLHR could alleviate the series of symptom in women with PCOS by regulating gut microbiota and butyrate metabolism. This study provides a scientific basis and new ideas for the therapy of PCOS.},
}

@article {pmid40185103,
year = {2025},
author = {Schwerdtfeger, LA and Montini, F and Lanser, TB and Ekwudo, MN and Zurawski, J and Tauhid, S and Glanz, BI and Chu, R and Bakshi, R and Chitnis, T and Cox, LM and Weiner, HL},
title = {Gut microbiota and metabolites are linked to disease progression in multiple sclerosis.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102055},
doi = {10.1016/j.xcrm.2025.102055},
pmid = {40185103},
issn = {2666-3791},
abstract = {Progressive multiple sclerosis (MS) is a neurological disease with limited understanding of the biology associated with transition from relapsing to progressive disease. Intestinal microbes and metabolites are altered in MS, but relation to disease progression is largely unknown. We investigate microbiota and metabolites in subjects with stable MS, those who worsened, and in those with relapsing MS who became progressive over 2 years. We find that Eubacterium hallii, Butyricoccaceae, Blautia, and other short-chain fatty-acid-producing microbes have beneficial associations with worsening of disability, 3T magnetic resonance imaging (MRI) measures, cognition, and quality of life, while Alistipes is detrimentally associated. Global metabolomics identified serum and stool metabolites that are altered in progressive MS and in relapsing subjects who transitioned to progressive disease. Most fecal metabolites associated with disease progression are decreased, suggesting a deficiency of protective factors in the gut. Using a unique MS cohort, our findings identify gut microbiome and metabolite pathways influencing progressive MS.},
}

@article {pmid40185096,
year = {2025},
author = {Abdeen, SK and Mastandrea, I and Stinchcombe, N and Puschhof, J and Elinav, E},
title = {Diet-microbiome interactions in cancer.},
journal = {Cancer cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ccell.2025.03.013},
pmid = {40185096},
issn = {1878-3686},
abstract = {Diet impacts cancer in diverse manners. Multiple nutritional effects on tumors are mediated by dietary modulation of commensals, residing in mucosal surfaces and possibly also within the tumor microenvironment. Mechanistically understanding such diet-microbiome-host interactions may enable to develop precision nutritional interventions impacting cancer development, dissemination, and treatment responses. However, data-driven nutritional strategies integrating diet-microbiome interactions are infrequently incorporated into cancer prevention and treatment schemes. Herein, we discuss how dietary composition affects cancer-related processes through alterations exerted by specific nutrients and complex foods on the microbiome. We highlight how dietary timing, including time-restricted feeding, impacts microbial function in modulating cancer and its therapy. We review existing and experimental nutritional approaches aimed at enhancing microbiome-mediated cancer treatment responsiveness while minimizing adverse effects, and address challenges and prospects in integrating diet-microbiome interactions into precision oncology. Collectively, mechanistically understanding diet-microbiome-host interactomes may enable to achieve a personalized and microbiome-informed optimization of nutritional cancer interventions.},
}

@article {pmid40184961,
year = {2025},
author = {Novau-Ferré, N and Papandreou, C and Rojo-Marticella, M and Canals-Sans, J and Bulló, M},
title = {Gut microbiome differences in children with Attention Deficit Hyperactivity Disorder and Autism Spectrum Disorder and effects of probiotic supplementation: A randomized controlled trial.},
journal = {Research in developmental disabilities},
volume = {161},
number = {},
pages = {105003},
doi = {10.1016/j.ridd.2025.105003},
pmid = {40184961},
issn = {1873-3379},
abstract = {BACKGROUND: Emerging evidence suggests a significant role of gut microbiota on neurodevelopmental disorders, including Attention Deficit Hyperactivity Disorder (ADHD) and Autism Spectrum Disorder (ASD).

AIMS: Our study aimed to compare gut microbiota composition between these disorders and evaluate the effect of probiotic supplementation.

METHODS: We conducted a 12-week randomized, double-blind, placebo-controlled trial with 80 children aged 5-14 years (39 with ADHD, 41 with ASD). Baseline and post-intervention fecal samples were analyzed using 16S rRNA gene sequencing to identify changes in gut microbiota composition.

RESULTS: We identified 22 taxa differentiating ADHD and ASD (AUC = 0.939), characterised by increased presence of Clostridia, Ruminococcaceae, and Lachnospiraceae in ADHD, and Bacteroides, Bacilli and Actinobacteria in ASD. These differences remained after accounting for potential confounders. ASD children receiving probiotics had significant increases in Chao 1, Fisher's alpha, and Shannon indices whereas no significant differences in α and β-diversity were found in ADHD. In ADHD, bacteria with potential adverse effects were under-represented. In ASD, the abundance of Eggerthellaceae, and other taxa associated with gastrointestinal problems and anxiety was decreased.

CONCLUSION: Variations in gut microbiota may influence responses in ADHD and ASD. Probiotic supplementation favorably altered gut microbiota composition, offering insights for future therapeutic strategies targeting the microbiome in neurodevelopmental disorders.

WHAT THIS PAPER ADDS: Recent research underscores the role of gut microbiota in ADHD and ASD, indicating that diet can significantly influence microbiota composition and potentially manage these neurodevelopmental disorders. This study reveals distinct differences in gut microbiota composition between children with ADHD and ASD and demonstrates that probiotic supplementation can modulate specific microbial genera in each disorder. These findings pave the way for the development of innovative microbiome-targeted therapies, offering a new avenue for the treatment of neurodevelopmental disorders. Understanding this relationship is crucial for designing future interventions.},
}

@article {pmid40184708,
year = {2025},
author = {He, D and Nong, Y and He, Y and Luo, Y and Li, C and Gao, J and Dang, C and Fu, J},
title = {Effect of pre-chlorination on bioelectricity production and stabilization of excess sludge by microbial fuel cell.},
journal = {Water research},
volume = {281},
number = {},
pages = {123564},
doi = {10.1016/j.watres.2025.123564},
pmid = {40184708},
issn = {1879-2448},
abstract = {Microbial fuel cell (MFC) is a technology that can generate electricity while degrading excess sludge. However, the complex components, intricate biological structures, and inhibitory compounds in sludge limit the application of MFC. Therefore, this study utilized chlorination as a sludge pretreatment method to improve the comprehensive performance of MFC in sludge treatment. Results showed that pre-chlorination at a dose of 0.2 mg/L increased output voltage of MFC by 500 % from approximately 100 mV to around 600 mV, and power density by 15.60 % from 3.15 W/m[3] to 3.64 W/m[3], and simultaneously increased the degradation of sludge MLSS (mixed liquor suspended solids), MLVSS (mixed liquor volatile suspended solids), EPS (extracellular polymeric substances) polysaccharide and protein by 9.64 %, 47.07 %, 18.63 % and 16.26 %, respectively. Molecular composition analysis of EPS in sludge by three-dimensional excitation emission matrix fluorescence spectroscopy (3D-EEM), Fourier transform infrared spectroscopy (FTIR) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) indicated pre-chlorination significantly promoted the molecular transformation in MFC. The microbiome analysis of anode biofilm in MFC by scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), metagenomics and metametabolomics revealed that pre-chlorination facilitated the development of biomass, enrichment of electricity-producing bacteria (EPB), enhancement of electricity-producing activity and metabolic activity. Moreover, the sludge EPS was the importance source for the microbial metabolites in MFC was validated by the joint analysis of FT-ICR-MS and metametabolomics.},
}

@article {pmid40184646,
year = {2025},
author = {Chen, L and Wang, Z and Wang, Y and Jiang, H and Ding, Y and Xia, Q and Cheng, X and Zhang, X},
title = {Alterations in fatty acid metabolism in patients with schizophrenia in a multi-omics perspective.},
journal = {Schizophrenia research},
volume = {279},
number = {},
pages = {94-105},
doi = {10.1016/j.schres.2025.03.036},
pmid = {40184646},
issn = {1573-2509},
abstract = {BACKGROUND: Recent research has extensively explored the involvement of gut microbes in various fatty acid metabolic processes, elucidating their crucial roles in host energy homeostasis and metabolism. Nevertheless, there remains a dearth of studies examining the comprehensive profile of fatty acid metabolites in schizophrenia and their potential connection to gut microbes.

METHOD: Conducting a thorough investigation, this study scrutinized the gut microbiome composition of 63 individuals, consisting of 35 schizophrenia (SZ) patients and 28 demographically matched healthy control (HC) subjects. Feces and serum samples were meticulously collected, with stool samples subjected to 16S rRNA sequencing targeting region V4 and untargeted metabolomics analysis, while serum samples underwent untargeted metabolomics assessment.

RESULTS: A total of 21 different genus-level species were identified in the SZ and HC groups. Predictive analysis of gut flora pathways revealed abnormal fatty acid degradation in schizophrenia. Notably, 17 differential fatty acid metabolites were found in feces, whereas 43 were found in serum fatty acid metabolites. A higher proportion of differential fatty acid metabolites were found in serum compared to those in feces. The predominant pathways enriched in fatty acid metabolites included biosynthesis of unsaturated fatty acids, arachidonic acid metabolism, and linoleic acid metabolism. Additionally, a significant correlation was noted between intestinal flora and fatty acids, as well as potential interactions between intestinal flora, fecal fatty acids and serum fatty acids.

CONCLUSIONS: Our multi-omics study provides new insights into the pathogenesis of schizophrenia, which may inform the treatment of neurodevelopmental disorders by modifying fatty acid metabolism through modulation of the gut microbiota.},
}

@article {pmid40184142,
year = {2025},
author = {Guo, L and An, T},
title = {Investigating the correlation between gut microbiota and prostate cancer through a two-sample Mendelian randomization analysis.},
journal = {Medicine},
volume = {104},
number = {1},
pages = {e41141},
pmid = {40184142},
issn = {1536-5964},
mesh = {Male ; Humans ; *Prostatic Neoplasms/microbiology/genetics/epidemiology ; Mendelian Randomization Analysis/methods ; *Gastrointestinal Microbiome/genetics ; Genome-Wide Association Study ; },
abstract = {Previous studies in observational epidemiology have suggested a potential correlation between the gastrointestinal tract microbiota and prostate cancer. However, the causal relationship between the 2 remains uncertain, our objective was to thoroughly examine the influence of the gut microbiome on the progression of prostate cancer. In this study, we focused on investigating the gut microbiome as an exposure factor, specifically analyzing data from the MiBioGen consortium, which had a substantial sample size of 18,340 participants. As our disease outcome, we utilized prostate cancer data from the FinnGen genome-wide association study, which involved 13,216 participants. To establish causal relationships, we conducted a comprehensive Mendelian randomization analysis employing multiple methods, including inverse variance-weighted, Mendelian randomization-Egger, maximum likelihood, and weighted median approaches. Additionally, we performed sensitivity analysis to address issues such as heterogeneity and horizontal pleiotropy, ensuring the robustness of our findings. The results obtained through inverse variance-weighted analysis revealed that certain microbial groups exhibited a protective effect on prostate cancer. Specifically, the phylum Verrucomicrobia, particularly the family Rikenellaceae, and the genera Anaerotruncus, Eisenbergiella, Olsenella, and Parabacteroides were found to have a beneficial impact. Conversely, the class Bacilli, class Erysipelotrichia, order Erysipelotrichales, order Lactobacillales, family Erysipelotrichaceae, and the genera Marvinbryantia, Romboutsia, Ruminococcaceae UCG002, and Sutterella had an adverse influence on prostate cancer. The sensitivity analysis did not reveal any such outliers, further strengthening the validity of our results. To summarize, a cause-and-effect connection was discovered between various types and prostate cancer. Nevertheless, additional randomized controlled experiments are required for validation.},
}

Male
Humans
*Prostatic Neoplasms/microbiology/genetics/epidemiology
Mendelian Randomization Analysis/methods
*Gastrointestinal Microbiome/genetics
Genome-Wide Association Study

@article {pmid40183945,
year = {2025},
author = {Budin, M and Sandiford, NA and Gehrke, T and Citak, M},
title = {Body mass index matters: morbid obese patients have different microorganism profiles in the setting of periprosthetic hip joint infections.},
journal = {International orthopaedics},
volume = {},
number = {},
pages = {},
pmid = {40183945},
issn = {1432-5195},
abstract = {PURPOSE: This study investigated the relationship between BMI and microorganism profiles, with a particular focus on gut microorganisms in patients with PJI following total hip arthroplasty (THA). It also explored comorbidities, that may contribute to these variations.

METHODS: This study included all patients treated at our institution for a PJI of a THA between 1996 and 2021. Patients were categorized into four distinct BMI groups: <30; 30-34.9; 35-39.9; ≥ 40. Bivariate and logistic regression analysis were conducted, with presentation of odds ratio (OR) and 95% confidence interval (CI).

RESULTS: A total of 3645 hip PJI cases were recruited for the final analysis. Patients with a BMI ≥ 40 had approximately a ten fold higher risk for Streptococcus dysgalactiae (p < 0.001; OR = 9.92; 95% CI 3.87-25.44) and a seven fold higher risk for Proteus mirabilis (p < 0.001; OR = 7.43; 95% CI 3.13-17.67) and Klebsiella pneumoniae (p < 0.001; OR = 6.9; 95% CI 2.47-19.31). Furthermore, polymicrobial infections (p < 0.001; OR = 2.17; 95% CI 1.50-3.15) were found to be significantly more prevalent in patients with a BMI ≥ 40.

CONCLUSION: Obese patients (BMI ≥ 30) displayed a distinct microorganism profile in hip PJIs, mainly dominated by Firmicutes and Proteobacteria. Comorbidities such as diabetes, hypertension, and hyperlipidaemia may contribute to a leaky gut syndrome, increasing PJI risk caused by gut microorganisms. Optimizing comorbidities may help reduce the risk of hip PJI. Further research is needed to clarify the relationship between obesity, gut microbiome alterations and hip PJI development.},
}

@article {pmid40183608,
year = {2025},
author = {Ichikawa, A and Takayama, T and Kojima, C and Fujie, S and Iemitsu, M and Inoue, K},
title = {Conversion Reaction of Stable-Isotope Oxygen Labeling of Carboxylic Acids for Accurate Screening LC-MS/MS Assay: Application of Behavioral Changes of Short-Chain Fatty Acids in Sports Athletes under Exercise Loading.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.4c05872},
pmid = {40183608},
issn = {1520-6882},
abstract = {Short-chain fatty acids (SCFAs) have attracted considerable interest as potential biomarkers, therapeutic targets, and nutritional factors in athletic training. SCFAs are typically produced by the intestinal microbiome and exhibit various structural forms, including linear- and branched-chain types. In particular, branched-chain SCFAs have been associated with muscle metabolism during exercise loading. Consequently, accurate and efficient analytical methods are essential for identifying these biomarkers. Liquid chromatography-tandem mass spectrometry is a suitable and accurate technique for SCFA analysis; however, stable isotope calibrations are required for all analytes. Because of technological limitations, the available species are restricted to certain types of SCFAs. To address this issue, this study performed a simple conversion reaction involving the incorporation of [18]O into the carboxyl group. Specifically, oxygen atoms in the carboxyl groups were substituted with [18]O sourced from commercially available H2[18]O. An SCFA mixture standard solution was successfully labeled under optimized conditions, and the SIL purity and amount were sufficient for isotope dilution (95.2-96.9%, 250 assays using 10 μL of H2[18]O). Moreover, no reversion to [16]O was observed during storage or analysis. Analytical validation was performed in human serum using the substituted isotopic standard mixture, achieving good accuracy (90-110%) and precision (<10% relative standard deviation) across three concentration levels. Finally, changes in SCFA patterns were examined in athletes during exercise loading.},
}

@article {pmid40183597,
year = {2025},
author = {Rios de Alvarez, L and Contreras-Correa, ZE and Lemley, C and Dearborn, L and Fan, P and Hsu, CY and Bernard, B and Pesato, M and Sandoval-Castro, C and Torres-Acosta, JF},
title = {Effect of Cottonseed diet on the Performance of Meat Does Artificially Infected with Haemonchus contortus.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf094},
pmid = {40183597},
issn = {1525-3163},
abstract = {Gossypol is a phenolic compound found in cottonseed. Phenolic compounds are plant secondary metabolites, known to have both, beneficial and negative effects on animals. The present experiment evaluated the beneficial and negative effects of cottonseed on growth, daily weight gain, parasite infection measured by fecal egg counts, liver function, and ruminal microbiome of growing female meat goats. Forty Boer x Spanish doelings were assigned to 4 groups (n = 10 per group) in a 2 x 2 factorial design consisting of CS-NP cottonseed supplementation (CS) (0.5% body weight-BW in kg) + no parasite infection (NP) CON-NP commercial pellets or control (CON) + no parasite infection (NP); CON-P commercial pellets or control (CON) + Haemonchus contortus artificial infection (P); and CS-P CS supplementation (CS) + H. contortus artificial infection (P). Artificial infection consisted of 4,000 H. contortus infective larvae (L3). The FEC were not affected by diet. The liver function showed a diet by parasite interaction (P = 0.03) for the mean velocity of the hepatic portal vein, which was decreased in CON-P compared with CS-NP indicating a reduction in metabolism. A diet by parasite interaction (P = 0.014) was also observed for the diameter of the hepatic portal vein, which was increased in the CS-P goats compared to all other groups. Liver weights were affected by diet, being decreased in the CS animals vs. the CON ones (P = 0.00), as well as the liver weight relative to the animal's BW (P = 0.01). Diet effect (P = 0.01) was observed for the liver blood flow relative to liver weight. For the rumen microbiome, the number of bacterial species was unaffected by CS but decreased by the parasite challenge (P = 0.03). In conclusion, the supplementation of female meat goats with CS did not affect BW, DWG, parasite infection, and FAMACHA©, but reduced the liver weights, influenced fiber-digesting bacteria in the rumen, and restored lipolytic bacteria in the rumen of goats with parasite challenge.},
}

@article {pmid40183593,
year = {2025},
author = {Bond, E and Reines, C and Thiel, V and Göker, M and Stamatis, D and Seshadri, R and Luna Lopez, C and Read, B},
title = {Draft genome sequence of Mesonia hippocampi DSM 29568[T] isolated from the brood pouch of a diseased male seahorse.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0004725},
doi = {10.1128/mra.00047-25},
pmid = {40183593},
issn = {2576-098X},
abstract = {Mesonia hippocampi was isolated from the brood pouch of a diseased seahorse, Hippocampus barbouri, and the 498,773,430 bp genome encoding 2,377 proteins was sequenced. Understanding the role of M. hippocampi can inform conservation strategies to improve the health and survival of wild and captive H. barbouri.},
}

@article {pmid40183585,
year = {2025},
author = {Goff, KL and Suresh, S and Stadfeld, JM and Bhatnagar, S},
title = {Complete genome sequences of nine isolates from microplastics in the Bow River, Calgary, Canada.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0108524},
doi = {10.1128/mra.01085-24},
pmid = {40183585},
issn = {2576-098X},
abstract = {We present the complete genome sequences of nine bacterial strains isolated from microplastics from water or sediments of the Bow River in Calgary, Alberta. These isolates provide insight into the freshwater microplastic microbiome and their plastic biodegradation potential.},
}

@article {pmid40183584,
year = {2025},
author = {Iqbal, M and Yu, Q and Tang, J and Xiang, J},
title = {Unraveling the gut microbiota's role in obesity: key metabolites, microbial species, and therapeutic insights.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0047924},
doi = {10.1128/jb.00479-24},
pmid = {40183584},
issn = {1098-5530},
abstract = {Obesity, characterized by excessive fat accumulation, stems from an imbalance between energy intake and expenditure, with the gut microbiota playing a crucial role. This review highlights how gut microbiota influences metabolic pathways, inflammation, and adipose tissue regulation in obesity. Specific bacteria and metabolites, such as lipopolysaccharides (LPS) and short-chain fatty acids (SCFAs), modulate gut permeability, inflammation, and energy harvest, impacting obesity development. Certain gut bacteria, including Clostridium XIVb, Dorea spp., Enterobacter cloacae, and Collinsella aerofaciens, promote obesity by increasing energy harvest, gut permeability, and inflammatory response through LPS translocation into the bloodstream. Conversely, beneficial bacteria like Akkermansia muciniphila, Lactobacillus spp., and Bifidobacterium spp. enhance gut barrier integrity, regulate SCFA production, and modulate fasting-induced adipose factor, which collectively support metabolic health by reducing fat storage and inflammation. Metabolites such as SCFAs (acetate, propionate, and butyrate) interact with G-protein coupled receptors to regulate lipid metabolism and promote the browning of white adipose tissue (WAT), thus enhancing thermogenesis and energy expenditure. However, LPS contributes to insulin resistance and fat accumulation, highlighting the dual roles of these microbial metabolites in both supporting and disrupting metabolic function. Therapeutic interventions targeting gut microbiota, such as promoting WAT browning and activating brown adipose tissue (BAT), hold promise for obesity management. However, personalized approaches are necessary due to individual microbiome variability. Further research is essential to translate these insights into microbiota-based clinical therapies.},
}

@article {pmid40183581,
year = {2025},
author = {Aminian-Dehkordi, J and Dickson, A and Valiei, A and Mofrad, MRK},
title = {MetaBiome: a multiscale model integrating agent-based and metabolic networks to reveal spatial regulation in gut mucosal microbial communities.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0165224},
doi = {10.1128/msystems.01652-24},
pmid = {40183581},
issn = {2379-5077},
abstract = {Mucosal microbial communities (MMCs) are complex ecosystems near the mucosal layers of the gut essential for maintaining health and modulating disease states. Despite advances in high-throughput omics technologies, current methodologies struggle to capture the dynamic metabolic interactions and spatiotemporal variations within MMCs. In this work, we present MetaBiome, a multiscale model integrating agent-based modeling (ABM), finite volume methods, and constraint-based models to explore the metabolic interactions within these communities. Integrating ABM allows for the detailed representation of individual microbial agents each governed by rules that dictate cell growth, division, and interactions with their surroundings. Through a layered approach-encompassing microenvironmental conditions, agent information, and metabolic pathways-we simulated different communities to showcase the potential of the model. Using our in-silico platform, we explored the dynamics and spatiotemporal patterns of MMCs in the proximal small intestine and the cecum, simulating the physiological conditions of the two gut regions. Our findings revealed how specific microbes adapt their metabolic processes based on substrate availability and local environmental conditions, shedding light on spatial metabolite regulation and informing targeted therapies for localized gut diseases. MetaBiome provides a detailed representation of microbial agents and their interactions, surpassing the limitations of traditional grid-based systems. This work marks a significant advancement in microbial ecology, as it offers new insights into predicting and analyzing microbial communities.IMPORTANCEOur study presents a novel multiscale model that combines agent-based modeling, finite volume methods, and genome-scale metabolic models to simulate the complex dynamics of mucosal microbial communities in the gut. This integrated approach allows us to capture spatial and temporal variations in microbial interactions and metabolism that are difficult to study experimentally. Key findings from our model include the following: (i) prediction of metabolic cross-feeding and spatial organization in multi-species communities, (ii) insights into how oxygen gradients and nutrient availability shape community composition in different gut regions, and (iii) identification of spatiallyregulated metabolic pathways and enzymes in E. coli. We believe this work represents a significant advance in computational modeling of microbial communities and provides new insights into the spatial regulation of gut microbiome metabolism. The multiscale modeling approach we have developed could be broadly applicable for studying other complex microbial ecosystems.},
}

@article {pmid40183155,
year = {2025},
author = {Duan, Y and Zhang, J and Petropoulos, E and Zhao, J and Jia, R and Wu, F and Chen, Y and Wang, L and Wang, X and Li, Y and Li, Y},
title = {Soil Acidification Destabilizes Terrestrial Ecosystems via Decoupling Soil Microbiome.},
journal = {Global change biology},
volume = {31},
number = {4},
pages = {e70174},
doi = {10.1111/gcb.70174},
pmid = {40183155},
issn = {1365-2486},
support = {2023449//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 24ZD13FA004//Gansu Provincial Science and Technology Planning Project/ ; 2019QZKK0305//Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; 31971466//National Natural Science Foundation of China/ ; 2017YFA0604803//National Key R&D Program of China/ ; },
mesh = {*Soil Microbiology ; *Microbiota ; *Soil/chemistry ; Hydrogen-Ion Concentration ; China ; Climate Change ; *Ecosystem ; Bacteria/classification ; Biodiversity ; },
abstract = {Soil microbiome is essential for terrestrial ecosystem preservation. β-diversity information on the former, although dynamic due to its sensitivity to environmental conditions driven by climate change, is limited. Our knowledge becomes poorer for microbiomes subjected to environmental gradients, especially for those across multiple ecosystems-information important for biological conservation management. In this study, using next generation sequencing and machine learning at samples from 207 locations among 4300 km of transects that spanned among six typical terrestrial ecosystems of China, we established the divergent distance-decay relationships between bacterial and eukaryotic communities in response to soil pH (pH as proxy of climate and edaphic conditions). The findings, pH-decrease results in lower β-diversity (convergent tendency) among the bacterial communities opposite to the eukaryotic ones (low pH-high β-diversity (divergent tendency)). Meanwhile, competition between bacteria and eukaryotes intensifies at lower pH while the predominant genera and communities are re-structured. Under these circumstances, potential soil acidification due to climate change or other factors could alter soil bacteria and eukaryotes into decoupling directions influencing ecosystems' stability. Thus, soil pH is a pivotal environmental variable that not only describes, but also controls, soil microbiome dynamics at a large scale under ongoing global changes; hence, a cornerstone variable for the biodiversity conservation of China's nature protected areas and not only.},
}

*Soil Microbiology
*Microbiota
*Soil/chemistry
Hydrogen-Ion Concentration
China
Climate Change
*Ecosystem
Bacteria/classification
Biodiversity

@article {pmid40182774,
year = {2025},
author = {Karaliute, I and Tilinde, D and Ramonaite, R and Lukosevicius, R and Nikitina, D and Bernatoniene, J and Kuliaviene, I and Valantiene, I and Petrauskas, D and Zigmantaite, V and Misiunas, A and Denkovskiene, E and Razanskiene, A and Gleba, Y and Kupcinskas, J and Skieceviciene, J},
title = {Bacteriocin KvarM versus conventional antibiotics: comparative effectiveness in treating Klebsiella pneumoniae infections in murine intestinal models.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1559865},
pmid = {40182774},
issn = {2235-2988},
mesh = {Animals ; *Klebsiella pneumoniae/drug effects/genetics ; *Klebsiella Infections/drug therapy/microbiology ; *Anti-Bacterial Agents/pharmacology/therapeutic use/administration & dosage ; *Bacteriocins/pharmacology/therapeutic use/administration & dosage ; Disease Models, Animal ; Mice ; Gastrointestinal Microbiome/drug effects ; Ciprofloxacin/pharmacology/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Intestines/microbiology ; Bacterial Load/drug effects ; Female ; },
abstract = {INTRODUCTION: The rapid emergence of multidrug-resistant bacterial species poses a critical threat by reducing the efficacy of antibiotics and complicating infection treatment. Bacteriocins, such as klebicin KvarM, have emerged as promising alternatives to traditional antibiotics due to their targeted antimicrobial activity. In this study, we evaluated the therapeutic potential of Eudragit-coated klebicin KvarM in a mouse model of Klebsiella pneumoniae intestinal colonization, assessing both its antimicrobial effectiveness and impact on commensal gut microbiota.

METHODS: Antimicrobial activity of KvarM in comparison to conventional antibiotic therapy with ciprofloxacin was tested in murine models for K. pneumoniae gastrointestinal (GI) tract infection. The haemolysin gene (khe) was chosen as the qualitative marker for Klebsiella genus identification, and 16S rRNA gene sequencing of V1-V2 hypervariable region was performed for analyses of gut microbiota.

RESULTS: Our results demonstrated that KvarM was highly effective in reducing K. pneumoniae colonization, showing the same efficacy as ciprofloxacin. Following K. pneumoniae inoculation, administration of KvarM resulted in a significant reduction in bacterial load indicating a 99% effectiveness. Furthermore, microbiome analysis of the gut microbiota revealed that KvarM therapy showed no significant changes in microbial composition compared with commensal microbiota composition, whereas administration of ciprofloxacin led to a significant decrease in microbial diversity.

DISCUSSION: These findings demonstrate that klebicin KvarM therapy is highly effective for treating intestinal K. pneumoniae infections and it does not affect the integrity of the gut microbiota.},
}

Animals
*Klebsiella pneumoniae/drug effects/genetics
*Klebsiella Infections/drug therapy/microbiology
*Anti-Bacterial Agents/pharmacology/therapeutic use/administration & dosage
*Bacteriocins/pharmacology/therapeutic use/administration & dosage
Disease Models, Animal
Mice
Gastrointestinal Microbiome/drug effects
Ciprofloxacin/pharmacology/therapeutic use
RNA, Ribosomal, 16S/genetics
Intestines/microbiology
Bacterial Load/drug effects
Female

@article {pmid39736385,
year = {2024},
author = {Kumar, A and Jayawardena, D and Priyamvada, S and Anbazhagan, AN and Chatterjee, I and Saksena, S and Dudeja, PK},
title = {SLC26A3 (DRA, the Congenital Chloride Diarrhea Gene): A Novel Therapeutic Target for Diarrheal Diseases.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {19},
number = {6},
pages = {101452},
doi = {10.1016/j.jcmgh.2024.101452},
pmid = {39736385},
issn = {2352-345X},
support = {I01 BX006626/BX/BLRD VA/United States ; IK6 BX005242/BX/BLRD VA/United States ; R01 DK054016/DK/NIDDK NIH HHS/United States ; I01 BX002011/BX/BLRD VA/United States ; IK2 BX004719/BX/BLRD VA/United States ; I01 BX005862/BX/BLRD VA/United States ; },
abstract = {Diarrhea associated with enteric infections, gut inflammation, and genetic defects poses a major health burden and results in significant morbidity and mortality. Impaired fluid and electrolyte absorption or secretion in the intestine are the hallmark of diarrhea. Electroneutral NaCl absorption in the mammalian GI tract involves the coupling of Na[+]/H[+] and Cl[-]/HCO3[-] exchangers. SLC26A3 (Down Regulated in Adenoma, DRA) is the major anion exchanger involved in luminal Cl[-] absorption and HCO3[-] secretion. Mutations in the SLC26A3 gene cause a severe disease called congenital chloride diarrhea (CLD). Multiple studies have shown that DRA function or expression is downregulated in infectious diarrheal disorders caused by EPEC, C rodentium, Salmonella, Clostridioides difficile and Cryptosporidium parvum infection. In addition, DRA levels are severely depleted in colonic mucosa of IBD patients and in mouse models of IBD (eg, DSS, TNBS, adoptive T-cell transfer, anti-CD-40, and IL-10 KO colitis). In addition, genetic defects exhibiting diarrhea including microvillus inclusion disease (MVID), keratin-8 depletion, knock-out mouse models of transcriptional factors (eg, CDX-2 and HNF1α/1β) also exhibit severe down regulation of DRA. Also, recent studies have shown that DRA is not only critical for chloride absorption but also plays a key role in maintaining gut epithelial barrier integrity, microbiome composition, and has now emerged as an IBD susceptibility gene. In this review, we provide strong evidence that DRA may serve as a novel therapeutic target with dual benefits in not only correcting diarrheal phenotype but also improving gut barrier integrity and inflammation in pathogen infection or IBD.},
}

@article {pmid40182773,
year = {2025},
author = {Amedei, A and Weiskirchen, R},
title = {Editorial: The microbiome in the development of gastrointestinal diseases.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1561143},
doi = {10.3389/fcimb.2025.1561143},
pmid = {40182773},
issn = {2235-2988},
}

@article {pmid40182766,
year = {2025},
author = {Lazarevic, V and Gaïa, N and Pham, TT and de Lorenzi-Tognon, M and Girard, M and Mauffrey, F and Charretier, Y and Renzi, G and Huber, C and Schrenzel, J},
title = {Identification of causative agents of infective endocarditis by metagenomic next-generation sequencing of resected valves.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1532257},
doi = {10.3389/fcimb.2025.1532257},
pmid = {40182766},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Male ; Middle Aged ; Female ; *Heart Valves/microbiology/surgery ; Sensitivity and Specificity ; Aged ; *Endocarditis/microbiology/diagnosis/surgery ; Prospective Studies ; *Bacteria/genetics/classification/isolation & purification ; DNA, Bacterial/genetics ; Adult ; Aged, 80 and over ; },
abstract = {BACKGROUND: Infective endocarditis (IE) is a rare and life-threatening condition with considerable mortality rates. Diagnosis is often complicated by negative blood culture results, limiting the accurate identification of causative pathogens. This study aimed to evaluate the effectiveness of metagenomic next-generation sequencing (mNGS) of cardiac valve specimens compared to conventional clinical laboratory methods for identifying pathogens in IE.

METHODS: Nineteen patients with suspected IE who were scheduled for surgical valve removal were prospectively enrolled. The metagenomic workflow included bacterial DNA enrichment from resected valves using the Molzym Ultra-Deep Microbiome Prep, sequencing of metagenomic libraries using the Illumina MiSeq platform, and Kraken 2 taxonomic assignments based on read data.

RESULTS: Valve mNGS achieved a sensitivity of 82.4% and a specificity of 100% relative to the final adjudicated pathogen diagnosis. Blood culture, considered the reference standard, exhibited slightly higher sensitivity (88.2%) with comparable specificity (100%). In comparison, valve culture (sensitivity: 29.4%, specificity: 50.0%) and microscopy (sensitivity: 35.3%, specificity: 100%) showed lower diagnostic performance. Delays between blood culture negativization and valve resection impacted mNGS sensitivity, likely due to pathogen clearance. Notably, valves resected within 12 days from blood culture negativization achieved 100% diagnostic accuracy, emphasizing the importance of timing for optimal mNGS results.

CONCLUSION: This study underscores mNGS as a valuable diagnostic tool for detecting IE pathogens, complementing traditional diagnostic methods. The detection of antibiotic resistance genes and multi-locus sequence typing profiles in some samples further demonstrated its utility.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Male
Middle Aged
Female
*Heart Valves/microbiology/surgery
Sensitivity and Specificity
Aged
*Endocarditis/microbiology/diagnosis/surgery
Prospective Studies
*Bacteria/genetics/classification/isolation & purification
DNA, Bacterial/genetics
Adult
Aged, 80 and over

@article {pmid40182701,
year = {2025},
author = {Manus, MB and Savo Sardaro, ML and Dada, O and Davis, M and Romoff, MR and Torello, SG and Ubadigbo, E and Wu, RC and Dominguez-Bello, MG and Melby, MK and Miller, ES and Amato, KR},
title = {Birth and household exposures are associated with changes to skin bacterial communities during infancy.},
journal = {Evolution, medicine, and public health},
volume = {13},
number = {1},
pages = {49-76},
doi = {10.1093/emph/eoae023},
pmid = {40182701},
issn = {2050-6201},
abstract = {BACKGROUND AND OBJECTIVES: Microbial exposures during infancy shape the development of the microbiome, the collection of microbes living in and on the body, which in turn directs immune system training. Newborns acquire a substantial quantity of microbes during birth and throughout infancy via exposure to microbes in the physical and social environment. Alterations to early life microbial environments may give rise to mismatches, where environmental, cultural and behavioral changes that outpace the body's adaptive responses can lead to adverse health outcomes, particularly those related to microbiome development and immune system regulation.

METHODS: This study explored the development of the skin microbiome among infants born in Chicago, USA. We collected skin swab microbiome samples from 22 mother-infant dyads during the first 48 h of life and again at 6 weeks postpartum. Mothers provided information about social environments and hygiene behaviors that may impact infants' microbial exposures.

RESULTS: Analysis of amplicon bacterial gene sequencing data revealed correlations between infant skin bacterial abundances shortly after birth and factors such as antibiotic exposure and receiving a bath in the hospital. The composition of the infant microbiome at 6 weeks of age was associated with interactions with caregivers and infant feeding practices. We also found shifts in maternal skin microbiomes that may reflect increased hygiene practices in the hospital.

CONCLUSIONS AND IMPLICATIONS: Our data suggest that factors related to the birth and household environment can impact the development of infant skin microbiomes and point to practices that may produce mismatches for the infant microbiome and immune system.},
}

@article {pmid40182595,
year = {2025},
author = {Gopika, AG and Sachdeva, N},
title = {New insights into the mechanisms of modified Pulsatilla decoction in alleviating chemotherapy-induced intestinal mucositis.},
journal = {World journal of gastroenterology},
volume = {31},
number = {12},
pages = {105162},
doi = {10.3748/wjg.v31.i12.105162},
pmid = {40182595},
issn = {2219-2840},
mesh = {*Mucositis/chemically induced/drug therapy/pathology/microbiology ; Animals ; *Intestinal Mucosa/drug effects/pathology/microbiology ; *Pulsatilla/chemistry ; Humans ; *Drugs, Chinese Herbal/therapeutic use/pharmacology ; Gastrointestinal Microbiome/drug effects ; Fluorouracil/adverse effects ; Mice ; Diarrhea/chemically induced/drug therapy ; Disease Models, Animal ; Oxidative Stress/drug effects ; *Antineoplastic Agents/adverse effects ; Cytokines/metabolism ; },
abstract = {Chemotherapy-induced intestinal mucositis (IM) is a prevalent complication affecting up to 80% of cancer patients undergoing treatment. Current therapies focus on symptomatic relief rather than addressing the underlying mechanism. Recent advances in integrative medicine highlight the potential of traditional Chinese medicine formulations as alternatives or adjuncts to existing therapies. In this context, this editorial discusses the recent results of a study published by Qiu et al, which investigates the multifaceted potential of modified Pulsatilla decoction (PD), a formulation of PD with licorice (Glycyrrhiza uralensis) and Ejiao (Colla corii asini), on 5-fluorouracil-induced IM in mice to alleviate clinical symptoms including diarrhea, weight loss, and intestinal damage. A series of histological, biochemical, bioinformatic, and microbiological assays evaluated body weight, diarrhea scores, inflammatory cytokine profiles, oxidative stress modulation, and microbiota composition. The findings indicated a reduction in diarrhea and oxidative stress, as well as an improvement in body weight and intestinal histopathology. Furthermore, the modified PD suppressed the TLR4/MyD88/nuclear factor kappa-B inflammatory pathway and down-regulated key pro-inflammatory cytokines. Moreover, the study underscores the role of gut microbiota in IM pathogenesis. Modified PD treatment reshaped microbial diversity by promoting beneficial genera such as Bacteroides acidifaciens while suppressing pathogenic species like Salmonella. These findings suggest that the therapeutic effects of the modified PD extend beyond inflammation modulation to encompass microbiome reprogramming and mucosal barrier repair. Although the study provides significant insights, several limitations still prevail. The broader implications of modified PD in gastrointestinal disorders and integrative oncology need further exploration.},
}

*Mucositis/chemically induced/drug therapy/pathology/microbiology
Animals
*Intestinal Mucosa/drug effects/pathology/microbiology
*Pulsatilla/chemistry
Humans
*Drugs, Chinese Herbal/therapeutic use/pharmacology
Gastrointestinal Microbiome/drug effects
Fluorouracil/adverse effects
Mice
Diarrhea/chemically induced/drug therapy
Disease Models, Animal
Oxidative Stress/drug effects
*Antineoplastic Agents/adverse effects
Cytokines/metabolism

@article {pmid40182115,
year = {2025},
author = {Dollas, MN and Nilsson, M and Larsen, T and Nygaard, N and Moser, C and Belstrøm, D},
title = {High prevalence of antibiotic resistance of Streptococcus species in saliva from non-hospitalized adults - a pilot study.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2486647},
doi = {10.1080/20002297.2025.2486647},
pmid = {40182115},
issn = {2000-2297},
abstract = {BACKGROUND: Antibiotic resistance (AR) is a recognized threat to global human health. However, the prevalence of AR in healthy adults is not well described. The present observational pilot study aimed to uncover the potential of using saliva samples for screening for antibiotic resistance.

METHODOLOGY: A laboratory protocol was developed for screening of AR in saliva samples, which was tested and validated using saliva samples collected from 100 study participants. The risk of AR was analyzed with descriptive statistics and evaluated using a risk-factor profile based on information on antibiotic usage within the last 12 months, education level and origin of birth.

RESULTS: AR was identified in 43 (48%) saliva samples, out of which 60,0% and 17,1% of resistant strains displayed resistance to clindamycin and penicillin, respectively. Streptococcus salivarius and Streptococcus parasanguinis were most often identified with AR (51,4% of all cases). The risk of AR was not associated with self-perceived oral or general health, antibiotic use within the latest 12 months or any demographic or socioeconomic parameters recorded. The risk-factor profile was observed in 44% in the AR group versus 30% in the non-AR group (p = 0.19).

CONCLUSION: The present study showed that it is possible to perform non-invasive saliva-based screening for AR with a frequency of 48% of the samples, highlighting that saliva samples could be a valuable supplement to current surveillance methodologies for AR in the oral microbiota.},
}

@article {pmid40182114,
year = {2025},
author = {Datorre, JG and Dos Reis, MB and Sorroche, BP and Teixeira, GR and Hatano, SS and de Carvalho, AC and Gama, RR and Rebolho Batista Arantes, LM and Reis, RM},
title = {Intratumoral Fusobacterium nucleatum is associated with better cancer-specific survival in head and neck cancer patients.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2487644},
doi = {10.1080/20002297.2025.2487644},
pmid = {40182114},
issn = {2000-2297},
abstract = {BACKGROUND: The oral microbiome, particularly Fusobacterium nucleatum (Fn), has been implicated in head and neck cancers (HNC), influencing local immunity and Human Papillomavirus (HPV) status. Here, we evaluated the presence of Fn and its association with HPV infection, TERT promoter (TERTp) mutations, and patient outcomes.

MATERIALS AND METHODS: We analyzed 94 formalin-fixed paraffin-embedded (FFPE) tumor tissues from HNC patients previously evaluated for TERTp mutations. Fn DNA was detected using droplet digital PCR (ddPCR), and HPV status was determined via p16 immunohistochemistry in pre-treatment samples. Associations between Fn presence, clinicopathological features, HPV, and TERTp mutation status were assessed.

RESULTS: Tumors primarily originated from the oropharynx (70.2%) and oral cavity (29.8%). Tobacco and alcohol use were reported in 87.2% and 79.8% of cases, respectively. Fn was present in 59.6% of cases, with higher prevalence in oropharyngeal (62.1%) than oral cavity (53.6%) tumors. No significant associations were found between Fn and clinicopathological features, TERTp, or HPV status. However, patients with Fn positivity showed significantly improved cancer-specific survival (61.5% vs. 39.1%, p = 0.013), similar to HPV-positive patients (72.7% vs. 42.7%, p = 0.014).

CONCLUSION: The presence of Fusobacterium nucleatum in HNC correlates with longer survival, highlighting its potential as a prognostic marker.},
}

@article {pmid40181971,
year = {2025},
author = {Vogrig, A and Dentoni, M and Florean, I and Cellante, G and Domenis, R and Iacono, D and Pelizzari, G and Rossi, S and Damato, V and Fabris, M and Valente, M},
title = {Prediction, prevention, and precision treatment of immune checkpoint inhibitor neurological toxicity using autoantibodies, cytokines, and microbiota.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1548897},
doi = {10.3389/fimmu.2025.1548897},
pmid = {40181971},
issn = {1664-3224},
mesh = {Humans ; *Immune Checkpoint Inhibitors/adverse effects ; *Cytokines/immunology/metabolism ; *Autoantibodies/immunology ; *Neoplasms/drug therapy/immunology ; Precision Medicine ; *Microbiota/immunology ; Biomarkers ; *Nervous System Diseases/prevention & control/chemically induced ; Immunotherapy/adverse effects ; },
abstract = {Cancer immunotherapy with immune checkpoint inhibitors (ICIs) has revolutionized oncology, significantly improving survival across multiple cancer types. ICIs, such as anti-PD-1 (e.g. nivolumab, pembrolizumab), anti-PD-L1 (e.g. atezolizumab, avelumab), and anti-CTLA-4 (e.g. ipilimumab), enhance T cell-mediated anti-tumor responses but can also trigger immune-related adverse events (irAEs). Neurological irAEs (n-irAEs), affecting 1-3% of patients, predominantly involve the peripheral nervous system; less commonly, n-irAEs can present as central nervous system disorders. Although irAEs suggest a possible correlation with treatment efficacy, their mechanisms remain unclear, with hypotheses ranging from antigen mimicry to cytokine dysregulation and microbiome alterations. Identifying patients at risk for n-irAEs and predicting their outcome through biomarkers would be highly desirable. For example, patients with high-risk onconeural antibodies (such as anti-Hu or Ma2), and elevated neurofilament light chain (NfL) levels often respond poorly to irAE treatment. However, interpreting neuronal antibody tests in the diagnosis of n-irAEs requires caution: positive results must align with the clinical context, as some cancer patients (e.g., SCLC) may have asymptomatic low antibody levels, and false positive results are common without tissue-based confirmation. Also, the use of biomarkers (e.g. IL-6) may lead to more targeted treatments of irAEs, minimizing adverse effects without compromising the anti-tumor efficacy of ICIs. This review provides a comprehensive overview of the latest findings on n-irAEs associated with ICIs, with a focus on their prediction, prevention, as well as precision treatment using autoantibodies, cytokines, and microbiota. The most interesting data concern neuronal antibodies, which we explore in their pathogenic roles and as biomarkers of neurotoxicity. Most of the available data on cytokines, both regarding their role as diagnostic and prognostic biomarkers and their role in supporting therapeutic decisions for toxicities, refer to non-neurological toxicities. However, in our review, we mention the potential role of CXCL10 and CXCL13 as biomarkers of n-irAEs and describe the current evidence, as well as the need for further studies, on the use of cytokines in guiding selection of second-line therapies for n-irAEs. Finally, no specific microbiome-related microbial signature has been proven to be linked to n-irAEs specifically, leading to the need of more future research on the topic.},
}

Humans
*Immune Checkpoint Inhibitors/adverse effects
*Cytokines/immunology/metabolism
*Autoantibodies/immunology
*Neoplasms/drug therapy/immunology
Precision Medicine
*Microbiota/immunology
Biomarkers
*Nervous System Diseases/prevention & control/chemically induced
Immunotherapy/adverse effects

@article {pmid40181808,
year = {2025},
author = {Farnetano, M and Carucci, L and Coppola, S and Oglio, F and Masino, A and Cozzolino, M and Nocerino, R and Berni Canani, R},
title = {Corrigendum: Gut microbiome features in pediatric food allergy: a scoping review.},
journal = {Frontiers in allergy},
volume = {6},
number = {},
pages = {1588779},
doi = {10.3389/falgy.2025.1588779},
pmid = {40181808},
issn = {2673-6101},
abstract = {[This corrects the article DOI: 10.3389/falgy.2024.1438252.].},
}

@article {pmid40181608,
year = {2025},
author = {Zhang, N and Zhang, X and Li, J and Li, B and Wang, S and Liu, X and Meng, H and Zhu, M},
title = {Development of Akkermansia Muciniphila Membrane-Coated Mesoporous Silica Nanoparticles with a Cerium Oxide Core for Inflammatory Bowel Disease Treatment.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e2405159},
doi = {10.1002/adhm.202405159},
pmid = {40181608},
issn = {2192-2659},
support = {2022YFA1206100//National Key R&D Program of China/ ; BJ-2022-103//National High-Level Hospital Clinical Research Funding/ ; Z230008//Beijing Natural Science Foundation/ ; 2021YFA1200902//National Key R&D Program of China projects/ ; 2022YFA1207300//National Key R&D Program of China projects/ ; 2021YFA1201100//National Key R&D Program of China projects/ ; 32271449//National Natural Science Foundation of China/ ; 32201158//National Natural Science Foundation of China/ ; 51773188//National Natural Science Foundation of China/ ; 82204300//National Natural Science Foundation of China/ ; 32271452//National Natural Science Foundation of China/ ; 22388101//Basic Science Center Project of the National Natural Science Foundation of China/ ; YSBR-036//CAS Project for Young Scientists in Basic Research/ ; },
abstract = {While convenient for patient compliance, the efficacy of oral treatments for inflammatory bowel disease (IBD) is often compromised by the dynamic and harsh chemical environment of the gastrointestinal tract, presenting challenges for effective therapeutic management. The pathological complexity of IBD frequently involves multiple factors such as oxidative stress, immune dysregulation, gut microbiome abnormality, and inadequate drug bioavailability, among others. To address these challenges, this project develops an oral nanomedicine platform based on mesoporous silica nanoparticles with a cerium oxide core, further coated with an outer membrane (OM) derived from Akkermansia muciniphila (Akk), a beneficial bacteria naturally present in the human gut. This novel nanocomplex, termed "OM-CeMeso," is evaluated for its enhanced stability, reactive oxygen species (ROS) scavenging capacity, and ability to restore microbiota homeostasis. This project demonstrates that the silica-based nanomaterials' acid-resistant yet base-degradable properties significantly improved stability in a murine IBD model. The incorporation of cerium oxide nanoparticles (CeO2 NPs) added further benefits by enhancing ROS scavenging. Notably, the Akk-derived OM coat also increases the diversity and abundance of beneficial gut microbiota. These complementary and integrated functions lead to significant symptom alleviation in murine IBD models while avoiding any unwanted toxicity.},
}

@article {pmid40181310,
year = {2025},
author = {Gao, ZW and Xu, ZN and Li, YL and Chang, L and Li, N and Liao, YC and Meng, WJ and Sun, H and Huang, L},
title = {Shifts in dominant tree species modulate phyllosphere microbial diversity and function in successional forests.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {195},
pmid = {40181310},
issn = {1471-2180},
support = {31870474//the National Natural Science Foundation of China/ ; 2023YFD1401304//the National Key R & D Program of China/ ; },
mesh = {*Forests ; *Bacteria/classification/isolation & purification/genetics ; *Plant Leaves/microbiology ; *Microbiota ; *Fungi/classification/isolation & purification/genetics ; *Trees/microbiology ; Biodiversity ; *Pinus/microbiology ; High-Throughput Nucleotide Sequencing ; Phylogeny ; },
abstract = {BACKGROUND: Phyllosphere microbiome plays a crucial role in maintaining plant fitness. However, its response to changes in dominant tree species during forest succession still remains poorly understood.

METHODS: In this study, microbial isolation and high-throughput sequencing techniques were used to analyze the community structure and diversity of phyllosphere microbes in pure Pinus massoniana forests, mixed P. massoniana and Liquidambar formosana forests, and pure L. formosana forests.

RESULTS: The results showed that the isolation rates of key plant fungal pathogens varied significantly in phyllosphere across forest types. In pure pine forest, Fusarium was most prevalent in pine needles, while in the mixed forest, Alternaria was dominant. For Liquidambar leaves, Phyllosticta dominated in pure forests, while Colletotrichum was prevalent in the mixed forests. Alpha diversity analysis revealed that higher microbial richness and diversity in the mixed forest compared to the pure forest. The bacterial community structure in Liquidambar leaves differed between the pure forest and the mixed forest. Co-occurrence networks confirmed more complex and stable microbial compositions and interactions in the mixed forest. Bacterial communities in pine needles exhibited higher functional capacity for methanotrophy and nitrogen fixation in the mixed forests.

CONCLUSIONS: The results demonstrate that the mixed forests foster greater microbial diversity, complexity, and functional potential in the phyllosphere compared to the pure forests, highlighting the importance of forest composition in shaping phyllosphere microbial communities.},
}

*Forests
*Bacteria/classification/isolation & purification/genetics
*Plant Leaves/microbiology
*Microbiota
*Fungi/classification/isolation & purification/genetics
*Trees/microbiology
Biodiversity
*Pinus/microbiology
High-Throughput Nucleotide Sequencing
Phylogeny

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

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

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

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

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

@article {pmid40181232,
year = {2025},
author = {Khavani, M and Mehranfar, A and Mofrad, MRK},
title = {Unravelling the Glycan Code: Molecular Dynamics and Quantum Chemistry Reveal How O-Glycan Functional Groups Govern OgpA Selectivity in Mucin Degradation by Akkermansia muciniphila.},
journal = {Microbial biotechnology},
volume = {18},
number = {4},
pages = {e70091},
doi = {10.1111/1751-7915.70091},
pmid = {40181232},
issn = {1751-7915},
mesh = {Molecular Dynamics Simulation ; *Mucins/metabolism/chemistry ; *Polysaccharides/metabolism/chemistry ; Substrate Specificity ; *Bacterial Proteins/metabolism/chemistry ; Quantum Theory ; Akkermansia ; },
abstract = {Mucins, heavily O-glycosylated glycoproteins, are a key component of mucus, and certain gut microbiota, including Akkermansia muciniphila, can utilise mucin glycans as a carbon source. Akkermansia muciniphila produces the O-glycopeptidase enzyme OgpA, which cleaves peptide bonds at the N-terminus of serine (Ser) or threonine (Thr) residues carrying O-glycan substitutions, with selectivity influenced by the O-glycan functional groups. Using molecular dynamics (MD) simulations and quantum chemistry calculations, we explored how different O-glycan groups affect OgpA's selectivity. Our results show that peptides bind to the enzyme via hydrogen bonds, π-π interactions, van der Waals forces and electrostatic interactions, with key residues, including Tyr90, Val138, Gly176, Tyr210 and Glu91, playing important roles. The primary determinant of selectivity is the interaction between the peptide's functional group and the enzyme's binding cavity, while peptide-enzyme interface interactions are secondary. Quantum chemistry calculations reveal that OgpA prefers peptides with a lower electrophilic character. This study provides new insights into mucin degradation by gut microbiota enzymes, advancing our understanding of this critical biological process.},
}

Molecular Dynamics Simulation
*Mucins/metabolism/chemistry
*Polysaccharides/metabolism/chemistry
Substrate Specificity
*Bacterial Proteins/metabolism/chemistry
Quantum Theory
Akkermansia

@article {pmid40180829,
year = {2025},
author = {Burananat, T and Wilantho, A and Kulalert, P and Nanthapisal, S and Tonglim, J and Deetienin, W and Wangkumhang, P and Tongsima, S and Thaweekul, P},
title = {The role of gut microbiota in obesity severity and metabolic risk in pediatric populations.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {},
number = {},
pages = {103970},
doi = {10.1016/j.numecd.2025.103970},
pmid = {40180829},
issn = {1590-3729},
abstract = {BACKGROUND AND AIMS: Childhood obesity is a considerable public health issue. Recent research has shown that alterations in gut microbiota can have an impact on developing obesity and other metabolic health problems in children. This study aimed to investigate whether the characteristics of gut microbiota in obese children and adolescents are associated with the severity of obesity and any metabolic complications.

METHODS AND RESULTS: During May 2022 to May 2023, a total of 56 children and adolescents with obesity, aged 6-18 years, were recruited at Thammasat Hospital, situated in provincial Pathumthani in central Thailand. Participants were allocated into two groups, characterized by the severity of their obesity. Demographic data, body composition, along with resting energy expenditures were determined. Serum samples were collected for the metabolic profile and inflammatory markers. Fecal samples were obtained for gut microbiota analysis via 16S rRNA Illumina. The obese group exhibited notably greater relative abundance of Actinobacteriota in comparison to the severely obese group, along with a lower abundance of Bacteroidota. There were no statistically significant differences in the relative abundance of Firmicutes and the Firmicutes to Bacteroidota ratio between the two cohorts. Bacteroidota positively correlated with FMI, while Actinobacteriota showed a negative correlation with FMI.

CONCLUSION: The data gathered from this study illustrated that children and adolescents with obesity and severe obesity in Thailand showed differences in the relative abundance of Actinobacteriota and Bacteroidota. Certain microbiome taxa showed correlations with various body and metabolic parameters.},
}

@article {pmid40180421,
year = {2025},
author = {Clavijo-Salomon, MA and Trinchieri, G},
title = {Unlocking the power of the microbiome for successful cancer immunotherapy.},
journal = {Journal for immunotherapy of cancer},
volume = {13},
number = {4},
pages = {},
doi = {10.1136/jitc-2024-011281},
pmid = {40180421},
issn = {2051-1426},
mesh = {Humans ; *Immunotherapy/methods ; *Neoplasms/therapy/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Fecal Microbiota Transplantation/methods ; *Microbiota ; },
abstract = {In recent years, evidence has shown that the gut microbiome significantly influences responses to immunotherapy. This has sparked interest in targeting it to improve therapy outcomes and predictions of response and toxicity. Research has demonstrated that dysbiosis, often resulting from antibiotic use, can diminish the effectiveness of immune checkpoint inhibitors, and this lack of efficacy could be linked to systemic inflammation. Certain bacterial species have been identified as having beneficial and harmful effects on immunotherapy in the clinic. While a clear consensus has yet to emerge on the optimal species for therapeutic use, introducing a new microbiome into immunotherapy-refractory patients may boost their chances of responding to further treatment attempts. State-of-the-art interventions targeting the microbiome-such as fecal microbiota transplantation-are being assessed clinically for their safety and potential to enhance treatment outcomes, with promising results. Additionally, the microbiome has been leveraged for its power to predict clinical outcomes using machine learning, and surprisingly, its predictive capability is comparable to that of other described multi-biomarker clinical scores. Here, we discuss developing knowledge concerning the microbiome's significance in cancer immunotherapy and outline future strategies for maximizing its potential in immuno-oncology.},
}

Humans
*Immunotherapy/methods
*Neoplasms/therapy/immunology/microbiology
*Gastrointestinal Microbiome/immunology
Fecal Microbiota Transplantation/methods
*Microbiota

@article {pmid40180180,
year = {2025},
author = {Diacova, T and Cifelli, CJ and Davis, CD and Holscher, HD and Kable, ME and Lampe, JW and Latulippe, ME and Swanson, KS and Karl, JP},
title = {Best Practices and Considerations for Conducting Research on Diet-Gut Microbiome Interactions and their Impact on Health in Adult Populations: An Umbrella Review.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100419},
doi = {10.1016/j.advnut.2025.100419},
pmid = {40180180},
issn = {2156-5376},
abstract = {Diet modulates gut microbiome composition and function. However, determining causal links between diet-gut microbiome interactions and human health is complicated by inconsistencies in the evidence, arising partially from variability in research methods and reporting. Widespread adoption of standardized best practices would advance the field but requires those practices be identified, consolidated and discussed. This umbrella review aimed to identify recommended best practices, define existing gaps, and collate considerations for conducting research on diet-gut microbiome interactions and their impact on human health outcomes. Reviews meeting inclusion criteria and published after 2013 were identified using a systematic search. Recommendations, considerations and gaps relating to best practices associated with study design, participant selection, dietary intervention/assessment, biological sample collection, and data analysis and reporting were extracted and consolidated. Eight narrative reviews were included. Several general points of agreement were identified, and a recurring theme was that best practices are dependent upon the research aims, outcomes and feasibility. Multiple gaps were also identified. Some, such as suboptimal diet assessment methods and lack of validated dietary intake biomarkers, are particularly relevant to nutrition science. Others, including defining a "healthy" gut microbiome and the absence of standardized sample and data collection/analysis protocols were relevant specifically to gut microbiome research. Gaps specific to diet-gut microbiome research include the underrepresentation of microbiome-modulating dietary components in food databases, lack of knowledge regarding interventions eliciting changes in the gut microbiome to confer health benefits, lack of in situ measurement methods and the need to further develop and refine statistical approaches for integrating diet and gut microbiome data. Future research and cross-disciplinary exchange will address these gaps and evolve best practices. In the interim, the best practices and considerations discussed herein, and the publications from which that information was extracted, provide a roadmap for conducting diet-gut microbiome research. PROSPERO registration: CRD42023437645.},
}

@article {pmid40180172,
year = {2025},
author = {Li, VW and Dong, TS and Funes, D and Hernandez, L and Kushnir, NR and Nair, D and Jacobs, JP and Reddy, ST and Mayer, EA and Chang, L and Meriwether, D},
title = {Mass spectrometric profiling of primary estrogens and estrogen metabolites in human stool and plasma partially elucidates the role of the gut microbiome in estrogen recycling.},
journal = {Molecular and cellular endocrinology},
volume = {},
number = {},
pages = {112534},
doi = {10.1016/j.mce.2025.112534},
pmid = {40180172},
issn = {1872-8057},
abstract = {Primary estrogens and estrogen metabolites are commonly measured in human plasma and serum, but there exist almost no recent reports for human stool. This knowledge gap limits our understanding of the relationships between systemic and gut estrogens. We developed a highly sensitive liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) method to determine, in human plasma and stool, the free and conjugated levels of estrone, estradiol, and estriol together with their additional hydroxyestrogen and methoxyestrogen metabolites. We investigated human stool and plasma estrogens in healthy control men; in follicular and luteal phase premenopausal women; and in postmenopausal women. Most estrogens were present in plasma and stool of all groups, while the plasma and stool levels of hydroxyestrogen and methoxyestrogen metabolites but not estrone were correlated. In stool, estrogens were higher in premenopausal women, with estrogens increasing across the menstrual cycle. We combined these LC-MS/MS measures with shotgun metagenomic sequencing of the stool microbiomes. Estrogen deconjugation enzyme gene copy numbers (β-glucuronidase and arylsulfatase) were higher in premenopausal women; while the gene copy number of β-glucuronidase + arylsulfatase, but not β-glucuronidase alone, correlated with deconjugated stool estrogens in all groups. Moreover, β-glucuronidase + arylsulfatase gene copy numbers correlated with combined plasma estrogens in men and with individual plasma estrogen metabolites in men and premenopausal women. These results support the hypothesis that gut microbial β-glucuronidase and arylsulfatase control the deconjugation of gut estrogens while modulating systemic levels through the uptake and recirculation of these deconjugated estrogens. The intestine may thus constitute an important additional compartment in estrogen physiology.},
}

@article {pmid40179831,
year = {2025},
author = {Verosky, BG and Bailey, MT and Gur, TL},
title = {The Metabolomic Mind: Microbial Metabolite Programming of Microglia.},
journal = {Neuroimmunomodulation},
volume = {},
number = {},
pages = {1-15},
doi = {10.1159/000545484},
pmid = {40179831},
issn = {1423-0216},
abstract = {The gut microbiota is increasingly recognized as a critical regulator of brain function, influencing neurodevelopment, adult brain physiology, and disease vulnerability in part through its interactions with microglia, the resident immune cells of the central nervous system. Emerging evidence demonstrates that microbial metabolites, beginning prenatally and persisting throughout the lifespan, regulate fundamental aspects of microglial biology including maturation, metabolic function, and activation. Microglia from germ-free mice exhibit persistent immaturity, altered energy metabolism, and blunted inflammatory responses, which are partially reversible by restoring microbial communities or supplementing key microbial metabolites. Short-chain fatty acids, tryptophan-derived indoles, and other bacterial metabolites derived from the gut microbiota shape microglial function to modulate neurons and synaptic architecture, and influence neuroinflammatory processes. These findings reveal distinct metabolite-driven pathways linking microbial composition to microglial phenotypes, positioning the microbiome as a potential key influencer of neurodevelopmental trajectories and the pathophysiology of psychiatric and neurological disorders. Despite recent advances, major knowledge gaps persist in understanding the precise molecular intermediaries and mechanisms through which metabolite signaling to microglia shape neural function to influence susceptibility or resilience to brain-based disorders. Understanding both the bacterial metabolomic landscape and its collective impact on microglial programming holds substantial therapeutic promise, offering avenues to target microbial metabolite production or administer them directly to modulate brain health.},
}

@article {pmid40179800,
year = {2025},
author = {Guvenc, F and Danska, JS},
title = {The intestinal microbiome in type 1 diabetes: bridging early childhood exposures with translational advances.},
journal = {Current opinion in immunology},
volume = {94},
number = {},
pages = {102553},
doi = {10.1016/j.coi.2025.102553},
pmid = {40179800},
issn = {1879-0372},
abstract = {Type 1 diabetes (T1D) results from T cell-mediated destruction of pancreatic β-cells, requiring lifelong insulin therapy and glycemic monitoring. While genetic risk, particularly HLA class II, is well established, rising T1D incidence and earlier onset suggest environmental modifiers. Mouse models show that microbiome alterations influence β-cell autoimmunity, and human studies link microbiome composition to T1D, though specific microbial regulators remain unidentified. We examine host-microbiome interactions, including studies implicating enteroviruses in modulating islet autoimmunity. Mechanistic discoveries of microbial effects on diabetes have emerged from mouse model studies. We consider clinical applications, including microbiota-targeted therapies and biomarkers of microbiome-immune crosstalk. Future research should integrate microbial, genetic, environmental, and immune data using multi-omic approaches. Collaborative efforts combining immunology, microbiology, and clinical metadata will drive discovery and precision medicine in T1D.},
}

@article {pmid40179789,
year = {2025},
author = {Liang, Y and Cao, Y and Xing, J and Tsai, IY and Zhao, C and Zhang, L and Xiao, Z and Levy, A and Eichen, Y and Achmon, Y},
title = {Impacts of different plastic residues on soil volatile profiles associated with microbiome dynamics.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138051},
doi = {10.1016/j.jhazmat.2025.138051},
pmid = {40179789},
issn = {1873-3336},
abstract = {Plastic pollution poses a significant threat to soil ecosystems, yet the role of volatile organic compounds (VOCs) in plastic degradation is not well-studied. The present research focuses on the impact of polyethylene (PE), polylactic acid (PLA), and poly(butylene-adipate-co-terephthalate) (PBAT) residues on soil in a 12-week long lab-scale aerobic experiment. The study focused on the dynamics of VOC profiles, soil physicochemical properties, and microbial communities. PBAT, known for its biodegradability, produced a distinct VOC profile with hazardous compounds such as 1,3-butadiene, which is consistently associated with cardiovascular diseases and leukemia. Microbial analysis of PBAT revealed distinct bacterial and fungal diversity responses, along with unique KEGG pathway profiles compared to PE and PLA, suggesting its biodegradation process may involve biofilm formation and quorum sensing. Correlation analysis based on the relevant abundance of specific microbes exhibited strong positive correlations, such as Streptomyces with propyne emission and Hydrogenispora with ethylene emission. These results demonstrated distinct biodegradation patterns of various plastics in soil, identified through the combination of VOC detection and microbiome analysis.},
}

@article {pmid40179568,
year = {2025},
author = {Caldeira, MO and McDonald, KS and Martinez, ESM and Moraes, JGN and Ramos, IS and Poock, SE and Ortega, MS and Lucy, MC},
title = {Short- and long-term effects of uterine disease on oocyte developmental capacity in postpartum dairy cows.},
journal = {Theriogenology},
volume = {240},
number = {},
pages = {117413},
doi = {10.1016/j.theriogenology.2025.117413},
pmid = {40179568},
issn = {1879-3231},
abstract = {The hypothesis was that early postpartum uterine disease would reduce the developmental capacity of oocytes thus contributing to the reduced fertility of dairy cows with uterine disease. Dairy cows were diagnosed healthy or with metritis at 7-10 d postpartum. The reproductive tract was collected at approximately 1 mo (Exp. 1) or approximately 80 or 165 d (Exp. 2) postpartum for the collection of cumulus-oocyte complexes (COC). The COC were matured, co-incubated with sperm for fertilization, and cultured to the blastocyst stage (8 d) in vitro. For Exp.1, the disease diagnosis (healthy or metritis) did not affect the number of collected COC or the subsequent embryo development to the blastocyst stage. The presence of purulent material in the uterine lumen (endometritis) at time of oocyte collection, however, was associated with a reduced cleavage rate evaluated 3 d following fertilization. For Exp. 2, there was no effect of disease diagnosis (healthy or metritis) on the number of COC or their subsequent development. Reduced cleavage rates were observed in COC retrieved from cows slaughtered at 80 d postpartum, but not at 165 d postpartum, and this reduction was associated with a vaginal microbiome indicative of uterine disease at 4-5 wk postpartum. Regression analyses that included plasma haptoglobin or energy metabolite concentrations or uterine bacterial genera abundance did not explain a large percentage of the variation in oocyte development in vitro. We conclude that there is an effect of uterine disease at one month postpartum on the oocyte and its capacity for development (Exp. 1) and this effect may be present at 80 d postpartum (Exp. 2). In later postpartum cows (165 d postpartum; Exp. 2) there was no effect of uterine disease on in vitro oocyte development.},
}

@article {pmid40179015,
year = {2025},
author = {Liao, Q and Zhou, X and Wu, L and Yang, Y and Zhu, X and Liao, H and Zhang, Y and Lian, W and Zhang, F and Wang, H and Ding, Y and Zhao, L},
title = {Gut microbial metabolite 4-hydroxybenzeneacetic acid drives colorectal cancer progression via accumulation of immunosuppressive PMN-MDSCs.},
journal = {The Journal of clinical investigation},
volume = {},
number = {},
pages = {},
doi = {10.1172/JCI181243},
pmid = {40179015},
issn = {1558-8238},
abstract = {Colorectal cancer (CRC) is characterized by an immune-suppressive microenvironment that contributes to tumor progression and immunotherapy resistance. The gut microbiome produces diverse metabolites that feature unique mechanisms of interaction with host targets, yet the role of many metabolites in CRC remains poorly understood. In this study, the microbial metabolite 4-hydroxybenzeneacetic acid (4-HPA) promoted the infiltration of polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) in the tumor microenvironment, consequently inhibiting the anti-tumor response of CD8+ T cells and promoting CRC progression in vivo. Mechanistically, 4-HPA activates the JAK2/STAT3 pathway, which upregulates CXCL3 transcription, thereby recruiting PMN-MDSCs to the CRC microenvironment. Selective knockdown of CXCL3 re-sensitized tumors to anti-PD1 immunotherapy in vivo. Chlorogenic acid (CGA) reduces the production of 4-HPA by microbiota, likewise abolishing 4-HPA-mediated immunosuppression. The 4-HPA content in CRC tissues was notably increased in patients with advanced CRC. Overall, the gut microbiome uses 4-HPA as a messenger to control chemokine-dependent accumulation of PMN-MDSC cells and regulate anti-tumor immunity in CRC. Our findings provide a scientific basis for establishing clinical intervention strategies to reverse the tumor immune microenvironment and improve the efficacy of immunotherapy by reducing the interaction between intestinal microbiota, tumor cells and tumor immune cells.},
}

@article {pmid40178925,
year = {2025},
author = {Handte-Reinecker, A and Sardeshpande, M},
title = {Microbiomes as Modulators of Human and Planetary Health: A Relational and Cross-Scale Perspective.},
journal = {Global change biology},
volume = {31},
number = {4},
pages = {e70152},
doi = {10.1111/gcb.70152},
pmid = {40178925},
issn = {1365-2486},
mesh = {*Microbiota ; Humans ; *Global Health ; *Public Health ; Biodiversity ; },
abstract = {The various human microbiomes play critical roles in maintaining health and well-being, and they are continuously shaped by a complex web of internal and external factors. Research on human and environmental microbiomes is generally discrete within disciplinary areas such as medicine, microbiology, molecular ecology, etc. This paper presents a perspective based on a scoping review of the literature, aiming to explore how these interconnected microbiomes shape human health and well-being and, in turn, planetary health. We explore the working of human microbiomes from cellular mechanisms to population outcomes, and the role of intrinsic and extrinsic factors influencing these microbiomes. We argue that global trends such as the homogenization of diets, environments, and medical practices are driving shifts in microbial diversity, with far-reaching implications for human health and well-being as well as planetary health. Disruptions to microbial feedback mechanisms at individual, community, and ecosystem levels are often interconnected and exacerbated by biodiversity loss and environmental change. We underscore the need for holistic public health interventions that account for microbiome stewardship across scales. By examining these connections, we aim to highlight the importance of a systems-level understanding of the microbiome in public health.},
}

*Microbiota
Humans
*Global Health
*Public Health
Biodiversity

@article {pmid39743984,
year = {2025},
author = {Blake, DP},
title = {Eimeria of chickens: the changing face of an old foe.},
journal = {Avian pathology : journal of the W.V.P.A},
volume = {54},
number = {3},
pages = {267-278},
doi = {10.1080/03079457.2024.2441180},
pmid = {39743984},
issn = {1465-3338},
mesh = {Animals ; *Chickens/parasitology ; *Coccidiosis/veterinary/parasitology/economics/epidemiology ; *Poultry Diseases/parasitology/economics/epidemiology/prevention & control ; *Eimeria/genetics/physiology/classification ; COVID-19/epidemiology ; },
abstract = {ABSTRACTEimeria are globally enzootic parasites that can cause coccidiosis in chickens. Until recently, remarkably little had changed over the last 40 years in the fundamental biology that underpins detection and control of Eimeria. Tools such as microscopy and lesion scoring remain central to diagnosis, and control still relies on routine supplementation of diets with anticoccidial drugs or application of live vaccines. However, refocusing on aspects of economics, molecular biology, and bacteriology that relate to coccidiosis has prompted considerable change in dogma. The cost of coccidiosis in chickens has been difficult to define, but updating models created in the 1990s suggested an annual cost to the global poultry industry of £10.4 billion in 2016, rising to a peak of £12.9 billion in 2022 under the influence of the COVID-19 pandemic and regional wars. Surveillance using genomic sequence-based diagnostics has suggested the presence of three new Eimeria species, supported by subsequent biological characterization of each line. Use of microbiome sequencing pipelines has revealed the breadth of impact Eimeria infection exerts on enteric microbiota, contributing to dysbiosis and deteriorating litter conditions. Enhanced understanding of Eimeria and the consequences of infection can be used to improve control and diagnosis with relevance to productivity and welfare, creating opportunities to optimize anticoccidial drug use.RESEARCH HIGHLIGHTSThe cost of coccidiosis in chickens fluctuates considerably, peaking in 2022.Three new Eimeria species can infect chickens and escape current vaccines.Eimeria infection exerts wide-ranging effects on enteric microbiota.},
}

Animals
*Chickens/parasitology
*Coccidiosis/veterinary/parasitology/economics/epidemiology
*Poultry Diseases/parasitology/economics/epidemiology/prevention & control
*Eimeria/genetics/physiology/classification
COVID-19/epidemiology

@article {pmid40178790,
year = {2025},
author = {Yuan, J and Yang, J and Sun, Y and Meng, Y and He, Z and Zhang, W and Dang, L and Song, Y and Xu, K and Lv, N and Zhang, Z and Guo, P and Yin, H and Shi, W},
title = {An early microbial landscape: inspiring endeavor from the China Space Station Habitation Area Microbiome Program (CHAMP).},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40178790},
issn = {1869-1889},
abstract = {China's progressing space program, as evidenced by the formal operation of the China Space Station (CSS), has provided great opportunities for various space missions. Since microbes can present potential risks to human health and the normal operation of spacecraft, the study on space-microorganisms in the CSS is always a matter of urgency. In addition, the knowledge on the interactions between microorganisms, astronauts, and spacecraft equipment will shed light on our understanding of life activities in space and a closed environment. Here, we present the first comprehensive report on the microbial communities aboard the CSS based on the results of the first two survey missions of the CSS Habitation Area Microbiome Program (CHAMP). By combining metagenomic and cultivation methods, we have discovered that, in the early stage of the CSS, microbial communities are dominated by human-associated microbes, with strikingly large differences in both composition and functional diversity compared to those found on the International Space Station (ISS). While the samples from two missions of CHAMP possessed substantial differences in microbial composition, no significant difference in functional diversity was found, although signs of accumulating antibiotic resistance were evident. Meanwhile, strong bacteria co-occurrence was noted within the station's microbiota. At the strain level, environmental isolates from the CSS exhibited numerous genomic mutations compared to those from the Assembly, Integration, and Test (AIT) center, potentially linked to the adaptation to the unique conditions of space. Besides, the intraspecies variation within four high-abundance species suggests possible propagation and residency effects between sampling sites. In summary, this study offers critical insights that not only advance our understanding of space microbiology but also lay the groundwork for effective microbial management in future long-term human space missions.},
}

@article {pmid40178645,
year = {2025},
author = {Li, N and Fang, X and Li, H and Liu, J and Chen, N and Zhao, X and Yang, Q and Chen, X},
title = {Ginsenoside CK modulates glucose metabolism via PPARγ to ameliorate SCOP-induced cognitive dysfunction.},
journal = {Metabolic brain disease},
volume = {40},
number = {4},
pages = {168},
pmid = {40178645},
issn = {1573-7365},
support = {81704001//National Natural Science Foundation of China/ ; 20200708056YY//Jilin Provincial Scientific and Technological Development Program/ ; YDZJ202301ZYTS466//Natural Science Foundation of Jilin Province/ ; },
mesh = {Animals ; *Ginsenosides/pharmacology/therapeutic use ; *Cognitive Dysfunction/metabolism/chemically induced/drug therapy ; *PPAR gamma/metabolism ; Mice ; *Glucose/metabolism ; Male ; Hippocampus/metabolism/drug effects ; Neurons/drug effects/metabolism ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Amyloid beta-Peptides/metabolism ; },
abstract = {Ginsenoside compound K (CK) exhibits neuroprotective properties; however, the underlying mechanisms behind these effects have not been investigated thoroughly. CK is the primary active compound derived from ginseng and is metabolized in the gut. It enhances neuronal function by modulating the gut microflora. Therefore, the present study aimed to elucidate the mechanism through which CK enhances cognitive function, employing gut microbiome and microarray analyses. The results revealed that CK upregulated the expression of peroxisome proliferator-activated receptor gamma (PPARγ), suppressed amyloid-β (Aβ) aggregation in hippocampal neurons, and influenced the expression of cyclin-dependent kinase-5 (CDK5), (including insulin receptor substrate 2) IRS2, insulin-degrading enzyme (IDE), glycogen synthase kinase-3 beta (GSK-3β), glucose transporter type 1 (GLUT1), and glucose transporter type 3 (GLUT3) proteins. These proteins play crucial roles in regulating brain glucose metabolism, increasing neuronal energy, and reducing neuronal apoptosis, thereby ameliorating cognitive impairment in mice.},
}

Animals
*Ginsenosides/pharmacology/therapeutic use
*Cognitive Dysfunction/metabolism/chemically induced/drug therapy
*PPAR gamma/metabolism
Mice
*Glucose/metabolism
Male
Hippocampus/metabolism/drug effects
Neurons/drug effects/metabolism
Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
Amyloid beta-Peptides/metabolism

@article {pmid40178319,
year = {2025},
author = {Herzog, E and Ishida, K and Scherlach, K and Chen, X and Bartels, B and Niehs, SP and Cheaib, B and Panagiotou, G and Hertweck, C},
title = {Antibacterial Siderophores of Pandoraea Pathogens and their Impact on the Diseased Lung Microbiota.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e202505714},
doi = {10.1002/anie.202505714},
pmid = {40178319},
issn = {1521-3773},
abstract = {Antibiotic-resistant bacteria of the genus Pandoraea, frequently acquired from the environment, are an emerging cause of opportunistic respiratory infections, especially in cystic fibrosis (CF) patients. However, their specialized metabolites, including niche and virulence factors, remained unknown. Through genome mining of environmental and clinical isolates of diverse Pandoraea species, we identified a highly conserved biosynthesis gene cluster (pan) that codes for a non-ribosomal peptide synthetase (NRPS) assembling a new siderophore. Using bioinformatics-guided metabolic profiling of wild type and a targeted null mutant, we discovered the corresponding metabolites, pandorabactin A and B. Their structures and chelate (gallium) complexes were elucidated by a combination of chemical degradation, derivatization, NMR, and MS analysis. Metagenomics and bioinformatics of sputum samples of CF patients indicated that the presence of the pan gene locus correlates with the prevalence of specific bacteria in the lung microbiome. Bioassays and mass spectrometry imaging showed that pandorabactins have antibacterial activities against various lung pathogens (Pseudomonas, Mycobacterium, and Stenotrophomonas) through depleting iron in the competitors. Taken together, these findings offer first insight into niche factors of Pandoraea and indicate that pandorabactins shape the diseased lung microbiota through the competition for iron.},
}

@article {pmid40178132,
year = {2025},
author = {Chedrawe, ER and Connors, J and Arra, A and Dunn, K and Blake, K and van Limbergen, J},
title = {Gut Microbiome Pilot Study of Patients With CHARGE Syndrome and Sibling Controls.},
journal = {American journal of medical genetics. Part A},
volume = {},
number = {},
pages = {e64053},
doi = {10.1002/ajmg.a.64053},
pmid = {40178132},
issn = {1552-4833},
support = {//CHARGE Syndrome Foundation/ ; //IWK Health Centre/ ; },
abstract = {Difficulties with feeding and digestion are common in individuals with CHARGE syndrome. Animal models with CHD7 gene variants demonstrate abnormal gut innovation and dysmotility. Our pilot study evaluated whether individuals with CHARGE syndrome have differences in their gut microbiome compared to unaffected siblings. Participants between the ages of 2-18 were recruited from Atlantic Canada with a confirmed genetic diagnosis of CHARGE syndrome. Gut Microbiome DNA analysis was performed on stool samples using 16S ribosomal RNA (rRNA) gene sequences. The PASSFP and PEDSQL served as GI symptom questionnaires. Eleven participants completed this study with one twin pair (CHARGE syndrome = 7, sibling controls = 4). The mean percent abundance for the four most common phyla in individuals with CHARGE versus Controls showed a trend towards increased Bacteroidetes, Proteobacteria, and a decrease in Firmicutes and Actinobacteria but was not significant. Microbiome comparisons based on abnormal (< 77) and normal (≥ $$ \ge $$ 77) GI scores, found significantly elevated Bacteroidetes (p = 0.042, 59.5% ± 15.1% vs. 33.1% ± 14.6%) and decreased Firmicutes (p = 0.042, 37.5% ± 15.9% vs. 62.4% ± 14.0%) with abnormal scores. Alpha diversity did not differ with either disease or GI symptom scores. Our data showed that, although there was a trend in changes in the gut microbiome in individuals with CHARGE compared to unaffected siblings, this change appears to be related to the severity of GI symptoms and not necessarily CHARGE itself, as differences were more pronounced in individuals with more difficulties with feeding and GI symptoms.},
}

@article {pmid40177999,
year = {2025},
author = {Delgado-Baquerizo, M and Singh, BK and Liu, YR and Sáez-Sandino, T and Coleine, C and Muñoz-Rojas, M and Bastida, F and Trivedi, P},
title = {Integrating ecological and evolutionary frameworks for SynCom success.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70112},
pmid = {40177999},
issn = {1469-8137},
abstract = {Use of synthetic microbial communities (SynComs) is a promising approach that harnesses nature-based solutions to support soil fertility and food security, mitigate climate change impacts, and restore terrestrial ecosystems. Several microbial products are in the market, and many others are at different stages of development and commercialization. Yet, we are still far from being able to fully harness the potential and successful applications of such biotechnological tools. The limited field efficiency and efficacy of SynComs have significantly constrained commercial opportunities, resulting in market growth falling below expectations. To overcome these challenges and manage expectations, it is critical to address current limitations, failures, and potential environmental consequences of SynComs. In this Viewpoint, we explore how using multiple eco-evolutionary theories can inform SynCom design and success. We further discuss the current status of SynComs and identify the next steps needed to develop and deploy the next-generation tools to boost their ability to support multiple ecosystem services, including food security and environmental sustainability.},
}

@article {pmid40177853,
year = {2025},
author = {Nelson, AS and Larson, MJ and Hammer, TJ},
title = {Core symbionts, age at inoculation and diet affect colonization of the bumblebee gut by a common bacterial pathogen.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.70029},
pmid = {40177853},
issn = {1365-2656},
support = {2023-67012-39357//National Institute of Food and Agriculture/ ; },
abstract = {Microbes shape the health of bumblebees, an important group of pollinators, including species of conservation concern. Most microbial research on bumblebees has focused on eukaryotic and viral pathogens or the core gut microbiome, a community of host-specialized bacterial symbionts that helps protect hosts against eukaryotic pathogens. Bumblebees also harbour a third class of microbes: non-core gut bacteria, which are non-host specific and vary among individuals. Understanding their functional role and how they interact with core symbionts is important for bumblebee ecology and management. We surveyed non-core bacteria in wild bumblebee workers (Bombus impatiens) and conducted laboratory experiments with gnotobiotic B. impatiens to examine factors shaping colonization by a focal non-core bacterium (Serratia marcescens) and its consequences for bee health. Non-core bacteria, including Serratia, frequently occur at high abundance in wild bumblebees, with roughly half of individuals harbouring at least 10% non-core gut bacteria. Experiments showed that Serratia marcescens better colonizes the gut when bees are inoculated early (within 1 day of adult emergence) and the core gut microbiome is disrupted. A mixed wildflower pollen diet facilitated the highest level of infection compared with two monofloral pollen treatments. We also provide evidence that Serratia is pathogenic: exposing bees with disrupted gut microbiomes to Serratia strongly reduced lifespan and, as a result, also reduced total reproduction. These results have three important implications: first, non-core bacteria are widespread in wild bumblebees, and some species are opportunistic pathogens. Second, the core gut microbiome plays a crucial role in protecting against these pathogens. Third, the timing of inoculation relative to bee age, as well as diet, is a key factor controlling bacterial pathogen colonization of the gut. Overall, these findings suggest that gut bacterial health could be an important target for monitoring and managing bumblebee health.},
}

@article {pmid40177842,
year = {2025},
author = {Larnder, AH and Manges, AR and Murphy, RA},
title = {The estrobolome: Estrogen-metabolizing pathways of the gut microbiome and their relation to breast cancer.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.35427},
pmid = {40177842},
issn = {1097-0215},
support = {/CAPMC/CIHR/Canada ; //Weston Family Foundation/ ; },
abstract = {Increasing evidence links the gut microbiome to carcinogenesis. Disruptions in estrogen regulation by the estrobolome-gut microbiota with estrogen-related functions-may promote breast cancer. However, precise information on estrobolome targets and their underlying mechanisms is limited. This review identifies relevant targets for measuring the estrobolome, focusing on enzymes and microbial taxa involved in processing estrogens, precursors, metabolites, and phytoestrogens, to facilitate the exploration of potential links to breast cancer. Evidence from breast cancer case-control studies is synthesized to assess alignment with these targets, highlight gaps in the evidence, and suggest new paths forward. Findings from case-control studies were heterogeneous and showed limited alignment with estrobolome targets, with only Escherichia coli and Roseburia inulinivorans identified as differentially abundant and functionally relevant between cases and controls. The lack of compelling evidence for estrobolome-specific mechanisms may reflect measurement challenges or may suggest that broader ecological changes in the microbiome, which influence a network of interacting mechanisms, are more influential for carcinogenesis. To clarify the estrobolome's role in breast cancer, future research should use advanced sequencing techniques and methods such as metabolomics and transcriptomics, while considering clinical and behavioral factors that may modify estrobolome mechanisms.},
}

@article {pmid40177692,
year = {2025},
author = {Speer, KA and Víquez-R, L and Frick, WF and Ibarra, A and Simmons, NB and Dittmar, K and Calderón, RS and Preciado, R and Medellín, R and Tschapka, M and Sommer, S and Perkins, SL},
title = {Comparative Community Ecology Reveals Conserved Ectoparasite Microbiomes Amidst Variable Host and Environment Microbiomes.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71120},
doi = {10.1002/ece3.71120},
pmid = {40177692},
issn = {2045-7758},
abstract = {The microbiome-the community of microorganisms that is associated with an individual animal-has been an important driver of insect biodiversity globally, enabling insects to specialize in narrow, nutrient-deficient diets. The importance of maternally inherited, obligate bacterial endosymbionts in provisioning nutrients missing from these narrow dietary niches has been well studied in insects. However, we know comparatively little about the processes that dictate the composition of non-maternally inherited bacteria in insect microbiomes, despite the importance of these bacteria in insect health, fitness, and vector competence. Here, we used two species of obligate insect ectoparasites of bats, the bat flies (Streblidae) Trichobius sphaeronotus and Nycterophilia coxata, to examine whether the microbiome, beyond obligate bacterial endosymbionts, is conserved or variable across geographic space, between ectoparasite species, or covaries with the external microbiome of their bat hosts or the cave environment. Our results indicate that ectoparasite microbiomes are highly conserved and specific to ectoparasite species, despite these species feeding on the blood of the same bat individuals in some cases. In contrast, we found high geographic variation in the fur microbiome of host bats and that the bat fur microbiome mimics the cave microbiomes. This research suggests that there is a constraint on blood-feeding insect ectoparasites to maintain a specific microbiome distinct from their host and the environment, potentially to meet their nutritional needs. Given that many of these bacteria are not known to be maternally inherited, this research lays the foundation for future examinations of how blood-feeding arthropods acquire and maintain bacteria in their microbiomes.},
}

@article {pmid40177686,
year = {2025},
author = {Argueta-Guzmán, M and Spasojevic, MJ and McFrederick, QS},
title = {Solitary Bees Acquire and Deposit Bacteria via Flowers: Testing the Environmental Transmission Hypothesis Using Osmia lignaria, Phacelia tanacetifolia, and Apilactobacillus micheneri.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71138},
doi = {10.1002/ece3.71138},
pmid = {40177686},
issn = {2045-7758},
abstract = {Microbial environmental transmission among individuals plays an important role in shaping the microbiomes of many species. Despite the importance of the microbiome for host fitness, empirical investigations on environmental transmission are scarce, particularly in systems where interactions across multiple trophic levels influence symbiotic dynamics. Here, we explore microbial transmission within insect microbiomes, focusing on solitary bees. Specifically, we investigate the environmental transmission hypothesis, which posits that solitary bees acquire and deposit their associated microbiota from and to their surroundings, especially flowers. Using experimental setups, we examine the transmission dynamics of Apilactobacillus micheneri, a fructophilic and acidophilic bacterium, between the solitary bee Osmia lignaria (Megachilidae) and the plant Phacelia tanacetifolia (Boraginaceae). Our results demonstrate that bees not only acquire bacteria from flowers but also deposit these microbes onto uninoculated flowers for other bees to acquire them, supporting a bidirectional microbial exchange. We therefore find empirical support for the environmental transmission hypothesis, and we discuss the multitrophic dependencies that facilitate microbial transmission between bees and flowers.},
}

@article {pmid40177558,
year = {2025},
author = {Xia, S and Jiang, D and Zhou, Q and Lyu, H and Voigt, AY and Zhou, X and Zhou, Z and Huang, Y},
title = {Unlocking the healthy human microbiome: Redefining core microbial signatures.},
journal = {Acta pharmaceutica Sinica. B},
volume = {15},
number = {2},
pages = {1189-1192},
doi = {10.1016/j.apsb.2025.01.001},
pmid = {40177558},
issn = {2211-3835},
}

@article {pmid40177547,
year = {2025},
author = {Dong, C and Zhou, B and Zhao, B and Lin, K and Tian, Y and Zhang, R and Xie, D and Wu, S and Yang, L},
title = {GLP-1RAs attenuated obesity and reversed leptin resistance partly via activating the microbiome-derived inosine/A2A pathway.},
journal = {Acta pharmaceutica Sinica. B},
volume = {15},
number = {2},
pages = {1023-1038},
doi = {10.1016/j.apsb.2024.12.006},
pmid = {40177547},
issn = {2211-3835},
abstract = {Extensive evidence has demonstrated that glucagon-like peptide-1 receptor agonists (GLP-1RAs) can ameliorate obesity. Our previous studies revealed that (Ex-4)2-Fc, a long-acting GLP-1RA we developed, depends on the leptin pathway to treat obesity. However, the mechanisms linking (Ex-4)2-Fc and leptin resistance remain largely unclear. To address this question, we explored the mechanism of GLP-1RAs from the perspective of the gut microbiota, as increasing evidence indicates an important link between the gut microbiota and obesity. This study aimed to explore the potential role of the gut microbiota in the treatment of GLP-1RAs. We found that (Ex-4)2-Fc treatment reshaped obesity-induced gut microbiota disturbances and substantially increased the abundance of Akkermansia muciniphila (Am). In addition, (Ex-4)2-Fc did not respond well in antibiotic-treated (ATB) Obese mice. Subsequent studies have shown that this defect can be overcome by gavage with Am. In addition, we found that Am enhanced (Ex-4)2-Fc therapy by producing the metabolite inosine. Inosine regulates the macrophage adenosine A2A receptor (A2A) pathway to indirectly reduce leptin levels in adipocytes Thus, elucidating the role of metabolites in regulating the leptin pathway will provide new insights into GLP-1RAs therapy and may lead to more effective strategies for guiding the clinical use of antidiabetic agents.},
}

@article {pmid40177486,
year = {2025},
author = {Yang, S and Chen, J and Zheng, J and Mao, H and Deng, F and Wu, D and Chai, J},
title = {Feeding systems influence the rumen resistome in yaks by changing the microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1505938},
doi = {10.3389/fmicb.2025.1505938},
pmid = {40177486},
issn = {1664-302X},
abstract = {The rumen microbiome serves as a reservoir of antibiotic-resistance genes (ARGs) with significant implications for public health. This study aimed to investigate the effects of different feeding systems on the rumen resistome in yaks. Yaks that grazed naturally on pasture were used as controls, while the experimental yaks were housed in a high-density pen environment and fed a specially designed diet to optimally meet their nutritional requirements, with increased interactions with farm workers. Metagenomic analysis was performed to assess changes in the rumen microbiome and resistome. Dietary factors influencing changes in the rumen microbiome and resistome were identified. A greater variety of microbiomes associated with carbohydrate digestion was found in yaks under a house-feeding system, such as Stomatobaculum longum and Succiniclasticum ruminis. Although grazing yaks exhibited various dominant antibiotic resistance genes (ARGs) at the class level, house-fed yaks were mainly enriched with tetracycline-resistant genes. A random forest model identified specific ARG signatures for each group, such as Sent_cmlA and Sliv_cmlR (Phenicol) and vanHD (Glycopeptide) prevalent in grazing yaks, while tet44, tetW, tetW/N/W, and tet40 were abundant in house-fed yaks. ARG interactions varied by feeding system, with signature ARGs in each group showing distinct correlations. Nevertheless, strong correlations among ARGs existed regardless of the treatments, such as the positive correlation between tetW and tetW/N/W in both groups. The rumen microbiome was strongly associated with the resistome, especially regarding abundant microbiomes and ARGs. Proteobacteria carrying ARGs were observed in grazing yaks, while Firmicutes served as hosts for ARGs in yaks under a housed feeding system. The specific bacteria contributing to the distinct ARGs in each group were identified. For instance, members of Firmicutes (Clostridium tepidiprofundi) carried their ARG signatures, such as tet44. These findings emphasized that diet, along with environmental factors and farmworker interactions, contributed to changes in the rumen resistome of yaks. This study is the first to discuss how multiple factors within a feeding regime influence the gut resistome, highlighting the drawbacks of intensive feedings with respect to the gut resistome.},
}

@article {pmid40177354,
year = {2025},
author = {Chen, G and Li, Y and Wei, S and Wang, X and Kuang, Z and Guo, W and Qin, J and Huang, T and Li, Y and Zhu, C},
title = {Role of gut microbiota in thalassemia: a review of therapeutic prospects.},
journal = {Frontiers in physiology},
volume = {16},
number = {},
pages = {1523448},
doi = {10.3389/fphys.2025.1523448},
pmid = {40177354},
issn = {1664-042X},
abstract = {In recent years, the study of gut microbiota has gradually become a research hotspot in the field of medicine, as gut microbiota dysbiosis is closely related to various diseases. Thalassemia, as a hereditary hemoglobinopathy, has a complex pathophysiological mechanism, and traditional treatment methods show limited efficacy. With a deeper understanding of the gut microbiome, researchers have begun to focus on its role in the pathogenesis of thalassemia and its therapeutic effects. This article aims to review the role of gut microbiota in thalassemia and its potential therapeutic prospects, analyze the latest research findings, and explore the impact and mechanisms of gut microbiota on patients with thalassemia, with the goal of providing new ideas and directions for future research and clinical treatment of thalassemia.},
}

@article {pmid40177291,
year = {2025},
author = {Chen, X and Cheng, Q and Zhang, GF},
title = {Elevated propionate and its association with neurological dysfunctions in propionic acidemia.},
journal = {Frontiers in molecular neuroscience},
volume = {18},
number = {},
pages = {1499376},
doi = {10.3389/fnmol.2025.1499376},
pmid = {40177291},
issn = {1662-5099},
abstract = {Propionate, a short-chain fatty acid (SCFA), has recently attracted attention for its various health benefits. However, elevated levels of propionate in certain pathological conditions can have adverse effects. Propionic acidemia (PA) is a rare metabolic disorder caused by mutations in the propionyl-CoA carboxylase (PCC) gene (PCCA or PCCB), leading to reduced PCC activity and impaired propionyl-CoA metabolism. This metabolic block at the PCC-mediated step results in the accumulation of propionyl-CoA and its metabolites, including propionate, contributing to various complications, such as neurological dysfunction, in patients with PA. This review examines propionate synthesis, its physiological role, its metabolism in healthy individuals and those with PA, and the pathological link between elevated propionate levels and neurological dysfunctions in PA patients. A deeper understanding of propionate metabolism under both normal and pathological conditions will help clarify the full spectrum of its metabolic effects.},
}

@article {pmid40176988,
year = {2025},
author = {Chen, Y and Peng, L and Li, Y and Peng, Y and Dai, S and Han, K and Xin, J},
title = {Amplicon-based analysis reveals link between adolescent acne and altered facial skin microbiome induced by negative emotional states.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1543616},
doi = {10.3389/fcimb.2025.1543616},
pmid = {40176988},
issn = {2235-2988},
mesh = {Humans ; Adolescent ; *Acne Vulgaris/microbiology/psychology ; *Skin/microbiology ; Male ; *Microbiota/genetics ; Female ; *Emotions ; High-Throughput Nucleotide Sequencing ; Severity of Illness Index ; *Face/microbiology ; Bacteria/classification/genetics/isolation & purification ; Skin Microbiome ; },
abstract = {INTRODUCTION: The skin microbiome is integral to maintaining skin homeostasis and is involved in the pathogenesis of acne. Emerging evidence supporting the 'brain-skin axis' suggests that psychological stress may exacerbate acne. Both negative emotional states and acne are highly prevalent among adolescents. Although research has begun to explore this relationship, the role of the skin microbiome in adolescents experiencing emotional disturbances and acne remains poorly understood.

METHODS: 166 adolescents aged 15-18 were divided into four distinct groups based on their emotional health and acne severity: no acne or negative emotions (NC), acne without negative emotions (NS), negative emotions without acne (YC), and acne with negative emotions (YS). Skin samples were collected from each participant's forehead and analyzed using high-throughput sequencing techniques, followed by comprehensive bioinformatics analyses to evaluate the microbial composition and diversity across the different groups.

RESULTS: Adolescents with both acne and negative emotions exhibited significantly higher acne severity (IGA 2.675 ± 0.090) compared to the group with acne but without negative emotions (IGA 1.952 ± 0.136). Distinct microbial community patterns emerged among the groups, with acne-affected individuals displaying increased α-diversity. Additionally, negative emotions were associated with heightened β-diversity differences between acne-affected individuals. The predominant bacterial phyla identified were Firmicutes, Bacteroidetes, Proteobacteria, and Fusobacteria, with Acinetobacter being more abundant, and Roseomonas and Cutibacterium being less prevalent in adolescents experiencing negative emotions.

CONCLUSION: This study revealed that the bacterial biomarkers of the disease change when acne is accompanied by negative emotions. Cutibacterium, Acinetobacter, and Roseomonas may be key contributors to acne exacerbation. These findings underscore the importance of considering both emotional and microbiological factors in the management of adolescent acne, particularly within the context of the brain-skin connection.},
}

Humans
Adolescent
*Acne Vulgaris/microbiology/psychology
*Skin/microbiology
Male
*Microbiota/genetics
Female
*Emotions
High-Throughput Nucleotide Sequencing
Severity of Illness Index
*Face/microbiology
Bacteria/classification/genetics/isolation & purification
Skin Microbiome

@article {pmid40176862,
year = {2025},
author = {Lin, YT and Lin, YC and Chen, HL and Lin, CC and Wu, MY and Chen, SH and Lin, ZH and Chang, YC and Sun, CH and Lu, SY and Chiang, MY and Tsai, HC and Shih, MJ and Chang, DR and Tsai, FJ and Chiang, HY and Kuo, CC},
title = {Mini-review of clinical data service platforms in the era of artificial intelligence: A case study of the iHi data platform.},
journal = {BioMedicine},
volume = {15},
number = {1},
pages = {6-22},
doi = {10.37796/2211-8039.1643},
pmid = {40176862},
issn = {2211-8020},
abstract = {In the past two decades, healthcare organizations have transitioned from the early stages of digitization and digitalization to a more comprehensive process of digital transformation, a shift significantly accelerated by the advent of artificial intelligence (AI). Consequently, the development of high-quality clinical data warehouses, derived from electronic health records (EHRs) and enriched with multidomain data, such as genomics, proteomics, and Internet of Things (IoT) information, has become essential for the creation of the modern patient digital twin (PDT). This approach is critical for leveraging AI in the evolving landscape of clinical practice. Leading medical centers and healthcare institutions have adopted this model, as summarized in this review. Since 2020, China Medical University Hospital (CMUH) has been constructing its data ecosystem by integrating EHRs with extensive genomic databases. This initiative has led to the development of a data service platform, the ignite Hyper-intelligence (iHi®) platform. The iHi platform serves as a case study exemplifying the workflow of the smart data chip, which facilitates the deep cleaning and reliable de-identification of clinical data while incorporating analytical platforms related to genomics and the microbiome to enhance insight extraction processes. The ability to predict complex interactions and disease trajectories among PDTs, digital counterparts of healthcare professionals, and virtual socioeconomic environments will be pivotal in advancing personalized healthcare and optimizing patient outcomes. Future challenges will involve the unification of cross-institutional data platforms and ensuring the interoperability of AI inferences-key factors that will define the next era of AI-driven healthcare.},
}

@article {pmid40176802,
year = {2025},
author = {Ramos-Lopez, O and Liu, C and Liu, HY},
title = {Editorial: Epigenetics in the microbiome-host crosstalk: from mechanisms to therapeutics.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1589656},
doi = {10.3389/fimmu.2025.1589656},
pmid = {40176802},
issn = {1664-3224},
}

@article {pmid40176488,
year = {2025},
author = {Winfrey, CC and Resasco, J and Fierer, N},
title = {Habitat specialization and edge effects of soil microbial communities in a fragmented landscape.},
journal = {Ecology},
volume = {106},
number = {4},
pages = {e70072},
doi = {10.1002/ecy.70072},
pmid = {40176488},
issn = {1939-9170},
support = {89303720SEM000037//U.S. Department of Energy/ ; DGE 1650115//National Science Foundation/ ; G-03583-01//National Science Foundation/ ; },
mesh = {*Soil Microbiology ; *Bacteria/classification ; *Ecosystem ; *Fungi/classification/physiology ; *Archaea/classification/physiology ; Mycorrhizae/physiology ; Soil/chemistry ; },
abstract = {Soil microorganisms play outsized roles in nutrient cycling, plant health, and climate regulation. Despite their importance, we have a limited understanding of how soil microbes are affected by habitat fragmentation, including their responses to conditions at fragment edges, or "edge effects." To understand the responses of soil communities to edge effects, we analyzed the distributions of soil bacteria, archaea, and fungi in an experimentally fragmented system of open patches embedded within a forest matrix. In addition, we identified taxa that consistently differed among patch, edge, or matrix habitats ("specialists") and taxa that showed no habitat preference ("nonspecialists"). We hypothesized that microbial community turnover would be most pronounced at the edge between habitats. We also hypothesized that specialist fungi would be more likely to be mycorrhizal than nonspecialist fungi because mycorrhizae should be affected more by different plant hosts among habitats, whereas specialist prokaryotes would have smaller genomes (indicating reduced metabolic versatility) and be less likely to be able to sporulate than nonspecialist prokaryotes. Across all replicate sites, the matrix and patch soils harbored distinct microbial communities. However, sites where the contrasts in vegetation and pH between the patch and matrix were most pronounced exhibited larger differences between patch and matrix communities and tended to have edge communities that differed from those in the patch and forest. There were similar numbers of patch and matrix specialists, but very few edge specialist taxa. Acidobacteria and ectomycorrhizae were more likely to be forest specialists, while Chloroflexi, Ascomycota, and Glomeromycota (i.e., arbuscular mycorrhizae) were more likely to be patch specialists. Contrary to our hypotheses, nonspecialist bacteria were not more likely than specialist bacteria to have larger genomes or to be spore-formers. We found partial support for our mycorrhizal hypothesis: arbuscular mycorrhizae, but not ectomycorrhizae, were more likely to be specialists. Overall, our results indicate that soil microbial communities are sensitive to edges, but not all taxa are equally affected, with arbuscular mycorrhizae in particular showing a strong response to habitat edges. In the context of increasing habitat fragmentation worldwide, our results can help inform efforts to maintain the structure and functioning of the soil microbiome.},
}

*Soil Microbiology
*Bacteria/classification
*Ecosystem
*Fungi/classification/physiology
*Archaea/classification/physiology
Mycorrhizae/physiology
Soil/chemistry

@article {pmid40176389,
year = {2025},
author = {Karsten, L and Harvey, BH and Stein, DJ and Valderrama, B and Bastiaanssen, TFS and Clarke, G and Cryan, JF and van der Sluis, R and Jaspan, H and Happel, AU and Wolmarans, W},
title = {Escitalopram alters tryptophan metabolism, plasma lipopolysaccharide, and the inferred functional potential of the gut microbiome in deer mice showing compulsive-like rigidity.},
journal = {Acta neuropsychiatrica},
volume = {},
number = {},
pages = {1-37},
doi = {10.1017/neu.2025.16},
pmid = {40176389},
issn = {1601-5215},
abstract = {OBJECTIVE: Compulsive-like rigidity may be associated with hyposerotonergia and increased kynurenine (KYN) pathway activity. Conversion of tryptophan (TRP) to kynurenine (KYN), which may contribute to hyposerotonergia, is bolstered by inflammation, and could be related to altered gut microbiota composition. Here, we studied these mechanisms in a naturalistic animal model of compulsive-like behavioural rigidity, i.e., large nest building (LNB) in deer mice (Peromyscus sp.).

METHODS: Twenty-four (24) normal nest building (NNB)- and 24 LNB mice (both sexes) were chronically administered either escitalopram (a selective serotonin reuptake inhibitor; 50 mg/kg/day) or a control solution, with nesting behaviour analysed before and after intervention. After endpoint euthanising, frontal cortices and striata were analysed for TRP and its metabolites, plasma for microbiota derived lipopolysaccharide (LPS) and its binding protein (LBP), and stool samples for microbial DNA.

RESULTS: LNB, but not NNB, decreased after escitalopram exposure. At baseline, LNB associated with reduced frontal cortical TRP concentrations and hyposerotonergia that was unrelated to altered KYN pathway activity. In LNB mice, escitalopram significantly increased frontal-cortical and striatal TRP without altering serotonin concentrations. Treated LNB, compared to untreated LNB- and treated NNB mice, had significantly reduced plasma LPS as well as a microbiome showing a decreased inferred potential to synthesise short-chain fatty acids and degrade TRP.

CONCLUSION: These findings support the role of altered serotonergic mechanisms, inflammatory processes, and gut microbiome involvement in compulsive-like behavioural rigidity. Our results also highlight the importance of gut-brain crosstalk mechanisms at the level of TRP metabolism in the spontaneous development of such behaviour.},
}

@article {pmid40176259,
year = {2025},
author = {Huang, R and Zhou, G and Cai, J and Cao, C and Zhu, Z and Wu, Q and Zhang, F and Ding, Y},
title = {Maternal consumption of urbanized diet compromises early-life health in association with gut microbiota.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2483783},
doi = {10.1080/19490976.2025.2483783},
pmid = {40176259},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Pregnancy ; *Diet/adverse effects ; *Maternal Nutritional Physiological Phenomena ; *Urbanization ; *Prenatal Exposure Delayed Effects ; Infant, Newborn ; Animals ; },
abstract = {Urbanization has significantly transformed dietary habits worldwide, contributing to a globally increased burden of non-communicable diseases and altered gut microbiota landscape. However, it is often overlooked that the adverse effects of these dietary changes can be transmitted from the mother to offspring during early developmental stages, subsequently influencing the predisposition to various diseases later in life. This review aims to delineate the detrimental effects of maternal urban-lifestyle diet (urbanized diet) on early-life health and gut microbiota assembly, provide mechanistic insights on how urbanized diet mediates mother-to-offspring transfer of bioactive substances in both intrauterine and extrauterine and thus affects fetal and neonatal development. Moreover, we also further propose a framework for developing microbiome-targeted precision nutrition and diet strategies specifically for pregnant and lactating women. The establishment of such knowledge can help develop proactive preventive measures from the beginning of life, ultimately reducing the long-term risk of disease and improving public health outcomes.},
}

Humans
*Gastrointestinal Microbiome/physiology
Female
Pregnancy
*Diet/adverse effects
*Maternal Nutritional Physiological Phenomena
*Urbanization
*Prenatal Exposure Delayed Effects
Infant, Newborn
Animals

@article {pmid40176140,
year = {2025},
author = {Ding, YP and Liu, CC and Yu, KD},
title = {RNA modifications in the tumor microenvironment: insights into the cancer-immunity cycle and beyond.},
journal = {Experimental hematology & oncology},
volume = {14},
number = {1},
pages = {48},
pmid = {40176140},
issn = {2162-3619},
support = {2023YFC3404100/2023YFC3404101/2023YFC2506400//National Key Research and Development Program of China/ ; 82325042, 82203860, 82072916//National Natural Science Foundation of China/ ; 2023-05-50//Shanghai Municipal Education Commission Scientific Research Innovation Project/ ; 32067502023-18-29//Wu Jieping Medical Foundation Research Project/ ; },
abstract = {The chemical modification of biological molecules is a critical regulatory mechanism for controlling molecular functions. Although research has long focused on DNA and proteins, RNA modifications have recently attracted substantial interest with the advancement in detection technologies. In oncology, many studies have identified dysregulated RNA modifications including m6A, m1A, m5C, m7G, pseudouridylation and A to I editing, leading to disrupted downstream pathways. As the concept of the tumor microenvironment has gained prominence, studies have increasingly examined the role of RNA modifications in this context, focusing on interactions among cancer cells, immune cells, stromal cells, and other components. Here we review the RNA modifications in the tumor microenvironment through the perspective of the Cancer-Immunity Cycle. The extracellular RNA modifications including exosomes and influence of microbiome in RNA modifications are potential research questions. Additionally, RNA modifying enzymes including FTO, ALKBH5, METTL3, PUS7 are under investigation as potential biomarkers and targets for combination with immunotherapies. ADCs and mimetics of modified RNA could be potential novel drugs. This review discusses the regulatory roles of RNA modifications within the tumor microenvironment.},
}

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

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

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

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