@article {pmid41052982,
year = {2025},
author = {Cao, Y and Fan, X and Zang, T and Qiu, T and Fang, Q and Bai, J and Liu, Y},
title = {Prenatal depression-associated gut microbiota induces depressive-like behaviors and hippocampal neuroinflammation in germ-free mice.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {383},
pmid = {41052982},
issn = {2158-3188},
support = {2023AFB710//Natural Science Foundation of Hebei Province (Hebei Provincial Natural Science Foundation)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; *Hippocampus/metabolism/pathology/immunology ; Mice ; Pregnancy ; Fecal Microbiota Transplantation ; *Depression/microbiology/metabolism ; *Dysbiosis/microbiology/complications ; Humans ; Lipopolysaccharides/blood ; Germ-Free Life ; *Neuroinflammatory Diseases/metabolism/microbiology ; Microglia ; *Pregnancy Complications/microbiology ; Disease Models, Animal ; Behavior, Animal ; Interleukin-6/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; },
abstract = {Numerous studies have described the role of the microbiome-gut-brain axis in depression. However, the molecular mechanisms underlying the involvement of gut microbiota in the development of prenatal depression are limited. In this study, fecal microbiota from women with prenatal depression was transplanted into germ-free mice to investigate the potential causal relationships between the gut microbiota and depressive phenotypes. Shotgun metagenomic sequencing and untargeted metabolomics approaches were used to investigate the characteristics of gut microbiota and microbial metabolites. The levels of neuroinflammation in the brain were detected using immunofluorescence and real-time quantitative PCR. We found significant changes in gut microbiota composition and metabolites in mice with fecal microbiota transplantation (FMT) from women with prenatal depression, including decreased Ligilactobacillus, increased Akkermansia, and abnormal glycerophospholipid metabolism. Besides, significant increase in plasma lipopolysaccharide (LPS) levels and significant proliferation of microglia in the hippocampus were observed in mice receiving FMT from women with prenatal depression, accompanied by a significant increase in the expression of nuclear factor-κB (NF-κB) p65, tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) mRNA. The gut microbiota and its metabolites were strongly associated with depressive-like behaviors, plasma LPS and neuroinflammation. Our study collectively demonstrates that dysbiosis of the gut microbiota may play a causal relationship in the development of prenatal depression. This process potentially involves the activation of neuroinflammation through the LPS-NF-κB signaling pathway.},
}

Animals
*Gastrointestinal Microbiome/physiology
Female
*Hippocampus/metabolism/pathology/immunology
Mice
Pregnancy
Fecal Microbiota Transplantation
*Depression/microbiology/metabolism
*Dysbiosis/microbiology/complications
Humans
Lipopolysaccharides/blood
Germ-Free Life
*Neuroinflammatory Diseases/metabolism/microbiology
Microglia
*Pregnancy Complications/microbiology
Disease Models, Animal
Behavior, Animal
Interleukin-6/metabolism
Tumor Necrosis Factor-alpha/metabolism

@article {pmid41052412,
year = {2025},
author = {Dias, ME and Breyer, GM and Torres, MC and Wuaden, CR and Rebelatto, R and Kich, JD and Dorn, M and Siqueira, FM},
title = {Overview of the microbiome and resistome of swine manure in commercial piglet farms and its application in grazing soils.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/09593330.2025.2566429},
pmid = {41052412},
issn = {1479-487X},
abstract = {The environmental spread of antimicrobial resistance genes (ARGs) through the use of animal manure in agriculture has become a significant concern. This study investigated the impact of applying swine manure treated through biodigestion on the spread of ARGs in agricultural soils in the Midwest region of Brazil. Samples of untreated and treated manure, fertilized soil, and unfertilized soil were collected from three piglet production units. Bacterial communities and ARGs were characterized through metagenomic sequencing and bioinformatics. Bacterial profiles in fertilized and unfertilized soils were highly similar across all farms. In contrast, biodigestion reduced the total number of ARGs in treated manure. Of the 399 ARGs detected in fertilized soils, 67% were also found in unfertilized soils, and 12% were shared exclusively with treated manure. The presence of numerous ARGs in unfertilized soils highlights the role of environmental dissemination routes, such as runoff, dust, or wildlife, in shaping soil resistomes even in areas without manure application. These findings suggest a stable bacterial and resistome profile in soils, regardless of manure application. Although antimicrobial residues were not evaluated, the results reinforce the need for responsible antibiotic use and effective manure management to minimize environmental ARG dissemination.},
}

@article {pmid41052276,
year = {2025},
author = {Sherwani, MK and Ruuskanen, MO and Feldner-Busztin, D and Nisantzis Firbas, P and Boza, G and Móréh, Á and Borman, T and Putu Erawijantari, P and Scheuring, I and Gopalakrishnan, S and Lahti, L},
title = {Multi-omics time-series analysis in microbiome research: a systematic review.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {5},
pages = {},
doi = {10.1093/bib/bbaf502},
pmid = {41052276},
issn = {1477-4054},
support = {952914//European Union's Horizon 2020 research and innovation programme/ ; },
mesh = {*Microbiota ; Humans ; *Computational Biology/methods ; Machine Learning ; *Genomics/methods ; Multiomics ; },
abstract = {Recent developments in data generation have opened up unprecedented insights into living systems. It has been recognized that integrating and characterizing temporal variation simultaneously across multiple scales, from specific molecular interactions to entire ecosystems, is crucial for uncovering biological mechanisms and understanding the emergence of complex phenotypes. With the increasing number of studies incorporating multi-omics data sampled over time, it has become clear that integrated approaches are pivotal for these efforts. However, standard data analytical practices in longitudinal multi-omics are still shaping up and many of the available methods have not yet been widely evaluated and adopted. To address this gap, we performed the first systematic literature review that comprehensively categorizes, compares, and evaluates computational methods for longitudinal multi-omics integration, with a particular emphasis on four categories of the studies: (i) host and host-associated microbiome studies, (ii) microbiome-free host studies, (iii) host-free microbiome studies, and (iv) methodological framework studies. Our review highlights current methodological trends, identifies widely used and high-performing frameworks, and assesses each method across performance, interpretability, and ease of use. We further organize these methods into thematic groups-such as statistical modeling, machine learning, dimensionality reduction, and latent factor approaches-to provide a clear roadmap for future research and application. This work offers a critical foundation for advancing integrative longitudinal data science and supporting reproducible, scalable analysis in this rapidly evolving field.},
}

*Microbiota
Humans
*Computational Biology/methods
Machine Learning
*Genomics/methods
Multiomics

@article {pmid41051602,
year = {2025},
author = {Pereira, HS and Rashid, M and Alissa, A and Keraidi, S and Wipf, N and Sowa, AM and McDonnell, JM and Darwish, S and Butler, JS},
title = {Exploring osteomicrobiology: A narrative review of the gut-bone axis in osteoporosis.},
journal = {Irish journal of medical science},
volume = {},
number = {},
pages = {},
pmid = {41051602},
issn = {1863-4362},
abstract = {Osteoporosis is a chronic condition that presents with decreased bone mass and changes in bone microarchitecture, leading to an increased fracture risk. While the relationship between the gut microbiome and the immune system is well established, its impact on bone health remains underexplored. This narrative review aims to investigate the relationship between gut microbiota, bone health, and osteoporosis. Key findings indicate that the gut microbiome influences bone density through various mechanisms. Specific bacterial strains such as Lactobacillus and Bifidobacterium enhance the absorption of calcium, magnesium, and phosphorus, increasing bone mineral density. Additionally, the ability to produce essential vitamins like K and B makes the gut microbiota crucial for bone synthesis and integrity. Studies also revealed notable differences in the gut microbiome composition of individuals diagnosed with primary osteoporosis (PO) compared to those who were healthy controls. PO patients exhibited higher microbiota diversity and certain distinctive phylogenetic shifts. Important bacterial taxa such as Bacteroidetes, Faecalibacterium, and Dialister exist in high numbers in PO and may be useful as biomarkers. Additionally, a correlation was found between H. Pylori infections and reduced lumbar spine bone mineral density in older males. The review identifies certain gaps in the current knowledge and research such as the role of viral and fungal components within the gut microbiome. This review highlights the potential role of the gut microbiome as a target for osteoporosis diagnosis, treatment and prevention, underscoring the need for dietary and lifestyle interventions to modify the microbiome and improve bone health.},
}

@article {pmid41051464,
year = {2025},
author = {Muigano, MN and Liu, J and Liu, X and Luo, P and Li, Z and Li, J},
title = {The Impact of Dietary Patterns on the Human Gut Microbiome and Its Health Significance: A Review.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {19},
pages = {e71072},
doi = {10.1096/fj.202502040R},
pmid = {41051464},
issn = {1530-6860},
support = {//Shanghai Stomatological Hospital & School of Stomatology/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diet ; Diet, Mediterranean ; Diet, Vegetarian ; Obesity/microbiology ; },
abstract = {The gut microbiome constitutes a dynamic and complex ecosystem within the human body, playing a crucial role in maintaining metabolic homeostasis, immune regulation, and disease prevention. Among the various factors shaping this ecosystem, dietary patterns represent a major determinant of microbial composition and function. Recent studies have identified dietary patterns as one of the primary factors influencing the composition and function of the gut microbiome. This review summarizes the effects of various dietary patterns, including the Mediterranean diet, vegetarianism, low-carbohydrate high-fat diets, and high-protein diets, on gut microbiome dynamics. Furthermore, it explores the mechanisms by which the gut microbiome contributes to the pathophysiology of multiple chronic diseases, such as obesity, diabetes, inflammatory bowel disease, osteoporosis, and neurodegenerative disorders. The potential of dietary interventions to improve health by modulating the gut microbiome is also evaluated, emphasizing recent findings that unveil the intricate network of dietary microbiome-host interactions. This review aims to provide a scientific basis for the development of future dietary strategies that leverage gut microbiome modulation, ultimately contributing to personalized nutrition and precision medicine.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Diet
Diet, Mediterranean
Diet, Vegetarian
Obesity/microbiology

@article {pmid41051418,
year = {2025},
author = {Seth, M and Mondal, M and Mukhopadhyay, SK},
title = {Paracoccus sp. PS1: a novel probiotic strain for the mitigation of cardiometabolic risk factors TMA, TMAO, and methylglyoxal.},
journal = {Archives of microbiology},
volume = {207},
number = {11},
pages = {285},
pmid = {41051418},
issn = {1432-072X},
support = {DST/INSPIRE Fellowship/2018/IF180258//Department of Science and Technology Innovation in Science Pursuit for Inspired Research (DST INSPIRE), Government of India/ ; },
mesh = {*Methylamines/metabolism ; *Pyruvaldehyde/metabolism ; *Probiotics ; Humans ; *Paracoccus/genetics/metabolism/isolation & purification/growth & development/physiology ; Gastrointestinal Microbiome ; *Cardiovascular Diseases/prevention & control ; Risk Factors ; Genome, Bacterial ; },
abstract = {The gut microbiome is increasingly recognized as a critical modulator of host health, particularly in the context of non-communicable diseases like cardiovascular disease and diabetes. Central to this connection are microbially-derived metabolites such as trimethylamine N-oxide (TMAO), trimethylamine (TMA), and methylglyoxal, which have emerged as significant biomarkers and mediators of disease progression. All these toxic metabolites are generated in the body by the type of food we consume on daily basis. As the epicentre of TMA mediated ailments is human gut, a probiotic microbial strain with TMA degrading ability may be useful in mitigating those ailments. Due to its strong TMA-degrading ability and non-pathogenic nature of our isolated strain Paracoccus sp. PS1 prompted further investigation of its other physio-biochemical properties to judge its suitability as a probiotic strain. With this aim, viability of PS1 under anaerobic and microaerophilic conditions, which mimic human gut, were examined. Strain PS1 showed positive growth under both microaerophilic and anaerobic conditions and also showed other probiotic features such as tolerance to bile, lysozyme, acidic pH, gastric juices (pepsin), hydrophobicity, aggregation, coaggregation, adhesion and antioxidant properties. Furthermore, analysis of the whole genome sequence of Paracoccus sp. PS1 identified the genes and their respective proteins responsible for its probiotic properties, supporting its potential for use as a novel probiotic strain. The present study is the first to identify and characterize a potential probiotic from the genus Paracoccus with the unique capacity to degrade TMA, TMAO, and methylglyoxal.},
}

*Methylamines/metabolism
*Pyruvaldehyde/metabolism
*Probiotics
Humans
*Paracoccus/genetics/metabolism/isolation & purification/growth & development/physiology
Gastrointestinal Microbiome
*Cardiovascular Diseases/prevention & control
Risk Factors
Genome, Bacterial

@article {pmid41051380,
year = {2025},
author = {Jendraszak, M and Andrusiewicz, M},
title = {Uncovering hidden connections: the role of the male reproductive system microbiome and gut microorganisms in implantation: a critical review.},
journal = {Critical reviews in clinical laboratory sciences},
volume = {},
number = {},
pages = {1-31},
doi = {10.1080/10408363.2025.2562894},
pmid = {41051380},
issn = {1549-781X},
abstract = {Recent advancements in sequencing technologies have uncovered complex and diverse microbial communities inhabiting various niches of the human body, including the reproductive system. This review explores the significance of the male genital and gut microbiomes in maintaining reproductive health, focusing on their potential roles in embryo implantation and pregnancy outcomes. A comprehensive literature search was conducted using MEDLINE, Web of Science, and Scopus for articles published between 2004 and 2024. Search terms included "microbiome," "implantation," "inflammation," "male reproductive system," "recurrent miscarriage," "recurrent implantation failure," and "probiotics." From an initial pool of 1,091 articles, 107 were selected after applying filters for clinical, comparative, and observational studies. Ultimately, 21 articles met the quality criteria and were included in the review. While the female genital microbiome has been extensively studied and its role in implantation and embryo development well established, research on the male genital microbiome remains limited, and its influence is not yet fully understood. Nevertheless, emerging data suggest that the male reproductive tract harbors its own distinct microbial community, which may affect fertility, implantation, and pregnancy outcomes. The presence of certain bacteria and leukocytes in semen has been associated with sperm DNA damage, potentially compromising fertility and embryo development. Moreover, microbial exchange between partners during intercourse may alter the composition of the female reproductive microbiome, potentially influencing implantation success. The male and female reproductive tracts are colonized by microbial communities that play crucial roles in preventing infections and supporting reproductive health. Disruptions in these ecosystems have been linked to infertility, miscarriage, and preterm birth. Additionally, the gut microbiome is believed to interact with the reproductive system, possibly influencing implantation through immune and metabolic pathways. A deeper understanding of these connections is essential for identifying new preventive and therapeutic strategies for individuals experiencing recurrent pregnancy loss or implantation failure. Identifying specific microbial patterns associated with dysbiosis is critical for the development of targeted interventions. Potential therapeutic approaches include probiotics, prebiotics, and antibiotics, which may help restore microbial balance, enhance fertility, and reduce the risk of miscarriage. Antibiotic treatment may also prove beneficial in addressing infections that disrupt implantation. As microbial exchange, sperm DNA integrity, and immune regulation are all influenced by the microbiome, further research is necessary to understand its role in reproductive outcomes fully. Microbiome-targeted therapies represent a promising frontier in reproductive medicine. However, their clinical efficacy must be validated through rigorous research. This review underscores the importance of characterizing the composition and functional roles of the genital and gut microbiomes in order to inform the development of novel diagnostic tools and therapeutic strategies aimed at improving reproductive health and pregnancy outcomes.},
}

@article {pmid41051239,
year = {2025},
author = {Hamidi Nia, L and Alqudah, S and Markley, RL and DeLucia, B and Bobba, V and Elmallah, J and Nemet, I and Sangwan, N and Claesen, J},
title = {The antimicrobial metabolite nisin Z reduces intestinal tumorigenesis and modulates the cecal microbiome in Apc[Min/+] mice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0155725},
doi = {10.1128/spectrum.01557-25},
pmid = {41051239},
issn = {2165-0497},
abstract = {UNLABELLED: Nisin Z, an antimicrobial metabolite produced by Lactococcus lactis, has been safely used as a food preservative for many years. Nisin Z also showed promising activity against various cancer types in vitro and significantly reduced tumor size in an ectopic head and neck cancer model. Here, we investigate the activity of nisin Z for colorectal cancer treatment and observed an in vitro reduction in cellular proliferation and a moderate enhancement in cell death. We next analyzed the effect of oral nisin Z administration in the Apc[Min/+] intestinal adenoma mouse model. We measured tumor burden along the gastrointestinal tract and observed a decrease in tumor burden in the middle region of the small intestine but not in the lower region or colon. Since tumor progression in the Apc[Min/+] model is exacerbated by an inflammatory environment, we next determined whether nisin Z impacts this in a direct or indirect manner. We show that nisin Z directly reduces NF-κB activation in a dose-dependent manner in a cell-based assay, and we observe a corresponding reduction in NF-κB protein expression in the middle region of the small intestine. In addition, nisin Z impacted the cecal microbiome composition as well as microbiota-associated plasma metabolites, leading to changes that are in part associated with beneficial outcomes. Interestingly, the Apc[Min/+] genotype differentially impacted the nisin Z-mediated differences in cecal microbiome composition and plasma metabolites compared to wild-type animals. In summary, our data suggest that the reduction in small intestinal tumor burden could be due to nisin Z's contribution to a reduced pro-inflammatory environment. Future studies will reveal whether nisin's localized effect is due to degradation of the peptidic compound in more distal regions of the gastrointestinal tract and focus on development of delivery systems to increase efficacy.

IMPORTANCE: With the increased incidence of colorectal cancer, especially among younger individuals, it is critical to study approaches that help with the prevention and treatment of this debilitating disease. Our study indicates that nisin Z, a bacterially produced peptide antibiotic, decreases the growth of colorectal cancer cells and moderately increases cell death in vitro. Oral administration of nisin Z in an intestinal adenoma mouse model revealed a reduction of tumor burden in the middle region of the small intestine. This decreased tumor burden might in part be attributed to a direct anti-inflammatory effect, as well as an indirect effect on the gut microbiota and their metabolites due to nisin Z's antibacterial activity. Overall, we demonstrate a potential activity for nisin Z in the prevention or amelioration of inflammation-associated colorectal cancer, underscoring the significance of investigating the properties of bacterial natural products in human health.},
}

@article {pmid41051180,
year = {2025},
author = {Ganesan, SM and Yadav, M and Ghimire, S and Lehman, PC and Patel, AJ and Woods, S and Olalde, H and Hoang, J and Paullus, M and Cherwin, C and Gill, C and Cho, T and Mangalam, AK},
title = {Relapsing-Remitting Multiple Sclerosis Is Associated With a Dysbiotic Oral Microbiome.},
journal = {Annals of clinical and translational neurology},
volume = {},
number = {},
pages = {},
doi = {10.1002/acn3.70212},
pmid = {41051180},
issn = {2328-9503},
support = {1RO1AI137075//National Institute of Allergy and Infectious Diseases, USA/ ; 1P20NR018081-01/NR/NINR NIH HHS/United States ; 5T90DE023520/GF/NIH HHS/United States ; T32AI007260/GF/NIH HHS/United States ; //Department of Pathology, University of Iowa/ ; 10.13039/100000002//National Institute of Health, USA/ ; //University of Iowa Environmental Health Sciences Research Center/ ; //Carver Trust/ ; 1I01CX002212//US department of Veterans Affairs/ ; },
abstract = {OBJECTIVE: Multiple sclerosis (MS) is a chronic autoimmune disorder characterized by inflammation, demyelination, and neurological impairment. While the gut microbiota's role in MS is extensively studied, the association between the oral microbiota and MS remains underexplored, particularly in North American cohorts. This study aimed to investigate the microbiota (bacterial) composition as well as functional pathways and immune profiles of the oral cavity in 60 patients with relapsing-remitting MS (RRMS), stratified by treatment status, compared to 44 healthy controls (HC).

METHODS: Unstimulated saliva was collected for genomic DNA extraction and salivary cytokine quantification. Oral bacterial composition and diversity were analyzed using 16S rRNA sequencing, with functional pathways inferred using PICRUSt2. Salivary cytokine levels were measured via multiplex immunoassays. LEfSe and random forest models identified key discriminatory taxa, and correlations between microbiota and cytokines were assessed using Spearman's rank analysis.

RESULTS: RRMS patients exhibited distinct microbial communities compared to HC and a higher Bacteroidota to Firmicutes ratio. Key taxa such as Campylobacter, Lachnoanaerobaculum, and Porphyromonas were enriched in RRMS. Functional profiling revealed 49 differentially abundant pathways, including the enrichment of lipopolysaccharide biosynthesis in MS. Elevated levels of IFN-γ, IL-6, and other cytokines correlated with the altered microbiome. IL-21, elevated in HC, correlated with anti-inflammatory pathways, suggesting a protective role in immune homeostasis.

INTERPRETATION: This study provides, for the first time, insights into oral microbiome-host interactions in North American RRMS patients, underscoring the interplay between microbial dysbiosis, functional pathways, and immune dysregulation. The oral microbiome shows potential as a biomarker for MS-related immune alterations.},
}

@article {pmid41051094,
year = {2025},
author = {Cheng, Z and Xia, W and McKelvey, S and He, Q and Chen, Y and Yuan, H},
title = {Building Predictive Understanding of the Activated Sludge Microbiome by Bridging Microbial Growth Kinetics and Microbial Population Dynamics.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c05925},
pmid = {41051094},
issn = {1520-5851},
abstract = {Modeling microbiomes can provide predictive insights into microbial ecology, but current modeling approaches suffer from inherent limitations. In this study, a novel modeling approach was developed based on the intrinsic connection between the growth kinetics of guilds and the dynamics of microbial populations. To implement this approach, 466 samples from four full-scale activated sludge systems were retrieved. The raw samples were processed using a data transformation method that tripled the data set size and enabled quantification of population dynamics. Of the 42 family level core populations, 36 showed overall dynamics statistically close to zero (within ± 0.05 d[-1]). Bayesian networks were built to classify the core populations into heterotrophic and autotrophic guilds. Topological data analysis was applied to identify keystone populations and time-dependent microbial interactions. The data-driven inferences were validated directly using the Microbial Database for Activated Sludge (MiDAS) and indirectly by predicting community structure using artificial neural networks. The Bray-Curtis similarity between predicted and observed communities was higher with microbial kinetic parameters than without these parameters (0.70 vs 0.66, t test, p < 0.05). Owing to the flexibility of the modeling framework, this proposed hybrid approach might potentially be adapted to time-dependent data from natural systems for predictive understanding of the involved microbiomes.},
}

@article {pmid41050887,
year = {2025},
author = {Lyu, WN and Shen, CY and Lee, YH and Chen, SK and Chuang, EY and Lou, PJ and Tsai, MH},
title = {Novel biomarker identification for oral squamous cell carcinoma development in nonsmoker, nondrinker, and nonchewer patients using third-generation sequencing of oral microbiome.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2565452},
pmid = {41050887},
issn = {2000-2297},
abstract = {BACKGROUND/OBJECTIVE: Oral squamous cell carcinoma (OSCC) in patients without tobacco, alcohol, or betel-quid habits is poorly understood and difficult to detect early. This study aimed to identify microbial biomarkers specific to this habit-free population using third-generation sequencing (TGS).

Twenty-seven habit-free OSCC patients were recruited at National Taiwan University Hospital (NTUH). Paired tumor and adjacent normal tissues were collected with informed consent and NTUH Research Ethics Committee approval (IRB 201902080RINC, 201304078RIND). Full-length 16S rRNA sequencing (PacBio Sequel IIe) was processed with DADA2 and SILVA. Biomarkers were identified using sparse partial least squares discriminant analysis (sPLS-DA) and random forest with cross-validation, and validated against three public OSCC cohorts.

RESULTS: A three-species panel-Eikenella corrodens, Slackia exigua, and Eggerthia catenaformis-discriminated tumor from normal tissues (AUC = 0.905 training; 0.733 testing). Functional and network analyses showed tumor-enriched taxa forming pro-inflammatory clusters linked to lipid and glutamine metabolism, while commensals correlated with homeostatic pathways. Cross-cohort comparison confirmed this panel's specificity to habit-free OSCC.

CONCLUSIONS: Using TGS, we revealed distinct microbial signatures in habit-free OSCC that may aid early diagnosis and underscore the role of microbiome-host interactions in carcinogenesis.},
}

@article {pmid41050878,
year = {2025},
author = {Chetty, C and Mafunda, N and Happel, AU and Khan, A and Cooley Demidkina, B and Yende-Zuma, N and Saidi, Y and Mahabeer Polliah, A and Lewis, L and Osman, F and Radebe, P and Passmore, JS and Kwon, D and Ravel, J and Ngcapu, S and Liebenberg, L and Symul, L and Holmes, S and Mitchell, CM and Potloane, D},
title = {Randomized trial of multi-strain Lactobacillus crispatus vaginal live biotherapeutic products after antibiotic therapy for bacterial vaginosis: study protocol for VIBRANT (vaginal lIve biotherapeutic RANdomized trial).},
journal = {Contemporary clinical trials communications},
volume = {48},
number = {},
pages = {101554},
pmid = {41050878},
issn = {2451-8654},
abstract = {BACKGROUND: Globally, approximately 30 % of women have bacterial vaginosis (BV). Antibiotic treatment is frequently followed by recurrence, likely due to lack of colonization with beneficial lactobacilli.

METHODS: This is a Phase 1, randomized, placebo-controlled trial of vaginal live biotherapeutic products (LBP) after antibiotic treatment for BV to establish Lactobacillus colonization. The LBP are vaginal tablets containing 6 L. crispatus strains (LC106) or 15 L. crispatus strains (LC115), at 2 x 10[9] colony forming units (CFU) per dose. Participants with BV in the United States and South Africa will receive seven days of oral metronidazole twice daily and will be randomized 1:1:1:1:1 to: seven days placebo; seven days LC106; three days LC106/four days placebo; seven days LC106 starting day 3 of the metronidazole course; or seven days LC115. Safety will be assessed by the number and percentage of ≥ Grade 2 related adverse events during or after product use. The primary outcome is LBP colonization defined as relative abundance ≥5 % of any LBP strain or ≥10 % of a combination of LBP strains by metagenomic sequencing any time in the 5 weeks after randomization. A generalized linear model will measure the association between treatment group and colonization, adjusting for site.

CONCLUSIONS: This study seeks to establish proof of concept for a multi-strain LBP to promote vaginal L. crispatus colonization in two geographically distinct populations.

TRIAL REGISTRATION: South African National Clinical Trials Registry (SANCTR DOH-27-102023-8342; October 27, 2023) and ClinicalTrials.gov (NCT06135974; November 11, 2023).

PROTOCOL VERSION: 2.0 dated October 03, 2023.},
}

@article {pmid41050755,
year = {2025},
author = {Wang, L and Zhang, J and Zhang, M and Xu, Z and Zheng, Y and Lv, B and Pan, M},
title = {Insights into the alteration of vaginal microbiota and metabolites in pregnant woman with preterm delivery: prospective cohort study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1580801},
pmid = {41050755},
issn = {2235-2988},
mesh = {Female ; Humans ; Pregnancy ; *Vagina/microbiology/metabolism ; *Premature Birth/microbiology ; Prospective Studies ; Adult ; *Microbiota ; *Bacteria/classification/isolation & purification/metabolism/genetics ; Metabolomics ; Young Adult ; },
abstract = {Disruptions in vaginal microbiota and metabolites during pregnancy may be the most important risk factor for preterm delivery, thus the difference in vaginal microbiota and metabolites between women who subsequently delivered at term and who eventually experienced preterm birth. In this study, 63 participants were enrolled before the cervical cerclage surgery (namely pre-cerclage), comprising women who subsequently delivered at term and who eventually experienced preterm birth. The cervical-vaginal fluid (CVF) was collected two days prior to the cervical cerclage surgery. Compared with the term birth groups (PrTG), the proportion of beneficial bacteria (Lactobacillus, Prevotella, Trichococcus, Neisseria and Gemella) in the preterm birth group (PrPG) were significantly reduced (p < 0.05), while the proportion of harmful bacteria (Thauera, Ochrobactrum, Gardnerella, Massilia, Phyllobacteriaceae and Atopobium) were significantly increased (p < 0.05). In addition, vaginal metabolomics-based LC-Orbitrap-MS/MS revealed that the contents of 2-Piperidone, Melphalan, N-acetylputrescine, Obatoclax, Eurostoside, Pregnanediol 3-O-glucuronide, O-Phospho-L-serine, 1-Kestose and N-arachidonylglycine were significantly decreased in the PrPG group compared with the PrTG group, while Acenocoumarol, Isopyrazam, Pentosidine, hexose, 7-Hydroxymitragynine, PE, Tamoxifen and 1-Deoxynojirimycin contents were significantly increased. These results suggest that specific bacterial species and metabolites may serve as potential biomarkers for preterm birth prediction, and approve the theoretical basis for the intervention of preterm birth.},
}

Female
Humans
Pregnancy
*Vagina/microbiology/metabolism
*Premature Birth/microbiology
Prospective Studies
Adult
*Microbiota
*Bacteria/classification/isolation & purification/metabolism/genetics
Metabolomics
Young Adult

@article {pmid41050748,
year = {2025},
author = {Castellano, P and Ceccarani, C and Djusse, ME and Mazzetti, M and Morselli, S and Camboni, T and Conti, S and Prinelli, F and Severgnini, M and Foschi, C and Dall'Asta, M and Consolandi, C and Marangoni, A},
title = {Linking antibiotic resistance genes in the vaginal microbiota to health-related behaviors and antibiotic awareness in reproductive-age women: a cross-sectional study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1640992},
pmid = {41050748},
issn = {2235-2988},
mesh = {Humans ; Female ; Cross-Sectional Studies ; *Vagina/microbiology ; *Microbiota/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; Adult ; RNA, Ribosomal, 16S/genetics ; Young Adult ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Drug Resistance, Bacterial/genetics ; Adolescent ; DNA, Bacterial/genetics ; },
abstract = {INTRODUCTION: The vaginal microbiota (VMB), predominantly shaped by Lactobacillus species, plays a crucial role in maintaining vaginal health and preventing infections. However, its delicate balance is increasingly challenged by the widespread use of antibiotics and the consequent rise in antibiotic resistance genes (ARGs). While the VMB has been recognized as a potential reservoir for ARGs, limited research has explored how microbial composition, antibiotic exposure, and individual behavioral factors converge to shape the vaginal resistome.

MATERIALS AND METHODS: In this cross-sectional study, vaginal swabs were collected from 105 reproductive-age Caucasian women. The VMB composition was characterized and classified into Community State Types (CSTs), by sequencing the hypervariable V3-V4 regions of the bacterial 16S rRNA gene. In order to highlight common patterns of abundance among taxa, a co-abundance groups (CAGs) analysis was performed. We assessed the distribution of 14 ARGs conferring resistance to macrolides, tetracyclines, beta-lactams, and quinolones along with two associated transposons by means of PCR. An overall composite ARGs score was also calculated. Participants completed detailed questionnaires assessing demographics and behavioral factors, with a particular focus on both health- and antibiotic-related behaviors. Statistical analyses examined associations between ARG prevalence, vaginal microbiome composition and relevant exposures.

RESULTS: CSTs I and III were the most prevalent, with the most frequently detected ARGs being erm(F), tet(M), erm(B), erm(A), and tet(W), each present in over 65% of participants. ARG presence was positively correlated with a higher vaginal microbiome alpha-diversity. Moreover, BV-associated bacterial taxa showed strong associations with ARGs, while Lactobacillus species generally exhibited negative correlations. Smoking, a higher body mass index (BMI), presence of Candida spp. and a history of antibiotic use were significantly associated with increased ARG prevalence, whereas oral contraceptive use and higher diet quality scores were negatively associated. Correlating together the relative abundances of the microbial CAGs and the presence/absence of specific ARGs, we found a positive association between several genes related to macrolide and tetracycline resistance and the Gardnerella-Prevotella CAG. Additionally, the Gardnerella-Prevotella, and the Streptococcus CAGs were positively correlated to the total ARG score, whereas the L. crispatus/jenesenii/gasseri CAG was negatively correlated.

CONCLUSIONS: These findings underscore the role of the VMB as a dynamic reservoir of ARGs and highlight the influence of individual lifestyle and antibiotic-related behaviors on ARG dissemination in the vaginal niche. This supports the need for integrated public health strategies that combine antibiotic stewardship with targeted lifestyle and behavioral interventions, as well as the development of individualized therapeutic approaches.},
}

Humans
Female
Cross-Sectional Studies
*Vagina/microbiology
*Microbiota/genetics/drug effects
*Anti-Bacterial Agents/pharmacology
Adult
RNA, Ribosomal, 16S/genetics
Young Adult
*Bacteria/genetics/drug effects/classification/isolation & purification
*Drug Resistance, Bacterial/genetics
Adolescent
DNA, Bacterial/genetics

@article {pmid41050727,
year = {2025},
author = {Humphreys, LR and Lucas, JM and Spicer, ME},
title = {Canopy Height and Epiphytic Bryophytes Shape Fungal Communities in a Temperate Rainforest.},
journal = {Ecology and evolution},
volume = {15},
number = {10},
pages = {e72241},
pmid = {41050727},
issn = {2045-7758},
abstract = {Fungal communities contribute to plant ecology and evolution in forested ecosystems. Their diverse interactions with associated host plants can vary along abiotic and biotic gradients, but these gradients are poorly understood in complex natural ecosystems. Given the high diversity of epiphytic plants in many ecosystems, forest canopies offer a unique and underexplored system for studying plant-associated microbial diversity and distribution. We explored both abiotic and biotic factors structuring arboreal fungal communities. Specifically, we hypothesized that bryophyte-associated fungal communities are structured by the vertical height gradient within host trees (from the ground to high in the canopy), vary across host plant species, and that living bryophytes host distinct fungal communities compared to dead bryophyte matter. To test these hypotheses, we sampled living and dead bryophytes (mosses and liverworts) across three different bryophyte host species and four heights, ranging from the forest floor to 18 m above the ground. We characterized the fungal community composition in each sample using metabarcoding. Fungal communities showed significant variation across substrates: bryophytes collected from the ground exhibited 17% greater Shannon diversity and 34% higher taxonomic richness than epiphytic bryophytes, while living bryophytes had 15% higher diversity and 30% greater richness than dead tissues. This pattern suggests that the diverse microhabitats within living bryophytes may drive microbial diversity. Community analysis identified a core fungal community across living bryophyte samples, but rare taxa accounted for a majority of reads, driving differences in community composition between different heights and bryophyte species. Synthesis: Epiphytic bryophyte-associated fungal communities show high heterogeneity across different substrates and heights, which provides insight into the structuring of the forest microbiome and epiphyte ecology. These results demonstrate the importance of exploring canopy-associated microbes to better understand microbial diversity and function in forest ecosystems.},
}

@article {pmid41050722,
year = {2025},
author = {Pfau, MJ and Weber, S and Kennedy, S and Krehenwinkel, H and Roderick, G and Gillespie, R},
title = {Invasive Spiders and Their Microbiomes: Patterns of Microbial Variation in Native and Invasive Species in Hawai'i.},
journal = {Ecology and evolution},
volume = {15},
number = {10},
pages = {e72175},
pmid = {41050722},
issn = {2045-7758},
abstract = {Invasive species can have detrimental impacts on the community structure and native species persistence, causing cascading impacts on ecosystem function. These effects are amplified in remote island ecosystems that are characterized by non-representative and often diverse biota. The mechanisms behind successful invasions, particularly of arthropods, are varied, but growing evidence suggests that invasive species escape from their native predators and competitors. Recent research has suggested that gut microbiota can play an important role in arthropod fitness, with vertically transmitted endosymbionts and horizontally acquired microbes performing different functions. Here, we explored the extent to which the microbiome may facilitate the ability of spiders to exploit and ultimately adapt to novel environments. We examined co-occurring pairs of native and invasive spiders across three locations in the Hawaiian Islands and compared them with mainland counterparts to test two core predictions: (1) gut microbiota would be shaped primarily by local environmental filters rather than invasion status, and (2) vertically transmitted endosymbionts would show stronger host-specificity and reduced diversity in invasives. Using 16S rRNA amplicon sequencing, we found that the site explained 11.7% of gut-microbial compositional variance compared to 6.5% for host species. These results suggest that each spider maintains a species-specific level of α-diversity but reassembles taxonomic composition according to local microbial pools, thus indicating high context dependence in environmental filtering. Invasive species were found to have a lower relative abundance of gut endosymbiont taxa, with one species, Badumna longinqua, showing little to no endosymbiont presence across sites, and the other, Steatoda grossa, exhibiting low but site-specific abundance. We observed a strong localization effect, suggesting that these endosymbionts are also being acquired from local environments, not carried from ancestral ranges. These results suggest host-symbiont interactions have differential impacts on native and invasive species and that microbiota may facilitate the success of spiders in novel environments.},
}

@article {pmid41050671,
year = {2025},
author = {Duan, H and Xu, B and Luo, P and Chen, T and Zou, J},
title = {Microbial metabolites and their influence on the tumor microenvironment.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1675677},
pmid = {41050671},
issn = {1664-3224},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Neoplasms/immunology/metabolism/therapy/microbiology ; Animals ; Immunotherapy ; *Microbiota/immunology ; Fatty Acids, Volatile/metabolism ; },
abstract = {While tumor immunotherapy has achieved remarkable progress in many hematological malignancies, its efficacy remains limited by key challenges, including the immunosuppressive microenvironment of solid tumors, metabolic abnormalities, and drug resistance. As a central mechanism underlying impaired immune function, metabolic reprogramming of immune cells has emerged as a pivotal focus for unraveling tumor immune evasion and therapeutic resistance. Advances in metagenomics have highlighted the significance of the human commensal microbiome as a 'second genome.' Microbial metabolites, whether circulating systemically or accumulating locally, serve as key messengers linking the microbiota to tumor immunometabolism. This review comprehensively examines the regulatory roles and metabolic mechanisms through which microbial metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan metabolites, and lipopolysaccharides (LPS)-modulate tumor immunity and immunotherapeutic responses via immune cell metabolism. These metabolites shape the tumor immune microenvironment and influence immunotherapeutic efficacy by reprogramming immune cell metabolic and biosynthetic pathways. This review underscores the central regulatory role of microbial metabolites as the 'second genome' in tumor immunometabolism, offering a theoretical foundation and potential targets to elucidate mechanisms of immunotherapeutic resistance and advance microbiota metabolism-based precision interventions.},
}

Humans
*Tumor Microenvironment/immunology
*Neoplasms/immunology/metabolism/therapy/microbiology
Animals
Immunotherapy
*Microbiota/immunology
Fatty Acids, Volatile/metabolism

@article {pmid41050662,
year = {2025},
author = {Wierzbińska, W and Kuźmycz, O and Kowalczyk, A and Stączek, P},
title = {The role of dysbiosis in shaping host immunity in endometrial cancer development.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1627285},
pmid = {41050662},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Endometrial Neoplasms/immunology/microbiology/pathology/etiology ; Female ; Tumor Microenvironment/immunology ; Animals ; Microbiota/immunology ; Carcinogenesis/immunology ; },
abstract = {In recent years, research into the background of carcinogenic processes has increasingly focused on the role of the tumor microenvironment (TME) in tumorigenesis. In addition to the presence of tumor cells and non-malignant components, which include immune cells, extracellular matrix elements, stroma, and endothelial cells, the microbiome is now increasingly being classified as an integral part of the TME. The establishment of the Human Microbiome Project (HMP) in 2007 along with the development of next-generation sequencing (NGS) techniques proved to be a breakthrough in terms of human microbiota research, shedding new light on the existing knowledge of microorganisms inhabiting various niches of the human body and their functions. Emerging scientific evidence from preclinical and clinical studies indicates significant differences in the microbiome composition between tumor tissues and benign controls. The presence of specific pathogenic strains within a tissue may play a key role in the initiation and progression of inflammation, which not only may be directly responsible for the stimulation of tumorigenic processes but may also affect the destabilization of the host genome, causing significant disruption of its metabolism. The role of microorganisms in the induction and promotion of pathological processes, including cancer, has been confirmed in many studies to date. Recent years of research on the microbiota of the female reproductive tract (FRT) have not only indicated that the endometrium has its unique microbial composition but have also made it possible to point out differences in composition between the microbiome of healthy and tumor-lesioned tissue, suggesting a potential role for dysbiotic disorders in the pathogenesis of endometrial cancer (EC). In this review, we aim to highlight the complex interplay between bacterial interactions and host immunity, and how this phenomenon contributes to the development and progression of endometrial cancer.},
}

Humans
*Dysbiosis/immunology/microbiology
*Endometrial Neoplasms/immunology/microbiology/pathology/etiology
Female
Tumor Microenvironment/immunology
Animals
Microbiota/immunology
Carcinogenesis/immunology

@article {pmid41050659,
year = {2025},
author = {Almansour, N and Al-Rashed, F and Choudhry, K and Alqaderi, H and Sindhu, S and Al-Mulla, F and Ahmad, R},
title = {Gut microbiota: a promising new target in immune tolerance.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1607388},
pmid = {41050659},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Immune Tolerance ; Animals ; Dysbiosis/immunology ; },
abstract = {Gut microbiota research has highlighted its pivotal role in human health and disease. Its composition is shaped by diet, genetics, age, and environmental factors. When the balance of these microbes is disrupted (dysbiosis), it can contribute to health problems like metabolic, inflammatory, and mental disorders. The microbiota supports digestion, fermentation, and vitamin production, which are essential for overall health. The gut microbiota has emerged as a critical modulator of immune function, with increasing evidence highlighting its role in establishing and maintaining immune tolerance. Despite significant advances in understanding the interactions between the gut microbiome and immune system, gaps remain in the literature regarding the specific mechanisms through which microbiota influences immune tolerance. This review aims to address these knowledge gaps by synthesizing current research on the microbiota impact on immune tolerance, emphasizing key factors such as microbial diversity, metabolic byproducts, and the microbiota interaction with immune cells, specifically focusing on the role of microbial tryptophan metabolites in PD-1/PD-L1 tolerance. We also highlight critical areas for future research, including the identification of microbial species or strains that can modulate immune tolerance, the influence of diet and environmental factors on microbiota composition, and the development of microbiota-based therapies. By bridging these gaps, this review seeks to provide a comprehensive understanding of the mechanistic role of microbiota immune tolerance and its potential as a novel therapeutic target for autoimmune and inflammatory diseases.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Immune Tolerance
Animals
Dysbiosis/immunology

@article {pmid41050155,
year = {2025},
author = {Widjaja, N and Agustina, C and Felicia, F and Wijaya, F and Limanjaya, J and Yulandi, A and Waturangi, DE and Simatupang, ST and Tan, S and Tjandrawinata, RR},
title = {Gut microbiome in adult Asians with obesity, type 2 diabetes mellitus, and a combination of obesity and type 2 diabetes mellitus.},
journal = {Bioscience of microbiota, food and health},
volume = {44},
number = {4},
pages = {251-260},
pmid = {41050155},
issn = {2186-6953},
abstract = {Obesity and type 2 diabetes (T2D) are two of the most common health problems in the world, particularly in adult Asians, with a significant impact on morbidity and mortality. Numerous studies have revealed that the gut microbiome of people with obesity and T2D differs significantly from those of healthy people. Those who suffer from certain illnesses often encounter disruption in their gut microbiome, leading to a decrease in richness diversity and diminished microbial activity. This disruption can also result in the loss of the gut mucosal barrier, increased gut permeability, and most likely, the development of a leaky gut. Recent studies have also emphasized the essential role of the gut microbiome in these conditions. However, conflicting findings were found between one study and another investigation. Therefore, this paper aims to provide an overview of gut microbiome characteristics in adult Asians with obesity, T2D, and the combination of both. In addition, this paper elaborates on the current understanding regarding the association of the gut microbiome with health status, thereby serving as a foundation for developing probiotics or prebiotics to modulate the gut microbiome and improve metabolic health.},
}

@article {pmid41049923,
year = {2025},
author = {Pedraza, A and Bonnice, S and Won, MN and Kesselman, MM and Demory Beckler, M},
title = {Impact of COVID-19 on the Gut Microbiome: A Review.},
journal = {Cureus},
volume = {17},
number = {9},
pages = {e91470},
pmid = {41049923},
issn = {2168-8184},
abstract = {Coronavirus Disease 2019 (COVID-19) has resulted in over 6 million deaths worldwide in fewer than four years and is a result of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The protein that mediates SARS-CoV-2 host cell entry is the angiotensin-converting enzyme 2 (ACE2), which is highly expressed on the membrane of gastrointestinal (GI) cells. Consequently, infection can lead to direct damage to the GI tract and gut dysbiosis, which is associated with an imbalance of microbiota, inflammation, and other systemic infections and diseases. In this review, we will focus on the impact of COVID-19 on the GI system. We will examine the pathophysiology of gut dysbiosis in COVID-19 patients, as well as emphasize the significance of probiotics in addressing this condition. Additionally, we will identify key areas of interest that warrant further investigation.},
}

@article {pmid41049881,
year = {2025},
author = {Nazari, H and Meibodi, AE and Bassami, M and Olfatifar, M and Yadegar, A},
title = {Association of Gut Microbiota With Performance Level Among Iranian Professional and Semi-Professional Runners: A Cross-Sectional Study.},
journal = {Health science reports},
volume = {8},
number = {10},
pages = {e71319},
pmid = {41049881},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: The gut microbiota is a diverse ecosystem with the potential to significantly enhance athletic metabolic capacity. Emerging research indicates that the gut microbiota plays a crucial role in modulating energy metabolism, immune function, oxidative stress, skeletal muscle dynamics, and neuroendocrine regulation, all of which are essential for optimizing athletic performance. This study investigates the composition of a selection of gut microbiota among Iranian professional and semi-professional runners from three different disciplines including endurance, middle-distance, and speed runners, and examines their association with performance levels.

METHODS: Fresh stool samples of 60 runners were collected and the relative abundance of a selection of intestinal microbiota at various taxonomic levels was assessed by RT-qPCR. The relative abundance of the selected microbiota revealed distinct patterns across different types of runners.

RESULTS: Predominant taxa in professional groups were Bacteroidetes, Firmicutes, and Prevotella spp., while semi-professional groups had a higher abundance of Firmicutes, Bacteroidetes, Actinobacteria, Clostridia, and Prevotella spp. Akkermansia muciniphila was mostly abundant among speed runners (40.95%), followed by endurance (27.025%) and middle-distance runners (23.525%). Fusobacterium nucleatum was more abundant in middle-distance (34.9%) and endurance runners (34.3%) compared to speed runners (22.3%). A negative correlation was found between performance levels and the abundance of Actinobacteria, Enterobacteriaceae, E-proteobacteria, Bifidobacterium spp., and Faecalibacterium prausnitzii, while a positive correlation was observed with Methanobrevibacter smithii.

CONCLUSION: This study illuminates the distinct microbial taxa detected in professional and semi-professional runners, which corroborates the relationship between running disciplines and the gut microbiota composition, as well as their impact on performance levels.},
}

@article {pmid41049590,
year = {2025},
author = {Vautier, RA and Sumners, EM and Raizada, MK and Pepine, CJ and Goel, R},
title = {The Gut Microbiome and Cardiac Arrhythmias.},
journal = {Federal practitioner : for the health care professionals of the VA, DoD, and PHS},
volume = {42},
number = {7},
pages = {264-269},
pmid = {41049590},
issn = {1078-4497},
abstract = {BACKGROUND: The relationship between the gut microbiome and overall human health is increasingly recognized. This review discusses new research that outlines pathways and intermediaries that may mediate the interaction between the gut microbiome and cardiac arrhythmias.

OBSERVATIONS: Gut microbial constituents and their products have been shown to influence human physiology, including the cardiovascular system, cardiac arrhythmia, and other disease processes. The effect of the human gut microbiome on cardiovascular diseases may improve understanding of disease pathophysiologic mechanisms and presents opportunities for therapeutic modification of the gut microbiome to positively affect disease outcomes.

CONCLUSIONS: Research into the gut microbiome and its overarching impact on the human body is still in its early stages. Continued investigation of its complex relationships may lead to the development of novel therapies and strategies to enhance patient safety.},
}

@article {pmid41049561,
year = {2025},
author = {Raspet, I and Gehret, E and Herman, C and Meilander, J and Manley, A and Simard, A and Bolyen, E and Caporaso, JG},
title = {Facilitating bootstrapped and rarefaction-based microbiome diversity analysis with q2-boots.},
journal = {F1000Research},
volume = {14},
number = {},
pages = {87},
pmid = {41049561},
issn = {2046-1402},
mesh = {*Microbiota ; *Software ; Humans ; Biodiversity ; *Computational Biology/methods ; },
abstract = {BACKGROUND: We present q2-boots, a QIIME 2 plugin that facilitates bootstrapped and rarefaction-based microbiome diversity analysis. This plugin provides eight new actions that allow users to apply any of thirty different alpha diversity metrics and twenty-two beta diversity metrics to bootstrapped or rarefied feature tables, using a single QIIME 2 Pipeline command, or more granular QIIME 2 Action commands.

RESULTS: Given a feature table, an even sampling depth, and the number of iterations to perform (n), the command qiime boots core-metrics will resample the feature table n times and compute alpha and beta diversity metrics on each resampled table. The results will be integrated in summary data artifacts that are identical in structure and type to results that would be generated by applying diversity metrics to a single table. This enables all the same downstream analytic tools to be applied to these tables and ensures that all collected data is considered when computing microbiome diversity metrics.

CONCLUSIONS: A challenge of this work was deciding how to integrate distance matrices that were computed on n resampled feature tables, as a simple average of pairwise distances (median or mean) does not account for the structure of distance matrices. q2-boots provides three options, and we show here that the results of these approaches are highly correlated. q2-boots is free and open source. Source code can be found at https://github.com/caporaso-lab/q2-boots; installation instructions and a tutorial can be found in the project's documentation at https://q2-boots.readthedocs.io.},
}

*Microbiota
*Software
Humans
Biodiversity
*Computational Biology/methods

@article {pmid41049463,
year = {2025},
author = {Zhang, H and Tang, Y and Ge, H and Tong, H and Yang, L and Zhang, T and Han, C and Liu, C},
title = {Sodium alginate supplementation can alleviate non-alcoholic fatty liver disease in rats by restoring hepatic lipid metabolism and gut microbiota.},
journal = {Current research in food science},
volume = {11},
number = {},
pages = {101199},
pmid = {41049463},
issn = {2665-9271},
abstract = {Nonalcoholic fatty liver disease (NAFLD) is a highly prevalent metabolic disorder with no approved pharmacological treatments. Several studies indicate that sodium alginate (SA) may hold promising potential in the treatment of NAFLD. However, whether SA can serve as a viable therapeutic dietary intervention for NAFLD remains unclear. Therefore, the current study aimed to explore whether supplementing with SA can alleviate NAFLD by regulating liver lipid metabolism via the gut microbiota. We used histopathology analysis, serum biochemistry assays, and scanning electron microscopy to assess the therapeutic effects of SA against NAFLD. Microbiome analysis, quantification of short-chain fatty acids, and liver lipidomics were further performed to elucidate the mechanisms underlying these therapeutic effects. Our results showed that SA significantly mitigated body fat deposition, hyperlipidemia and liver injury in rats fed with the high-fat and high-cholesterol diet (HFHCD). Additionally, SA supplementation remodeled the HFHCD-induced imbalance in gut microbiota. SA treatment substantially increased the abundance of butyrate-producing bacteria, reduced lipid metabolites associated with liver steatosis, promoted glycerophospholipid metabolism, and regulated several lipid metabolism-related signaling pathways. It also restored the imbalanced expression of the sterol regulatory element-binding protein-1c (SREBP-1c), acetyl-CoA carboxylase (ACC), fatty acid synthase (FAS), stearoyl-CoA desaturase 1 (SCD1), and carnitine palmitoyltransferase 1 (CPT1) in HFHCD-fed rats. Taken together, our results show that SA supplementation can potentially be used as a therapeutic dietary intervention for alleviating NAFLD. In addition, our findings provide a theoretical foundation for the development of SA as a nutraceutical raw agent.},
}

@article {pmid41049421,
year = {2025},
author = {Yan, J and Zhao, J and Naizemuding, P and Zhao, W and Sun, J and Wang, Y and Yang, J and Li, D and Zhang, F and Cao, H},
title = {Unraveling the Anti-Obesity Potential of White Kidney Bean α-Amylase Inhibitors: Mechanistic Insights From Enzyme Kinetics to Gut Microbiota Modulation.},
journal = {Food science & nutrition},
volume = {13},
number = {10},
pages = {e71043},
pmid = {41049421},
issn = {2048-7177},
abstract = {The global rise in obesity, driven largely by excessive carbohydrate consumption, highlights the demand for innovative dietary interventions targeting starch digestion. This study investigates the anti-obesity effects of α-amylase inhibitors (α-AI) extracted from white kidney beans, employing a multidisciplinary strategy encompassing botanical screening, enzyme kinetics, clinical trials, and gut microbiota profiling. Among 10 varieties evaluated, the A10 strain from Jilin Province demonstrated the highest α-AI activity, characterized by noncompetitive inhibition that remains effective across varying starch concentrations. In an 8-week randomized controlled trial, α-AI supplementation significantly reduced body weight, BMI, waist circumference, and hip circumference compared to placebo. Further, 16S rRNA sequencing revealed dual mechanisms: enrichment of SCFA-producing bacteria (e.g., Bifidobacterium and Bacteroides ovatus) and modulation of microbial lipid metabolic pathways. These results highlight α-AI as a dual-action anti-obesity agent, combining direct enzymatic inhibition with microbiome-mediated metabolic effects. By bridging phytochemical characterization with clinical outcomes, this work proposes a novel therapeutic approach that simultaneously targets carbohydrate absorption and gut microbial ecology, supporting the development of standardized α-AI formulations as potential nutraceuticals for metabolic syndrome.},
}

@article {pmid41049070,
year = {2025},
author = {Liu, Z and Jiang, Y and Fan, Q and Li, S and Wang, Y},
title = {The Role of Butyric Acid and Microorganisms in Chronic Inflammatory Diseases and Microbiome-Based Therapeutics.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {13465-13487},
pmid = {41049070},
issn = {1178-7031},
abstract = {Butyric acid, produced by gut microbiota fermentation, has gained significant attention over the past decade. It shows strong therapeutic potential in both experimental and clinical treatments for inflammatory diseases across multiple systems. However, factors such as the host's environment, genetics, and microbial lineage transmission influence gut microecology and butyric acid metabolism, resulting in variable and sometimes opposing, therapeutic effects. Consequently, precise personalized medicine is essential for diseases related to microbes and butyric acid. This review first introduces the fundamentals of butyric acid, focusing on its immune mechanisms and its effects on early-life microbiota. It then summarizes how microbes and butyric acid contribute to the treatment of systemic inflammatory diseases (eg, autoimmune diseases (AIDs), asthma, metabolic syndrome) and discusses the concept of Microbial Precision Therapy (MPT). Understanding butyric acid provides deeper insight into managing inflammatory diseases and supports precise medication and personalized therapy. This approach may offer more effective and safer strategies for multi-system inflammatory disorders.},
}

@article {pmid41048701,
year = {2025},
author = {Swaney, MH and Newman, DJ and Mao, J and Hilton, AC and Worthington, T and Li, M},
title = {Aging-dependent skin microbiome alterations across body sites in a United Kingdom cohort.},
journal = {Frontiers in aging},
volume = {6},
number = {},
pages = {1644012},
pmid = {41048701},
issn = {2673-6217},
abstract = {INTRODUCTION: The aging process profoundly influences not only the health and visual appearance of the skin, but also the composition of the microbial communities residing on its surface.

METHODS: To investigate these microbial changes, we employed a comprehensive, multi-scale approach that probes community composition, species interactions, and predicted metabolic function of the skin microbiome of the face and forearm in young and old age individuals from the United Kingdom using 16S rRNA gene sequencing.

RESULTS: Our findings revealed significant and site-specific age-related shifts in the microbiome involving diversity, interpersonal heterogeneity, network connectivity, and metabolic potential, suggesting loss of microbiome robustness and a shift towards a hyperdiversified, fragile microbial community in old age. Furthermore, we applied Dirichlet Multinomial Mixtures to uncover novel age-driven microbiome profiles unique across each skin site, highlighting Cutibacterium acnes, Staphylococcus hominis, and microbial community diversity as key differentiating biomarkers of the skin microbiome across the lifespan.

DISCUSSION: Overall, through examining the aging skin microbiome from a systems perspective, our study reinforces and enhances the findings from previous aging microbiome studies and underscores the importance of site-specific differences in skin microbiome dynamics with age. These insights suggest that microbial interventions could mitigate age-related changes, enhancing skin health and wellbeing throughout life.},
}

@article {pmid41048671,
year = {2025},
author = {Vander Donck, L and Gehrmann, T and Ahannach, S and Van den Bosch, S and Hiel, M and Delanghe, L and Allonsius, CN and Cauwenberghs, E and Spacova, I and Oerlemans, E and Wittouck, S and De Boeck, I and Donders, G and Verhoeven, V and Lebeer, S},
title = {The female intimate microbiome space.},
journal = {npj women's health},
volume = {3},
number = {1},
pages = {55},
pmid = {41048671},
issn = {2948-1716},
abstract = {Despite its importance in health, the female intimate skin microbiome remains understudied. In this Isala study we explored microbial dispersal across intimate body sites, including the vagina, groins, breast and mouth. Microbial similarity correlated with physical proximity, suggesting dispersal influenced by hygiene or sexual activity. Notably, lactobacilli were unexpectedly abundant on breast skin. These findings highlight the need for research into microbiome dynamics and their implications for women's health.},
}

@article {pmid41048510,
year = {2025},
author = {Mieremet, A and van der Wurff, M and Pagan, L and Ferrer-González, E and Seo, J and Schuren, FHJ},
title = {Taxonomic and functional profiling of the vulvar microbiome indicates variations related to ecological signatures, aging, and health status.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1633147},
pmid = {41048510},
issn = {1664-302X},
abstract = {INTRODUCTION: The vulvar microbiome is adjacent to that of the skin and the vagina and connects microbiomes present on a stratified epithelial barrier to that of a mucosal barrier. Yet, the characterization of the microbiome in the vulvar region of the body is understudied, although dysbiosis in the microbiome of the skin or vagina have been linked to impairments in women's health.

METHODS: To better understand the role of the vulvar microbiome during healthy aging or during presentation of vulvar diseases, we analyzed the vulvar microbiome by shotgun metagenomic sequencing on composition at species level and for functional capacity. This was performed in a large population enrolled in the Vulvar Microbiome Leiden Cohort (VMLC), including a total of 58 healthy women in a broad age range (22-82 years). Moreover, we analyzed vulvar microbiome derived from 9 participants presenting a vulvar disease, including vulvar lichen sclerosus (LS; N = 6), or high-grade squamous intraepithelial lesion (HSIL; N = 3).

RESULTS: Compositional analyses showed a skin-, vagina-, or multispecies mixture- dominant bacterial signature, which revealed differences in the alpha diversity and functional capacity of the microbiome. Upon aging the presence of Lactobacillus iners, L. crispatus, and L. gasseri in the vulvar microbiome shifted toward reduction. In the microbiome of individuals with a vulvar disease, higher abundance of Staphylococcus hominis, Micrococcus luteus, Corynebacterium amycolatum, and Corynebacterium simulans was detected, and an altered functional capacity for the L-histidine pathway.

DISCUSSION: In conclusion, we identified variations in microbial taxa and functional capacities in the vulvar microbiome that are associated with age and disease (LS and HSIL), which can be targeted to develop microbiome-based vulvar therapies promoting women's health.},
}

@article {pmid41048507,
year = {2025},
author = {Fu, X and Yu, H and Li, Y and Li, G and Bi, X and Li, Y and Hu, F and Dong, W},
title = {Geographic variation in fungal diversity associated with leaf spot symptoms of Coffea arabica in Yunnan, China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1568029},
pmid = {41048507},
issn = {1664-302X},
abstract = {In China, the small grain coffee plants (Coffea arabica) are mainly cultivated in Yunnan province, yet the diversity of associated fungi remains poorly characterized. In this study we collected symptomatic leaves from 16 locations across Pu'er City and Xishuangbanna Dai Autonomous Prefecture (n = 48 samples, triplicate controls). Fungal communities were analyzed via ITS amplicon sequencing (Illumina MiSeq). We identified 3,638 fungal OTUs, dominated by Ascomycota (92%), including pathogens (Colletotrichum gloeosporioides, Cercospora coniogrammes), saprophytes, and beneficial entomopathogens (Lecanicillium, Simplicillium). The fungal communities showed significant geographical variation, with Pu'er City exhibiting a higher relative abundance of pathogenic fungi such as Colletotrichum gloeosporioides and Cercospora coniogrammes, while Xishuangbanna had a greater presence of beneficial entomopathogenic fungi such as Lecanicillium and Simplicillium. We classified abundant fungal OTUs into 48 different species colonizing leaves of coffee plants. Our core microbiome analysis revealed the presence of Cercospora coniogrammes (2%), the Fusarium equiseti of Nectriaceae family (5%), and the novel pathogenic fungi Colletotrichum gloeosporioides and Cercospora coniogrammes. Interestingly, we also identified the anti-phytopathogenic fungi belonging to the genus Simplicillium (9%) and entomopathogenic fungi known as lecanicillium (11%). This first report of C. coniogrammes and C. gloeosporioides in Yunnan coffee highlights the need for region-specific disease management. The prevalence of entomopathogenic fungi in Xishuangbanna suggests untapped biocontrol potential. Our data provide a foundation for monitoring leaf-associated fungi to improve crop resilience.},
}

@article {pmid41048504,
year = {2025},
author = {Ai, X and Huang, C and Liu, Q and Duan, R and Ma, X and Li, L and Shu, Z and Miao, Y and Shen, H and Lv, Y and Jiang, Z and Luo, H and Long, Z},
title = {Gut microbiome dynamics and functional shifts in healthy aging: insights from a metagenomic study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1629811},
pmid = {41048504},
issn = {1664-302X},
abstract = {INTRODUCTION: Population aging represents a significant challenge in contemporary society. The gut microbiome plays a critical role in maintaining host health and physiological functions, and its alterations with advancing age are closely associated with the process of healthy aging.

METHODS: This study conducted a comprehensive analysis of the gut microbiome in hundred healthy elderly individuals (aged ≥60) residing in Changshou Town, Zhongxiang City, Hubei Province, utilizing metagenomic sequencing technology. The primary objective was to investigate the changes in the gut microbiome and its potential functions during the latter stages of life. Participants were categorized into three distinct age groups: the Young-Old group (YO, ages 60-74), the Middle-Old group (MO, ages 75-89), and the Long-Lived Old group (LO, ages 90-99).

RESULTS: The findings indicate that the diversity of the gut microbiome tends to diminish with age. However, a significant reversal was observed among healthy longevity elderly individuals. Our analysis specifically focused on the trends in the alterations of gut microbiome species and their potential functions as age increases, revealing that the changes in major differential functions closely align with the trends in major differential species, demonstrating a strong positive correlation. The YO group exhibited a more diverse array of differential microbial characteristics and functional traits. Notably, there was a significant enrichment of Bacteroides stercoris in the YO group, which displayed a continuous decline with age, alongside a marked enrichment of pathways associated with xenobiotic biodegradation and metabolism. Furthermore, species significantly linked to aging-related pathways, such as oxidative phosphorylation, were identified through species functional correlation analysis. Specifically, Collinsella bouchesdurhonensis and Prevotella stercorea were enriched in the LO and YO groups, respectively. In total, we successfully obtained two hundred and thirty eight high-quality bins through metagenomic assembly, which included the identification of four species with 100% completeness, as well as the genomic information of the Methanobrevibacter smithii A across all groups.

DISCUSSION: This study characterizes the age-associated trends in gut microbiome composition and function during later-life healthy aging, providing exploratory insights that may inform future microecological intervention strategies, pending validation in longitudinal studies.},
}

@article {pmid41048500,
year = {2025},
author = {Sabater, C and Neacsu, M and Duncan, SH},
title = {Harnessing beneficial soil bacteria to promote sustainable agriculture and food security: a one health perspective.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1638553},
pmid = {41048500},
issn = {1664-302X},
abstract = {Harnessing beneficial soil bacteria for use in agricultural practices offers an exciting and promising pathway to achieving sustainable farming. Soil microbes, including bacteria and fungi, play a pivotal role in nutrient cycling, enhancing soil structure, and promoting plant growth. Certain plant growth-promoting bacteria, such as Bacillus and Paenibacillus species, are particularly notable for their ability to improve nutrient uptake, suppress pathogens, and enhance plant resilience to environmental stress. By employing these natural bacterial species, farmers can rely less on chemical fertilisers and pesticides, helping the environment and improving soil health. Moreover, soil bacteria may possess potent enzymes systems for breaking down complex carbohydrates, so that the simpler sugars can be used to nourish plants. Genome mining of soil representatives can be used to design novel consortia of soil bacteria (including Paenibacillus odorifer, P. xylanilyticus and Streptococcus cellostaticus) to cover the maximum number of complementary enzyme activities acting on cellulosic and hemi cellulosic materials. Similarly, the combination of these strains and Arthobacter humicola could be of great interest to maximize the metabolisation of lignocellulosic substrates and to reduce and re-valorise food waste from the food production cycle. Soil bacteria play a pivotal role in advancing One Health by mediating interactions across human, animal, and environmental health. Future research and development should focus on optimizing microbial delivery to different soils and also understanding the complex interactions within the soil microbiome to maximize their benefits in diverse farming systems.},
}

@article {pmid41048499,
year = {2025},
author = {Lyu, L and Shi, J and Gao, P and Cai, Z and Li, F},
title = {EM biofertilizer and organic fertilizer co-application modulate vegetation-soil-bacteria interaction networks in artificial grasslands of alpine mining regions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1659475},
pmid = {41048499},
issn = {1664-302X},
abstract = {To address vegetation establishment challenges caused by poor soil in the alpine mining areas of the Qinghai-Tibet Plateau. Through three-year field experiments, this study systematically investigated the effects of combined EM microbial fertilizer and organic fertilizer application on vegetation community characteristics, soil physicochemical properties, and bacterial community diversity/functional structure in artificial grasslands of alpine mining areas. Key findings include: (1) The synergistic treatment of EM biofertilizer and organic fertilizer significantly improved the physical and chemical properties of soil and the characteristics of vegetation community. The Y2E2 treatment consistently enhanced vegetation community characteristics and soil physicochemical metrics in 2023 and 2024. Compared to the control (CK), it increased soil total nitrogen (TN) by 68.92 and 76.31%, reduced pH by 8.31 and 11.11%, and boosted biomass by 75.97 and 84.02%, confirming its efficacy in alleviating nutrient stress and promoting plant growth. (2) Microbiome analysis revealed that biofertilizer treatments significantly improved soil bacterial community structure. The Y2E2 and Y2E3 showed the highest OTU numbers (2,481 and 2,501 respectively). The Y2E3 increased relative abundance of Actinomycetota (+18.2%) and Acidobacteria (+12.7%) compared to CK (organic fertilizer 0.00 kg m[-2] + EM biofertilizer 0.00 kg m[-2]), while reducing Pseudomonadota (-14.3%). The Y2E2 improved Shannon (2.36%), Ace (6.44%), and Chao1 (5.05%) indices versus CK. Y1E1 exhibited 67.11% positive correlations in microbial co-occurrence networks. (3) Environmental drivers and functional activation: Mantel tests and RDA revealed soil electrical conductivity (SEC) and pH were negatively correlated with bacterial diversity indices (except Simpson). Other soil physical and chemical indexes and plant community indexes are positively correlated with soil bacterial diversity index except Simpson index. Soil pH emerged as the key driver of bacterial community construction. Combined fertilization neutralized alkalinity, activated manganese-oxidizing and photosynthetic microbes, while excessive application triggered heterotroph competition. In summary, the combined application of EM microbial fertilizer and organic fertilizer accelerates biomass accumulation in plant communities by regulating soil pH and improving the structure, function, and diversity of soil bacterial communities. These ecological processes involving plant-soil-microbe interactions expedite the restoration of ecological functions in artificial grasslands within alpine mining areas. Among the treatments, Y2E2 demonstrated the best performance, with an application rate of 600.00 kg of EM biofertilizer per hectare combined with 20.00 tons of organic fertilizer.},
}

@article {pmid41048498,
year = {2025},
author = {Pinos, A and Alonso-Alonso, P and Correa-Carmona, Y and Holzmann, KL and Yon, F and Brehm, G and Steffan-Dewenter, I and Peters, MK and Weinhold, A and Keller, A},
title = {Host identity, more than elevation, shapes bee microbiomes along a tropical elevation gradient.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1671348},
pmid = {41048498},
issn = {1664-302X},
abstract = {Understanding how host-microbiome interactions respond to abiotic and biotic factors is key to elucidating the mechanisms influencing ecological communities under current climate change scenarios. Despite increasing evidence that gut microbial communities associated with bees influence their health and fitness, including key roles in nutrient assimilation, toxin removal, defense against pathogens, and immune responses, the distribution of gut microbial communities and the dynamics of these associations along environmental gradients remain poorly understood. In this study, we assessed how environmental changes with elevation and host taxonomic identity influence the bacterial gut microbiome of wild bees collected along a 3,600 m elevation gradient in the Peruvian Andes. We applied DNA metabarcoding on the 16S rRNA region of gut samples from five bee tribes: Apini (honey bees), Bombini (bumble bees), Meliponini (stingless bees), Euglossini (orchid bees), and Halictini (sweat bees). Our findings indicate a general decrease in bacterial diversity and a high turnover of microbial taxa along the elevation gradient, with notable differences among host tribes. Host taxonomic identity was a strong predictor of gut microbial community composition, despite a high turnover of microbial and host taxa along the gradient. Within tribes, the turnover of microbial compositions was mainly explained by environmental changes with elevation in bumble and stingless bees. The observed variations in gut microbial diversity and composition at different elevations and different host taxa suggest that both factors significantly impact the gut microbiomes. As climate change continues to influence environmental conditions in the Andean-Amazonian forests it is crucial to consider how these changes may affect host-microbiome relationships. This highlights the necessity of understanding both abiotic and biotic factors in the context of climate change.},
}

@article {pmid41048436,
year = {2025},
author = {Jiang, H and Wang, X and Zhou, W and Huang, Z and Zhang, W},
title = {Gut microbiota dysbiosis in diabetic nephropathy: mechanisms and therapeutic targeting via the gut-kidney axis.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1661037},
pmid = {41048436},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology/therapy ; *Diabetic Nephropathies/microbiology/therapy/metabolism ; Animals ; *Kidney/metabolism/microbiology ; },
abstract = {Diabetic kidney disease (DKD) is the primary microvascular complication of diabetes and a leading cause of chronic kidney disease (CKD) and end-stage renal disease (ESRD) worldwide, with its prevalence on the rise. Recent evidence has highlighted the crucial involvement of gut microbiota (GM) dysbiosis in the pathogenesis and progression of DKD, mediated through the gut-kidney axis. At the core of this process is a dynamic network involving metabolic, immune, and barrier dysfunction. Renal impairment-such as that seen in uremia-disrupts gut microbial composition and metabolic function. In turn, dysbiosis compromises intestinal barrier integrity, resulting in increased exposure to endotoxins and a reduction in the production of beneficial metabolites, notably short-chain fatty acids (SCFAs). This triad manifests as: (1) impaired metabolism, marked by decreased SCFAs (e.g., acetate), which weaken anti-inflammatory and immunomodulatory effects, alongside an accumulation of uremic toxins like trimethylamine N-oxide (TMAO) that trigger inflammatory pathways and renal fibrosis; (2) immune dysregulation, where increased endotoxin translocation (e.g., lipopolysaccharide, LPS) provokes systemic inflammation, oxidative stress, and immune cell infiltration (such as macrophages), contributing to renal inflammatory and fibrotic responses; and (3) barrier dysfunction, in which compromised intestinal barrier accelerates the translocation of detrimental microbial components, perpetuating a vicious cycle that exacerbates glomerulosclerosis, tubular injury, and renal function decline.Collectively, metabolic, immune, and barrier alterations reinforce one another and drive DKD progression via gut-derived metabolites and immune activation. Targeted interventions aiming to modulate the GM-using probiotics, prebiotics, or synbiotics-show promise in improving metabolic profiles, restoring gut barrier function, and mitigating DKD phenotypes. This review systematically elucidates the metabolism-immunity-barrier mechanisms by which GM dysbiosis contributes to DKD and discusses the translational potential of microbiome-targeted therapies. Further studies are needed to validate these findings and assess their long-term clinical efficacy.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Dysbiosis/microbiology/therapy
*Diabetic Nephropathies/microbiology/therapy/metabolism
Animals
*Kidney/metabolism/microbiology

@article {pmid41048220,
year = {2025},
author = {Pereira, SMS and José, VPBS and da Silva, A and Martins, KVC and Leite, LB and Forte, P and Natali, AJ and Martino, HSD and Lucia, CMD and Bressan, J},
title = {Can physical exercise modify intestinal integrity and gut microbiota composition? A systematic review of in vivo studies.},
journal = {Biology of sport},
volume = {42},
number = {4},
pages = {13-28},
pmid = {41048220},
issn = {0860-021X},
abstract = {There is little evidence about how physical exercise affects the gut microbiota since studies in the field are relatively recent. Thus, we aimed to systematically review the main effects of regular physical exercise on the intestinal integrity and microbiota composition in animal models, discuss the mechanisms involved, and indicate future directions. Searches for original articles were performed in PubMed/MEDLINE, Scopus, Web of Science, and Embase. A total of 18 studies were selected. These studies suggest that physical exercise has a significant impact on the gut microbiota. Voluntary running increased the thickness of duodenal villi and microbiota diversity but reduced its richness. Low-intensity treadmill running increased the abundance of the phylum Actinobacteria and the family Bifidobacteriaceae, while that of moderate-intensity reduced the Bacteroides/Prevotella ratio. High-intensity swimming and treadmill running altered the gut microbiota, evidenced by β-diversity, and increased the Shannon and Chao indices but reduced short-chain fatty acids. Resistance exercise increased the Chao index and altered the functionality of the gut microbiota, increasing carbohydrate metabolism and reducing lipid and amino acid metabolism. Thus, regular physical exercise of different intensities and types can modify the gut microbiota, and the exercise benefits appear to be positively associated with training intensity.},
}

@article {pmid41048034,
year = {2025},
author = {Wright, SL and Abdul-Aziz, M and Blaha, GN and Ta, CK and Gancz, A and Ademola-Popoola, IJ and Szécsényi-Nagy, A and Sereno, PC and Weyrich, LS},
title = {Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70054},
doi = {10.1111/1755-0998.70054},
pmid = {41048034},
issn = {1755-0998},
abstract = {Ancient DNA (aDNA) analysis of archaeological dental calculus has provided a wealth of insights into ancient health, demography and lifestyles. However, the workflow for ancient metagenomics is still evolving, raising concerns about reproducibility. Few systematic investigations have examined how DNA extraction methods and library preparation protocols influence ancient oral microbiome recovery, despite evidence from modern populations suggesting that they do. This leaves a gap in our understanding of how wet-lab protocols impact aDNA recovery from dental calculus. In this study, we apply two DNA extraction and two library preparation methods in the aDNA field on dental calculus samples from Hungary and Niger. Samples from each context have similar chronological ages, but differences in their levels of aDNA preservation are notable, providing additional insights into how the efficacy of wet-lab protocols is impacted by sample preservation. Several metrics were employed to assess intra- and inter-sample variability, such as DNA fragment length recovery, GC content, clonality, endogenous content, DNA deamination and microbial composition. Our findings indicate that both DNA extraction and library preparation protocols can considerably impact ancient DNA recovery from archaeological dental calculus. Furthermore, no single protocol consistently outperformed the others across all assessments, and the effectiveness of specific protocol combinations depended on the preservation of the sample. These findings highlight the challenges of meta-analyses and underscore the need to account for technical variability. Lastly, our study raises the question of whether the field should strive to standardise methods for comparability or optimise protocols based on sample preservation and specific research objectives.},
}

@article {pmid41047993,
year = {2025},
author = {Paaske, SE and Baunwall, SMD and Rubak, T and Rågård, N and Kelsen, J and Hansen, MM and Lødrup, AB and Lyhne, S and Glavind, E and Fernis, CMC and Hald, S and Erikstrup, LT and Vinter-Jensen, L and Lal, S and Mikkelsen, S and Erikstrup, C and Dahlerup, JF and Hvas, CL},
title = {Improving Clinical Outcomes of Encapsulated Faecal Microbiota Transplantation for Clostridioides difficile Infection Through Empirical Donor Selection and Optimised Dosing: A Quality Improvement Study.},
journal = {Alimentary pharmacology & therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.70395},
pmid = {41047993},
issn = {1365-2036},
support = {8056-00006B//Innovationsfonden/ ; },
abstract = {BACKGROUND: Faecal microbiota transplantation (FMT) is effective for Clostridioides difficile infection (CDI), but real-world effectiveness data are warranted to refine treatment algorithms. We previously found that FMT effectiveness varied with donors, and the effect of a single capsule FMT administration was lower than expected.

AIMS: To improve FMT outcomes through empirical donor exclusion and application of an optimised capsule FMT dosing regimen.

METHODS: In this multi-site Danish quality improvement study, we included patients with CDI treated with capsule-based FMT from 24 June 2019 to 30 September 2024. The primary outcome was cure of C. difficile-associated diarrhoea (CDAD) 8 weeks after FMT. We assessed this using statistical process control charts monitored separately for the primary FMT centre and the external FMT sites. We used multivariable, mixed-effect logistic regression analysis to evaluate the impact of FMT dosing while adjusting for patient, donor and CDI-related factors.

RESULTS: We included 1176 patients (1707 FMT treatments). At external FMT sites, the cure rate from one FMT treatment changed from 50% (95% confidence interval (CI): 45%-56%) to 59% (55%-63%) following the exclusion of three low-performing donors in November 2022. After implementing a two-dose capsule FMT dosing regimen in February 2024, the cure rate increased to 72% (65%-77%). The impact of the two-dose capsule FMT dosing regimen remained statistically significant after adjustment (odds ratio 1.22; 95% CI 1.16-1.28; p < 0.001).

CONCLUSION: Empirical donor selection and a two-dose capsule FMT regimen improved clinical outcomes in a large-scale system treating patients with CDI.},
}

@article {pmid41047836,
year = {2025},
author = {Reddy, LB and Saier, MH},
title = {Microbiome: Friend or Friendly Foe.},
journal = {Microbial physiology},
volume = {},
number = {},
pages = {},
doi = {10.1159/000548748},
pmid = {41047836},
issn = {2673-1673},
abstract = {The human microbiome is a dynamic, polymicrobial ecosystem that plays an essential role in nutrition, immune development, barrier integrity, and host physiology, acting as a mutualistic partner under balanced conditions. However, its ecological complexity, genetic adaptability through horizontal gene transfer, and interactions with other prokaryotes as well as protozoan and metazoan parasites can transform commensals into pathobionts, resulting in weakened host's barriers, immunity declines with the progression of age, and community composition shifts toward dysbiosis. Factors such as diet, genetics, aging, immune-senescence, impaired autophagy, and environmental exposure, all influence this delicate balance, determining whether the microbiome remains protective or becomes an opportunistic source of inflammation and disease. This review focuses on the study of the intestinal microbiome in humans. Maintaining microbiome homeostasis is promoted through (a) dietary diversity, (b) limited antimicrobial use, (c) use of probiotics, (d) support for gut barrier function, and (e) healthy lifestyle improvements. These actions and considerations are critical to prevent the emergence of pathogenic states and preserving the microbiome's vital role in host health throughout life.},
}

@article {pmid41047664,
year = {2025},
author = {Cho, JH and Jin, SY},
title = {Diagnosis and treatment of Helicobacter pylori infection: past, present, and future.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/17460913.2025.2568326},
pmid = {41047664},
issn = {1746-0921},
abstract = {Helicobacter pylori infects more than half of the world's population. Chronic H. pylori infection is associated with the development of precancerous gastric conditions, including chronic atrophic gastritis and intestinal metaplasia, which may progress to peptic ulcer disease and gastric cancer. In 2020, an estimated 1.09 million new cases of gastric cancer were reported worldwide. Gastric cancer continues to pose a significant health burden and is the fourth leading cause of cancer-related deaths globally, with an estimated 769,000 deaths occurring annually. To decrease gastric cancer-related deaths, international guidelines recommend H. pylori eradication in all infected individuals. Increasing antibiotic resistance of H. pylori has significantly compromised the effectiveness of standard eradication regimens, highlighting the urgent need for alternative and effective treatment strategies. Over the past decade, molecular technologies and genome sequencing have advanced H. pylori diagnosis and treatment. This comprehensive review discusses the latest evidence on H. pylori management to guide the development of effective testing and treatment strategies. It also offers updates for clinicians, including the optimized H. pylori diagnosis, the history of H. pylori treatment and guideline development, updated empirical H. pylori treatment regimens, molecular testing for tailored H. pylori eradication, and next-generation sequencing of the gastric microbiome.},
}

@article {pmid41047527,
year = {2025},
author = {Sellmann, H and Williams, JE and Udekwu, K and McDonough, A and Heckathorn, K and Nuñez, L and Chen, Y},
title = {The relationship between infant feeding types, gut microbiome, intestinal inflammation, and neurodevelopment in a neonatal piglet model.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpen.70019},
pmid = {41047527},
issn = {1941-2444},
support = {//The project described was supported by an American Society for Parenteral and Enteral Nutrition Rhoads Research Foundation Research Grant. This publication was made possible by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health (NIH), the NIH Office of Women's Health and the NIH Office of Nutrition Research under grant #P20GM152304. Additional funding was provided by the National Center for Advancing Translational Sciences of the NIH under award No. KL2TR002317/ ; },
abstract = {BACKGROUND: The influences of nutrition on the infant's developing gastrointestinal (GI) microbiome, intestinal tract, and brain is unclear. Human milk (HM) is associated with beneficial immune and cognitive development compared with infant formula (IF). This study used a neonatal piglet model to determine the effects of infant feeding exposures (HM vs IF) on the GI microbiome, intestinal inflammation, and brain oligodendrocyte maturation.

METHODS: Six pairs of piglets received HM or IF for 28 days. Fecal samples were collected weekly and GI regions (jejunum, ileum, and colon) and brains were harvested at necropsy. Fecal microbiome composition was determined by 16S ribosomal RNA (16S rRNA) sequencing. Intestinal inflammation was assessed via quantification of intestinal interleukin (IL)-1β, IL-8, IL-10, tumor necrosis factor (TNF)-α, and fecal calprotectin. Neurodevelopment was evaluated by quantifying mature and immature oligodendrocytes in gray and white matter.

RESULTS: Bacterial community composition differed between feeding groups (P < 0.002) and over time (P = 0.001). Various highly abundant genera were associated with changes over time (P < 0.05) and only Escherichia-Shigella was associated with feeding group by time interactions (P < 0.05). No differences were found in intestinal inflammatory markers between feeding types, but mature oligodendrocytes in white matter were higher in HM-fed piglets (P = 0.004). Various intestinal inflammatory markers and relatively highly abundant genera were significantly associated.

CONCLUSION: Piglet fecal bacterial compositions differed by feeding group and over time, with several relatively highly abundant genera associated with intestinal inflammatory markers. Additionally, HM may support proper white matter development. Future research should investigate mechanisms underlying these relationships.},
}

@article {pmid41047258,
year = {2025},
author = {Pirovano, E and Marino, F and Rossi, E and Gennari, A and Rasini, E and Uslenghi, M and Figueira, I and Iacoviello, L and Ferrari, M and Cosentino, M},
title = {Modified Mediterranean diet effects on Parkinson's disease (MED-PARK): a single-centre randomised controlled trial protocol.},
journal = {BMJ open},
volume = {15},
number = {10},
pages = {e101946},
doi = {10.1136/bmjopen-2025-101946},
pmid = {41047258},
issn = {2044-6055},
mesh = {Humans ; *Diet, Mediterranean ; *Parkinson Disease/diet therapy/physiopathology ; Randomized Controlled Trials as Topic ; Aged ; Middle Aged ; Adult ; Male ; Aged, 80 and over ; Female ; Quality of Life ; Gastrointestinal Microbiome ; Metabolomics ; },
abstract = {INTRODUCTION: Only symptomatic treatments are available for patients with Parkinson's disease (PD), the second most common chronic neurodegenerative disease worldwide, and it is therefore imperative to identify disease-modifying interventions that can alter the course of the disease. Epidemiological studies in PD patients suggest that a Mediterranean diet is associated with better motor and non-motor symptoms, slower progression and reduced mortality. Few interventional studies, however, investigated the relationship between diet and PD severity and progression. This study aims to determine whether a Mediterranean nutritional intervention can benefit motor and non-motor symptoms experienced by PD patients. As a secondary aim, the effects of a modified Mediterranean diet on the immune system, metabolomics and microbiome will also be assessed.

METHODS AND ANALYSIS: This is an interventional, non-pharmacological, superiority, randomised, controlled, single-centre, masked study with two parallel groups to evaluate the efficacy and safety of a modified Mediterranean diet on motor and non-motor patient-reported symptoms. PD patients meeting inclusion criteria will be enrolled (44 participants, aged between 40 years and 85 years), block-randomised and split into two parallel arms to either maintain their usual diet (control) or follow a modified Mediterranean diet for 6 months (intervention).Patient-reported symptomatology is the primary outcome, measured through the Movement Disorders Society Unified PD Rating Scale (MDS-UPDRS) I+II score. Secondary outcomes include the immunophenotype of circulating cells of the adaptive immune system, the nasal and faecal microbiome composition, faecal and urinary metabolites and the measurement of inflammatory and metabolic markers. Disease severity (MDS-UPDRS III), non-motor symptomatology (Non-Motor Symptoms Scale), participant's well-being (36-Item Short Form Health Survey), gastrointestinal symptomatology (Gastrointestinal Symptom Rating Scale and the Patient Assessment of Constipation Quality of Life) and intensity of dopaminergic replacement therapy (levodopa equivalents) will also be assessed. Evaluations will be conducted before the start and at the end of the intervention.

ETHICS AND DISSEMINATION: The Ethical Committee 'Comitato Etico Territoriale Lombardia 5' first approved this study on 17 September 2024 Prot. Nr. 420/24. Findings will be disseminated via peer-reviewed research papers and conference presentations.

TRIAL REGISTRATION NUMBER: NCT06705517.},
}

Humans
*Diet, Mediterranean
*Parkinson Disease/diet therapy/physiopathology
Randomized Controlled Trials as Topic
Aged
Middle Aged
Adult
Male
Aged, 80 and over
Female
Quality of Life
Gastrointestinal Microbiome
Metabolomics

@article {pmid41047121,
year = {2025},
author = {Yadav, S and Yadav, J and Jones, D and Humphrey, MB},
title = {Osteoimmunology: the little niche with the big impact.},
journal = {The American journal of the medical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.amjms.2025.09.014},
pmid = {41047121},
issn = {1538-2990},
abstract = {Osteoimmunology, which emerged in the early 2000s, was paradigm-shifting in its integration of immunology and skeletal research, recognizing the pivotal role of immunoreceptors on preosteoclasts, immune cells, and proinflammatory cytokines contributing to inflammatory bone remodeling. Numerous immunoreceptors and key signaling pathways were defined that regulate osteoclastogenesis. A dynamic interplay between lymphocytes and osteoclasts was found to be fundamental to maintaining bone homeostasis and contributing to pathological bone resorption in inflammatory arthritis or malignant metastasis. Osteoimmunology has expanded to include crosstalk between osteoclasts and osteoblasts, the role of bone marrow stromal cells in maintaining the hematopoietic stem cell niche, and the influence of the microbiome on lymphocytes that drive bone remodeling. Deciphering the intricate mechanisms that govern the immune system's regulation of bone remodeling remains a central objective in osteoimmunology, offering promising avenues for the development of targeted therapeutic strategies aimed at restoring skeletal equilibrium.},
}

@article {pmid41047001,
year = {2025},
author = {Dai, J and Dai, W and Heianza, Y and Qi, L},
title = {Phenome-wide associations of coffee intake in the human phenotype project.},
journal = {Metabolism: clinical and experimental},
volume = {},
number = {},
pages = {156412},
doi = {10.1016/j.metabol.2025.156412},
pmid = {41047001},
issn = {1532-8600},
abstract = {OBJECTIVE: Coffee is one of the most widely consumed beverages globally and has been linked to favorable health outcomes. However, its system-wide relationships with human biology and the underlying mechanisms remain poorly characterized. This study aimed to investigate the relationship between coffee consumption and continuous glucose monitoring (CGM) metrics and other biological systems in healthy adults.

RESEARCH DESIGN AND METHODS: In the Human Phenotype Project, 8666 generally healthy Israeli adults provided two weeks of real-time dietary logs, from which coffee intake was estimated. Participants wore CGM devices throughout this period, and multimodal data spanning 11 additional systems (e.g., gut microbiome, serum lipidomics, and body composition) were collected. We employed machine learning approaches to quantify the extent to which each system reflected coffee intake. We performed linear regression to identify individual traits associated with coffee intake, with false discovery rates < 0.05 considered significant.

RESULTS: This cross-sectional study identified continuously-monitored glucose regulation and gut microbial composition as the most reflective systems of coffee intake, with further analyses revealing favorable glycemic profiles spanning diverse aspects of glucose regulation with increasing coffee intake, and Clostridium phoceensis (i.e., Lawsonibacter asaccharolyticus) as the most significant species positively associated with coffee intake. Additionally, coffee intake was favorably associated with traits across body composition, serum lipidomics, and hepatic, hematopoietic, and renal systems.

CONCLUSIONS: This study found that habitual coffee intake was linked to multifaceted favorable glucose control captured by CGM and favorable profiles across multiple biological systems, providing mechanistic insights that may guide precision nutrition strategies for diabetes prevention.},
}

@article {pmid41046872,
year = {2025},
author = {Yang, S and Yang, M and Jennings, M and Timek, H and Haley, AE and Romee, R and Li, J},
title = {Repurposing the bacterial surface display technology for drug delivery.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {115701},
doi = {10.1016/j.addr.2025.115701},
pmid = {41046872},
issn = {1872-8294},
abstract = {Bacteria have emerged as versatile platforms for therapeutic delivery, owing to their inherent adaptability, genetic tractability, and ability to interface with the human microbiome and immune system. This review explores the evolution of bacterial engineering for medical applications, emphasizing drug delivery strategies enabled by bacterial surface display technologies. We outline the advantages of surface display-such as enhanced localization, prolonged therapeutic activity, and reduced systemic toxicity-over conventional bacterial secretion and lysis-based delivery methods. The review details key biological mechanisms of surface display in both Gram-negative and Gram-positive bacteria, including outer membrane proteins, sortase-mediated anchoring, and spore-based systems. We also highlight emerging applications of surface-displayed cytokines, nanobodies, and immunomodulatory proteins in cancer therapy, vaccine development, microbiome engineering, and animal health. Innovative approaches combining bacterial display with conjugation systems and biosensors expand the potential of these living therapeutics for precise, responsive, and programmable interventions. Furthermore, we propose a future roadmap that leverages computational tools such as AlphaFold and in silico screening to rationally identify optimal outer membrane anchors, accelerating the design of next-generation surface display platforms. While challenges remain-including regulatory hurdles and microbial stability-continued interdisciplinary innovation with synthetic biology promises to transform engineered bacteria into clinically viable therapeutic agents. This review positions bacterial surface display as a powerful and underexplored modality for targeted drug delivery, bridging synthetic biology, immune engineering, and translational medicine.},
}

@article {pmid41046786,
year = {2025},
author = {Liu, D and Hsieh, ML and Ding, Y},
title = {Strategies for engineering domesticated and undomesticated human microbes.},
journal = {Current opinion in biotechnology},
volume = {96},
number = {},
pages = {103368},
doi = {10.1016/j.copbio.2025.103368},
pmid = {41046786},
issn = {1879-0429},
abstract = {Human-associated microbes hold immense therapeutic potential, yet most species remain undomesticated due to cultivation barriers and limited genetic tools. Recent advances in genetic engineering are overcoming these challenges, enabling the precise manipulation of both domesticated and previously intractable microbes. This review highlights established strategies for engineering domesticated strains, such as Escherichia coli Nissle 1917 and lactic acid bacteria, for diverse therapeutic applications. We also discuss emerging tools, including optimized transformation protocols for skin commensals and genome-editing approaches for Clostridium species and undomesticated E. coli, that address key barriers in non-model microbes and expand the potential of engineered microbiome therapeutics.},
}

@article {pmid41046740,
year = {2025},
author = {Guerrieri, A and Abedini, D and White, F and Bleeker, J and Kramer, G and Dong, L},
title = {Cycloartenol-derived triterpenoid pathway genes alter the root metabolome and microbiome in tomato.},
journal = {Plant physiology and biochemistry : PPB},
volume = {229},
number = {Pt C},
pages = {110584},
doi = {10.1016/j.plaphy.2025.110584},
pmid = {41046740},
issn = {1873-2690},
abstract = {Plant triterpenoids derived from cycloartenol are central to sterol homeostasis and specialized metabolite production, yet their roles in shaping rhizosphere interactions remain poorly understood. Here, we investigated the function of key cycloartenol-derived triterpenoid biosynthetic genes in tomato (Solanum lycopersicum) by transiently silencing CYCLOARTENOL SYNTHASE 1 (SlCAS1), STEROL METHYLTRANSFERASE 1 (SlSMT1), STEROL SIDE CHAIN REDUCTASE 2 (SlSSR2), and PHYTOENE DESATURASE (SlPDS). SlCAS1 suppression caused severe growth inhibition, confirming the essential role of cycloartenol for plant development. Silencing of SlSMT1 and SlSSR2 altered root sterol composition, with SlSMT1 reducing β-sitosterol and stigmasterol, and SlSSR2 causing decreases in cholesterol as well as significant reductions in steroidal glycoalkaloids (SGAs) and steroidal saponins (SAs). By contrast, SlPDS silencing unexpectedly led to elevated sterol levels and broad metabolome shifts. Untargeted metabolomics revealed gene-specific alterations in root and exudate profiles, while molecular networking highlighted the rapid loss of SGAs in exudates, suggesting microbial degradation. Integration of metabolomic and 16S rRNA sequencing data showed that changes in sterols, SGAs, and saponins were associated with distinct bacterial families, including Comamonadaceae and Sphingomonadaceae. Together, these findings demonstrate that cycloartenol-derived triterpenoid pathway genes strongly influence root metabolite composition and shape the assembly of tomato root-associated microbial communities.},
}

@article {pmid41046701,
year = {2025},
author = {Yao, H and Yu, J and Yang, X and Xu, J},
title = {Mechanisms of disruption of the gut-brain axis by environmental endocrine disruptors.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119124},
doi = {10.1016/j.ecoenv.2025.119124},
pmid = {41046701},
issn = {1090-2414},
abstract = {Environmental endocrine disruptors (EEDs) are exogenous chemicals that impair physiological health by disrupting endocrine function. The gut-brain axis represents a complex bidirectional communication network integrating the gut microbiome, immune system, neural signaling, and endocrine pathways to maintain systemic homeostasis. Within this interconnected system, gut microbiota influence mood regulation, immune activity modulates neural processes, and neural signaling governs circadian and sleep cycles. This review explores the multi-system impacts of EEDs across four key physiological domains: (1) gut microbial ecology, (2) immune function, (3) neuroendocrine regulation, and (4) developmental processes. Evidence indicates that EED exposure disrupts intestinal microbial composition, leading to dysbiosis marked by the depletion of beneficial taxa and the expansion of pathogenic species. Concurrently, EEDs impair gut-associated immune cell populations (T cells, B cells, and macrophages), undermining mucosal immunity and increasing susceptibility to inflammatory bowel disease, autoimmune conditions, and gastrointestinal malignancies. At the endocrine level, EEDs interfere with the hypothalamic-pituitary-adrenal and hypothalamic-pituitary-gonadal axes, contributing to hormonal imbalances and impaired reproductive development. Neurochemically, they disrupt the synthesis, release, and degradation of key neurotransmitters, including norepinephrine, dopamine, and serotonin, while exerting direct neurotoxic effects such as cerebrovascular abnormalities and delayed cerebellar myelination. In summary, this review delineates the mechanistic pathways through which EEDs perturb gut-brain axis homeostasis. These insights provide a scientific basis for designing targeted therapeutic interventions and shaping evidence-based public health policies.},
}

@article {pmid41046586,
year = {2025},
author = {Kwiatkowska, AM and Guzmán, JA and Lafaurie, GI and Castillo, DM and Cardona, AF},
title = {Exploring the role of the oral microbiome in saliva, sputum, bronchoalveolar fluid, and lung cancer tumor tissue: A systematic review.},
journal = {Translational oncology},
volume = {62},
number = {},
pages = {102557},
doi = {10.1016/j.tranon.2025.102557},
pmid = {41046586},
issn = {1936-5233},
abstract = {OBJECTIVE: To explore the association between the oral microbiome and the presence or progression of lung cancer (LC) using metagenomic sequencing techniques.

METHODS: Databases, including PubMed and EMBASE, were reviewed. Eligible studies included the study of oral microorganisms via genomic sequencing and molecular mechanisms associated with LC in saliva, sputum, bronchoalveolar lavage fluid (BALF), or tumor tissue from LC patients. A quality analysis of the studies was carried out, and a qualitative synthesis was performed according to the localization and sample type. Meta-analysis was performed on alpha diversity indexes.

RESULTS: Of the 1880 scrutinized articles, 50 studies were selected, comprising 29 cross-sectional, 7 case-control, and 14 cohort studies. The quality analysis sheds light on potential biases. The findings revealed a conspicuous overgrowth of specific microbial taxa in LC patients' saliva BALF samples of Veillonella and Streptococcus. Conversely, the Bacteroides genus, related to periodontal disease, exhibited no significant correlation with LC. Microorganisms in tumoral tissue were associated with poor prognosis. Veillonella was associated with a better response to ICIs therapy. Oral microorganisms were related to metabolic reprogramming with xenobiotic biodegradation, amino acid, sugar, sucrose, and lipidic metabolism, immune modulation, and proinflammatory responses.

CONCLUSION: Overgrowth of specific oral microorganisms in the saliva and BALF is associated with diagnosis, poor prognosis, and low response to immunotherapy. Veillonella could be a marker for response to ICIs therapy. Further well-designed studies should evaluate the impact of the oral microbiome on the response to ICIs.},
}

@article {pmid41046274,
year = {2025},
author = {Sadeghloo, Z and Ebrahimi, S and Hakemi-Vala, M and Totonchi, M and Sadeghi, A and Fatemi, N},
title = {Fusobacterium nucleatum and non-coding RNAs: orchestrating oncogenic pathways in colorectal cancer.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {78},
pmid = {41046274},
issn = {1757-4749},
abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, with mounting evidence implicating the gut microbiome in its pathogenesis. Among the microbial agents, Fusobacterium nucleatum has emerged as a prominent contributor, frequently detected in CRC tissues and associated with advanced disease stages and poor prognosis. This review highlights the complex interplay between F. nucleatum and host non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), in modulating CRC biology. F. nucleatum influences the expression of several ncRNAs, which in turn regulate key signaling pathways such as Wnt/β-catenin (e.g., miR-1246, miR-135b), PI3K/AKT (e.g., miR-22, miR-135b), and TLR4/NF-κB (e.g., miR-31, lnc-NEAT1). Through these mechanisms, F. nucleatum contributes to tumor cell proliferation, immune evasion, metastasis, and chemoresistance. Additionally, its impact on ncRNA expression is implicated in reduced efficacy of standard chemotherapy. Emerging microbiota-based therapies, including probiotics and fecal microbiota transplantation, show promise in modulating gut flora and potentially reversing ncRNA dysregulation; however, their mechanistic effects on the F. nucleatum-ncRNA axis require further investigation. This review underscores the critical role of F. nucleatum-regulated ncRNAs in CRC and presents new opportunities for biomarker discovery and targeted therapeutics.},
}

@article {pmid41046045,
year = {2025},
author = {Chavarria, X and Shatta, A and Park, HS and Choi, DY and Kang, D and Oh, S and Lee, D and Kim, M and Choi, JH and Cho, YH and Yi, MH and Kim, JY},
title = {Microbiome of Dipteran vectors associated with integron and antibiotic resistance genes in South Korea.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107858},
doi = {10.1016/j.actatropica.2025.107858},
pmid = {41046045},
issn = {1873-6254},
abstract = {The spread of antibiotic resistance genes (ARGs) across the environment and the role that organisms that interact with humans play as reservoirs of resistant bacteria pose important threats to public health. Flies are two-winged insects composing the order Diptera, which includes synanthropic species with significant ecological roles as pollinators, vectors, and decomposers. Here, we used iSeq100 metabarcoding to characterize the microbiome of six dipteran species in South Korea: Lucilia sericata, Lucilia illustris, Culex pipiens, Aedes vexans, Psychoda alternata and Clogmia albipunctata. We profiled a panel of common ARGs and performed correlation network analysis of the microbiome and resistome to identify co-occurrence patterns of bacterial bacterial amplicon sequence variants (ASVs) and resistance genes. We detected blaTEM, ermB, tetB, tetC, aac(6')-Ib-cr, cat2, sul1, qepA, int1 and int2, but no blaSHV, mecA, tetA or cat1. Notably, co-occurrence analysis showed highly mobile genes such as qepA, ermB and sul1 were associated with integron of class 1 integrase presence. These, along with aac(6')-Ib-cr were detected at higher rates across multiple species. Microbiome composition was distinct across species. amplicon sequence variants (ASVs) of Pseudomonas, Corynebacterium, Clostridium, Ignatzschineria, Bacteroides, Streptococcus, Treponema and Dietzia showed strong co-occurrence with multiple ARGs. This study contributes to the understanding of the role of dipterans as reservoirs of antibiotic resistance.},
}

@article {pmid41045888,
year = {2025},
author = {Zhang, M and Zhang, W and Jiang, Q and Zhao, C and Han, F and Chen, H and Li, Y and Zhuge, Y and Zhou, W},
title = {Assimilation overwhelms nitrification in saline wastewater nitrogen removal: From heterotrophic nitrification and aerobic denitrification strains to microbiomes.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124694},
doi = {10.1016/j.watres.2025.124694},
pmid = {41045888},
issn = {1879-2448},
abstract = {Heterotrophic nitrification and aerobic denitrification (HN-AD) represents an innovative biological nitrogen removal strategy for saline wastewater treatment. However, how HN-AD microbes could be applied to environmental microbiomes and conduct nitrogen metabolic performance remains ambiguous. Here we established synthetic heterotrophic microbiomes using halophilic HN-AD strains - biofilm-forming Pseudomonas kunmingens 8-C and Acinetobacter johnsonii 2-1-H, and characterized nitrogen metabolism in pure-cultured strains and microbiomes. The pure-cultured HN-AD strains removed ammonium primarily via ammonium assimilation (> 46 % contribution) and heterotrophic nitrification, comprehensively validated by nitrogen balance, [15]N stable isotopic labeling tests, enzyme activity assays and functional gene identification. Four synthetic halophilic microbiomes constructed by biofilm-forming and HN-AD strains achieved ammonium and total nitrogen removal efficiencies of 76-92 % and 72-86 %. Biofilm-forming strains facilitated heterotrophic microbiome assembly by shaping microbial communities through the deterministic assembly process. Notably, initial functional strains selectively recruited environmental microbes with efficient ammonium-assimilating capacity, manifested as a stable and relatively high abundance of glnA gene in microbiomes. But the invasion of microbes consequently led to the overwhelming dominance of ammonium assimilation over nitrification in microbiomes. Our results provided a framework for constructing environmental microbiomes using functional microbes and highlighted the distinct nitrogen metabolism shifting from HN-AD pure-cultured bacteria to microbial consortia.},
}

@article {pmid41045839,
year = {2025},
author = {He, T and Zhang, J and Zhao, A and Luo, S and Jiang, H and Tang, M and Zhang, Y},
title = {Docosahexaenoic acid supplementation in pregnancy and early lactation: Impacts on breast milk docosahexaenoic acid and Maternal-Infant gut microbiota - A randomized controlled trial.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {54},
number = {},
pages = {71-82},
doi = {10.1016/j.clnu.2025.09.006},
pmid = {41045839},
issn = {1532-1983},
abstract = {AIM: This study aimed to evaluate whether docosahexaenoic acid (DHA) supplementation during pregnancy increases DHA concentrations in colostrum among Chinese women, and to determine whether continued postpartum supplementation is necessary to sustain DHA levels throughout lactation. Additionally, the study examined the impact of maternal DHA supplementation on the gut microbiota of both mothers and their infants.

METHODS: 79 pregnant women were enrolled in this multicenter, double-blinded, randomized, placebo-controlled, parallel trial and were randomized to three groups (CC, control group; FC, DHA supplementation in the third trimester; FF, DHA supplementation from the third trimester to 42 days postpartum). Participants in the FF and FC groups were administered 100 mg/day DHA via milk powder and those in the CC group were administered milk powder without DHA fortification. Breast milk was collected - on days 3 and 42 postpartum. Fatty acid composition in breast milk was measured with gas chromatography and expressed as percentage of total fatty acids by weight. Fecal samples from mothers (at gestational week 28, 38 and 42 days postpartum) and infants (at 3 and 42 days of age) were collected, then analyzed using 16S rRNA sequencing.

RESULTS: The FF group had significantly higher levels of DHA in colostrum than the other two groups (FF: 1.49%, FC: 1.27%, CC: 1.11, P-ANCOVA = 0.018) but not in early mature milk (FF: 0.94%, FC: 0.82%, CC: 0.85%, P-ANCOVA = 0.646). At 42 days postpartum, both mothers and infants in the FF group exhibited a higher abundance of the genus Lactobacillus in the fecal microbiome.

CONCLUSION: In this cohort of Chinese women, maternal supplementation with 100 mg/day of DHA starting from the third trimester of pregnancy significantly increased DHA concentrations in colostrum. However, 100 mg/day may be insufficient to sustain DHA levels beyond colostrum. Additionally, maternal DHA supplementation was found to influence Lactobacillus abundance at 42 days postpartum of both mothers and their infants. Future studies should explore higher DHA doses for long-term lactation stability, and investigate dynamic changes in other gut microbiota taxa and microbiota-mediated health effects.

CLINICAL TRIAL REGISTRATION: ChinaClinicalTrial.gov (ChiCTR1800019461).},
}

@article {pmid41045629,
year = {2025},
author = {Ouyang, Y and Sun, L and Yu, D and Li, Q and Du, S and Wang, X and Wang, M and Xu, G and Ye, W and Liu, X},
title = {Exogenous chemical exposures and metabolic disruptions in hyperuricemia: a multi-omics mediation study.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109832},
doi = {10.1016/j.envint.2025.109832},
pmid = {41045629},
issn = {1873-6750},
abstract = {BACKGROUND: Hyperuricemia has emerged as a significant public health concern. However, the relationship between hyperuricemia and both individual and mixed exogenous chemicals remains poorly understood, and the underlying mechanisms are still unclear.

OBJECTIVES: This study aimed to elucidate the risk factors and biological mechanisms underlying hyperuricemia by integrating multi-omics data.

METHODS: UPLC-MS-based methods were employed to quantify 186 exogenous chemicals and profile metabolites from serum samples of 298 pairs of hyperuricemia patients and matched control subjects.

RESULTS: Significant disturbances in amino acid metabolism, energy metabolism, and gut microbiota-related metabolism were observed in hyperuricemia patients. The concentrations of perfluoroheptanoic acid, perfluorobutanesulfonate, sodium 4-chlorophenoxyacetate, and indole-3-butyric acid were significantly higher in hyperuricemia patients. A positive association was observed between combined exposures and hyperuricemia risk, with indole-3-butyric acid being the most significant contributor. Perfluorinated compounds may affect uric acid excretion via gut microbiome-related metabolites. Indole-3-butyric acid might modulate the enzymatic activity of various acyl-CoA dehydrogenases, leading to disruptions in fatty acid metabolism and an increased risk of hyperuricemia. Furthermore, genetic susceptibility appears to further increase the risk of hyperuricemia.

CONCLUSIONS: In summary, hyperuricemia is related to the interplay of environmental exposures and individual genetic susceptibility, with metabolic dysregulation serving as a crucial mediating link. These findings offer novel insights into the potential health risks associated with exogenous chemical exposures.},
}

@article {pmid41045571,
year = {2025},
author = {Chang, C and Gupta, R and Sedighian, F and Louie, A and Gonzalez, DM and Le, C and Cho, JM and Park, SK and Castellanos, J and Ting, TW and Dong, TS and Arias-Jayo, N and Lagishetty, V and Navab, M and Reddy, S and Sioutas, C and Hsiai, T and Jacobs, JP and Araujo, JA},
title = {Corrigendum to "Subchronic inhalation exposure to ultrafine particulate matter alters the intestinal microbiome in various mouse models" [Environ. Res. 248 (2024) 118242].},
journal = {Environmental research},
volume = {286},
number = {Pt 3},
pages = {122855},
doi = {10.1016/j.envres.2025.122855},
pmid = {41045571},
issn = {1096-0953},
}

@article {pmid41045547,
year = {2025},
author = {Yang, X and Li, Y and Wang, T and Li, Z and Zhuang, Q and Liang, C and Wang, X and Tian, J},
title = {GmSPX5 regulates arbuscular mycorrhizal colonization and phosphate acquisition through modifying transcription profile and microbiome in soybean.},
journal = {The Plant journal : for cell and molecular biology},
volume = {124},
number = {1},
pages = {e70511},
doi = {10.1111/tpj.70511},
pmid = {41045547},
issn = {1365-313X},
support = {2021YFF1000500//National Key Research and Development Program of China/ ; 2024A1515013054//Guangdong Basic and Applied Basic Research Foundation/ ; 2023ZD04072//STI 2030-Major Project/ ; 2022B0202060005//Key Areas Research and Development Programs of Guangdong Province/ ; 2022SDZG07//the Open Competition Program of Ten Major Directions of Agricultural Science and Technology Innovation for the 14th Five-Year Plan of Guangdong Province/ ; 32172658//National Natural Science Foundation of China/ ; 32172659//National Natural Science Foundation of China/ ; 32302662//National Natural Science Foundation of China/ ; },
mesh = {*Glycine max/microbiology/genetics/metabolism ; *Mycorrhizae/physiology ; *Phosphates/metabolism ; Symbiosis ; *Plant Proteins/genetics/metabolism ; Plants, Genetically Modified ; Gene Expression Regulation, Plant ; Plant Roots/microbiology/metabolism ; *Microbiota/genetics ; },
abstract = {Symbiosis with arbuscular mycorrhizal (AM) fungi is a crucial strategy for plant adaptation to low phosphorus (P) stress. However, the mechanisms underlying how phosphate (Pi) signaling regulators participate in AM colonization remain largely unknown in soybean (Glycine max). In this study, the expression of GmSPX5, one member of the SPX (SYG1/Pho81/XPR1) family, was induced by AM fungal inoculation in soybean roots. Furthermore, the expression of GmSPX5 seems to overlap with AM infection structures through analyzing GUS activity of transgenic soybean plants harboring ProGmSPX5:GUS. Four transgenic lines with GmSPX5 overexpression (OX8 and OX12) and suppression (Ri9 and Ri11) were subsequently used to examine the functions of GmSPX5 on AM symbiosis and Pi acquisition. Despite no difference between Ri and wild-type (WT), the overexpression of GmSPX5 significantly increased AM colonization as reflected by 8.4% in OX8 and 8.7% in OX12, respectively. Consistently, the dry weight and total P content of OX8 and OX12 were higher than WT. Furthermore, a total of 3483 genes were found to exhibit differential expression patterns in roots between OX12 and WT, including genes related to linolenic acid metabolism and flavonoid metabolism. Meanwhile, the composition of the bacterial community in the roots of OX12 was distinct from that in WT through β-diversity analysis. Particularly, an ASV19 (Sphingomonadales) was enriched in OX12 roots, which was positively related to total P content and AM fungi colonization. Taken together, these results highlight that GmSPX5 can regulate AM symbiosis, as well as Pi acquisition in soybean. Our findings advance the understanding of SPX functions in plant-microbe interaction.},
}

*Glycine max/microbiology/genetics/metabolism
*Mycorrhizae/physiology
*Phosphates/metabolism
Symbiosis
*Plant Proteins/genetics/metabolism
Plants, Genetically Modified
Gene Expression Regulation, Plant
Plant Roots/microbiology/metabolism
*Microbiota/genetics

@article {pmid41045399,
year = {2025},
author = {Moon, J and Liu, Z and Park, T},
title = {PSM-SMOTE: propensity score matching and synthetic minority oversampling for handling unbalanced microbiome data.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {41045399},
issn = {2092-9293},
support = {NRF-2022R1A2C1092497//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: Predictive models using microbiome data often suffer from covariate imbalance and class imbalance, biasing results. Propensity Score Matching (PSM) balances covariates but reduces sample size, while borderline synthetic minority oversampling technique (borderline-SMOTE) oversamples minority classes but can generate uninformative examples.

OBJECTIVE: To develop and evaluate PSM-SMOTE, a novel hybrid sampling method that integrates PSM and borderline-SMOTE to handle both covariate and class imbalance in microbiome data.

METHODS: We developed PSM-SMOTE, a three-step hybrid sampling algorithm for microbiome data: (1) PSM at four caliper levels to balance covariates, (2) selection of at least ten robust differential markers via seven statistical tests with false discovery rate correction, and (3) application of borderline-SMOTE on the marker-based distance matrix to oversample minority classes. We evaluated PSM-SMOTE on three publicly available microbiome case-control datasets: pancreatic ductal adenocarcinoma (PDAC), colorectal cancer (CRC), and obesity, using logistic regression (LR), random forest (RF), and support vector machine (SVM) classifiers. Performance was assessed via area under the ROC curve (AUC).

RESULTS: PSM-SMOTE improved test AUCs in multiple model-dataset combinations compared with using PSM alone. Notably, for the RF model, PSM-SMOTE consistently enhanced AUC across nearly all oversampling settings in the PDAC and obesity cohorts. For the SVM model, PSM-SMOTE also achieved a significant AUC increase in the CRC cohort. For the LR model, PSM-SMOTE showed modest improvement under strict matching.

CONCLUSION: PSM-SMOTE effectively addresses dual imbalance in microbiome data and consistently enhances performance, providing a practical solution for imbalanced data analyses.},
}

@article {pmid41045195,
year = {2025},
author = {Green Buzhor, M and Longobardi, G and Kandli, O and Krinsky, A and Avramoff, O and Katyal, A and Salomon, K and Miari, A and Venkert, D and Barnatan, TT and García Alvarado, A and Greenberg, S and Satchi-Fainaro, R},
title = {Harnessing Next-Generation 3D Cancer Models to Elucidate Tumor-Microbiome Crosstalk.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e03198},
doi = {10.1002/adhm.202503198},
pmid = {41045195},
issn = {2192-2659},
support = {835227//European Research Council (ERC) Advanced/ ; 3DBrainStrom//European Research Council (ERC) Advanced/ ; 862580//ERC PoC/ ; 3DCanPredict//ERC PoC/ ; 101113390//ERC PoC/ ; ImmuNovation//ERC PoC/ ; 101214384//The European Innovation Council (EIC)/ ; TIMNano//The European Innovation Council (EIC)/ ; ISF 3706/24//Israel Science Foundation/ ; PROF-18-602//Israel Cancer Research Fund (ICRF)/ ; LCF/PR/HR19/52 160 021//"La Caixa" Foundation/ ; LCF/PR/HR22/52 420 016//"La Caixa" Foundation/ ; LCF/PR/HR24/00968//"La Caixa" Foundation/ ; //Morris Kahn Foundation/ ; },
abstract = {The tumor microenvironment (TME) is a complex and dynamic ecosystem increasingly recognized for its interplay with the microbiome. In colorectal, breast, lung, liver, and brain cancers, bacterial communities and their metabolites are shown to influence tumor progression, immune responses, and therapeutic outcomes. To study these interactions in physiologically relevant contexts, advanced 3D in vitro models have emerged, including spheroids, organoids, microfluidic organ-on-a-chip platforms, and 3D-bioprinted constructs. These systems provide spatial organization, mechanical cues, and co-culture capabilities that facilitate investigation of host-microbiome-tumor cross-talk. Incorporation of live bacteria, their metabolites, and immune components into these platforms has yielded new insights into how the microbiome shapes cancer behavior, inflammation, and drug resistance. This review outlines recent advances in 3D model development for studying tumor-microbiome interactions, highlighting organ-specific applications, extracellular matrix-mimicking hydrogels, and biofabrication strategies. It also addresses key challenges, including maintaining microbiome viability, modeling temporal dynamics, and integrating immune complexity. Overcoming these limitations requires interdisciplinary approaches that merge bioengineering, microbiology, and oncology. Evolving 3D platforms offer powerful tools for microbiome-informed cancer modeling and hold significant promise for advancing therapeutic screening and precision oncology.},
}

@article {pmid41045140,
year = {2025},
author = {Pongpamorn, P and Zwart, M and Bouwmeester, HJ},
title = {The Role of Soil Microbiota in the Control of Parasitic Weeds.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcaf125},
pmid = {41045140},
issn = {1471-9053},
abstract = {Parasitic weeds from the Orobanchaceae family, particularly Striga, Orobanche and Phelipanche spp., are responsible for substantial agricultural losses worldwide. A better understanding of the intricate chemical interaction between parasitic plants and their host crops, and the effect the rhizosphere microbiome may have on this, offers potential for developing sustainable and effective biocontrol strategies. We review the biology of parasitic plants, with a focus on host-derived signaling molecules such as strigolactones (SLs) and haustorium inducing factors (HIFs) that coordinate key stages of their lifecycle, and hence are potential targets for control through microorganisms. We highlight several examples of pathogenic microorganisms, and plant growth-promoting rhizobacteria (PGPR) and fungi (PGPF) that have been shown to suppress parasitic weeds. These microbes act through multiple mechanisms: direct antagonism of the parasite, enhancement of the host's defense responses, and interference with chemical signaling between host and parasite. Both laboratory and field studies are reviewed to evaluate the efficacy and future potential of these biological control agents.},
}

@article {pmid41045128,
year = {2025},
author = {Xia, S and Huang, S and Wu, J and Lin, H and Duan, J and Ye, W and Xie, T and Cai, J and Sun, Y and Luo, X and Song, Y},
title = {Molecular Pathogenesis of Ovarian Endometrioma: Mechanistic Insights and Therapeutic Implications.},
journal = {Biology of reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1093/biolre/ioaf219},
pmid = {41045128},
issn = {1529-7268},
abstract = {Ovarian endometrioma (OMA), the most prevalent and clinically consequential subtype of endometriosis, represents a chronic inflammatory disorder characterized by ectopic endometrial-like lesions. This condition manifests as progressive dysmenorrhea, ovarian reserve depletion, and subfertility, imposing substantial physical and psychosocial burdens. Current diagnostic modalities remain constrained by the absence of reliable biomarkers, while surgical interventions often yield suboptimal outcomes marked by incomplete lesion resolution and elevated recurrence rates. Despite growing recognition of endometriosis as a systemic disease, the distinct pathogenic mechanisms underlying OMA formation-particularly the interplay between immune dysregulation, steroid hormone hypersensitivity, and microenvironmental reprogramming-remain insufficiently characterized. Emerging evidence implicates multifaceted pathophysiological cascades involving chronic peritoneal inflammation, T-cell polarization anomalies, vascular endothelial growth factor (VEGF)-mediated neoangiogenesis, progesterone resistance, and reactive oxygen species accumulation. Notably, microbiome-derived metabolites and multi-omics integration have redefined paradigms of disease progression by elucidating mechanisms sustaining lesion viability. This review consolidates recent advances in OMA pathogenesis, dissecting molecular drivers of cellular survival, adhesive interactions, and inflammatory cascades within the ovarian microenvironment.},
}

@article {pmid41044998,
year = {2025},
author = {Modin, O and Zheng, D and Schnürer, A and Lundwall, T and Bolanos, SE and Olsson, J},
title = {From Low-Loaded Mesophilic to High-Loaded Thermophilic Anaerobic Digestion: Changes in Reactor Performance and Microbiome.},
journal = {Microbial biotechnology},
volume = {18},
number = {10},
pages = {e70238},
doi = {10.1111/1751-7915.70238},
pmid = {41044998},
issn = {1751-7915},
support = {//Käppalaförbundet/ ; //The Swedish Research Council (VR)/ ; },
mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *Sewage/microbiology ; Methane/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Temperature ; *Microbiota ; *Archaea/classification/genetics/metabolism ; Metagenomics ; },
abstract = {This study investigated temporal dynamics in reactor performance and microbial community structure during anaerobic digestion of sewage sludge when the temperature was changed from 37°C to 55°C, followed by an increase in organic loading rate (OLR). Performance instability was observed immediately following the temperature increase and in the end of the study when the OLR was 11.1 ± 0.3 kgVS m[-3]d[-1]. The specific methane production peaked at 0.31 ± 0.06 Nm[3] kg[-1] volatile solids (VS) during thermophilic operation and when the OLR was 3.5 ± 0.9 kgVS m[-3]d[-1]. Using metagenomic sequencing, 304 species-representative genome bins (SGB) were assembled. Network analysis revealed that 186 SGB were associated with thermophilic conditions and several new species putatively involved in key reactor functions were identified. When reactor function initially stabilised, two hydrogenotrophic and one aceticlastic methanogen (Methanothermobacter spp. and Methanosarcina thermophila), the hydrolytic Coprothermobacter proteolyticus, and putative syntrophic propionate oxidisers (e.g., Pelotomaculaceae) had high relative abundance. During the peak in specific gas production, the community was dominated by one hydrogenotrophic Methanothermobacter species coexisting with syntrophic acetate oxidising bacteria (Thermacetogenium phaeum and other species). Finally, when the reaction function deteriorated due to high OLR, new hydrolytic taxa emerged and the same aceticlastic methanogen as seen during the initial acclimatisation phase returned.},
}

*Bioreactors/microbiology
Anaerobiosis
*Sewage/microbiology
Methane/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
Temperature
*Microbiota
*Archaea/classification/genetics/metabolism
Metagenomics

@article {pmid41044986,
year = {2025},
author = {Chen, R and Wu, X and Yin, N and Xie, E and Sun, S and Shen, J and Chen, Y and Zhou, F and Li, T and Li, Q and Su, D and Fu, F and Li, G and Li, X and Shan, Y},
title = {Mechanisms of flavonoid-mediated amelioration of MASLD: flavonoids, their metabolites or impact on gut microbes?.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-24},
doi = {10.1080/10408398.2025.2566391},
pmid = {41044986},
issn = {1549-7852},
abstract = {Metabolic syndrome (MetS), characterized by symptoms like hyperlipidemia, abdominal obesity, and insulin resistance, is closely associated with metabolic dysfunction-associated steatotic liver disease (MASLD), an established disease burden worldwide. Health-promoting, side-effect-free preventative, and treatment strategies for MetS are required. Flavonoids, which are active phytochemicals easily obtained from dietary sources, have been shown in animal and population studies to improve lipid metabolism disorders and offer protective support against MASLD. However, it remains unclear which among flavonoids, their metabolites, or indirect mechanisms such as impact on gut microbiota most significantly ameliorates MASLD. This review first explores the diverse mechanisms through which flavonoids attenuate the onset and progression of MASLD. It then summarizes the flavonoid metabolites that have enhanced MASLD protection. Additionally, certain flavonoids can mitigate MASLD by reshaping the specific or entire gut microbiome. Finally, the review outlines the potential for developing prebiotic-probiotic systems with flavonoids and discusses potential directions for identifying causal relationship between flavonoids and MASLD amelioration.},
}

@article {pmid41044807,
year = {2025},
author = {Kim, H and Kim, A and Kim, H and Seo, D and Son, S and Kim, D and Shin, JU},
title = {Differential Modulation of Skin Barrier Proteins and Lipid Synthesis by Staphylococcus aureus, Staphylococcus hominis, and Cutibacterium acnes.},
journal = {Annals of dermatology},
volume = {37},
number = {5},
pages = {276-285},
doi = {10.5021/ad.25.020},
pmid = {41044807},
issn = {2005-3894},
support = {RS-2023-KH140992/MOHW/Ministry of Health and Welfare/Korea ; RND2023-103//Aekyung Co., Ltd./Korea ; },
abstract = {BACKGROUND: The skin microbiome plays a critical role in regulating epidermal differentiation and immune responses. Understanding of how individual microbial species influence the expression of barrier proteins and lipid synthesis pathways is essential for elucidating their contributions to skin barrier function.

OBJECTIVE: This study aimed to investigate the distinct effects of Staphylococcus aureus (S. aureus), Staphylococcus hominis (S. hominis), and Cutibacterium acnes (C. acnes) on the skin barrier protein expression and lipid synthesis, thereby clarifying their roles in maintaining skin barrier integrity and homeostasis.

METHODS: Keratinocyte 2-dimensional monolayer cultures and self-assembled 3-dimensional skin models were treated with S. aureus, S. hominis, or C. acnes. Alterations in skin barrier proteins and lipid synthesis were assessed using quantitative real-time polymerase chain reaction, immunofluorescence staining, and Oil Red O staining.

RESULTS: S. aureus significantly downregulated the messenger ribonucleic acid expression of skin barrier proteins and lipid synthesis enzymes, resulting in reduced lipid accumulation. In contrast, S. hominis upregulated barrier protein expression and enhanced lipid accumulation. Similarly, C. acnes increased the expression of both skin barrier proteins and lipid synthesis enzymes, leading to a marked increase in lipid accumulation.

CONCLUSION: Collectively, these findings suggest that S. aureus compromises the skin barrier function by downregulating the expression of barrier-associated proteins and lipid synthesis enzymes, whereas S. hominis and C. acnes enhance barrier integrity by upregulating these components. These differential microbial effects elucidate potential mechanisms by which the skin microbiome contributes to barrier homeostasis.},
}

@article {pmid41044805,
year = {2025},
author = {Hong, JY and Kwon, D and Park, KY},
title = {Microbiome-Based Interventions for Skin Aging and Barrier Function: A Comprehensive Review.},
journal = {Annals of dermatology},
volume = {37},
number = {5},
pages = {259-268},
doi = {10.5021/ad.25.009},
pmid = {41044805},
issn = {2005-3894},
support = {H12300860/MOHW/Ministry of Health and Welfare/Korea ; },
abstract = {The skin microbiome, a dynamic ecosystem of microorganisms, is essential for maintaining skin health by protecting against pathogens, modulating immunity, and enhancing barrier function. External factors such as pollutants, harsh skincare products, and aging disrupt microbial balance, leading to compromised skin health and accelerated aging. Aging-related changes, including reduced microbial diversity, loss of beneficial metabolites, and increased oxidative stress, contribute to inflammaging. Microbiome-supportive skincare, incorporating probiotics, prebiotics, and postbiotics, offers promising solutions to restore microbial balance, strengthen the skin barrier, and delay aging. These formulations work by reducing inflammation, enhancing antioxidant defenses, and regulating skin pH. However, challenges in microbiome research and product development persist, including individual variability in microbial composition, formulation complexities, and a limited understanding of microbe-skin interactions. Future innovations such as personalized microbiome skincare, genetically engineered probiotics, and advanced diagnostic tools could enable more targeted and effective interventions. Long-term clinical trials and detailed mechanistic studies are crucial to validate the efficacy of microbiome-focused skincare and optimize formulations for diverse populations. By addressing these challenges and advancing research, microbiome-supportive skincare has the potential to revolutionize approaches to skin health, preserving resilience and combating aging through tailored microbial interventions.},
}

@article {pmid41044758,
year = {2025},
author = {Pérez-Pérez, L and Galisteo, C and Sanjuán, JMO and Cobo-Díaz, JF and Puente, H and Rubio, P and Carvajal, A and Arguello, H},
title = {Severity of Brachyspira hyodysenteriae colitis correlates to the changes observed in the microbiota composition and its associated functionality in the large intestine.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {105},
pmid = {41044758},
issn = {2524-4671},
support = {PRE2020-093762//Ministerio de Ciencia, Innovación y Universidades/ ; JDC2023-051122-I//Ministerio de Ciencia, Innovación y Universidades/ ; LE088P23//Junta de Castilla y León/ ; },
abstract = {BACKGROUND: The gut microbiota is essential for maintaining nutritional, physiological and immunological processes, but colonic infections such as swine dysentery, caused by Brachyspira hyodysenteriae (B. hyo) disrupt this homeostasis. This study uses shotgun and full-length 16S rRNA sequencing in faeces, colonic contents and mucosa from pigs challenged with B. hyo to provide a high-resolution characterisation of the taxa, functions and metagenome-assembled genomes (MAGs) of interest, disclose their association with the primary pathogen and how they are affected by the pathological changes of the infection.

RESULTS: Changes in the microbiota were associated with disease severity. In early infection, no major findings were observed in diversity or abundance analyses, whereas in acute infection, B. hyo load, mucosal neutrophil infiltration, epithelial ulceration and mucosal thickness were clearly associated with changes in microbiota ordination, which were also associated with a decrease in species richness. Changes included a significant increase in Acetivibrio ethanolgignens, Campylobacter hyointestinalis and Roseburia inulinivorans, which, with the exception of C. hyointestinalis, established themselves as part of the core microbiota and shifted the colonic enterotype in acutely infected animals. MAGs analyses revealed that no major virulence genes were detected in the genomes of the species co-interacting with B. hyo in acute infection. Similarly, functional changes were observed only after the onset of clinical signs, with an increase in functions related to inflammation and toxic effects on the colonic epithelium.

CONCLUSIONS: Our study shows that in colitis caused by B. hyo, changes in the microbiota are mainly a consequence of the lesions that occur in the intestine, with no differences observed in early infection. Similarly, the bacterial species that are increased at the onset of clinical signs may promote intestinal inflammation caused by B. hyo infection, but the analysis of their genomes rule out their participation in the primary infection.},
}

@article {pmid41044750,
year = {2025},
author = {Kang, L and Li, Y and Wang, J and Fu, J and Li, Q and Jiang, Q and Zhou, H and Xiao, H and Zhang, Z and Hong, M},
title = {Seasonal dynamics, dietary patterns, and bamboo leaf nutrition shape the phyllosphere-associated gut microbiota of red pandas.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {104},
pmid = {41044750},
issn = {2524-4671},
support = {grant no. 32470516//National Natural Science Foundation of China/ ; grant no. KCXTD2022-7//Innovation Team Funds of China West Normal University/ ; grant no. 2024NSFSC2082//Sichuan Natural Science Foundation/ ; },
abstract = {BACKGROUND: The gut microbiota of bamboo-eating red pandas (Ailurus fulgens) comprises a intricate and multifaceted ecosystem influenced by numerous factors. Despite considerable research dedicated to captive red pandas, the microbial dynamics observed in wild populations are still not well understood. To address this research gap, our study employed advanced techniques such as high-throughput sequencing and metagenomic analysis to characterize the microbial communities and their functional profiles in fresh fecal samples from wild red pandas and in samples of their primary food source. Our objective was to conduct a thorough examination of how seasonality, diet, bamboo leaf nutrition, and phyllosphere-associated microorganisms affect the gut microbiota of red pandas.

RESULTS: Our findings reveal that seasonal variations have a notable impact on the composition, structure, and functionalities of red pandas' gut microbiota. Specifically, autumn and winter exhibit heightened microbial diversity and richness. Moreover, during different feeding phases (leaf-feeding, shoot-feeding, and mixed-feeding), the gut microbiota displays varied cellulose-digesting abilities, marked by increased expression of key enzymes during high-fiber dietary phases. Our analysis reveals robust correlations between bamboo nutrients and microbial communities in both bamboo and red panda guts. Notably, bamboo's crude protein and phosphorus content are pivotal in shaping the phyllosphere and gut microbial communities, while crude fat, crude protein, and phosphorus emerge as key drivers of microbial structure. Seasonal fluctuations in microbial populations of both bamboo and red panda guts with shared genera, underscore their tight linkage and interconnected seasonal adaptations.

CONCLUSIONS: In conclusion, our study provides a comprehensive understanding of how seasonality, diet, and bamboo leaf nutrition shape the gut microbiota of red panda connected to bamboo microbiome. It underscores the gut microbes' indispensable role in facilitating red pandas' adaptation to their bamboo-based diet, crucial for their survival in natural habitats.},
}

@article {pmid41044695,
year = {2025},
author = {Cun, H and He, P and Ahmed, A and He, P and Wu, Y and Jiang, Y and Zhang, H and Tang, G and Kong, B and Youssef, SA and Munir, S and He, Y},
title = {Intercropping between persimmon and apple enriched the leaf endophytes and rhizosphere communities against apple root rot.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1307},
pmid = {41044695},
issn = {1471-2229},
support = {202202AE090025//Technology Special Project of Yunnan Province/ ; 2022YFD140070//National Key Research and Development Program of China/ ; },
mesh = {*Malus/microbiology/growth & development ; *Rhizosphere ; *Endophytes/physiology ; Plant Leaves/microbiology ; Plant Roots/microbiology ; *Plant Diseases/microbiology/prevention & control ; Soil Microbiology ; *Diospyros/microbiology/growth & development ; Microbiota ; },
abstract = {BACKGROUND: Root rot disease has seriously restricted the development of the apple industry Worldwide. After being infected by pathogens, the microbial communities of rhizosphere soil and leaves may change. We found that apple and persimmon intercropping can reduce the occurrence of apple root rot achieving a relative control efficacy of 80.3% following persimmon intercropping.

RESULTS: Here, we investigate the effect of intercropping with persimmon tree on rhizosphere microbiome and leaf endophytes. For this, we tested the rhizosphere soil and leaves of healthy and infected apple trees during intercropping. The soil and leaves of healthy and infected root rot apple trees, persimmon trees, and intercropping were collected (during sampling time, apple trees were 5 years old, and persimmon trees were 3 years old). The high-throughput sequencing was performed on the Illumina Miseq platform to analyze the leaf endophytic bacterial and soil microbial communities. We further revealed that infection by root rot pathogens severely impacts the synergistic effects between endophytes and the composition of rhizosphere microbial communities. The intercropping between apple and persimmon trees can modulate apple leaf endophytes and rhizosphere microbial communities. Importantly, the relative abundance of Pantoea and Serratia increased significantly in the leaves of apple trees affected by root rot. We argue that bacteria such as Pantoea and Serratia are conducive to the occurrence of root rot. Notably, Bacillus and Trichoderma were significantly reduced in the rhizosphere of apples with root rot trees; however, persimmon trees and apple trees can maintain the relative abundance of beneficial species or improve the abundance compared with healthy apple trees.

CONCLUSIONS: The overall study concludes that intercropping apples and persimmons maintains the beneficial microbial balance and plant growth and helps to prevent dysbiosis caused by pathogens. Based on this shift in microbiome balance, a management strategy for apple root rot is discussed.},
}

*Malus/microbiology/growth & development
*Rhizosphere
*Endophytes/physiology
Plant Leaves/microbiology
Plant Roots/microbiology
*Plant Diseases/microbiology/prevention & control
Soil Microbiology
*Diospyros/microbiology/growth & development
Microbiota

@article {pmid41044678,
year = {2025},
author = {Ren, C and Meng, Y and Liu, Y and Wang, Y and Wang, H and Liu, Y and Liu, C and Fan, X and Zhang, S},
title = {Probiotic Bacillus subtilis enhances silkworm (Bombyx mori) growth performance and silk production via modulating gut microbiota and amino acid metabolism.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {103},
pmid = {41044678},
issn = {2524-4671},
support = {No. SDAIT-18//Modern Agricultural Technology System of Shandong Province/ ; No. CARS-18//China Agriculture Research System of MOF and MARA/ ; },
abstract = {BACKGROUND: Artificial diet-reared silkworms (Bombyx mori) exhibit reduced gut microbial diversity and impaired growth performance compared to mulberry-fed counterparts. While Bacillus subtilis is widely used as a probiotic in livestock and aquaculture, its impact on silkworms remains unexplored. This study investigates whether dietary supplementation with B. subtilis enhances larval development and elucidates the underlying mechanisms involving gut microbiota and metabolic pathways.

RESULTS: Supplementing artificial diets with B. subtilis (6 × 10[5] CFU/g) significantly increased larval body weight by 9.1-22.1% during instar stages and improved feed utilization efficiency (FUE) by 4.09%-6.80% compared to controls. Cocoon quality metrics, including cocoon shell weight (+ 9.77% in females) and cocoon shell ratio (+ 6.56%), also improved. Mechanistically, B. subtilis did not colonize the midgut but transiently modulated gut physiology: it elevated midgut fluid pH and enhanced α-amylase, trypsin, and lipase activities. 16 S rRNA sequencing revealed reduced gut microbial diversity (Shannon index, P < 0.01) and shifts in community structure, with decreased abundances of potential pathogens (e.g., Pseudomonas) and commensals (e.g., Lactobacillus). Targeted metabolomics identified a 3.1-fold increase in phenylalanine levels in hemolymph, linked to upregulated aromatic amino acid metabolism pathways (KEGG). Dietary phenylalanine supplementation (0.4%) replicated B. subtilis-induced growth promotion, confirming its pivotal role in host-microbe interactions.

CONCLUSIONS: B. subtilis enhances silkworm growth and silk production through multi-faceted mechanisms: reshaping gut microbiota composition, improving digestive enzyme activity, and elevating phenylalanine biosynthesis. These findings establish B. subtilis as a promising probiotic for optimizing artificial diet systems in Lepidoptera and highlight the central role of amino acid metabolism in insect-microbiome symbiosis.},
}

@article {pmid41044628,
year = {2025},
author = {Chun, SJ and Cui, Y and Kim, J and Lee, JW and Nam, KH},
title = {Multidimensional sampling framework reveals plant-driven effects on microbial spatial heterogeneity and niche differentiation in a natural ecosystem.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {125},
pmid = {41044628},
issn = {2524-6372},
support = {NIE-A-2025-10; NIE-A-2025-04; NIE-A-2025-11//The Ministry of Environment (MOE) of the South Korea/ ; },
abstract = {BACKGROUND: The identification of complex spatial patterns of microbial communities in relation to their ecological niches is fundamental to understanding the mechanisms of ecological interactions among diverse organisms. This study introduces a novel three-dimensional (3D) sampling approach to examine the spatial dynamics of microbial populations and niche differentiation influenced by plant-mediated effects in natural ecosystem.

RESULTS: Microbial communities across horizontal and vertical dimensions were systematically mapped, and we found that the total microbial diversity, particularly among eukaryotes, increased more than ten-fold compared to that obtained via single-grid sampling, emphasizing the importance of spatial heterogeneity in shaping microbial dynamics. Moreover, the 3D framework enabled us to identify taxa specifically associated with particular plants, offering insights into plant-microbe interactions, pathogen prevalence, and ecological consequences of plant-driven effects on local communities.

CONCLUSIONS: Collectively, these findings demonstrate that 3D sampling approach provides a reproducible and scalable methodology for investigating microbial spatial heterogeneity, pathogen ecology, and niche differentiation in natural environments.},
}

@article {pmid41044486,
year = {2025},
author = {Huang, P and Liu, Y and Li, N and Zhang, Q and Luo, Y and Zhang, Y and Zhou, Y and Mu, W and Yuan, M and Liu, Y and Xin, Y and Li, H and Peng, Y and Wang, X and Zhao, M and Yu, K and Wang, C},
title = {Causal relationship between gut microbiota and pneumonia: a Mendelian randomization and retrospective case-control study.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {449},
pmid = {41044486},
issn = {1471-2466},
support = {U20A20366//the National Natural Science Foundation of China-Regional Innovation and Development Joint Fund/ ; No.82430069//the National Natural Science Foundation of China/ ; No.82472198//the National Natural Science Foundation of China/ ; },
mesh = {Humans ; Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; Retrospective Studies ; Case-Control Studies ; *Pneumonia/microbiology/genetics ; Male ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Aged ; Genome-Wide Association Study ; },
abstract = {BACKGROUND: The relationship between microbiota and the gut-lung axis has been extensively studied in both experimental and epidemiological contexts. However, it is still unclear whether the gut microbiome plays a causal role in the development of pneumonia.

METHODS: Our study initially identified the genetic instruments in the gut microbiota GWAS across phylum, class, order, family, and genus levels. Pneumonia data were sourced from the open GWAS project of the Integrated Epidemiology Group (IEU). Mendelian randomization (MR) analysis employed several methods such as inverse variance weighting (IVW), weighted median, and MR-Egger, with Cochran's Q were calculated to assess heterogeneity via IVW and MR-Egger. Additionally, MR-PRESSO and MR-Egger intercepts were utilized to mitigate horizontal pleiotropy. A retrospective case-control study collected anal swab samples from severe pneumonia patients on the 1st and 3rd days after ICU admission. Samples were analyzed using 16S ribosomal ribonucleic acid (16S rRNA) and PERMANOVA analysis.

RESULTS: Eleven potential causal relationships between the gut microbiome and pneumonia (critical care), as well as nine potential causal relationships between the gut microbiome and pneumonia (28-day death in critical care) were identified. By integrating the results of PERMANOVA analysis with Mendelian randomization analysis, we were able to determine a negative correlation between genus Akkermansia and lactate levels, as well as length of ICU days in patients with septic acute respiratory distress syndrome (ARDS). Moreover, we found a potential negative causal relationship between the genus Akkermansia and pneumonia (28-day death in critical care) (OR 0.42, 95% CI 0.22-0.79, P = 0.007).

CONCLUSIONS: Our Mendelian randomization analysis has provided evidence for a potential causal relationship between gut microbiota and pneumonia. Furthermore, we observed that the genus Akkermansia may decrease the risk of pneumonia (28-day death in critical care), as observed in septic ARDS patients which Akkermansia could reduce ICU days and lactate levels. These findings provide valuable insights into the gut-lung axis and have the latent to inform future research in this field.

TRIAL REGISTRATION: The study was registered at the Chinese Clinical Trial Registry (https://www.chictr.org.cn/index.html , ChiCTR2300075450).},
}

Humans
Mendelian Randomization Analysis
*Gastrointestinal Microbiome/genetics
Retrospective Studies
Case-Control Studies
*Pneumonia/microbiology/genetics
Male
Female
Middle Aged
RNA, Ribosomal, 16S/genetics
Aged
Genome-Wide Association Study

@article {pmid41044437,
year = {2025},
author = {Kwa, M and Hussey, G and Novik, Y and Franke, AA and Volkova, A and Flores, K and Blaser, MJ and Speyer, J and Oratz, R and Meyers, M and Jhaveri, K and Fadel, E and Heguy, A and Schluter, J and Ruggles, KV and Adams, S},
title = {Evaluation of the gut microbiome and sex hormones in postmenopausal women with newly diagnosed hormone receptor-positive breast cancer versus healthy women: a prospective case-control study.},
journal = {Journal of cancer research and clinical oncology},
volume = {151},
number = {10},
pages = {275},
pmid = {41044437},
issn = {1432-1335},
support = {P30CA71789/NH/NIH HHS/United States ; 5P30CA16087-40/NH/NIH HHS/United States ; },
mesh = {Humans ; Female ; *Breast Neoplasms/microbiology/metabolism/pathology/blood ; *Postmenopause ; Case-Control Studies ; Prospective Studies ; *Gastrointestinal Microbiome ; Middle Aged ; Aged ; Receptors, Progesterone/metabolism ; Receptors, Estrogen/metabolism ; *Gonadal Steroid Hormones/blood/urine/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {PURPOSE: The functional composition and diversity of the gut microbiome may affect breast cancer risk by modulation of systemic sex hormones. Gut bacteria with β-glucuronidase enzymatic activity may deconjugate estrogens, leading to increased estrogen reabsorption into the circulation thereby increasing breast cancer risk. We investigated the relationship between the gut bacterial microbiome and endogenous estrogens and related sex hormones in women with hormone receptor-positive breast cancer compared to healthy control women. The goal was to determine if the estrobolome (i.e., bacteria capable of modulating the body's circulated estrogen levels) was altered in those with breast cancer compared with controls.

METHODS: In this prospective case-control study, postmenopausal women (n = 46) with newly diagnosed stage I-III estrogen and/or progesterone receptor-positive breast cancer were compared with healthy postmenopausal female controls (n = 22). Bacterial composition of the gut microbiome was analyzed by 16S rRNA gene sequencing from fecal specimens. Plasma and urine sex hormones were quantified using high-performance liquid chromatography/mass spectrometry.

RESULTS: We found evidence that some β-glucuronidase positive bacteria were enriched in the breast cancer patients compared to healthy controls, whereas abundances of some β-glucuronidase negative bacteria were reduced. There was also a wide distribution of prevalence of β-glucuronidase positive taxa in both breast cancer subjects and healthy controls, as well as higher probability of breast cancer subjects having higher average β-glucuronidase levels. Significant differences were found in endogenous progesterone levels between the breast cancer patients and healthy controls.

CONCLUSION: This pilot study showed differences in the gut microbiome and endogenous progesterone levels among postmenopausal women with hormone receptor-positive breast cancer compared with healthy controls. These interesting findings may have implications for breast cancer risk and prevention and warrant further exploration.},
}

Humans
Female
*Breast Neoplasms/microbiology/metabolism/pathology/blood
*Postmenopause
Case-Control Studies
Prospective Studies
*Gastrointestinal Microbiome
Middle Aged
Aged
Receptors, Progesterone/metabolism
Receptors, Estrogen/metabolism
*Gonadal Steroid Hormones/blood/urine/metabolism
RNA, Ribosomal, 16S/genetics

@article {pmid41044363,
year = {2025},
author = {Catacutan, DB and Tran, V and Arnold, A and Alexander, J and Corso, G and Yousefi, Y and Tu, MM and McLellan, S and Tertigas, D and Magolan, J and Surette, MG and Brown, ED and Coombes, BK and Barzilay, R and Stokes, JM},
title = {Discovery and artificial intelligence-guided mechanistic elucidation of a narrow-spectrum antibiotic.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41044363},
issn = {2058-5276},
abstract = {Current clinical antibiotics are largely broad-spectrum agents that can alter the gut microbiome and promote colonization by Enterobacteriaceae, which are often drug resistant. This includes adherent-invasive Escherichia coli (AIEC), particularly in patients with inflammatory bowel disease, in which dysbiosis creates a niche for this pathogen to colonize. There is an urgent and unmet need for novel narrow-spectrum and microbiome-sparing antibiotics. Here we screened 10,747 bioactive small molecules for antibacterial activity against AIEC and discovered enterololin, an antibacterial compound with targeted activity against Enterobacteriaceae species. Enterololin could overcome intrinsic and acquired resistance mechanisms in clinical isolates when combined with a subinhibitory concentration of SPR741, a polymyxin B analogue used here to increase outer membrane permeability in Gram-negative bacteria. Molecular substructure- and deep learning-guided mechanism-of-action investigations revealed that enterololin perturbs lipoprotein trafficking through a mechanism involving the LolCDE complex, laboratory-evolved resistant mutants predominantly mapped to lolC and lolE, with an in vitro frequency of resistance of ~10[-8] to 10[-7]. Enterololin showed low mammalian cytotoxicity (HEK293 half-maximal inhibitory concentration ~100 µg ml[-1]) and suppressed AIEC infection in mouse models when administered in combination with SPR741, while largely preserving the overall microbiome composition. This study highlights the utility of deep learning methods for predicting molecular interactions and identifies a promising Enterobacteriaceae-specific antibacterial candidate for further development.},
}

@article {pmid41044104,
year = {2025},
author = {Hafeez, SH and Khalid, A and Ahmed, S and Umrani, F and Qureshi, AK and Ahmed, K and Shaheen, F and Hotwani, A and Kabir, F and Moore, SR and Ali, SA and Iqbal, J and Iqbal, NT},
title = {Fermented pickles improve gut microbiota and immune profile in women in a community trial in rural Pakistan.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34522},
pmid = {41044104},
issn = {2045-2322},
support = {5D43TW007585-13//National Institute of Health's Fogarty International Center/ ; 5D43TW007585-13//National Institute of Health's Fogarty International Center/ ; 5D43TW007585-13//National Institute of Health's Fogarty International Center/ ; 5D43TW007585-13//National Institute of Health's Fogarty International Center/ ; INV- 033567//Bill & Melinda Gates Foundation/ ; INV- 033567//Bill & Melinda Gates Foundation/ ; INV- 033567//Bill & Melinda Gates Foundation/ ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Adult ; Rural Population ; Pakistan ; Biomarkers ; Feces/microbiology ; *Fermented Foods ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Peroxidase ; Prospective Studies ; Lipocalin-2 ; },
abstract = {A gut microbiome-targeted diet can potentially mitigate chronic diseases, including malnutrition. In a prospective 12-week intervention trial, we evaluated the effects of six different plant-based fermented pickles (~ 50 g/day) on clinical, inflammatory, and gut microbiota parameters in a cohort of women (n = 230) in a rural setting with a high prevalence of undernutrition. Blood was collected at two, whereas stool was collected at three timepoints. Among fecal biomarkers, myeloperoxidase (MPO), Lipocalin-2 (LCN2), and 16S rRNA gene sequencing were measured at baseline, 8[th,] and 12[th] weeks. Overall, the compliance rate was > 70%. Among radish group, WBCs (p = 0.002, two-tailed paired T-test) decreased, whereas neutrophils and platelets decreased among both radish (p = 0.016, p = 0.017, two-tailed paired T-test) and carrot (p = 0.005, p = 0.006, two-tailed paired T-test) groups after intervention. Similarly, in lemon-chilli group, platelets decreased while mean corpuscular hemoglobin (MCH) increased (p < 0.001, p = 0.022, two-tailed paired T-test). In onion and lemon-chilli groups, α- (р =0.001 and p = 0.0005, Kruskal-Wallis Test, respectively) and β-diversity indices (p = 9e-04 and p = 0.022, pairwise PERMANOVA, respectively) were significantly increased, post-intervention. Linear discriminant analysis (LDA) of lemon-chilli group identified 25 bacterial taxa markers in 8[th] and 12[th] week, which included Eggerthellaceae and Oscillospiraceae, Erysipelatoclostridiaceae and Subdoligranulum. Correlation analysis revealed six taxa negatively associated with inflammatory markers such as C-reactive protein (CRP), LCN2, and platelets. Our study provides preliminary evidence that the consumption of traditional fermented pickles leads to beneficial changes in women's hematological and gut microbiota profiles.},
}

Humans
Female
*Gastrointestinal Microbiome
Adult
Rural Population
Pakistan
Biomarkers
Feces/microbiology
*Fermented Foods
RNA, Ribosomal, 16S/genetics
Middle Aged
Peroxidase
Prospective Studies
Lipocalin-2

@article {pmid41044018,
year = {2025},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {Soil microbes: below-ground defenders against desertification.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2025.09.014},
pmid = {41044018},
issn = {1872-8383},
abstract = {Soil microbes act as below-ground defenders against desertification by several mechanisms, such as rhizosheath formation, necromass accumulation, biological soil crusts, exopolysaccharide (EPS) production, hyphal networks, and calcium carbonate precipitation. Here, we discuss how soil microbes drive ecosystem recovery in drylands, offering promising, nature-based strategies for restoring soils in the face of desertification.},
}

@article {pmid41039216,
year = {2025},
author = {Ma, Y and Wang, D and Yu, X and Fan, Y and Yang, Z and Gao, X and Huang, X and Meng, J and Cheng, P and Liu, X and Liu, Z and Li, X},
title = {Moderate altitude exposure induced gut microbiota enterotype shifts impacting host serum metabolome and phenome.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {591},
pmid = {41039216},
issn = {1471-2180},
support = {2023YFE0114300//National key research and development program intergovernmental key projects/ ; No.2024A1515012697//Guangdong Provincial Basic and Applied Basic Research Fund Project/ ; No. 202206010044//Science and Technology Program of Guangzhou, China/ ; No. U24A20652//The Joint Funds of the Natural Science Foundation of China/ ; No. 82272246//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Consistent patterns of gut microbiota variations, particularly in relative abundance, have been identified in the adult human gut. Enterotype, another general measure of the gut microbiota, is a valuable approach for categorizing the human gut microbiota into distinct clusters. The impact of different enterotypes on human health varies, and the changes induced by moderate altitude exposure remain unclear. This study aimed to conduct a comprehensive investigation of the cascade effects triggered by enterotype shifts following moderate altitude exposure.

RESULTS: Using shotgun metagenome sequencing, participants before and after moderate-altitude exposure were classified into cluster BL (dominated by Blautia) and cluster BA (dominated by Bacteroides). Relative to cluster BL, cluster BA consisted predominantly of individuals exposed to moderate altitude. Compared to cluster BL, Cluster BA exhibited rewired metabolism of serum metabolites (i.e., amino acids, fatty acids and bile acids) and gut microbiota, lower inflammatory factor levels (i.e., tumor necrosis factor-α (TNF-α)), and sparser correlations among these parameters. Individuals with baseline BL enterotype who transitioned to the BA enterotype following moderate-altitude exposure showed prominent improvement in fasting blood glucose (FBG) levels, with higher abundance of Bacteroidetes species (e.g., Bacteroides thetaiotaomicron, and Bacteroides uniformis), but lower Proteobacteria species abundance (e.g., Escherichia coli) and decreased L-Glutamic acid levels. Furthermore, fecal microbiota transplantation (FMT) from moderate-altitude exposed individuals to high-fat diet (HFD) fed mice confirmed increased Bacteroides abundance shifts associated with improvements in glucose homeostasis regulation and rewired amino acid metabolism. In addition, significant increases in alanine aminotransferase (ALT) levels but decreased serum creatinine (Scr), arterial oxygen saturation (SaO2), 4-Hydroxyproline, L-Glutamic acid, L-Asparagine, L-Threonine, L-Citrulline, L-Lysine and Isovaleric acid levels were identified as potentially important signals for individuals upon moderate altitude exposure, regardless of the gut microbiota enterotype.

CONCLUSIONS: Moderate altitude exposure could induce enterotype switching, and a Bacteroides-dominant enterotype may be a beneficial pattern of the gut microbiome related to host metabolism. Moderate-altitude exposure has potential implications for glycemic control, suggesting new avenues for managing FBG levels in future.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04245-4.},
}

@article {pmid41043862,
year = {2025},
author = {Jeong, SH and Kim, YJ and Shin, JY and Oh, KW and Lee, JW and Lee, PH},
title = {DPP-4 inhibitor alleviates gut-brain axis pathology in Parkinson's disease.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-334988},
pmid = {41043862},
issn = {1468-3288},
abstract = {BACKGROUND: Dipeptidyl peptidase-4 inhibitors (DPP-4is) have been reported to exhibit therapeutic effects in Parkinson's disease (PD), increasing their potential for drug repurposing. One aspect of PD pathogenesis is thought to be associated with the gut-brain axis, where α-synuclein from the gut is transmitted to the brain via the vagus nerve (VN).

OBJECTIVE: We explored whether sitagliptin, a DPP-4i, exhibits a protective effect in a low-dose rotenone-treated gut-brain axis-associated PD model.

DESIGN: To explore the effect of sitagliptin, we used the oral rotenone-treated mouse model, which showed spreading of pathological α-synuclein from the intestine in a stereotypic manner via the VN into the midbrain with motor deficits.

RESULTS: Sitagliptin mitigated rotenone-induced gut inflammation and toll-like receptor 2 (TLR2) expression, reduced α-synuclein accumulation in the gut, VN and brain and lessened neuronal loss in the medulla and midbrain with recovery of motor performance. In addition, sitagliptin suppressed inflammation in response to a TLR2 agonist and rotenone in macrophages, enteric glial cells and enteroendocrine cell lines in vitro. In secretin tumour cell 1, an enteroendocrine cell line, sitagliptin also decreased rotenone-induced endogenous α-synuclein levels. The beneficial effects of sitagliptin were maintained even under glucagon-like peptide-1 receptor blockade. Notably, sitagliptin significantly altered the gut microbiome, shifting towards a profile that may counteract PD pathology.

CONCLUSION: These findings demonstrated that sitagliptin alleviated α-synuclein deposition in the gut and brain through modulation of TLR2-mediated inflammation and altered the gut microbiome composition towards a more favourable profile, which indicates that DPP-4is can offer a novel therapeutic avenue for managing PD.},
}

@article {pmid41043686,
year = {2025},
author = {Biruete, A and Buobu, PS and Considine, R and Hoxha, EM and Eicher-Miller, HA and Kinzig, KP and Panjwani, AA and Running, CA and Rutigliani, G and Savaiano, DA and Veile, AJ and Wolf, PM and Mattes, R},
title = {Ingestive Behavior and Precision Nutrition: Part of the Puzzle.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100531},
doi = {10.1016/j.advnut.2025.100531},
pmid = {41043686},
issn = {2156-5376},
abstract = {The marked individual variability in response to common dietary exposures necessitates tailoring of dietary guidance to individuals, or small groups of individuals with similar needs, to optimize health. This is a complex task requiring integration of environmental, cultural, psychological and biological contributions. Work in the area of precision nutrition is an effort to translate science into practice. A research roadmap developed through an National Institutes of Health (NIH) conference identified many of the inputs that require quantification. Better characterization of ingestive behaviors is one key area. The aim of this narrative review is to summarize current understanding of the influences of age, sex, Body Mass Index (BMI), ethnicity and genetics on ingestive behaviors, including culture, sensory function, appetite, dietary intake, the gut-brain axis and microbiome. To do so, the extant literature was accessed through search engines relevant to the various topics covered. Outcomes assessed varied topically. In addition to compiling evidence on the nature and magnitude of these relationships, this review highlights the degree of individual variability in attributes or responses to an intervention. More broadly, it: a) documents that cause and effect relationships are difficult to establish as most are dynamic and interactive; b) there are inherent and learned contributions to both behavior and biology that will require different considerations and offer different opportunities for manipulation; c) a focus on intuitive approaches may not be as successful as desired; d) that external influences can, and often do, override internal influences of biology; and e) there are multiple ways to construct healthful diets. At the same time, it is vital that improved methods to characterize the multiple relevant inputs to ingestive behavior be developed. It is hoped the evidence compiled here will inform efforts to develop precision nutrition guidance.},
}

@article {pmid41043678,
year = {2025},
author = {Kumar, P and Gulati, M and Kapoor, B and Yadav, AK and Hussain, MS and Kumar, R},
title = {Beyond the HCG test: Microbiome-based diagnosis of pregnancy.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {},
number = {},
pages = {120639},
doi = {10.1016/j.cca.2025.120639},
pmid = {41043678},
issn = {1873-3492},
abstract = {The complex but definitive relationship between pregnancy and the body microbiota offers a significant opportunity for novel diagnostic techniques. This work proposes a new diagnostic method that correlates the significant changes in the gut, vaginal, and oral microbiota composition that occur in the early stages of pregnancy. The main premise is identification of those microbial indicators that are strongly linked to early pregnancy by describing the periodic shifts in these microbial ecosystems. Early and precise pregnancy identification may be made possible by these biomarkers' potential as highly sensitive and precise indicators. More importantly, understanding of the fundamental processes by which the microbiota in various organs affects pregnancy outcomes, tailored therapies to enhance the health of both the mother and the foetus may be considered as a long-term goal. Analysis of vaginal swabs or saliva is proposed as a non-invasive method that might transform prenatal care. Healthcare professionals might monitor pregnancy progress, understand and mitigate the expected problems, and initiate prompt measures by identifying early pregnancy indicators. Finding microbiome-based indicators of pregnancy complications may also make it possible to identify at-risk patients early and implement individualised treatment plans. We may get fresh understanding of the intricacies of pregnancy and create creative methods to enhance the health of both mothers and children by utilizing the potential of the human microbiome.},
}

@article {pmid41043575,
year = {2025},
author = {Ahmed, LA and Al-Massri, KF},
title = {Insights into the Role of Gut Microbiota Modulation in the Management of Various Cardiovascular Diseases: A New Approach for Improving the Efficacy of Current Cardiovascular Medications.},
journal = {European journal of pharmacology},
volume = {},
number = {},
pages = {178210},
doi = {10.1016/j.ejphar.2025.178210},
pmid = {41043575},
issn = {1879-0712},
abstract = {Gut microbiome is an emerging contributor to various cardiovascular diseases (CVDs) where gut dysbiosis increases the risk of development and progression of atherosclerosis, coronary artery diseases, hypertension, and heart failure. Microbiota can also affect the metabolism of medications including cardiovascular drugs, resulting in alteration of their pharmacokinetics and pharmacodynamics or producing metabolites which can interfere with response of these drugs. Importantly, CVDs require prolonged pharmacological interventions with medications which may have impacts on the diversity and composition of gut microbiota. Gut microbiota modulation using diets, prebiotics, probiotics, fecal microbiota transplantation, and microbial trimethylamine-lyase inhibitors, has also shown benefits in the management of CVDs where gut microbiota and their metabolites have recently been studied as potential targets for the management of these diseases. Specifically, using innovative microbiota therapies in combination with traditional pharmacological agents have been evaluated for additional benefits in various CVDs. However, assessing the interactions among host factors, gut microbiome, and drug response will be essential for the development of new therapeutic targets for cardiovascular disorders, ultimately hoping better prognosis and patient's quality of life for those affected with CVDs.},
}

@article {pmid41043335,
year = {2025},
author = {He, B and Ma, Y and Wang, K and Bing, P and Ji, L and Tian, G and Liu, H and He, P and Yang, J},
title = {Microbiome-transcriptome-histology triad enhances survival risk stratification in multiple cancers.},
journal = {Computational biology and chemistry},
volume = {120},
number = {Pt 2},
pages = {108703},
doi = {10.1016/j.compbiolchem.2025.108703},
pmid = {41043335},
issn = {1476-928X},
abstract = {Accurate prognostic stratification is essential for optimizing postoperative therapeutic strategies in oncology. While deep learning approaches have shown promise for survival prediction through unimodal analyses of histopathological images, transcriptomic profiles, and microbial signatures, their clinical utility remains limited due to fragmented biological insights. In this study, we introduce HMTsurv, a multimodal survival prediction framework that integrates digital histopathology, host transcriptomics, and tumor-associated microbiome features. Utilizing multi-omics datasets from four major malignancies-colorectal, gastric, hepatocellular, and breast cancers-our model exhibited superior prognostic accuracy (c-index: 0.68-0.72) when compared to single-modality benchmarks, as validated through rigorous cross-validation methods. Notably, our model achieved robust risk stratification (log-rank p < 0.001 across all cohorts) as demonstrated by Kaplan-Meier analysis, effectively distinguishing patients into distinct survival trajectories. Systematic examination of multimodal signatures identified 14 pan-cancer survival biomarkers, including MAGE family genes, which were consistently upregulated in high-risk subgroups. Additionally, we elucidated distinct histopathological patterns, dysregulated microbial communities, and altered gene-microbiota co-expression networks that were predictive of adverse outcomes. This study not only establishes a generalizable multimodal architecture for cancer prognosis but also elucidates the intricate interactions among histological, molecular, and ecological determinants of survival, providing a clinically actionable framework for precision oncology.},
}

@article {pmid41043307,
year = {2025},
author = {Ji, Z and Liu, S and Tian, Z and Guo, N and Wei, W and Jiang, Q},
title = {Tooth Loss-Induced Gut Dysbiosis Promotes Neuroinflammation via L-Asparagine-Mediated Neuronal Toxicity.},
journal = {International dental journal},
volume = {75},
number = {6},
pages = {103929},
doi = {10.1016/j.identj.2025.103929},
pmid = {41043307},
issn = {1875-595X},
abstract = {INTRODUCTION AND AIMS: Tooth loss is not only a dental issue but also affects gut microbial composition and downstream physiological responses. This study investigates how tooth loss-induced alterations in the gut microbiota influence metabolic and neural function. This study aimed to elucidate the mechanistic links between microbiota dysbiosis, metabolic imbalance, and neuroinflammation following tooth loss.

METHODS: Using a murine model, the first molars of C57BL/6 mice were extracted, followed by the collection of fecal samples, serum, and brain tissue for subsequent metagenomic sequencing, metabolomics, and transcriptomics. Pro-inflammatory markers (IL-6, TNF-α) and PSD95 expression were assessed. The neurotoxic effects of key metabolite L-Asparagine were validated using HT22 neuronal cell models.

RESULTS: Tooth loss induced gut microbiota dysbiosis, which subsequently mediated pathological alterations in brain tissue, characterised by a reduction in beneficial Butyribacter and an increase in pathogenic taxa. Corresponding shifts in systemic metabolism were observed, along with changes in brain gene expression, particularly in genes related to neuroinflammation. In vitro experiments further demonstrated that L-Asparagine directly induced neurotoxicity in HT22 hippocampal neurons through ROS overproduction, apoptosis, and inflammatory activation.

CONCLUSION: Tooth loss induced gut microbiota dysbiosis, systemic metabolic disruptions, and neuroinflammatory responses. Our findings demonstrated that tooth loss exacerbated neuroinflammation via gut-derived L-Asparagine, providing a mechanistic link in the oral-gut-brain axis.

CLINICAL RELEVANCE: This study demonstrated that molar extraction in mice disrupted gut microbiota and promoted neuroinflammation via L-Asparagine, suggesting that maintaining oral integrity might help preserve neurological health. This could open new avenues for microbiota-targeted interventions in neurodegenerative disease prevention.},
}

@article {pmid41043233,
year = {2025},
author = {Sun, C and Liu, X and Wang, M and Zhang, Q and Geng, H and Ji, X and Wang, H and Li, S and Jin, E and Zhang, F},
title = {Metagenome-metabolome responses to linarin alleviate hepatic inflammatory response, oxidative damage, and apoptosis in an ETEC-challenged weaned piglet model.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119145},
doi = {10.1016/j.ecoenv.2025.119145},
pmid = {41043233},
issn = {1090-2414},
abstract = {Enterotoxigenic Escherichia coli (ETEC), present in contaminated food, water, and environments, can induce hepatic injury via the gut-liver axis, posing a serious threat to ecological systems and public health. Linarin, a flavonoid extracted from Chrysanthemum indicum, exhibits anti-inflammatory and antioxidant properties, but its protective effects against ETEC-induced hepatic injury remain unclear. In this study, 24 weaned piglets were randomly assigned to four groups: BD+NB (basal diet + nutrient broth), LN+NB (basal diet + 150 mg/kg linarin + nutrient broth), BD+ETEC (basal diet + ETEC challenge), and LN+ETEC (basal diet + 150 mg/kg linarin + ETEC challenge). Dietary linarin significantly increased ADFI and the genes related to oxidative damage and bile acid metabolism, while decreasing F:G ratio, liver index, serum liver function-related parameters, and the genes related to inflammatory response and apoptosis. It also significantly altered the relative abundances of gut microbiota, which were closely associated with key hepatic metabolic pathways, including nicotinate and nicotinamide metabolism and fatty acid biosynthesis. Our study suggests that linarin alleviated ETEC-induced hepatic inflammation and apoptosis, enhanced antioxidant capacity, and regulated bile acid metabolism. The potential mechanism involves linarin modulating gut microbiota-mediated key hepatic metabolic pathways to exert protective effects. In contrast to previous flavonoid-ETEC studies that primarily focused on the gut, this study, based on the gut-liver axis, investigates the potential mechanisms by which linarin is associated with the alleviation of ETEC-induced hepatic injury through integrated analysis of gut microbiome metagenomics and liver metabolomics.},
}

@article {pmid41043219,
year = {2025},
author = {Gugescu, L and Yang, Y and Kool, JF and Fyhrquist, N and Wincent, E and Alenius, H},
title = {Microbiota modulates compound-specific toxicity of environmental chemicals: A multi-omics analysis in zebrafish embryos.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109828},
doi = {10.1016/j.envint.2025.109828},
pmid = {41043219},
issn = {1873-6750},
abstract = {Interactions between gut microbiota and environmental chemicals critically influence toxicological outcomes, yet mechanistic insights remain limited. Here, we combine developmental toxicity with full-length 16S rRNA gene sequencing, transcriptomic, and metabolomic analyses in germ-free (GF) and conventionally colonized wild-type (WT) zebrafish embryos to elucidate the microbiota's role in modulating chemical toxicity. Using representative compounds from major classes of environmental contaminants, we show that microbial presence significantly alters toxicity profiles in a compound-specific manner. The perfluorinated contaminant PFOS (perfluorooctanesulfonic acid) induced the strongest microbiota-dependent effects, with a greater number of differentially expressed genes in WT embryos and pronounced changes in immune and stress-related pathways. The pesticide boscalid and bisphenol F elicited distinct microbiota-modulated transcriptional and metabolic responses. Gene network analysis identified baseline microbial regulation of immune and metabolic programs, while metabolomics showed PFOS-dependent changes in L-tryptophan and its microbe-associated metabolites, including inosine, indoxyl sulfate and indole acetaldehyde, exclusively in WT embryos. These findings establish a mechanistically grounded framework for microbiota-chemical interactions and highlight the importance of integrating microbiome context into environmental health assessments.},
}

@article {pmid41043062,
year = {2025},
author = {Malogan, J and Hallowell, HA and Francis, B and Suez, J},
title = {Supplementation and Elimination of Microbiome-Produced Metabolites in the Treatment of Human Disease.},
journal = {Annals of the New York Academy of Sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/nyas.70103},
pmid = {41043062},
issn = {1749-6632},
abstract = {The human gut microbiome has a complex and influential relationship with host physiology that is governed through commensal-derived metabolites, small molecules, and endogenous microbial patterns. Indeed, microbial metabolites from the gut microbiome have been implicated in promoting health as well as contributing to the pathogenesis of microbiome-associated diseases. Live microbial therapeutics, such as probiotics and fecal microbiota transplantations, have been extensively utilized to establish health-promoting assemblages of bacteria and their associated beneficial metabolites. However, broad clinical use of live microbial therapeutics is limited by efficacy, specificity, and safety concerns. To circumvent this, a postbiotic approach can be taken, in which a beneficial effect may be achieved by direct administration of bacterially derived bioactive molecules. Alternatively, in cases where microbiome-derived metabolites drive disease, specific oral inhibitors can be used to restrict compound production. In this review, we examine the use of postbiotics to alleviate disease and highlight recent translational successes. Additionally, we discuss emerging approaches for precision elimination of disease-causing metabolites, as well as the exciting possibility of utilizing bacteriophages to modulate the production of metabolites in the microbiome.},
}

@article {pmid41042689,
year = {2025},
author = {Gao, S and Li, L and Wang, J and Wang, Y and Dong, Y},
title = {MicroSTNet: a spatio-temporal graph-based framework for time-series microbiome analysis.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001519},
pmid = {41042689},
issn = {2057-5858},
mesh = {Humans ; *Microbiota/genetics ; Mouth/microbiology ; Spatio-Temporal Analysis ; *Gastrointestinal Microbiome ; Algorithms ; Machine Learning ; },
abstract = {The structure and function of microbial communities are profoundly influenced by spatio-temporal dynamics. While existing machine learning algorithms are extensively used for phenotype prediction based on microbial communities, particularly for disease forecasting, they fail to fully utilize the spatio-temporal dynamics embedded in microbial data. Moreover, data collected at a single time point often proves inadequate for the accurate prediction of host or environmental phenotypes. This study investigates the interaction dynamics of microbial communities in closed environments using data from two independent research projects. We introduce the microbial spatio-temporal network model, which combines two-stream spatio-temporal graph convolutional networks with long short-term memory to predict dynamic microbial abundance in the human oral cavity and gut. The model captures the temporal trajectories of microbes together with spatial features embedded in network structures, enabling accurate prediction of future community trends. Experimental validation confirmed its ability to track temporal patterns with high accuracy, even for micro-organisms exhibiting significant fluctuations. Ablation experiments demonstrated that the integrated model outperforms individual components, harnessing the strengths of both approaches. This technology presents a promising strategy for low-cost, non-invasive early diagnosis of human diseases, offering valuable insights into future health risks.},
}

Humans
*Microbiota/genetics
Mouth/microbiology
Spatio-Temporal Analysis
*Gastrointestinal Microbiome
Algorithms
Machine Learning

@article {pmid41042595,
year = {2025},
author = {Bywater-Brenna, KK and Unnikrishnan, M},
title = {Unravelling three-way interactions between Clostridioides difficile, microbiota and the host.},
journal = {Journal of medical microbiology},
volume = {74},
number = {10},
pages = {},
doi = {10.1099/jmm.0.002067},
pmid = {41042595},
issn = {1473-5644},
mesh = {*Clostridioides difficile/physiology ; Humans ; *Clostridium Infections/microbiology/immunology ; *Gastrointestinal Microbiome ; Animals ; Dysbiosis/microbiology ; *Host-Pathogen Interactions ; },
abstract = {Clostridioides difficile infection is a global issue, representing a huge financial burden on healthcare systems worldwide which is further exacerbated by high recurrence rates. Infection is closely linked with the gut microbiome status, with successful C. difficile colonization usually occurring when there is dysbiosis. Our understanding of the molecular mechanisms underlying microbiota-mediated colonization resistance has advanced significantly in recent years, although the nuanced crosstalk occurring between C. difficile, the gut microbiota and host mucosa has yet to be fully elucidated. Deciphering these three-way interactions is critical for the development of effective therapeutic and prophylactic strategies. This review will discuss known interactions between this pathogen, the microbiota and the host in addition to the tools available to dissect complex microbial interchanges.},
}

*Clostridioides difficile/physiology
Humans
*Clostridium Infections/microbiology/immunology
*Gastrointestinal Microbiome
Animals
Dysbiosis/microbiology
*Host-Pathogen Interactions

@article {pmid41042593,
year = {2025},
author = {Varliero, G and Bauder, A and Stierli, B and Qi, W and Frey, B},
title = {Host-virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001524},
pmid = {41042593},
issn = {2057-5858},
mesh = {*Ice Cover/microbiology/virology ; *Bacteria/genetics/virology/classification ; *Microbiota/genetics ; *Viruses/genetics/classification/isolation & purification ; Switzerland ; Metagenomics/methods ; Ecosystem ; Host Specificity ; },
abstract = {Glaciers are retreating rapidly, altering ecosystem dynamics and increasing meltwater outflow into populated areas. Understanding microbial-virome interactions is crucial for predicting the consequences of this release. We sampled ice from four shallow pits in the weathering crust of the Rhonegletscher, Swiss Alps, and found a microbiome dominated by bacteria and microeukaryotes, alongside a metavirome infecting both groups. Viruses exhibited variable host specificity, with some targeting particular taxa and others showing a broader infectivity range. Variable genomic regions, including metagenomic and metaviromic islands, were enriched in genes related to replication, recombination, repair and transposable elements. Detected auxiliary metabolic genes were primarily involved in host coenzyme biosynthesis, uptake or utilization and in altering bacterial methylation patterns to evade detection. These findings underscore the major role of viruses in regulating microbial dynamics in glaciers and their potential downstream environmental impacts.},
}

*Ice Cover/microbiology/virology
*Bacteria/genetics/virology/classification
*Microbiota/genetics
*Viruses/genetics/classification/isolation & purification
Switzerland
Metagenomics/methods
Ecosystem
Host Specificity

@article {pmid41042542,
year = {2025},
author = {Torrez Lamberti, MF and Thompson, S and Harrison, NA and Gardner, CL and da Silva, DR and Teixeira, LD and Kondepudi, KK and Gonzalez, CF and Chukkapalli, SS and Lorca, GL},
title = {Lactobacillus johnsonii N6.2 Improves Glycemia, and Reduces Diabetes-induced Organ Injury in the db/db Mice Model.},
journal = {The Journal of endocrinology},
volume = {},
number = {},
pages = {},
doi = {10.1530/JOE-25-0184},
pmid = {41042542},
issn = {1479-6805},
abstract = {Diabetes mellitus is a complex metabolic disorder characterized by hyperglycemia as well as the associated comorbidities. Type 2 diabetes is also associated with dysfunction of liver, kidney and nervous system. In addition, an altered microbiota is frequently observed in subjects with Type 2 diabetes. In this study a db/db (diabetic) mouse model of Type 2 diabetes was used to elucidate the beneficial effects of the probiotic Lactobacillus johnsonii N6.2. To evaluate metabolic effects, we performed metabolomics on liver samples, and RNA-seq from liver and visceral adipose tissue, followed by qRT-PCR validation. Using L. johnsonii N6.2 extracellular vesicles we evaluated lipid accumulation in hepatocytes. Finally, the gut microbiome of db/db mice was profiled using 16S rRNA sequencing. We observed that administration of the probiotic improved glycemic levels and decreased diabetes scores, as well as Type 2 diabetes-associated injury to the pancreas, liver and kidneys. Liver metabolomic and transcriptome analyses identified biomarkers of L. johnsonii N6.2 activity, including modulation of the vitamin K pathway, upregulation of FGF21-, a key regulator of glucose and lipid metabolism, and alternations in selected circadian genes. This study elucidates the beneficial effects of L. johnsonii N6.2, against the common symptoms of type 2 diabetes, highlighting its potential as an adjuvant therapeutic agent.},
}

@article {pmid41042396,
year = {2025},
author = {Wu, J and Zhou, J and Zhao, Q and Yang, C and Bai, Y},
title = {Metagenomic analysis of microbial community dynamics in konjac rhizosphere during soft rot disease progression.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {212},
pmid = {41042396},
issn = {1432-0614},
support = {32072558//the Nature Science Foundation of China/ ; 2024-620-000-001-007//Hubei Agricultural Science and Technology Innovation Center Innovation Team Project/ ; },
mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Soil Microbiology ; Metagenomics ; *Amorphophallus/microbiology ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation & purification ; Fungi/genetics/classification ; },
abstract = {Amorphophallus konjac, the sole glucomannan-rich species in the Araceae family, faces significant yield and quality losses due to soft rot disease. Understanding the relationship between soil microbial communities and soft rot incidence is critical for sustainable konjac production. Metagenomic profiling was employed to systematically characterize the spatiotemporal dynamics of rhizosphere microbiomes during disease progression. Microbial alpha diversity (Chao1 index) exhibited a significant peak in the rhizosphere of diseased plants at the mature stage, contrasting with stable diversity patterns in healthy and latently infected groups, indicating dysbiosis-associated richness inflation during disease progression. Principal coordinate analysis (PCoA) revealed significant divergence in rhizosphere microbial structures between diseased and healthy/latently infected groups, with higher compositional variability observed in diseased samples. At the phylum level, Chloroflexi and Acidobacteria abundances in healthy mature plants exceeded those in diseased plants by 11.54% and 4.6%, respectively, while pathogenic Rhizopus arrhizus and Rhizopus microsporus were significantly enriched in diseased mature plants. Correlation analyses demonstrated predominantly negative associations between bacterial species and soil factors, contrasting with positive fungal correlations. KEGG pathway annotation identified carbohydrate metabolism and amino acid synthesis as core microbial functions in the konjac rhizosphere. Collectively, Chloroflexi and Acidobacteria were validated as putative biocontrol agents, while Rhizopus spp. emerged as key drivers of soft rot development. These findings provide mechanistic insights for designing microbiome-based biocontrol strategies to mitigate konjac soft rot, offering a sustainable alternative to conventional agrochemical reliance. KEY POINTS: • Diseased konjac microbial richness peaks; healthy plants enrich Chloroflexi/Acidobacteria. • Rhizopus pathogens drive soft rot; bacteria and fungi show opposing soil factor links. • Lays groundwork for microbiome approaches to cut agrochemicals in konjac rot control.},
}

*Rhizosphere
*Plant Diseases/microbiology
*Soil Microbiology
Metagenomics
*Amorphophallus/microbiology
*Microbiota/genetics
Bacteria/classification/genetics/isolation & purification
Fungi/genetics/classification

@article {pmid41042380,
year = {2025},
author = {Wang, S and Jiang, H and Yao, T},
title = {Integrative genomics and functional immunology reveal Clostridia species as modulators of neuroinflammation in amyotrophic lateral sclerosis.},
journal = {Inflammation research : official journal of the European Histamine Research Society ... [et al.]},
volume = {74},
number = {1},
pages = {136},
pmid = {41042380},
issn = {1420-908X},
support = {2020B22//Doctoral Fund of the First Affiliated Hospital of Harbin Medical University/ ; 2023ZX07D06//The key research and development project of Heilongjiang Province/ ; 2022-KYYWF-0301//Innovative Scientific Research Funding Project of Harbin Medical University/ ; PL2024H140//Natural Science Foundation of Heilongjiang Province,China/ ; },
mesh = {Humans ; *Amyotrophic Lateral Sclerosis/immunology/microbiology/genetics ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Cytokines/immunology ; Genomics ; *Neuroinflammatory Diseases/immunology/microbiology/genetics ; Aged ; Myeloid-Derived Suppressor Cells/immunology ; Mendelian Randomization Analysis ; },
abstract = {OBJECTIVE: This multiomics study investigated causal relationships between the gut microbiota (GM), immune dysregulation, and amyotrophic lateral sclerosis (ALS) pathogenesis using Mendelian randomization (MR) with experimental validation.

MATERIALS: Analyses incorporated genome-wide data from 87,347 participants (GM: n = 7738; ALS: 20,806 patients, 59,804 controls; immune phenotypes: n = 3757), transcriptomic data from 71 subjects (56 ALS patients, 15 controls), and experimental validation in matched cohorts (n = 6 subjects per group).

METHODS: Two-sample bidirectional MR and mediation analysis were used to evaluate associations. Experimental validation employed flow cytometry for myeloid-derived suppressor cell quantification, enzyme-linked immunosorbent assay for cytokines, and real-time polymerase chain reaction for bacterial validation. Statistical analyses included inverse variance weighted methods with Cohen's d calculations.

RESULTS: Sixteen bacterial taxa, including p_Firmicutes.c_Clostridia, displayed protective associations with the risk of ALS, whereas sixteen showed harmful associations. Mediation analysis suggested that p_Firmicutes.c_Clostridia may confer protection through CD33+HLA-DR-myeloid-derived suppressor cell upregulation (23.8% mediation effect). Experimental validation confirmed fewer myeloid-derived suppressor cells in ALS patients (4.0 ± 0.8% vs. 7.5 ± 1.0%, p < 0.001, Cohen's d = 1.4) and lower levels of anti-inflammatory cytokines (TGF-β1: Cohen's d = 1.8, p < 0.001).

CONCLUSIONS: These findings support causal associations between gut microbial taxa and the ALS risk, which are mediated through immunoregulatory mechanisms, highlighting therapeutic targets within the gut‒immune‒brain axis.},
}

Humans
*Amyotrophic Lateral Sclerosis/immunology/microbiology/genetics
*Gastrointestinal Microbiome
Male
Female
Middle Aged
Cytokines/immunology
Genomics
*Neuroinflammatory Diseases/immunology/microbiology/genetics
Aged
Myeloid-Derived Suppressor Cells/immunology
Mendelian Randomization Analysis

@article {pmid41042228,
year = {2025},
author = {Paccou, J and Gagnon, C and Yu, EW and Rosen, CJ},
title = {Effects of weight-loss interventions on bone health in people living with obesity.},
journal = {Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research},
volume = {},
number = {},
pages = {},
doi = {10.1093/jbmr/zjaf135},
pmid = {41042228},
issn = {1523-4681},
abstract = {Strategies to reduce weight in people living with obesity (PwO) include calorie restriction, metabolic and bariatric surgery (MBS), and anti-obesity drugs including glucagon-like peptide-1 receptor agonists (GLP-1Ra), such as liraglutide and semaglutide. Although weight loss in PwO has many health benefits, it can result in increased bone loss and fracture risk. Indeed, the consequences of weight loss interventions are well known: (i) significant weight loss induced by caloric restriction and MBS results in high turnover bone loss and (ii) unlike calorie restriction, PwO experience a substantial deterioration in bone microarchitecture and strength associated with an increased risk of fracture after MBS, especially malabsorptive procedures. GLP-1 may enhance bone metabolism and improve bone quality, and liraglutide appears to have a positive effect on bone health despite significant weight loss in several rodent models. However, most of the positive effects on bone have been observed at concentrations much higher than those approved for obesity care in humans. The effects of GLP-1Ra on bone health in PwO are still limited; however, significant weight loss induced by GLP-1Ra may also result in accelerated bone turnover and bone loss, and semaglutide could lead to an increased risk of fractures in the at-risk population. The mechanisms responsible for the adverse skeletal effects of MBS are not yet fully understood, and there are insufficient human studies supporting pathophysiological hypotheses. However, data suggest that multiple mechanisms are involved, including nutritional factors, mechanical unloading, hormonal factors, adipokines, and alterations in the gut microbiome. Recommendations for the prevention and treatment of osteoporosis secondary to MBS are now available, and the efficacy of anti-osteoporosis medications in preventing bone loss has been evaluated in two randomized controlled trials. Priorities for future research include the development of effective approaches to reduce fracture risk in PwO following MBS and investigation of the effects of anti-obesity drugs on bone health.},
}

@article {pmid41041974,
year = {2025},
author = {Najafpour, B and Canario, AVM and Power, DM},
title = {Bacterial 16S Ribosomal Gene Fingerprints as a Tool to Diagnose and Mitigate Fish Larvae Gut Dysbiosis.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70187},
doi = {10.1111/1758-2229.70187},
pmid = {41041974},
issn = {1758-2229},
support = {UIDP/04326/2020//Portuguese national funds from FCT-Foundation for Science and Technology/ ; LA/P/0101/2020//Portuguese national funds from FCT-Foundation for Science and Technology/ ; 727610//European Unions Horizon 2020 research and innovation programme, PerformFISH/ ; 871108//European Unions Horizon 2020 research and innovation programme (AQUAEXCEL3.0)/ ; EMBRC.PT ALG-01-0145-FEDER-022121//The operational programmes CRESC Algarve 2020 and COMPETE 2020/ ; BIODATA.PT ALG-01-0145-FEDER-022231//The operational programmes CRESC Algarve 2020 and COMPETE 2020/ ; },
mesh = {Animals ; *Dysbiosis/microbiology/diagnosis/veterinary ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification/isolation & purification ; *Bass/microbiology ; *Sea Bream/microbiology ; Phylogeny ; *Fish Diseases/microbiology/diagnosis ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; },
abstract = {Dysbiosis is associated with shifts in the diversity or relative abundance of beneficial versus harmful bacteria, leading to health issues in organisms. This study investigated gut bacterial dysbiosis associated with larval quality using 16S rRNA gene sequencing. The gut microbiome of gilthead sea bream and European sea bass, key commercial species and vertebrate models, was examined in high- and low-quality larvae batches from several European hatcheries. Larval quality, hatchery site and species influenced bacterial diversity in the gut. Individuals from larval batches that performed well had higher microbial diversity in the gut and individuals from batches that performed poorly had a gut microbiota dominated by pathogenic Vibrio (e.g., V. aestuarianus and V. cortegadensis). The bacterial dysbiosis index revealed a notable predominance of Fusobacteriota and Firmicutes phyla, Thermoanaerobacteria class and Lactobacillaceae, Moritellaceae, Clostridiaceae, Thiotrichaceae and Shewanellaceae families in good-quality larvae batches, and a prevalence of the Proteobacteria phylum, Gammaproteobacteria class, Sphingomonadaceae and Vibrionaceae families in the gut of individuals from poor-quality larvae batches. A positive dysbiosis index (cutoff > 0.4) was associated with a high risk of decreased larval performance and quality. Additionally, the abundance of Clostridium_sensu_stricto_15, Shewanellaceae_unclassified, Cetobacterium, Psychrilyobacter, Moritella and Latilactobacillus genera in the gut of good production batches, and the Vibrio genus in the gut of poor production batches, identified these genus as potential markers for diagnosing and mitigating bacterial dysbiosis in fish and potentially other vertebrates.},
}

Animals
*Dysbiosis/microbiology/diagnosis/veterinary
Larva/microbiology
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
*Bacteria/genetics/classification/isolation & purification
*Bass/microbiology
*Sea Bream/microbiology
Phylogeny
*Fish Diseases/microbiology/diagnosis
DNA, Bacterial/genetics/chemistry
Sequence Analysis, DNA

@article {pmid41041899,
year = {2025},
author = {Ganamurali, N and Sabarathinam, S},
title = {β-Sitosterol targets the gut-brain-clock axis to ameliorate circadian disruption and metabolic dysfunction: A herb-pharmacomicrobiomic perspective.},
journal = {Chronobiology international},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/07420528.2025.2568586},
pmid = {41041899},
issn = {1525-6073},
abstract = {β-Sitosterol (BS) is a phytosterol that may contribute to circadian and metabolic regulation through multiple predicted mechanisms. Using network pharmacology, gene expression profiling, and microbiome analysis, this study suggests that BS could interact with nuclear receptors (PPARγ, PPARα, RORα, RORγ) and potentially influence CLOCK:BMAL1 transcriptional rhythms in peripheral tissues. BS was also predicted to be associated with PER2-related feedback and the synchronization of gluconeogenic and lipogenic pathways with the light-dark cycle. In addition, computational and preclinical evidence indicates that BS may influence the gut microbiome, supporting short-chain fatty acid-producing bacteria, intestinal barrier integrity, and inflammatory balance. Limited preclinical findings further suggest a potential role for BS in mitigating circadian misalignment and insulin resistance, with possible implications for lipid homeostasis. Future clinical studies are warranted to investigate BS supplementation across different chronotypes and dietary conditions in order to evaluate its chronotherapeutic potential. While the findings are promising, they remain preliminary, and human validation is essential to determine dosing strategies and therapeutic relevance. This study, therefore, highlights BS as a candidate compound with potential relevance to circadian disruptions and metabolic disorders, pending further experimental confirmation.},
}

@article {pmid41041846,
year = {2025},
author = {Zhao, Y and Yu, C and Zhang, J and Yao, Q and Zhu, X and Zhou, X},
title = {The gut‑skin axis: Emerging insights in understanding and treating skin diseases through gut microbiome modulation (Review).},
journal = {International journal of molecular medicine},
volume = {56},
number = {6},
pages = {},
doi = {10.3892/ijmm.2025.5651},
pmid = {41041846},
issn = {1791-244X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Skin Diseases/therapy/microbiology ; *Skin/microbiology/pathology ; Probiotics/therapeutic use ; Animals ; Prebiotics ; },
abstract = {Emerging evidence indicates a significant association between the composition and functionality of the gut microbiome and various skin disorders, including psoriasis, atopic dermatitis, acne and several dermatological conditions. The gut‑skin axis theory describes a complex bidirectional communication network between the gut and the skin, providing mechanistic insights into the pathogenesis of certain cutaneous diseases. Specifically, the gut microbiome influences skin health through the regulation of systemic immunity, inflammatory responses and metabolic pathways. Advances in high‑throughput sequencing and bioinformatics technologies have substantially enhanced the understanding of the role of the gut microbiome in skin pathology. Clinical and preclinical studies have demonstrated that restoring gut microbial homeostasis via interventions such as faecal microbiota transplantation, probiotics and prebiotics can ameliorate symptoms of skin diseases. Furthermore, personalized microbiome‑based therapies, next‑generation probiotics and dietary modifications hold promise for refining gut‑skin interactions and advancing precision medicine in dermatology. Therapeutic strategies targeting the gut‑skin axis offer novel avenues for innovative dermatological treatments, with future breakthroughs potentially involving microbial community engineering, postbiotics and artificial intelligence in microbiome‑related diagnostics. This narrative review summarizes recent advances in gut‑skin axis research, explores its potential in the prevention and management of selected dermatoses and discusses future trends and scientific developments in the field.},
}

Humans
*Gastrointestinal Microbiome
*Skin Diseases/therapy/microbiology
*Skin/microbiology/pathology
Probiotics/therapeutic use
Animals
Prebiotics

@article {pmid41041828,
year = {2025},
author = {Wang, J and Jiang, Y and Kuzyakov, Y and Han, Z and Liu, S and Huang, Y and Smith, P and van Groenigen, KJ and Zou, J},
title = {Toward Climate-Smart Rice Systems: Moving Beyond Cultivar Improvement.},
journal = {Global change biology},
volume = {31},
number = {10},
pages = {e70545},
doi = {10.1111/gcb.70545},
pmid = {41041828},
issn = {1365-2486},
mesh = {*Oryza/genetics/growth & development/physiology ; *Climate Change ; *Agriculture/methods ; Methane/metabolism ; *Plant Breeding/methods ; Crops, Agricultural/growth & development ; },
abstract = {Rice is one of the world's most important staple crops and a major source of agricultural methane emissions. Breeding strategies such as photosynthate allocation modification and biomass enhancement show potential, but their effectiveness is highly context dependent, shaped by water regimes and soil organic carbon levels. Cultivars effective under continuous flooding may fail, or even increase emissions, under optimized water regimes. This perspective argues for integrated strategies that combine cultivar improvement with water and organic matter management, microbiome regulation, and climate-resilient breeding to build climate-smart rice systems that ensure both yield stability and methane mitigation.},
}

*Oryza/genetics/growth & development/physiology
*Climate Change
*Agriculture/methods
Methane/metabolism
*Plant Breeding/methods
Crops, Agricultural/growth & development

@article {pmid41041568,
year = {2025},
author = {Klatt, N and Swanson, E and Broedlow, C and Cherenack, E and Nogueira, N and Basting, C and Yue, P and Chakrawarti, A and Schroeder, T and Salazar, A and Acosta, L and Raccamarich, P and Gale, M and Fein, L and Alcaide, M},
title = {Host-microbe interactions characterized by gene expression of cervical adhesion molecules, cytokines, and growth factors define the recurrence of bacterial vaginosis.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7576831/v1},
pmid = {41041568},
issn = {2693-5015},
abstract = {Bacterial vaginosis (BV) is a common vaginal condition with a high recurrence rate after treatment. In this longitudinal multi-omics study, we integrated cervical microbial metatranscriptomics, host transcriptomics, cytokine profiles, and behavioral data to investigate factors driving BV recurrence in women from Miami-Dade county (N24). Recurrence at 6 months occurred in 46% of participants after metronidazole treatment. Recurrence was preceded by increased transcriptional activity of Gardnerella and Fannyhessea, enriched for glycogen and maltose metabolism and iron scavenging. Host transcriptomic analysis of cervical tissue revealed reduced CEACAM5-7 expression and increased IL6 and EREG, indicating impaired epithelial integrity and persistent inflammation. Cytokine-gene correlations and Bayesian mediation models identified CEACAM7 as a key mediator linking inflammation and microbial activity to recurrence. Intravaginal practices further amplified risk. These findings uncover for the first time dynamic host-microbiome disruptions that persist after treatment and reveals new targets for diagnostic and therapeutic strategies to reduce BV recurrence.},
}

@article {pmid41041532,
year = {2025},
author = {Niraula, S and Khan, I and Jung, J and Stirewalt, SL and Alagna, M and Du, J and Xiong, L and Elmasri, A and Wu, E and Seed, P and Green, SJ and Ho, KJ},
title = {Comparative study of sample storage conditions on gut dysbiosis in peripheral artery disease.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7483387/v1},
pmid = {41041532},
issn = {2693-5015},
abstract = {BACKGROUND: Large-scale gut microbiome studies rely on fecal sample storage prior to batch sample preparation, sequencing, and analysis. Effects of storage methods have largely been studied using samples from healthy participants, where the microbial communities and the metabolic environment are in concordance. In diseased states, dysbiosis is more prone to environmental perturbation, which causes variable shifts in the communities. Cardiovascular diseases are associated with gut dysbiosis, but the effect of storage methods on the qualitative and quantitative aspects of dysbiosis is unknown. Thus, we examined the effects of 3 sample storage conditions on the fecal samples of patients with peripheral artery disease (PAD), a form of cardiovascular disease, and non-PAD controls.

METHODS AND RESULTS: This is a cross-sectional study of fecal samples collected from adults with PAD and non-PAD controls. All participants (12 non-PAD and 18 PAD) followed the home fecal sample collection protocol. Each sample was immediately frozen (IF), placed in modified Cary-Blair (CB), and stored in an OMNIgene•Gut vial. All samples were subjected to 16S rRNA gene amplicon sequencing of the hypervariable V4 region. A subset of glycerol stocks from IF and CB samples was thawed and cultured to compare revivification. We found significant differences in microbial composition and community structure between non-PAD and PAD groups based on storage conditions. Although we did not see the effect of an interaction term (disease group*storage condition) at the community level, we observed storage condition-specific differential abundance of genera in the PAD compared to the non-PAD group. The high number of differentially variable taxa in the PAD group samples further emphasize the need for standardizing storage conditions. The subset of samples stored in CB had less revivification potential than IF samples under both anaerobic and aerobic processing conditions.

CONCLUSIONS: Sample storage conditions and room temperature storage time differentially affect the microbial communities of fecal samples and revivification of glycerol stocks from non-PAD and PAD groups. The effects of storage conditions can bias microbiome-related disease biomarker discovery. Careful consideration should be given to sample storage conditions when analyzing fecal samples from diseased populations and when combining data from cohorts with samples stored in different conditions.},
}

@article {pmid41041324,
year = {2025},
author = {Alsayb, MA},
title = {Innovations in immunotherapy for autoimmune diseases: recent breakthroughs and future directions.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1647066},
pmid = {41041324},
issn = {1664-3224},
mesh = {Humans ; *Autoimmune Diseases/therapy/immunology ; *Immunotherapy/methods/trends ; Animals ; Antibodies, Bispecific/therapeutic use ; Immune Checkpoint Inhibitors/therapeutic use ; },
abstract = {Millions of people worldwide suffer from chronic and devastating autoimmune disorders, challenging contemporary medicine. These disorders develop when the immune system attacks its own tissues, causing inflammation and damage. Traditional treatments have focused on widespread immunosuppression, which can relieve symptoms but has serious adverse effects and does not address immunological dysregulation. This review discusses the current and future trends in immunotherapy for the management of autoimmune diseases, including advancements such as CAR T-cell therapy, bispecific antibodies, next-generation immune checkpoint modulators, targeted cytokine therapies, and microbiome-based interventions. The discussion is grounded in current scientific literature, focusing on mechanisms of action, recent breakthroughs, limitations, and potential future directions. Each of the related sections presents cutting-edge advancements, current challenges, and future opportunities for research and clinical translation.},
}

Humans
*Autoimmune Diseases/therapy/immunology
*Immunotherapy/methods/trends
Animals
Antibodies, Bispecific/therapeutic use
Immune Checkpoint Inhibitors/therapeutic use

@article {pmid41041139,
year = {2025},
author = {Berlanga, M and Martín-García, A and Guerrero, R and Riu-Aumatell, M and López-Tamames, E},
title = {Changes in healthy Wistar rat gut microbiome by short-term dietary cava lees intervention.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1641612},
pmid = {41041139},
issn = {2296-861X},
abstract = {INTRODUCTION: The gut microbiome plays a crucial role in host health through complex host-microbe interactions. Beta-glucans, structural polysaccharides found in yeast cell walls, have emerged as promising modulators of immune function and microbial ecology. Cava lees, a by-product of sparkling wine production composed of Saccharomyces cerevisiae cell walls, represent a rich source of beta-glucans that could be upcycled for nutritional and therapeutic applications.

METHODS: Twenty-four Wistar rats (12 males, 12 females) were randomly divided into control and treatment groups. The treatment group received daily doses of 2,000 mg lees/kg body weight for 14 days. Shotgun metagenomic analysis was performed to assess microbial composition and functional changes.

RESULTS: A 14-day cava lees supplementation study revealed significant shifts in gut microbiota composition and function. Baseline microbiota was dominated by Bacillota (64-72%) and Bacteroidota (23-32%) with sex-specific differences at the family level. Post-supplementation analysis showed increased Shannon diversity across both sexes, with beneficial enrichment of Bifidobacteriaceae and Rikenellaceae families and reduction of Eubacteriaceae. While global metabolic profiles remained stable, targeted functional pathways were significantly changed, including butyrate production genes. Females exhibited particularly elevated secondary bile acid modification genes (Mann-Whitney-Wilcoxon test p = 0.032), and male oxidative stress response pathways (Mann-Whitney-Wilcoxon test p = 0.016) showing both a potentially sex-dependent responses to dietary intervention.

CONCLUSION: Working with healthy individuals provides a clear understanding of the normal, baseline microbiota composition and function before any intervention. These findings suggest a degree of plasticity of the gut microbiome and its responsiveness to dietary modifications. Beta-glucans from cava lees appear to create a favorable environment for beneficial bacteria, with sex-specific changes of certain bacterial families and functions. These findings provide a foundation for future translational research in humans. Nonetheless, to establish their true impact on human health, these observations in rodent models must be validated through appropriately designed human clinical studies.},
}