@article {pmid41187758,
year = {2025},
author = {Yilmaz, B and Baertschi, I and Meier, KHU and Le Gac, C and Jordi, SBU and Black, C and Li, J and Lindholm, AK and , and König, B and Sauer, U and Stelling, J and Macpherson, AJ},
title = {A global survey of taxa-metabolic associations across mouse microbiome communities.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.10.010},
pmid = {41187758},
issn = {1934-6069},
abstract = {Host-microbiota mutualism is rooted in the exchange of dietary and metabolic molecules. Microbial diversity broadens the metabolite pool, with each taxon contributing distinct compounds in varying proportions. In the human microbiome, high variability in consortial composition is largely compensated by similar metabolic functions across different taxa. However, the extent of compensation in lower diversity mouse models, and whether vivaria are metabolically equivalent, is unknown. We provide a searchable resource of microbiome composition variability across 51 murine vivaria and 12 wild mouse colonies worldwide, with vivarium-specific variants mapped according to predicted 3D structures for each microbial species. Our matched metabolomics data show that realized metabolic potential has relatively low variability, providing functional evidence for metabolic compensation. Additionally, variability is related to taxonomic composition rather than vivarium, revealing taxa-metabolite associations that are potentially relevant to phenotypic differences between vivaria. Collectively, this resource offers tools to strengthen microbiome studies and collaborative science.},
}

@article {pmid41187701,
year = {2025},
author = {Li, N and Yin, L and Wang, J and Zhang, J and Tong, Y},
title = {Programmable probiotics as next-generation living therapeutics: bridging synthetic biology and precision medicine.},
journal = {Current opinion in biotechnology},
volume = {96},
number = {},
pages = {103375},
doi = {10.1016/j.copbio.2025.103375},
pmid = {41187701},
issn = {1879-0429},
abstract = {Engineered probiotics are rapidly redefining what's possible for living therapeutics. Instead of acting passively, these microbes can now home to disease sites, sense local signals, and deliver precisely the therapeutic activities our patients need - directly in situ and for extended periods. With the help of modular genetic circuits, synthetic biology is transforming once-commensal bacteria into sophisticated, programmable medicines. In this review, we highlight how these designer microbes are tackling inflammatory bowel disease, metabolic conditions, and cancer, and we offer a critical look at the strategies underpinning their safety, efficacy, and clinical translation. We also discuss the translational bottlenecks, such as biocontainment, regulatory complexity, and microbiome variability, that must be overcome as these living medicines move from concept toward routine clinical use. Ultimately, programmable probiotics stand poised to reshape pharmaceutical biotechnology, sitting squarely at the intersection of microbiology, engineering, and precision medicine.},
}

@article {pmid41187575,
year = {2025},
author = {Fooladi, AAI and Cho, WC and Reiter, RJ and Alimohammadi, M and Farahani, N and Hushmandi, K},
title = {Staphylococcal enterotoxins in cancer immunotherapy: An overview of translational advances and targeting strategies.},
journal = {Pathology, research and practice},
volume = {276},
number = {},
pages = {156283},
doi = {10.1016/j.prp.2025.156283},
pmid = {41187575},
issn = {1618-0631},
abstract = {Staphylococcal enterotoxins (SEs) are superantigens that polyclonally activate T cells by cross-linking MHC class II on antigen-presenting cells with T cell receptor (TCR) Vβ regions, generating potent IL-2/IFN-γ/TNF responses distinct from conventional peptide-MHC-restricted activation. This review synthesizes mechanistic and translational evidence for SEs in oncology, emphasizing disease-relevant contexts and advanced engineering strategies that improve therapeutic index. Preclinical studies demonstrate antitumor activity across melanoma, glioblastoma, renal cell carcinoma, bladder cancer, hepatocellular carcinoma, colorectal cancer, breast cancer, squamous cell carcinoma, and hematologic malignancies (e.g., acute myeloid leukemia, lymphoma). Tumor-targeted superantigen platforms, such as antibody or ligand-SE fusion proteins and oncolytic vectors encoding Ses, concentrate activity intratumorally, increase intratumoral IFN-γ/TNF, reduce proliferation and angiogenesis, and enhance necrosis while limiting systemic exposure. Engineered SE variants (for example, SEB with attenuated pyrogenicity) and localized delivery further mitigate risks associated with cytokine release. Early clinical experiences with SE-based constructs and SE-modified tumor vaccines report feasibility and signals of activity in head and neck cancer, glioma, renal cell carcinoma, and myeloma, but small, heterogeneous studies limit definitive conclusions. Although SEs can trigger cytokine storm and off-target activation via MHC II on healthy tissues, risk can be reduced through intratumoral/regional dosing, tumor-targeted fusions, dose-schedule optimization, and indication selection informed by MHC II biology; paradoxical, disease-specific effects (e.g., in cutaneous T-cell lymphoma) highlight the importance of microbiome-aware protocols. Priorities for translation include disease-focused development in MHC II-II-permissive tumors, combinations with immune checkpoint inhibitors, and biomarker-anchored trials integrating multi-omics and patient selection. With targeted engineering and controlled delivery, SEs can evolve from broadly inflammatory agents into precise immuno-oncology tools with meaningful clinical impact. This review underscores that, with targeted engineering, controlled delivery, and biomarker-guided patient selection, SEs can be advanced from broadly inflammatory agents to precise immuno-oncology platforms ready for rigorous clinical evaluation.},
}

@article {pmid41187545,
year = {2025},
author = {Al-Huqail, AA and Darwish, DBE and Melebari, DM and Osman, HES and Alasimi, SM and Alghanem, SMS and Alhaithloul, HAAS and Khan, KA and Abeed, AHA and Peijnenburg, W},
title = {Nanoparticle-driven defense in wheat (Triticum aestivum L.): Enhancing antioxidant and rhizosphere responses under arsenic and microplastic stress.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119334},
doi = {10.1016/j.ecoenv.2025.119334},
pmid = {41187545},
issn = {1090-2414},
abstract = {Soil contamination with toxic heavy metals such as arsenic (As) and microplastics (MPs) is becoming a serious global problem due to rapid industrial and agriculture expansion. Although nanoparticles (NPs) are the major protectants to alleviate metal toxicity. A pot-based study was conducted to evaluate the effects of silicon (Si-NPs), silicon dioxide (SiO2-NPs), and silver (Ag-NPs) nanoparticles on wheat (Triticum. Aestivum L.) exposed to As and MPs stress, focusing on key physiological, biochemical, and molecular assessments including oxidative stress responses, antioxidant activities, proline metabolism, and rhizosphere microbiome dynamics. Our results depicted that As and MPs exposure significantly reduced plant biomass (by 42-46 %), photosynthetic efficiency (by 38 %), mineral uptake (by 35 %), and rhizosphere microbiome diversity (by 30 %), while increasing malondialdehyde (MDA) and H2O2 contents (by 55-60 %), indicating oxidative stress, health risk indices, and molecular mechanisms. Antioxidant enzymes (SOD, POD, CAT, and APX) were enhanced at 100 mg kg[-1] As and 2 mg L[-1] MPs but declined at 200 mg kg[-1] As and 4 mg L[-1] MPs. As and MPs stress also suppressed anthocyanins and soluble proteins while increasing As accumulation in roots and shoots (by up to 48 %). Application of Si-NPs, SiO2-NPs, and Ag-NPs mitigated these adverse effects by improving growth (30-40 %), photosynthesis (25-33 %), antioxidant defenses (40-50 %), regulating AsA-GSH cycle, proline metabolism, and cellular fractionation, mineral uptake, reducing oxidative damage and HI indices (25-30 %). These treatments also lowered As retention in plant tissues (by 35-40 %). Research findings, therefore, suggested that application of Si-NPs, SiO2-NPs, and Ag-NPs can ameliorate As toxicity in T. aestivum seedlings and resulted in improved plant growth and composition under metal stress.},
}

@article {pmid41187543,
year = {2025},
author = {Lan, W and Zhou, Y and Duan, S and Yang, F and Xiao, Y and Yang, H},
title = {Rhizosphere microbiome-mediated cadmium and lead mobilization in Erigeron canadensis across a regional contamination gradient: Trade-offs between diversity loss and functional gene enrichment.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119341},
doi = {10.1016/j.ecoenv.2025.119341},
pmid = {41187543},
issn = {1090-2414},
abstract = {Erigeron canadensis, an invasive plant with significant biomass and heavy metal tolerance, has the potential for phytoremediation of soil heavy-metal contaminants. This study aimed to screen the key factors for improving the phytoremediation capacity of E. canadensis by examining rhizospheric ecological characteristics under varying levels of heavy metal pollution. Results showed that E. canadensis exhibited greater ability to enrich Cd and Pb in mildly polluted environments, with distinct mechanisms driving this pattern across three groups: HX (Huayuan County), LX (Liuyang City), and YX (Yueyang City), which represented different levels of pollution. Soil properties such as pH, total nitrogen, alkaline-hydrolyzed nitrogen (readily available nitrogen), and organic matter significantly influenced heavy metal uptake. Furthermore, the rhizosphere environment facilitated the adaptation of plant and enrichment of heavy metals by altering the microbial community, specifically by reducing overall diversity while increasing the relative abundance of key taxa characterized by metal resistance and plant growth-promoting abilities, including Lysobacter, Corynebacterium, Humicola, and Colletotrichum. These microorganisms adapted to Cd/Pb stress with some specific genes (e.g., Fur, PerR, and CueR) and enzymes (e.g., P-type ATPases, catalase, and alcohol dehydrogenase) related to heavy metal transport and uptake. This study elucidated the relationship between rhizospheric ecological factors and the regulatory mechanisms of phytoremediation. Selected microbial taxa might be developed as bioinoculants, improving phytoremediation efficiency and enhancing the ecological restoration capacity while also providing insights for the management of invasive species.},
}

@article {pmid41187250,
year = {2025},
author = {Issa, NT and Baldwin, H and Wroblewski, K and Kircik, L},
title = {The Dark Side of Oral Antibiotics: Adverse Events of Consideration in Dermatology.},
journal = {Journal of drugs in dermatology : JDD},
volume = {24},
number = {11},
pages = {s4-s12},
doi = {10.36849/JDD.99182},
pmid = {41187250},
issn = {1545-9616},
mesh = {Humans ; *Anti-Bacterial Agents/adverse effects/administration & dosage ; Administration, Oral ; Gastrointestinal Microbiome/drug effects ; Dermatology/methods ; Antimicrobial Stewardship/methods ; Drug Resistance, Bacterial/drug effects ; Drug Therapy, Combination ; Acne Vulgaris/drug therapy/microbiology ; Dermatologic Agents/administration & dosage/adverse effects ; },
abstract = {Antibiotics remain a cornerstone in the management of dermatologic conditions such as acne and hidradenitis suppurativa, underscoring the need for responsible antibiotic stewardship. This article explores the “dark side” of antibiotics, highlighting their role in disrupting the gut microbiome, elevating risks for infections like Clostridium difficile, and increasing resistance in Cutibacterium acnes and other microbes. Emerging evidence also links antibiotic use to reduced vaccine efficacy and diminished responses to cancer immunotherapy. To mitigate these risks, dermatologists should prioritize narrow-spectrum antibiotics and incorporate combination topical therapies containing benzoyl peroxide (BPO), such as the triple-combination of clindamycin, adapalene, and BPO, to help curb antibiotic resistance. Prudent antibiotic use, combined with topical regimens utilizing BPO, optimizes treatment outcomes while minimizing systemic adverse effects and resistance. Ongoing education and research are essential to refine prescribing practices that balance therapeutic benefits with long-term patient and public health.},
}

Humans
*Anti-Bacterial Agents/adverse effects/administration & dosage
Administration, Oral
Gastrointestinal Microbiome/drug effects
Dermatology/methods
Antimicrobial Stewardship/methods
Drug Resistance, Bacterial/drug effects
Drug Therapy, Combination
Acne Vulgaris/drug therapy/microbiology
Dermatologic Agents/administration & dosage/adverse effects

@article {pmid41187215,
year = {2025},
author = {Lee, K and Corbett, E and Hafner, R and Barnett, J},
title = {Public perceptions of biospecimen sampling and uncertainty in the context of personalised nutrition.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0335733},
doi = {10.1371/journal.pone.0335733},
pmid = {41187215},
issn = {1932-6203},
mesh = {Humans ; Female ; Male ; *Precision Medicine/psychology ; Uncertainty ; Adult ; Middle Aged ; Surveys and Questionnaires ; Nutritional Status ; *Specimen Handling ; Young Adult ; Feces/microbiology ; Aged ; },
abstract = {Personalised nutrition based on analysis of biospecimen generates individual-specific dietary recommendations and potentially, improved health. However, the science underpinning these approaches is evolving and uncertain. Additionally, users must provide a biological sample appropriate to the analytic approach being taken. This two-part quasi-experimental study sought to understand the impact of certainty and sample type on affective responses and attitudes to personalised nutrition. Participants (n716) completed a free association task and an attitudinal survey. Participants responded with more positive affect and attitudes to personalised nutrition when the science was characterised as certain. Attitudes to personalised nutrition were not affected by sample type, although contemplating providing a stool sample elicited more negative affective responses than other samples. This suggests that the need to provide a stool sample could be a barrier to microbiome-based personalised nutrition. We consider the implications of our findings in relation to future research and to providers of personalised nutrition.},
}

Humans
Female
Male
*Precision Medicine/psychology
Uncertainty
Adult
Middle Aged
Surveys and Questionnaires
Nutritional Status
*Specimen Handling
Young Adult
Feces/microbiology
Aged

@article {pmid41186727,
year = {2025},
author = {Shah, D and Phan, F and Yu, Z and Choi, JDW and Toh, JWT},
title = {Is the microbiome the answer to inflammatory bowel disease: systematic review.},
journal = {Langenbeck's archives of surgery},
volume = {411},
number = {1},
pages = {2},
pmid = {41186727},
issn = {1435-2451},
mesh = {Humans ; *Gastrointestinal Microbiome ; Dysbiosis ; *Colitis, Ulcerative/microbiology ; *Inflammatory Bowel Diseases/microbiology ; *Crohn Disease/microbiology ; },
abstract = {PURPOSE: Inflammatory bowel disease (IBD) encompasses two main conditions - Crohn's disease (CD) and ulcerative colitis (UC). Its pathogenesis is vastly unknown but genetics, environmental factors and the gut microbiome are thought to play vital roles. While dysbiosis is thought to be a feature of IBD, its exact role in pathogenesis is unclear.

METHODS: Relevant studies were identified through searching Medline and Embase from database inception to January 2025. Only gastrointestinal microbiome studies comparing IBD human patients with healthy controls (HC), performed on faecal, mucosal biopsy, saliva, or oral swab samples were examined. Studies were excluded if they included ≤ 10 IBD patients, did not compare IBD to HC, reported on IBD with other gastrointestinal infections, all were taking IBD medications, or included post-operative bowel resection patients.

RESULTS: Of 83 identified observational studies, most reported reduced alpha and beta diversity in IBD, more prevalent in CD than UC. There was depletion of protective butyrate producing Firmicutes bacteria including Faecalibacterium (specifically F. prausnitzii), Eubacteria, Roseburia, Lachnospiraceae, Ruminococcaceae (mainly R. bromii). There was decreased Bacteroidetes phylum in IBD, with depletion of Bacteroides genus in CD but increased in UC. There was increased Proteobacteria and its family Enterobacteriaceae in IBD.

CONCLUSIONS: The gut microbiome in IBD demonstrated reduced biodiversity, more pronounced in CD, with increased pathogenic and reduced beneficial bacteria. While this study demonstrated important associations between the microbiome and IBD, the exact mechanism, whether it be from a multistep process, a causative agent, or interplay between mucosal immunology and dysbiosis, is yet be elucidated.},
}

Humans
*Gastrointestinal Microbiome
Dysbiosis
*Colitis, Ulcerative/microbiology
*Inflammatory Bowel Diseases/microbiology
*Crohn Disease/microbiology

@article {pmid41186720,
year = {2025},
author = {Aijaz, M and Ahmad, M and Ahmad, S and Afzal, M and Kothiyal, P},
title = {The gut-brain axis: role of gut microbiota in neurological disease pathogenesis and pharmacotherapeutics.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {41186720},
issn = {1432-1912},
abstract = {The gut-brain axis is a highly complex, bidirectional communication link between the gut and the central nervous system (CNS), mainly through neural, endocrine, immunological, and metabolic pathways. This review outlines the growing contribution of gut microbiota in the remediation of neurological health and also emphasizes the controlling role of gut microbiota on the synthesis of neurotransmitters. Emerging evidence indicates that dysbiosis of the gut is related to a variety of neurodegenerative and neuropsychiatric diseases such as Parkinson's disease (PD), Alzheimer's disease (AD), multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS), Huntington's disease (HD), autism spectrum disorders (ASD), depression, and glioblastoma. Mechanistic understandings show that gut microbes critically contribute to neuroimmune and blood-brain barrier (BBB) signaling. The peripheral association of gut microflora, networked with inflammasome activation, nuclear factor kappa B (NF-κB), and type-I IFN pathways highlights their role in CNS inflammation. Microbiota-targeted interventions with probiotics, prebiotics, synbiotics, antibiotics, dietary modifications, and fecal microbiota transplantation are examined for their therapeutic potential. These strategies appear to be promising to reinstate microbial balance, enhance neuroplastic responses, and ameliorate the disease symptoms. The review highlights personalized microbiome-based algorithms, underpinned by integrated multi-omics technologies and machine-learning-driven diagnostics. Future research should address underlying microbial mechanisms and perform large, randomized controlled trials in order to establish microbiota-based therapies for neurological disorders.},
}

@article {pmid41186505,
year = {2025},
author = {Khalifa, R and Al-Naamani, K and Elbadry, M and Alswat, K and El-Kassas, M},
title = {Intermittent fasting and liver disease: Insights from the Ramadan model.},
journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association},
volume = {},
number = {},
pages = {},
pmid = {41186505},
issn = {1998-4049},
abstract = {Intermittent fasting (IF) has gained growing interest for its potential metabolic benefits. However, the unique physiological aspects of Ramadan fasting (RF), a culturally and religiously significant form of dry IF, remain underexplored, particularly regarding liver disease. RF imposes distinct metabolic and circadian challenges through prolonged daily fasting and altered meal timing, placing considerable demands on hepatic adaptability. Given the liver's essential role in energy balance, metabolism, and inflammation, as well as the high prevalence of liver disease in many Muslim-majority regions, it is crucial to better understand how RF impacts liver health. This review synthesizes current evidence on how RF can impact liver function, including its effects on insulin sensitivity, autophagy, gut microbiota, gene expression, and inflammation-related pathways. We further reviewed the clinical implications of RF across the broad spectrum of liver conditions, from metabolic dysfunction-associated steatotic liver disease (MASLD) to advanced cirrhosis, hepatocellular carcinoma (HCC), and post-transplant states. By addressing this knowledge gap, this review offers an evidence-based foundation for culturally sensitive and risk-stratified fasting recommendations in individuals with liver disease.},
}

@article {pmid41186490,
year = {2025},
author = {Yoon, SJ and Jutte, PC and Soriano, A and Zijlstra, WP and Wouthuyzen-Bakker, M},
title = {Systemic and local antimicrobial strategies to prevent Periprosthetic joint infection.},
journal = {Expert review of anti-infective therapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14787210.2025.2586067},
pmid = {41186490},
issn = {1744-8336},
abstract = {INTRODUCTION: Periprosthetic joint infection (PJI) is a severe complication of total joint arthroplasty and necessitates comprehensive strategies for prevention. One of the key features in infection prevention is the optimal selection of antimicrobial strategies.

AREAS COVERED: This review evaluates systemic and local antimicrobial approaches to PJI prevention, including systemic antibiotic prophylaxis, nasal and skin decolonization of Staphylococcus aureus, local antimicrobial delivery into the joint space, and antimicrobial modification of the implant surface. We conducted a literature search of the MEDLINE, Web of Science, Cochrane and ClinicalTrials.gov databases for recent evidence from randomized and observational studies, as well as current orthopedic guidelines concerning these topics.

EXPERT OPINION: Further reductions in the incidence of PJI through antimicrobial strategies will require: (1) the adoption of alternative trial designs such as registry-nested and adaptive platform trials to study outcomes with low event rates; (2) improved adherence to established best practices, particularly in systemic antibiotic prophylaxis; (3) precision prevention informed by validated risk stratification tools; and (4) novel interventions targeting emerging biological mechanisms such as the gut microbiome.},
}

@article {pmid41186403,
year = {2025},
author = {Lugli, GA and Argentini, C and Tarracchini, C and Longhi, G and Mancabelli, L and Bianchi, MG and Taurino, G and Amaretti, A and Candeliere, F and Bussolati, O and Milani, C and Turroni, F and Ventura, M},
title = {Host interactions of Lactococcus lactis and Streptococcus thermophilus support their adaptation to the human gut microbiota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0154725},
doi = {10.1128/aem.01547-25},
pmid = {41186403},
issn = {1098-5336},
abstract = {UNLABELLED: Within the human gut microbiota, lactic acid bacteria (LAB) play a crucial role in host health by producing lactic acid, which has been shown to shape microbial interactions and support intestinal homeostasis. However, despite their importance, there are limited insights regarding how LAB species interact with the host and other gut commensals. In this study, the investigation of the human gut microbiota of 10,000 healthy adults allowed the identification of Lactococcus lactis and Streptococcus thermophilus as commonly detected food bacteria. Further in silico analyses led to the identification of reference strains of the L. lactis and S. thermophilus species within the human gut, represented by PRL2024 and PRL2025 strains, respectively, which can represent nomadic bacteria. In vitro experiments revealed that both strains are ecologically adapted to survive and interact within the human gastrointestinal tract, while also highlighting their metabolic capacity to utilize a broad range of carbon sources. Specifically, the lactose metabolism was investigated, revealing that S. thermophilus PRL2025, despite high lactic acid output, incompletely metabolizes galactose, whereas L. lactis PRL2024 ensures full galactose utilization with lower acid production.

IMPORTANCE: The identification and functional characterization of Lactococcus lactis PRL2024 and Streptococcus thermophilus PRL2025 as human-adapted reference strains provide a valuable foundation for further in vivo experimentation. Given their ecological resilience, metabolic versatility, and interaction potential with beneficial gut microbes, these strains represent promising candidates as microbiota-targeted functional foods.},
}

@article {pmid41186329,
year = {2025},
author = {Liu, Y and Liu, X and Hu, Y and Gao, F and Yu, W and Cheng, F},
title = {Evaluating untargeted metabolomics pipelines for sports nutrition research: a review.},
journal = {Analytical methods : advancing methods and applications},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5ay01484k},
pmid = {41186329},
issn = {1759-9679},
abstract = {Untargeted metabolomics has emerged as a transformative approach in sports nutrition research, offering an unbiased means to characterize the complex biochemical responses to exercise, training, and dietary interventions. Unlike targeted assays restricted to predefined metabolites, untargeted strategies capture broad metabolic perturbations across lipid, carbohydrate, amino acid, and nucleotide pathways, enabling the discovery of novel biomarkers and unanticipated physiological mechanisms. This review critically evaluates the design and application of untargeted metabolomic pipelines in the context of exercise and nutrition science, from pre-analytical sample handling and analytical platforms such as NMR, LC-MS, and GC-MS, to data processing using tools like XCMS, MZmine, and MS-DIAL, and subsequent statistical and bioinformatic interpretation. Key applications include delineating acute metabolic shocks induced by endurance exercise, identifying athlete-specific metabolic phenotypes shaped by chronic training, and assessing the impact of nutritional interventions such as fruit intake, amino acid supplementation, or polyphenol-rich foods on exercise recovery and oxidative stress. The integration of metabolomics with other omics, particularly microbiome metagenomics and lipidomics, highlights the potential for systems-level insights into host-microbe-diet interactions. Nonetheless, significant challenges remain, including the reproducibility of findings, difficulties in metabolite identification, and the translational gap between large datasets and actionable nutritional strategies. By synthesizing current strengths, limitations, and controversies, this review emphasizes that the future of sports metabolomics lies in methodological standardization, multi-omics integration, and validation of candidate biomarkers in independent cohorts. Collectively, these efforts position untargeted metabolomics as a cornerstone for advancing precision nutrition and personalized performance monitoring in athletes.},
}

@article {pmid41186233,
year = {2025},
author = {Yang, JW and Denef, VJ},
title = {Dissecting two contrasting phytoplankton-symbiont interaction modes based on population dynamics and gene expression patterns.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0080325},
doi = {10.1128/msystems.00803-25},
pmid = {41186233},
issn = {2379-5077},
abstract = {UNLABELLED: Microbial symbionts play vital roles in the health, fitness, and ecological dynamics of most eukaryotic species, making it essential to understand how host-microbe interactions shape the microbiome. Building on our previous work, we hypothesized that symbionts with diverse functions are maintained in the microbiome via a trade-off between two host-microbe interaction modes: either by better utilizing host-derived dissolved organic matter (DOM) without direct interaction with the host (unidirectional interaction) or by engaging in feedback interactions with the host that alter DOM composition to their advantage (bidirectional interaction). By screening symbionts isolated from C. sorokiniana (host), we examined growth and gene expression responses of two representative symbionts and the host. We found Curvibacter sp. thrived on spent medium from axenic C. sorokiniana with host-derived dissolved organic matter (DOM) in unidirectional interaction, whereas Falsiroseomonas sp. grew best with live C. sorokiniana cells in bidirectional interaction and exhibited a greater shift in gene expression between modes despite larger growth phase differences between treatments for Curvibacter sp. Specifically, Falsiroseomonas sp. showed differential expression of metabolic pathways that could benefit (e.g., synthesis of cofactors) or antagonize (e.g., metabolism of defensive secondary metabolites) toward the host under bidirectional interaction conditions. In response, host co-cultured with Falsiroseomonas sp. reduced its growth and triggered its higher expression of nitrogen-rich amino acid metabolism which may provide a nutritional benefit to Falsiroseomonas sp. These findings demonstrated that distinct host-microbe interaction modes drive differential symbiont strategies and play an important role in microbiome assembly.

IMPORTANCE: Deciphering how host-microbe interactions shape microbiome structure is crucial for understanding host health and ecosystem function. Given the inherent complexity of host-microbe interactions, we simplified the system by separating interactions into unidirectional and bidirectional modes. Using this framework, we observed contrasting effects on the growth of two representative bacterial taxa isolated from the same host microbiome. These growth responses were further coupled with distinctive gene expression profiles in both hosts and bacteria under the different interaction modes. Together, these findings underscore the importance of considering host-microbe interaction modes in microbiome research. For example, our findings help explain how hosts can harbor functionally diverse microbial assemblages, where contrasting metabolic strategies are maintained through distinct interaction modes. Such insights are fundamental for predicting, managing, or engineering microbiomes, as well as understanding the ecological processes that drive microbiome diversity and function within host-microbiome systems in nature.},
}

@article {pmid41185751,
year = {2025},
author = {Huang, Y and Zhang, Z and Xue, L and Zhang, X and He, C},
title = {Advances in Nanomedicine-Mediated Modulation of the Microbiome for Cancer Therapy.},
journal = {International journal of nanomedicine},
volume = {20},
number = {},
pages = {13079-13096},
pmid = {41185751},
issn = {1178-2013},
mesh = {Humans ; *Neoplasms/therapy/microbiology/drug therapy ; *Nanomedicine/methods ; Tumor Microenvironment/drug effects ; Animals ; Probiotics/therapeutic use/administration & dosage ; Fecal Microbiota Transplantation/methods ; *Microbiota/drug effects ; Liposomes/chemistry ; Drug Delivery Systems ; Antineoplastic Agents/administration & dosage ; Gastrointestinal Microbiome/drug effects ; },
abstract = {The microbiome is closely related to the development of cancer, and it is feasible to modulate the microbiome for cancer therapy. Strategies based on the modulation of the microbiome, such as probiotic therapy and fecal microbiota transplantation (FMT), have achieved certain results in cancer therapy. However, poor targeting and low survival rate of the microbiome limited their further application in cancer therapy. Nanomaterials such as liposomes and micelles are widely used as carriers for drug delivery due to their good biocompatibility and stability. The latest evidence indicates that some nanomedicines can reverse cancer-promoting effects (such as promoting cell proliferation and accelerating tissue inflammation) by eliminating cancer-related microbiota, or increase the proportion of beneficial bacteria, which further enhance the production of beneficial metabolites, facilitate immune cell infiltration, and reshape the tumor microenvironment (TME), thereby inhibit tumor growth. Thus, it is promising to enhance the efficacy of cancer therapy by regulating microbiota through nanomedicines. This review highlights recent advances in the integration of nanomedicine and microbiota modulation for cancer treatment, aiming to provide insights into the design of innovative therapeutic strategies and broaden treatment options for cancer patients.},
}

Humans
*Neoplasms/therapy/microbiology/drug therapy
*Nanomedicine/methods
Tumor Microenvironment/drug effects
Animals
Probiotics/therapeutic use/administration & dosage
Fecal Microbiota Transplantation/methods
*Microbiota/drug effects
Liposomes/chemistry
Drug Delivery Systems
Antineoplastic Agents/administration & dosage
Gastrointestinal Microbiome/drug effects

@article {pmid41185633,
year = {2025},
author = {Villarreal, CX and Chan, DD},
title = {Multiomic Integration Reveals Taxonomic Shifts Correlate to Serum Cytokines in an Antibiotics Model of Gut Microbiome Disruption.},
journal = {Cellular and molecular bioengineering},
volume = {18},
number = {5},
pages = {369-385},
pmid = {41185633},
issn = {1865-5025},
abstract = {PURPOSE: The gut microbiome interacts with many systems throughout the human body. Microbiome disruption reduces bone tissue mechanics but paradoxically slows osteoarthritis progression. The microbiome also mediates inflammatory and immune responses, including serum cytokines. Towards our long-term goal of studying how the gut microbiome interacts with synovial joint health and disease, we examined how antibiotics-induced changes to microbial taxa abundance associated to serum cytokine levels.

METHODS: Mice (n = 5 + ) were provided ad libitum access to water containing antibiotics (1 g/L neomycin, 1 g/L ampicillin, or 1 g/L ampicillin with 0.5 g/L neomycin) or control water from 5- to 16-weeks old, corresponding in skeletal development to ~ 10 to ~ 25 years in humans. At humane euthanasia, we collected cecum contents for 16S metagenomics and blood for serum cytokine quantification for comparison to control and among antibiotic groups. We used dimensional reduction techniques, multiomic integration, and correlation to discriminate antibiotic groups and identify specific relationships between high-abundance taxa and serum cytokines.

RESULTS: Antibiotic treatment significantly lowered diversity, altered phylum relative abundance, and resulted in significant association with specific taxa. Dimensional reduction techniques and multiomic integration revealed distinct antibiotic-associated clusters based on genera relative abundance and cytokine serum concentration. Cytokines IL-6, MIP-1B, and IL-10 significantly contributed to antibiotic discrimination, significantly different among antibiotic treatments, and had significant correlations with specific taxa.

CONCLUSIONS: Antibiotic treatment resulted in heterogenous response in gut microbiome and serum cytokines, allowing significant microbe-cytokine links to emerge. The relationships identified here will enable further investigation of the gut microbiome's role in modifying joint health and disease.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12195-025-00861-2.},
}

@article {pmid41185450,
year = {2025},
author = {Amaro, AR and Darbinyan, H and Kardashian, A},
title = {Liver disease in women with HIV.},
journal = {Current opinion in HIV and AIDS},
volume = {},
number = {},
pages = {},
doi = {10.1097/COH.0000000000000992},
pmid = {41185450},
issn = {1746-6318},
abstract = {PURPOSE OF REVIEW: Chronic liver disease is the leading cause of non-HIV-related mortality in women with HIV (WWH). We review the pathophysiology of liver injury in WWH, natural history and management of common liver diseases, and role of viral, pharmacologic, and sex hormone-related factors in exacerbating liver disease progression in WWH.

RECENT FINDINGS: In the current era of effective antiretroviral therapy (ART), viral hepatitis related liver disease has decreased in prevalence, while alcohol-associated and metabolic dysfunction associated steatotic liver disease (MASLD) have become more common. Several mechanisms cause accelerated fibrogenesis in WWH, including direct cytopathic effects from HIV, ART, gastrointestinal barrier impairments, and microbiome alterations. The menopausal transition is a critical period in which WWH develop a profibrogenic state exacerbated by HIV-associated estrogen deficiency. Glucagon-like peptide-1 use in WWH holds promise in reversing hepatic steatosis. Higher rates of hazardous alcohol use and psychiatric comorbidities in WWH, compared to men with HIV, increases the risk of alcohol and viral hepatitis related liver disease.

SUMMARY: WWH experience unique challenges to achieving optimal liver disease care due to social marginalization, biological sex differences, and HIV infection itself. Future research investigating mechanisms and potential interventions is needed to improve liver health outcomes in this high-risk population.},
}

@article {pmid41185347,
year = {2025},
author = {Deng, W and Guo, Y and Mo, Q and Liu, J and Su, Y and Wei, Z and Ma, R and Chen, J and Song, Y and Chen, T and Wang, P and Yu, W and Lu, S},
title = {Exploring the mechanisms of torularhodin in alleviating diabetic kidney disease: a microbiome and metabolomics approach through the gut-kidney axis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 4},
pages = {117597},
doi = {10.1016/j.foodres.2025.117597},
pmid = {41185347},
issn = {1873-7145},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Diabetic Nephropathies/drug therapy/metabolism/microbiology ; Metabolomics ; Mice ; *Kidney/drug effects/metabolism ; Oxidative Stress/drug effects ; Male ; Antioxidants/pharmacology ; Mice, Inbred C57BL ; NF-E2-Related Factor 2/metabolism ; Diabetes Mellitus, Experimental ; Signal Transduction/drug effects ; },
abstract = {This study primarily investigates the pivotal role of torularhodin in alleviating diabetic nephropathy in mice. Oral administration of torularhodin at a dose of 30 mg/kg/day for 8 weeks significantly improved diabetic symptoms and mitigated kidney tissue damage in a mouse model of diabetic nephropathy. Integrating findings from both network pharmacology and in vivo experiments, the study confirmed that torularhodin activates the Nrf2 signaling pathway, thereby promoting the expression of multiple antioxidant enzymes to directly reduce oxidative stress and mitochondrial damage in renal tissues. Moreover, combined analyses of metabolomics and gut microbiota profiling revealed that torularhodin increased the abundance of Muribaculaceae, Moraxellaceae, and Erysipelotrichaceae, while decreasing the abundance of Lactobacillaceae and Enterobacteriaceae. These microbial shifts were accompanied by increased levels of key metabolites, such as Glycerol 3-Phosphate and d-Fructose 6-Phosphate, which helped alleviate amino acid metabolic disorders, restore energy metabolism, and reduce oxidative stress in the kidneys via the gut-kidney axis. This study demonstrates that the protective effects of torularhodin against diabetic nephropathy arise both from its direct antioxidant and mitochondrial protective actions, and partly from modulation of the gut microbiota and their metabolites. These findings provide new insights into the mechanisms of torularhodin and establish a theoretical basis for its potential use as a therapeutic strategy for diabetic nephropathy.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Diabetic Nephropathies/drug therapy/metabolism/microbiology
Metabolomics
Mice
*Kidney/drug effects/metabolism
Oxidative Stress/drug effects
Male
Antioxidants/pharmacology
Mice, Inbred C57BL
NF-E2-Related Factor 2/metabolism
Diabetes Mellitus, Experimental
Signal Transduction/drug effects

@article {pmid41185328,
year = {2025},
author = {Wang, D and Ren, Y and Liao, Y and Pan, L and Su, Y and Zhu, W},
title = {Differential characteristics of meat flavor compounds, colonic microbiome and metabolome between Duroc × Landrace × Yorkshire pigs with high and low intramuscular fat of longissimus dorsi muscles.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 4},
pages = {117579},
doi = {10.1016/j.foodres.2025.117579},
pmid = {41185328},
issn = {1873-7145},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Swine ; Volatile Organic Compounds/analysis ; *Taste ; *Metabolome ; *Muscle, Skeletal/metabolism ; *Pork Meat/analysis ; *Adipose Tissue/metabolism ; *Colon/microbiology ; *Red Meat/analysis ; },
abstract = {Pork flavor has received widespread attention from consumers and producers, but the flavor differences and microbial differences in pigs with different intramuscular fat (IMF) content remain unclear. This study aimed to investigate differential characteristics of meat flavor compounds, colonic microbiome and metabolome between Duroc × Landrace × Yorkshire pigs with high and low IMF using multi-omics analyses. High IMF (H-IMF) pork had higher marbling scores, tenderness, and overall acceptability than low IMF (L-IMF) pork. The overall flavor profiles were similar between H-IMF and L-IMF pork. The main enriched volatile flavor compounds (VOCs) in H-IMF pork belonged to esters and were mainly represented by 3-methylbutanal, ethyl acetate, (E)-2-decenal, ethyl nonanoate, 2-nonanone, methional, and ethyl decanoate. Dorea was significantly enriched and showed a positive correlation with main VOCs, whereas Treponema, Alloprevotella, and Cryptobacteroides were significantly reduced in the colon of H-IMF pigs. Differential metabolites were mainly enriched in nucleotide and pyrimidine metabolic pathways. Dorea and metabolites cytidine, 2'-deoxycytidine-5'-monophosphate, and 2'-deoxythymidine-5'-monophosphate participated in nucleotide and pyrimidine metabolic pathways and potentially influenced the production of flavor compounds. Overall, the results imply that IMF influences pork flavor compounds and is closely associated with the gut microbiota, indicating potential to improve flavor attributes through microbial regulation.},
}

Animals
*Gastrointestinal Microbiome/physiology
Swine
Volatile Organic Compounds/analysis
*Taste
*Metabolome
*Muscle, Skeletal/metabolism
*Pork Meat/analysis
*Adipose Tissue/metabolism
*Colon/microbiology
*Red Meat/analysis

@article {pmid41185310,
year = {2025},
author = {Wu, S and Li, Y and Zhang, H and Pan, Y and Yang, H and Tan, Y},
title = {Microbial community reshaping: Calcium chloride-heat treatment synergy in fresh-cut jackfruit preservation via antagonistic yeast enrichment.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 4},
pages = {117558},
doi = {10.1016/j.foodres.2025.117558},
pmid = {41185310},
issn = {1873-7145},
mesh = {*Calcium Chloride/pharmacology ; *Food Preservation/methods ; *Hot Temperature ; *Food Microbiology/methods ; *Fruit/microbiology ; *Artocarpus/microbiology ; Penicillium/drug effects/growth & development ; *Yeasts/drug effects/growth & development ; Antibiosis ; },
abstract = {Fresh-cut jackfruit is highly susceptible to microbial contamination and rapid spoilage due to mechanical damage and its nutrient-rich substrate. We evaluated calcium chloride combined with heat treatment (CH, 2 % CaCl2 - 55 °C) for controlling spoilage and preservation of fresh-cut jackfruit. The results identified Gilbertella hainanensis, Penicillium kongii, and P. citrinum as the dominant spoilage fungi in fresh-cut jackfruit. CH inhibited these fungi with in vitro inhibition rates of 80.14 %, 43.75 %, and 52.94 %, and corresponding in vivo rates of 83.1 %, 77.9 %, and 83.7 %, respectively. In vitro assays indicated CH compromises fungal membrane integrity, causing leakage of cellular contents. Further analysis revealed that CH markedly increased the relative abundance of the antagonistic yeast Meyerozyma guilliermondii (42.82 %, 8.13-fold vs. control) and was associated with reduced relative abundance of plant pathogenic and saprotrophic fungi. Correlation analysis linked dominant yeast genera to higher total phenolic content and reduced weight loss and other quality deterioration. Overall, CH treatment effectively delayed spoilage and preserved fruit physicochemical and nutritional quality, likely via direct antifungal effects and beneficial reshaping of the surface microbiome. These findings advance understanding of jackfruit postharvest microbial ecology and CH as a promising preservation strategy for fresh-cut jackfruit fruit.},
}

*Calcium Chloride/pharmacology
*Food Preservation/methods
*Hot Temperature
*Food Microbiology/methods
*Fruit/microbiology
*Artocarpus/microbiology
Penicillium/drug effects/growth & development
*Yeasts/drug effects/growth & development
Antibiosis

@article {pmid41185061,
year = {2025},
author = {Mekuria, Z and Deblais, L and Ojeda, A and Mummed, B and Singh, N and Gebreyes, W and Havelaar, AH and Rajashekara, G and , },
title = {Host clustering of Campylobacter species and enteric pathogens in a longitudinal cohort of infants, family members and livestock in rural Eastern Ethiopia.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {225},
pmid = {41185061},
issn = {2049-2618},
support = {OPP11755487//Bill and Melinda Gates Foundation/ ; OPP11755487//Bill and Melinda Gates Foundation/ ; OPP11755487//Bill and Melinda Gates Foundation/ ; },
mesh = {Animals ; Humans ; *Campylobacter/classification/genetics/isolation & purification ; Infant ; *Campylobacter Infections/microbiology/epidemiology/veterinary ; Ethiopia/epidemiology ; *Livestock/microbiology ; Rural Population ; Longitudinal Studies ; Female ; Male ; Chickens/microbiology ; Feces/microbiology ; Metagenomics/methods ; Gastrointestinal Microbiome ; Adult ; Cluster Analysis ; Family ; Child, Preschool ; },
abstract = {BACKGROUND: Livestock are recognized as major reservoirs for Campylobacter species and other enteric pathogens, posing infection risks to humans. High prevalence of Campylobacter during early childhood has been linked to environmental enteric dysfunction and stunting, particularly in low-resource settings.

METHODS: A total of 280 samples from Campylobacter positive households with complete metadata were analyzed by shotgun metagenomic sequencing followed by bioinformatic analysis via the CZ-ID metagenomic pipeline (Illumina mNGS Pipeline v7.1). Further statistical analyses in JMP PRO 16 explored the microbiome, emphasizing Campylobacter and other enteric pathogens. Two-way hierarchical clustering and split k-mer analysis examined host structuring, patterns of co-infections and genetic relationships. Principal component analysis was used to characterize microbiome composition across the seven sample types.

RESULTS: The study identified that microbiome composition was strongly host-driven, with more than 3844 genera detected, and two principal components explaining 62% of the total variation. Twenty-one dominant (based on relative abundance) Campylobacter species showed distinct clustering patterns for humans, ruminants, and broad hosts. The broad-host cluster included the most prevalent species, C. jejuni, C. concisus, and C. coli, present across sample types and a sub-cluster within C. jejuni involving humans, chickens, and ruminants. Campylobacter species from chickens showed strong positive correlations with mothers (r = 0.76), siblings (r = 0.61) and infants (r = 0.54), while co-occurrence analysis found a higher likelihood (Pr > 0.5) of pairs such as C. jejuni with C. coli, C. concisus, and C. showae. Analysis of the top 50 most abundant microbial taxa showed a distinct cluster uniquely present in human stool and absent in all livestock. The study also found frequent co-occurrence of C. jejuni with other enteric pathogens such as Salmonella, and Shigella, particularly in human and chicken. Additionally, instances of Candidatus Campylobacter infans (C. infans) were identified co-occurring with Salmonella and Shigella species in stool samples from infants, mothers, and siblings.

CONCLUSIONS: A comprehensive analysis of Campylobacter diversity in humans and livestock in a low-resource setting revealed that infants can be exposed to multiple Campylobacter species early in life. C. jejuni is the dominant species with a propensity for co-occurrence with other notable enteric bacterial pathogens, including Salmonella, and Shigella, especially among infants. Video Abstract.},
}

Animals
Humans
*Campylobacter/classification/genetics/isolation & purification
Infant
*Campylobacter Infections/microbiology/epidemiology/veterinary
Ethiopia/epidemiology
*Livestock/microbiology
Rural Population
Longitudinal Studies
Female
Male
Chickens/microbiology
Feces/microbiology
Metagenomics/methods
Gastrointestinal Microbiome
Adult
Cluster Analysis
Family
Child, Preschool

@article {pmid41184906,
year = {2025},
author = {Singh, H and Balusamy, SR and Sukweenadhi, J and Saravanan, M and Aruchamy, M and Mijakovic, I and Singh, P},
title = {Smart hybrid nanomaterials for chronic infections: microbiome-responsive and sustainable therapeutic platforms.},
journal = {Journal of nanobiotechnology},
volume = {23},
number = {1},
pages = {698},
pmid = {41184906},
issn = {1477-3155},
}

@article {pmid41184733,
year = {2025},
author = {Valido, E and Bertolo, A and Stoyanov, J},
title = {Quantitative profiling of bacterial communities via full length 16S rRNA gene sequencing with internal controls: optimization and validation across diverse human microbiomes.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {710},
pmid = {41184733},
issn = {1471-2180},
}

@article {pmid41184709,
year = {2025},
author = {Kiecka, A and Szczepanik, M},
title = {Dietary modulation of the gut microbiome as a supportive strategy in the treatment of amyotrophic lateral sclerosis - a narrative review.},
journal = {Pharmacological reports : PR},
volume = {},
number = {},
pages = {},
pmid = {41184709},
issn = {2299-5684},
abstract = {Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease leading to permanent damage to the central and peripheral motor neurons. Currently, there is no effective treatment for ALS, and therapy focuses solely on slowing the progression of the disease. Recent studies show that gut microbiota plays an important role in the development of neurodegenerative diseases. Altered gut microbiota has also been found in ALS. These changes have prompted the search for alternative forms of ALS treatment, focusing on changing the microbial composition of the gut. It has been noted that diet, probiotics, prebiotics and vitamins can all influence the course of ALS. Another interesting issue is fecal microbiota transplantation, which is already used in the treatment of certain intestinal diseases and could potentially be useful in the treatment of ALS. This review summarizes current knowledge on the impact of gut microbiota on the neurodegenerative process in ALS, with particular emphasis on the role of diet and probiotics. It also discusses potential mechanisms and highlights future research directions in this emerging field.},
}

@article {pmid41184615,
year = {2025},
author = {Zhang, S and Qiu, CW and Shi, SH and Sreesaeng, J and Gao, ZF and Zhang, C and Mao, W and Ali, MA and Chen, ZH and Wu, F},
title = {Trichoderma genome and multiomics insight into promoting yield and reducing grain cadmium in barley and wheat.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.70063},
pmid = {41184615},
issn = {1744-7909},
support = {3211101286//National Natural Science Foundation of China/ ; //Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding, China/ ; },
abstract = {Soil cadmium (Cd) contamination poses significant risks to human health and environmental sustainability. Despite advances in bioremediation, effective bioagents with clear mechanistic insights for Cd detoxification are lacking. We first deciphered the whole-genome sequence of a novel Cd-tolerant Trichoderma nigricans T32781 and its in vivo heavy metal tolerance. In five independent pot and field trials, we revealed the T32781-induced alleviation mechanisms of plant-microbe-soil interactions in wheat and barley in response to Cd toxicity using a combination of agronomic, physiological, microbiome and metabolome approaches. We discovered that T32781 inoculation in soil significantly increased grain yield and decreased grain Cd concentration in barley and wheat exposed to different soil Cd levels. T32781 predominantly colonized soils, mitigating Cd toxicity by reducing soil Cd availability and promoting beneficial soil microbial communities and metabolites. These beneficial effects were further validated in the field, where the exogenous application of key metabolites induced by T32781 inoculation in soils and plants significantly increased grain yield and reduced grain Cd concentration in barley. This work highlights the potential of T32781 to enhance plant‒microbe-soil interactions and support sustainable and safe crop production in Cd-contaminated soils, addressing the increasing global demand for cereal production for food and feed.},
}

@article {pmid41184590,
year = {2025},
author = {Li, G and Wu, Y and Huang, X and Du, M and Tang, H},
title = {A gut-brain-gut axis orchestrates host responses counteracting microbiome-induced iron insufficiency.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {41184590},
issn = {1460-2075},
support = {32350015//MOST | National Natural Science Foundation of China (NSFC)/ ; 32530030//MOST | National Natural Science Foundation of China (NSFC)/ ; 32070565//MOST | National Natural Science Foundation of China (NSFC)/ ; 31871465//MOST | National Natural Science Foundation of China (NSFC)/ ; 2019YFA0802900//MOST | National Key Research and Development Program of China (NKPs)/ ; 202209003//HRHI program of the Westlake Laboratory of Life Sciences and Biomedicine/ ; 202109007//HRHI program of the Westlake Laboratory of Life Sciences and Biomedicine/ ; LQN25C070002//Zhejiang Provincial Natural Science Foundation of China/ ; LQ23C040002//Zhejiang Provincial Natural Science Foundation of China/ ; },
abstract = {The brain monitors changes in the gut microbiome to maintain health, but the impact of specific bacterial alterations, as well as the underlying mechanisms, remains largely unclear. Here, we discovered an unexpected neuronal regulation of iron metabolism, mediating the neuronal surveillance of gut bacterial activity in C. elegans. Specifically, through a genome-wide screen, we identified 29 E. coli genes, mainly linked to metabolism regulation, whose inactivation could increase dopamine and serotonin biosynthesis in C. elegans head neurons. These neurons respond to the lack of respiratory chain genes in E. coli in the gut by perceiving intestinal mitochondrial impairment resulting from bacterial-induced reduction in host labile iron levels. Such neuronal responses subsequently promote intestinal ferritin-1 expression to counteract bacterially induced labile iron reduction, thus maintaining mitochondrial function. Our findings reveal how alterations in bacterial metabolism can elevate dopamine and serotonin levels in the host brain, demonstrating that the nervous system not only senses microbiome-caused changes in the gut but also feeds back to revert them.},
}

@article {pmid41184414,
year = {2025},
author = {Van Thanh Le, T and Vuong, TBT and Le, GHL and Do, DM},
title = {Scraping enhances microbial DNA recovery over swabbing in sensitive facial skin: a pilot study of 10 patients.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38359},
pmid = {41184414},
issn = {2045-2322},
mesh = {Humans ; Pilot Projects ; *Skin/microbiology ; Male ; Female ; *DNA, Bacterial/isolation & purification/genetics ; *Microbiota/genetics ; Middle Aged ; *Face/microbiology ; *Specimen Handling/methods ; Adult ; *DNA, Fungal/isolation & purification/genetics ; Bacteria/genetics/isolation & purification ; Aged ; },
abstract = {Sensitive skin is a common condition with a complex pathogenesis involving both host-related factors and microbial interactions. Emerging evidence suggests a bidirectional relationship between skin microbiome dysbiosis and sensitive skin, although whether microbial shifts are causal or consequential remains unclear. Characterizing the microbiome in this population is particularly challenging due to low microbial biomass and heightened skin reactivity, both of which may compromise sampling and data quality. While swabbing remains the most common method for skin microbiome collection, it may fail to yield sufficient DNA, especially from delicate facial areas. In this pilot study of 10 patients with sensitive facial skin, we compared swabbing to gentle scraping using a sterile No. 10 surgical blade. Swabbing consistently failed to recover detectable microbial DNA. In contrast, scraping was well-tolerated and enabled one-time sampling that yielded sufficient DNA for both bacterial and fungal sequencing. DNA concentrations ranged from 0.065 to 13.2 ng/µL for bacteria and 0.104 to 30.0 ng/µL for fungi. Genus-level classification rates exceeded 99.7% for bacteria and 97% for fungi. Shannon diversity indices ranged from 0.03 to 2.85 for bacteria and 0.106 to 2.849 for fungi. PCoA revealed substantial inter-individual variation in community composition. Dominant taxa included Staphylococcus aureus group, Cutibacterium acnes group, Malassezia restricta, and Malassezia globosa. These findings indicate that skin scraping is a feasible and reproducible method for microbiome studies of sensitive skin, providing comprehensive taxonomic and ecological profiling in a single, non-invasive session.},
}

Humans
Pilot Projects
*Skin/microbiology
Male
Female
*DNA, Bacterial/isolation & purification/genetics
*Microbiota/genetics
Middle Aged
*Face/microbiology
*Specimen Handling/methods
Adult
*DNA, Fungal/isolation & purification/genetics
Bacteria/genetics/isolation & purification
Aged

@article {pmid41184333,
year = {2025},
author = {Ghosh, A and Maile, A and Nagarajaram, HA},
title = {Prokaryotic co-occurrence patterns in diverse Indian mangrove ecosystems.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38283},
pmid = {41184333},
issn = {2045-2322},
mesh = {India ; *Wetlands ; Biodiversity ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Phylogeny ; Soil Microbiology ; },
abstract = {Mangrove ecosystems are unique coastal zones known to harbour a rich biodiversity of flora and fauna, including microbial communities. These microorganisms play a crucial role in nutrient cycling and sustain the primary productivity driven by plants within this ecosystem. Recent advancements in microbial ecology research emphasise that microbial community structure and composition are critical for an ecosystem to thrive. Studies have focused on the microbial diversity within Indian mangrove forests; however, there is a limited understanding of the co-occurrence patterns and functional roles of microbial communities in these ecosystems. This study explores prokaryotic diversity, primarily focusing on community interactions across three major Indian mangrove forests: the Bhitarkanika mangrove forest in Odisha, the Goan mangroves, and the Sundarbans in West Bengal. By analysing the publicly available 16 S rRNA amplicon datasets of the Indian mangrove microbiomes and performing co-occurrence network analysis on these datasets, we identified positively correlated genera and their predicted functional roles. Furthermore, the findings revealed the co-occurrence of several pathogenic bacteria in two of the mangrove ecosystems. Overall, our study highlights the shared functional roles adopted by co-occurring microbes in three major Indian mangrove ecosystems and suggests the need for large-scale studies in these understudied Indian ecosystems.},
}

India
*Wetlands
Biodiversity
*Bacteria/genetics/classification/isolation & purification
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
*Ecosystem
Phylogeny
Soil Microbiology

@article {pmid41184254,
year = {2025},
author = {Wang, Y and Ge, M and Wang, J and Xu, Y and Wang, N and Xu, S},
title = {Metabolic reprogramming in ischemic stroke: when glycolytic overdrive meets lipid storm.},
journal = {Cell death & disease},
volume = {16},
number = {1},
pages = {788},
pmid = {41184254},
issn = {2041-4889},
support = {22205254, 82174496, 82374574//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Ischemic Stroke/metabolism/pathology ; *Glycolysis ; Animals ; *Lipid Metabolism ; Metabolic Reprogramming ; },
abstract = {Ischemic stroke, a leading cause of global disability and mortality, remains inadequately treated beyond reperfusion, with persistent translational failures in neuroprotection. We posit metabolic reprogramming in ischemic stroke (MRIS) as the unifying pathophysiological driver, where acute compensatory glycolysis collides with enzymatic lipid peroxidation to ignite neuroinflammation and early deficits. This metabolic crisis transcends neuron-centric models, integrating single-cell heterogeneity with bidirectional brain-peripheral crosstalk: hepatic ketogenesis releases neuroprotective β-hydroxybutyrate; adipose lipolysis fuels inflammatory storms; and gut dysbiosis disrupts barrier integrity, amplifying neuroinflammation. MRIS progresses through temporally stratified phases. An acute glycolytic-excitotoxic crisis and nicotinamide adenine dinucleotide (NAD[+]) depletion trigger neuroimmune dysfunction. Subacute lipid peroxidation cascades trigger ferroptosis and microglial polarization, whereas chronic-phase recovery of executive networks is scaffolded by sirtuin-mediated mitochondrial biogenesis and the interplay between adenosine monophosphate-activated protein kinase (AMPK) and mechanistic target of rapamycin (mTOR). Spatial metabolomics and single-cell omics decode cell-type-specific vulnerabilities, revealing astrocytic lipid droplets, microglial succinate accumulation, and neuron-glia lactate shuttles as targetable nodes. Chronobiology further dictates therapeutic windows: lactate dehydrogenase A (LDHA) inhibition mitigates hyperacute acidosis, while NAD[+] salvage pathways optimize chronic mitochondrial plasticity. We propose that metabolic reprogramming is a central amplifier of both ischemic injury and recovery, linking cerebral vascular occlusion to systemic organ dysfunction. By reframing stroke within a vascular-metabolic continuum, MRIS shifts the paradigm from a neuron-centric view to one of systemic bioenergetic failure, accounting for past translational gaps and opening pathways for precision therapies, from pentose phosphate pathway modulation to nanoparticle-based metabolite delivery and microbiome interventions. In this framework, metabolic plasticity becomes not just a consequence but a therapeutic target, transforming stroke from an untreatable vascular event to a modifiable metabolic disorder.},
}

Humans
*Ischemic Stroke/metabolism/pathology
*Glycolysis
Animals
*Lipid Metabolism
Metabolic Reprogramming

@article {pmid41183797,
year = {2025},
author = {Lee, I and Kim, BS and Suk, KT and Lee, SS},
title = {Corrigendum to: Gut Microbiome-Based Strategies for the Control of Carbapenem-Resistant Enterobacteriaceae.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e35004},
doi = {10.4014/jmb.2025.3511.C01},
pmid = {41183797},
issn = {1738-8872},
}

@article {pmid41183502,
year = {2025},
author = {Marshall, D and Ueland, M and Nadort, A and Söderström, B},
title = {Using the postmortem epinecrotic microbiome as a tool for time since death estimations.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf274},
pmid = {41183502},
issn = {1365-2672},
abstract = {The estimated time since death, or postmortem interval (PMI), is a crucial piece of information in forensic death investigations. Current scientific methods used to estimate this timeframe do not always provide the most accurate predictions and often rely on subjective interpretations. The microbiome has recently been recognised as a large impactor of human decomposition and current research shows its potential to provide additional accuracy to PMI estimations. As bacteria are ubiquitous, persistent, and due to recent advancements in technology genetically identifiable, microbial analysis effectively complements other forensic science approaches. However, this new field of forensic research requires standardisation, foundational validity, and research collaboration if it is to be considered reliable for use as evidence in the court of law. This review discusses the potential for forensic microbiology to be used as an additional estimator for the PMI, the advantages of epinecrotic microbiome sampling and outlines further steps needed for the integration of this discipline into forensic practice.},
}

@article {pmid41183500,
year = {2025},
author = {Eastwood, J and van Hemert, S and Poveda, C and Elmore, S and Williams, C and Lamport, D and Walton, G},
title = {Using in vitro models to ascertain whether multi-probiotic supplementation influences neurotransmitter and SCFA production in the absence of human cells.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf272},
pmid = {41183500},
issn = {1365-2672},
abstract = {AIMS: The present study aimed to explore microbial production of neurotransmitters related to cognitive function in the faecal microbiota of healthy older adults, and assess whether a multi-strain probiotic formula may influence production of these neuroactive metabolites, short-chain fatty acids, and the bacterial community.

METHOD AND RESULTS: The current study employed a three-stage continuous culture system with faecal microbiota from three healthy older adult donors. Neuroactive compounds were quantified using liquid chromatography mass spectroscopy, SCFAs using gas chromatography, and the bacterial community was assessed using fluorescence in situ hybridisation with flow cytometry and 16S rRNA sequencing. Addition of the probiotic supplement (Bifidobacterium lactis W51, Bifidobacterium lactis W52, Lactobacillus acidophilus W37, Lactobacillus salivarius W24, Lactobacillus casei W56, Bifidobacterium bifidum W23, Lactobacillus brevis W63, Lactococcus lactis W19, Lactococcus lactis W58) significantly increased the relative abundance of Lactococcus lactis in the transverse region, alongside a trend for increased Roseburia across the three colon regions modelled, valerate in the distal region and GABA in the proximal region.

CONCLUSIONS: Whilst administration of the probiotic only had a small effect of trending increases in the synthesis of GABA and valerate, this highlights important mechanisms by which probiotics could be involved in the gut-brain axis. The model also enabled the observation of limited microbial production of other neurotransmitters. Further exploration in human studies is therefore warranted. Probiotics were confirmed to lead to microbial changes, both directly (Lactococcus) and indirectly (Roseburia). This research helps to support mechanistic understanding of probiotics and the gut brain axis.},
}

@article {pmid41183484,
year = {2025},
author = {Arad, N and Pauli, D and Truco, M and Lavelle, D and Michelmore, R and Arnold, AE},
title = {Diversity of leaf- and root microbiomes among genotypes and market classes of desert-grown lettuce (Lactuca sativa L.).},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf121},
pmid = {41183484},
issn = {1574-6968},
abstract = {Plant microbiomes are increasingly acknowledged both as extensions of plant characteristics and as biological factors that influence plant traits important for nutrition and resilience. In the context of global change, manipulation of microbiomes has the potential to complement genetic approaches to enhance crop health and productivity under rising heat and drought stress. Understanding the factors that influence microbial communities and their variation across plant genotypes is essential for developing such capabilities. We employed metabarcoding via the Illumina sequencing platform to investigate microbial communities that occur within healthy leaves and roots of 12 lettuce genotypes (Lactuca sativa L.) grown in a desert agriculture environment. We detected diverse foliar- and root-endophytic fungi and bacteria in field-grown lettuce at the Maricopa Agricultural Center (Arizona, USA). The composition of microbial community structure varied with foliar chemistry and root traits. Notably, levels of zinc and other beneficial nutrients in the leaves were strongly linked with specific endophytes. These results document the lettuce microbiome in desert farming and provide insights into endophytes in lettuce leaves, which are noteworthy because they remain after washing and are regularly ingested.},
}

@article {pmid41183305,
year = {2025},
author = {Yang, R and Ma, J and Abebe, H and Tu, Y},
title = {Divergent Responses of Soil Microbiome Structure and Function to Salinity and Depth Gradients.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c08498},
pmid = {41183305},
issn = {1520-5118},
abstract = {Soil salinization profoundly threatens agricultural ecosystems by disrupting soil microbial communities and functions, yet the interplay of salinity and depth on microbiome structure and function is unclear. In the present experiment, soils from two depths (0-20 and 20-40 cm) across a low (LS), medium (MS), and high (HS) salinity gradient were collected. The results indicated that the soil electrical conductivity, available sodium, and available potassium were significantly elevated in HS soil. 16S rRNA gene sequencing identified three key microorganisms associated with soil salinity, including Sphingomonas, Bradyrhizobium, and Chloracidobacterium. Metagenomic analysis indicated that the abundances of carbon and nitrogen cycle genes such as amyA, xylA, nifH, nirK, narG and amoA were significantly upregulated in LS soils. In conclusion, the experiment systematically elucidated the intricate restructuring of soil microbiome responses across distinct salinity gradients and depths, providing new theoretical support for the remediation of soil salinization.},
}

@article {pmid41182672,
year = {2025},
author = {El-Demerdash, FE and Mohammed, OA and Mohamed, HH and Doghish, AS},
title = {Microbiome alterations in healthy pregnancy and pregnancy disorders in association with autoimmune diseases.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {41182672},
issn = {1874-9356},
abstract = {Pregnancy induces significant alterations in the maternal microbiome, which are critical for fetal development and maternal health. Gynecological diseases, along with infertility, have increased due to excessive personal care product usage, which contains endocrine-disrupting chemicals (EDCs). Mammalian immune systems develop during pregnancy and after birth owing to crucial inputs from the environment. The growing incidence of autoimmune diseases (AIMDs) emphasizes the need to understand the environmental elements that play a role in their development, with the microbiome emerging as a key player. Exposure to EDCs with oxidative stress (OS) induces microbiome disruptions to promote AIMDs and negatively impacts female reproductive health and fetuses. Because the body changes in a number of ways to provide ideal conditions for fetal growth, pregnancy is a special moment in a woman's life. All microorganisms undergo changes, and their quantity and composition vary over the three trimesters of pregnancy. Recent research suggests a connection between pregnancy issues and the microorganisms present during pregnancy. This review explores the pivotal role of the human microbiome in pregnancy health, emphasizing how microbiome dynamics influence immune development and long-term immunity in offspring. It examines the impact of environmental factors, particularly EDCs, on maternal microbiota and their association with pregnancy complications such as hypertensive disorders and autoimmune diseases. The manuscript highlights current research findings and discusses potential microbiome-targeted interventions to promote maternal and fetal well-being.},
}

@article {pmid41182240,
year = {2025},
author = {Gui, F and Gafforov, Y and Vílchez, JI and Zhao, J and Ma, Z and Lv, T and Wang, M},
title = {Epigenetic landscape underlying plant-microbiome chemical communication.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf249},
pmid = {41182240},
issn = {1751-7370},
abstract = {Chemical communication, a universal mode among the interactive members within dynamic plant-microbiome systems, fundamentally drives coevolutionary trajectories. Emerging evidence suggests the critical role of epigenetic regulation in chemical communication, though its mechanistic insights are yet not well understood, a gap that has limited the precise mining of microbiomes function in modern agriculture. Here, we synthesize recent findings from chemistry to epigenetics to illuminate the overlooked epigenetic landscape in plant-microbiome chemical communication. Revisiting the traditional plant-pathogen interaction model and a more complex ternary model involving the plant resident microbiota, we not only present knowledge gaps but also critically dissect the paradoxical roles of resident microbiota by proposing four chemo-epigenetic patterns that fine-tune the interactions among plants, resident microbiota and pathogens. Further, Intelligent Click Chemistry (ICC), an innovative interdisciplinary strategy integrating click chemistry and artificial intelligence, is proposed and discussed, with the aim of unraveling the complex chemo-epigenetic events underlying plant-microbiome chemical communication. Untangling the epigenetic landscape underpinning plant-microbiome chemical communication would enable the strategic and precise exploitation of beneficial microbial traits and suppression of detrimental interactions for sustainable agriculture.},
}

@article {pmid41182235,
year = {2025},
author = {Bisschop, K and Goel, N and Coone, M and Vanoverberghe, I and Greffe, A and Asselman, J and Decaestecker, E},
title = {Host-microbiota matching and epigenetic modulation drive Daphnia magna responses to cyanobacterial stress.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf247},
pmid = {41182235},
issn = {1751-7370},
abstract = {Microbial communities are crucial in host adaptation to stressors, particularly in dynamic ecosystems. In aquatic environments, Daphnia magna is ideal for studying host-microbiome interactions due to its ecological importance and sensitivity. Adaptation to toxins, such as those produced by cyanobacteria, may involve both host and microbial gene repertoires. Yet, the influence of microbiota composition and function on host performance remains poorly understood. Because epigenetic mechanisms such as DNA methylation regulate gene expression and mediate adaptive responses, we also investigated whether these associations are reflected in DNA methylation levels. To address this, we conducted a fully factorial transplant experiment using microbiota-depleted Daphnia colonised with microbiota from the same or different genotype, previously exposed to toxic or non-toxic diets, or left uncolonised. We assessed life-history traits, microbial composition (16S rRNA genes), functional profiles (whole-genome-resequencing), and DNA methylation (colorimetric quantification). Daphnia fed non-toxic diets grew larger and reproduced more. Increased methylation occurred when microbiota donors differed from the host genotype and was strongest under toxic diet. Dysbiosis and reduced performance were noted in individuals colonised with toxic-diet microbiota from another genotype, where Limnohabitans spp. was reduced or absent. Signs of hormesis emerged when Daphnia received microbiota from their own genotype reared on non-toxic diets. DNA methylation of both host and microbiota was associated with functional pathways, including increased mitochondrial fatty acid biosynthesis. These findings highlight the importance of host-microbiota matching and microbial environmental history in shaping host performance and epigenetic responses, emphasizing the need to consider host-microbe-environment interactions in evolutionary and ecological studies.},
}

@article {pmid41181663,
year = {2025},
author = {Ibrahim, SM and Khalel, AM},
title = {Using the Immune System for Effective Periodontal and Caries Management.},
journal = {BioMed research international},
volume = {2025},
number = {},
pages = {6385469},
pmid = {41181663},
issn = {2314-6141},
mesh = {Humans ; *Dental Caries/immunology/therapy/microbiology ; *Periodontal Diseases/immunology/therapy/microbiology ; Immunity, Innate ; *Immune System/immunology ; Microbiota/immunology ; Adaptive Immunity ; Animals ; },
abstract = {The immune system plays a critical, albeit complex, role in oral health, mediating the host response to microbial challenges that lead to prevalent diseases like periodontal disease and dental caries. While essential for protection, immune responses, particularly chronic inflammation, can paradoxically contribute significantly to tissue destruction. This comprehensive review uniquely integrates recent advances in oral immunology with clinical applications, providing novel insights into immunomodulatory therapeutic strategies that distinguish it from previous reviews by emphasizing translational approaches and personalized immunogenetic-based interventions. This review synthesizes current understanding of the intricate interplay between the oral microbiome, innate and adaptive immunity, and the pathogenesis of periodontal disease and caries. We investigate how key immune cells (neutrophils, macrophages, and lymphocytes) and mediators (cytokines and chemokines) orchestrate responses that can lead to alveolar bone loss and enamel demineralization. Saliva's crucial role in modulating oral immunity is also highlighted. The clinical significance of this work lies in its potential to guide evidence-based immunomodulatory treatments, improve patient outcomes through personalized therapeutic approaches, and reduce the systemic health burden associated with chronic oral inflammatory diseases. By dissecting these immunological mechanisms, this article is aimed at underscoring the potential for developing novel, targeted immunomodulatory strategies-including vaccines, host modulation therapies, and personalized approaches based on immunogenetics-for more effective prevention and management of these common oral diseases, ultimately promoting better oral and systemic health.},
}

Humans
*Dental Caries/immunology/therapy/microbiology
*Periodontal Diseases/immunology/therapy/microbiology
Immunity, Innate
*Immune System/immunology
Microbiota/immunology
Adaptive Immunity
Animals

@article {pmid41181529,
year = {2025},
author = {Moutzoukis, MK and Argyriou, K and Manolakis, A and Kapsoritakis, A and Christodoulou, D},
title = {Endoscopic bariatrics: Current status and emerging technologies.},
journal = {World journal of gastrointestinal endoscopy},
volume = {17},
number = {10},
pages = {109031},
pmid = {41181529},
issn = {1948-5190},
abstract = {Endoscopic bariatrics has emerged as a minimally invasive alternative to traditional bariatric procedures. Over the last decade, significant progress in endoscopic techniques and technologies has improved the safety, efficacy, and accessibility of these procedures. Current methods, such as intragastric balloons, endoscopic sleeve gastroplasty, and endoscopic-assisted gastrojejunostomy, have promoted weight loss, improving the metabolic health of obese individuals, with emerging evidence suggesting that their combination with pharmacological agents could further maximize their benefit. Emerging technologies, such as robotic-assisted endoscopic devices, advanced imaging systems, and biodegradable implants, could enhance procedural precision, minimize complications, and provide more personalized treatment options. In contrast, novel approaches such as microbiome modulation and tissue regeneration could have an adjunct role in improving patient outcomes. This review provides a brief overview of the current status of endoscopic bariatrics, highlighting the most common procedures and emerging technologies. It also discusses the challenges and future directions for the field, emphasizing the importance of multidisciplinary collaboration, patient selection, and research priorities to establish the long-term benefit and effectiveness of the available endoscopic bariatric interventions.},
}

@article {pmid41181495,
year = {2025},
author = {Rahman, A and Faiz, M and Khalid, M and Talha, M and Waafira, A},
title = {Gut instinct: microbiome as a modifiable target in the management of neurologic symptoms in myoclonic epilepsy with ragged-red fibers (MERRF).},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {10},
pages = {6904-6905},
pmid = {41181495},
issn = {2049-0801},
abstract = {Myoclonic epilepsy with ragged-red fibers (MERRF) is a rare mitochondrial disorder primarily driven by mutations in mitochondrial DNA, particularly the m.8344A>G variant in MT-TK, and is characterized by epilepsy, myoclonus, ataxia, and other multisystemic features. With no curative therapy, recent attention has turned to the gut microbiome as a modifiable factor influencing neurologic symptoms in mitochondrial diseases. Dysbiosis-induced by antibiotics, diet, or preservatives-has been linked to altered microbial metabolites such as short-chain fatty acids and indoxyl sulfate, which may exacerbate neurological dysfunction. Preliminary clinical trials and preclinical studies suggest that probiotics and dietary interventions can modestly improve disease burden and symptoms such as constipation. However, significant challenges remain, including lack of standardization in analytical protocols, heterogeneous host-microbiota responses, and inadequate patient stratification. To fully realize the therapeutic potential of microbiome-based approaches in MERRF, coordinated multicenter trials, clear regulatory guidelines, and machine learning-enhanced stratification will be essential.},
}

@article {pmid41181349,
year = {2025},
author = {Yang, S and Hao, S and Ye, H and Zhang, X},
title = {Crosstalk Between Oral Microbiome and Cancer: Emerging Trends and Insights.},
journal = {The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale},
volume = {2025},
number = {},
pages = {6639127},
pmid = {41181349},
issn = {1712-9532},
abstract = {Background: Emerging scientific evidence suggests a connection between the oral microbiome (OM) and cancer (CA). This paper is designed to delve into the scientific output within this domain, pinpoint highly cited articles, and explore the latest research hotspots and emerging trends in OM/CA studies. Methods: On January 25, 2025, a comprehensive search was conducted to investigate research on the relationship between OM and CA. The search terms pertinent to both OM and CA were utilized. Key information was extracted from WoSCC. A suite of tools including Biblioshiny from R packages, Excel, and VOSviewer were utilized for comprehensive data visualization. Co-citation analysis was conducted to delineate the conceptual landscape of the field and to highlight influential publications. Results: A total of 1663 papers related to OM/CA were retrieved. The number of papers (Np) in OM/CA is proliferated from 2010 to 2024. The United States and China occupied leading positions and made the most significant contributions. Karolinska Institutet and Harvard University were the most productive institutions. The most prolific authors were Tina Dalianis and Anders Naesman. Oral Oncology garnered the most Np, whereas Gut received the highest total citations (TCs). A historical citation analysis traced the evolution of OM/CA research over time. The key topics encompassed the impact of OM on the initiation and progression of CA, the characteristics of OM in CA, the role of OM in screening and prognosis of CA, the effect of OM on CA treatment, and the underlying mechanisms through which OM is involved in CA. Emerging research hotspots in this field may include Mendelian randomization, applications of machine learning, biofilm formation, cytolethal distending toxin, and nanoparticles, along with the roles of Fusobacterium nucleatum and Porphyromonas gingivalis in disease pathogenesis. Conclusion: This study assessed worldwide production in OM/CA research, examining its quantitative characteristics. It pinpointed several pivotal papers and compiled data on the current status, emerging hotspots, and evolving trends within OM/CA research. The findings of this research may offer a fresh perspective for both academics and practitioners in the field.},
}

@article {pmid41181343,
year = {2025},
author = {Jeyaraman, N and Jeyaraman, M and Dhanabal, P and Ramasubramanian, S and Ambrosio, L and Vadalà, G and Muthu, S},
title = {Implications of the gut microbiome in spinal cord injuries.},
journal = {Frontiers in surgery},
volume = {12},
number = {},
pages = {1668225},
pmid = {41181343},
issn = {2296-875X},
abstract = {Spinal cord injuries (SCIs) present complex challenges in medical treatment and rehabilitation, profoundly affecting the patient's physiological and neurological status. Emerging research on the gut microbiome has unveiled its potential role in influencing SCI outcomes and recovery. The gut microbiome undergoes significant changes following SCIs, which influence systemic inflammation and increase susceptibility to secondary complications, such as infections and chronic pain. These effects are linked to altered permeability, immune system dysregulation, and activation of the gut-brain axis, which represent promising therapeutic targets for the treatment of these conditions. Insights into the mechanisms underlying these effects were explored, highlighting the roles of microbial-derived metabolites like short-chain fatty acids, which have been shown to possess anti-inflammatory properties and support neuroprotective responses. The implications of these findings are significant, suggesting that interventions aimed at modulating the gut microbiome, such as the use of probiotics, prebiotics, and faecal microbiota transplantation, could complement existing SCI treatments and support recovery processes. This review aims to synthesise current knowledge on the interplay between the gut microbiome and SCIs, exploring how this relationship can influence immune modulation, inflammation, and neuroplasticity, thereby affecting recovery trajectories and the necessity for interdisciplinary research approaches that integrate neurology, microbiology, and nutrition to develop holistic, effective treatment strategies for SCI patients.},
}

@article {pmid41181328,
year = {2025},
author = {Jo, JW and Kim, SK and Byun, JY and Hong, SM and Kim, BS},
title = {The association between the adenoid microbiome and chronic otitis media with effusion in children differs according to age.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1660939},
pmid = {41181328},
issn = {2235-2988},
mesh = {Humans ; *Otitis Media with Effusion/microbiology ; Child ; *Adenoids/microbiology ; Male ; Female ; Child, Preschool ; Age Factors ; Chronic Disease ; *Microbiota ; Feces/microbiology ; Streptococcus pneumoniae/isolation & purification ; Haemophilus influenzae/isolation & purification ; Gastrointestinal Microbiome ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Infant ; },
abstract = {INTRODUCTION: Chronic otitis media with effusion (COME) can adversely affect childhood development, and while the adenoid has been considered a reservoir for bacterial pathogens contributing to the pathogenesis of COME, the role of the adenoid microbiome in COME remains unclear. This study analyzed both the adenoid and gut microbiome in children with and without COME to identify their potential roles in the disease's pathogenesis.

METHODS: Adenoid samples were collected during surgery for adenoid microbiome analysis, while fecal samples were collected for gut microbiome analysis. Microbiome was analyzed using whole metagenome sequencing and subsequent bioinformatic analysis.

RESULTS: A significant association between the adenoid microbiome and COME was detected, while no such association observed for the gut microbiome. The adenoid microbiome varied by age in the control group, but this age-dependent variation was perturbed in the COME group. Notably, in children aged 6-12 years, the adenoid microbiome was significantly associated with COME based on the type of middle ear fluid, where Streptococcus pneumoniae and Haemophilus influenzae were prominent indicators in the mucoid form of COME. The proliferation of these species in mucoid COME group was correlated with indicators for the serous COME group. The altered microbiome in COME patients may influence immune responses through the synthesis of spermidine and acetate, contributing to disease development.

DISCUSSION: This study highlights the age-dependent contribution of the adenoid microbiome-particularly in children aged 6 to 12 years-to the pathogenesis of COME.},
}

Humans
*Otitis Media with Effusion/microbiology
Child
*Adenoids/microbiology
Male
Female
Child, Preschool
Age Factors
Chronic Disease
*Microbiota
Feces/microbiology
Streptococcus pneumoniae/isolation & purification
Haemophilus influenzae/isolation & purification
Gastrointestinal Microbiome
Metagenomics
Bacteria/classification/genetics/isolation & purification
Infant

@article {pmid41181327,
year = {2025},
author = {Qian, Z and Bai, W and Li, J and Rao, X and Huang, G and Zhang, X and Wu, W and Liu, J and Wei, W},
title = {Gut microbiome-mediated epigenetic modifications in gastric cancer: a comprehensive multiomics analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1585881},
pmid = {41181327},
issn = {2235-2988},
mesh = {Humans ; *Stomach Neoplasms/genetics/microbiology ; *Epigenesis, Genetic ; DNA Methylation ; *Gastrointestinal Microbiome ; Cell Line, Tumor ; Computational Biology ; Gene Regulatory Networks ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Transcriptome ; Epigenomics ; Multiomics ; },
abstract = {BACKGROUND: Gastric cancer (GC), a malignant and highly proliferative disease, has profoundly impacts a substantial global population and is associated with several variables, including genetic, epigenetic, and environmental impacts. Global variance is associated with Helicobacter pylori infection and dietary factors.

OBJECTIVES: The aim of the present study was to understand and identify key genes significantly modulated by epigenetic changes that can serve as biomarkers and therapeutic targets for gastric cancer.

METHODS: This study employed an integrative multiomics approach to investigate gut microbiome-mediated epigenetic modifications in gastric cancer by utilizing publicly available transcriptomic and DNA methylation datasets, Quality control, normalization and deferentially expressed gene analysis of sequencing data were performed via standard bioinformatics pipelines. Functional enrichment analyses, including GO and KEGG pathway mapping, were performed to elucidate the biological pathways influenced by these interactions and network analysis was conducted using Cytoscape to identify hub genes. We conducted in vitro assays using the gastric adenocarcinoma cell lines AGS and MKN45, and the normal gastric epithelial cell line GES-1. The expression of selected candidate genes was evaluated using real-time PCR in these cell lines.

RESULTS: The GEO2R and coexpression network analyses revealed that six genes MAPK1, NOXO1, CUL1, CDK1, CDK2, and CCNB1 were significantly altered by modified DNA methylation and mRNA expression in GC. Owing to their identification across all epigenetic, transcriptomic, and miRNA datasets, we have designated these genes as shared genes. The results showed that the relative gene expression levels of MKN45 and AGS cell lines were higher than those in the GES-1 cell line in the control., and the results were aligned with the in silico findings.

CONCLUSIONS: CDK1, CDK2, NOXO1, CUL1, MAPK1, and CCNB1 play pivotal roles in GC carcinogenesis and hold promise as early diagnostic biomarkers and therapeutic targets for GC.},
}

Humans
*Stomach Neoplasms/genetics/microbiology
*Epigenesis, Genetic
DNA Methylation
*Gastrointestinal Microbiome
Cell Line, Tumor
Computational Biology
Gene Regulatory Networks
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
Transcriptome
Epigenomics
Multiomics

@article {pmid41181324,
year = {2025},
author = {Paul, LS and Hameed, HC and K V, L and Sharma, A and Lee, J and Shemesh, M and Rajasekharan, SK},
title = {Nomadic Lactobacilli as cell factory for antibiofilm therapy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1668573},
pmid = {41181324},
issn = {2235-2988},
mesh = {Humans ; *Probiotics/therapeutic use ; *Biofilms/growth & development/drug effects ; *Lactobacillus/physiology ; *Candida albicans/physiology/growth & development ; *Candidiasis, Vulvovaginal/therapy/microbiology ; Female ; Vagina/microbiology ; *Antibiosis ; Quorum Sensing ; Hydrogen-Ion Concentration ; },
abstract = {Vulvovaginal candidiasis (VVC) is an infection caused by Candida albicans that presents an escalating threat to humans. Lactobacilli may play a critical role in maintaining microbiome balance in the gut and vagina as well as limiting fungal colonization, including C. albicans. Certain Lactobacilli, classified as nomadic groups is gaining immense popularity in antifungal defense due to its unique morphological adaptations. One significant adaptation is the V-shaped cell chaining observed under low pH conditions governed by the LuxS-mediated quorum-sensing system. This structural adaptation potentiates altered secondary metabolite secretion. These geometric forms are not solely survival responses but reflect a structurally coordinated strategy that enhances both antibiofilm and antihyphal activities. In this perspective, we argue that morphology-driven transitions identify nomadic Lactobacilli as a promising frontier in probiotic therapy. By shifting from conventional probiotic formulations to structured microbial interventions, we propose the development of novel sustainable therapeutics for anticandidal therapy.},
}

Humans
*Probiotics/therapeutic use
*Biofilms/growth & development/drug effects
*Lactobacillus/physiology
*Candida albicans/physiology/growth & development
*Candidiasis, Vulvovaginal/therapy/microbiology
Female
Vagina/microbiology
*Antibiosis
Quorum Sensing
Hydrogen-Ion Concentration

@article {pmid41181319,
year = {2025},
author = {Wang, Z and Song, L and Li, D and Jin, Y},
title = {From commensalism to pathogenesis: the hidden role of the respiratory virome.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1693796},
pmid = {41181319},
issn = {2235-2988},
mesh = {Humans ; *Virome ; *Microbiota ; *Symbiosis ; *Respiratory System/virology/microbiology ; Bacteriophages ; *Viruses/classification/genetics ; Animals ; Metagenomics ; Host-Pathogen Interactions ; Respiratory Tract Infections/virology ; },
abstract = {The respiratory virome, encompassing both eukaryotic viruses and bacteriophages, is an essential but often overlooked component of the airway microbiome. Recent advances in metagenomics have revealed that a diverse viral community exists even in healthy individuals, contributing to immune regulation and microbial balance. However, the field faces several challenges: the baseline composition of the respiratory virome remains incompletely defined, its immunomodulatory functions are not fully understood, and its contributions to respiratory diseases are only beginning to be elucidated. This mini-review summarizes current knowledge of the respiratory virome under physiological conditions, highlights emerging insights into how resident viruses and phages shape host immunity, and discusses alterations observed in asthma, chronic obstructive pulmonary disease, pulmonary fibrosis, and pneumonia. By integrating evidence across these conditions, we emphasize the significance of the virome in both health and disease. A deeper understanding of its dynamics may yield novel diagnostic markers and therapeutic strategies, underscoring the importance of future longitudinal and mechanistic studies in this rapidly evolving field.},
}

Humans
*Virome
*Microbiota
*Symbiosis
*Respiratory System/virology/microbiology
Bacteriophages
*Viruses/classification/genetics
Animals
Metagenomics
Host-Pathogen Interactions
Respiratory Tract Infections/virology

@article {pmid41181176,
year = {2025},
author = {Abidov, A and Bayer, DK},
title = {Atopic dermatitis, primary atopic disorders, and the cutaneous microbiome: current understanding of an expanding field.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1670623},
pmid = {41181176},
issn = {2296-2360},
abstract = {Atopic dermatitis is a common inflammatory skin disease with rapidly expanding worldwide prevalence. Increasingly, cases of severe and early-onset dermatitis have been identified and found to be due to underlying monogenic mutations, leading to immune dysregulation. These conditions, called primary atopic disorders, have become an area of extensive study over the last 30 years. Simultaneously, our understanding of the human microbiome has steadily grown, and there is clear evidence that dysbiosis plays a major role in atopic dermatitis, not only in severity of disease and as a potential trigger but also offering clues for targeted treatment strategies. Unfortunately, despite our growing understanding of the cutaneous microbiome and the expanding availability of genetic testing allowing for diagnosis of primary atopic disorders, there remains very limited understanding regarding the microbiomics changes that underlie these disorders. Here we review the current research regarding atopic dermatitis in the setting of primary atopic disorders, understanding regarding primary atopic disorders and associated cutaneous dysbiosis, and identify specific gaps in knowledge.},
}

@article {pmid41181150,
year = {2025},
author = {Guo, X and Wang, S and Ding, J and Liu, W and Xu, J and Wang, M and Sun, H and Ma, Y and Liu, W and Zhang, L and Liu, M},
title = {Periodontopathic bacteria in rheumatoid arthritis pathogenesis: bridging clinical associations to molecular mechanisms.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1681037},
pmid = {41181150},
issn = {1664-3224},
mesh = {Humans ; *Arthritis, Rheumatoid/microbiology/immunology/etiology ; *Periodontitis/microbiology/immunology/complications ; *Porphyromonas gingivalis/immunology ; Animals ; Microbiota/immunology ; Dysbiosis ; Disease Susceptibility ; },
abstract = {Periodontitis (PD) is a chronic inflammatory disease linked to microbial dysbiosis, while rheumatoid arthritis (RA) is an autoimmune disorder characterized by anti-citrullinated protein antibodies (ACPA). Despite their distinct etiologies, a clinical and serological association between PD and RA has been observed. Oral microorganisms, especially Porphyromonas gingivalis (P. gingivalis), may contribute to RA onset or progression through dissemination to joints or systemic inflammation. This review explores a: the role of oral microbiota and immune responses in RA b; clinical pathogenic pathways from oral pathogens to the joints c; mechanistic studies on the impact of periodontal pathogens on RA; and d. preventive and therapeutic strategies. P. gingivalis and other periodontal pathogens have been detected in synovial tissues and fluids of RA patients. Microbiome analyses show a more diverse oral microbiota with elevated periodontal disease-associated bacteria in RA patients. Studies demonstrate that P. gingivalis can induce citrullination, autoantibody production, and inflammation, exacerbating joint damage. Future research should investigate the impact of periodontal therapy and RA treatments on the oral microbiota, while large-scale clinical trials are needed to validate the causal relationship between periodontal pathogens and RA.},
}

Humans
*Arthritis, Rheumatoid/microbiology/immunology/etiology
*Periodontitis/microbiology/immunology/complications
*Porphyromonas gingivalis/immunology
Animals
Microbiota/immunology
Dysbiosis
Disease Susceptibility

@article {pmid41181130,
year = {2025},
author = {Li, K and Zeng, H and Liu, T and Huo, S and Zhang, C and Li, W and Deng, J and Zhong, X and Tao, Y and Lin, B and Liu, J and Xie, B and Zhong, X},
title = {Gut microbiome as a potential mediator linking sexual behaviors to immune profiles in HIV-negative men who have sex with men: a multi-omics study.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1659556},
pmid = {41181130},
issn = {1664-3224},
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/immunology ; *Homosexuality, Male ; Adult ; *Sexual Behavior ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; HIV Seronegativity ; Leukocytes, Mononuclear/immunology ; Transcriptome ; Multiomics ; },
abstract = {INTRODUCTION: The effects of sexual behaviors on the gut microbiome and immune system in men who have sex with men (MSM) remain unclear. Here, we conducted a multi-omics study in MSM to investigate how sexual behaviors shape gut microbiome composition and immune profiles in this population. The interplay among high-risk sexual behaviors, gut microbiome, and systemic immune activation was also explored.

METHODS: HIV-negative MSM were enrolled in this study. Fecal samples were collected and subjected to 16S rRNA gene sequencing. Bulk and single-cell transcriptome sequencing of peripheral blood mononuclear cells (PBMCs) were performed to investigate the systemic immune profiles. Primary component analysis and spearman correlation analysis were used to assess the associations between gut microbiome and immune signatures. BayesPrism algorithm was applied to predict cellular composition and gene expression in individual cell types by integrating bulk RNA sequencing and sc-RNA sequencing. Causal mediation analysis evaluated the contribution of gut microbiome in linking sexual behaviors to immune outcomes.

RESULTS: The gut microbiome of HIV-negative MSM was dominated by Segatella. Receptive anal intercourse had the most significant impact on the gut microbiome, characterized by increased diversity, depletion of Xylanibacter, and enrichment of Holdemania. We also identified altered immune gene expression, an elevated CD8:CD4 ratio, distinctive CD4[+] T cell communications, and higher expression of CXCR4 in CD4[+] T cells in MSM engaged in receptive anal intercourse. Mediation analysis indicated that Bilophila potentially mediated the effects of receptive anal intercourse on CD4[+] T cell proportions (P = 0.026). MSM exposed to group sex and illicit drug had elevated HIV susceptibility index, possibly mediated by Bifidobacterium (P = 0.012, P = 0.02 respectively).

CONCLUSION: Our study indicates that gut microbiome partially mediates the immunomodulatory effects of sexual behaviors, providing mechanistic insights into HIV susceptibility. These findings underscore the gut-immune axis as a potential target for HIV prevention strategies in high-risk MSM.},
}

Humans
Male
*Gastrointestinal Microbiome/immunology
*Homosexuality, Male
Adult
*Sexual Behavior
RNA, Ribosomal, 16S/genetics
Middle Aged
HIV Seronegativity
Leukocytes, Mononuclear/immunology
Transcriptome
Multiomics

@article {pmid41181090,
year = {2025},
author = {Lu, Y and Yuan, H and Liang, S and Li, D and Jiang, P and Wang, X and Zhang, K and Liu, D},
title = {Microbial metabolite-driven immune reprogramming in tumor immunotherapy: mechanisms and therapeutic perspectives.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1603658},
pmid = {41181090},
issn = {1664-3224},
mesh = {Humans ; *Neoplasms/immunology/therapy/metabolism/microbiology ; *Immunotherapy/methods ; Tumor Microenvironment/immunology ; *Gastrointestinal Microbiome/immunology ; Animals ; Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Tryptophan/metabolism ; Cellular Reprogramming ; Fatty Acids, Volatile/metabolism ; Bile Acids and Salts/metabolism ; },
abstract = {The gut microbiome critically regulates antitumor immunity through its metabolic byproducts, which serve as pivotal mediators of host-microbe crosstalk in tumor immunotherapy. This review synthesizes cutting-edge evidence on how microbial metabolites-including short-chain fatty acids (SCFAs), tryptophan derivatives, and bile acids-reprogram immune cell dynamics and remodel the tumor microenvironment (TME). Mechanistically, metabolites such as butyrate and indole-3-propionic acid (IPA) enhance immune checkpoint inhibitor (ICI) efficacy by epigenetic modulation or metabolic reprogramming. Conversely, kynurenine (a tryptophan metabolite) and secondary bile acids drive resistance by polarizing macrophages toward an immunosuppressive phenotype or exhausting cytotoxic T cells. Metabolite-targeted interventions (such as probiotics, dietary modulation, and engineered microbes) show synergistic potential with ICIs, but require resolution of causal inference limitations, interindividual variability, tumor-context specificity, and dose optimization. Precision microbiome engineering, guided by multi-omics profiling and artificial intelligence, may unlock personalized strategies to overcome immunotherapy resistance.},
}

Humans
*Neoplasms/immunology/therapy/metabolism/microbiology
*Immunotherapy/methods
Tumor Microenvironment/immunology
*Gastrointestinal Microbiome/immunology
Animals
Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Tryptophan/metabolism
Cellular Reprogramming
Fatty Acids, Volatile/metabolism
Bile Acids and Salts/metabolism

@article {pmid41181082,
year = {2025},
author = {Agake, SI and Damo, JLC and Rai, H and Stacey, G and Yasuda, M and Ohkama-Ohtsu, N},
title = {Comparative analysis of Bacillus pumilus TUAT1 endospores and vegetative cells: Implications for plant growth promotion and soil microbiome modulation.},
journal = {Plant biotechnology (Tokyo, Japan)},
volume = {42},
number = {3},
pages = {327-334},
pmid = {41181082},
issn = {1342-4580},
abstract = {Bacillus pumilus TUAT1, a gram-positive and spore-forming plant growth-promoting rhizobacterium, has been utilized as a biofertilizer due to its robust ability as spores to withstand environmental stresses and ensure long-term viability. This study investigated the mechanisms underlying the plant growth-promoting effects of spores and vegetative cells. Elemental analyses revealed that endospores are enriched in carbon, calcium, and manganese, which contribute to their protective properties, while vegetative cells are richer in nitrogen and phosphorus. Notably, both viable and dead spores and vegetative cells promoted the growth of Setaria viridis in natural soil. Microbial community analysis showed that bacterial alpha diversity was not changed across treatments, whereas beta diversity varied significantly, forming distinctly separated groups influenced by planting and inoculation. Fungal community analysis exhibited increased alpha diversity due to Setaria planting but no significant effects from bacterial treatments. Enrichment of Bdellovibrio spp., Bacteriovorax spp., and Pseudomonas spp. in soil inoculated with viable and dead vegetative cells and spores highlighted the capability of indirect mechanisms through microbial interactions rather than direct nutrient supply from bacterial residues. We believe that bacterial inoculants, including dead cells, modulate soil microbial communities to enhance plant growth, emphasizing their potential in sustainable agriculture.},
}

@article {pmid41181072,
year = {2025},
author = {Nakamura, N and Sugiyama, A},
title = {Developmental stage-specific triterpenoid saponin accumulations in Ardisia crenata rhizosphere and its influence on rhizosphere microbial communities.},
journal = {Plant biotechnology (Tokyo, Japan)},
volume = {42},
number = {3},
pages = {357-369},
pmid = {41181072},
issn = {1342-4580},
abstract = {Plant-specialized metabolites (PSMs) act as candidate drivers of rhizosphere microbiome assembly by recruiting specific microbial taxa. The resulting PSM-microbe interactions influence the host-plant fitness and population dynamics, ultimately impacting the aboveground biodiversity. Although saponins are widely distributed PSMs in the angiosperms, their dynamics and impact on soil microbiomes in a natural ecosystem remain unclear. Here, we investigated the ecological role of a triterpenoid saponin, ardisiacrispin, synthesized by the shade-tolerant shrub Ardisia crenata (Primulaceae), in a forest ecosystem. First, we quantified the saponin concentrations in both the roots and rhizosphere soils of A. crenata at two different developmental stages (i.e., seedling and adult). Next, we assessed how saponin treatment alters the microbial communities in forest soil. Finally, we integrated 16S rRNA and the internal transcribed spacer region sequencing data from the field-collected A. crenata rhizosphere with the results from in vitro saponin-treatment experiments to determine whether saponins selectively enrich or deplete specific microbial taxa. We found that the rhizosphere saponin content primarily varies with the developmental stages of A. crenata, with higher saponin concentrations in adults than in seedlings. The saponin-treatment experiments revealed that ardisiacrispins modify the soil microbial diversity and community structure in accordance with their concentration. Moreover, several microbial taxa were consistently enriched or depleted in the saponin-treated soil, which mirrors the shifts observed from seedling to adult rhizospheres. Thus, ardisiacrispin can mediate rhizosphere microbial community assembly in a natural ecosystem. Our findings highlight the importance of the developmental stage-specific accumulation of saponins in the rhizosphere for plant-microbe interactions.},
}

@article {pmid41181071,
year = {2025},
author = {Hemelda, NM and Noutoshi, Y},
title = {Root-exuded sugars as drivers of rhizosphere microbiome assembly.},
journal = {Plant biotechnology (Tokyo, Japan)},
volume = {42},
number = {3},
pages = {215-227},
pmid = {41181071},
issn = {1342-4580},
abstract = {Sugars in root exudates play a pivotal role in shaping plant-microbe interactions in the rhizosphere, serving as carbon sources and signaling molecules that orchestrate microbial behavior, community structure, and plant resilience. Recent research has shed light on the dynamics of sugar levels in root exudates, the factors that influence their secretion, and the mechanisms by which these sugars drive microbial colonization and community assembly in the rhizosphere. Microbial communities, in turn, contribute to plant physiological changes that enhance growth and stress tolerance. While well-studied sugars such as glucose, sucrose, and fructose are known to promote chemotaxis, motility, and biofilm formation, emerging evidence suggests that less-studied sugars like arabinose and trehalose may also play significant roles in microbial interactions and stress resilience. Key challenges remain, including the accurate measurement of labile sugars that are rapidly metabolized by microbes, and the elucidation of genetic mechanisms underlying rhizosphere metabolic interactions in both host plants and microbes. Addressing these challenges will advance our understanding of sugar-mediated interactions and inform the development of sustainable agricultural innovations.},
}

@article {pmid41181069,
year = {2025},
author = {Osayande, IS and Han, X and Tsuda, K},
title = {Dynamic shifts in plant-microbe relationships.},
journal = {Plant biotechnology (Tokyo, Japan)},
volume = {42},
number = {3},
pages = {271-277},
pmid = {41181069},
issn = {1342-4580},
abstract = {Plant-microbe interactions encompass a continuum from mutualism and commensalism to parasitism. Mutualists confer benefits such as nutrient acquisition or stress tolerance, whereas pathogens compromise host health, and commensals coexist without detectable harm or benefit. Importantly, these relationships are not fixed but are dynamic, shifting between interaction modes in response to host physiology, microbial adaptation, and environmental conditions. Such shifts can influence plant health, agricultural productivity, and ecosystem stability. This review synthesizes the mechanisms underlying these functional transitions and discusses how understanding the drivers of interaction shifts can inform sustainable agriculture and ecosystem management.},
}

@article {pmid41181040,
year = {2025},
author = {Jeyaraman, M and Balasubramanian, E and Jeyaraman, N and Nallakumarasamy, A and Muthu, S},
title = {Metagenomic analysis of gut microbiome and spondyloarthropathy: A systematic review.},
journal = {World journal of orthopedics},
volume = {16},
number = {10},
pages = {108374},
pmid = {41181040},
issn = {2218-5836},
abstract = {BACKGROUND: Spondyloarthritis (SpA), a prevalent chronic inflammatory disorder, predominantly impacts the axial skeleton, including the spine and sacroiliac joints. Emerging evidence implicates gut dysbiosis in the pathogenesis of SpA.

AIM: To evaluate the association between gut microbiome alterations and SpA through metagenomic sequencing analyses.

METHODS: A systematic review was conducted by querying English-language databases, including PubMed, EMBASE, and Google Scholar, spanning 2000 to 2023. From an initial pool of 150 studies, four articles meeting stringent inclusion and exclusion criteria were selected for analysis.

RESULTS: The reviewed studies identified an enrichment of opportunistic pathogenic bacterial species, such as Clostridium spp., Prevotella spp., and Bacteroides spp., alongside viral families including Gratiaviridae and Quimbyviridae, in individuals with ankylosing spondylitis compared to healthy controls. Dysregulated metabolic pathways were highlighted as potential mediators of chronic inflammation and arthritic manifestations. Notably, treatment with tumor necrosis factor inhibitors demonstrated efficacy in mitigating SpA symptoms and restoring gut microbial balance.

CONCLUSION: The findings underscore a significant presence of pathogenic gut microbiota in SpA patients, suggesting a pivotal role in disease progression. Future investigations should focus on species-specific microbial targets to develop innovative therapies for preventing and managing SpA and associated gut dysbiosis.},
}

@article {pmid41180995,
year = {2025},
author = {Anis, MA and Shahid, Y and Majeed, AA and Abid, S},
title = {Microbiome and gut-liver interactions: From mechanisms to therapies.},
journal = {World journal of gastroenterology},
volume = {31},
number = {40},
pages = {111409},
pmid = {41180995},
issn = {2219-2840},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/physiology/drug effects ; *Dysbiosis/therapy/microbiology/immunology ; *Liver/microbiology/immunology/metabolism/pathology ; Probiotics/therapeutic use ; *Liver Diseases/microbiology/therapy/immunology ; Fecal Microbiota Transplantation ; Bile Acids and Salts/metabolism ; Anti-Bacterial Agents/therapeutic use ; Precision Medicine/methods ; Animals ; Host Microbial Interactions/immunology ; },
abstract = {The gut-liver axis represents a bidirectional and dynamic communication system between the gastrointestinal tract and liver, critically modulated by gut microbiota, bile acids, immune responses, and metabolic pathways. Disruption of this finely tuned axis contributes to the pathogenesis of several liver diseases, including alcohol-associated hepatitis, metabolic dysfunction-associated steatotic liver disease, cirrhosis, hepatic encephalopathy, and cholangiopathies like primary biliary cholangitis and primary sclerosing cholangitis. Dysbiosis, marked by reduced microbial diversity and dominance of pathogenic species, alters bile acid metabolism, increases gut permeability, and fuels hepatic inflammation. In cholangiopathies, the gut microbiome modulates immune dysregulation and fibrosis through complex microbial-host interactions. Emerging therapies targeting the microbiota, such as fecal microbiota transplantation, antibiotics (e.g., rifaximin, vancomycin), bile acid modulators, and probiotics, show promise in restoring microbial equilibrium, improving liver biochemistry, and reducing disease progression. Precision medicine strategies integrating genomics, metabolomics, and microbiomics offer a tailored approach for therapy and prognosis. This review highlights the central role of the gut-liver axis in liver diseases and the potential of microbiome-based interventions to shift management from symptomatic relief toward disease modification and personalized hepatology, underscoring a new frontier in liver disease therapeutics.},
}

Humans
*Gastrointestinal Microbiome/immunology/physiology/drug effects
*Dysbiosis/therapy/microbiology/immunology
*Liver/microbiology/immunology/metabolism/pathology
Probiotics/therapeutic use
*Liver Diseases/microbiology/therapy/immunology
Fecal Microbiota Transplantation
Bile Acids and Salts/metabolism
Anti-Bacterial Agents/therapeutic use
Precision Medicine/methods
Animals
Host Microbial Interactions/immunology

@article {pmid41180884,
year = {2025},
author = {Sharma, P and Kapoor, N and Langer, S},
title = {Comparative Analysis of Gut Bacterial Communities in Fish and Shellfish of Great Himalayan River System.},
journal = {Indian journal of microbiology},
volume = {65},
number = {3},
pages = {1734-1747},
pmid = {41180884},
issn = {0046-8991},
abstract = {The gut microbiota comprises a unique micro-ecosystem and plays important role in various metabolic functions of the host. Cirrhinus mrigala and Maydelliathelphusa masoniana are two important species of fish and shellfish found in Chenab and Ravi rivers of Himalayan river system. This is the first report on the core gut microbiota of M. masoniana and C. mrigala using Illumina Miseq Sequencing. Gut bacterial diversity of crabs and fishes are studied from the rivers as well as farms. The core microbiome of crab gut samples consists of genera: Bacteroides, Dysgonomonas, Lactobacillus, Leptotrichia, Acinetobacter, Prevotella, Prevotella 1, Pseudomonas, Fusobacterium and Streptococcus. The core microbiome of fish gut samples consists of genera: Acinetobacter, Lactobacillus, Methanosaeta, Prevotella and Pseudomonas. The result shows higher relative abundance of Bacteroides and Lactobacillus in river Ravi than Chenab. Gut bacterial diversity of fishes and crabs of river Chenab is comparatively lower than the river Ravi. Three genera (Bacteroides, Oceanobacillus and Lactococcus) show significant variation (p value < 0.05) in fishes and crabs. Our study generated sequencing data on the gut microbiota of M. masoniana and C. mrigala can establish a base for the development of therapeutic approaches in dealing with the health conditions of diseased fishes and crabs. Gut microbial characterization will not only help in growth and development of the host but also helps in minimizing the disease susceptibility.},
}

@article {pmid41180801,
year = {2025},
author = {Hattori, Y and Fujii, T and Tochio, T and Kumamoto, T and Hiro, J and Matsuoka, H and Masumori, K and Funasaka, K and Ohno, E and Hirooka, Y and Suda, K and Otsuka, K},
title = {Postoperative Gut Microbiota Changes after Colorectal Cancer Surgery: A Comparative Study Based on Resection Sites.},
journal = {Journal of the anus, rectum and colon},
volume = {9},
number = {4},
pages = {447-454},
pmid = {41180801},
issn = {2432-3853},
abstract = {OBJECTIVES: Colorectal cancer (CRC) is a major global health concern, and surgical resection remains its primary treatment. However, the impact of different surgical procedures on gut microbiota and their influence on postoperative outcomes remain unclear. This study investigated changes in the gut microbiota following three types of CRC resections: right-sided colectomy (RSC), left-sided colectomy (LSC), and low anterior resection (LAR).

METHODS: Fecal samples were collected from 34 patients with CRC who underwent curative resection at Fujita Health University Hospital between April 2022 and December 2023. Bacterial profiling was performed using 16S rRNA gene amplicon sequencing. The results were compared with data from 85 healthy controls.

RESULTS: Significant alterations in gut microbiota composition were observed in surgical groups compared to the healthy control (Ctrl) group. The RSC group exhibited the greatest reduction in alpha diversity, likely because of ileocecal valve loss. Beta-diversity analysis revealed distinct microbial profiles between the Ctrl group and the surgical groups, with notable alterations in key bacterial species. The RSC group exhibited significant reduction in beneficial bacteria, including Faecalibacterium prausnitzii and Bifidobacterium spp., alongside increase in Escherichia coli, suggesting a shift toward a pro-inflammatory environment. In contrast, the LSC and LAR groups exhibited enrichment of Akkermansia muciniphila, which may promote gut barrier integrity and immune modulation.

CONCLUSIONS: CRC resection induces site-specific changes in gut microbiota composition. These microbial alterations may affect postoperative inflammation, metabolism, and cancer recurrence risk. Further studies are necessary to explore microbiome-targeted strategies for improving postoperative outcomes in cases of CRC.},
}

@article {pmid41180703,
year = {2025},
author = {Amir, Q and Gyaneshwari, and Khalid, M and Talha, M and Waafira, A},
title = {Probiotics in the fight against necrotizing enterocolitis: a cost-effective yet underutilized strategy in neonatal care.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {11},
pages = {6905-6906},
pmid = {41180703},
issn = {2049-0801},
abstract = {Necrotizing enterocolitis (NEC) remains a leading cause of gastrointestinal morbidity and mortality among preterm and very low birth weight infants. Probiotics, particularly multi-strain formulations including Bifidobacteria, Lactobacillus, and Enterococcus, have shown considerable promise in reducing the incidence and severity of NEC by modulating the neonatal gut microbiome, enhancing mucosal barrier integrity, and reducing systemic inflammation. Recent meta-analyses confirm their efficacy in lowering NEC risk and associated mortality. Nevertheless, routine use in clinical practice remains limited due to heterogeneity in neonatal intensive care unit practices, uncertainty around optimal strains, dosage, and treatment duration, and insufficient long-term safety data. Given their cost-effectiveness and strong evidence base, integrating probiotics into standard neonatal care protocols, while addressing existing research gaps, could significantly improve outcomes for this vulnerable population.},
}

@article {pmid41180493,
year = {2025},
author = {Choi, JM and Wu, X and Zhang, L},
title = {FastST: an efficient tool for inferring decomposition and directionality of microbial communities.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20161},
pmid = {41180493},
issn = {2167-8359},
mesh = {*Microbiota ; Humans ; Bayes Theorem ; Computer Simulation ; *Software ; *Computational Biology/methods ; },
abstract = {Microbiomes play crucial roles in human health, disease development, and global ecosystem functioning. Understanding the origins, movements, and compositions of microbial communities is essential for unraveling the principles governing microbial ecology. Microbial source tracking (MST) approaches have emerged as valuable tools for quantifying the proportions of different microbial sources within target communities, enabling researchers to track transmissions between hosts and environments, identify similarities between microbiome samples, and determine sources of contamination in various settings. Current MST methods like SourceTracker2 and FEAST have advanced the field by employing Bayesian and expectation-maximization approaches, respectively, but are limited by computational inefficiency with high-dimensional data and inability to infer directionality in source-sink relationships. This study presents a novel computational framework for microbial source tracking called FastST. FastST infers the relative contributions of source environments to sink microbiomes while also determining directionality when source-sink relationships are not predefined. Through extensive simulation studies with varying numbers of sources and complexity, FastST demonstrates superior performance in both accuracy and computational efficiency compared to FEAST and SourceTracker2, maintaining consistent execution times even as the number of source environments increases. Furthermore, the proposed method achieved over 90% accuracy in directionality inference across all tested scenarios, even when multiple major sources are present, broadening its applicability in practical microbiome research and environmental monitoring. FastST and data simulation codes are publicly available at https://github.com/joungmin-choi/FastST.},
}

*Microbiota
Humans
Bayes Theorem
Computer Simulation
*Software
*Computational Biology/methods

@article {pmid41180402,
year = {2025},
author = {Chen, C and Xu, D and Jiang, B and Lu, X and Yu, C and Wang, Y and Wang, H and Li, J and Zhu, J},
title = {Precipitation-driven restructuring of rhizosphere microbiota enhances alpine plant adaptation.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1641511},
pmid = {41180402},
issn = {1664-462X},
abstract = {INTRODUCTION: Climate-driven precipitation changes are increasingly threatening alpine ecosystems, yet the adaptive responses of soil microbiomes to rainfall variability remain poorly characterized. This knowledge gaphinders our ability to predict ecosystem resilience under future climate scenarios.

METHODS: We combined metagenomic sequencing with detailed physicochemical analyses to examine how natural precipitation events reshape the microbial communities in both rhizosphere and bulk soils associated with Poa alpigena in the alpine sandy ecosystems of Qinghai Lake.

RESULTS: Rainfall significantly reduced bacterial alpha diversity, particularly in bulk soils, and triggered a compositional shift from drought-resistant taxa (e.g., Geobacter, Pseudomonas) to moisture-adapted genera (e.g., Azospirillum, Methylobacterium). Actinobacteria remained consistently dominant (31.56-34.62%), while Proteobacteria abundance decreased markedly in the rhizosphere post-rainfall. Metabolic reconstruction revealed a transition from pre-rainfall carbohydrate catabolism to post-rainfall anaerobic energy production and carbon fixation pathways. The rhizosphere microbiome uniquely displayed drought-induced biofilm formation and rainfall-enhanced branched-chain amino acid metabolism. Soil moisture and total carbon were identified as primary drivers of microbial restructuring in bulk soils, whereas root exudates conferred stability to rhizosphere communities against hydrological fluctuations.

DISCUSSION: These results elucidate microbiome-mediated adaptive strategies to precipitation changes in alpine sandy ecosystems, highlighting the critical buffering role of plant-microbe interactions. The study provides a mechanistic basis for predicting and restoring climatevulnerable wetlands under increasingly variable hydrological regimes.},
}

@article {pmid41180233,
year = {2025},
author = {Naveenprasath, T and Ummat, BH and Tarique, F and Chawade, A and Kushwaha, S},
title = {Metatranscriptome analysis to unveil the molecular signatures of transcriptionally active pathogens associated with bovine mastitis.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1642351},
pmid = {41180233},
issn = {2297-1769},
abstract = {Bovine mastitis, a multi-etiological disease, is driven by complex microbial consortia; however, the transcriptional activity of pathogens and their underlying molecular mechanisms remains insufficiently explored. To the best of our knowledge, no metatranscriptome study on bovine mastitis is available in the public domain that identifies transcriptionally active pathogens and their associated molecular signatures. In this study, an in silico metatranscriptomics approach is employed on publicly available bovine mastitis RNA sequencing (RNA-Seq) datasets to identify transcriptionally active pathogens and their gene expression signatures. The analysis of unmapped reads (those not mapped to the bovine genome) identified 25 transcriptionally active pathogenic genera, accounting for 8,995 sequences, approximately from 500 bacterial strains of different species. Major findings of the study includes: (I) list of emerging pathogens "Pseudomonas, Stenotrophomonas, Comamonas, and Sphingomonas" actively contributing to disease development alongside well-known pathogens; (II) expression profiling of 4,121 virulence proteins, 484 peptidases, 432 secretory proteins, and 74 antimicrobial resistance genes; (III) identification of numerous hypothetical proteins in Staphylococcus (112), Mycoplasma (69), and Escherichia (32), representing potential source for diagnostics and multi-epitope vaccine candidates; and (IV) negative correlations between beneficial bacteria (Blautia, Bacillus, Lactobacillus) and pathogenic species in microbial co-occurrence interaction networks, suggesting opportunities for microbiome-based therapeutic strategies to treat subclinical mastitis. This study demonstrated the advantages of the metatranscriptomics approach and publicly available dual RNA-Seq datasets in unraveling the complexity of polymicrobial infectious diseases.},
}

@article {pmid41179940,
year = {2025},
author = {Panneerselvam, VP and Kagithakara Vajravelu, L and Harikumar Lathakumari, R and Baskar Vimala, P and M Nair, D and Thulukanam, J},
title = {Bacteriophage-based therapies in oral cancer: A new frontier in oncology.},
journal = {Cancer pathogenesis and therapy},
volume = {3},
number = {6},
pages = {453-465},
pmid = {41179940},
issn = {2949-7132},
abstract = {The human oral cavity harbors a diverse and dynamic microbial ecosystem, including bacteriophages (phages), which play a critical role in shaping the microbial community structure. Bacteriophages, viruses that specifically target and infect bacteria, have been increasingly recognized for their potential to influence both microbial balance and disease progression within the oral environment. Recent studies suggest that bacteriophages not only modulate the composition of the oral microbiome but also play an essential role in the pathogenesis and treatment of oral cancer. This review aims to explore the complex crosstalk between bacteriophages and oral health related to oral carcinogenesis, with a particular focus on their emerging roles in oral carcinogenesis and therapeutic interventions. Oral cancer, a major global health concern, is often associated with microbial dysbiosis and chronic inflammation, both of which contribute to tumor progression. Fusobacterium nucleatum, a key bacterial species implicated in oral carcinogenesis, has been shown to promote tumor growth, enhance immune evasion, and exacerbate inflammation within the tumor microenvironment. Bacteriophages offer a promising strategy to selectively target and eliminate such pathogenic bacteria such as Fusobacterium nucleatum, thereby restoring microbial balance and reducing the pro-tumorigenic effects of bacterial infections. Through the disruption of tumor-associated biofilms and modulation of cancer-promoting bacterial populations, phages may help mitigate the inflammatory responses that drive oral cancer progression. Additionally, phage therapy could complement existing treatments by sensitizing cancer cells to chemotherapy and immunotherapy. Beyond their direct antibacterial effects, genetically engineered bacteriophages present novel opportunities for targeted cancer therapy. Advances in synthetic biology have enabled the development of phages capable of delivering therapeutic payloads, such as anti-cancer peptides, cytotoxic agents, and immune modulators. These engineered phages can be designed to selectively target bacterial species that influence tumor progression, offering a highly specific and precision-based approach to oncology. Moreover, phages can serve as vectors for cancer vaccines, facilitating antigen presentation and enhancing immune responses against tumor cells. In addition to therapeutic applications, bacteriophages hold promise in the field of cancer diagnostics. The ability of phages to selectively bind to specific bacterial biomarkers associated with oral cancer could be leveraged for early disease detection and non-invasive screening. Phage-based biosensors, for instance, have shown potential in identifying cancer-associated microbial signatures, paving the way for innovative diagnostic tools that could improve early intervention and patient outcomes. Despite their potential, several challenges must be addressed before phage-based strategies can be fully integrated into clinical practice. Phage resistance, immune system clearance, and regulatory barriers pose significant hurdles to the widespread adoption of phage therapy. Additionally, the complex interactions between bacteriophages, host immunity, and the tumor microenvironment require further investigation to optimize therapeutic efficacy and safety. Advancing research on bacteriophages in the context of oral cancer could revolutionize current treatment paradigms, providing more targeted, efficient, and patient-friendly alternatives to conventional therapies. By harnessing the natural specificity and adaptability of bacteriophages, clinicians and researchers can develop innovative approaches to combat oral cancer, ultimately improving patient care and clinical outcomes.},
}

@article {pmid41179893,
year = {2025},
author = {Vavricka, SR and Bartoli, C and Castillo, C},
title = {Primary care and specialist physicians' prescribing preferences for concurrent probiotic-antibiotic therapy: a multinational clinical practice survey across 13 countries.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1685840},
pmid = {41179893},
issn = {2296-858X},
abstract = {Antibiotic-induced intestinal microbiota disruption represents a significant clinical concern, yet physician practices regarding concurrent probiotic supplementation remain poorly characterized across international healthcare systems. We investigated physician attitudes, knowledge, and prescribing behaviors in 390 physicians from 13 countries concerning probiotic-antibiotic co-administration and evaluated receptivity to innovative probiotic formulations with a cross-sectional online survey conducted in June 2025. Sampling included random selection of direct email outreach to known internal medicine specialists, general practitioners, and family physicians. Participants included internal medicine specialists (42%), general practitioners (46%), and family physicians (12%). There was an overall response rate of 52%. While 98% of physicians demonstrated high awareness of antibiotic-induced microbiota disruption, only 37% consistently recommended probiotics when prescribing antibiotics, with substantial variation in co-prescribing practices: 7% prescribed probiotics to nearly all patients, 13% to 1-10, 20% to 11-25, 33% to 26-50, and 27% to 51-99% of antibiotic recipients. Regional variations showed Lithuania, Colombia and Peru had the highest co-prescription rates (50% of physicians prescribing to >50% of patients), while Finland demonstrated more conservative patterns (50% prescribing to <25% of patients). During cold and flu season, antibiotic prescribing rates were evenly distributed across physician groups but decreased substantially outside peak respiratory illness periods. Most physicians (68%) found probiotics useful when taken with antibiotics, with 96% considering them for patients with prior antibiotic-associated diarrhea history. Physician receptivity to advanced probiotic formulations was consistently high, with 92% welcoming products that could be taken simultaneously with antibiotics and 92% willing to recommend such products to patients with special concerns, indicating that while physicians maintain high awareness of antibiotic microbiome impact, probiotic co-prescribing practices remain inconsistent globally with regional variations reflecting differences in healthcare policies and clinical guidelines.},
}

@article {pmid41179493,
year = {2025},
author = {Gul, F and Herrema, H and Ameer, A and Davids, M and Nasir, A and Gerasimidis, K and Ijaz, UZ and Javed, S},
title = {Dietary composition and fasting regimens differentially impact the gut microbiome and short-chain fatty acid profile in a Pakistani cohort.},
journal = {Frontiers in systems biology},
volume = {5},
number = {},
pages = {1622753},
pmid = {41179493},
issn = {2674-0702},
abstract = {PURPOSE: Fasting is known to have beneficial effects on human physiology and health due to changes in gut microbiota and its associated metabolites. We investigated the effects of intermittent and Ramadan fasting on the gut microbial composition, diversity, and short-chain fatty acid (SCFA) profile in a Pakistani population.

METHODS: Paired fecal samples-a total of 29 for Ramadan fasting (divided into three groups, before and after completion and after 3 months) and 22 for intermittent fasting (divided into two groups, day 1 and day 10)-were collected for both 16S rRNA microbiome profiling and SCFA analysis. Study volunteers also provided a detailed questionnaire about the dietary regimen before and during the fasting period. Descriptive statistics were applied to ascertain variations in the gut microbiome and SCFAs attributable to changes in food consumption during fasting.

RESULTS: Ramadan fasting increased the bacterial taxonomic and functional diversity and decreased the abundance of certain harmful microbes such as Blautia, Haemophilus, Desulfovibrio, Lachnoclostridium, and Porphyromonas. Intermittent fasting showed increased abundance of Prevotella, Lactobacillus, and Anaerostipes. Ramadan fasting also led to a significant increase in SCFAs including C7, iC4, and iC6, accounting for variability in microbial composition and phylogeny, respectively. In intermittent fasting, C5, iC5, and iC6 contributed to variability in microbial composition, phylogeny, and function, respectively.

CONCLUSION: Both fasting regimens impacted gut microbiome and metabolic signatures, but Ramadan fasting showed a more drastic effect due to the 30 days compliance period and water restriction than intermittent fasting. Ramadan fasting also improved metabolic health by increasing the abundance of SCFA-producing microbes. With Ramadan fasting, most microbial taxa reverted to their prefasting state after resumption of normal feeding patterns with few exceptions, indicating impact on microbial niche creation with prolonged fasting regimens that benefit Enterococcus, Turibacter, and Klebsiella colonization. The dietary regimen adopted during fasting, especially the consumption of high-fat-content food items, accounted for persistent gut microbial changes.},
}

@article {pmid41179483,
year = {2025},
author = {Fanous, N and Talley, NJ and Chaemsupaphan, T and Lee, E and Rayamajhee, B and Baradaran Ghavami, S and Kazemifard, N and Asadzadeh Aghdaei, H and Chuang, E and Leong, RW},
title = {Microbiota-targeted strategies in IBD: therapeutic promise of 2'-fucosyllactose and beyond.},
journal = {Therapeutic advances in gastroenterology},
volume = {18},
number = {},
pages = {17562848251386319},
pmid = {41179483},
issn = {1756-283X},
abstract = {Inflammatory bowel diseases (IBD) are chronic and recurrent conditions of the gastrointestinal tract. IBD is often challenging to manage due to the complex etiology and involvement of multiple dysregulated immune pathways. Current treatments, including biologics and immunosuppressants, are associated with significant risks and side effects, highlighting the need for safer alternatives. Human milk oligosaccharides (HMOs), a group of bioactive carbohydrates found in human breast milk, play a crucial role in shaping the infant gut microbiome, modulating microbial metabolism and immune responses, and reducing inflammation. Notably, HMOs have no nutritional value for the infant and travel undigested through the upper gastrointestinal tract, serving as selective substrates for beneficial gut bacteria and supporting intestinal epithelial health. Among these, 2'-fucosyllactose (2'-FL) is the most abundant and well-studied HMO, functioning as a trisaccharide prebiotic. Emerging evidence suggests that the benefits of HMOs extend beyond infancy, with potential therapeutic applications in modulating immune responses, promoting epithelial health, and reducing inflammation in IBD. This review summarizes current research on the role of 2'-FL in inflammation and colitis, exploring its potential role in treating IBD.},
}

@article {pmid41179353,
year = {2025},
author = {Carboni, S and Poirier, AC and Peralta-Aguilar, AP and Watsa, M and Erkenswick, G and Melin, AD},
title = {The Scent Gland Microbiomes of Wild Tamarins Provide New Insight Into Microbial Contributions to Olfactory Communication.},
journal = {Ecology and evolution},
volume = {15},
number = {11},
pages = {e72335},
pmid = {41179353},
issn = {2045-7758},
abstract = {The microbiome of mammalian scent glands is thought to contribute to the production of odorant compounds involved in sensory communication. Yet, the extent to which glandular microbiomes contain bacteria relevant to odor production and vary by host species, scent marking behavior, or gland morphology remains poorly understood, particularly in wild animals. We sampled microbes collected from skin swabs of suprapubic and sternal scent glands in wild Peruvian saddleback tamarins (Leontocebus weddelli; n = 19) and emperor tamarins (Tamarinus imperator; n = 20) to better understand glandular microbial communities. We aimed to: (1) profile glandular microbiomes of both species, focusing on odor-related taxa and metabolic pathways, and (2) determine whether suprapubic glands, more often in contact with the external environment, had higher diversity and distinct composition of odor-related taxa and pathways compared to sternal glands. We generated metagenomic reads using short-read DNA shotgun sequencing from glandular swabs. We identified 18 odor-associated microbial taxa in both tamarin species, mainly Staphylococcus and Corynebacterium, and 26 pathways, including pyruvate fermentation and amino acid metabolism. Suprapubic glands had lower Shannon alpha diversity relative to sternal glands, especially in L. weddelli. The glands of L. weddelli also differed in taxonomic composition, with odor-related taxa more abundant in suprapubic glands. Our results provide evidence for the involvement of scent gland microbiomes in host communication biology. Glandular specializations differed not only between closely related tamarin species but also between gland types within the same individuals, suggesting a nuanced pattern of host-microbe coevolution that may shape interactions important for olfactory communication.},
}

@article {pmid41179309,
year = {2025},
author = {Yan, L and He, B and Deng, Q and Qiu, Y and Lin, L and Shi, B and Wang, J and Chen, F},
title = {Is systemic inflammation a missing link between oral microbiome and oral squamous cell carcinoma? Results from multi-omics integration analyses.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2574326},
pmid = {41179309},
issn = {2000-2297},
abstract = {OBJECTIVES: To investigate whether systemic inflammation mediates the relationship between oral microbiome alterations and oral squamous cell carcinoma (OSCC) through multi-omics integration analyses.

METHODS: Metagenomic sequencing of unstimulated saliva samples from 65 OSCC patients and 65 matched controls was performed. Plasma levels of 34 inflammatory cytokines were profiled using Luminex assay. Six machine learning models identified potential diagnostic microbial markers. Mediation analysis assessed whether inflammation serves as a mechanistic link between oral microbiota and OSCC.

RESULTS: OSCC patients exhibited reduced species richness and significant beta diversity alterations. Among 155 differential species identified, 25 were enriched in OSCC, including Capnocytophaga sputigena, Gemella haemolysans, Staphylococcus aureus, and several Streptococcus species, with higher abundance in poor oral hygiene conditions. The Boruta-CatBoost model achieved exceptional diagnostic performance (bootstrap AUC = 0.991; 5-fold cross-validation AUC = 0.947). Functional profiling revealed 22 metabolic pathways over-represented in OSCC, notably lipopolysaccharide biosynthesis. Nine circulating cytokines (IL-22, IL-6, IL-2, CCL5, GM-CSF, IL-1β, TNF-α, IL-18, IFN-α) were significantly elevated in OSCC patients. Mediation analysis revealed that IL-22 partially mediated the effect of Staphylococcus aureus on OSCC risk, while CCL5 mediated associations of Gemella haemolysans and Streptococcus species with OSCC (mediation proportions: 29.9-50.1%).

CONCLUSION: Our multi-omics integration suggests that systemic inflammation, particularly through IL-22 and CCL5 upregulation, serves as a mechanistic link between specific oral bacteria and OSCC risk, which could provide new strategies for OSCC prevention and early intervention.},
}

@article {pmid41178995,
year = {2025},
author = {Watawana, M and Lima, EMF and Quecan, BXV and Sherry, M and Granato, D and Schmalenberger, A and Hoffmann, C and Pinto, UM and Hoffmann Sarda, FA},
title = {Impact of non-nutritive sweeteners on bacterial quorum sensing and phenotypic expression: implications for gut microbiome dynamics.},
journal = {Gut microbiome (Cambridge, England)},
volume = {6},
number = {},
pages = {e19},
pmid = {41178995},
issn = {2632-2897},
abstract = {Non-nutritive sweeteners (NNSs) are popular sugar substitutes, valued for their potential to reduce caloric intake and associated health risks. However, their long-term effects on the human gut microbiome remain debatable. This study investigates the impact of tagatose, allulose, Rebaudioside-A (Reb-A), and saccharin on quorum-sensing (QS)-regulated phenotypes and gene expression in QS biosensor model bacteria. It sheds light on their potential influence on the gut microbiome. Our study revealed diverse effects among the NNSs. Tagatose and allulose demonstrated QS phenotypic inhibition in Chromobacterium violaceum (≈50%) and Pseudomonas aeruginosa (20-50%) in a concentration-dependent manner. Additionally, tagatose and allulose decreased the P. aeruginosa lasI gene expression. Reb-A and saccharin presented a significant, however less prominent, phenotypic inhibition on C. violaceum (25-30%) and P. aeruginosa swarming motility (≈20%). Both NNSs decreased the expression of the lasI gene of P. aeruginosa. Molecular docking of QS regulatory proteins showed that saccharin and Reb-A have significantly higher binding affinity compared to allulose and tagatose, relative to native inducers. These results suggest the complex interactions mediated by NNSs in QS regulatory pathways. These findings provide valuable insights into the varied, species and dose-dependent effects of NNS on microbial communication, suggesting potential implications for the gut microbiome.},
}

@article {pmid41178971,
year = {2025},
author = {Du, H and Hao, X and Lin, B and Zhu, Y and Yang, Y and Tang, M and Wu, W and Wang, D and Lin, B and Liang, Y and Tang, W and Xu, H and Li, J and Gao, F and Du, X},
title = {Exploring the role of intestinal microbiota in mitigating acute radiation-induced intestinal injury through high-energy X-ray FLASH radiotherapy via metagenomic analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1601244},
pmid = {41178971},
issn = {1664-302X},
abstract = {OBJECTIVES: This study preliminarily examines the potential correlation between the gut microbiome and the protective effects of FLASH radiotherapy (FLASH-RT) on intestinal tissue using metagenomic analysis.

METHODS: Compact single high-energy X-ray source (CHEXs) FLASH-RT was employed for FLASH irradiation, while EBT3 radiochromic film and a fast current transformer were used to measure the absolute dose and the pulsed beam characteristics. Sham radiotherapy (control), FLASH-RT (333 Gy/s), and Conventional dose rate radiotherapy (CONV-RT, 0.07 Gy/s) were performed on whole abdomen of normal C57BL/6J female mice (10 Gy, 12 Gy, 14 Gy). At 72 h post-irradiation, intestinal contents from normal C57BL/6J female mice were collected for metagenomic analysis. The survival status, body weight, and damage to normal tissues were observed.

RESULTS: At 28 days post-whole abdomen irradiation with doses of 12 Gy, the survival rate of the FLASH group was higher than that of the CONV group (p < 0.05). Histological analysis of intestinal tissues by H&E staining revealed significantly less acute intestinal damage and inflammation in the FLASH group compared to the CONV group. Further macrobiome analysis using LEfSe indicated that the abundance of beneficial bacteria, including Weissella, Lactobacillus ruminis and Lactobacillus taiwanensis was significantly higher in the FLASH group than in the CONV group. Moreover, compared to the CONV group, the FLASH group exhibited significant upregulation of several signaling pathways, including the glycosaminoglycan degradation, PI3K/Akt and arabinogalactan biosynthesis Mycobacterium signaling pathway.

CONCLUSION: Compared to CONV-RT, high-energy X-ray FLASH irradiation exerts radioprotective effects on normal intestinal tissue. Alterations in the gut microbiota and associated signaling pathways may be linked to the protective effects of FLASH.},
}

@article {pmid41178963,
year = {2025},
author = {Whitehead, K and Eppinger, J and Srinivasan, V and Ugalde, JA},
title = {Microbial cross contamination in household laundering and microbial ecology of household washing machines.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1667606},
pmid = {41178963},
issn = {1664-302X},
abstract = {Household washing machines host diverse microbial communities that may include opportunistic pathogens, potentially impacting laundry hygiene and human health. However, our understanding of these communities and their transfer abilities remains limited. We examined microbial communities from 10 household washing machines (five front-load and five top-load) using surface swabs from specific hotspots and sterile sentinel washcloths. Samples were analyzed using culture-based methods and 16S rRNA/ITS metabarcoding. We tested microbial transfer during washing cycles with and without clothing and evaluated the effects of machine drying on this transfer. Front-load machines had significantly higher microbial loads than top-load machines (average bacterial counts: 6.50 ± 2.46 Log10/swab vs. 3.79 ± 1.73 Log10/swab). The microbial community composition was mainly shaped by the machine user rather than the machine type or sampling location. The dominant bacterial genera included Pseudomonas, Micrococcus, and Sphingomonas, while Aspergillus, Cladosporium, and Penicillium dominated the fungal communities. Opportunistic microorganisms were identified, but no highly pathogenic species (pathogenicity score 3) were found. Machine drying did not significantly decrease microbial loads, whereas the presence of soiled clothing impacted community composition. Household washing machines host user-specific microbial communities, including potential opportunistic pathogens. Current laundry practices may be inadequate for the complete elimination of pathogens, especially in immunocompromised individuals. These results support the need for additional household laundry sanitization strategies.},
}

@article {pmid41178925,
year = {2025},
author = {Pacheco-Barcia, V and Mariño-Mendez, A and Hernandez-Jimenez, E and Jimenez-Fonseca, P and Muñoz Martín, AJ and Custodio-Cabello, S and Palka-Kotlowska, M and Gonzalez-Diaz, I and Cabezon-Gutierrez, L},
title = {Gut microbiome and nutritional strategies in gastrointestinal cancers: Clinical implications and therapeutic perspectives.},
journal = {World journal of clinical oncology},
volume = {16},
number = {10},
pages = {107877},
pmid = {41178925},
issn = {2218-4333},
abstract = {Gastrointestinal malignancies, particularly pancreatobiliary and gastroesophageal cancers, are associated with poor prognosis due to their frequent late-stage diagnosis. Many of these tumors contribute to anorexia-cachexia syndrome and malnutrition, further exacerbating disease progression. Inflammation plays a crucial role in tumor proliferation, and growing evidence suggests that gut microbiome significantly influence inflammatory responses and clinical outcomes in these patients. Additionally, the gut microbiome contributes to carcinogenesis through multiple mechanisms, including DNA damage, activation of oncogenic pathways, and modulation of immune responses. The emerging field of nutritional interventions highlight the microbiome's impact on anticancer drug responses, affecting both chemotherapy and molecular-targeted treatments. Given its pivotal role, microbiome modulation through probiotics, fecal microbiome transplantation, and antibiotics represents a promising approach for cancer prevention and treatment. In this review, we explore the intricate interplay between gut microbiome, inflammation, and nutritional status in gastrointestinal cancers, emphasizing potential therapeutic strategies to improve patient outcomes.},
}

@article {pmid41178889,
year = {2025},
author = {Rong, Y and Nie, CY and Zhou, JD and Wang, ZC and Wu, DL and Wu, SW and Xie, ZY},
title = {Intestinal reengineering: Scientific advances in intestinal transplantation.},
journal = {World journal of gastrointestinal surgery},
volume = {17},
number = {10},
pages = {111672},
pmid = {41178889},
issn = {1948-9366},
abstract = {Intestinal transplantation (ITx) has emerged as a pivotal life-saving intervention for patients with irreversible intestinal failure unresponsive to conventional medical and nutritional therapies. Despite its growing clinical acceptance, ITx remains among the most immunologically complex and technically demanding procedures in the field of solid organ transplantation. This review comprehensively summarizes the historical evolution, clinical indications, and advancements in surgical techniques, with emphasis on innovations in vascular anastomosis, multivisceral transplantation, and ex vivo preservation. Special attention is given to the unique immunological challenges of ITx, including bidirectional immune responses-host-vs-graft and graft-vs-host disease-immune-microbiota interactions, and the distinct roles of key immune cells. Pediatric and adult recipients exhibit divergent etiologies, immune responses, and complication profiles, necessitating individualized approaches. Although novel immunotherapeutic strategies and bioengineering innovations have improved short-term outcomes, chronic rejection, graft dysfunction, and immunosuppressive toxicity remain significant barriers. Looking ahead, future directions should prioritize precision immunomodulation, microbiome-targeted therapies, and integrated platforms for gene editing, 3D bioprinting, and immune monitoring. Through multidisciplinary collaboration and translational research, ITx is poised to evolve from a high-risk salvage therapy into a personalized, sustainable solution that enhances long-term survival and patient quality of life.},
}

@article {pmid41178417,
year = {2025},
author = {Bicakci, C and Cavus, I and Tunali, V and Ozel, Y and Ozbilgin, A and Alten, B and Vaselek, S},
title = {Vector microbiota and parasite infection: bacteria-mediated effects on Leishmania in Phlebotomus papatasi and culture.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/17460913.2025.2582361},
pmid = {41178417},
issn = {1746-0921},
abstract = {AIM: Microbes are increasingly being explored as tools to control leishmaniasis and sandfly populations. This study investigated the interactions between sandflies, Leishmania, and their microbiota.

METHODS: The in vitro and in vivo survival and development of Leishmania major in the presence of seven bacterial species were assessed. In vitro experiments included Leishmania co-cultures with bacteria applied at different concentrations (10[2]-10[8] CFU/ml), monitoring parasite survival/development at early (30-120 min) and late (12-240 h) time points. In vivo experiments in Phlebotomus papatasi examined Leishmania infection rate and intensity on days 2, 6, and 8 post co-infection with the same bacterial species (10[8] CFU/ml).

RESULTS: All bacteria demonstrated negative effects on Leishmania survival and development. Under in vitro conditions, the speed of Leishmania ablation (48-216 h) depended on the bacterial species and concentration, impacting Leishmania motility and viability, and halting the development of metacyclic forms. In vivo studies demonstrated that bacterial overgrowth negatively impacted the intensity of Leishmania infection and percentage of stomodeal valve colonization (27.58-82.14%).

CONCLUSIONS: The observed effect of bacteria on Leishmania under in vitro and in vivo conditions points out toward the potentially greater role of microbes in Leishmania survival in vectors, highlighting the need for deeper investigations of sandfly-Leishmania-microbiota interactions.},
}

@article {pmid41178126,
year = {2025},
author = {Gawałko, M and Kociemba, W and Sanders, P and Linz, D},
title = {Gut microbiome and atrial fibrillation: mechanistic insights metabolites and comorbidities. Systematic review.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2570423},
doi = {10.1080/19490976.2025.2570423},
pmid = {41178126},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Atrial Fibrillation/microbiology/metabolism/epidemiology ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Comorbidity ; Animals ; Methylamines/metabolism ; Fatty Acids, Volatile/metabolism ; },
abstract = {Emerging evidence indicates that the gut microbiome (GM) and its metabolites may play a role in the development of cardiometabolic diseases, including atrial fibrillation (AF). Although the current data are limited, studies suggest that the GM composition in AF mirrors that observed in associated conditions such as heart failure, hypertension, diabetes, and coronary artery disease (characterized by increased genera Lactobacillus, Enterococcus, Streptococcus, and decreased genus Faecalibacterium). Additionally, patients with AF appear to have distinct microbial alterations, including increased abundances of the genera Dialister, Dorea, Haemophilus, Klebsiella, Lachnospira, Parabacteroides, Ruminococcus, and Veillonella and decreased abundances of the genera Butyricicoccus, Hungatella, and Prevotella. Gut-derived metabolites also show associations with AF. Trimethylamine N-oxide and choline have been linked to new-onset and postoperative AF, potentially via autonomic, inflammatory, and fibrotic pathways. In contrast, short-chain fatty acids, which are reduced in AF patients, may offer protective effects. Elevated lipopolysaccharide levels are correlated with AF onset and recurrence through inflammation and structural remodeling. Indoxyl sulfate and bile acids may contribute to arrhythmogenesis via oxidative stress, apoptosis, and disrupted calcium signaling. These mechanisms contribute to AF by disrupting conduction and increasing automaticity. Emerging evidence also links gut microbes to other arrhythmias, but more research is needed to clarify causality and therapeutic potential.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Atrial Fibrillation/microbiology/metabolism/epidemiology
*Bacteria/classification/metabolism/genetics/isolation & purification
Comorbidity
Animals
Methylamines/metabolism
Fatty Acids, Volatile/metabolism

@article {pmid41177823,
year = {2025},
author = {Zuo, T},
title = {Pushing the frontier of gut microbiome health cross-kingdom and cross-organ.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {41177823},
issn = {1759-5053},
}

@article {pmid41177624,
year = {2026},
author = {Zheng, L and Tian, Q and Tan, Q and Wang, X and Xing, Y and Zhang, Y},
title = {Biogeography and diversity of wetland soils bacterial communities across temperature zones based on independent studies.},
journal = {Journal of environmental sciences (China)},
volume = {160},
number = {},
pages = {439-449},
doi = {10.1016/j.jes.2025.04.025},
pmid = {41177624},
issn = {1001-0742},
mesh = {*Wetlands ; *Soil Microbiology ; *Bacteria/classification ; Biodiversity ; *Microbiota ; Temperature ; *Environmental Monitoring ; },
abstract = {Wetlands are vital ecosystems that perform essential functions such as climate regulation, environmental purification, material circulation and energy flow. They play an essential role in global biogeochemical cycles, driven primarily by microorganisms. Understanding the distribution of wetland microorganisms across different temperature zones is key to comprehending their ecological roles. A meta-analysis of 704 wetland soil samples on microbial communities was conducted, using statistical methods like analysis of variance, principal component analysis, non-metric nultidimensional scaling, and structural equation modeling to examine biogeography and diversity across temperature zones. Our findings revealed a clear latitudinal diversity gradient pattern, with the highest microbial abundance in the tropics and the lowest in the southern temperate zone, which differed significantly from other temperature zones. Proteobacteria (37.76 %-51.04 %), Acidobacteria (5.11 %-30.70 %) and Bacteroidetes (3.43 %-16.16 %) dominanted the bacterial communities. Notably, the southern temperate zone showed significant variations, with a higher prevalence of Acidobacteria (30.07 %). To investigate the causes of this variability, we screened 177 core microbiome and identified latitude as the core environmental factor influencing microbial community composition. Moreover, soil microorganisms exhibited strong nitrogen cycling potentials (particularly nirD and nirB) and carbon cycling potentials (especially accA), with gene abundances showing little variation across temperature zones. Wetland bacterial communities also demonstrated high stability, with average variation degree index values ranging from 0.1 to 0.3. Our results improve the understanding of the diversity and biogeographic mechanisms of wetland bacterial communities and hold significant implications for the management and conservation of wetlands.},
}

*Wetlands
*Soil Microbiology
*Bacteria/classification
Biodiversity
*Microbiota
Temperature
*Environmental Monitoring

@article {pmid41177523,
year = {2025},
author = {Kroeger, E and Malloy, C and Chen, CX and Gondwe, KW and Kamp, K},
title = {Awareness of the Vaginal Microbiome and Willingness to Undergo Vaginal Microbiota Transplant.},
journal = {Journal of obstetric, gynecologic, and neonatal nursing : JOGNN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jogn.2025.10.009},
pmid = {41177523},
issn = {1552-6909},
abstract = {OBJECTIVE: To examine awareness of the vaginal microbiome and vaginal microbiota transplant, willingness to undergo vaginal microbiota transplant, and factors that influence the decision to undergo the procedure.

DESIGN: Cross-sectional descriptive survey study.

SETTING: Online distribution from October 2024 to January 2025.

PARTICIPANTS: Respondents (N = 210) who self-identified as women (n = 198), men (n = 2), gender nonconforming (n = 14), transgender (n = 3), other (n = 2), and not specified (n = 2) and had vaginas.

METHODS: The survey included questions about patient demographics, gynecologic and pelvic symptoms and conditions, and vaginal microbiota transplantation awareness and willingness. We used descriptive statistics to summarize the quantitative data and conducted conventional content analysis to examine responses to open-ended questions about factors to undergo vaginal microbiota transplantation.

RESULTS: Most respondents (n = 176, 83.8%) had not heard of vaginal microbiota transplant. However, more than 50% of respondents were willing or very willing to undergo vaginal microbiota transplantation for each presented indication: prevent yeast infections, bacterial vaginosis, or cytolytic vaginosis (n = 131, 62.4%); reduce risk of sexually transmitted infections (n = 130, 61.9%); alleviate menstrual pain (n = 126, 60.0%); prevent urinary tract infections (n = 126, 60.0%); alleviate vaginal symptoms (n = 120, 57.1%); prevent preterm births (n = 119, 56.7%). We identified five categories from 180 responses about factors that influenced the decision to undergo vaginal microbiota transplantation: Evidence, Procedure Logistics, Health Care Factors, Personal Factors, and Donor Health.

CONCLUSION: Increased awareness about the vaginal microbiome and vaginal microbiota transplantations is necessary. Factors that influence willingness to undergo the procedure should be addressed in designing and implementing this new intervention.},
}

@article {pmid41177495,
year = {2025},
author = {Yoon, DS and Kim, JH and Kim, IC and Wang, Y and Yang, Z and Lee, MC and Lee, JS},
title = {Effects of environmental factors on host-microbiota interactions in the guts of aquatic organisms: A review.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {},
number = {},
pages = {110381},
doi = {10.1016/j.cbpc.2025.110381},
pmid = {41177495},
issn = {1532-0456},
abstract = {Aquatic environments are dynamic systems where multiple factors influence the intricate interactions between hosts and their gut microbiomes. This review explores how various stressors alter the gut microbiota of fish and aquatic invertebrates, by examining factors that include water characteristics, photoperiod, external pollutants such as heavy metals and microplastics, food availability, and practical aquaculture feed additives, for example, ethoxyquin. Across these diverse factors, common patterns emerge, including disruptions to microbial diversity, compromised gut barrier integrity, and the induction of oxidative stress. Conversely, beneficial additives like probiotics and astaxanthin are shown to mitigate these negative effects by reinforcing gut structure and modulating the microbial community. Collectively, these findings underscore the critical role of the gut microbiota in mediating host responses to environmental changes. Future research should therefore focus on elucidating specific toxicological pathways like the gut-organ axis, investigating the transgenerational effects of pollutants, and developing probiotic-based strategies to enhance the resilience and sustainability of aquaculture.},
}

@article {pmid41177416,
year = {2025},
author = {Bashir, B and Gulati, M and Vishwas, S and Hussain, MS and Gupta, G and Kumar, P and Negi, P and Mittal, N and Dua, K and Singh, SK},
title = {Bridging the gap in the management of Alzheimer's disease using fecal microbiota transplantation.},
journal = {Molecular and cellular neurosciences},
volume = {},
number = {},
pages = {104052},
doi = {10.1016/j.mcn.2025.104052},
pmid = {41177416},
issn = {1095-9327},
abstract = {Alzheimer's disease (AD) is a neurodegenerative disease that greatly impairs the health status of human beings and creates significant burdens on individuals, families, and society. AD is characterized by the buildup of pathological proteins and glial cell dysregulated activity. Additional hallmark features include oxidative stress, neuroinflammation, impaired autophagy, cellular senescence, mitochondrial dysfunction, epigenetic alterations, reduced neurogenesis, increased blood-brain barrier permeability, and age-inappropriate intestinal dysbiosis. There is significant evidence that shows that microbiota in the gut affects the development and progression of AD. As a result, gut microbiota modulation has been identified as a new method of clinical management of AD, and more and more efforts have been devoted to identifying new methodologies for its prevention and treatment. This paper will discuss the role of gut microbiome in the etiopathogenesis of AD and consider the possibilities of fecal microbiota extract (FME) supplementation, commonly referred to as fecal microbiota transplantation (FMT). It is both a prophylactic and curative approach. The FMT therapy is grounded on the premise that anti-inflammatory effects, modifications of amyloid β, improved synaptic plasticity, short-chain fatty acids, and histone acetylation are the principles behind the enhancement of AD. The current review will present an overview of the linkage between FMT and AD as well. It further examines and evaluates the effects of FMT on aging-based mechanisms that support the development of AD. It also provides a broad description of the recent clinical and preclinical evidence on the application of FMT to AD.},
}

@article {pmid41177336,
year = {2025},
author = {Bari, AK and Xavier, BB and Severs, T and Sinha, B and Rossen, JWA and , },
title = {Comparison of three commercial DNA extraction kits and assemblers for AMR determinant detection in Pseudomonas aeruginosa and Enterobacter cloacae using long-read sequencing.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107317},
doi = {10.1016/j.mimet.2025.107317},
pmid = {41177336},
issn = {1872-8359},
abstract = {BACKGROUND: Pseudomonas aeruginosa and Enterobacter cloacae, both members of the ESKAPE group, are multidrug-resistant pathogens that pose significant challenges in clinical care. The high GC-content (~67 %) of the P. aeruginosa genome complicates DNA extraction and long-read sequencing, with downstream effects on genome assembly and analyses. We compared three commercial extraction kits for isolating high-quality DNA suitable for Oxford Nanopore sequencing from clinical isolates of P. aeruginosa and E. cloacae.

METHODS: Genomic DNA was extracted from P. aeruginosa (n = 63; 3 × 21) and E. cloacae (n = 96; 3 × 32) clinical isolates using the MagAttract HMW DNA Kit (Qiagen), the DNeasy UltraClean Microbial Kit (Qiagen), and the MagMAX™ Microbiome Ultra Nucleic Acid Isolation Kit (ThermoFisher). DNA quantity/quality was assessed by spectrophotometry (NanoDrop, Thermo Fisher Scientific), fluorometry (Qubit, ThermoFisher), and capillary electrophoresis (TapeStation 2200, Agilent). Libraries were prepared and sequenced using Oxford Nanopore Technologies platforms. Assemblies were generated with Unicycler (v.0.5.1) and Flye (v.2.9.6); quality was assessed with QUAST (v.5.3). Genome completeness was evaluated by CheckM (v.1.1.6). Antimicrobial resistance determinants were identified with AMRFinderPlus (v.4.1.19).

RESULTS: DNeasy yielded up to 4.7× higher DNA and ~ 50 % higher sequencing output than MagAttract, while MagAttract produced higher DNA integrity and more contiguous assemblies. The choice of assembly had a greater impact on the detection of AMR determinants than the extraction method alone. Across workflows, Flye outperformed Unicycler, increasing detection by 2-14 percentage points. The best-performing combination (DNeasy + Flye) achieved 95.2 % AMR determinants, compared to 67.8 % for MagMAX + Unicycler, with the most difference (37.5 %) in efflux pump genes.

CONCLUSIONS: This systematic comparison highlights trade-offs between DNA yield, integrity, and downstream assembly performance, demonstrating that assembler choice critically impacts the detection of AMR determinants. These findings provide practical guidance for optimizing long-read-based sequencing workflows to support AMR surveillance and genomic epidemiology.},
}

@article {pmid41177025,
year = {2025},
author = {Singh, DP and Bijalwan, V and Poonam, J and Lal, R and Palkhade, R and Viramgami, A and Vidhani, H and Kumar, A and Bishnoi, M and Das, S},
title = {Bisphenol-A at an environmentally plausible dose caused gut microbiota-led impaired cognitive performances in adult mice.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140254},
doi = {10.1016/j.jhazmat.2025.140254},
pmid = {41177025},
issn = {1873-3336},
abstract = {Omnipresent Bisphenol-A (BPA) exposure is linked to neurobehavioral deficits and gut dysbiosis. However, studies assessed its impact on cognitive performance at environmentally unrealistic doses. Nevertheless, the exact mechanism underlying the neurobehavioral phenotype, linking the role of gut microbiota is poorly understood. Here, we evaluated the effects of environmentally plausible dose of BPA-exposure on cognitive task performances with the functional analysis of gut metagenome to elucidate the role of microflora-gut-brain axis in behavioural regulation. Swiss albino mice were exposed to BPA for 5 weeks assessed for working and spatial navigation task performances. qRT-PCR based gene expression, histological investigation, gut permeability, molecular and biochemical markers of neuro-inflammation, leaky gut, oxido-nitrosative stress and 16 s rRNA gene based metagenomics with functional analysis were performed. BPA exposure altered the cognitive task performances (mean difference for transfer latency in elevated plus maze 20.84 ± 5.64 sec in and -13.12 ± 3.53 in Morris' water maze), changed serotonin levels (-70.95 ± 21.43) and acetylcholinesterase activity (0.0032 ± 0.0008), enhanced ileal permeability (12.36 ± 3.56) and systemic and tissue level inflammation (increased brain LPS, TNF-a, IL-1b, IL-6 and circulating TNF-a and IL-1b), coupled with reduced SCFAs levels (acetate; 32.48 ± 8.48, and butyrate; 28.16 ± 9.86). Faecal microbial transplant cohort replicated similar behavioural, biochemical and molecular patterns, suggesting the role of gut-microbiota in the phenotype determination. Functional pathways prediction suggested altered serotonin, dopamine, SCFAs metabolism and LPS biosynthesis. BPA at a much lower but environmentally relevant dose altered the cognitive performances, which has potential linkage to gut-microbiota mediated pathways.},
}

@article {pmid41176845,
year = {2025},
author = {Kadriu, E and Qin, S and Prezioso, SM and Christendat, D},
title = {The interplay between glucose and aromatic compound regulation by two IclR-type transcription factors, LigR1 and LigR2, in Pseudomonas putida KT2440.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128382},
doi = {10.1016/j.micres.2025.128382},
pmid = {41176845},
issn = {1618-0623},
abstract = {Carbon utilization strategies are fundamental to microbial proliferation within complex ecosystems like the soil microbiome. These strategies dictate how microbes prioritize, and metabolize available carbon compounds, shaping community dynamics and ecological outcomes. Pseudomonas putida KT2440, a soil bacterium renowned for its metabolic versatility, exemplifies this adaptive capacity. However, the regulatory mechanism it employs to prioritize sugars vs aromatic compounds for their energy requirement remains poorly understood. Here, we investigated two IclR-type transcriptional regulators, LigR1 and LigR2, which control expression of the lig1 and lig2 operons. Functional analyses reveal that LigR1 and LigR2 activate lig1 but repress the lig2 operon. 4-hydroxybenzoate binding to LigR1 represses gene expression, whereas quinate, protocatechuate, and 4-hydroxybenzoate bind to LigR2 to induce lig2 operon expression. Additionally, ligR1 deletion causes growth defects on glucose and 4-hydroxybenzoate, accompanied by cell elongation and aggregation. We propose that the lig1 operon mediates dual influx of glucose and aromatics via its major facilitator superfamily transporter, while the lig2 operon catalyzes aromatic breakdown through a protocatechuate intermediate and meta-cleavage pathway, supplying oxaloacetate to the TCA cycle. Importantly, P. putida prioritizes shikimate pathway intermediates as energy sources under specific metabolic conditions, such as their accumulation. Overall, these findings redefine the metabolic flexibility of soil pseudomonads and reveal a novel mechanism for thriving in chemically diverse environments. By illuminating a dual regulatory system, our study offers new insight into microbial carbon flux and on the traditional biosynthetic paradigm of the shikimate pathway, revealing its unexpected role in supplying the organism with energy generating compounds.},
}

@article {pmid41176763,
year = {2025},
author = {Lu, A and Meyer, K and Zhou, G and Chen, X and Zhu, D and Yu, Z and Wan, X and Feng, L and Deng, Z and Ye, H and Wang, T and Wang, M and Singh, BK and Delgado-Baquerizo, M and Liu, S and Huang, Z},
title = {Neighbourhood Tree Competition Promotes Microbial Diversity in Phyllosphere.},
journal = {Ecology letters},
volume = {28},
number = {11},
pages = {e70240},
doi = {10.1111/ele.70240},
pmid = {41176763},
issn = {1461-0248},
support = {31930077//National Natural Science Foundation of China/ ; 32271842//National Natural Science Foundation of China/ ; 32572033//National Natural Science Foundation of China/ ; },
mesh = {*Biodiversity ; *Trees/microbiology/physiology ; *Microbiota ; *Plant Leaves/microbiology ; China ; Forests ; *Fungi/classification ; Bacteria/classification ; },
abstract = {The microbiome inhabiting the surface of leaves is essential for supporting forest health and productivity. Yet, the relevance of host selection and neighbourhood conditions in supporting phyllosphere microbial diversity remains poorly understood. Here, we used a large-scale forest biodiversity experiment in subtropical China to elucidate the mechanisms driving phyllosphere microbial diversity. Our results showed that bacterial diversity depends more on plant traits associated with resource-acquisitive strategy, while fungal diversity was more closely related to the trade-off between plant productivity and defence. Additionally, bacterial diversity was highly structured by neighbourhood tree competition, whereas fungal diversity was mainly shaped by host plant functional traits. Furthermore, the relationship between microbial diversity and host traits was enhanced as tree species diversity increased. Together, our work provides novel evidence that tree competition plays crucial roles in promoting microbial diversity in the phyllosphere and highlights the importance of plant-microbe interaction in supporting ecosystem sustainability.},
}

*Biodiversity
*Trees/microbiology/physiology
*Microbiota
*Plant Leaves/microbiology
China
Forests
*Fungi/classification
Bacteria/classification

@article {pmid41176741,
year = {2025},
author = {Wang, D and Zhao, YY and Huang, Y},
title = {Associations between gut microbiota and multiple system atrophy: a Mendelian randomization study.},
journal = {Journal of neurology},
volume = {272},
number = {11},
pages = {743},
pmid = {41176741},
issn = {1432-1459},
support = {82071417//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; *Multiple System Atrophy/genetics/microbiology ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; },
abstract = {BACKGROUND: Multiple system atrophy (MSA) is a rare and progressive neurodegenerative disorder characterized by Parkinsonism, cerebellar dysfunction, and autonomic failure. Emerging evidence suggests that gut microbiota may contribute to neurodegeneration, but whether these associations are causal remains unclear.

METHODS: We conducted a two-sample Mendelian randomization (MR) analysis using genome-wide association study (GWAS) summary statistics of gut microbiota (n = 18,340) from the MiBioGen consortium and MSA (888 cases, 7,128 controls) from a recent European study. Single nucleotide polymorphisms associated with 196 bacterial taxa were selected as instrumental variables. The primary MR method was inverse-variance weighting, complemented by weighted median, MR-Egger, and MR-PRESSO. Sensitivity analyses assessed pleiotropy, heterogeneity, and robustness.

RESULTS: Six taxa showed nominal associations with MSA risk. Lentisphaeria (OR = 1.57, p = 0.035), Oscillospira (OR = 1.76, p = 0.034), Victivallales (OR = 1.57, p = 0.035), and Peptococcus (OR = 1.46, p = 0.025) were positively associated with increased risk, whereas Veillonella (OR = 0.40, p = 0.004) and Erysipelotrichaceae UCG-003 (OR = 0.60, p = 0.041) were associated with reduced risk. No evidence of pleiotropy or heterogeneity was found. None survived multiple-testing correction.

CONCLUSIONS: This MR study provides hypothesis-generating evidence suggesting potential causal relationships between gut microbiota and MSA. These taxa nominate candidate microbial targets for future mechanistic and translational studies.},
}

Humans
Mendelian Randomization Analysis
*Gastrointestinal Microbiome/genetics
*Multiple System Atrophy/genetics/microbiology
Genome-Wide Association Study
Polymorphism, Single Nucleotide

@article {pmid38710643,
year = {2025},
author = {Chen, PC and Hsu, HY and Liao, YC and Lee, CC and Hsieh, MH and Kuo, WS and Wu, LS and Wang, JY},
title = {Moonlighting glyceraldehyde-3-phosphate dehydrogenase of Lactobacillus gasseri inhibits keratinocyte apoptosis and skin inflammation in experimental atopic dermatitis.},
journal = {Asian Pacific journal of allergy and immunology},
volume = {43},
number = {3},
pages = {472-485},
doi = {10.12932/AP-211123-1733},
pmid = {38710643},
issn = {0125-877X},
mesh = {Animals ; *Dermatitis, Atopic/immunology/pathology/therapy ; Mice ; Disease Models, Animal ; Mice, Inbred BALB C ; Apoptosis ; *Lactobacillus gasseri/enzymology ; *Keratinocytes/immunology/pathology ; Female ; *Probiotics ; *Skin/pathology/immunology ; Asthma/immunology ; Gastrointestinal Microbiome ; Humans ; },
abstract = {BACKGROUND: Lactic acid bacteria may be used as probiotics to prevent or treat various diseases, and Lactobacillus delbrueckii has an inhibitory effect on the development of atopic diseases.

OBJECTIVE: This study explored the effects of L. delbrueckii subsp. lactis strain LDL557 administration on a mouse asthma model resulting from Dermatophoides pteronyssinus (Der p) sensitization and investigated the associated gut microbiota.

METHODS: Der p-sensitized and challenged BALB/c mice were orally administered with three different doses of live (low, 107 colony-forming units (CFU); medium, 108 CFU; high, 109 CFU) and heat-killed (109 cells) LDL557 in 200 μL of PBS daily, starting 2 weeks before Der p sensitization and lasting 4 weeks. After the allergen challenge, airway responsiveness to methacholine and the influx of inflammatory cells to the lungs were assessed. The gut microbiome was obtained by sequencing the V3-V4 region of the 16S rRNA gene from mice stool samples.

RESULTS: LDL557 in the live (109 CFU) and heat-killed (109 cells) conditions reduced the airway hyper-responsiveness after stimulation with methacholine, inflammatory cell infiltration, and mucus production. These effects were similar to those in groups treated with dexamethasone. No significant change in the gut microbiota was observed after LDL557 treatment, except for the tendency of heat-killed LDL557 to change the gut microbial profile to a greater extent than live LDL557.

CONCLUSION: In summary, we found that live and heat-killed LDL557 had the beneficial effect of preventing Der p-induced allergic inflammation in a mouse model of asthma.},
}

Animals
*Dermatitis, Atopic/immunology/pathology/therapy
Mice
Disease Models, Animal
Mice, Inbred BALB C
Apoptosis
*Lactobacillus gasseri/enzymology
*Keratinocytes/immunology/pathology
Female
*Probiotics
*Skin/pathology/immunology
Asthma/immunology
Gastrointestinal Microbiome
Humans

@article {pmid41176223,
year = {2025},
author = {Chen, L and Yang, X and Su, Z and Guan, X and Wang, Z and Huang, T},
title = {Sustainable tea plantations: Harnessing chemical-microbial synergy and smart application triangulation for targeted weed control.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.10.054},
pmid = {41176223},
issn = {2090-1224},
abstract = {BACKGROUND: Over 200 weed species-predominantly from the Poaceae and Asteraceae families-infest tea plantations. These weeds compete aggressively with tea plants for essential resources (light, water, and nutrients), serve as reservoirs for pathogens and pests, and bioaccumulate phytotoxic compounds (e.g., pyrrolizidine alkaloids and heavy metals), jeopardizing agroecosystem health. Although chemical herbicides are currently the most effective and economical method, their long-term overuse poses ecological risks and threatens agricultural sustainability, highlighting an urgent need for sustainable alternatives. Although chemical herbicides remain the most effective and economical method, their long-term overuse causes ecological risks and challenges agricultural sustainability.

AIM OF REVIEW: This review synthesizes current knowledge on sustainable weed management in tea plantations by evaluating the strengths and limitations of chemical and microbial herbicides. It further advances the novel concepts of chemical-microbial synergy and smart application triangulation-integrated strategies not explicitly addressed in previous reviews-that provide new directions for developing next-generation sustainable weed control.

This review systematically examines three critical aspects of weed management in tea plantations: (1) characterizing weed biodiversity and assessing multidimensional threats through taxonomic profiling of invasive species, with particular focus on their cascading impacts on tea agroecosystems including resource competition, disease transmission, and soil toxicity; (2) evaluating the mechanisms and trade-offs of current herbicide approaches through comparative analysis of chemical herbicides (noting their efficiency but ecological concerns) and microbial herbicides (considering their environmental benefits but field performance variability); (3) exploring sustainable optimization strategies by investigating innovative approaches such as precision herbicide formulations (nano-formulations, smart delivery systems) and integrated weed management solutions (microbiome engineering, epigenome editing).},
}

@article {pmid41176097,
year = {2025},
author = {Lu, X and Yang, Y and Peng, Y and Li, R and Chen, C and Luo, Y and Jiang, Y and Xu, M and Wang, Z and Meng, F},
title = {Integrative microbiome-metabolomics identifies Pseudomonas as a potential pathogenic factor in endometriosis.},
journal = {Genomics},
volume = {},
number = {},
pages = {111149},
doi = {10.1016/j.ygeno.2025.111149},
pmid = {41176097},
issn = {1089-8646},
abstract = {Endometriosis (EMS) is a chronic disease characterized by unclear etiology, influenced by various genetic and environmental factors, with no definitive biomarkers available for early screening. Recent studies suggest that the abdominal microbiome and its metabolites, shaped by the host's genetic composition and environmental exposures, play significant roles in the pathogenesis and regulation of EMS. This study aims to integrate microbiome and metabolomics analyses to identify bacteria and metabolites critical to the progression of EMS. Multi-omics characterization was performed on pelvic cavity washings (PCW) from 7 EMS patients and 8 matched controls using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC-MS). A validation cohort of 42 EMS patients and 42 controls was assessed for clinical measures. Metabolomics revealed 7 metabolites across 12 metabolic pathways, with three uniquely distinguished in the endometriosis group. Microbial diversity analysis identified 2471 operational taxonomic units (OTUs), showing significant compositional disparities between groups. Notably, Pseudomonas enrichment in PCW was associated with advanced disease progression, especially in stage III and IV EMS, characterized by extensive pelvic adhesions and larger lesion sizes. Our findings highlight Pseudomonas as a potential biomarker for EMS severity, advancing the understanding of its pathogenesis and offering promising implications for non-hormonal therapeutic strategies. KEY MESSAGE: Comprehensive analyses show significant interactions between Pseudomonas and its metabolite guanylate in endometriosis patients. Increased Pseudomonas levels correlate with larger lesions and more severe pelvic adhesions, suggesting it may serve as a biomarker and potential driver of disease severity, informing new preventive strategies and non-hormonal treatments.},
}

@article {pmid41176044,
year = {2025},
author = {Sodré, IC and Prist, PR and Mancini, MCS and Bettoni-Rodríguez, G and de Andreazzi, CS and Tambosi, LR and Dos Santos, AFA and da Costa, MDF and Bueno, MG},
title = {Forest cover influences the fecal virome of Oligoryzomys nigripes in Atlantic Forest remnants, Brazil.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107894},
doi = {10.1016/j.actatropica.2025.107894},
pmid = {41176044},
issn = {1873-6254},
abstract = {Landscape changes driven by human activities can alter host-pathogen interactions, favoring generalist mammal species that act as reservoirs for zoonotic pathogens, potentially leading to spillover events and outbreaks. Here, we investigated how forest cover influences viral diversity in Oligoryzomys nigripes, a generalist rodent known to harbor zoonotic viruses in the Brazilian Atlantic Forest. We employed high-throughput sequencing to explore the fecal virome of 20 specimens collected across three landscapes with varying forest cover (20%, 40%, and 60%) within Atlantic Forest fragments in São Paulo state. We identified 48 viral families, predominantly bacteriophages and vertebrate-associated viruses. Some, found for the first time in this host, exhibited zoonotic potential, including Papillomaviridae, Herpesviridae, Polyomaviridae, Adenoviridae, Alloherpesviridae, Arenaviridae, Paramyxoviridae, Peribunyaviridae, and Picornaviridae. Alpha and beta diversity indices were used to assess the viral community structure. Although alpha diversity indices did not show a statistically significant difference among landscapes, a significant compositional difference in viral community was detected through beta diversity index (Jaccard dissimilarity), indicating that forest cover may shape the composition of viral families present. The presence of a core virome shared across all landscapes, including families with pathogenic potential, reinforces O. nigripes role as a natural reservoir. While forest cover influences viral community structure, it doesn't necessarily reflect greater ecological complexity within fragments, indicating that other landscape-related factors must also be considered. This pioneering study characterizes the fecal virome of O. nigripes, revealing how forest cover may shape viral communities in wild rodents and underscoring their potential for zoonotic virus surveillance.},
}

@article {pmid41175891,
year = {2025},
author = {Minari, TP and Pisani, LP},
title = {The Role of Gut Microbiota in Chronic Noncommunicable Diseases: An Overview of the Last Decade.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuaf200},
pmid = {41175891},
issn = {1753-4887},
abstract = {The gut microbiota has emerged as a key modulator of various health outcomes, including chronic noncommunicable diseases (NCDs). Obesity, diabetes, and hypertension represent important clinical challenges. Recent research suggests that gut dysbiosis may contribute to the pathophysiology of NCDs through metabolic and inflammatory pathways. This narrative review evaluates current scientific evidence on the role of gut microbiota in NCDs, examining its impact on blood pressure, glucose regulation, and weight control. It also explores interactions with medications, prebiotics, probiotics, fecal transplants, and lifestyle changes while identifying research gaps to advance understanding and inform innovative therapeutic strategies. An extensive review was conducted across multiple scientific databases, including PubMed, Web of Science, CrossRef, Google Scholar, and Scopus. Articles published between 2015 and 2025 were collected. A total of 115 relevant studies were identified and analyzed. The findings demonstrate consistent associations between gut dysbiosis and NCDs. Genera such as Akkermansia muciniphila, Faecalibacterium prausnitzii, and Fusicatenibacter were depleted in disease states, while Prevotella and Clostridium sensu stricto 1 were often enriched in obesity, diabetes, and hypertension. Microbial imbalances, including altered Bacillota/Bacteroidota ratios and reduced short-chain fatty acid production, were implicated in low-grade inflammation and metabolic disruption. Current findings suggest that fecal transplantation, prebiotics, postbiotics (bioactive compounds resulting from probiotic activity), and probiotics have limited effectiveness in improving gut microbiota, emphasizing the need for further human studies. Several drugs can positively or negatively alter the composition of the microbiota. Gut microbiota imbalances contribute meaningfully to the onset and progression of major NCDs. Although emerging therapies offer promise, clinical translation requires more robust, longitudinal studies integrating microbiome profiling, metabolic outcomes, and personalized strategies. Advancing microbiota-targeted approaches may help bridge current gaps in NCD prevention and management.},
}

@article {pmid41175763,
year = {2025},
author = {Lv, Z and Liu, Z and Li, D and Cai, M and Liu, J and Zhang, XH and Shi, X},
title = {Anthropogenic PAHs reshape sedimentary microbiomes and ecotoxicological risks in polar regions: A pan-Arctic/Antarctic metagenomic study.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140321},
doi = {10.1016/j.jhazmat.2025.140321},
pmid = {41175763},
issn = {1873-3336},
abstract = {The analysis of the composition and functional gene responses of sedimentary microbial communities to polycyclic aromatic hydrocarbons (PAHs) is essential for evaluating the pollution status of PAHs in polar regions. PAH concentrations and microbiome characteristics are quantified using advanced instrumental detection combined with metagenomic analysis. Overall, PAHs exhibit relatively high levels of contamination in polar regions, whereas variations in the abundance of functional genes indicate potential degradation propensities among different sedimentary microbial communities. The PAHs in the study area are primarily attributed to fossil fuel combustion, with local anthropogenic emissions considered the main drivers of contaminant accumulation. Sedimentary bacterial communities and their functions are significantly influenced by PAH contamination. Correlation analysis identifies 4H-Naphthalene, Naphthalene, 1-Indanone, Anthracene, Benzo[c]phenanthrene and 1,4-Naphthoquinone as the most critical compounds affecting microbial communities. The co-occurrence of PAH degradation genes with nitrogen- and sulfur-cycling genes in several MAGs suggests that PAH biodegradation may be enhanced through the utilization of nitrate and sulfate as electron acceptors. Within a pan-Arctic and Antarctic framework, the responses of sedimentary microbiomes to PAH contamination are examined, providing novel insights into the comprehensive evaluation of PAH pollution levels and associated ecological risks in polar regions.},
}

@article {pmid41175755,
year = {2025},
author = {Tang, K and Cao, X and Geng, X and Huang, W and Liu, H and Yan, Z and Wu, Z and Yang, C and Tang, J and Zhou, Z},
title = {Microbiome dysbiosis and decreased survival in coral larvae exposed to environmentally relevant concentrations of nanoplastics and sulfamethoxazole.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140297},
doi = {10.1016/j.jhazmat.2025.140297},
pmid = {41175755},
issn = {1873-3336},
abstract = {Scleractinian corals are increasingly threatened by environmental contaminants such as nanoplastics (NPs) and antibiotics. The early life stages of corals are particularly vulnerable to environmental stressors, yet their impacts under environmentally relevant concentrations remain poorly understood. Here, we exposed Pocillopora damicornis larvae to NPs (100 μg/L) and sulfamethoxazole (SMX, 0.1 μg/L) for 48 h to assess their effects on larval survival, settlement, tissue structure, and bacterial symbionts. Exposure to NPs and SMX significantly reduced larval survival, caused tissue necrosis and mesenterial filament dissociation, and altered the composition of bacterial symbionts, such as a decrease in Pseudoalteromonas abundance. Compared to the single exposure group, co-exposure to NPs and SMX induced more severe tissue damage and broader functional shifts in microbial communities, including elevated methylotrophy, photoheterotrophy, photoautotrophy, and reduced anaerobic respiration. These findings suggest that coral larvae are highly sensitive to NPs and SMX, which can alter bacterial symbiont community to disturb nutrient cycling and energy metabolism, cause tissue damage, and ultimately impair larval survival, thereby threatening coral reef replenishment and recovery.},
}

@article {pmid41175729,
year = {2025},
author = {Fan, X and Liao, C and Cai, C and Shen, M},
title = {The inhibitory effect of strontium on colorectal cancer and its impact on the gut microbiome.},
journal = {Bioorganic chemistry},
volume = {166},
number = {},
pages = {109138},
doi = {10.1016/j.bioorg.2025.109138},
pmid = {41175729},
issn = {1090-2120},
abstract = {Colorectal cancer (CRC) is one of the most prevalent malignant tumors worldwide. Strontium (Sr) is an essential trace element in the human body, and Sr compounds have been shown to inhibit the growth of various cancer cell types. However, the mechanism of action of SR in CRC remains unclear. In our previous study, we found that serum Sr levels in patients with CRC were lower than those in the normal population. But its role in CRC development and its influence on the gut microbiome remain unclear. To articulate the mechanism of action of Sr in CRC, we conducted CCK8, plate cloning, cell scratch, and Transwell migration assays. Mitochondrial membrane potential measurements were used to evaluate the effects of Sr on the biological functions of CRC cells. By constructing a nude mouse xenograft model, the pathological changes in CRC tumors and colon tissues, as well as the expression levels of CaSR, Bcl-2, and Caspase-3 proteins, were analyzed. Changes in the gut microbiota were analyzed using 16S rRNA gene sequencing. SrCl2 and SrRan significantly inhibited CRC cell proliferation (P < 0.05), migration (P < 0.05), and invasion (P < 0.001), while inducing G1/S phase arrest and apoptosis mediated by the mitochondrial pathway. Animal experiments demonstrated a 68.60 % reduction in tumor volume in the strontium-treated group, accompanied by a marked downregulation of Ki67 expression. In addition,16S rRNA sequencing revealed that strontium modulated the gut microbiota composition in CRC nude mice, characterized by a significant increase in the relative abundance of Lactobacillus species (P < 0.05). This study suggests that strontium supplementation may provide a theoretical basis for the treatment of colorectal cancer and the optimization of comprehensive treatment strategies for this condition.},
}

@article {pmid41175683,
year = {2025},
author = {López-Bucio, J and Jiménez-Vázquez, KR and Martínez-Romero, E},
title = {Indole-3-acetic acid from plants and microbes in human health.},
journal = {Current opinion in immunology},
volume = {98},
number = {},
pages = {102683},
doi = {10.1016/j.coi.2025.102683},
pmid = {41175683},
issn = {1879-0372},
abstract = {The production of indole-3-acetic acid (IAA, auxin) is universal in microbes and plants, and contributes to human wellness, acting as an anticancer and anti-inflammatory agent. This review highlights the ubiquity of IAA production by microbes and plants, as well as its role in human health. A high-fat diet decreases IAA levels in the intestine and serum, whereas intake of IAA as part of plant or microbial-derived food, or engineering the endogenous microbiome with IAA-producing bacteria, offers suitable alternatives against diseases. The aryl hydrocarbon receptor found in immune cells in the intestine has affinities for IAA and regulates both adaptive and innate immune responses. In plants, IAA receptors are well known, as well as the molecular responses elicited. Clearly, IAA is a key molecule in plant and human health, and plant and human health are interrelated.},
}

@article {pmid41175426,
year = {2025},
author = {Meher, MM and Afrin, M},
title = {Global surge of human metapneumovirus (hMPV) and its interactions with microbiome to disease severity.},
journal = {Journal of infection and public health},
volume = {19},
number = {1},
pages = {103024},
doi = {10.1016/j.jiph.2025.103024},
pmid = {41175426},
issn = {1876-035X},
abstract = {Human metapneumovirus (hMPV) is a significant virus of the lungs that causes diversified symptoms such as mild colds to severe pneumonia in people of all ages, especially in children, the elderly, and immunosuppressed individuals. The review highlights the global escalation of hMPV and explores how the human microbiome may shape the susceptibility of infections, immune responses and disease severity. The virus can form inclusion bodies inside the host cells and increase hMPV virulence to induce severe viral infection. hMPV also exploits immune-evasion strategy that weaken the host-body's defenses. Disturbances of gut-lung-microbiota can weaken the host immunity and worsen the disease severity. Nevertheless, intestinal microbes may promote the lung health through the compounds e.g., short-chain fatty acids. Although no particular treatment exists, there is an increasing concern in microbiome-based therapeutic approaches and personalized medicine. Understanding the microbiome interaction to hMPV may develop strategies to predict, prevent, and manage the hMPV infections.},
}

@article {pmid41175312,
year = {2025},
author = {Miller, BC and Haggler, JA and Chaudhari, DS and Shukla, R and Kumar, V and Mishra, SP and Masternak, MM and Holland, P and Labyak, C and Golden, A and Dangiolo, M and Arikawa, AY and Kociolek, J and Fraser, A and Williams, C and Agronin, M and Aymat, M and Pledger, W and Yadav, H and Jain, S},
title = {Gut microbiome signatures predict cognitive impairment in older cancer survivors.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {41175312},
issn = {2509-2723},
support = {22A17//Florida Department of Health/ ; },
abstract = {Cancer treatments are improving, and the population of cancer survivors is steadily increasing. However, many survivors experience long-term side effects, including chemobrain and other age-related geriatric disorders like cognitive impairment (CI), severely impacting their quality of life. Emerging studies suggest that the gut microbiome plays a central role in cognitive health. However, the long-term effects of cancer treatments on the microbiome, and how these changes impact cognitive health in survivors, remain largely unknown. Shotgun metagenomic data from 150 older adults (≥ 60 years old, including 49 cancer survivors and 101 controls) from the Microbiome in Aging Gut and Brain (MiaGB) consortium revealed that Tyzzerella, Eggerthella lenta, and Bacteroides vulgatus were specific markers of the cancer survivor gut and could differentiate cancer survivorship in this cohort. Microbiome signatures were distinct in cancer survivors with CI compared to those without and differed from those seen in non-cancer individuals with CI. Bacterial taxa including Streptococcus thermophilus and Firmicutes bacterium CAG 114 were significantly reduced in cancer survivors and strongly associated with CI. Importantly, metabolic pathway analysis revealed that microbial neurotransmitter synthesis was significantly depleted in the gut of cancer survivors, suggesting a mechanistic link to CI. Our results suggest that microbiome signatures predict cancer survivorship and the risk of CI in older adults, potentially by depleting neurotransmitter synthesis in the gut. These findings aid in establishing the role of the microbiome in predicting cancer survivorship and CI risk, which is valuable in the development of novel therapies to support the growing population of cancer survivors.},
}

@article {pmid41175215,
year = {2025},
author = {Ichibakase, F and Naito, T and Kaji, N},
title = {Fabrication and installation of a flexible polydimethylsiloxane (PDMS) porous membrane as a substitute for a rigid, conventional, track-etched polyethylene terephthalate (PET) membrane on cell culture inserts for gut barrier co-culture.},
journal = {Analytical and bioanalytical chemistry},
volume = {},
number = {},
pages = {},
pmid = {41175215},
issn = {1618-2650},
support = {24K01322//Japan Society for the Promotion of Science/ ; },
abstract = {We report a simple, clean-room-free strategy for fabricating an ultrathin (≈ 5 µm) and highly flexible polydimethylsiloxane (PDMS) porous membrane that functions as a mechanically dynamic scaffold for an intestine-on-a-chip platform capable of co-culturing human epithelial cells and gut bacteria. The membrane is produced by a two-dimensional phase separation process in which polystyrene (PS) of defined molecular weight (MW = 1300-170,000) acts as the sacrificial layer in a PDMS/toluene matrix. Systematic variation of phase separation time (3-24 h), PS molecular weight, and PS:PDMS:toluene mixing ratio revealed that PS of MW = 5780 at a 1:7.5:7.5 weight ratio generated through pores 10-100 µm in diameter, whereas PS of MW = 1300 yielded sub-2 µm pores but required optimization to secure pore continuity. Scanning electron microscopy images confirmed homogeneous lateral distribution of the pores and negligible surface collapse after sacrificial removal of PS by overnight toluene extraction and subsequent thermal curing. Fluorescein permeability assays demonstrated that membranes fabricated with PS of MW = 5780 or 1300 displayed solute transport rates that showed a similar trend to 1.0 µm track-etched polyethylene terephthalate (PET) inserts at 12 h, underscoring successful formation of through pores despite an order of magnitude reduction in overall thickness. Importantly, Caco-2 colon epithelial cells adhered, proliferated, and formed confluent monolayers within 7 days on collagen-coated PDMS membranes, whereas confluent cultures on PET required 10 days. Long-term culture experiments (up to 18 days in our setting) highlighted contrasting behaviors: cells cultured on the larger-pore (10-100 µm) membranes detached after ≈13 days, likely due to accumulation of autocrine inhibitors on the impermeable basal side; in contrast, cells on the smaller pore (≈2 µm) PDMS membranes remained viable, although some cells migrated through the membrane to the lower chamber, illustrating the need to match pore size distribution to cell diameter. The present methodology eliminates photolithography and plasma bonding steps commonly associated with PDMS microfabrication and can be completed with benchtop spin coating and solvent-casting equipment in <48 h. Because the resulting membrane combines (i) compliance suitable for pneumatically driven peristaltic deformation, (ii) molecular permeability that showed a similar trend to conventional PET inserts, and (iii) optical transparency for real-time microscopy, it provides a versatile foundation for constructing gut-on-a-chip systems that more faithfully recapitulate the biochemical and mechanical microenvironment of the intestinal epithelium. Beyond microbiome-epithelium interaction studies, the platform is readily adaptable to barrier-function assays, drug-transport screening, and host-pathogen investigations involving mechanically active mucosal tissues.},
}

@article {pmid41175138,
year = {2025},
author = {Balan, P and Leite, FRM and Tay, JRH and Hartanto, J and Nascimento, GG and Romandini, M},
title = {Oral Microbiome Signatures in Periodontitis and Edentulism-A Population-Based Study.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70046},
pmid = {41175138},
issn = {1600-0765},
abstract = {AIM: To examine the association between the oral microbiome, periodontitis, and edentulism in a nationally representative sample of the U.S.

METHODS: A total of 5299 adults aged 30-69 years were examined (NHANES 2009-2012). Oral rinse samples were collected and analyzed through 16S rRNA gene sequencing. Periodontitis presence, stage, extent, and grade were assessed according to the 2017 AAP/EFP classification using the ACES framework, with edentulism considered as a distinct category. Bacterial diversity and taxonomic composition were evaluated using alpha and beta diversity metrics and multivariable linear models (MaAsLin2), adjusted for relevant confounders.

RESULTS: Alpha diversity increased with periodontitis severity, extent, and grade, peaking in Stage III generalized periodontitis. In Stage IV, extensive tooth loss was associated with a decrease in alpha diversity. Edentulous individuals exhibited the lowest alpha diversity, falling below levels observed in those without periodontitis. Beta diversity differences across periodontitis severity, extent, and grade were subtle (< 0.2%). Taxonomically, increasing severity, extent, and grade of periodontitis were associated with enrichment of established periodontitis-related genera (e.g., Dialister, Filifactor, Fusobacterium, Porphyromonas, Prevotella, Tannerella) and Jonquetella, alongside depletion of health-related genera (e.g., Rothia, Veillonella). A total of 13 genera were commonly altered in both edentulous individuals and those with Stage III-IV periodontitis, relative to participants with no or localized Stage I-II disease.

CONCLUSION: Periodontitis is characterized by an increase in alpha diversity with advancing severity, extent, and grade, followed by a decline with extensive tooth loss and edentulism. However, it accounted for only a small fraction of the overall variation in oral microbiome composition. Taxonomic shifts included enrichment of established periodontitis-related genera and Jonquetella, alongside depletion of health-related genera. The persistence of periodontitis-associated bacteria in edentulous individuals may have important implications for implant dentistry.},
}

@article {pmid41174950,
year = {2025},
author = {Vega-Abellaneda, S and Román, E and Soler, Z and Ortiz, MÀ and Rossi, G and Biagini, L and Sánchez, E and Pons-Tarin, M and Laghi, L and Mengucci, C and Kaur, N and Poca, M and Cuyàs, B and Serrano-Gomez, G and Alvarado, E and Manichanh, C and Soriano, G},
title = {A Metagenomics Approach to Frailty in Patients With Cirrhosis Undergoing a Multifactorial Intervention.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {45},
number = {12},
pages = {e70418},
doi = {10.1111/liv.70418},
pmid = {41174950},
issn = {1478-3231},
support = {PI19/00275//Instituto de Salud Carlos III/ ; PR-455/2020//Col.legi Oficial d'Infermeres i Infermers de Barcelona/ ; //MENDES SA/ ; //Infisport/ ; },
mesh = {Humans ; *Liver Cirrhosis/complications/therapy/microbiology ; *Frailty/therapy/microbiology ; Male ; Metagenomics ; *Gastrointestinal Microbiome ; Female ; *Probiotics/therapeutic use ; Middle Aged ; Aged ; Feces/microbiology ; Amino Acids, Branched-Chain/therapeutic use ; },
abstract = {The relationship between frailty and gut microbiota has not been previously addressed in patients with cirrhosis. We studied by metagenomic shotgun sequencing the faecal microbiota composition associated with frailty in 29 patients with cirrhosis from a previous study (Román, Hepatol Commun 2024). Frail and prefrail patients were randomised to a multifactorial intervention (home exercise, branched-chain amino acids and a multistrain probiotic) or control for 12 months. We observed a positive correlation between the abundance of Rothia dentocariosa and the Liver frailty index (LFI), and between Bacteroides faecis and gait speed. After the multifactorial intervention, LFI improved and the main changes in the microbiota composition were a decrease in the abundance of Akkermansia muciniphila, and an increase in Streptococcus thermophilus, Lactobacillus acidophilus and several species of Bifidobacterium. We conclude that frailty in patients with cirrhosis was associated with a distinct microbiome signature. After a long-term multifactorial intervention, frailty improved in parallel with changes in microbiome composition. Trial Registration: ClinicalTrials.gov identifier: NCT04243148.},
}

Humans
*Liver Cirrhosis/complications/therapy/microbiology
*Frailty/therapy/microbiology
Male
Metagenomics
*Gastrointestinal Microbiome
Female
*Probiotics/therapeutic use
Middle Aged
Aged
Feces/microbiology
Amino Acids, Branched-Chain/therapeutic use

@article {pmid41174806,
year = {2025},
author = {Dong, Q and Ma, B and Zhou, X and Huang, P and Gao, M and Yang, S and Jiao, Y and Zhou, Y and Shi, Z and Deng, Q and Hua, D and Wang, X and Liu, L and Zhang, C and Zhang, C and Kong, M and He, C and Wu, T and Zou, H and Shi, J and Sheng, Y and Wang, Y and , and Tang, L and Hu, S and Zhong, H and Sun, W and Chen, W and Zhai, Q and Kong, X and Zheng, Y and Chen, L},
title = {Expanded gut microbial genomes from Chinese populations reveal population-specific genomic features related to human physiological traits.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {137},
pmid = {41174806},
issn = {1756-994X},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Asian People/genetics ; Phylogeny ; China ; *Genome, Bacterial ; *Genomics/methods ; East Asian People ; },
abstract = {BACKGROUND: A comprehensive and representative reference database is crucial for accurate taxonomic and functional profiling of the human gut microbiome in population-level studies. However, as approximately 70% of current microbial reference data originate from European and North American populations, other regions, including East Asia-and particularly China-remain significantly underrepresented.

METHODS: We constructed the human Gut Microbiome Reference (GMR), comprising 478,588 high-quality microbial genomes from Chinese (247,134) and non-Chinese (231,454) populations. Species-level clustering and protein annotations were performed to characterize microbial diversity and function. We further integrated novel microbial genomes into taxonomic profile database and validated the improvements using independent cohort data.

RESULTS: The GMR dataset spans 6664 species, including 26.4% newly classified species, and encodes over 20 million unique proteins, with 47% lacking known functional annotations. Notably, we observed that 35.35 and 32.46% of species unique to Chinese and non-Chinese populations, respectively. For 2145 species shared between populations, 74% of 304 species with balanced prevalence between populations exhibited population-specific phylogenetic stratification, involving health relevant functionalities such as antibiotic resistance. Integration of novel genomes into taxonomic improved population-level species profiling by up to 23% and uncovered replicable associations between novel species and host physiological traits.

CONCLUSIONS: Our study largely expands the compositional and functional landscape of the human gut microbiome, providing a crucial resource for studying the role of gut microbiome for regional health disparities.},
}

Humans
*Gastrointestinal Microbiome/genetics
Asian People/genetics
Phylogeny
China
*Genome, Bacterial
*Genomics/methods
East Asian People