@article {pmid41117995,
year = {2025},
author = {Marik, D and Sadhukhan, A},
title = {Unearthing the hidden organ: vital role of the root in drought tolerance of plants.},
journal = {Plant molecular biology},
volume = {115},
number = {6},
pages = {119},
pmid = {41117995},
issn = {1573-5028},
support = {I/SEED/ASK/20220015//Indian Institute of Technology Jodhpur/ ; SRG/2022/000169//Science and Engineering Research Board, Govt. of India/ ; },
}

@article {pmid41117771,
year = {2025},
author = {Miranda de Souza Junior, S and Chenoll, E and Howard-Varona, A and Lamelas, A and Martinez-Blanch, JF and Davenport, GM and Nixon, S and He, F and de Godoy, MRC},
title = {Effects of Supplementation with Bifidobacterium Animalis Subsp. Lactis CECT 8145 -In Live Probiotic and Heat-Treated Postbiotic Form-on Fecal Metabolites, Fecal Microbiota, Blood Metabolites and Systemic Biomarkers of Oxidative Stress and Inflammation, and White Blood Cell Gene Expression of Adult Cats.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf355},
pmid = {41117771},
issn = {1525-3163},
abstract = {Probiotics and postbiotics have been linked with enhancement of gastrointestinal health. This study aimed to evaluate the longitudinal effects of daily supplementation of a pro- and a postbiotic on metabolic health, blood metabolites and systemic biomarkers of oxidative stress and inflammation, fecal fermentative end-products, the gastrointestinal microbiota and white blood cell gene expression of adult cats. The study was a double-blind parallel randomized design with 36 cats divided into 3 groups. Animals were fed a standard extruded commercial diet. The groups were control diet + placebo (maltodextrin carrier) (CON), control diet + probiotic (Bifidobacterium animalis subsp. lactis CECT8145; daily dosage: 1010 CFU/day) (PRO), and control diet + postbiotic (Heat-treated Bifidobacterium animalis subsp. lactis CECT8145,) 1x1010 cells/day (POST). Longitudinal analyses were performed every 30 days for a total of 90 days. There was no observed effect on body weight (P > 0.05). At a species level, cats in the PRO group had an increased abundance of Bifidobacterium animalis over time (P < 0.05). Over time, CAZy genes between the PRO and POST groups presented similar output when compared to the CON group. There was no treatment by day effect of serum cytokines and chemokines (P > 0.05). Overall, the supplementation of the probiotic and postbiotic was safe and well tolerated during the supplementation period, showing similar physiological responses in this population of adult cats.},
}

@article {pmid41117697,
year = {2025},
author = {Li, Z and Kuang, X and Ling, J and Shen, T and Shan, G and Wu, J},
title = {Mouse chymase mast cell protease-4 facilitates blood feeding of Aedes aegypti (Diptera: Culicidae) mosquitoes.},
journal = {Journal of medical entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jme/tjaf137},
pmid = {41117697},
issn = {1938-2928},
support = {24 3505 Pj//Swedish Cancer Society/ ; //Guizhou High-level Innovative Talents Training Program (Qiankehe Platform Talents-GCC[2022]033-1)/ ; //Science and Technology Innovation Talent Team of Guizhou Province (Qian Ke He Platform Talent-CXTD [2022]004)/ ; ZK[2021]430]//Guizhou Provincial Basic Research Program (Natural Science)/ ; 21NSFCP29//Incubation Funding of Guizhou Medical University National Natural Science Foundation/ ; },
abstract = {Aedes aegypti (Linnaeus) are rapidly spreading across the globe. Evidence suggests that a Type I hypersensitivity reaction, characterized by IgE-mediated mast cell degranulation, may enhance the blood-feeding behavior of Ae. aegypti. Chymases, the mast cell-specific proteases, may play a critical role in this process. To investigate the role of mouse chymase mast cell protease-4 (mMCP-4) on mosquito blood feeding, we incubated bone marrow-derived mast cells with serum from mice sensitized by female Ae. aegypti bites and subsequently challenged the cells with salivary gland proteins (SGPs) from female mosquito. And the degradation of SGPs by mMCP-4 was assessed. Then, the MCP-4 deficient mice were sensitized twice by Ae. aegypti, the first bite on day 0 and the second on day 3. Throughout these experiments, we recorded the total blood meal duration, probing time, and blood feeding of the mosquitoes and analyzed the cutaneous microbiota. We discovered that serum from sensitized mice enhanced mast cell degranulation and chymase release. And mMCP-4 degraded some SGPs, in particular, potentially cleaving the blood-feeding-related salivary protein D7. Mcpt-4 deficiency resulted in prolonged blood-feeding duration during the second exposure, without affecting initial probing behavior. Moreover, Mcpt-4-deficient mice exhibited a reduced proportion of mosquitoes achieving rapid engorgement. Skin microbiome profiling revealed that Mcpt-4 deficiency attenuated the bite-induced expansion of potentially harmful bacterial taxa, including the dominant genus Corynebacterium (Mycobacteriales: Corynebacteriaceae). These findings identify mMCP-4 as a critical mediator of mosquito blood-feeding behavior and a modulator of skin microbial ecology in response to Ae. aegypti bites.},
}

@article {pmid41117680,
year = {2025},
author = {Karakayalı, EM and Tuğlu, Mİ},
title = {The contribution of probiotics to combined cellular therapy in skin wound healing in diabetic rats.},
journal = {Ulusal travma ve acil cerrahi dergisi = Turkish journal of trauma & emergency surgery : TJTES},
volume = {31},
number = {10},
pages = {925-936},
doi = {10.14744/tjtes.2025.37711},
pmid = {41117680},
issn = {1307-7945},
mesh = {Animals ; *Probiotics/therapeutic use/pharmacology ; *Wound Healing/drug effects ; Rats ; *Diabetes Mellitus, Experimental/complications ; Male ; Skin/injuries ; *Cell- and Tissue-Based Therapy/methods ; },
abstract = {BACKGROUND: Diabetes-related wound care is still a major issue due to chronic and non-healing ulcers that are prone to infection and ultimately amputation. In recent years, cellular therapy (CT) products such as mesenchymal stem cells (MSC), platelet-rich plasma (PRP), and stromal vascular fraction (SVF) have been widely used. A combined cellular therapy (CCT) has not yet been tested as a triple combination, although its use alone and in dual combinations has been investigated. Probiotics (PB) accelerate healing by altering the intestinal microbiota. This study aims to examine the role of PB in enhancing the effects of CCT on diabetic wound healing.

METHODS: A 1×1 cm2 full-thickness cutaneous wound was created after administering 40 mg/kg streptozotocin intraperitoneally (STZ i.p.) to induce a diabetic (DB) animal model. Animals were divided into four groups: DB, DB+PB, DB+CCT, and DB+CCT+PB, each with six adult Albino rats. The wound edges were treated with a total of 300 µL of solution, consisting of 30 µL each of 100 µL 1×106 MSC, 100 µL SVF, and 100 µL PRP as CCT. PB was administered orally at a dose of approximately 200 mg daily. Histochemical analyses were performed using hematoxylin and eosin (HE) and Masson's trichrome (MT). Immunohistochemical analyses were conducted for endothelial nitric oxide synthase (eNOS), Caspase-3, interleukin-10 (IL-10), vascular endothelial growth factor (VEGF), and Collagen I. The intestinal microbiome was examined through metagenomic analyses of taxonomic structure.

RESULTS: Combined cellular therapy provided more effective and faster healing in DB animals. It was discovered that PB further accelerated this process, leading to greater improvement. CCT was observed to reverse high eNOS, Caspase-3, and IL-10 expression, as well as low VEGF and Collagen I levels. Moreover, PB therapy significantly enhanced the positive effects of CCT. CCT in combination with PB significantly improved wound healing by preventing oxidative stress, apoptosis, and inflammation, while promoting vascularization and collagen organization.

CONCLUSION: Probiotic support was considered important for diabetic wound healing and was suggested to improve patients' quality of life.},
}

Animals
*Probiotics/therapeutic use/pharmacology
*Wound Healing/drug effects
Rats
*Diabetes Mellitus, Experimental/complications
Male
Skin/injuries
*Cell- and Tissue-Based Therapy/methods

@article {pmid41117558,
year = {2025},
author = {Maltz, MR and Topacio, TM and Lo, DD and Zaza, M and Freund, L and Botthoff, J and Swenson, M and Cocker, D and Biddle, T and Yisrael, K and Del Castillo, D and Drover, RW and Aronson, E},
title = {Lung microbiomes' variable responses to dust exposure in mouse models of asthma.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0020925},
doi = {10.1128/msphere.00209-25},
pmid = {41117558},
issn = {2379-5042},
abstract = {UNLABELLED: Inhalation of dust is significant and relevant to health effects. As pollution and climate change worsen in dryland regions, wind currents entrain loose sediment and dust. This potentially disperses toxic geochemical and microbial burdens throughout the region. When inhaled environmental dust and host-associated microbiomes mingle, they pose exposure risks to host respiratory health. The Salton Sea, California's largest lake, is shrinking, thus exposing nearby communities to playa dust. Therefore, we analyze the effect of Salton Sea dust exposure in murine models to relate lung microbial communities and respiratory health. We used an environmental chamber to expose mice to dust filtrate or ambient air and examined the effects of those exposures on lung microbiomes. We found that lung microbial composition varied by dust exposure. Furthermore, dust elicited neutrophil recruitment and immune responses more than mice exposed to ambient air. Sources of dust differentially affected the composition of the lung core microbiome. Lung microbial diversity correlated with neutrophil recruitment as lungs associated with inflammatory responses harbored more diverse microbiomes. Although Salton Sea dust influences dust microbiomes and prevalent taxa, these responses are variable. The composition of lungs exposed to dust collected further from the Salton Sea was more similar to lungs from ambient air exposures; in contrast, dust collected near the Salton Sea yielded lung microbiomes that clustered further from lungs exposed to ambient air. As lakes continue to dry out, we expect greater public health risks in proximal dryland regions, which may correlate with dust microbial dispersal-related changes to lung microbiomes.

IMPORTANCE: Dust inhalation can lead to health effects, especially when toxic chemicals and microbes mix in with the dust particles. As California's Salton Sea dries up, it exposes lake bottom sediments to wind, which disperses the dried sediments. To mimic the effect of inhaling Salton Sea dust, we collected and filtered airborne dust to use in exposure experiments with mice in environmental chambers. We predicted that inhaling small dust particles, chemicals, and microbial residues found in this dust would affect mouse respiratory health or change the microbes found inside their lungs. We found that inhaling dust led to lung inflammation, and the dust source influenced the type of microbes found inside mouse lungs. As lakes continue to dry out, we expect greater health risks and changes to lung microbiomes.},
}

@article {pmid41117551,
year = {2025},
author = {Jablonska, S and Nelson, L and Finger, G and Kula, A and Putonti, C},
title = {Draft genome of Corynebacterium glycinophilum S209 isolated from healthy human skin.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0080925},
doi = {10.1128/mra.00809-25},
pmid = {41117551},
issn = {2576-098X},
abstract = {Corynebacterium glycinophilum is an understudied species of this genus, although it has been identified in dairy products as well as the human skin microbiome. Recently, we isolated a strain from the skin of a healthy human female, and here, we present the draft genome of this isolate, C. glycinophilum S209.},
}

@article {pmid41117288,
year = {2025},
author = {Zhu, X and Cheng, S and Ge, J and Weng, C and Fang, K and Chen, J and Yang, R and Shi, B and Shao, D and Zhao, L and Leong, KW and Wu, Y and Huang, H},
title = {Periodontitis Induces Arterial Microbiota Shifts and Immune Dysregulation Contributing to Peripheral Vascular Inflammation.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70055},
pmid = {41117288},
issn = {1600-051X},
support = {82301148//National Natural Science Foundation of China/ ; 82170970//National Natural Science Foundation of China/ ; 81970944//National Natural Science Foundation of China/ ; 2024T170605//China Postdoctoral Science Foundation/ ; 2025ZNSFSC0758//Sichuan Province Science and Technology Support Program/ ; TB2022005//Sichuan Postdoctoral Science Foundation/ ; 24QNMP060//Health Commission of Sichuan Province Medical Science and Technology Program/ ; RCDWJS2024-7//Research Funding from West China School/Hospital of Stomatology Sichuan University/ ; RD-03-202105//Cross-disciplinary Innovation Project, West China School of Stomatology, Sichuan University/ ; },
abstract = {AIM: To explore periodontitis-induced changes in the femoral artery microbiota and their impact on the immune system, seeking to clarify the mechanisms underlying the link between periodontitis and peripheral arterial diseases (PADs).

MATERIALS AND METHODS: A ligature-induced periodontitis mouse model was used. 2bRAD sequencing for microbiome (2bRAD-M) was applied to analyse the femoral artery microbiota, and single-cell RNA sequencing (scRNA-seq) was used to characterise the arterial immune microenvironment.

RESULTS: Periodontitis significantly altered the femoral artery microbiota. There was increase in the relative abundance of anaerobic bacteria and reduction in aerobic and facultative anaerobic bacteria. Lipopolysaccharide (LPS) concentrations in both blood and the femoral artery were elevated. scRNA-seq showed an increase in fatty acid binding protein 4 (FABP4[+]) endothelial cells (ECs). FABP4[+] ECs were more responsive to LPS, which promoted neutrophil infiltration and T-cell differentiation.

CONCLUSION: These findings identify FABP4[+] ECs as key mediators in the connection between periodontitis and PADs. The study provides new insights into the systemic effects of periodontitis and offers a basis for developing preventive and therapeutic strategies for periodontitis-associated vascular diseases.},
}

@article {pmid41117273,
year = {2025},
author = {Oba, S and Hosoya, T and Iwai, H and Yasuda, S},
title = {Long COVID: mechanisms of disease, multisystem sequelae, and prospects for treatment.},
journal = {Immunological medicine},
volume = {},
number = {},
pages = {1-24},
doi = {10.1080/25785826.2025.2570902},
pmid = {41117273},
issn = {2578-5826},
abstract = {Long COVID has emerged as a significant global health issue, affecting individuals across a wide spectrum of initial disease severity. While its definition and prevalence vary across studies, persistent symptoms such as fatigue, cognitive dysfunction, respiratory difficulties, and cardiovascular complications have been widely reported. Multiple pathophysiological mechanisms have been proposed, including incomplete viral clearance, reactivation of latent viruses, immune dysregulation, autoimmunity, endothelial dysfunction, microbiome alterations, and mitochondrial impairment. These interconnected processes are thought to contribute to chronic inflammation and multi-organ disease. To date, there are no established therapies for Long COVID, and management primarily focuses on symptomatic relief and rehabilitation. Vaccination has been shown to reduce the incidence of Long COVID, and emerging strategies, including antiviral agents, immune-modulating therapies, microbiome restoration, and mitochondria-targeted interventions, are under investigation. This review summarizes the current understanding of the epidemiology, pathophysiology, organ-specific manifestations, and potential therapeutic approaches for Long COVID, aiming to provide insights into future research directions and clinical management strategies.},
}

@article {pmid41117146,
year = {2025},
author = {Tran, MN and Eubank, TA and Kullar, R and McFarland, LV and Garey, KW and Goldstein, EJ},
title = {New investigational agents for the treatment of clostridioides difficile infections.},
journal = {Expert opinion on investigational drugs},
volume = {},
number = {},
pages = {},
doi = {10.1080/13543784.2025.2579016},
pmid = {41117146},
issn = {1744-7658},
abstract = {INTRODUCTION: The Centers for Disease Control and Prevention (CDC), estimates that Clostridioides difficile infection (CDI) results in 250,000 hospitalizations yearly in the U.S.A. an annual mortality of 12,800 and recurrence in 15-30% of patients. Consequently, new approaches and agents are needed to treat CDI. We review the current developmental pipeline for various categories of CDI therapies.

AREASCOVERED: We searched various data bases to identify relevant data.

EXPERT OPINION: Ibezapolstat, CRS3123, and ridinilazole were identified with unique mechanisms of action and narrow spectrums of activity that result in gut microbiome preservation and reduced recurrent CDI (rCDI) rates. One cannot predict the potential efficacy of these new agents under study until further studies are done. Some may emerge as only supplemental therapies, while others may fail or be shelved and hopefully at least one will emerge as a primary CDI therapy and to prevent rCDI. Some have the ability to restore the microbiome (VE303) or preserve intestinal integrity (e.g. REC-3964, LMN-201, AQ). Regardless, patients and clinicians need new agents. CDI is a significant burden to the healthcare system and the quality of life for patients who suffer from CDI and rCDI. Further development of these investigational agents to prevent this cycle are of upmost importance.},
}

@article {pmid41117133,
year = {2025},
author = {Jacob, AA and Rout, S and Dash, R and Venugopal, G and Punde, AR and John, JK and Varghese, SS and Cherupanakkal, C and Mattethra, GC and Ramadass, B},
title = {Gut microbiome differences in Parkinson's disease patients in Central Kerala population.},
journal = {Neurodegenerative disease management},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/17582024.2025.2574204},
pmid = {41117133},
issn = {1758-2032},
abstract = {BACKGROUND AND OBJECTIVES: Gut microbiota dysbiosis is increasingly implicated in Parkinson's disease (PD). This study aimed to find gut microbiota diversity and composition of PD patients in Central Kerala population, India.

METHODS: 16 PD patients were enrolled and their spouse formed the controls. Fecal Microbiome analysis was performed by 16S rRNA amplicon sequencing.

RESULTS: Seven microbial species significantly contributed to the differences in beta diversity between the PD and control groups (p = 0.007). On network analysis Bifidobacterium longum, Bacteroides fragilis, Blautia obeum and Roseburia faecis represented the PD group communities and Ruminococcus bromii and Ruminococcus gnavus represented the controls. Faecalibacterium prausnitzii and Ruminococcus gnavus enhanced centrality in the spouse control network and Bifidobacterium longum, Eubacterium biforme, and Roseburia faecis in PD group.

CONCLUSIONS: This study offers initial evidence for identifying PD associated gut microbiome alterations in the Kerala population to be further explored with larger and more detailed longitudinal study.},
}

@article {pmid41116947,
year = {2025},
author = {Almazrouei, KM and Mishra, V and Pandya, H and Sambhav, K and Bhavsar, SN},
title = {Tumor Microenvironment and Its Role in Cancer Progression: An Integrative Review.},
journal = {Cureus},
volume = {17},
number = {9},
pages = {e92707},
pmid = {41116947},
issn = {2168-8184},
abstract = {The tumor microenvironment (TME) plays a crucial role in cancer progression, metastasis, immune evasion, and treatment resistance. However, the current literature often studies its components separately. This review offers an integrated view of the dynamic interactions among fibroblasts, immune and vascular cells, the extracellular matrix, cytokines, exosomes, and microbiota within the TME. It discusses classical mechanisms such as epithelial-mesenchymal transition, stromal remodeling, and metabolic rewiring alongside emerging paradigms like microbiome-driven immunomodulation and exosome-mediated therapy resistance. Spatial heterogeneity and the temporal evolution of the tumor niche are examined using recent advances in single-cell and spatial transcriptomics, 3D bioprinting, and patient-derived organoid models. Key findings emphasize the microbiome's influence on immune responses and the role of exosomes in transferring resistance traits and regulating intercellular signaling. By connecting molecular insights with clinical perspectives, the review explores translational strategies targeting the TME, including checkpoint inhibitors, stromal modulators, anti-angiogenic agents, and engineered CAR-T therapies. This comprehensive view highlights the importance of considering cancer as a complex, evolving ecosystem rather than just a cell-autonomous disease and provides a foundational framework for precision oncology approaches aimed at disrupting harmful TME interactions to improve therapeutic effectiveness and patient outcomes.},
}

@article {pmid41116875,
year = {2025},
author = {Abtin, S and Ziveh, T and Rezaee-Tavirani, M},
title = {The complicated relationship between inflammation and metabolic dysfunction.},
journal = {Journal of diabetes and metabolic disorders},
volume = {24},
number = {2},
pages = {237},
pmid = {41116875},
issn = {2251-6581},
abstract = {The prevalence of metabolic diseases, including obesity, type 2 diabetes, cardiovascular diseases, metabolic syndrome, and non-alcoholic fatty liver disease, is rising steadily and has emerged as a global health issue. Evidence indicates that chronic inflammation plays a crucial role in the development and progression of metabolic diseases. This review article addresses the intricate and reciprocal link between chronic inflammation and disrupted glucose and lipid metabolism. Furthermore, it explores the influence of factors such as the gut microbiome, socio-psychological variables, and aging. The article ultimately discusses future research directions and the need for a better understanding of the complexities between inflammation and metabolism. Addressing these factors could provide effective strategies for preventing and managing metabolic disorders, improving quality of life and public health.},
}

@article {pmid41116872,
year = {2025},
author = {Huang, J and Yu, Y and Feng, Z and Yin, Y and Liu, Y and Liu, X and Yu, R},
title = {Cross - Kingdom Dialogue of Microbial Messengers: Multi - Target Regulatory Mechanisms and Therapeutic Strategies of Gut Microbiota - Derived Extracellular Vesicles in Metabolic Diseases.},
journal = {International journal of nanomedicine},
volume = {20},
number = {},
pages = {12573-12591},
pmid = {41116872},
issn = {1178-2013},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Extracellular Vesicles/metabolism ; *Metabolic Diseases/microbiology/therapy ; Animals ; Probiotics ; Insulin Resistance ; },
abstract = {Gut microbiota-derived extracellular vesicles (GMEVs) serve as pivotal mediators of cross-communication between microorganisms and their hosts, playing a complex and central role in the onset and progression of metabolic diseases. This review systematically summarizes the biological characteristics, molecular composition, and regulatory mechanisms of GMEVs in metabolic disorders such as obesity, diabetes, and non-alcoholic fatty liver disease. GMEVs facilitate dialogue along the "gut-organ axis" by transporting active molecules such as lipopolysaccharides (LPS), flagellin, nucleic acids, and metabolic products, thereby mediating bidirectional regulation of host metabolic homeostasis. GMEVs derived from pathogenic bacteria promote metabolic inflammation and insulin resistance by compromising the intestinal barrier, activating inflammatory pathways, and inhibiting insulin signaling. Conversely, GMEVs originating from probiotics exert protective effects by enhancing tight junction functionality, modulating immune responses, and improving lipid metabolism. Notably, the dynamic fluctuations of GMEVs are closely linked to disease progression, and their microbiota-specific molecular characteristics offer novel biomarkers for the early diagnosis of metabolic diseases. Despite the challenges posed by standardization of isolation and elucidation of underlying mechanisms, the potential applications of GMEVs in the precise prevention and treatment of metabolic diseases are vast, providing a theoretical foundation for the development of novel microbiome-based intervention strategies. Future research should further elucidate the heterogeneity of GMEVs and their spatiotemporal dynamics in host interactions, facilitating the transition from fundamental research to clinical application.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Extracellular Vesicles/metabolism
*Metabolic Diseases/microbiology/therapy
Animals
Probiotics
Insulin Resistance

@article {pmid41116849,
year = {2025},
author = {Suleiman, KY and Akorede, GJ and Afisu, B and Onimajesin, AO and Saadudeen, A and Lawal, MO},
title = {The epigenetic influence of diet-induced gut microbiome changes in precision nutrition - a systematic review.},
journal = {Gastroenterology and hepatology from bed to bench},
volume = {18},
number = {3},
pages = {270-285},
pmid = {41116849},
issn = {2008-2258},
abstract = {AIM: This systematic review aimed to comprehensively evaluate the existing literature on the epigenetic influence of diet-induced gut microbiome changes in the context of precision nutrition.

BACKGROUND: Diet influences gut microbiome composition, which regulates epigenetic modifications affecting inflammation, metabolism, and disease susceptibility. Precision nutrition seeks to personalize dietary strategies based on these interactions, yet the role of microbiome-driven epigenetic regulation remains under investigation.

METHODS: A systematic review was conducted in 2025 following PRISMA guidelines. Studies exploring the relationship between dietary interventions, gut microbiome composition, and epigenetic changes were identified via PubMed and Google Scholar. Thirty-five studies, including randomized controlled trials, cohort studies, and observational research, met the inclusion criteria. Data on dietary interventions, microbial composition, epigenetic modifications, and health outcomes were synthesized.

RESULTS: Diets rich in fiber and polyphenols enhanced microbial diversity, increased short-chain fatty acid production, and positively influenced epigenetic markers related to metabolic health. In contrast, Western-style and high-fat diets were associated with gut dysbiosis, inflammation, and negative epigenetic changes linked to metabolic disorders. Dietary interventions impacted DNA methylation, histone modifications, and microRNA expression, influencing long-term health.

CONCLUSION: This review highlights the key role of diet-induced changes in the gut microbiome in modulating epigenetic mechanisms like DNA methylation and histone modifications. These alterations influence metabolic health, disease risk, and precision nutrition strategies. While dietary interventions show promise, challenges such as individual variability and methodological inconsistencies require further research to refine clinical applications of microbiome-driven nutrition.},
}

@article {pmid41116203,
year = {2025},
author = {Li, H and Hu, Y and Chen, S and Gafforov, Y and Wang, M and Liu, X},
title = {Harnessing chemical communication in plant-microbiome and intra-microbiome interactions.},
journal = {Journal of Zhejiang University. Science. B},
volume = {26},
number = {10},
pages = {923-934},
doi = {10.1631/jzus.B2500099},
pmid = {41116203},
issn = {1862-1783},
support = {2025YFE0104500//the National Key R&D Program of China/ ; LD25C140002//the Zhejiang Provincial Natural Science Foundation of China/ ; 2024SZRZDC 130001//the Natural Science Foundation of Hangzhou/ ; U21A20219 and 32122074//the National Natural Science Foundation of China/ ; },
mesh = {*Microbiota/physiology ; *Plants/microbiology ; Artificial Intelligence ; Ecosystem ; },
abstract = {Chemical communication in plant-microbiome and intra-microbiome interactions weaves a complex network, critically shaping ecosystem stability and agricultural productivity. This non-contact interaction is driven by small-molecule signals that orchestrate crosstalk dynamics and beneficial association. Plants leverage these signals to distinguish between pathogens and beneficial microbes, dynamically modulate immune responses, and secrete exudates to recruit a beneficial microbiome, while microbes in turn influence plant nutrient acquisition and stress resilience. Such bidirectional chemical dialogues underpin nutrient cycling, co-evolution, microbiome assembly, and plant resistance. However, knowledge gaps persist regarding validating the key molecules involved in plant-microbe interactions. Interpreting chemical communication requires multi-omics integration to predict key information, genome editing and click chemistry to verify the function of biomolecules, and artificial intelligence (AI) models to improve resolution and accuracy. This review helps advance the understanding of chemical communication and provides theoretical support for agriculture to cope with food insecurity and climate challenges.},
}

*Microbiota/physiology
*Plants/microbiology
Artificial Intelligence
Ecosystem

@article {pmid41116050,
year = {2025},
author = {Deraison, C and Vergnolle, N},
title = {Proteases in intestinal health and disease.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {41116050},
issn = {1759-5053},
abstract = {Extracellular proteases, originating from the host or the microbiota, are key signalling molecules involved in cellular communication with the environment. They signal through a wide array of mechanisms, ranging from receptor activation to protein transformation and even degradation. Protease signals are irreversible, as it involves the cleavage of proteins. Therefore, proteases are tightly controlled, and must be understood within the context of the complex networks in which they operate - their activity is tightly regulated by access to specific substrates and the presence of inhibitors. The intestine is particularly exposed to extracellular proteases, which have major roles in gut physiology: digestion, food antigen processing, barrier function, epithelial renewal and microbiome homeostasis. Dysregulated proteolytic balance is associated with intestinal pathologies including inflammatory bowel disease, irritable bowel syndrome, coeliac disease and colorectal cancer. Extracellular proteases are major contributors to a number of gut dysfunctions, including microbiota dysbiosis, barrier dysfunction, matrix remodelling, activation of mucosal immunity and nociceptive or motility abnormalities. Consequently, proteolytic homeostasis at the intestinal mucosa surface has become a goal for intestinal health, and new therapeutic options targeting the interplay among proteases, their inhibitors and their substrates have been explored.},
}

@article {pmid41116021,
year = {2025},
author = {Morgan, KM and Shivanna, B},
title = {Initial insights into perinatal gut microbiome and early infantile respiratory tract infections.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {41116021},
issn = {1530-0447},
}

@article {pmid41115965,
year = {2025},
author = {Göttert, S and Thiele Orberg, E and Fan, K and Heinrich, P and Matthe, DM and Khalid, O and Klostermeier, L and Suriano, C and Strieder, N and Gebhard, C and Vonbrunn, E and Mamilos, A and Hirsch, D and Meedt, E and Kleigrewe, K and Hiergeist, A and Schwarz, A and Gläsner, J and Ghimire, S and Joachim, L and Voll, F and Neuhaus, K and Janssen, KP and Perl, M and Pielmeier, F and Ruland, J and Kreutz, M and Weber, D and Schmidl, C and Köhler, N and Tschurtschenthaler, M and Hoffmann, P and Edinger, M and Wolff, D and Bassermann, F and Rehli, M and Haller, D and Evert, M and Hildner, K and Büttner-Herold, M and Herr, W and Gessner, A and Heidegger, S and Holler, E and Poeck, H},
title = {The microbial metabolite desaminotyrosine protects against graft-versus-host disease via mTORC1 and STING-dependent intestinal regeneration.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9282},
pmid = {41115965},
issn = {2041-1723},
support = {324392634//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; *Graft vs Host Disease/prevention & control ; *Mechanistic Target of Rapamycin Complex 1/metabolism ; *Gastrointestinal Microbiome/drug effects ; Mice ; Hematopoietic Stem Cell Transplantation/adverse effects ; Humans ; *Intestines/physiology/drug effects ; *Membrane Proteins/metabolism/genetics ; *Regeneration/drug effects ; Mice, Inbred C57BL ; *Tyrosine/analogs & derivatives/pharmacology/metabolism ; Male ; Female ; Fecal Microbiota Transplantation ; Transplantation, Homologous ; },
abstract = {Changes in the intestinal microbiome and microbiota-derived metabolites predict clinical outcomes after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Here, we report that desaminotyrosine (DAT), a product of bacterial flavonoid metabolism, correlates with improved overall survival and reduced relapse rates in patients receiving allo-HSCT. In preclinical mouse models, treatment with synthetic DAT prevents graft-versus-host disease by protecting the intestinal barrier and promoting intestinal regeneration and contributes to graft-vs.-leukemia responses. DAT´s beneficial effects on intestinal regeneration remain effective despite broad-spectrum antibiotics-induced dysbiosis, also when administered by fecal microbiota transfer with flavonoid-degrading F. plautii. Mechanistically, DAT promotes mTORC1-dependent activation and proliferation of intestinal stem cells, with concomitant engagement of the innate immune receptor STING required to mitigate metabolic stress and maintain an undifferentiated stem cell state independently of type-I interferon responses. Additionally, DAT can skew T cells towards an effector phenotype to modulate graft-versus-leukemia responses. Our data uncover DAT's dual, tissue- and immune-modulating properties and underscore its potential in precision microbiome-based therapies to improve tissue regeneration and minimize immune-mediated side effects.},
}

Animals
*Graft vs Host Disease/prevention & control
*Mechanistic Target of Rapamycin Complex 1/metabolism
*Gastrointestinal Microbiome/drug effects
Mice
Hematopoietic Stem Cell Transplantation/adverse effects
Humans
*Intestines/physiology/drug effects
*Membrane Proteins/metabolism/genetics
*Regeneration/drug effects
Mice, Inbred C57BL
*Tyrosine/analogs & derivatives/pharmacology/metabolism
Male
Female
Fecal Microbiota Transplantation
Transplantation, Homologous

@article {pmid41115949,
year = {2025},
author = {Morais, LH and Stiles, L and Freeman, M and Oguienko, AD and Hoang, JD and Ji, J and Jones, J and Quan, B and Devine, J and Bois, JS and Chou, TF and Trinh, J and Picard, M and Gradinaru, V and Mazmanian, SK},
title = {The gut microbiome promotes mitochondrial respiration in the brain of a Parkinson's disease mouse model.},
journal = {NPJ Parkinson's disease},
volume = {11},
number = {1},
pages = {301},
pmid = {41115949},
issn = {2373-8057},
support = {Postdoctoral fellowship//American Parkinson Disease Association/ ; ASAP-020495//Aligning Science Across Parkinson's/ ; ASAP-020495//Aligning Science Across Parkinson's/ ; PD160030//U.S. Department of Defense/ ; },
abstract = {The pathophysiology of Parkinson's disease (PD) involves gene-environment interactions that impair various cellular processes including mitochondrial dysfunction. Mitochondria-associated mutations increase PD risk, respiration is altered in the PD brain, and mitochondria-damaging toxicants cause PD-like motor and gastrointestinal symptoms in animal models. The gut microbiome is altered in PD, representing an environmental risk, however a relationship between mitochondrial function and the microbiome in PD has not been previously established. Herein, we discover that dysregulation of mitochondria-associated genes and hyperactive striatal mitochondria are induced by the microbiome in α-synuclein-overexpressing (Thy1-ASO) mice. Thy1-ASO mice elaborate increased reactive oxygen species in the striatum whereas germ-free counterparts express increased oxygen scavenging proteins. Indeed, treatment with an antioxidant drug improves motor performance in Thy1-ASO mice and blocking oxidant scavenging in germ-free mice enhances motor deficits in an α-synuclein dependent manner. Thus, the gut microbiome promotes motor symptoms in a mouse model of PD via increased mitochondrial respiration and oxidative stress in the brain.},
}

@article {pmid41115930,
year = {2025},
author = {Fitzjerrells, RL and Meza, LA and Yadav, M and Olalde, H and Hoang, J and Paullus, M and Cherwin, C and Cho, TA and Brown, G and Ganesan, SM and Mangalam, AK},
title = {Multiple sclerosis patients exhibit oral dysbiosis with decreased early colonizers and lower hypotaurine level.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {199},
pmid = {41115930},
issn = {2055-5008},
support = {F31DE033564/DE/NIDCR NIH HHS/United States ; T90DE023520/DE/NIDCR NIH HHS/United States ; R03DE030527/DE/NIDCR NIH HHS/United States ; 1P20NR018081-01/NR/NINR NIH HHS/United States ; 1RO1AI137075//National Institute of Allergy and Infectious Diseases/ ; 1I01CX002212//U.S. Department of Veterans Affairs/ ; P30 ES005605/ES/NIEHS NIH HHS/United States ; },
mesh = {Humans ; *Dysbiosis/microbiology ; Female ; Male ; Adult ; *Taurine/analogs & derivatives/analysis/metabolism ; Middle Aged ; Metagenomics ; *Mouth/microbiology ; *Multiple Sclerosis, Relapsing-Remitting/microbiology ; Metabolomics ; *Bacteria/classification/genetics/isolation & purification ; Microbiota ; Fusobacterium nucleatum/isolation & purification ; Metabolome ; *Multiple Sclerosis/microbiology ; Actinomyces/isolation & purification ; Porphyromonas gingivalis/isolation & purification ; },
abstract = {Although gut microbiome dysbiosis is implicated in the pathobiology of multiple sclerosis (MS), the role of the oral microbiome (OM), the second largest microbiome, remains poorly understood. Additionally, while the salivary metabolome has been linked to other neurodegenerative diseases; its role in people with Relapsing-Remitting MS (pwRRMS), the most prevalent form of MS, is unknown. Combining shotgun metagenomics with untargeted metabolomics, we identified a reduced abundance of several early colonizing species including Streptococcus and Actinomyces in pwRRMS and an enrichment of bacteria with pathogenic potential including Fusobacterium nucleatum, Porphyromonas gingivalis, and several Prevotella species. pwRRMS had an altered metabolite profile including a decreased hypotaurine compared to healthy controls. Thus we report altered oral microbiome and metabolome in pwRRMS which might contribute to MS pathobiology. These findings offer potential microbiome-metabolome based diagnostic biomarkers for MS and pave the way for novel therapeutic interventions to improve disease management and patient outcomes.},
}

Humans
*Dysbiosis/microbiology
Female
Male
Adult
*Taurine/analogs & derivatives/analysis/metabolism
Middle Aged
Metagenomics
*Mouth/microbiology
*Multiple Sclerosis, Relapsing-Remitting/microbiology
Metabolomics
*Bacteria/classification/genetics/isolation & purification
Microbiota
Fusobacterium nucleatum/isolation & purification
Metabolome
*Multiple Sclerosis/microbiology
Actinomyces/isolation & purification
Porphyromonas gingivalis/isolation & purification

@article {pmid41115870,
year = {2025},
author = {Tanevska, E and Leyton, CE and Seamark, R},
title = {The usefulness of microbiome profiling for geriatric patients with neuropsychiatric conditions: a scoping review.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {420},
pmid = {41115870},
issn = {2158-3188},
mesh = {Humans ; Aged ; *Mental Disorders/microbiology/diagnosis ; *Gastrointestinal Microbiome ; *Alzheimer Disease/microbiology/diagnosis ; },
abstract = {INTRODUCTION: Neuropsychiatric disorders encompass psychiatric and neurodegenerative diseases. These conditions are particularly challenging to diagnose in the elderly due to their overlapping cognitive, affective, and behavioural symptoms. Recent studies indicate microbiota imbalances exist in both psychiatric and neurodegenerative conditions, suggesting potential biomarkers for diagnosis and prognosis. The objective of this scoping review is to provide a comprehensive overview of how microbiome profiling has been used in research to develop diagnostic and prognostic models for elderly patients with neuropsychiatric conditions.

METHODS: Following JBI guidelines, a comprehensive search was conducted across four electronic databases (MEDLINE, PsycINFO, SCOPUS, EMBASE) with strategies developed alongside academic librarians. Two independent reviewers screened titles, abstracts, and full texts based on pre-specified inclusion criteria. Data was extracted focusing on participants, study methods, and key findings.

RESULTS: Thirty-one studies employing microbiome-based predictive models were identified, primarily targeting Alzheimer's and Parkinson's diseases, with limited research on psychiatric conditions which was only found for depression and schizophrenia. Most studies used 16S rRNA gene sequencing and machine learning models. Findings highlight the potential of gut microbiota data to enhance predictions of neuropsychiatric conditions, though limitations included small, non-diverse cohorts and a lack of methodological standardisation. The review highlights the need for larger, longitudinal, multicentere studies to validate models and improve clinical applicability.

DISCUSSION: Microbiome-based predictive models for neuropsychiatric conditions in the elderly show promise. Future research should focus on longitudinal studies and expanding profiling methods to validate findings in larger, diverse cohorts.},
}

Humans
Aged
*Mental Disorders/microbiology/diagnosis
*Gastrointestinal Microbiome
*Alzheimer Disease/microbiology/diagnosis

@article {pmid41115834,
year = {2025},
author = {Facey, FSB and Maharjan, R and Dinh, H and Buchanan, JS and Connal, LA and Tay, AP and Paulsen, IT and Cain, AK},
title = {Characterising the Multiple-Plastic Degrading Strain of Bacillus subtilis GM_03 From the Galleria mellonella Microbiome.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70216},
doi = {10.1111/1758-2229.70216},
pmid = {41115834},
issn = {1758-2229},
support = {W911NF2320155//US Department of Defense/ ; FT220100152//Australian Research Council Future Fellowship/ ; 20235185//FSBF was supported by Macquarie University Research Excellence Scholarship Programme/ ; },
mesh = {Animals ; *Bacillus subtilis/metabolism/genetics/isolation & purification/classification ; Larva/microbiology ; *Moths/microbiology ; Biodegradation, Environmental ; *Plastics/metabolism ; *Microbiota ; Polyethylene/metabolism ; Polyurethanes/metabolism ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; Gastrointestinal Microbiome ; },
abstract = {Plastic waste is a mounting global problem with over 400 million tons of plastic produced annually and over 50% ending up in landfill after its intended use. Two types of plastics are particularly problematic and are difficult to recycle: low-density polyethylene (LDPE) and polyurethane (PU). Fortuitously, nature may offer a potential solution; Galleria mellonella larvae can digest various plastics, including LDPE, which is believed to be driven by microbes in their gut microbiome. Although some studies have examined their gut microbiota on a metagenomic level, little is known about their ability to degrade plastics. Here, we isolated six bacterial strains from G. mellonella larvae feeding on LDPE. One of them, identified as Bacillus subtilis GM_03, has the capacity to break down commercial PU (Impranil), in addition to LDPE. This bacterium encodes a suite of genes required for plastic degradation. Directed evolution was used to enhance this strain's plastic degrading rate by over six-fold. Sequencing of the evolved culture revealed four genes, srfAB, fadD, appA and citS, associated with this increased PU degradation rate. This is the first time that B. subtilis isolated from G. mellonella larvae has been shown to be capable of degrading multiple types of plastics.},
}

Animals
*Bacillus subtilis/metabolism/genetics/isolation & purification/classification
Larva/microbiology
*Moths/microbiology
Biodegradation, Environmental
*Plastics/metabolism
*Microbiota
Polyethylene/metabolism
Polyurethanes/metabolism
Phylogeny
Bacterial Proteins/genetics/metabolism
Gastrointestinal Microbiome

@article {pmid41115749,
year = {2025},
author = {Pichon, M and Bouleti, C and , and Hery-Arnaud, G and Burucoa, C and , },
title = {Heterogeneity and lack of standardisation in gut microbiome testing: a comparative assessment of French medical biology laboratories.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336981},
pmid = {41115749},
issn = {1468-3288},
}

@article {pmid41115624,
year = {2025},
author = {Mishra, R and Harvey, A and Guo, A and Tillotson, G and Feuerstadt, P and Khanna, S and Shannon, WD and Blount, KF},
title = {Microbiome and metabolome changes after fecal microbiota, live-jslm, administration are associated with health-related quality of life improvements.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {103006},
doi = {10.1016/j.anaerobe.2025.103006},
pmid = {41115624},
issn = {1095-8274},
abstract = {OBJECTIVES: Increasing evidence indicates a gut microbiome-brain axis, but more robust statistical methods are needed to solidify this connection. In a large phase 3, randomized, placebo-controlled clinical trial (PUNCH CD3; NCT03244644), fecal microbiota, live-jslm (REBYOTA; RBL, previously RBX2660), was effective in preventing recurrent Clostridium difficile infections, and trial participants had significant gut microbiome and metabolome shifts concurrent with significant changes in health-related quality of life (HRQOL). Advanced statistical methods were applied to data from this trial to further explore and demonstrate associations between changing HRQOL and microbiome or metabolome changes.

METHODS: A categorical statistical analysis queried whether patient-reported Cdiff32 HRQOL scores were more likely to improve after RBL than after placebo among PUNCH CD3 participants, and a Dirichlet-multinominal recursive partitioning model assessed whether mental domain Cdiff32 HRQOL scores were linked to participants' fecal microbiome or bile acid compositions.

RESULTS: Cdiff32 mental domain HRQOL scores were more likely to be improved after RBL administration compared with placebo among treatment responders. Cdiff32 mental domain scores were associated with changing gut microbiome and metabolome compositions, with a gradient of increased Clostridia and Bacteroidia and increased secondary bile acid predominance associated with better Cdiff32 scores.

CONCLUSIONS: The microbiota-gut-brain axis is posited to modulate health-related quality of life, microbiome, and metabolome changes through immune, gastrointestinal, and central nervous system functions in patients with recurrent C. difficile infection following RBL administration. These analyses provide a novel approach for investigating multi-omics data and categorical health-related quality of life questionnaires and generate new insights for further clinical studies.

CLINICAL TRIAL REGISTRATION: NCT03244644.},
}

@article {pmid41114648,
year = {2025},
author = {Graf, T and Moser, F and Embleton, H and Niklaus, PA and Grabenweger, G},
title = {Which factors influence the virulence of entomopathogenic fungi? Effect of spore type, oosporein, application method, and pathway of entry on the infectiveness of Beauveria brongniartii against Melolontha melolontha.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf259},
pmid = {41114648},
issn = {1365-2672},
abstract = {AIMS: The control of the common cockchafer Melolontha melolontha using the entomopathogenic fungus (EPF) Beauveria brongniartii is one of the most successful biological control systems. This study aimed to identify factors influencing the outcome of laboratory bioassays, which are crucial early steps in the development of biocontrol products, by using this system as a role model.

METHODS AND RESULTS: We combined spray and injection applications of conidio- and blastospores of the host-specific pathogen B. brongniartii BIPESCO2 (Bip2) and the generalist EPF Metarhizium brunneum Ma 43 and applied the treatments to cockchafer adults and larvae. Furthermore, the mycotoxin oosporein was tested alone or with Bip2 blastospores, as well as Bip2 conidiospores, in immersion, spray, and injection treatments of larvae. The most efficient spore suspension was applied to different larval body parts and to their food. Bip2 and Ma 43 infected adults frequently, but larvae resisted topical spray applications. Injection treatments revealed that adult cuticles offered limited protection, whereas the larval cuticle acted as an effective barrier. Larval thorax and legs, with articulations and intersegmental membranes, were more susceptible than the abdomen. Oosporein synergized with blastospores in larval immersion treatments, but alone had no effect. We propose that oosporein's antibiotic activity disrupts the larval cuticle microbiome, facilitating infection.

CONCLUSION: Contrary to the assumption that laboratory bioassays overestimate EPF performance under field conditions, we found the opposite. We therefore argue that more elaborate studies are required for realistic evaluation of candidate biocontrol agents, considering host-pathogen traits and test conditions.},
}

@article {pmid41114647,
year = {2025},
author = {Basso, TO and Venturini, AM and Ceccato-Antonini, SR and Gombert, AK},
title = {Microbial Ecology Applied to Fuel Ethanol Production from Sugarcane.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf100},
pmid = {41114647},
issn = {1574-6941},
abstract = {The production of fuel ethanol in sugarcane biorefineries is a non-aseptic industrial operation, which employs cell recycling and the use of adapted Saccharomyces cerevisiae strains. Microbial contaminants are present and, depending on the conditions, may lead to process performance deterioration. Past studies have identified the main microbial species present in this environment, using culture-dependent techniques. A few recent studies started to deploy culture-independent techniques to better understand this microbiota and its dynamics. In both cases, lactic acid bacteria have been identified as the main contaminating microorganisms. Less than a handful of reports are available on the interactions between yeast and contaminating bacteria, using synthetic microbial communities, proposing that interactions are not necessarily always detrimental. The present mini-review aims at systematizing the current knowledge on the microbiota present in the alcoholic fermentation environment in sugarcane biorefineries and setting the ground and claiming the need for a microbial ecology perspective to be applied to this system, which in turn might lead to future process improvements.},
}

@article {pmid41114585,
year = {2025},
author = {Aries Marchington, M and Gasvoda, H and Michelotti, M and Rodriguez-Caro, F and Gooman, A and Perez, A and Hensley-McBain, T},
title = {APOE genotype and sex drive microbiome divergence after microbiome standardization in APOE-humanized mice.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0042925},
doi = {10.1128/msphere.00429-25},
pmid = {41114585},
issn = {2379-5042},
abstract = {The APOE4 allele is the greatest known genetic factor for sporadic or late-onset Alzheimer's Disease (LOAD). Gut microbiome (GMB) dysbiosis can lead to poorer outcomes in disease. The intersection of sex, APOE genotype, inflammation, and gut microbiota is incompletely understood. Previous studies in humans and humanized APOE mice have demonstrated APOE-genotype-specific differences in the GMB. However, most of these studies were unable to resolve bacteria to the species level. It remains unclear how GMB changes with age and sex in the context of APOE genotype. In this study, humanized male mice with either APOE 2, 3, or 4 genotype were bred with the same two C57BL/6J sisters to standardize microbiomes across lines and monitor divergence based on APOE allele. Stool samples were collected at breeder set up and from the heterozygous (F1) and homozygous (F2) generations at wean and 6 months old. Stool was assessed via shallow shotgun sequencing to enable species and strain-level taxonomic resolution. The heterozygous pups' microbiome resembled each other at wean across all genotypes. However, the heterozygous pups and their homozygous offspring continued to diverge, particularly the APOE2 females. In homozygous mice, the GMB demonstrated significant divergence at 6 months of age based on sex and APOE genotype. In comparison to their APOE3 and APOE4 counterparts, APOE2 females and males demonstrated an increased quantity of bacteria associated with anti-inflammatory profiles, including in the Lachnospiraceae family (Lachnospiraceae bacterium UBA3401) and decreased quantities in the Turicibacteraceae family (higher levels are associated with LOAD).IMPORTANCEThe APOE4 allele is implicated as a significant risk factor for many diseases, including cardiovascular disease (responsible for more deaths than any other disease) and sporadic or late-onset Alzheimer's Disease (accounts for an estimated 60%-80% of all dementia cases). It is known that the gut microbiome (GMB) is affected by different genotypes and disease states. Mouse model studies have environmental and genetic controls, allowing a specific gene to be studied. This study aims at discovering key GMB species differences allowing for future therapeutic targets. The GMB of the experimental mice was standardized, and genotype and sex-specific divergence was observed with species and even strain level taxonomic resolution. Reported here are the first data demonstrating GMB divergence over time driven by APOE genotype from an inherited source and the first data to identify APOE genotype-specific bacteria species that may serve as therapeutic targets in APOE-driven disease.},
}

@article {pmid41114583,
year = {2025},
author = {Xia, Y and Yang, J and Lu, S and Cheng, W and Ren, M and Liu, Z and Yang, L and Shen, Q and Liang, Y and Huang, H and Chen, M and Zhou, X and Yu, M and Ji, F and Xu, C},
title = {Microbial changes resulting from VSG attenuate MASLD by modulating bile acid metabolism and the intestinal FXR-FGF19 axis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0063425},
doi = {10.1128/msystems.00634-25},
pmid = {41114583},
issn = {2379-5077},
abstract = {UNLABELLED: Vertical sleeve gastrectomy (VSG) is a highly effective intervention for metabolic dysfunction-associated steatotic liver disease (MASLD) and is associated with significant alterations in the gut microbiota. However, the precise mechanisms underlying its metabolic benefits remain poorly understood. In this study, we revealed that VSG mitigates MASLD by reshaping gut microbiota-mediated bile acid metabolism. Through integrated 16S rRNA sequencing, targeted metabolomics, and functional validation experiments, we demonstrated that VSG markedly enhances bile salt hydrolase (BSH) activity within the gut microbiota, resulting in elevated levels of unconjugated bile acids. These unconjugated bile acids serve as potent agonists for the intestinal farnesoid X receptor (FXR), thereby activating the intestinal FXR-fibroblast growth factor 19 signaling pathway. This activation leads to significant improvements in metabolic health, including enhanced glucose regulation and attenuated hepatic lipid accumulation. Fecal microbiota transplantation (FMT) from VSG-treated rats replicated these metabolic improvements, whereas antibiotic treatment abolished these beneficial effects, highlighting the indispensable role of the gut microbiota in mediating the anti-MASLD effects of VSG. Importantly, inhibition of intestinal FXR signaling negated the metabolic benefits of FMT, further emphasizing the critical role of the gut microbiota-BSH-FXR axis. Our findings reveal a novel mechanism by which VSG alleviates MASLD through gut microbiota-dependent activation of intestinal FXR, offering new perspectives for microbiome-targeted therapeutic strategies in MASLD.

IMPORTANCE: Fecal transplantation from bariatric surgery patients and mice to germ-free mice has shown that the gut microbiota may contribute to metabolic benefits after bariatric surgery. However, the mechanisms by which the gut microbiota contributes to metabolic benefits after bariatric surgery require further investigation. To address this gap, we investigated the effects of the vertical sleeve gastrectomy (VSG) gut microbiota on metabolic dysfunction-associated steatotic liver disease (MASLD) in vivo and elucidated its underlying mechanisms. Our study demonstrated that VSG significantly improved the gut microbiota, especially by increasing bile salt hydrolase (BSH) activity, in MASLD rats. Increased BSH activity significantly increased the proportion of FXR-agonistic bile acids and further activated the intestinal FXR-FGF19 axis, thereby improving MASLD. These findings explored the key roles and mechanisms of the gut microbiota in the metabolic benefits of VSG, offering new microbiome-based treatment strategies.},
}

@article {pmid41114579,
year = {2025},
author = {Powell, CE and McCurry, MD and Quevedo, SF and Ventura, L and Krishnan, K and Dave, M and Mahmood, SD and Specht, K and Bordia, R and Sargen, MR and Pratt, DS and Korzenik, JR and Devlin, AS},
title = {Cultured bacteria isolated from primary sclerosing cholangitis patient bile induce inflammation and cell death.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0055025},
doi = {10.1128/msphere.00550-25},
pmid = {41114579},
issn = {2379-5042},
abstract = {Primary sclerosing cholangitis (PSC) is a chronic liver disease characterized by inflammation and progressive fibrosis of the biliary tree. PSC pathogenesis remains poorly understood, and there are no effective therapies. Previous studies have observed associations between colonic and biliary microbiome alterations and PSC. We aimed to determine whether bacterial isolates cultured from PSC patient bile induce disease-associated phenotypes in cells, specifically cell death, epithelial permeability, inflammation, and changes in host-protective pathways. Bile was collected from PSC patients by endoscopic retrograde cholangiography and from non-PSC controls undergoing cholecystectomies. Biliary bacteria were cultured anaerobically, and 50 colonies per sample were identified by 16S sequencing. No bacteria were isolated from non-PSC controls, while bacteria were cultured from most PSC patients. The PSC bile microbiomes exhibited reduced diversity compared to the gut or oral cavity, with one or two species predominating. The effects of supernatants from seven PSC-associated bacterial isolates on cellular phenotypes were characterized using human colonic (Caco-2), hepatic (HepG2), and biliary (EGI-1) cells. Overall, PSC-associated bacteria produced factors cytotoxic to hepatic and biliary cells. An Enterococcus faecalis isolate, and to a lesser extent a Veillonella parvula isolate, induced epithelial permeability, while Escherichia coli, Fusobacterium necrophorum, and Klebsiella pneumoniae isolates induced inflammatory cytokines in biliary cells. Our data suggest that bacteria cultured from PSC bile induce cellular changes characteristic of PSC pathogenesis, with different isolates inducing distinct cellular responses. Our work provides a starting point for future research into bacterial contributions to PSC with the eventual goal of developing therapies for this disease.IMPORTANCEPrimary sclerosing cholangitis (PSC) is a chronic liver disease in which inflammation and scarring of the bile ducts cause bile to build up in the liver, leading to liver damage and eventually liver failure. The causes of this disease are poorly understood, and the only current treatment is a liver transplant. To develop new treatments, we must first better understand what leads to this disease. We examined whether bacteria isolated from PSC patient bile can cause disease-related responses in human biliary, liver, and intestinal cells. We observed that different PSC-associated bacteria can induce distinct disease-related cellular changes, including inflammation and cell death. These data suggest that the microbial community in PSC patients may indeed be linked to disease development. Our findings provide new starting points for further exploration into the poorly understood origins of PSC.},
}

@article {pmid41114526,
year = {2025},
author = {Schroll, M and Amar, Y and Krüger, P and Neuhaus, K and Djabali, K},
title = {Baricitinib Augments Lonafarnib Therapy to Preserve Colonic Homeostasis and Microbial Balance in a Mouse Model of Progeria.},
journal = {Aging cell},
volume = {},
number = {},
pages = {e70273},
doi = {10.1111/acel.70273},
pmid = {41114526},
issn = {1474-9726},
support = {2022-82//Progeria Research Foundation/ ; },
abstract = {Hutchinson-Gilford Progeria Syndrome (HGPS) is a fatal genetic disorder caused by progerin, a mutant lamin A variant that disrupts nuclear architecture and drives systemic cellular dysfunction. Gastrointestinal (GI) involvement in HGPS remains poorly understood, despite growing evidence of gut abnormalities and microbial dysbiosis in progeroid mouse models. Here, we provide the first comprehensive characterization of colonic pathology in Lmna[G609G/G609G] mice and assess the therapeutic impact of baricitinib (Bar), a JAK-STAT inhibitor, lonafarnib (FTI), the only FDA-approved therapy, and their combination on colonic health. Bar + FTI combination therapy most effectively lowered progerin levels, preserved colonic architecture and epithelial regeneration markers, while also reducing inflammation, cellular senescence, and early fibrotic changes. Notably, FTI monotherapy aggravated inflammation via STAT1 activation, an effect reversed by Bar co-administration. Bar also emerged as the primary driver in mitigating colonic tissue senescence, highlighting its role in supporting intestinal homeostasis. In addition, we observed marked microbial dysbiosis in HGPS mice, particularly in late-stage disease. While both monotherapies induced distinct shifts in gut microbiota, combination therapy preserved a profile more closely resembling healthy controls. These findings expand the current understanding of GI involvement in HGPS and identify the colon as a site where JAK-STAT inhibition enhances the therapeutic profile of FTI.},
}

@article {pmid41114510,
year = {2025},
author = {Leao, L and Esmail, GA and Miri, S and Mottawea, W and Hammami, R},
title = {In vitro modeling of the female gut microbiome: effects of sex hormones and psychotropic drugs.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0235025},
doi = {10.1128/spectrum.02350-25},
pmid = {41114510},
issn = {2165-0497},
abstract = {Sex hormones play a crucial role in shaping gut microbiome composition and metabolism, with significant implications for mental health. This study investigated the effects of sex hormones and the psychotropic drug aripiprazole on the gut microbiome, using a novel in vitro colonic fermentation model adapted from the PolyFermS system. Fecal samples from four male and female donors were used to develop sexually divergent models, with the female model subjected to hormonal treatments mimicking different phases of the menstrual cycle. Microbiome composition and short-chain fatty acid (SCFA) metabolism were analyzed. The results demonstrated that sex hormones significantly influenced microbiota structure and diversity, with the female model exhibiting reduced α-diversity and distinct bacterial associations with SCFAs. Hormonal fluctuations across menstrual phases induced specific shifts in bacterial composition, notably increasing Bacteroidota while decreasing Bacillota and Pseudomonadota. In the female model, aripiprazole treatment led to increased microbial diversity and altered SCFA profiles, although the changes in SCFAs were not statistically significant (P > 0.05). Differential abundance analysis revealed sex-specific enrichment of bacterial genera, such as Eubacterium coprostanoligenes and Agathobacter. These findings underscore the importance of considering sex-specific microbiome profiles and hormonal influences when optimizing psychotropic treatments for mental health disorders.IMPORTANCEThe gut microbiome plays a crucial role in human health, affecting metabolism, immunity, and brain function. However, the role of sex hormones in shaping the gut microbiome composition and metabolism remains largely unexplored. This study introduces a novel in vitro colonic fermentation model to investigate the effects of sex hormone fluctuations and psychotropic drug exposure on the gut microbiome. By simulating a sexually divergent human colon environment and mimicking hormonal variations throughout the menstrual cycle, this model provides a controlled setting for studying microbiome response to external stimuli. Our findings revealed that sex hormones, such as estrogen, progesterone, and testosterone, shape microbial diversity and alter the microbiome composition compared to the control group. Additionally, this study examined the effect of psychotropic drug exposure on the microbiota of a simulated female colon, revealing alterations in the microbial composition and metabolism. These results highlight the importance of considering the role of the gut microbiome in drug response, given the widespread use of psychiatric medications, particularly among women. This novel colonic fermentation model offers a valuable tool for studying sex-specific microbiome dynamics and their broader implications for health.},
}

@article {pmid41114501,
year = {2025},
author = {Gou, L and Luo, G and Xia, Z and Zhang, W and Li, S and Ji'e, K and Gao, T and Abi, K and Yang, F},
title = {Influence of breast milk microbiota on the composition of the early intestinal microbial community in goat kids: a study of composition and correlations.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0264224},
doi = {10.1128/spectrum.02642-24},
pmid = {41114501},
issn = {2165-0497},
abstract = {Colonization of gut microbes in young ruminants plays a fundamental role in their lifelong health. Although the relationship between breast milk (BM) and the gut microbiota of young animals has been reported, its specific impact on goats has yet to be thoroughly explored. Therefore, this study aimed to comprehensively reveal the influence of breast milk feeding on the development of intestinal microorganisms in goat kids and the interactions between breast milk microbiome and fecal microbiome. The results showed that there was a significant difference in the richness of breast milk microbiota between the BMD1, BMD7, and BMD14 groups (P < 0.05). At the genus level, the bacterial microbiota in breast milk across different days of age was predominantly composed of Pseudomonas, Asticcacaulis, Mannheimia, Sphingomonas, and Staphylococcus. In contrast, the fecal microbiota of goat kids was primarily dominated by Escherichia-Shigella, Butyricicoccus, Bacteroides, Lactobacillus, and Limosilactobacillus. Significant correlations (P < 0.05) were observed between the microbial communities of breast milk and the fecal microbiota of goat kids. Specifically, Delftia in breast milk was positively correlated with Limosilactobacillus and Lactobacillus and negatively correlated with Lachnoclostridium in the rectal feces of goat kids, and Lactobacillus in breast milk was positively correlated with Ruminococcus_gnavus_group. These results suggest that the structure of the breast milk microbiota may influence the colonization of the intestinal microbiota in goat kids, especially for some probiotic genera such as Lactobacillus. In conclusion, this study elucidates the dynamic changes in breast milk microbiota and the shifts in goat kid fecal microbiota following breast milk feeding, as well as the correlations between them. These findings provide a scientific foundation for enhancing goat kid growth, development, and health through early microbiota modulation in practical production.IMPORTANCEThe gastrointestinal (GI) microbiota has a profound effect on host health, especially in resisting pathogen colonization and promoting intestinal function (T. Zhong, Y. Wang, X. Wang, A. Freitas-de-Melo, et al., Front Microbiol 13:1020657, 2022, https://doi.org/10.3389/fmicb.2022.1020657). The results show that the stability of rumen microbial communities and their associated functions in lambs is not achieved until they reach at least 20 days of age (B. Brooks, B. A. Firek, C. S. Miller, I. Sharon, et al., Microbiome 2, 2014, https://doi.org/10.1186/2049-2618-2-1). From a nutritional perspective, young animals, such as lambs, can be considered non-ruminants (Y. Li, L. Ren, Y. Wang, J. Li, et al., Nutrients, 14, 2022, https://doi.org/10.1017/S1751731119003148). The gut is not only a key organ for digestion and absorption of nutrients, but also plays a variety of important roles in maintaining overall health. Thus, udder feeding may have a significant effect on the construction of the gut microbiota in lambs until 20 days of age. Although the relationship between breast milk (BM) and the gut microbiota of young animals has been reported, its specific impact on goats has yet to be thoroughly explored. Therefore, this study aimed to comprehensively reveal the influence of breast milk feeding on the development of intestinal microorganisms in goat kids and the interaction relationships between breast milk microbiome and fecal microbiome.},
}

@article {pmid41114498,
year = {2025},
author = {Tarquinio, KM and Farrell, J and Varga, JJ and Zhao, C and Mehlferber, E and Brown, SP},
title = {Mapping the respiratory microbiome in intubated children over time.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0044825},
doi = {10.1128/spectrum.00448-25},
pmid = {41114498},
issn = {2165-0497},
abstract = {Children who require airway intubation are almost always treated with empiric antibiotics, pending clinical microbiology results. Positive pathogen results are near inevitable, due to the frequent presence of potential opportunistic pathogens, whether they are causing disease or not. This pattern leads to potential antibiotic over-prescribing, to the detriment of both patients who do not require antibiotics and to antimicrobial stewardship goals. To assess our hypothesis that opportunistic pathogens are more common in children with prior lung disease, we prospectively profiled tracheal aspirate (TA) microbiome samples in children with and without prior lung disease. An IRB approval was obtained, and TAs were collected longitudinally. Samples were analyzed using 16S rDNA sequencing and conventional cultures. Patient demographics and clinical courses were obtained using electronic medical records. Thirteen subjects were included, producing 39 TA samples. Microbiome analysis identified 98 bacterial genera, dominated by Pseudomonas and Streptococcus. Patient identity was a significant determinant of TA sample variation, indicating a robust individual TA microbiome despite the presence of substantial antibiotic exposures. In contrast, clinical category and time since intubation were not significant predictors, in the context of substantial inter-patient variation. Our results reveal substantial inter-patient variation in TA microbiome structure, limiting our ability to test for significant impacts of clinical category on microbiome structure. Our results provide information for the design of larger-scale studies to evaluate the role of clinical history and specific taxa in governing the interplay between antibiotics and pathogen dynamics in critically ill children.IMPORTANCEClinicians often prescribe empirical antibiotics for critically ill, intubated children with suspected respiratory infections, contributing to antibiotic overuse and challenging antimicrobial stewardship. Our longitudinal tracheal aspirate analysis of cultures and 16S rDNA sequencing revealed significant inter-patient variability, regardless of the primary reason for intubation. We observed both concordance and discrepancies between clinical microbiology and sequencing results-gram-negative organisms aligned well between methods, whereas Streptococcus was detected in 34 of 39 samples by 16S rDNA but only once by culture. Our findings emphasize the value of longitudinal airway microbiome analysis in pediatric patients. Given the heterogeneous pathologies and diverse age groups in pediatric intensive care, future large-scale studies should account for antibiotic exposure, commensal bacterial interactions, and clinical conditions that influence microbiome dynamics. Expanding research in this area could improve our understanding of microbial shifts in critically ill children and inform more targeted treatment strategies.},
}

@article {pmid41114153,
year = {2025},
author = {Bera, S and Fouladi, F and Peddada, S},
title = {Cluster Based Association Measures with Applications.},
journal = {Sankhya. Series B. [Methodological.]},
volume = {},
number = {},
pages = {},
pmid = {41114153},
issn = {0581-5738},
abstract = {It is well recognized that relationships between variables are not always linear or even monotonic. For example, the expressions of cell-cycle, or circadian clock genes, or the abundance of microbes in a dynamic ecology are not expected to be linear. Furthermore, unknown to the researcher, there may be heterogeneous subgroups or clusters in the data. Researchers may be interested in discovering those clusters and derive an overall measure of association between variables of interest accounting for the different clusters as well as deriving associations within each cluster. Although standard concepts of correlations, such as the Pearson or Spearman, are widely used to describe overall associations, they can be misleading in such situations. As researchers continue to generate complex high dimensional data with hidden substructures or clusters, there is an urgent need for a measure that correctly quantifies associations between variables while agnostically accounting for hidden clusters in the data. Using clustering algorithms which are able to detect hidden clusters and association measures which are suitable for quantifying arbitrary relationships within each clusters, we develop a novel association procedure called CLuster based Association Measures (CLAM) to describe association between pairs of univariate as well as multivariate variables. The method is not limited to any specific form of association and is well-suited for heterogeneous data with hidden clusters, which are common in biomedical research. Performance of CLAM is evaluated using a synthetic data as well as real data from diverse applications, such as fission yeast (S. pombe) cell-cycle genes data, intestinal microbiome data from IBD patients, and three well-known imaging data sets, namely DrivFace data, Landsat data, and COIL data.},
}

@article {pmid41114144,
year = {2025},
author = {Shoaib, M and Li, G and Liu, X and Arshad, M and Zhang, H and Asif, M and Brestic, M and Skalicky, M and Wu, J and Zhang, S and Hu, F and Li, H},
title = {Nanoplastic alters soybean microbiome across rhizocompartments level and symbiosis via flavonoid-mediated pathways.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1676933},
pmid = {41114144},
issn = {1664-462X},
abstract = {Plastic pollution, particularly its breakdown into nanoplastics (NPs), poses a significant threat to ecosystem services, with notable effects on soil-plant-microbe interactions in agricultural systems. However, there is limited understanding of how NPs influence the soil microbiome and plant symbiotic functions. In this study, we applied polypropylene (PP) and polyethylene (PE) NPs, measuring 20 to 50 nm, to soybean growing conditions. We evaluated soil physicochemical properties, nodule counts, nitrogenase activity, and bacterial community composition in nodule, rhizosphere, and bulk soil under different concentrations of these NPs (200, 500, and 1000 mg/kg of soil w/w). Our results revealed that the impact of NPs on soil physicochemical properties was type-dependent, with PE-NPs exerting a more pronounced effect on soil enzyme activities than PP-NPs. Both NPs treatments accelerated nodulation and increased nitrogenase activity, with lower doses inducing more significant effects. Furthermore, PE and PP-NPs enriched bacterial species such as Ensifer and Arthrobacter, which positively interact with diazotrophs such as Bradyrhizobium, supporting symbiosis and biological nitrogen fixation. NPs treatments also significantly affected the bacteriome assembly process in the bulk soil, rhizosphere, and nodule, with an increased source ratio from the rhizosphere to the nodule and homogenous selection in the nodule bacteriome, likely benefiting bacteria involved in nodulation. Exposure to 500 mg/kg of both NPs caused alterations in the metabolic exudation profile of the plant rhizosphere, particularly influencing the biosynthesis pathways of flavonoids and isoflavonoids. Metabolites such as genistein and naringenin emerged as key mediators of plant-microbe interactions, further enhancing plant symbiotic processes under NPs exposure. This study demonstrates that NPs influence plants' symbiotic potential both directly, by altering the composition of the soil bacteriome, and indirectly, by affecting exudation potential. It provides strong evidence that NPs, especially those smaller than a micrometer, can have long-term effects on the stability and functionality of agricultural ecosystems.},
}

@article {pmid41114113,
year = {2025},
author = {Wu, TT and Zhou, X and Huang, Q and Yang, Q},
title = {Effectiveness of multi-region 16S rRNA gene sequencing in studying the microbiome of gastric cancer tissues.},
journal = {World journal of gastrointestinal oncology},
volume = {17},
number = {10},
pages = {110997},
pmid = {41114113},
issn = {1948-5204},
abstract = {BACKGROUND: The gastric microbiome is closely associated with gastric cancer, and single-region 16S rRNA sequencing has limitations in analyzing its characteristics, necessitating the search for a better sequencing method.

AIM: To evaluate the effectiveness of multi-region 16S rRNA gene sequencing in studying the microbiome of gastric cancer tissues.

METHODS: Patients with gastric cancer (n = 118) who underwent surgery at Liyang People's Hospital from January 2022 to December 2024 were enrolled. Fifty-nine paraffin-embedded and 59 fresh tissue samples were obtained. The ZymoBIOMICS[TM] microbial community standard and Escherichia coli ATCC 25922 were used as positive controls. Multi-region and single-region 16S rRNA gene sequencing were performed. Species identification, detection rates at varying microbial abundances, operational taxonomic unit (OTU) counts, and alpha diversity indices in gastric cancer tissues were compared between the two methods.

RESULTS: Multi-region 16S rRNA sequencing identified more species (eight species and eight genera) in the positive controls compared with single-region sequencing (one species and six genera). Detection rates at concentrations of 10[3], 10[2], and 10 CFU/mg were significantly higher using multi-region sequencing (P < 0.05). Multi-region sequencing also revealed significantly higher OTU counts and alpha diversity indices (Shannon, Simpson, and Chao1) in gastric cancer tissues (P < 0.05).

CONCLUSION: Compared with single-region sequencing, multi-region 16S rRNA gene sequencing demonstrates superior species resolution and detection sensitivity, providing a more comprehensive profile of microbial diversity in gastric cancer tissues.},
}

@article {pmid41114103,
year = {2025},
author = {Liu, XX and Yang, B and Tang, DX},
title = {Bidirectional regulation of the gut microbiome-immune axis in the immune microenvironment of colorectal cancer and targeted interventions.},
journal = {World journal of gastrointestinal oncology},
volume = {17},
number = {10},
pages = {109503},
pmid = {41114103},
issn = {1948-5204},
abstract = {The initiation and progression of colorectal cancer (CRC) are profoundly influenced by the complex interplay between the gut microbiota and the immune system, underscoring the clinical importance of exploring the bidirectional regulatory mechanisms of the microbiota-immune axis within the CRC immune microenvironment. Emerging evidence indicates that the composition and functional capacity of the gut microbiota play a vital role in modulating the host's immune responses, while the immune system, in turn, can reciprocally regulate the structure and function of the microbiota. Despite significant insights into the role of the microbiota-immune axis in CRC progression, several critical questions remain unanswered-including how microbial heterogeneity affects therapeutic outcomes and the specific consequences of dysregulated regulatory mechanisms on the immune microenvironment. This review aims to provide a comprehensive analysis of the compositional features of the CRC immune microenvironment, examine the bidirectional molecular mechanisms underpinning the microbiota-immune axis, and evaluate the potential of targeted therapeutic strategies, thereby offering novel research perspectives and clinical applications for CRC treatment.},
}

@article {pmid41114048,
year = {2025},
author = {Andermann, TM and Zeng, K and Guirales-Medrano, S and Groth, A and Ramachandran, BC and Sun, S and Sorgen, AA and Hill, L and Bush, AT and Liu, H and Jones, C and Roach, J and Conlon, BP and Rao, G and Chao, NJ and Fodor, AA and Sung, AD},
title = {Duration of Hospitalization is Associated with the Gut Microbiome in Patients Undergoing Hematopoietic Stem Cell Transplantation: Early Results from a Randomized Trial of Home Versus Hospital Transplantation.},
journal = {OBM transplantation},
volume = {9},
number = {3},
pages = {},
pmid = {41114048},
issn = {2577-5820},
abstract = {Home-based hematopoietic stem cell transplantation (HCT) is an innovative care model with growing interest, but its impact on the gut microbiome remains unexplored in a randomized setting. We present interim results from the first randomized controlled trials (RCT) evaluating the effect of HCT location-home versus hospital-on gut microbial diversity and antimicrobial resistance (AMR) gene carriage. We hypothesize that patients randomized to undergo home HCT would have higher gut taxonomic diversity and lower AMR gene abundance compared to those undergoing standard hospital HCT. We analyzed stool samples from the first 28 patients enrolled in ongoing Phase II RCTs comparing home (n = 16) and hospital (n = 12) HCT at Duke University using shotgun metagenomic sequencing to compare taxa and AMR gene composition between groups. We also performed a secondary analysis comparing patients who received transplants at outpatient infusion clinics versus inpatient standard HCT to evaluate the influence of hospitalization duration. In the primary RCT analysis, taxonomic and AMR gene α- and β-diversity were comparable between home and hospital groups, reflecting similar durations of hospitalization despite group allocation. In contrast, secondary analyses demonstrated that patients transplanted in outpatient infusion clinics who experienced significantly reduced hospitalization had higher gut taxonomic α-diversity and differential β-diversity, although AMR gene diversity remained unchanged. In summary, randomization by transplant location did not impact the gut microbiota to the same extent as the duration of hospitalization, although secondary analyses were heavily confounded. Even when taxonomic differences were observed, AMR genes were similar between groups. This RCT represents a novel investigation into how care setting influences the gut microbiome during HCT. Our findings suggest that hospital duration, rather than randomization allocation alone, is the primary driver of microbial disruption. These results underscore the potential for reducing hospital duration to mitigate microbiome injury, thereby informing future interventions to reduce infection risk and improve patient outcomes.},
}

@article {pmid41114005,
year = {2025},
author = {Sun, R and Xu, W and Xu, Y and Xu, Z and Tan, Y and Li, J and Liu, H and Yung, CCM},
title = {Environmental gradients shape viral-host dynamics in the Pearl River estuary.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf164},
pmid = {41114005},
issn = {2730-6151},
abstract = {Marine viruses play critical roles in shaping microbial communities and driving biogeochemical cycles, yet their dynamics in estuarine systems are not well characterized. Here, we conducted a comprehensive metagenomic analysis of viral communities and virus-host interactions across the Pearl River estuary, a dynamic subtropical estuary in southern China. Using 24 metagenomic libraries from eight sampling sites, we identified 29,952 viral populations, with Uroviricota and potential Uroviricota accounted for 80.48% of taxa, underscoring their ecological importance. A key finding of our integrated analysis is the unexpectedly high abundance of nucleocytoplasmic large DNA viruses in offshore waters, which suggests a more significant role for eukaryotic viruses in coastal ecosystems than previously acknowledged and correlates with elevated levels of their eukaryotic hosts. Environmental variables, particularly salinity and nutrient availability, emerged as key drivers of viral and host distribution patterns. By linking environmental gradients to distinct community "envirotypes" and their underlying genomic features, we revealed novel virus-host interactions and highlighted the impact of environmental gradients on microbial ecology. Additionally, viral auxiliary metabolic genes linked to phosphorus and nitrogen metabolism suggest critical roles in modulating host metabolic pathways and influencing nutrient cycling. Our findings demonstrate how spatial heterogeneity and environmental gradients shape viral and microbial ecology in estuarine ecosystems. Our findings provide a holistic, multi-domain view of microbial and viral ecology, demonstrating how integrating prokaryotic, eukaryotic, and viral community analyses offers a more complete understanding of ecosystem function in these critical transition zones.},
}

@article {pmid41113903,
year = {2025},
author = {Cheng, CH and Hung, CC and Wu, CY and Lin, CM and Fang, JT and , },
title = {Beyond the Pillow: Linking Subjective and Objective Sleep Measures to Gut Microbiome Composition in Community-Dwelling Older Adults.},
journal = {Nature and science of sleep},
volume = {17},
number = {},
pages = {2657-2668},
pmid = {41113903},
issn = {1179-1608},
abstract = {BACKGROUND: Sleep-related complaints are common among older adults, and recent research indicates that changes in sleep patterns may be associated with alterations in the composition of the gut microbiome (GM). However, investigations into the relationship between sleep measures and GM abundance among older adults have been limited thus far. This study represents the first large-scale effort to comprehensively explore the connection between GM composition and both subjective and objective sleep measures in older adults.

METHODS: The study included 279 cognitively-normal older adults from the community who had not used sleep medication, antibiotics, or probiotics for at least one month before providing stool samples. Participants were categorized as good sleepers (GS) or poor sleepers (PS) based on the Pittsburgh Sleep Quality Index (PSQI) scores. GM diversity and relative abundance were compared between both groups, and their associations with PSQI scores and objective sleep measures were also examined.

RESULTS: Alpha and beta diversity did not show significant differences between the GS and PS groups. However, significant differences in GM relative abundance across various taxonomic levels were found between the GS and PS groups. In the overall sample, higher PSQI scores were linked to lower abundance of the species Hungatella_hathewayi (p = 0.005, false discovery rate = 0.035). However, there were no significant associations between GM abundance and objective sleep measures after corrections for multiple comparisons.

CONCLUSION: These findings suggest that specific gut microbial taxa are associated with subjective sleep disturbances in older adults.},
}

@article {pmid41113721,
year = {2025},
author = {Ou, Y and Wang, H and Zhou, C and Chen, Y and Lyu, J and Feng, M and Huang, X},
title = {Endometriosis-associated infertility: Multi-omics insights into pathogenesis and precision therapeutics.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1613334},
pmid = {41113721},
issn = {1664-2392},
mesh = {Humans ; *Endometriosis/complications/therapy/metabolism/genetics ; Female ; *Infertility, Female/etiology/therapy/metabolism ; *Precision Medicine/methods ; Multiomics ; },
abstract = {INTRODUCTION: Endometriosis is a prevalent, estrogen-dependent, inflammatory disease that impairs fertility via hormonal dysregulation, immune dysfunction, oxidative stress/ferroptosis, genetic and epigenetic alterations, and microbiome imbalance. We summarize multi-omics insights and clinical implications for endometriosis-associated infertility.

METHODS: This article is a Systematic Review that synthesizes recent multi-omics and clinical evidence on mechanisms (hormonal, immune-inflammatory, oxidative stress/ferroptosis, genetic/epigenetic, microbiome/metabolic) and appraises therapeutic strategies spanning surgery, hormonal suppression, assisted reproductive technologies (ART), and emerging adjuncts. Mechanistic and clinical findings are integrated to map targets, biomarkers, and precision-care opportunities across disease phenotypes.

RESULTS: Evidence indicates local estrogen dominance with progesterone resistance, pervasive immune dysregulation, and oxidative stress with iron-driven ferroptosis that particularly injures granulosa cells, alongside disease-relevant genetic/epigenetic regulators and reproductive-tract/gut microbiome dysbiosis. Clinically, endometriosis detrimentally affects ovarian reserve and oocyte competence, disrupts endometrial receptivity/decidualization, and remodels pelvic anatomy through adhesions and fibrosis, cumulatively reducing fecundity. Current management includes laparoscopic excision/ablation, hormonal suppression (e.g., progestins, GnRH analogs/antagonists), and ART tailored to goals and disease severity. Adjunctive antioxidant and immune-modulating approaches show promise but require robust clinical validation. Biomarker discovery-including epigenetic regulators and microbiome-derived signals-may enable earlier diagnosis and personalization. Innovative avenues include immunotherapy targeting nociceptor-immune crosstalk, ferroptosis modulation, microbiota manipulation, and diet-based metabolic strategies.

DISCUSSION: The pathogenesis of endometriosis-associated infertility is multifactorial and interconnected. While current treatments offer benefits, their efficacy is variable. The integration of multi-omics data is unveiling novel diagnostic biomarkers and therapeutic targets. Future management requires a patient-centered, multidisciplinary precision medicine approach that combines mechanistic insights with individualized treatment strategies to improve reproductive outcomes across the disease spectrum.},
}

Humans
*Endometriosis/complications/therapy/metabolism/genetics
Female
*Infertility, Female/etiology/therapy/metabolism
*Precision Medicine/methods
Multiomics

@article {pmid41113655,
year = {2025},
author = {Mote, S and De, K and Nanajkar, M and Gupta, V},
title = {Unraveling the bacterial composition of a coral and bioeroding sponge competing in a marginal coral environment.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1550446},
pmid = {41113655},
issn = {1664-302X},
abstract = {The newly described bioeroding sponge Cliona thomasi, part of the Cliona viridis complex, is contributing to coral decline in the central eastern Arabian Sea, the West Coast of India. While its morphological and allelopathic mechanisms in coral invasion are well investigated, the role of its microbial communities in spatial competition is underexplored. This study focuses on the coral Turbinaria mesenterina and sponge C. thomasi, both known for their distinct symbiotic associations with Symbiodiniaceae. A 16S rRNA V3-V4 amplicon next-generation sequencing approach, followed by processing through the DADA2 algorithm, was used to analyze the bacterial composition. The results showed higher bacterial richness and diversity in coral samples, identifying 30 distinct phyla, compared to 14 in sponge samples. The coral samples were dominated by Proteobacteria, Actinobacteria, Firmicutes, Cyanobacteria, Planctomycetes, Chloroflexi, and Patescibacteria, while Proteobacteria, Cyanobacteria, Planctomycetes, and Actinobacteria were dominant in the sponge. Enrichment analysis revealed higher dominance of Acidobacteria, Actinobacteria, Chloroflexi, Dadabacteria, Firmicutes, Fusobacteriota, and Patescibacteria in the coral samples, while the sponge samples showed enrichment for Cyanobacteria, Planctomycetes, and Bdellovibrionota. Beta-diversity analysis (PERMANOVA and nMDS) showed significant differences, with an average dissimilarity of 81.44% between sponge and coral samples (SIMPER). These differences highlight variations in microbial profiles between sponges and corals, competing in the same vulnerable environment. Exploring the microbiome aspect, therefore, may elucidate physiological and ecological functions of the holobiont while also representing a health status biomarker for corals, supporting their conservation.},
}

@article {pmid41113651,
year = {2025},
author = {Lan, R and De Paula Ramos, L and Chen, Z and Carrouel, F},
title = {Editorial: Exploring the oral-gut microbiome interactions: pathways to therapeutic strategies and implications for systemic health.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1691238},
pmid = {41113651},
issn = {1664-302X},
}

@article {pmid41113648,
year = {2025},
author = {Dong, L and Du, Y and Qiu, F and Zhang, M and Wang, X and Zhu, X and Yao, Y and Li, J and Ji, X and Zhu, X},
title = {Metagenomic insights reveal the differences in the community composition and functional characteristics of the sea turtle microbiomes based on host species and tissue region.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1652229},
pmid = {41113648},
issn = {1664-302X},
abstract = {INTRODUCTION AND METHODS: Sea turtles have been proposed as health indicators of marine ecosystems for their characteristic of longevity and migratory, but they are facing serious threats due to various factors. The microbial communities within animals play an important role in health and disease. Our study aims to explore a thorough evaluation of the sea turtle microbiome by examining the oral, nasal, and cloacal microbial communities of three species: green turtles, hawksbills, and loggerheads, through metagenomic sequencing.

RESULTS: Utilizing approximately 705.81 GB of metagenomic sequencing data from 63 samples collected from different turtle species and tissue regions, we created a nonredundant sea turtle microbial gene catalog (STMGC) containing 10,733,232 unique genes through the de-redundancy of open reading frames (ORFs). Our findings revealed that the sea turtle microbiomes were primarily composed of Pseudomonadota (formerly Proteobacteria) and Bacteroidota (formerly Bacteroidetes). The tissue region was a key factor affecting the variability in the sea turtle microbiome, with green turtles showing notable differences among the three turtle species. Pseudomonadota was significantly more abundant in oral samples, while Bacteroidota was more prevalent in nasal samples. Campylobacterota was identified as significantly more abundant in cloacal samples. Importantly, we discovered 389 genera and 1,445 species of potential pathogens within the sea turtle microbiome, indicating potential pathogenic risks that warrant further investigation alongside culturomics. Additionally, our study highlighted significant functional differences among the three turtles and tissue regions. It is worth noting that among the three sea turtles, antibiotic resistance genes are more prevalent in hawksbills, while virulence genes are more abundant in loggerheads. Moreover, within the three tissue regions, antibiotic resistance genes are higher in oral samples, while virulence genes are more extensive in cloacal samples.

CONCLUSION: The findings in our study demonstrate that the microbial composition and function in these sea turtles exhibit both species-specific and region-specific variations. The implications of these associations and the underlying mechanisms not only provide valuable insights for future studies on the microbial communities of turtles, but also lay the foundation for further research on the health interrelationships among sea turtles, marine and terrestrial animals, humans and the environment, and for defining "One Health" factors.},
}

@article {pmid41113646,
year = {2025},
author = {Chen, X and Wu, J and Fan, D and Zhang, P and Li, Y and Cao, Y and Cao, M},
title = {Gut viral metagenomics identifies viral signatures and their role in depression.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1573851},
pmid = {41113646},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiome has been implicated in the onset and progression of depression. Yet, the role of the gut virome in depression remains unexplored, and a diagnostic model has not been satisfactorily constructed.

METHODS: Herein, we analysed the gut virome profiles of 29 patients with depression and 33 healthy controls using bulk metagenome sequencing.

RESULTS: A total of 45 differentially abundant viral taxa were identified, among which four, s_Stenotrophomonas_virus_Pokken, g_Pokkenvirus, s_Dickeya_virus_AD1, and g_Alexandravirus, demonstrated strong diagnostic potential (AUCs > 0.8). These four viruses also exhibited strong correlations, suggesting they may constitute a synergistic ecological cluster. Function annotation revealed seven metabolic pathways with significant differences, including alanine, aspartate, and glutamate metabolism, branched-chain amino acid (BCAA) biosynthesis, and energy metabolism in patients with depression.

CONCLUSION: This study identified four distinct viral signatures for depression and proposes novel viral biomarkers for the diagnosis of depression, offering a robust diagnostic approach and new insights into the pathological mechanisms of depression.},
}

@article {pmid41113645,
year = {2025},
author = {Durán-González, E and Ramírez-Tejero, JA and Pérez-Sánchez, M and Morales-Torres, C and Gómez-Morano, R and Díaz-López, C and Martínez-Lara, A and Cotán, D},
title = {Fibromyalgia diagnosis from a multi-omics approach: a gut feeling.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1641185},
pmid = {41113645},
issn = {1664-302X},
abstract = {BACKGROUND: Fibromyalgia is a complex disorder whose main symptoms are chronic widespread pain and fatigue and affects between 0.2 and 6.6% of the world population. Nowadays, there are no molecular biomarkers that could facilitate diagnosis. The latest efforts by researchers have focused on studying problems at the level of central nervous system sensitivity, inflammation, and oxidative disorders.

METHODS: A total of 892 women were initially enrolled in the study. For individuals who met the inclusion criteria, a plasma proteome analysis was conducted using blood samples. Briefly, blood was collected, centrifuged, and analyzed by liquid nano-chromatography coupled to tandem mass spectrometry. After the raw data analysis, proteins with statistically significant differential abundance and a fold change over 1.2 (20% increase in fibromyalgia compared with control samples) or under 0.8 (20% decrease in fibromyalgia compared with control samples) in fibromyalgia were selected. For fecal metagenome analysis, fecal samples were collected and processed for DNA extraction. Amplicon sequencing of V3-V4 regions from the 16S ribosomal RNA gene was performed using the Illumina MiSeq platform. The statistical analysis was conducted using R v4.3.2 base packages.

RESULTS: After applying exclusion criteria, 242 women (199 patients and 43 age- and environmentally paired controls) provided plasma and feces samples, as well as properly filled health questionnaires. A total of 30 proteins and 19 taxa were differentially expressed in fibromyalgia patients, and their integration into an algorithm allows for discrimination between cases and controls. The multi-omic approach for biomarker discovery in this study proposes a multifactorial connection between gut microbiota and mitochondria-derived oxidative stress and inflammation.

CONCLUSIONS: Plasma and fecal multi-omics analysis suggest an intricate and multifactorial connection between gut microbiota and mitochondria-derived oxidative stress and inflammation in FM patients, with glyceraldehyde-3-phosphate dehydrogenase and Streptococcus salivarius as leading actors.

TRIAL REGISTRATION: NCT05921409.},
}

@article {pmid41113638,
year = {2025},
author = {Verma, D and Zhang, Z and Liu, J},
title = {Editorial: Tobacco disease and biological control.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1694523},
pmid = {41113638},
issn = {1664-302X},
}

@article {pmid41113630,
year = {2025},
author = {Ngari, C and Poulet, V and Percoco, G and Peno-Mazzarino, L and Seyer, D},
title = {Early skin colonization by Staphylococcus epidermidis and Staphylococcus aureus reveals environment-dependent synergistic effects.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1677214},
pmid = {41113630},
issn = {1664-302X},
abstract = {INTRODUCTION: The skin microbiome is crucial for skin health and homeostasis. It contributes to immune defense, promotes epidermal differentiation, and supports a robust skin barrier function. Despite its importance, few studies have used model skin systems to examine how simple bacterial communities interact and how they impact the skin.

METHODS: We studied the interaction between a skin commensal, Staphylococcus epidermidis, and a pathogen, Staphylococcus aureus, by performing inoculations and co-inoculations on Reconstructed Human Epidermis (RHE) models maintained under classical humid conditions (>90% relative humidity) or dry conditions (<25% RH). In parallel, inoculations were conducted on human skin explants using a novel culture setup preserving physiological humidity levels (40-60% RH). Bacterial attachment was assessed 4 h post-inoculation. At 24 h, histology was examined, three natural moisturizing factors (NMFs) were quantified. Filaggrin (FLG) and ceramide levels were analyzed to assess the skin barrier function.

RESULTS: In contrast to previous findings at 24 h, co-inoculation increased S. epidermidis and S. aureus attachment in RHEs, but only under humid conditions. Only RHE maintained in dry conditions and skin explant revealed an effect of co-inoculation on filaggrin (FLG), yet an increase in RHEs and a decrease in skin explants. In both RHEs maintained in dry conditions and skin explants, NMF levels were consistently reduced following co-inoculation. In RHEs and skin explants, inoculation with S. aureus alone also lowered NMFs, with co-inoculation further amplifying this effect. Finally, ceramide levels increased similarly across both inoculations and co-inoculation.

DISCUSSION: Revealing unexpected early interactions between S. epidermidis, S. aureus, and the skin, our results could suggest that co-inoculation may trigger a synergetic disruption of the barrier function. Alternatively, it could imply that co-inoculation might reinforce the epidermal barrier via a S. aureus-mediated stimulation of the protective functions of S. epidermidis. Further studies are needed to confirm these effects and determine whether they are strain-specific or more broadly applicable.},
}

@article {pmid41113141,
year = {2025},
author = {Waseem, MH and Abideen, ZU and Shoaib, A and Rehman, N and Osama, M and Sajid, B and Ahmad, R and Fahim, Z and Ansari, MW and Aimen, S and Cheema, AH and Thada, PK},
title = {Fecal Microbiota Transplantation for Treatment of Parkinson's Disease: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.},
journal = {Journal of central nervous system disease},
volume = {17},
number = {},
pages = {11795735251388781},
pmid = {41113141},
issn = {1179-5735},
abstract = {BACKGROUND: Emerging evidence has indicated gut dysbiosis as a potential modifiable contributor to the pathogenesis of Parkinson's disease (PD). Fecal microbiota transplantation (FMT), a microbiome-centric model aimed at modulating the intestinal microbial taxa, represents a novel therapeutic approach. However, its safety and efficacy profile in improving PD symptoms remains inadequately researched.

METHODS: PubMed, ScienceDirect, and the Cochrane Central Registry were searched to retrieve relevant articles from inception till February 2025. Risk ratios (RR) and Mean differences (MD), along with 95% confidence intervals (CI), were pooled under the random-effect model for dichotomous and continuous outcomes, respectively. The primary outcomes of interest were change in Movement Disorder Society Unified Parkinson's Disease Rating Scale part 1 (MDS-UPDRS 1), change in MDS-UPDRS 2. Secondary endpoints of interest were change in MDS-UPDRS 3 (on medication), change in MDS-UPDRS 3 (off medication), change in MDS-UPDRS 4, change in Irritable Bowel Severity Scoring System (IBS-SSS), change in Montreal Cognitive Assessment (MoCA), change in Parkinson Disease Questionnaire Summary Index (PDQ-39 SI), and GI adverse events. The Cochrane Risk of Bias 2.0 (RoB 2.0) tool was used for the quality assessment of the included randomized controlled trials (RCTs). A Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) assessment was done for the certainty of evidence.

RESULTS: This systematic review and meta-analysis included 145 patients across 3 RCTs. FMT and placebo were comparable regarding the primary outcomes that include MDS-UPDRS Part I (MD = -0.36; 95% CI:[-2.18,1.45]; P = .70; I[2] = 33%), Part II (MD = -0.46; 95% CI:[-1.91,0.99]; P = .53; I[2] = 0%). The secondary outcomes, involving MDS-UPDRS Part III on-medication (MD = 1.41; 95% CI:[-2.14,4.42]; P = .50; I[2] = 17%), Part III off-medication (MD = 1.26; 95% CI:[-2.27,4.79]; P = .48; I[2] = 0%), and Part IV (MD = -0.39; 95% CI:[-1.63,0.85]; P = .54; I[2] = 24%) were also comparable between the two groups. No significant changes were observed in IBS-SSS (MD = -15.91; 95% CI:[-63.17,31.89]; P = .51; I[2] = 76%), PDQ-39 SI (MD = -2.13, 95% CI:[-5.62,1.36]; P = .23; I[2] = 0%), and MOCA scores (MD = 0.11; 95% CI:[-1.34,1.57]; P = .88; I[2] = 68%). However, the FMT group had more frequent adverse gastrointestinal events (RR = 3.32; 95% CI: [1.01,10.87]; P = .05; I[2] = 39%).

CONCLUSION: FMT shows no evidence of superiority compared to placebo. Variations in the findings of existing studies suggest that donor fecal composition, host-microbiota interactions, and methodological heterogeneity may determine outcomes. Further RCTs employing tailored microbiota and standardized endpoint metrics are required to establish a correlation between FMT and PD.},
}

@article {pmid41113084,
year = {2025},
author = {Curto, A and Iamello, RG and Lynch, EN and Galli, A},
title = {Advancing the management of primary biliary cholangitis: From pathogenesis to emerging therapies.},
journal = {World journal of clinical cases},
volume = {13},
number = {30},
pages = {109028},
pmid = {41113084},
issn = {2307-8960},
abstract = {Primary biliary cholangitis is a chronic cholestatic autoimmune liver disease that progressively damages the bile ducts, leading to cholestasis and, in advanced stages, cirrhosis. While it primarily affects middle-aged women, recent data indicate a rising incidence in men. The interplay between genetic susceptibility, environmental exposures, and gut microbiome alterations is thought to drive disease onset. Diagnosis relies on persistent cholestatic enzyme elevation, disease-specific autoantibodies, and, in select cases, liver biopsy. Ursodeoxycholic acid remains the cornerstone of treatment, but many patients show an incomplete response. The recent withdrawal of obeticholic acid from the market, due to insufficient evidence of long-term benefit, has highlighted the urgent need for effective second-line therapies. Agonists of peroxisome proliferator- activated receptors, such as elafibranor and seladelpar, have demonstrated promising biochemical improvements and may reshape the therapeutic landscape. Future research is focused on refining risk assessment, optimizing treatment combinations, and addressing symptoms such as fatigue and pruritus to enhance patient well-being. A shift toward early intervention and personalized treatment strategies may further improve long-term outcomes in primary biliary cholangitis.},
}

@article {pmid41112829,
year = {2025},
author = {Tansarawut, P and Boonsoongnern, P and Kamlangdee, A and Woonwong, Y and Boonsoongnern, A},
title = {Gut Health Evaluation Using Gut Microbiome and Intestinal Alkaline Phosphatase Levels in Postweaning Diarrhoea.},
journal = {Veterinary medicine international},
volume = {2025},
number = {},
pages = {4499017},
pmid = {41112829},
issn = {2090-8113},
abstract = {Postweaning diarrhoea (PWD) poses a significant threat to the swine industry by causing notable declines in productivity and mortality. Gut health diagnosis in pigs typically involves complex methods such as gut microbiome analysis, which can be costly and can require specialised skills. This study aimed to assess gut health in postweaning piglets by measuring and comparing gut microbiome profiles and levels of intestinal alkaline phosphatase (IALP) in faecal samples from pigs with and without PWD. This study revealed significant differences between the nondiarrhoea and diarrhoea groups of piglets in terms of IALP levels and gut microbiome composition. Nondiarrhoeal piglets had greater IALP levels than did diarrhoeal piglets (p=0.003). Additionally, faecal flora richness (observed (p=0.0007) and Chao1 (p=0.0007)) indices of the faecal microflora in the nondiarrhoeal pigs. At the phylum level, Firmicutes and Bacteroidetes were predominantly abundant in both groups, while Firmicutes (p=0.0008) and Patescibacteria (p=0.0334) showed significantly lower abundances in the nondiarrhoea group and Bacteroidetes (p=0.0003) exhibited greater abundance. The Clostridia class was significantly more abundant in the diarrhoea group than the nondiarrhoea group (p=0.0159). The diarrhoea group had a significantly greater relative abundance of the Clostridiaceae family than did the nondiarrhoea group (p=0.0007). At the genus level, the relative abundance of Prevotellaceae NK3B31 was significantly greater in the nondiarrhoea group than the diarrhoea group (p=0.0032). Moreover, the relative abundances of some pathogenic bacteria, including Clostridium sensu stricto (Clostridiaceae) 1, were significantly greater in the diarrhoea group than in the nondiarrhoea group (p=0.0007). IALP levels and gut microbiome diversity in faecal samples can be used to assess the gut health of nursery pigs. These results contribute to the understanding and manipulation of postweaning piglet gut health.},
}

@article {pmid41112728,
year = {2025},
author = {Zhou, Z and Liu, B and Shen, J and Yan, C and Yang, G and Zhang, Y and Zhao, J and Chen, L},
title = {Milk fat globule membrane supplementation in formula modulates the gut microbiome and metabolic status of piglets and normalizes intestinal development.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1632519},
pmid = {41112728},
issn = {2296-861X},
abstract = {Milk fat globule membrane (MFGM) supplementation of infant formula demonstrates potential efficacy in modulating gut microbiota and metabolic profiles. However, the associated site-specific effects on intestinal microbial composition remain unclear. In this study, we used a neonatal piglet model to investigate the mechanisms associated with the metabolic regulation of supplemental MFGM and characterized the compartment-specific modulatory effects on intestinal microbial communities. A total of 20 piglets were randomly allotted to one of the following three groups: breastfed (BF), standard formula (SF), and MFGM-supplemented formula (EF). These diets were administered until weaning, with subsequent provision of commercial feed until euthanasia. Morphometric, microbial, and serum metabolomic analyses revealed that compared to piglets in the SF group, those in the EF group were characterized by significantly enhanced jejunal villus height (p < 0.05) and reduced cecal Oxalobacter (p < 0.05) and Pasteurella abundances, which were comparable to the levels detected in the BF group. Metabolically, piglets in the SF group demonstrated significantly lower levels of tyrosine, phenylalanine, and β-alanine (p < 0.05) and higher levels of 3-methyl-2-oxovalerate (p < 0.05) than those in BF piglets. In contrast, compared to the SF piglets, EF piglets exhibited significantly elevated levels of betaine (p < 0.05) and lysine. Spearman's correlation analysis revealed significant positive associations between Oxalobacter abundance and creatinine, dimethyl sulfone, phenylalanine, tyrosine, and β-alanine concentrations, with inverse correlations observed for 3-methyl-2-oxovalerate and lysine levels. In conclusion, these findings revealed that MFGM supplementation contributes to maintaining a normal intestinal architecture, modulates site-specific microbiota, and mitigates metabolic disparities between formula-fed and breastfed neonates. Notably, these effects are primarily mediated via choline pathway regulation and competitive inhibition of pathogenic bacteria.},
}

@article {pmid41112578,
year = {2025},
author = {Chen, J and Xu, Q and Zhang, L and Zhang, D and Wu, X},
title = {Enrichment of prevotella melaninogenica in the lower respiratory tract links to checkpoint inhibitor pneumonitis and radiation pneumonitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1594460},
pmid = {41112578},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; Middle Aged ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; *Radiation Pneumonitis/microbiology ; *Prevotella/isolation & purification/genetics/classification ; Microbiota ; Lung Neoplasms/drug therapy ; *Immune Checkpoint Inhibitors/adverse effects ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Pneumonia/microbiology ; Lung/microbiology ; },
abstract = {BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) and radiation pneumonitis (RP) lead to anti-cancer therapy discontinuation and poor diagnosis. The human microbiome is related to various respiratory diseases. However, the role of the lung microbiome in CIP and RP remains unknown. Our study aimed to explore the lower respiratory tract (LRT) microbiome in CIP/RP patients.

METHODS: The study enrolled 61 patients with pneumonitis or pneumonia, including 23 with CIP/RP, and 38 with lung cancer with pneumonia (LC-P). Metagenomic next-generation sequencing (mNGS) was performed to identify the microbiota in bronchoalveolar lavage fluid (BALF), and bioinformatics methods were used to compare the microbial differences between CIP/RP and LC-P groups. Correlation analysis was conducted to explore the relationship between LRT microbiota and clinical features.

RESULTS: The Prevotella was the dominant genus in both groups. The Prevotella melaninogenica, which belongs to the Prevotella genus, was the dominant species in the CIP/RP group and the second most abundant species in the LC-P group. Compared to the LC-P group, the CIP/RP group had significantly high levels of Prevotella melaninogenica species and lymphocyte percentage in BALF but significantly low levels of lymphocytes, eosinophils and albumin in peripheral blood. In addition, the Prevotella melaninogenica species had a negative correlation with peripheral blood lymphocytes.

CONCLUSION: The enrichment of Prevotella melaninogenica species in LRT and a decreased level of peripheral blood lymphocytes are associated with CIP/RP.},
}

Humans
Male
Female
Middle Aged
Aged
Bronchoalveolar Lavage Fluid/microbiology
*Radiation Pneumonitis/microbiology
*Prevotella/isolation & purification/genetics/classification
Microbiota
Lung Neoplasms/drug therapy
*Immune Checkpoint Inhibitors/adverse effects
High-Throughput Nucleotide Sequencing
Metagenomics
*Pneumonia/microbiology
Lung/microbiology

@article {pmid41112491,
year = {2025},
author = {Kumari V S, S and Potdar, V and Shinde, M and Parashar, D and Alagarasu, K and Cherian, S and Lavania, M},
title = {Dysbiosis of the oropharyngeal microbiota in COVID-19: distinct profiles in patients with severe respiratory symptoms.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2569523},
pmid = {41112491},
issn = {2000-2297},
abstract = {BACKGROUND: COVID-19 has been strongly associated with alterations in the oropharyngeal microbiota, yet the microbial features linked to disease severity remain unclear.

OBJECTIVE: This study aimed to elucidate the microbial signatures associated with COVID-19 disease severity.

DESIGN: 16S rRNA gene sequencing was employed to profile the oropharyngeal microbiota of patients with varying degrees of COVID-19 severity.

RESULTS: A significant reduction in alpha diversity suggests a major microbial dysbiosis in critically ill patients compared to less severe cases and healthy individuals, whereas beta diversity analysis revealed a broadly conserved community structure across different groups. Comparative analysis showed significant depletion of the phylum Fusobacteriota and enrichment of bacterial families, including Corynebacteriaceae, Methylobacteriaceae, Acetobacteraceae, Bradyrhizobiaceae, Lactobacillaceae, Staphylococcaceae, Propionibacteriaceae, and Moraxellaceae. Rothia mucilaginosa was notably enriched in patients with severe respiratory symptoms, and many of the enriched taxa are known opportunistic pathogens associated with respiratory infections.

CONCLUSION: The marked dysbiosis and enrichment of opportunistic pathogens in the oropharyngeal microbiota of critically ill patients indicate their possible role in respiratory complications. The identified microbial patterns highlight the potential of microbiome profiling as a tool for disease prognosis and guide further research into the role of microbes in COVID-19 pathogenesis and implications for treatment protocols.},
}

@article {pmid41112298,
year = {2025},
author = {Ma, T and Zhang, T and Peng, C and Liu, K and Xiong, Y and Chen, K and Peng, N and Wei, Z and Kuang, J and Ou, L},
title = {Immune cells: the key mediator between the gut microbiota and osteoporosis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1680021},
pmid = {41112298},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Osteoporosis/immunology/microbiology/metabolism/therapy/etiology ; Animals ; Bone and Bones/immunology/metabolism ; Probiotics ; },
abstract = {As the body's largest immunological interface, the intestine harbors a complex ecosystem of gut microbiota (GM) that orchestrates mucosal immune maturation while sustaining local immunological equilibrium. Emerging evidence reveals the gut's influence on skeletal homeostasis via neuro-immune-endocrine pathways-termed the gut-bone axis-though its mechanistic intricacies remain incompletely defined. Since the concept of osteoimmunology was proposed in 2000 by Arron & Choi, immune-skeletal interactions have garnered significant research traction. Immune cells primarily contribute to the maintenance of bone homeostasis through the release of pro- and anti-inflammatory factors. Consequently, the immune system represents a crucial intermediary in understanding the relationship between GM and metabolic bone diseases. This review synthesizes the interrelationships among gut microbiota, immune cells, and osteoporosis, and elucidates how GM modulate bone metabolism in osteoporosis through this critical intermediary. Furthermore, building upon the microbiome-immune-bone axis, we highlight several emerging microbiota-targeted interventions-such as probiotics, prebiotics, dietary modifications, fecal microbiota transplantation, and engineered microbes-and evaluate their clinical translational potential, with the aim of advancing diagnostic and therapeutic strategies for metabolic bone disorders.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Osteoporosis/immunology/microbiology/metabolism/therapy/etiology
Animals
Bone and Bones/immunology/metabolism
Probiotics

@article {pmid41112283,
year = {2025},
author = {Pei, X and Yu, M and Wang, Y and Zong, S and Qi, F and Wang, K},
title = {What is the relationship between microorganisms in the human body and upper tract urothelial carcinoma?.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1636782},
pmid = {41112283},
issn = {1664-3224},
mesh = {Humans ; *Microbiota/immunology ; *Urologic Neoplasms/microbiology ; Tumor Microenvironment/immunology ; *Carcinoma, Transitional Cell/microbiology ; },
abstract = {Upper Tract Urothelial Carcinoma (UTUC) is a highly malignant tumor originating from the epithelium of the upper urinary tract with diverse pathogenesis, but currently available diagnostic and therapeutic strategies have some limitations. In recent years, human microbiome-related studies have provided new ideas for the exploration of the pathogenesis and treatment of UTUC. In this paper, we review the research progress of human microbiome related to UTUC. Focusing on the urinary microbiome, the role of the microbiome in the pathogenesis of UTUC is investigated through the mechanisms of chronic inflammation, genotoxic damage, immune microenvironmental imbalance and metabolic reprogramming. The pyelo-ureteric microbiome of healthy populations is dominated by commensal bacteria such as Lactobacillus and Streptococcus, whereas pathogenic bacteria such as Escherichia coli (E. coli) and Enterococcus faecalis are significantly enriched in patients with UTUC, which results in the development of DNA damage, inflammatory response and immunosuppression. In addition, microbiome metabolites (e.g., short-chain fatty acids, tryptophan derivatives) can influence tumor progression by modulating immune checkpoints (e.g., PD-1/PD-L1, B7-H4) and metabolic pathways (e.g., Warburg effect). In diagnostic and therapeutic applications, urinary microbial markers (e.g., E. coli-specific gene clusters) can be combined with circulating tumor DNA (ctDNA) assays to improve diagnostic sensitivity and specificity, and indices of intestinal flora diversity (e.g., Simpson's index) are significantly correlated with the response rate to chemotherapy and prognostic course. In the future, we need to overcome the challenges of difficult sample acquisition, unknown causal mechanisms, and etiologic heterogeneity interference, and promote multi-omics joint modeling as well as cross-ethnicity and geographic research, and bidirectional regulation mechanisms of the gut-kidney axis in order to develop more accurate UTUC diagnosis and treatment strategies.},
}

Humans
*Microbiota/immunology
*Urologic Neoplasms/microbiology
Tumor Microenvironment/immunology
*Carcinoma, Transitional Cell/microbiology

@article {pmid41112258,
year = {2025},
author = {Filippi Xavier, L and Gacesa, R and da Rocha, GHO and Broering, MF and Scharf, P and Lima, FDS and Faber, KN and Harmsen, H and Hoffmann, C and Farsky, SHP},
title = {Annexin A1 levels affect microbiota in health and DSS-induced colitis/inflammatory bowel disease development.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1679071},
pmid = {41112258},
issn = {1664-3224},
mesh = {Animals ; *Annexin A1/genetics/metabolism ; *Gastrointestinal Microbiome ; Humans ; Mice ; Mice, Knockout ; *Colitis/chemically induced/microbiology/metabolism ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; *Inflammatory Bowel Diseases/microbiology/metabolism ; Female ; Disease Models, Animal ; Dysbiosis ; Feces/microbiology ; Adult ; Middle Aged ; },
abstract = {BACKGROUND: Inflammatory Bowel Diseases (IBDs) are characterized by intestinal dysbiosis and immune dysregulation. Annexin A1 (AnxA1) promotes epithelial repair and inhibits immune responses during IBD. However, AnxA1's impact on gut microbiota during IBD remains unclear. Here, we experimentally investigated the microbiota profile during colitis in wild-type (WT) and AnxA1-deficient mice (AnxA1[-/-]), and evaluated an observational cohort in IBD patients with high or low AnxA1 expression.

METHODS: Colitis was induced in C57BL/6 WT and AnxA1 [[-]/[-]] mice via oral administration of 2% DSS for six days. Fecal samples were collected at baseline, peak inflammation (day 6), and during the recovery phase (day 10) for 16S rRNA sequencing. Human microbiota data from the Lifelines Dutch Microbiome Project cohort, including IBD and healthy subjects, were analyzed for AnxA1 expression using R software.

RESULTS: Healthy AnxA1[-/-] mice exhibited reduced microbial richness and a distinct gut microbiota composition, marked by increased Proteobacteria and Parasutterella, and reduced Deferribacterota, Campylobacterota, and Verrucomicrobiota. During DSS-induced colitis, AnxA1[-/-] mice showed greater weight loss and heightened inflammation, displaying earlier and more pronounced microbial shifts, including increased Proteobacteria, Cyanobacteria, Parabacteroides, Bacteroides, and Escherichia-Shigella. In contrast, WT mice exhibited delayed changes, with expansion of Alloprevotella, Akkermansia, and Faecalibaculum after day 6. In human IBD samples, Crohn's disease (CD) patients with low AnxA1 expression and active inflammation presented an altered microbiota enriched in Lachnoclostridium and Parabacteroides, while ulcerative colitis (UC) patients showed phylum-level shifts modulated by AnxA1 levels. Notably, non-inflamed CD and UC patients with low AnxA1 differed significantly in microbiota composition. Moreover, inflamed CD patients with high AnxA1 expression showed microbial profiles resembling those of healthy controls, while low AnxA1 expression was associated with a more pronounced dysbiotic state.

CONCLUSION: AnxA1 is implicated in microbiota control under healthy and IBD conditions. Accordingly, the microbiota of healthy AnxA1[-/-] mice, colitic AnxA1[-/-] mice, and IBD patients with low AnxA1 expression exhibit dysbiosis compared to their respective controls. Together, these unprecedented findings reveal AnxA1 as a potential regulatory protein in the immune-microbiota axis involved in IBD pathogenesis.},
}

Animals
*Annexin A1/genetics/metabolism
*Gastrointestinal Microbiome
Humans
Mice
Mice, Knockout
*Colitis/chemically induced/microbiology/metabolism
Mice, Inbred C57BL
Dextran Sulfate
Male
*Inflammatory Bowel Diseases/microbiology/metabolism
Female
Disease Models, Animal
Dysbiosis
Feces/microbiology
Adult
Middle Aged

@article {pmid41112171,
year = {2025},
author = {Muneer, MA and Huang, R and Xiaojun, Y and Pang, Z and Munir, MZ and Ji, B and Wu, L and Zheng, C},
title = {Mg-enriched nutrient management enhances phyllosphere bacterial diversity, community structure, and functional traits in pomelo orchards.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100476},
pmid = {41112171},
issn = {2666-5174},
abstract = {Phyllosphere, the aerial surface of plants, harbors a tremendous diversity of microbes that significantly influences plant health and ecosystem functionality. Nevertheless, a holistic understanding of the effects of nutrient management, particularly magnesium (Mg) supplementation, on phyllosphere endophytes remains elusive. Herein, we conducted a five-year field experiment to investigate the impact of different nutrient management practices, including farmer practice of high N.P.K input (FP), reduced N.P.K input (OPT), and OPT supplemented with Mg (OPT+Mg), on the phyllosphere endophytic bacterial community (Illumina 16S sequencing) associated with fruit and leaf of pomelo trees across different growth stages, i.e., June (S1), July (S2), and September (S3). The results demonstrated that Mg-enriched nutrient management (OPT+Mg), significantly enhanced microbial diversity and restructured community composition, with notable increases in the relative abundance of beneficial phyla such as Actinobacteriota, Bacteroidota, and Chloroflexi compared with FP across all growing seasons. Similarly, both OPT and OPT+Mg generally supported higher microbial diversity than FP in fruit and leaf samples. Principal Coordinate Analysis (PCoA) and PERMANOVA confirmed significant differences in bacterial community structures among treatments. Ternary plot analysis further indicated the enrichment of beneficial genera under OPT and OPT+Mg treatments, which can play key roles in promoting plant growth and enhancing resilience against various stresses. In addition, Mg application was associated with more complex co-occurrence networks, highlighting its impact on promoting robust microbial communities in leaf and fruit samples. Functional predictions (FAPROTAX) suggested that Mg application was associated with higher predicted carbon and nitrogen cycling functions and lower predicted relative abundances of potential plant pathogens and intracellular parasites. This study is the first to provide long-term field-based evidence of how Mg supplementation modulates phyllosphere microbiota in fruit orchards, offering critical insights into microbiome-informed nutrient strategies. These findings highlight the unexplored role of Mg in shaping aerial plant microbiomes and present a novel avenue for enhancing sustainable pomelo production through targeted nutrient-microbiome interventions.},
}

@article {pmid41112052,
year = {2025},
author = {Xu, J and Dai, D and Yang, Y and Gao, S and Yang, J and Dong, C and Yang, W and Yuan, J and Wang, T and Tian, T and Yang, Y and Luo, F and Jiang, P and Wu, C and Sun, X and Sui, Y and Gao, G and Ma, W and Wu, Y and Zhang, J and Li, J and Guo, C and Cui, C and Guo, T and Zhao, X and Yuan, J and Qiao, S and Hu, F and Gao, X and Luo, X and Peng, H and Wang, D and Wu, J and Wu, C and He, J and Chen, WH and Yang, Y and Fu, J},
title = {Distinct microbial and metabolic shifts characterize acute coronary syndrome and recovery.},
journal = {iMeta},
volume = {4},
number = {5},
pages = {e70079},
pmid = {41112052},
issn = {2770-596X},
abstract = {Early identification of patients at risk of acute coronary syndrome (ACS) remains a major unmet need, particularly among those with stable coronary artery disease (sCAD), where timely intervention could markedly improve outcomes. The gut microbiota has been implicated in coronary artery disease (CAD), but its ability to distinguish ACS from sCAD is not well defined. Here, we performed cross-sectional multi-omics profiling of fecal microbiota and plasma metabolites in 548 individuals, including participants with normal coronary arteries (N = 175), primary sCAD (N = 161), and ACS (N = 212). To assess whether disease-associated changes resolve with treatment, we further analyzed an independent cohort of ACS patients (N = 52) who transitioned to sCAD following standard therapy. We identified profound ACS-associated alterations in gut microbial composition and systemic metabolism, marked by enrichment of pro-inflammatory taxa such as Streptococcus spp. and elevated circulating levels of 3-hydroxybutyrate (3-HB). Strikingly, many of these ACS-specific microbial and metabolic signatures, including 3-HB and related microbial functional pathways, were restored toward sCAD-like levels after clinical recovery. Integrative models combining microbial taxa, metabolites, and clinical biomarkers robustly discriminated ACS from healthy controls (AUC = 0.91) and from sCAD (AUC = 0.83), significantly outperforming clinical markers alone (AUC = 0.69 for NCA vs. ACS; 0.59 for sCAD vs. ACS). These findings establish the gut microbiome and its metabolic outputs as key discriminators of ACS, reveal their dynamic resolution during disease recovery, and highlight their potential as biomarkers and therapeutic targets for cardiovascular risk stratification and management.},
}

@article {pmid41112047,
year = {2025},
author = {Xu, M and Guan, S and Zhong, C and Ma, M and Tao, L and Huang, G},
title = {Characterizing the microbiome of "sterile" organs in experimental mice and evidence of translocation of bacteria from the gut to other internal organs.},
journal = {iMeta},
volume = {4},
number = {5},
pages = {e70081},
pmid = {41112047},
issn = {2770-596X},
abstract = {Using culturomics and metagenomics, we demonstrate the existence of non-pathogenic microbiota in the internal organs of healthy experimental mice, challenging the traditional dogma of organ sterility. Based on the analysis of 104 commercially sourced mice (C57BL/6J, BALB/c, ICR), the study reveals that over 20% of the analyzed mice harbored a high microbial burden in the internal organs and identified a total of 463 microbial species. Several species, including Ligilactobacillus murinus, Alcaligenes faecalis, Micrococcus luteus, Pseudochrobactrum asaccharolyticum, Escherichia coli, and Microbacterium sp., were frequently identified and were abundant in the mouse tissues. Further investigation implies that microorganisms in the "sterile" tissues could be associated with the gut microbiota. Given the wide use of experimental mice in medical and biological research, these findings of resident microorganisms in the animal's internal organs raise concerns about potential variability in experimental outcomes.},
}

@article {pmid41112042,
year = {2025},
author = {Lin, A and Xiong, M and Jiang, A and Huang, L and Wong, HZH and Feng, S and Zhang, C and Li, Y and Chen, L and Chi, H and Zhang, P and Ye, B and Zhang, H and Zhang, N and Zhu, L and Mou, W and Shen, J and Li, K and Xu, W and Ying, H and Zhang, C and Zeng, D and Xie, J and Deng, X and Wang, Q and Xu, J and Shi, W and Qi, C and Qu, C and Huang, X and Hajdu, A and Li, C and Peng, C and Cao, X and Pei, G and Zhang, L and Huo, Y and Xu, J and Glaviano, A and Szöllősi, AG and Bian, S and Li, Z and Tang, H and Tang, B and Liu, Z and Zhang, J and Miao, K and Cheng, Q and Wei, T and Yuan, S and Luo, P},
title = {The microbiome in cancer.},
journal = {iMeta},
volume = {4},
number = {5},
pages = {e70070},
pmid = {41112042},
issn = {2770-596X},
abstract = {The human microbiome is now recognized as a central regulator of cancer biology, intricately shaping tumor development, immune dynamics, and therapeutic response. This comprehensive review delineates the multifaceted roles of bacteria, viruses, and fungi in modulating the tumor microenvironment and systemic immunity across diverse cancer types. We synthesize current evidence on how microbial dysbiosis promotes carcinogenesis via chronic inflammation, metabolic reprogramming, genotoxic stress, immune evasion, and epigenetic remodeling. This review emphasizes organ-specific microbiome signatures and highlights their potential as non-invasive biomarkers for early detection, treatment stratification, and prognosis. Furthermore, we explore the impact of intratumoral microbiota on cancer therapies, uncovering how microbial metabolites and host-microbe interactions shape therapeutic efficacy and resistance. Finally, advances in microbiome-targeted strategies, such as probiotics, fecal microbiota transplantation, and engineered microbes offer new avenues for adjunctive cancer therapy. This review provides a roadmap for future investigation and underscores the transformative promise of microbiome modulation in cancer prevention and treatment.},
}

@article {pmid41112009,
year = {2025},
author = {Guo, YC and Hong, Y and Huang, L and Xu, XW and Sun, JQ and Ji, KK and Li, CN},
title = {Beyond biomarkers: An integrated traditional Chinese medicine-machine learning approach predicts hepatic steatosis in high metabolic risk populations.},
journal = {World journal of gastroenterology},
volume = {31},
number = {38},
pages = {112166},
pmid = {41112009},
issn = {2219-2840},
mesh = {Humans ; *Machine Learning ; *Medicine, Chinese Traditional/methods ; Biomarkers/blood/analysis ; Risk Assessment/methods ; *Non-alcoholic Fatty Liver Disease/diagnosis ; Risk Factors ; Predictive Value of Tests ; Liver/pathology ; },
abstract = {Tian et al present a timely machine learning (ML) model integrating biochemical and novel traditional Chinese medicine (TCM) indicators (tongue edge redness, greasy coating) to predict hepatic steatosis in high metabolic risk patients. Their prospective cohort design and dual-feature selection (LASSO + RFE) culminating in an interpretable XGBoost model (area under the curve: 0.82) represent a significant methodological advance. The inclusion of TCM diagnostics addresses metabolic dysfunction-associated fatty liver disease (MAFLD's) multisystem heterogeneity-a key strength that bridges holistic medicine with precision analytics and underscores potential cost savings over imaging-dependent screening. However, critical limitations impede clinical translation. First, the model's single-center validation (n = 711) lacks external/generalizability testing across diverse populations, risking bias from local demographics. Second, MAFLD subtyping (e.g., lean MAFLD, diabetic MAFLD) was omitted despite acknowledged disease heterogeneity; this overlooks distinct pathophysiologies and may limit utility in stratified care. Third, while TCM features ranked among the top predictors in SHAP analysis, their clinical interpretability remains nebulous without mechanistic links to metabolic dysregulation. To resolve these gaps, we propose external validation in multiethnic cohorts using the published feature set (e.g., aspartate aminotransferase/alanine aminotransferase, low-density lipoprotein cholesterol, TCM tongue markers) to assess robustness. Subtype-specific modeling to capture MAFLD heterogeneity, potentially enhancing accuracy in high-risk subgroups. Probing TCM microbiome/metabolomic correlations to ground tongue phenotypes in biological pathways, elevating model credibility. Despite shortcomings, this work pioneers a low-cost screening paradigm. Future iterations addressing these issues could revolutionize early MAFLD detection in resource-limited settings.},
}

Humans
*Machine Learning
*Medicine, Chinese Traditional/methods
Biomarkers/blood/analysis
Risk Assessment/methods
*Non-alcoholic Fatty Liver Disease/diagnosis
Risk Factors
Predictive Value of Tests
Liver/pathology

@article {pmid41112002,
year = {2025},
author = {Saadeh, M and Donohue, S and Ailawadi, S and Hong, G and Johnson, DA},
title = {Oral microbiome and inflammatory bowel disease: New understanding and call to action.},
journal = {World journal of gastroenterology},
volume = {31},
number = {38},
pages = {111210},
pmid = {41112002},
issn = {2219-2840},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/immunology/therapy ; *Dysbiosis/microbiology/immunology ; *Mouth/microbiology/immunology ; *Microbiota/immunology ; Gastrointestinal Microbiome ; },
abstract = {The oral microbiome is the second largest microbial community in the human body after the gut microbiome. It includes an array of fungi, bacteria, amoebae, flagellates, archaea, and viruses, all of which are potential pathogens. This microbiome can act as a facilitator not only for protection but also for aggravation when dysbiosis occurs. Although conventional thought is this is primarily in terms of oral health issues, such as dental caries and gingival disease. The systemic effects of the oral microbiome however, are relevant to both gastrointestinal (GI) disease and non-GI disease. These systemic risks occur for several reasons, including upregulation of cytokines, adhesion cell-like processes, toll-like receptors, reactive oxidative species or generation of mutation inducing DNA changes. Additionally, there is translocation risk of potential active pathogens or their metabolic byproducts. There is a substantial and growing body of evidence that the oral microbiome influences diseases including Barrett's esophagus, metabolic-associated steatosis liver disease, and GI cancers. Additionally, there is burgeoning evidence of a causal association with systemic inflammatory diseases, including inflammatory bowel disease. This report discusses the most recent evidence of this association and highlights new approaches to potentially enhance our "best practice" strategies for optimal care of patients with inflammatory bowel disease.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/immunology/therapy
*Dysbiosis/microbiology/immunology
*Mouth/microbiology/immunology
*Microbiota/immunology
Gastrointestinal Microbiome

@article {pmid41110993,
year = {2025},
author = {Jang, KB and Seo, E and Kim, Y},
title = {Dynamic Interactions between the Gut Microbiome, Health, and Metabolic Disorders in Preterm Infants.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2508033},
doi = {10.4014/jmb.2508.08033},
pmid = {41110993},
issn = {1738-8872},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Infant, Premature/growth & development ; Infant, Newborn ; Dysbiosis/microbiology ; *Metabolic Diseases/microbiology ; Probiotics ; Gastrointestinal Tract/microbiology ; },
abstract = {Preterm birth, which occurs before the entire gestation is completed, causes serious health challenges for newborns. The gastrointestinal tract often shows delayed development and poor function in nutrient utilization and immune response. Preterm neonates are faced with difficulties in growth, are more vulnerable to infections, and have a higher risk of developing inflammatory diseases. One key factor in these outcomes is the abnormal development of intestinal microbiota. In premature neonates, gut microbes tend to show lower diversity and changes in several bacteria. The gut dysbiosis can disrupt gut function and contribute to complications like necrotizing enterocolitis, sepsis, and even long-term metabolic and neurodevelopmental disorders. This review brings together current research on how premature birth affects the growth, gut development, and overall health of infants, with a focus on changes in microbial colonization. In addition, we discuss how gut microbiota plays a role in shaping the immune system and influencing brain development. There is growing interest in using breast milk, specialized nutrition, and probiotics to improve microbial balance in premature infants. Preterm birth alters intestinal development and microbial colonization, making infants vulnerable to gut dysbiosis and disease. These changes contribute to a heightened risk of neonatal diseases such as NEC, sepsis, and long-term neurodevelopmental and metabolic disorders. Evidence highlights the critical role of commensal microbes and their metabolites in promoting epithelial maturation, immune balance, and gut-brain signaling. Advancing neonatal care will require precision approaches based on microbial profiling, targeted nutritional strategies, and a deeper understanding of host-microbe interactions to improve health in preterm infants. Therefore, this review focuses on integrating recent evidence of microbial development and preterm infant health, highlighting the gut-brain axis in relation to metabolic disorders, and emphasizing how gut dysbiosis links clinical outcomes with mechanistic insights in neonatal care.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Infant, Premature/growth & development
Infant, Newborn
Dysbiosis/microbiology
*Metabolic Diseases/microbiology
Probiotics
Gastrointestinal Tract/microbiology

@article {pmid41110987,
year = {2025},
author = {Hong, HH and Lee, SY and Jang, DH and Ju, SE and Shim, JE and Kim, TH and Kang, HS and Kim, SM},
title = {Multiomics Integration Reveals Microbial Gene Interactions Shaping Host Responses in a DSS-Induced Colitis Mouse Model.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2507010},
doi = {10.4014/jmb.2507.07010},
pmid = {41110987},
issn = {1738-8872},
mesh = {Animals ; Dextran Sulfate ; *Colitis/microbiology/chemically induced/immunology/genetics ; Disease Models, Animal ; Mice ; *Gastrointestinal Microbiome/genetics ; Inflammatory Bowel Diseases/microbiology/immunology ; Mice, Inbred C57BL ; Amino Acyl-tRNA Synthetases/genetics/metabolism ; Metabolic Networks and Pathways/genetics ; *Bacteria/genetics/classification ; Transcriptome ; Multiomics ; },
abstract = {Inflammatory bowel disease (IBD) has been studied with a multi-omics approach to identify key contributors and unravel the biological complexity of its pathogenesis, aiding in the development of early diagnostic markers and therapeutic targets. The dextran sulfate sodium (DSS)-induced colitis mouse model, a widely used system for studying IBD, induces gut barrier disruption and proinflammatory responses, making it an ideal model for investigating host-microbiome interactions. This study emphasizes the intricate relationship between microbial transcriptomic changes and host immune responses, revealing regulation of microbial genes, particularly in metabolic pathways related to carbohydrate metabolism, nucleotide metabolism, and aminoacyl-tRNA biosynthesis under inflammatory conditions. We identified key hub microbes and microbial genes that are closely associated with host immunological pathways, with particular focus on microbial aminoacyl-tRNA synthetases (aaRSs), which play significant roles in immune cell activation and inflammatory pathways. These findings offer valuable insights into the microbial contributions to inflammation and immune modulation in IBD, highlighting the potential role of aaRSs in regulating immune responses beyond their traditional function in translation. This lays the foundation for future research into host-microbiome interactions in inflammatory diseases and the development of novel therapeutic strategies that target microbial aaRSs to manipulate immune response.},
}

Animals
Dextran Sulfate
*Colitis/microbiology/chemically induced/immunology/genetics
Disease Models, Animal
Mice
*Gastrointestinal Microbiome/genetics
Inflammatory Bowel Diseases/microbiology/immunology
Mice, Inbred C57BL
Amino Acyl-tRNA Synthetases/genetics/metabolism
Metabolic Networks and Pathways/genetics
*Bacteria/genetics/classification
Transcriptome
Multiomics

@article {pmid41110985,
year = {2025},
author = {Lee, HW and Ha, JH},
title = {High-Resolution Characterization of the Bacterial Microbiome in Chili Pepper Powder Using SMRT Sequencing.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2506003},
doi = {10.4014/jmb.2506.06003},
pmid = {41110985},
issn = {1738-8872},
mesh = {*Capsicum/microbiology ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; Powders ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; China ; Republic of Korea ; Food Microbiology ; Phylogeny ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; },
abstract = {Chili pepper powder is an essential ingredient of Korean cuisine and kimchi products. As such, ensuring its microbiological safety is crucial from a public health perspective. In this study, the bacterial microbiomes of Korean and Chinese chili pepper powder samples were compared using high-resolution single-molecule real-time sequencing. Nine samples each from Korea and China were analyzed, yielding high-quality sequencing data with N50 values exceeding 1,460 bp and quality scores greater than Q30. Based on alpha diversity analysis, Chinese samples exhibited higher microbial diversity, whereas Korean samples had a more selective and clustered microbial structure, composed predominantly of Bacillus. Taxonomically, Chinese samples contained a wider range of genera, including Pantoea, Weissella, and Klebsiella, in contrast, Korean samples were dominated by Firmicutes, primarily Bacillus species. Although Salmonella enterica was detected in some Korean samples, viability was not confirmed. This may have indicated residual DNA or viable but nonculturable cells due to the low water activity of chili powders. Beta diversity analysis indicated moderate separation between the two groups, with Korean samples showing tighter clustering and Chinese samples displaying greater variability. Linear discriminant analysis effect size identified Bacillus altitudinis and Bacillus safensis as biomarkers for Korean samples, and Pantoea agglomerans and Weizmannia coagulans as biomarkers for Chinese samples. Overall, despite slightly lower microbial diversity, Korean chili pepper powder samples exhibited a more stable microbial community structure. Selection of chili pepper powder characterized by a stable and controlled microbiome could play an essential role in promoting the hygienic production and microbial safety of kimchi.},
}

*Capsicum/microbiology
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
Powders
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics
China
Republic of Korea
Food Microbiology
Phylogeny
Sequence Analysis, DNA
High-Throughput Nucleotide Sequencing

@article {pmid41110780,
year = {2025},
author = {Sreekutti, S and Ndomondo, S and Sharma, P and Patel, R and Mevada, V},
title = {Forensic application of metagenomics: Methods and future directions.},
journal = {Journal of microbiological methods},
volume = {239},
number = {},
pages = {107300},
doi = {10.1016/j.mimet.2025.107300},
pmid = {41110780},
issn = {1872-8359},
abstract = {The microbial communities are found commonly in our environment, making it impossible to touch any surface without interfering with them. The human microbiome, primarily bacteria in the saliva, skin, and gut, can be used for forensic purposes. Human-associated and environmental samples, such as soil, water, etc., carry the microbiome, which can be used for geolocation inference. These microbiomes have considerable potential for use in forensic investigations, including many instances of sexual violence, post-mortem examinations, individual identification, and location identification. Recent developments in metagenomic sequencing have greatly contributed to microbial analysis. Yet, because of certain issues and challenges, the forensic application of microbiomes is still in its infancy. This article reviewed the use of metagenomics in forensic science and some of the main obstacles that are faced by experts in this area. The first and foremost issues noted were the lack of standardization protocols and a poor reference database for research studies. Some limitations, such as storage sensitivity and limited samples, are also indicated. Future research studies should concentrate on more standardized investigations to overcome these difficulties and explore the enormous potential of microbiomes for beneficial applications in forensic contexts.},
}

@article {pmid41110769,
year = {2025},
author = {Alqudah, S and DeLucia, B and Osborn, LJ and Markley, RL and Bobba, V and Preston, SM and Thambidurai, T and Nia, LH and Fulmer, CG and Sangwan, N and Nemet, I and Claesen, J},
title = {The diet-derived gut microbial metabolite 3-phenylpropionic acid reverses insulin resistance and obesity-associated metabolic dysfunction.},
journal = {Molecular metabolism},
volume = {},
number = {},
pages = {102272},
doi = {10.1016/j.molmet.2025.102272},
pmid = {41110769},
issn = {2212-8778},
abstract = {Obesity-associated metabolic disorders, including type 2 diabetes and metabolic dysfunction associated fatty liver disease (MAFLD), are major global health burdens. While dietary polyphenols have shown promise in ameliorating these conditions, their efficacy is dependent on specialized gut microbial metabolism, and the underlying molecular mechanisms remain mostly elusive. Here, we demonstrate that dietary supplementation with polyphenol-rich elderberry (Eld) extract abrogates the effects of an obesogenic diet in a gut microbiota-dependent manner, preventing insulin resistance and reducing hepatic steatosis in mice. We developed a targeted, quantitative liquid chromatography-tandem mass spectrometry method for detection of gut bacterial polyphenol catabolites and identified 3-phenylpropionic acid as a key microbial metabolite in the portal plasma of Eld supplemented animals. Next, we showed that 3-phenylpropionic acid potently activates hepatic AMP-activated protein kinase α, explaining its role in improved liver lipid homeostasis. We further uncovered the metabolic pathway cumulating in 3-phenylpropionic acid for the common gut commensal Clostridium sporogenes. Our findings establish 3-phenylpropionic acid as a diet-derived, microbiota-dependent metabolite with insulin-sensitizing and anti-steatotic activities and provide a molecular basis for prebiotic interventions to improve host metabolic health.},
}

@article {pmid41110752,
year = {2025},
author = {Hong, G and Zhao, Y and Hou, X},
title = {Impact of four-week rifaximin treatment on abdominal symptoms, psychological state and gut microbiome in diarrhea-predominant irritable bowel syndrome: a pilot study.},
journal = {European journal of pharmacology},
volume = {1007},
number = {},
pages = {178271},
doi = {10.1016/j.ejphar.2025.178271},
pmid = {41110752},
issn = {1879-0712},
abstract = {Previous studies have revealed the effect of two-week rifaximin treatment on abdominal symptoms and gut microbiota in diarrhea-predominant irritable bowel syndrome (IBS-D), but they failed to observe the influence of rifaximin intervention for a longer period. This pilot study is designed to describe gut microbial profiles in IBS-D and to evaluate the impact of four-week rifaximin treatment on IBS-associated symptoms and gut microbiota for the first time. IBS-D patients who fulfilled the Rome III criteria and healthy controls (HC) were enrolled in the study. Then, 400 mg rifaximin was orally administered to IBS-D patients three times daily for four weeks. Abdominal symptoms and mental state were evaluated before treatment, after two weeks of treatment, and after four weeks of treatment. Fecal samples were collected to characterize the gut microbiota by performing 16S rRNA sequencing. A total of 40 healthy volunteers and 33 IBS-D patients were recruited, and all IBS-D patients agreed to receive rifaximin treatment. IBS-D patients exhibited decreased microbial diversity and a different microbial structure compared with HC. Microbial composition differed between HC and IBS-D at the phylum and genus levels. Administration of rifaximin for four weeks improved abdominal symptoms and anxiety in IBS-D patients. Potential enteropathogens including Haemophilus, Escherichia, and Veillonella were inhibited by rifaximin. Rifaximin upregulated arginine and proline metabolism in the gut microbiota. This is the first study demonstrating that four-week rifaximin treatment exerts good efficacy in relieving abdominal symptoms and anxiety in IBS-D, possibly through suppressing three potential enteropathogens and enhancing arginine and proline metabolism.},
}

@article {pmid41110468,
year = {2025},
author = {Maqsood, S and Asif, M and Shakoor, S and Saddiqa, A},
title = {Modulating Metabolism and Reproductive Health through Microbiome Driven Gut-Brain Axis Therapies.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108113},
doi = {10.1016/j.micpath.2025.108113},
pmid = {41110468},
issn = {1096-1208},
abstract = {The gut microbiome plays a crucial role in regulating metabolic and reproductive health through the gut-brain axis. This review underscores the therapeutic potential of modulating gut microbiota to alleviate conditions such as obesity and polycystic ovarian syndrome (PCOS). Gut dysbiosis as an imbalance microbiome, has direct effect on insulin resistance, hormonal imbalances, and systemic inflammation. It contributes to metabolic and reproductive disparities. This study reveals the coordination between dysbiosis and obesity, and PCOS. Alterations in gut-microbiota is the major contributor of insulin-resistance, menstrual dysfunction, and hormonal imbalances. It also focuses on the efficacy of probiotic and relevant microbes. Considering the literature, microbiome-potential and its role in treating the interventions is significantly important. Outcomes recommend that gut-dysbiosis aggravates metabolic and reproductive health illnesses by making worse hormonal inequalities and inflammation. The therapy probiotic has indicated favorable outcomes in enhancing insulin-resistance and menstrual cycle regulation, highlighting its capability as a reliable treatment for PCOS and obesity. Nevertheless, well-monitored clinical trials are necessary on large scale to make it optimized microbiome-focused treatments for long-term results and safety.},
}

@article {pmid41110352,
year = {2025},
author = {Yuan, Y and Hu, J and Lu, X and Han, H and Wang, M and Zhang, W and Jiao, Y and Li, Y and Lin, Z and Liang, C and Yu, Y and Xie, C and Li, J and Mao, T},
title = {Oral rhein attenuate nonalcoholic steatohepatitis in mice through the modulation of gut microbiota and Th17 cell differentiation.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157409},
doi = {10.1016/j.phymed.2025.157409},
pmid = {41110352},
issn = {1618-095X},
abstract = {BACKGROUND: Non-alcoholic steatohepatitis (NASH) is an important clinical issue and a challenge in the field of global public health. However, there are very few clinically approved drugs that can effectively treat NASH. Rhein is a natural organic compound with anti-inflammatory and antioxidant properties, but the specific role and mechanism on NASH remain unexplored.

PURPOSE: This study investigated the role and associated mechanism of rhein in NASH mice.

METHODS: The effects of rhein on lipid accumulation were evaluated in NASH mice through systemic signs of obesity, biochemical parameters, and histological changes. Network pharmacology was employed to determine the main bioactive compounds and key targets of rhein for the NASH treatment. Additionally, antibiotics treatment and fecal microbiota transplantation (FMT) were performed to investigate the role of microbiota in the treatment of NASH with rhein. Bacterial 16S rRNA amplicon sequencing, LC-MS/MS analysis and flow cytometric were employed to investigate the mechanisms underlying rhein's regulatory effects on gut microbiota, BA metabolism and immune balance. Finally, in vitro cell experiments were conducted to explore the effects of metabolites on Th17 cell differentiation.

RESULTS: Our results showed that mice treated with rhein showed a significant alleviating effect from high-fat diet (HFD)-induced liver lipid accumulation and pathological changes compared to those in HFD group. The protective effects of rhein are gut microbiota dependent, as demonstrated by fecal microbiome transplantation and antibiotics treatment. Microbiota transferred from rhein-treated mice displayed a similar role in attenuating hepatic lipid deposition as rhein on NASH in mice, and depletion of the gut microbiota through antibiotics treatments diminished the protective effects of rhein on NASH mice. Moreover, the results from bacterial 16S rRNA sequencing suggested that rhein partially attenuated HFD-induced gut dysbiosis in NASH mice. Network pharmacology analyses was implemented and showed that Th17 cell differentiation might be the potential target in the treatment of rhein against NASH, which was confirmed by flow cytometric analysis showing markedly decrease of the percentage of Th17 cells, corresponded with upregulated Treg cells in rhein-treated NASH mice. Furthermore, targeted bile acid metabolomics analysis showed that supplement with rhein greatly increased the levels of primary bile acids β-MCA and AlloLCA, positively correlated with the relative abundances of Bifidobacterium_choerinum, which may play the key role by which rhein-altered gut microbiota promoted the restoration of Th17/Treg balance in NASH mice. Subsequent in vitro experiments confirmed that AlloLCA directly inhibits Th17 cell differentiation, with suppression of glycolysis potentially serving as the underlying mechanism for the immunomodulatory effects of AlloLCA.

CONCLUSIONS: Collectively, our results suggested that orally administrated rhein reduced hepatic lipid deposition through the modulation of dysregulated gut microbiota and bile acids metabolism, thus regulating Th17/Treg immune balance. This study uncovers a novel mechanistic axis in NASH pathogenesis and providing new research directions for microbiota-targeted clinical strategies.},
}

@article {pmid41110294,
year = {2025},
author = {Muthukumar, S and Suresh Babu, HW and George, A and Maurya, BM and Mahalaxmi, I and Yadav, MK and HariKrishna Reddy, D and Arvinder Wander, and Narayanasamy, A and Ganesan, R and Lakhanpal, V and Vellingiri, B},
title = {The role of cytochrome P450 and gut microbiome in drug metabolism: Insights into Parkinson disease treatment.},
journal = {Drug metabolism and disposition: the biological fate of chemicals},
volume = {53},
number = {11},
pages = {100166},
doi = {10.1016/j.dmd.2025.100166},
pmid = {41110294},
issn = {1521-009X},
abstract = {Parkinson disease (PD) is a complex neurodegenerative condition marked by progressive motor and nonmotor symptoms. Cytochrome P450 (P450) enzymes, notably those from the CYP1 and CYP2 families, are increasingly recognized as significant factors in the development of PD. This review examines the role of P450 enzymes in PD, covering genetic variations, copy number variations, and single nucleotide polymorphisms linked to PD pathogenicity. It also explores the regulatory mechanisms controlling P450 expression in PD and the influence of the gut microbiome and metabolites on P450 activity. Additionally, the review discusses how P450 enzymes metabolically activate drugs used to treat PD and investigates the intricate relationship between P450s and mitochondrial dysfunction. Finally, it underscores the therapeutic potential of targeting P450 enzymes for PD treatment. Understanding the diverse roles of P450 enzymes in PD may lead to innovative treatment approaches and personalized interventions for this challenging neurological disorder. SIGNIFICANCE STATEMENT: Cytochrome P450 (P450) enzymes significantly influence Parkinson disease (PD) development through their roles in drug metabolism and detoxification. Single nucleotide polymorphisms in P450 genes can alter enzyme activity, affecting PD susceptibility and progression. Gut microbiota modulates P450 function, impacting detoxification of PD-related toxins and influencing gut and blood-brain barrier integrity. Additionally, P450-mitochondrial interactions contribute to energy deficits and oxidative stress, exacerbating neurodegeneration in PD. Understanding these pathways may uncover novel therapeutic targets and personalized treatment strategies.},
}

@article {pmid41109629,
year = {2025},
author = {Vahed, A and Molanouri Shamsi, M and Siadat, SD and Behmanesh, M and Negaresh, R and Agh-Mohammadi, S and Ebrahimi, M},
title = {Effects of home-based exercise training on gut microbiota and possible relations with cognitive function and metabolic health in postmenopausal women with type 2 diabetes mellitus: a randomized control trial.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {112908},
doi = {10.1016/j.diabres.2025.112908},
pmid = {41109629},
issn = {1872-8227},
abstract = {AIM: Evidence suggests that the gut microbiome is involved in type 2 diabetes mellitus (T2DM). This study investigates the association between gut microbiota composition, cognitive function, and metabolic health in postmenopausal women with T2DM following a 12-week home-based multi-task exercise intervention.

METHODS: Seventy postmenopausal women with T2DM were randomly assigned to either an intervention group, which performed home-based multi-task exercises, or a control group. Gut microbiota, cognitive function, physical fitness, and metabolic indices were assessed before and after the intervention.

RESULTS: Exercise training significantly increased Akkermansia muciniphila and Faecalibacterium levels, and reduced Lactobacillus abundance (p < 0.05). Participants showed improvements in HDL levels, cognitive function, and physical fitness (p < 0.05). Among the microbial changes, an increased abundance of Akkermansia was significantly correlated with improvements in high-density lipoprotein (HDL) levels (r = 0.41) and cognitive function (r = 0.49).

CONCLUSION: This study supports the potential effectiveness of multi-task exercise programs in enhancing physical fitness and metabolic health in postmenopausal women with T2DM. The findings also suggest a possible connection between the gut and the brain, with Akkermansia muciniphila emerging as a potential mediator. Investigating the Akkermansia-to-brain pathway represents a promising and emerging area of research that warrants further exploration.},
}

@article {pmid41109625,
year = {2025},
author = {Rattanapitoon, NK and Thanchonnang, C and Padchasuwan, NH and Rattanapitoon, SK},
title = {Extracellular vesicles and PET microplastics: toward a biomarker framework for systemic endocrine-microbiome disruption.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127281},
doi = {10.1016/j.envpol.2025.127281},
pmid = {41109625},
issn = {1873-6424},
}

@article {pmid41109441,
year = {2025},
author = {Yu, Q and Liao, H and Tan, W and Xu, L and Lin, G and Ai, Z and Xie, Q and Liu, Y and Li, Y and Yang, X and Su, Z and Ma, G and Xie, J and Lai, Z},
title = {Mechanistic insights into metformin's anti-hyperuricemic effect: Targeting PPP/DNPB/XOD-mediated purine pathway, purinosome assembly, and gut microbiota homostasis in rats.},
journal = {Chemico-biological interactions},
volume = {},
number = {},
pages = {111783},
doi = {10.1016/j.cbi.2025.111783},
pmid = {41109441},
issn = {1872-7786},
abstract = {Hyperuricemia has become a public threat to human health, and conventional medical treatment only aims to inhibit xanthine oxidase (XOD). Endogenous purine biosynthesis and purinosome formation are neglected in research of medical mechanism. In this study, the therapeutic effect and mechanism of metformin was explored in chronic high-fructose-induced hyperuricemic rats. Results indicated that four weeks of metformin administration effectively reduced uric acid (UA), creatinine, and urea levels, ameliorated renal and hepatic injuries, and promoted glycogen synthesis in hyperuricemic rats. Furthermore, metformin remarkedly downregulated the mRNA and protein expression of core enzymes in pentose phosphate pathway (PPP), and de novo purine biosynthesis (DNPB) of endogenous purine. Metformin was found to markedly inhibit the purine salvage pathway (PSP) and XOD to retard purine recycling and metabolism. Additionally, metformin effectively restored physiological purinosome architecture, preventing aberrant enzyme clustering and subcellular redistribution. The hepatic levels of IMP, inosine, hypoxanthine and xanthine in hyperuricemic rats were remarkably decreased by metformin. Besides, metformin favorably maintained the gut microbiome homeostasis and normalized purine metabolism to lower purine levels in intestine. Taken together, the results for the first time indicated that metformin exerted appreciable anti-hyperuricemic effect, at least partly, via inhibiting original biosynthetic and metabolic pathways of endogenous purine simultaneously mediated by PPP/DNPB/XOD, purinosome assembly, and modulating gut microflora profile. This work provided a scientific basis for its potential application in hyperuricemia therapy beyond its classical use in diabetes.},
}

@article {pmid41109435,
year = {2025},
author = {Rao, Z and Shi, Y and She, M and Liu, C and Zhu, J and Yu, Y},
title = {Associations among microbial enterotype, brain structure, and working memory: A combined structural and diffusion MRI study.},
journal = {NeuroImage},
volume = {},
number = {},
pages = {121536},
doi = {10.1016/j.neuroimage.2025.121536},
pmid = {41109435},
issn = {1095-9572},
abstract = {BACKGROUND: Enterotype analysis classifies individuals based on gut microbial community composition using clustering techniques. Despite evidence suggesting the important role of enterotype in affecting brain function and working memory, little is known about the brain structural substrates.

METHODS: We collected fecal samples and utilized 16S rDNA amplicon sequencing to identify three enterotypes (Bacteroides, Prevotella, and Ruminococcaceae) among 511 healthy young adults through unsupervised clustering. Structural and diffusion MRI techniques were adopted to assess gray matter morphology and white matter integrity. Inter-enterotype differences in brain structure were tested, followed by correlation and mediation analyses to investigate the potential relationships among enterotype, brain structure, and working memory.

RESULTS: The three enterotypes exhibited significant differences in cortical thickness of the prefrontal cortex and mean diffusivity of the cerebral peduncle and cingulum. Moreover, prefrontal cortical thickness was correlated with working memory and further acted as a significant mediator of the association between enterotype and working memory.

CONCLUSIONS: Our findings may contribute to the growing literature on the microbiota-brain-cognition relationship, setting the stage for for future longitudinal and interventional research.},
}

@article {pmid41109419,
year = {2025},
author = {Li, J and Zhang, W and Li, X and Liu, Z and Yan, H},
title = {Bupropion administration significantly impacts the gut microbiome, serum metabolites, and immune factors in chronic stress depression rats.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {120457},
doi = {10.1016/j.jad.2025.120457},
pmid = {41109419},
issn = {1573-2517},
abstract = {Emerging evidence suggests that the gut microbiota plays a crucial role in the pathogenesis of depression through the microbiota-gut-brain axis. Our previous research demonstrated that oral antidepressants were potent in regulating gut microbiome in depressive rats. Bupropion is a common antidepressant, but its regulatory mechanisms on the gut microbiota in the treatment of depression remain unclear. Here, we evaluated the potential mechanisms underlying the microbe-mediated behavioral effects of oral and injectable bupropion in chronic restraint stress (CRS)-induced depressive rat model through integrated microbiome, metabolome, and biochemical techniques. Oral bupropion modulated the gut microbiota composition in favor of beneficial bacteria such as Romboutsia and Muribaculum, while reducing potentially harmful bacteria, including Staphylococcus, Streptococcus, and Bacteroides. Metabolomic results revealed that oral bupropion improved the abnormal levels of acetic acid, butyric acid, tryptophan and its derivatives, nicotinamide, and biotin. Moreover, oral bupropion significantly reduced the percentage of CD4[+] T lymphocytes and the levels of IL-1β and CXCL2. In comparison, injectable administration may not fully replicate the effects of oral administration on these alterations. Moreover, significant changes in the gut microbiota composition, particularly Muribaculum and Bacteroides, as well as tryptophan metabolites (L-tryptophan, 5-hydroxy-L-tryptophan, and indole-3-acetic acid), and immune indicators (CXCL2 levels and CD4[+] T lymphocyte percentages), were correlated. Notably, bupropion administration may also selectively exert negative effects on the gut microbiota, metabolites, and immune factors. Collectively, this study presents the first comprehensive overview of changes in the gut microbiome, metabolome, and immune indicators after bupropion treatment, highlighting their role in mediating antidepressant effects.},
}

@article {pmid41109237,
year = {2025},
author = {Dorsey, ER and De Miranda, BR and Hussain, S and Bloem, BR and Elbaz, A and Llibre-Guerra, J and Lo, RY and Goldman, SM and Tanner, CM},
title = {Environmental toxicants and Parkinson's disease: recent evidence, risks, and prevention opportunities.},
journal = {The Lancet. Neurology},
volume = {24},
number = {11},
pages = {976-986},
doi = {10.1016/S1474-4422(25)00287-X},
pmid = {41109237},
issn = {1474-4465},
mesh = {Humans ; *Parkinson Disease/prevention & control/etiology/epidemiology ; *Environmental Exposure/adverse effects/prevention & control ; Pesticides/adverse effects ; Risk Factors ; *Environmental Pollutants/adverse effects ; },
abstract = {The global burden of Parkinson's disease is rising. Large-scale genetic studies have confirmed that extrinsic or environmental factors, rather than genetic predisposition, play a dominant role in its cause. Increasing evidence implicates three classes of toxicants-certain pesticides, the dry-cleaning chemicals trichloroethylene and perchloroethylene, and air pollution-in the development of Parkinson's disease. These toxicants are widely prevalent, impair mitochondrial or lysosomal function, or both, and contribute to, if not cause, the disease. Parkinson's disease could be thus largely preventable. Uncertainties remain regarding the relevant doses, timing, and routes of exposure, the nature of genetic and environmental interactions, the effects of combined exposures, the role of the microbiome, and the identity of other environmental risks. Methodological limitations and structural challenges hinder our understanding. However, improved measurement of toxicant exposure in individuals and the environment, long-term prospective studies, increased funding for prevention, and policy changes can precipitate the fall of the burden of Parkinson's disease.},
}

Humans
*Parkinson Disease/prevention & control/etiology/epidemiology
*Environmental Exposure/adverse effects/prevention & control
Pesticides/adverse effects
Risk Factors
*Environmental Pollutants/adverse effects

@article {pmid41109046,
year = {2025},
author = {Xu, S and Wang, R and Liu, X and Zhang, P and Luo, C and Zou, K and Xiang, C and Huan, X and Yao, W and Li, X and Zhang, J and Wu, Z},
title = {Yiqi Huayu Jiedu decoction enhances pathological response in neoadjuvant chemotherapy-treated gastric cancer patients: A prospective, randomized controlled trial.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157410},
doi = {10.1016/j.phymed.2025.157410},
pmid = {41109046},
issn = {1618-095X},
abstract = {BACKGROUND: While neoadjuvant chemotherapy (NAC) shows suboptimal pathological responses in advanced gastric cancer (GC), Yiqi Huayu Jiedu decoction (YHJD) demonstrates potential as a synergistic agent.

METHODS: This study represents an interim analysis of a prospective, double-arm, single-center, randomized controlled clinical trial (ChiCTR2300072742) conducted at Jiangsu Provincial Hospital of Traditional Chinese Medicine. A total of 122 patients with locally advanced GC were enrolled between June 2023 and December 2024. The study aimed to evaluate the efficacy and safety of YHJD in enhancing the neoadjuvant FLOT regimen. The primary endpoint was tumor pathological regression (TRG).

RESULTS: The YHJD group demonstrated superior pathological responses (TRG 1-3: YHJD group vs CON group: 44/68 [68.8%] vs 29/58 [50.0%], p = 0.043) while maintaining a safety profile comparable to chemotherapy alone. Gut microbiota analysis revealed that YHJD significantly reduced the abundance of Lactobacillus salivarius (L.salivarius) during NAC, with lower levels correlating with improved treatment response. Notably, depletion of intratumoral L.salivarius in the YHJD paralleled enhanced NAC efficacy. Further analysis revealed that enrichment of L. salivarius was associated with immunosuppressive microenvironment, it showed positive correlations with T regulatory cells (Tregs; r = 0.512, p < 0.0001) and M2 macrophages (r = 0.411, p = 0.002).

CONCLUSIONS: YHJD enhanced the pathological response rates in GC patients receiving FLOT-based NAC, possibly through modulation of the immuno-oncology-microbiome axis, potentially by downregulating L. salivarius-mediated immunosuppression.},
}

@article {pmid41108937,
year = {2025},
author = {Yang, MT and Xie, LH and Wang, L and Gao, YQ and Liu, R and Ma, H and Lei, CC and Jiang, J and Su, JW and Zhang, XX and Ni, HB and Nan, FL},
title = {Metagenomic analysis of bile acid biotransformation by gut microbiota in wild birds.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {105956},
doi = {10.1016/j.psj.2025.105956},
pmid = {41108937},
issn = {1525-3171},
abstract = {Although gut microbiota-mediated bile acid (BA) metabolism is well characterized in mammals, its mechanisms in wild birds remain largely unknown, hindering our understanding of their ecological adaptation and health. In this study, metagenomic analysis was performed on 10,455 metagenome-assembled genomes (MAGs) derived from 718 wild bird gut samples, from which 1,034 high-quality non-redundant MAGs were selected for further analysis. Functional annotation analysis identified 755 MAGs encoding genes associated with BA biotransformation pathways, primarily derived from the phyla Bacillota_A, Bacteroidota, and Bacillota, with dominant genera including Helicobacter_G and Ligilactobacillus. Subsequent genomic analysis identified 379 MAGs encoding bile salt hydrolase (BSH), with phylogenetic classification demonstrating predominant affiliation to the Bacteroidota and Bacillota_A phyla. Compared to the BSH-producing microbiota in the human and chicken gut, the phylum Bacillota exhibited a notably higher relative abundance in wild birds. Within the wild bird gut microbiome, Helicobacter_G was identified as the predominant BSH-encoding genus, whereas its relative abundance was substantially lower in both humans and chickens. Moreover, migratory birds (MB) displayed significantly higher diversity of BA biotransformation genes than resident birds (RB), with Helicobacter_G being notably enriched at the genus level in MB, potentially associated with their heightened energy and nutritional demands during migration. Notably, in addition to residency status, host species emerged as the most influential factor shaping the compositional variation of BA biotransformation genes, followed by environmental factors and dietary habits. In summary, this study systematically elucidates the potential functions of gut microbiota in BA metabolism and their close associations with host ecological traits in wild birds, not only advancing our understanding of host-microbe interactions and metabolic adaptation mechanisms but also providing a theoretical foundation for future interventions targeting gut microbiota to improve wildlife health.},
}

@article {pmid41108672,
year = {2025},
author = {Thelen, AC and Andreani, N and Korten, NM and Neumann, M and Verspohl, V and van Egmond, M and Kneisel, L and Voelz, C and Blischke, L and Baines, JF and Baier, J and Schumacher, J and Kiessling, F and Herpertz-Dahlmann, B and Beyer, C and Keller, L and Seitz, J and Trinh, S},
title = {The Influence of Omega-3 Fatty Acids and Probiotics on Hippocampal Inflammation and Glial Cells in a Chronic Anorexia Nervosa Rat Model.},
journal = {The International journal of eating disorders},
volume = {},
number = {},
pages = {},
doi = {10.1002/eat.24574},
pmid = {41108672},
issn = {1098-108X},
support = {START 16/22//University Hospital Aachen, RWTH Aachen/ ; //Bundesministerium für Bildung und Forschung/ ; 01EW1906A-01EW1906B//EU (European Research Association (ERA-)NET NEURON)/ ; //Deutsche Forschungsgemeinschaft/ ; },
abstract = {OBJECTIVE: Anorexia nervosa (AN) is a severe eating disorder associated with brain volume reduction, glial cell loss, microbiome alterations, and dysregulated pro-inflammatory mechanisms. However, the underlying cellular mechanisms remain inadequately elucidated, and interventions addressing these alterations are lacking.

METHOD: This study employed a chronic activity-based anorexia (ABA) rat model to investigate hippocampal glial and neuronal cell alterations, inflammation, and microbial modifications in the gut. Omega-3 fatty acids and a multi-strain probiotic were examined as potentially protective agents. Cell count, proliferation, and apoptosis rates of microglia, neurons, astrocytes, and oligodendrocytes were analyzed in the hippocampus. Furthermore, local gene expression of pro-inflammatory cytokines and microRNA was measured. The hippocampal volume was determined longitudinally using 7-Tesla MRI scans before and after starvation. Finally, the fecal microbiome was analyzed to identify potential associations with brain and clinical characteristics.

RESULTS: Results confirmed the previously described reduction in astrocytes and newly demonstrated a decrease in oligodendrocytes in the hippocampus. Increased levels of IBA1-positive cells and pro-inflammatory cytokines suggest microglial activation in this region. Administering omega-3 and probiotics to starved animals reduced neuroinflammation and microglial activation in the hippocampus, resulting in significantly increased neuronal cell counts in the omega-3 group. Microbiome composition was primarily affected by the ABA model, and to a lesser extent by omega-3 and probiotics.

DISCUSSION: These findings support the involvement of microglial activation in the pathogenesis of AN, potentially relevant to hippocampal re-learning and thus important for psychotherapy. Further, omega-3 and probiotics may serve as adjunct therapeutic strategies by modifying inflammation.},
}

@article {pmid41108591,
year = {2025},
author = {Officer, A and Meng, W and Spellman, D and Martin, J and Bracci, PM and McGrath, M and Huang, Y and Gao, SJ},
title = {Oral Microbiome and Inferred Functions Predict Kaposi's Sarcoma Progression.},
journal = {Journal of medical virology},
volume = {97},
number = {10},
pages = {e70647},
doi = {10.1002/jmv.70647},
pmid = {41108591},
issn = {1096-9071},
support = {//National Institutes of Health./ ; //This study was supported by grants from the National Institutes of Health (CA096512, CA284554, CA278812, CA291244 and CA124332 to S.-J. Gao), UPMC Hillman Cancer Center Startup Fund to S.-J. Gao, S10OD028483 to the Center for Research Computing of the University of Pittsburgh, and in part by award P30CA047904. A. Officer is supported by T32CA186873./ ; },
mesh = {Humans ; *Sarcoma, Kaposi/microbiology/pathology/virology ; *Microbiota ; Disease Progression ; RNA, Ribosomal, 16S/genetics ; Male ; *Mouth/microbiology ; Female ; Middle Aged ; Adult ; Herpesvirus 8, Human ; Sequence Analysis, DNA ; Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; AIDS-Related Opportunistic Infections ; },
abstract = {Kaposi's sarcoma (KS) is a common cancer among people living with HIV and is caused by infection with Kaposi's sarcoma-associated herpesvirus (KSHV). While previous studies have linked the oral microbiome to KSHV infection and KS development, its role in KS progression remains poorly defined. We performed 16S rRNA gene sequencing targeting the V1-V2 and V3-V4 hypervariable regions to characterize the microbiome in 20 patients with AIDS-associated KS, including 10 with nonprogressive disease and 10 with progressive disease. Samples were obtained from three anatomical sites: oral cavity, peripheral blood, and tumor biopsies. The highest number of microbes were identified in the oral cavity at species, genus, and family levels. Beta diversity analysis revealed significant compositional differences in the oral microbiome between progressive and nonprogressive KS (p value = 0.044). Differential abundance analysis identified 16 species in the oral cavity associated with disease progression, compared to only three species in tumors and one in blood (p value < 0.05). Notably, Prevotella pallens and Megasphaera micronuciformis, both known producers of short-chain fatty acids, were significantly enriched in the oral microbiome of patients with progressive KS (log-fold changes = 2.8 and 2.4, respectively). Functional pathway inference revealed 39 differentially abundant microbial pathways in the oral cavity, including pathways related to denitrification, ubiquinone biosynthesis, and arginine metabolism (all p values < 0.05). Our findings provide the first evidence that specific oral microbiome alterations are associated with KS progression. The enrichment of short-chain fatty acid-producing bacteria and changes in microbial metabolic pathways may promote inflammation and KSHV lytic replication, offering potential mechanistic insights into KS pathogenesis and highlighting novel microbiome-based prognostic markers.},
}

Humans
*Sarcoma, Kaposi/microbiology/pathology/virology
*Microbiota
Disease Progression
RNA, Ribosomal, 16S/genetics
Male
*Mouth/microbiology
Female
Middle Aged
Adult
Herpesvirus 8, Human
Sequence Analysis, DNA
Bacteria/classification/genetics/isolation & purification
DNA, Bacterial/genetics/chemistry
DNA, Ribosomal/genetics/chemistry
AIDS-Related Opportunistic Infections

@article {pmid41108536,
year = {2025},
author = {Siddiqui, S and Siddiqui, H and Riguene, E and Nomikos, M},
title = {Zebrafish: A Versatile and Powerful Model for Biomedical Research.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e70080},
doi = {10.1002/bies.70080},
pmid = {41108536},
issn = {1521-1878},
support = {//NPRP-Blue Skies Research Award/ ; NPRP-BSRA1-0504-210082//Qatar Research Development and Innovation Council (QRDI), Doha, Qatar/ ; },
abstract = {Zebrafish (Danio rerio) have become a versatile model in precision medicine, bridging fundamental biology with translational applications. Their optical transparency, rapid development, and high genetic conservation with humans enable real-time imaging and cost-efficient high-throughput screening. Advances in CRISPR/Cas9, prime editing, and morpholino approaches have expanded their utility for modeling diverse human diseases. In addition to well-established roles in cardiovascular, neurological, metabolic, oncological, and infectious disease research, emerging applications include non-invasive larval urine assays, functional validation of rare human variants, host-microbiome interactions, and automated behavioral profiling for neuropsychiatric conditions. Limitations such as species-specific lipid metabolism and limited antibody availability remain, yet recent integration of single-cell transcriptomics, computational modeling, and machine learning is enhancing translational relevance. Collectively, these innovations position zebrafish as a scalable and powerful platform for disease modeling and personalized therapeutic strategies, underscoring their growing impact in the evolving landscape of precision medicine.},
}

@article {pmid41108334,
year = {2025},
author = {Chang, A and Oh, J and Shin, A and Oser, M and Manitius, N and Ghaffari, A and Limketkai, BN},
title = {Similar Symptoms, Distinct Syndromes: Multi-modal Approach to the Patient with an IBD-IBS Overlap.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {41108334},
issn = {1573-2568},
abstract = {Inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) are distinct gastrointestinal conditions, but they frequently share overlapping clinical symptoms such as abdominal pain, bloating, and altered bowel habits. IBD is defined by the presence of chronic immune-mediated inflammation, and IBS is characterized by gastrointestinal symptoms in the absence of endoscopic and histologic inflammation. When patients with IBD continue to experience IBS-like symptoms despite remission of inflammation, this phenomenon is commonly referred to as IBD-IBS overlap. These patients pose diagnostic and therapeutic challenges, as symptom persistence may reflect lingering immune activation, disrupted barrier function, visceral hypersensitivity, gut-brain axis dysfunction, or microbiome alterations. This review synthesizes emerging evidence on the shared mechanisms underlying IBD and IBS and outlines a multimodal treatment approach that includes pharmacologic management, dietary interventions, mind-body therapies, and microbiome-directed strategies such as probiotics and fecal microbiota transplantation.},
}

@article {pmid41108224,
year = {2025},
author = {Agrawal, R and Lathia, T},
title = {Obesity during pregnancy: contemporary evidence and clinical implications.},
journal = {Current opinion in endocrinology, diabetes, and obesity},
volume = {},
number = {},
pages = {},
doi = {10.1097/MED.0000000000000936},
pmid = {41108224},
issn = {1752-2978},
abstract = {PURPOSE OF REVIEW: Obesity during pregnancy is a growing global health concern with implications for maternal, fetal, and intergenerational outcomes. This review highlights pathophysiological mechanisms, clinical risks, and evidence-based management strategies across the preconception, antenatal, and postpartum periods.

RECENT FINDINGS: Maternal obesity amplifies pregnancy-associated insulin resistance, disrupts adipokine balance, and promotes inflammation, placental hormone dysregulation, and aberrant mTOR signaling. These mechanisms increase risks of gestational diabetes, hypertensive disorders, cesarean delivery, and macrosomia. Epigenetic modifications contribute to fetal metabolic programming, raising offspring risk of obesity, type 2 diabetes, and cardiovascular disease. Recent advances emphasize early risk stratification using continuous glucose monitoring, lipid and inflammatory biomarkers, and integration of telehealth-based lifestyle interventions. Precision medicine and microbiome-targeted therapies represent emerging frontiers.

SUMMARY: Management of obesity in pregnancy requires a continuum of care. Preconception optimization through lifestyle interventions and, in select cases, bariatric surgery improves outcomes. Antenatal care demands individualized metabolic monitoring, adherence to gestational weight gain targets, and pharmacologic interventions such as metformin when indicated. Postpartum priorities include structured weight management, diabetes prevention, and lactation support. Multidisciplinary, culturally tailored strategies are essential to mitigate the global burden of maternal obesity and its intergenerational consequences.},
}

@article {pmid41108133,
year = {2025},
author = {Wang, YF and Dong, SS and Chen, Y and Zeng, YH and Chen, ZX and Zhang, LL},
title = {Caries Control by CAPE Toothpaste: In Vitro, In Vivo, and In Situ Analysis.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345251374959},
doi = {10.1177/00220345251374959},
pmid = {41108133},
issn = {1544-0591},
abstract = {Dental caries is closely associated with microbiome dysbiosis. Incorporating antimicrobial agents can enhance the efficacy of fluoride toothpaste. Our previous studies showed that caffeic acid phenethyl ester (CAPE), derived from propolis, effectively inhibited cariogenic bacteria. To formulate a novel CAPE-containing fluoridated toothpaste and establish a multistage evaluation system assessing its caries-controlling efficacy. The CAPE toothpaste's physicochemical properties were characterized. Its in vitro antimicrobial activity against Streptococcus mutans was examined using quantitative suspension and checkerboard microdilution assays. In vivo anticaries efficacy and biosafety were evaluated in a rat caries model (n = 9/group) comparing 5 groups: untreated control (group NC), base toothpaste without CAPE (group B, 600 ppm F[-]), CAPE-fluoride toothpaste (group C, 0.16 mg/mL CAPE + 600 ppm F[-]), fluoride control (group F, DARLIE[®], 600 ppm F[-]), and propolis nonfluoride control (group P, Red Seal[®]). Caries severity was scored using the Keyes method. Finally, in situ enamel repair (n = 24 enamel blocks) and plaque microbiome modulation (n = 6 samples) were assessed in a 7-d clinical study (ChiCTR2400089643) with 4 groups (groups NC, C, F, and P). The novel formulation showed stable physicochemical properties. Group C reduced S. mutans by 1.5-log10 within 3 min (P = 0.0062 vs NC), and CAPE plus fluoride exhibited additive antibacterial properties (fractional inhibitory concentration index = 0.75). In rats, group C showed the lowest smooth-surface score (21.0 ± 1.7, P < 0.005 vs. all) and reduced sulcal lesion severity (slight dentinal lesions: P = 0.0181 vs. NC and P = 0.0318 vs. F). In situ, group C achieved 27.58% surface microhardness recovery (P < 0.01 vs. all), with significant reductions in mineral loss and lesion depth (P < 0.001 vs. all). Microbiome analysis revealed a preserved microbial diversity, increased Streptococcus oralis, and reduced cariogenic populations. The novel CAPE-containing fluoridated toothpaste effectively inhibited the onset and development of caries. Wider-ranging and longer-term clinical investigations are still needed.},
}

@article {pmid41108124,
year = {2025},
author = {Manzoor, M and Putaala, J and Zaric, S and Leskelä, J and Dong, A and Könönen, E and Lahti, L and Paju, S and Pussinen, PJ},
title = {Oral Microbial Determinants of Saliva and Serum Lipopolysaccharide Activity.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345251370995},
doi = {10.1177/00220345251370995},
pmid = {41108124},
issn = {1544-0591},
abstract = {Lipopolysaccharide (LPS) is a virulence factor of gram-negative bacteria, and endotoxemia or translocation of LPS in serum plays a significant role in oral and systemic pathologies. The contribution of the oral microbiome composition to saliva LPS activity and endotoxemia remains unclear. We investigated whether salivary and serum LPS levels are associated with oral microbiome diversity, taxonomic profiles, and functional characteristics. The oral microbiome was analyzed using metagenomic sequencing of saliva from 298 individuals enrolled in a multicenter case-control study, SECRETO (NCT01934725). Serum and salivary LPS activities were measured, and multiple linear regression models were fitted to identify the microbial taxa that predicted LPS levels. MaAsLin2 (Microbiome Multivariable Associations with Linear Models) was used to determine the associations of microbial functional features and LPS levels. Salivary alpha diversity was positively associated with serum LPS but negatively associated with salivary LPS, smoking, and antibiotic use in the preceding 1 to 6 mo. Community composition (beta diversity) differed between the salivary LPS tertiles (P = 0.001) but not between serum LPS tertiles. In total, 10 oral taxa associated with serum LPS tertiles and 59 with salivary LPS tertiles were identified. Prevotella, Neisseria, Leptotrichia, and Porphyromonas had significant positive associations with salivary LPS, whereas Fusobacterium had a negative association. Among these genera, Prevotella sp. E13_17, P. gingivalis, L. wadei, and F. nucleatum were the species with the strongest associations. Among the 1,016 oral microbiome metabolic features, several were linked to the biosynthesis of LPS, lipid A, and O-antigen pathways. The oral microbiome composition was strongly associated with salivary LPS activity in addition to weaker links to serum LPS. Oral microbiota-derived LPS activity in saliva was associated with microbial metabolism characterized by the predominance of proliferation and biosynthesis pathways. Our study indicates that dysbiosis of the oral microbiome is a source of increased salivary and serum LPS activity.},
}

@article {pmid41108123,
year = {2025},
author = {Boubsi, F and Anckaert, A and Argüelles-Arias, A and Ongena, M},
title = {Pectin-derived oligogalacturonides shape mutualistic interactions between Bacillus and its host plant.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf232},
pmid = {41108123},
issn = {1751-7370},
abstract = {Certain beneficial bacteria of the root-associated microbiome such as B. velezensis protect plants against diseases and are promising biocontrol agents exploited in sustainable agriculture. Unveiling the molecular dialogue governing mutualistic interactions between these beneficials and their host is essential to better understand their ecological behavior and to optimize their use as bioprotectants. However, the chemical diversity and functionality of mediators involved in this interkingdom crosstalk remain largely unexplored. In this study, we uncover a strategy by which B. velezensis exploits the root cell wall polymer pectin to prime its host for enhanced resistance against phytopathogens and to ensure a safe environment enabling its efficient root establishment. Thanks to the activity of its two conserved pectinolytic enzymes, the bacterium generates a specific pattern of short oligogalacturonides that act as efficient triggers of plant systemic defense against leaf pathogens. Moreover, these oligomers induce only weak immune responses in root cells and dampen local defense reaction in response to the perception of the bacterium itself. Our data emphasize the key role of short oligogalacturonides as mediators in the intricate interplay between plants and their bacterial associates, providing new insights into the mechanisms that enable beneficial bacteria to coexist with their host plant.},
}

@article {pmid41108012,
year = {2025},
author = {Woolley, CSC and Muwonge, A and de C Bronsvoort, BM and Schoenebeck, JJ and Handel, IG and Chamberlain, K and Rose, E and Clements, DN},
title = {The gut microbiota of Labrador retriever puppies: a longitudinal cohort study.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {108},
pmid = {41108012},
issn = {2524-4671},
support = {BB/ J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/ J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/ J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/ J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/ J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/ J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/ J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/ J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {BACKGROUND: Most research into the development of the canine gut microbiota has featured cross-sectional studies, and there has been limited exploratory research into how it is affected by external factors. We aimed to longitudinally characterise the gut microbiota and its development in Labrador Retriever puppies and identify whether alterations in the gut microbiota are associated with factors related to demography, lifestyle, antibiotic usage and gastrointestinal health.

RESULTS: 76 Labrador Retriever puppies were recruited via Dogslife, a UK-based online cohort study. Faecal samples were collected at three to four, seven, and 12 months of age and analysed using 16 S rRNA gene sequencing alongside questionnaire data. Alpha and beta diversity were assessed using linear mixed effects models and permutational multivariate analysis, accounting for repeated measures. Differential abundance was evaluated using multivariable association with linear models. Associations were identified between puppies' gut microbiota and age, sex, coat colour, household smoking status, dietary indiscretions (e.g. household waste, coprophagia), contact with other dogs and horses, recent oral/injected antibiotic use, and recent vomiting and diarrhoea. The greatest source of variation was individual identity, explaining approximately 25% of alpha diversity and 50% of beta diversity. Alpha diversity declined between three and 12 months, with age-related shifts in community composition and dispersion. Coprophagia was associated with increased alpha diversity and contributed to variation in community structure. Antibiotic use was associated with reduced alpha diversity, altered composition, and changes in taxa across Firmicutes, Proteobacteria, and Tenericutes. These effects were largely transient, with the largest shifts occurring within one week of treatment. Puppies with recent diarrhoea showed increased alpha diversity and differential abundance in several taxa within four weeks of the episode. Helicobacter was more frequently detected in samples from puppies with recent diarrhoea.

CONCLUSIONS: This longitudinal study characterises the development of gut microbiota in Labrador Retriever puppies and identifies associations with demographic, environmental, and health-related factors. These findings underscore the value of longitudinal sampling in microbiome research, offer novel insights for owners and veterinarians, and lay a foundation for future studies investigating causal mechanisms and potential interventions.},
}

@article {pmid41107739,
year = {2025},
author = {Wu, F and Jiang, X and Chen, G and Zhang, L},
title = {Integrated Microbiome and metabolome analysis reveals Microbial-Metabolic interactions in psoriasis pathogenesis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {665},
pmid = {41107739},
issn = {1471-2180},
support = {82370785//National Natural Science Foundation of China/ ; ZR2024MH220//Shandong Provincial Natural Science Foundation/ ; },
mesh = {Humans ; *Psoriasis/microbiology/metabolism ; Female ; Male ; *Skin/microbiology/metabolism ; *Metabolome ; *Microbiota ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metabolomics ; Corynebacterium ; Lipid Metabolism ; },
abstract = {BACKGROUND: Psoriasis is a chronic inflammatory skin disorder with unclear etiology. The roles of skin microbiome and metabolic dysregulation in psoriasis pathogenesis are not yet fully understood.

METHODS: We conducted an integrated microbiome and untargeted metabolomic analyses on skin samples from 29 patients with psoriasis and 31 healthy controls. The skin microbiota was characterized using 16 S rRNA gene sequencing, and untargeted metabolomic profiling was performed using LC-MS/MS. Multivariate statistical analyses were used to identify differential microbes and metabolites, followed by correlation analyses to explore microbe-metabolite interactions.

RESULTS: Psoriatic lesions exhibited significantly higher skin microbial alpha diversity compared to healthy controls. Principal component analysis revealed distinct microbial community structures between the two groups. At the genus level, Corynebacterium and Staphylococcus were significantly enriched in psoriatic lesions, while Cutibacterium was notably reduced. Metabolomic analysis identified 63 differential metabolites, with 39 upregulated and 24 downregulated in psoriatic lesions. These metabolites were primarily involved in lipid metabolism (particularly phospholipids and sphingolipids), amino acid metabolism, and inflammatory mediator pathways. Correlation analysis revealed significant associations between microbial alterations and metabolic dysregulation. Cutibacterium abundance was negatively correlated with inflammatory lipids and positively correlated with antioxidant metabolites, whereas Staphylococcus and Corynebacterium exhibited the opposite pattern. Notably, the abundance of Propionibacteriaceae strongly correlated with glutathione levels (r = 0.821, P < 0.001), indicating a potential role of microbiome-mediated oxidative stress in psoriasis.

CONCLUSIONS: This study highlights significant alterations in both the skin microbiome and metabolome in patients with psoriasis, revealing complex microbe-metabolite interaction networks. The findings suggest that microbial dysbiosis, particularly the decreased abundance of Cutibacterium and the increased abundance of Staphylococcus/Corynebacterium, may contribute to psoriasis pathogenesis by modulating lipid metabolism, inflammatory pathways, and oxidative stress responses.},
}

Humans
*Psoriasis/microbiology/metabolism
Female
Male
*Skin/microbiology/metabolism
*Metabolome
*Microbiota
Adult
Middle Aged
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/metabolism/isolation & purification
Metabolomics
Corynebacterium
Lipid Metabolism

@article {pmid41107717,
year = {2025},
author = {Khan, MSI and Wu, J and Hou, S and Ji, S and Li, H and Chang, Y and Sui, B and Tan, D and Yin, J},
title = {Bile modulates phage-host interactions in multidrug-resistant Pseudomonas aeruginosa.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {666},
pmid = {41107717},
issn = {1471-2180},
support = {2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; },
mesh = {*Pseudomonas aeruginosa/virology/drug effects/genetics/physiology ; *Bile/metabolism ; *Drug Resistance, Multiple, Bacterial ; Biofilms/growth & development/drug effects ; *Pseudomonas Phages/physiology ; Lipopolysaccharides/biosynthesis ; Pseudomonas Infections/microbiology ; *Host-Pathogen Interactions ; },
abstract = {Biliary tract infections (BTIs) arise within a bile-rich environment that profoundly shapes microbial ecology and pathogen adaptation. Pseudomonas aeruginosa, a major opportunistic pathogen in nosocomial settings, exhibits remarkable physiological plasticity, that enable persistence in such challenging niches. However, the influence of bile on P. aeruginosa's adaptive responses and phage-host interactions remains largely unexplored. Here, we demonstrate that ox-bile imposes concentration-dependent stress on P. aeruginosa strain ZS-PA-35, indicative of host-derived selective pressure. Notably, ox-bile enhances biofilm formation and promotes swarming and twitching motilities while concurrently suppressing swimming motility. Moreover, ox-bile modulates phage susceptibility, likely through altered receptor expression: exposure to ox-bile sensitizes P. aeruginosa to the type IV pili (T4P)-dependent phage phipa2, whereas susceptibility to the lipopolysaccharide (LPS)-targeting phage phipa10 remains unchanged. Genome-wide mutagenesis identified resistance-conferring mutations affecting T4P structures, LPS biosynthesis, and associated regulatory pathways. Among these, phage-resistant mutants ΔpilT and ΔgalU retained high fitness under ox-bile stress, accompanied by enhanced swarming and swimming motilities. Furthermore, in a lysogenic context, ox-bile markedly suppressed prophage accumulation in the T4P-dependent strain ZS-PA-05. These findings reveal that bile acts as a critical environmental cue shaping both adaptive physiology and phage susceptibility in P. aeruginosa, with broad implications for microbiome dynamics and the development of phage-based therapies targeting bile-impacted infections.},
}

*Pseudomonas aeruginosa/virology/drug effects/genetics/physiology
*Bile/metabolism
*Drug Resistance, Multiple, Bacterial
Biofilms/growth & development/drug effects
*Pseudomonas Phages/physiology
Lipopolysaccharides/biosynthesis
Pseudomonas Infections/microbiology
*Host-Pathogen Interactions

@article {pmid41107577,
year = {2025},
author = {Meng, L and Liu, J and Ong, HH and Wang, DY and Shi, L},
title = {MUC1 in the upper-lower airway inflammatory continuum: an endotype-centered perspective.},
journal = {Inflammation research : official journal of the European Histamine Research Society ... [et al.]},
volume = {74},
number = {1},
pages = {143},
pmid = {41107577},
issn = {1420-908X},
support = {82371117//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Mucin-1/immunology ; Animals ; *Inflammation/immunology ; *Respiratory Tract Diseases/immunology ; },
abstract = {Emerging evidence indicates that upper and lower airway diseases share anatomical and pathophysiological features. Infections often begin in the upper airway and progress downward, suggesting common immunological mechanisms. Mucin 1 (MUC1), a membrane-bound glycoprotein abundantly expressed in airway epithelial cells, has attracted increasing attention for its immunoregulatory and barrier functions. This review summarizes recent findings on MUC1's involvement in airway inflammation driven by Th1, Th2, and Th17 immune responses. In Th1-type inflammation, MUC1 negatively regulates Toll-like receptor (TLR)-NF-κB signaling pathways, thereby limiting excessive inflammatory responses to bacterial and viral infections. In Th2-type inflammation, MUC1 influences eosinophil survival, maintains epithelial integrity, and modulates glucocorticoid sensitivity, exerting both protective and pathological effects. In Th17-type inflammation, characterized by neutrophil infiltration and elevated IL-17A and IL-22, MUC1 expression alleviates chronic inflammation and may impact microbiome dysbiosis. While MUC1's roles in lower airway disorders are increasingly understood, its specific function and regulatory mechanisms in upper airway diseases remain unclear. This review adopts the unified airway disease (UAD) framework to examine the endotype-specific roles of MUC1 across the upper and lower airways. Rather than providing a disease-by-disease summary, we synthesize evidence through Th1/Th2/Th17 endotypes, link shared mechanisms to biomarker-based patient stratification, and outline MUC1-targeted therapeutic strategies. By applying an endotype- and UAD-centered perspective, the review distinguishes itself from previous work and highlights actionable opportunities for precision medicine. Furthermore, we emphasize the translational potential of MUC1 as both a diagnostic biomarker and a therapeutic target, focusing on advances in small peptides, monoclonal antibodies, RNA interference, and natural compounds that modulate MUC1-related pathways. These developments may ultimately enable the creation of personalized therapies for airway inflammation.},
}

Humans
*Mucin-1/immunology
Animals
*Inflammation/immunology
*Respiratory Tract Diseases/immunology

@article {pmid41107300,
year = {2025},
author = {Urrutia-Angulo, L and Ocejo, M and Yergaliyev, T and Oporto, B and Aduriz, G and Camarinha-Silva, A and Hurtado, A},
title = {Exploring colostrum microbiota and its influence on early calf gut microbiota development using full-length 16S rRNA gene metabarcoding.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36350},
pmid = {41107300},
issn = {2045-2322},
support = {PRE2020-096275//MICIU/AEI/10.13039/501100011033 and ESF Investing in your future/ ; },
mesh = {*Colostrum/microbiology ; Animals ; Cattle ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; DNA Barcoding, Taxonomic/methods ; Female ; Phylogeny ; },
abstract = {The early gut microbiota of calves is seeded by colostrum and shaped by diet, environment, disease, and antibiotic treatments. This study analyzed the colostrum microbiota of 42 cows and tracked their calves' gut microbiota during early life (days d1, d16, and d57), assessing the impact of antimicrobial dry cow therapy and infection treatments. The full-length 16S rRNA gene was sequenced using Oxford Nanopore, enabling taxonomic classification down to species level. Microbial richness and diversity were lowest at d1 and increased afterwards. Beta diversity analysis showed that d16 samples had microbial profiles intermediate to those of d1 and d57. The most abundant phyla (Pseudomonadota, Bacillota, and Bacteroidota) were common to all sample categories, while genus-level composition showed greater variability. Colostrum was dominated by Paraclostridium, Romboutsia, and Staphylococcus, while Escherichia/Shigella and Clostridium were more abundant in d1 feces, later replaced by Succinivibrio and Faecalibacterium at d16 and d57. Notably, 56.2% of species in d1 feces were also present in colostrum, and 37.4% of colostrum species persisted in feces at d57, highlighting colostrum´s role in bacterial gut colonization. Interindividual variability in gut microbiota decreased over time as richness and diversity increased. Antimicrobial treatments did not significantly alter microbiota diversity or composition, suggesting a limited long-term impact.},
}

*Colostrum/microbiology
Animals
Cattle
*RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/classification/isolation & purification
Feces/microbiology
DNA Barcoding, Taxonomic/methods
Female
Phylogeny

@article {pmid41107061,
year = {2025},
author = {Carraro, P and Naeem, Y and Girardi, F and Botton, A and Varotto, S and Ruperti, B and Bonghi, C},
title = {A Rootstock-Centered Perspective on the Regulation of Alternate Bearing in Fruit Trees.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf460},
pmid = {41107061},
issn = {1460-2431},
abstract = {Alternate bearing in most perennial fruit tree species refers to the phenomenon where high-yielding on-years are followed by low or nearly no fruiting off-years. This variability complicates orchard management, especially under unpredictable weather patterns. Alternate bearing is regulated by both endogenous and environmental signals, and recent studies suggest that rootstocks could play a role on its modulation. Beyond affecting scion growth and nutrient status, rootstocks influence developmental behavior through long-distance signaling. They participate in hormonal metabolism, nutrient uptake, water transport, and chromatin conformation in scion tissues. Epigenetic changes, including DNA methylation and histone marks, have been implicated in regulating flowering-related genes in response to environmental and developmental cues. This review explores possible contributions of the rootstock to alternate bearing through physiological, molecular, and epigenetic signals-such as signaling molecules and chromatin states associated with flowering-as working hypotheses. The role of rootstocks in shaping source-sink dynamics, interpreted throughout the resource budget model, and their potential influence on stress responses are also discussed in relation to the AB rhythmicity. Finally, emerging strategies aimed at mitigating alternate bearing intensity, including genome editing, marker-assisted selection, and microbiome-based strategies, are highlighted as promising for stabilizing productivity under changing climate conditions.},
}

@article {pmid41107018,
year = {2025},
author = {Marietta, E and Rubio-Tapia, A},
title = {Intestinal Bacteria and Gluten Interactions in Celiac Disease.},
journal = {Gastrointestinal endoscopy clinics of North America},
volume = {35},
number = {4},
pages = {869-880},
doi = {10.1016/j.giec.2025.02.012},
pmid = {41107018},
issn = {1558-1950},
mesh = {Humans ; *Celiac Disease/microbiology ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/complications ; *Glutens/immunology/metabolism ; Probiotics/therapeutic use ; Intestinal Mucosa/microbiology ; },
abstract = {Dysbiosis exists in both the small intestinal mucosa, as well as the fecal microbiome of patients with celiac disease. However, no clear signal has been associated with every patient with celiac disease. Rather, the intestinal microbiome of each patient with celiac disease differs from the controls. Clinical trials with probiotics have not demonstrated any consistent reversals of intestinal pathology, but they have shown promising results with amelioration of symptoms. It is unlikely that intestinal dysbiosis plays a direct role in the pathogenesis of celiac disease. Instead, it may play an aggravating role in either the pathogenesis or healing.},
}

Humans
*Celiac Disease/microbiology
*Gastrointestinal Microbiome
*Dysbiosis/microbiology/complications
*Glutens/immunology/metabolism
Probiotics/therapeutic use
Intestinal Mucosa/microbiology

@article {pmid41107011,
year = {2025},
author = {Weekley, K and Gardinier, D and Lee, AR and Weisbrod, V},
title = {The Gluten-Free Diet for Celiac Disease.},
journal = {Gastrointestinal endoscopy clinics of North America},
volume = {35},
number = {4},
pages = {753-773},
doi = {10.1016/j.giec.2025.01.009},
pmid = {41107011},
issn = {1558-1950},
mesh = {Humans ; *Celiac Disease/diet therapy/psychology ; *Diet, Gluten-Free/adverse effects/psychology ; Quality of Life ; Micronutrients/deficiency ; },
abstract = {A gluten-free diet (GFD) is the only treatment of celiac disease (CeD). A GFD is free from any food or substance with wheat, rye, and barley. CeD can be associated with micronutrient deficiencies including iron, folate, vitamin B12, vitamin D, zinc, and copper. Foods that are high in fat, added sugars, total calories are more often consumed, increasing the risk of obesity and a poor microbiome. There are psycho-social demands of a GFD including emotional burden, anxiety, social isolation, and relationship strain. People with CeD on a GFD should be monitored for nutrient deficiencies, other comorbidities, and overall quality of life.},
}

Humans
*Celiac Disease/diet therapy/psychology
*Diet, Gluten-Free/adverse effects/psychology
Quality of Life
Micronutrients/deficiency

@article {pmid41106736,
year = {2025},
author = {Tampanna, N and Lim, SJ and Rahman, HA and Sofian-Seng, NS and Razali, NSM and Mustapha, WAW and Wichienchot, S},
title = {Human gut microbiome modulation and butyrogenic effects of fucoidan from Sargassum binderi: A prebiotic activity in in vitro simulated digestion and human fecal fermentation.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {148327},
doi = {10.1016/j.ijbiomac.2025.148327},
pmid = {41106736},
issn = {1879-0003},
abstract = {The fucoidan extract from Sargassum binderi, a brown algae-derived marine polysaccharide, is rich in fucose, and are a potent candidate for functional food, and nutraceutical applications. This study uniquely investigated the prebiotic potential of S. binderi fucoidan through in vitro simulated digestion and human fecal fermentation. The fucoidan extract demonstrated higher resistance to simulated upper gastrointestinal digestion (88.27 %) than inulin (81.13 %), allowing a substantial portion to reach the colon, which was metabolized by gut microbiota into beneficial metabolites. Fucoidan selectively modulated the gut microbiome by increasing the relative abundance of Megamonas and decreasing Bacteroides. Our current findings proved that the Megamonas enrichment, a carbohydrate-fermenting genus, contributed to a substantial rise in short-chain fatty acid (SCFA) production, including butyric acid (10.24-fold), acetic acid (5.89-fold), and propionic acid (4.92-fold), higher than those produced by inulin, indicating a strong butyrogenic effect. These microbiome shifts and enhanced SCFA production suggest that S. binderi fucoidan may help maintain gut microbiome balance. Overall, the current findings highlight the potential of S. binderi-derived fucoidan to formulate functional foods with a butyrogenic effect, for promoting gut health.},
}

@article {pmid41106731,
year = {2025},
author = {Kamath, S and Ariaee, A and Abdelhafez, A and Asif, Z and Chan, NSL and Collins, K and Hunter, A and Joyce, P},
title = {Microbiome-active drug delivery systems (MADDS): Leveraging microbial stimuli for controlled drug release.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {115720},
doi = {10.1016/j.addr.2025.115720},
pmid = {41106731},
issn = {1872-8294},
abstract = {The human microbiome comprises diverse microbial communities that inhabit tissues and biofluids throughout the body, including the gastrointestinal tract, lungs, vagina, and skin. These sites create dynamic microenvironments rich in enzymes, metabolites, and chemical gradients that act both as biological barriers and as localised targets for drug delivery. This review provides an overview of Microbiome-Active Drug Delivery Systems (MADDS), an emerging class of platforms that exploit microbial stimuli for site-specific therapeutic release. Unlike conventional systems that simply coexist with the microbiome, MADDS harness resident microbes and their metabolites to trigger drug activation, retention, or release. This enables spatially precise delivery of small molecules, biologics, and live biotherapeutic products (LBPs). Key strategies include enzyme-, environment-, metabolite-, biofilm-, and receptor-responsive designs, each tailored to microbial niches and applied across infectious, inflammatory, and metabolic disorders. However, challenges remain, including microbiome variability between individuals, regulatory uncertainty around hybrid biologic-material systems, and the need for scalable GMP-compliant manufacturing. This review therefore outlines the current approaches for engineering MADDS and the future steps required for clinical translation. By exploiting microbial cues for controlled drug release, MADDS offer a practical route to more targeted and patient-specific therapies.},
}

@article {pmid41106704,
year = {2025},
author = {Heckmann, ND and Culler, M and Atallah, LM and Mont, MA and Lieberman, JR and Parvizi, J},
title = {Emerging Concepts in Periprosthetic Joint Infection Research: Infection Recurrence and Microbe Persistence.},
journal = {The Journal of arthroplasty},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arth.2025.10.033},
pmid = {41106704},
issn = {1532-8406},
abstract = {Recurrent periprosthetic joint infection (PJI) is a highly morbid complication following total joint arthroplasty (TJA). Despite appropriate medical and surgical management with targeted antimicrobial therapies, many patients who suffer from a PJI experience clinically relevant episodes of recurrence. Though the majority of these recurrent infections are due to microbes that are different from the species initially isolated at the index infection, approximately 15 to 50% of subsequent PJIs are attributed to recurrence with the same causative organism. Treatment resistance, contamination during revision surgery, hematogenous spread of bacteria from a distant source, and the presence of resilient biofilms have long been implicated in these recurrent infections. However, recent preclinical and clinical evidence has demonstrated that certain organisms that commonly cause PJI, namely staphylococcal species, can undergo phenotypic transformation into viable, but non-culturable (VBNC) and quasi-dormant small colony variant (SCV) forms that may persist intracellularly and lead to recurrent infection. Moreover, some organisms are known to infiltrate the osteocyte lacuno-canalicular network (OLCN) and invade eukaryotic cells to avoid targeting by the host immune system and antimicrobial agents. In doing so, they create microbial reservoirs that may be capable of reactivating to cause symptomatic infection locally or after being transported to the joint by circulating phagocytic cells. Commensal species present in the human microbiome may also become pathogenic and lead to recurrent PJI. Evidence suggests dysbiosis, a pathological imbalance in the composition and function of the microbiome, may induce the translocation of resident organisms from the gut into the bloodstream. Recent studies have also identified joint microbiota signatures that vary in accordance with the presence or absence of certain pathologies, including PJI.},
}

@article {pmid41106636,
year = {2025},
author = {Chen, T and Tang, Q and Yu, B and Tang, L and Lin, J and Zhang, L and Shan, W and Yu, H},
title = {Investigation of the mechanism involved in high-fat diet-induced depressive behavior based on energy metabolism.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {120505},
doi = {10.1016/j.jad.2025.120505},
pmid = {41106636},
issn = {1573-2517},
abstract = {BACKGROUND: The specific mechanisms underlying high-fat diet (HFD) and depressive behaviors remain elusive. Meanwhile, the impact of calorie restriction (CR) on the development of depression has not been explored in-depth. Thus, we aimed to examine the pathways underlying how long-term HFD intake leads to depression, focusing on energy metabolism.

METHODS: C57BL/6J mice were randomly divided into four groups-control (CK) group, CR group, HFD group, and chronic unpredictable mild stress (CUMS) group. Enzyme-linked immunosorbent assay, western blot, metabolomics and 16s rRNA gene sequencing analysis were undertaken to investigate the 5-hydroxytryptamine system, glucolipid metabolism, brain energy metabolism and gut microbiome.

RESULTS: Mice with HFD- and CUMS-induced depressive-like symptoms exhibited a significant decrease in serotonergic activity in the hippocampus. The behaviors of CR mice did not differ significantly from CK mice. Fasting blood glucose levels, fatty acid contents, and reactive oxygen species (ROS) levels were all negatively affected in unrestricted HFD and CUMS mice, suggestive of energy metabolism disruption. Metabolomic analysis revealed that tricarboxylic acid cycle activity was inhibited in the HFD and CUMS groups but not in the CR group. Additionally, analysis of the gut microbiome revealed that [Ruminococcus] gnavus exhibited higher predictive potential for HFD-induced depression, while Allobaculum showed greater predictive potential for stress-induced depression.

LIMITATIONS: Causal relationship between brain energy metabolism and gut microbiome unclear.

CONCLUSION: An unrestricted HFD promotes dysbiosis of the gut microbiota, impairs energy metabolism in the brain, affects the serotonergic system, and ultimately induces depressive-like behaviors.},
}