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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

DESIGN: Cross-sectional descriptive survey study.

SETTING: Online distribution from October 2024 to January 2025.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid41174753,
year = {2025},
author = {Xing, Y and Liu, C and Zhang, C and Zhou, D and Hu, B and Jiang, Q and Chen, J and Lin, Z and Wang, T and Yan, H and Liu, A and Lu, W and Ben, X and Yang, K and Yuan, JX and Zhan, W and Wang, J},
title = {Antibiotic-driven and microbiota-targeted therapy for advanced management of pulmonary hypertension.},
journal = {Respiratory research},
volume = {26},
number = {1},
pages = {303},
pmid = {41174753},
issn = {1465-993X},
support = {82120108001//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Hypertension, Pulmonary/drug therapy/microbiology/physiopathology ; *Anti-Bacterial Agents/therapeutic use/pharmacology/administration & dosage ; Male ; Retrospective Studies ; Rats ; Humans ; Middle Aged ; Female ; *Gastrointestinal Microbiome/drug effects/physiology ; Aged ; Rats, Sprague-Dawley ; *Disease Management ; Cohort Studies ; *Microbiota/drug effects ; },
abstract = {BACKGROUND: Pulmonary hypertension (PH), particularly secondary to hypoxic lung diseases like chronic obstructive pulmonary disease (COPD), lacks effective targeted therapies. Emerging evidence suggests that microbiota imbalances contribute to PH progression, raising the possibility of microbiome-targeted interventions. This study explores the role of antibiotics in modulating microbiota and ameliorating PH.

METHODS: A retrospective cohort analysis was conducted using the Medical Information Mart for Intensive Care (MIMIC) database to assess changes in mean pulmonary artery pressure (mPAP) after antibiotic treatment. Subsequently, clinical data of 220 PH patients (including group 1, 3, and 4 PH) from single clinical center were analyzed, with 16S rRNA sequencing performed on pharyngeal and fecal samples to evaluate microbiota composition. A hypoxia-induced PH rat model was used to investigate the effects of antibiotic treatment on hemodynamics, pulmonary vascular remodeling, and gut microbiota.

RESULTS: Antibiotic use was associated with reduced mPAP in PH patients, particularly in hypoxic associated PH. Microbiota diversity decreased with antibiotic treatment, but probiotic species like Lactobacillus were enriched. In hypoxia-induced PH rats, antibiotics attenuated right ventricular systolic pressure (RVSP), reduced pulmonary vascular thickening, and preserved gut villi integrity. Lactobacillus and Anaerostipes correlated negatively with PH severity, suggesting a protective role.

CONCLUSION: Antibiotic-driven microbiota modulation may alleviate PH progression by targeting dysbiosis and reducing inflammation. These findings support further investigation into optimized antibiotic regimens as a therapeutic strategy for PH, particularly in hypoxic lung disease-associated cases.},
}

Animals
*Hypertension, Pulmonary/drug therapy/microbiology/physiopathology
*Anti-Bacterial Agents/therapeutic use/pharmacology/administration & dosage
Male
Retrospective Studies
Rats
Humans
Middle Aged
Female
*Gastrointestinal Microbiome/drug effects/physiology
Aged
Rats, Sprague-Dawley
*Disease Management
Cohort Studies
*Microbiota/drug effects

@article {pmid41174528,
year = {2025},
author = {Sharma, D and Valmiki, H and Chayal, P and Kumar, S and Chhotaray, S},
title = {Microbiome study of Murrah buffalo mastitis milk with emphasis on Acinetobacter species.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {703},
pmid = {41174528},
issn = {1471-2180},
}

@article {pmid41174251,
year = {2025},
author = {Dass, M and Abbai, NS and Ghai, M},
title = {The human skin microbiome: factors affecting individuality and application in forensic investigations.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {41174251},
issn = {1437-1596},
abstract = {Differences in microbial communities have been observed across various skin sites, such as dry, moist, and sebaceous areas. These skin types influence the diversity of microbials present in each microenvironment. Commonly found skin microbes include Staphylococcus epidermidis, Cutibacterium acnes and Corynebacterium sp. Ethnicity, age, gender and health status are a few individual-specific factors that shape the skin microbiome. Every individual retains unique and distinct skin microbial communities despite constant exposure to environmental changes. In forensic investigations, human identification can be achieved through skin microbial trace analysis left behind on surfaces and objects. Temporal stability of the microbial profile, on skin, for up to two weeks, is an attractive feature for the implementation of skin microbiome analysis in forensic applications. Additionally, microbial traces can assist in determining geolocation and estimating postmortem interval. Although high-throughput sequencing technologies have accelerated microbiome research and provide species-level information, the skin is a low-biomass sample, and there are currently no standardised protocols from sample collection to analysis. Machine learning is rapidly advancing skin microbiome research by enabling the analysis of large and complex datasets to uncover patterns. These patterns can be used for predicting skin health conditions, matching skin samples to specific microenvironments, identifying individuals and inferring biogeographic origins. The present review highlights current research in the application of skin microbiome analysis for forensics and future potential applications for age and gender determination. Additionally, the factors affecting the skin microbiome diversity are discussed. Skin microbiome research will accelerate enrichment of microbiome databases, which could complement the standard STR typing in accurate human identification.},
}

@article {pmid41173905,
year = {2025},
author = {Adhikary, R and Alkhatib, AEA and Hazra, S},
title = {Resistome profiling and bacterial community structure of semi-urban gutter ecosystems of India.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38127},
pmid = {41173905},
issn = {2045-2322},
mesh = {India ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; *Drug Resistance, Bacterial/genetics ; beta-Lactamases/genetics/metabolism ; Gastrointestinal Microbiome ; Metagenomics/methods ; Humans ; Microbiota ; Metagenome ; },
abstract = {Environmental factors contribute to antimicrobial resistance, a global health threat. Contaminated gutter water in urban areas spreads resistant bacteria, disrupting ecosystems and promoting biofilm formation, causing widespread concern. This study aimed to evaluate antibiotic-resistant bacterial populations across six gutter ecosystems in Roorkee, Uttarakhand, India during summer against different classes of antibiotics, identify presence of beta-lactamase, and explores total bacterial communities, and predicting metabolic pathways through 16S rRNA based metagenomic approach of V3 region. The highest resistant bacterial population was found in HL_NS-6, and HL_NS-2, with highly resistance to Penicillin (ampicillin and oxacillin), Cephalosporin (Cephalothin), aminoglycoside (Kanamycin), fluoroquinolone (ciprofloxacin), and Antifolate (Trimethoprim) class antibiotics. Beta-lactamase activity was detected in all samples except HL_NS-5, indicated by nitrocefin hydrolysis. The microbial community in the six samples were composed with the major families enterobacteriaceae (15.4%) and pseudomonadaceae (8.29%), covering 23.7% of the total population. The highest taxa were found in HL_NS-2 and HL_NS-4, while the largest genera were Pseudomonas (8.3%), Escherichia (8.2%), Hydrogenophaga (6.85%), and Candidatus Moranella (5.4%). There were 21.25% common bacterial genera were present as core microbiome and rest were signified the population diversity among the six-gutter microbiome. The coexistence of common metabolic pathways (citric acid cycle, carbon, nitrogen metabolism etc.), and streptomycin, glycosphingolipid, lipopolysaccharide, cyanoamino acid metabolism pathways might be induced the development of antibiotic resistance in gutter microbiome. This study suggests the presence of antibiotic-resistant bacteria with antibiotic resistant metabolic pathways, and beta-lactamase genes in urban gutter water, which could be harmful to both human health and environmental ecosystems.},
}

India
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects/classification
RNA, Ribosomal, 16S/genetics
*Ecosystem
*Drug Resistance, Bacterial/genetics
beta-Lactamases/genetics/metabolism
Gastrointestinal Microbiome
Metagenomics/methods
Humans
Microbiota
Metagenome

@article {pmid41173853,
year = {2025},
author = {Huang, Y and Li, H and Zhu, B and Feng, S and Liu, C and Zhang, Z and Ning, Y and Wu, K and Wu, F},
title = {The association between gut microbiota and functional connectivity in cognitive impairment of first-episode major depressive disorder.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {449},
pmid = {41173853},
issn = {2158-3188},
support = {82301688//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82301688//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82301688//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82301688//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82301688//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82301688//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82301688//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82301688//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Cognitive Dysfunction/physiopathology/microbiology/diagnostic imaging ; *Depressive Disorder, Major/microbiology/physiopathology/complications/diagnostic imaging ; Male ; Female ; Adult ; Magnetic Resonance Imaging ; Young Adult ; *Brain/physiopathology/diagnostic imaging ; Case-Control Studies ; *Nerve Net/physiopathology/diagnostic imaging ; Connectome ; },
abstract = {The pathogenesis of major depressive disorder(MDD) and cognitive impairment has been linked to gut microbiota; however, the relationship between cognitive impairment and gut microbiota in patients with MDD and their underlying mechanisms remain unclear. This study aimed to investigate the brain-gut axis involved in cognitive impairment among patients with first-episode MDD through neuroimaging and microbiome analyses. 43 microbial species were different between patients with first-episode MDD and healthy controls. Notably, the relative abundances of Amycolatopsis sp. Hca4 and Shewanella livingstonensis were lower in patients with MDD compared to healthy controls, with Amycolatopsis sp. Hca4 negatively correlated with processing speed and Shewanella livingstonensis positively correlated with verbal learning. Brain network analysis revealed significant connectivity between subnetworks in patients with MDD, with cognitive function closely associated with connections between somatomotor-limbic, default mode-limbic and frontoparietal-limbic networks. Additionally, Amycolatopsis sp. Hca4 was found to modulate the relationship between the functional connectivity of the middle frontal gyrus and parahippocampal gyrus and working memory, with this correlation varying according to the abundance of Amycolatopsis sp. Hca4. These findings suggest that gut microbiota disturbances in patients with first-episode MDD serve as a regulatory factor for brain dysfunction and cognitive impairment.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Cognitive Dysfunction/physiopathology/microbiology/diagnostic imaging
*Depressive Disorder, Major/microbiology/physiopathology/complications/diagnostic imaging
Male
Female
Adult
Magnetic Resonance Imaging
Young Adult
*Brain/physiopathology/diagnostic imaging
Case-Control Studies
*Nerve Net/physiopathology/diagnostic imaging
Connectome

@article {pmid41173690,
year = {2025},
author = {Strunk, T and Steer, J and Currie, A},
title = {Neonatal skin: barrier, immunity and infection prevention in the NICU.},
journal = {Seminars in fetal & neonatal medicine},
volume = {},
number = {},
pages = {101681},
doi = {10.1016/j.siny.2025.101681},
pmid = {41173690},
issn = {1878-0946},
abstract = {The neonatal skin is central to early survival and immune development. Far from being a passive mechanical barrier, it integrates physical, chemical, and microbial defences that together protect the infant in the immediate postnatal period. In preterm infants, structural immaturity, reduced antimicrobial capacity, and altered microbial colonisation confer heightened vulnerability to infection and inflammation. At the same time, the neonatal period represents a critical window during which skin-microbe interactions shape tolerance and long-term immune trajectories. This review summarises recent advances in understanding the development of the skin barrier, antimicrobial and innate immune defences, and the role of commensals in immune programming. Translational opportunities for neonatal care are discussed, including skin protective practices, antisepsis, and emollient use that may reduce infection risk in the neonatal intensive care unit. Finally, we consider future directions in microbiome-informed and skin-centred strategies.},
}

@article {pmid41173568,
year = {2025},
author = {Díaz Perdigones, CM and Hinojosa Nogueira, D and Rodríguez Muñoz, A and Subiri Verdugo, A and Vilches-Pérez, A and Mela, V and Tinahones, FJ and Moreno Indias, I},
title = {Taxonomic and functional characteristics of the gut microbiota in obesity: A systematic review.},
journal = {Endocrinologia, diabetes y nutricion},
volume = {72},
number = {9},
pages = {501624},
doi = {10.1016/j.endien.2025.501624},
pmid = {41173568},
issn = {2530-0180},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Obesity/microbiology/metabolism ; Bacteria/classification ; },
abstract = {Obesity is a growing public health problem. In recent decades, scientific evidence has linked gut microbiota to obesity. This systematic review summarizes current knowledge on the composition and functional differences in gut microbiota between individuals with obesity and those with normal weight. Following PRISMA 2020 recommendations, studies published in adult populations between January 2014 and May 2024 were reviewed. PubMed, Web of Science, and Scopus databases were searched for observational studies that had used advanced sequencing methods, such as 16S rRNA and shotgun metagenomics, to assess gut microbiota. The quality of these studies was also analyzed using the Newcastle-Ottawa scale. Our review of 16 studies shows a reduction in microbial diversity in individuals with obesity. In addition, a higher relative abundance of the phylum Firmicutes, the families Enterobacteriaceae, Gemellaceae, Prevotellaceae, Streptococcaceae and Veillonellaceae, as well as the genera Blautia, Butyricimonas, Collinsella, Megamonas, and Streptococcus, while beneficial bacteria such as the families Porphyromonadaceae and Rikenellaceae, and the genera Bifidobacterium spp. and Faecalibacterium prausnitzii, were depleted. Functional analysis showed a tendency to an increase in metabolic pathways associated with carbohydrate and lipid metabolism, with reduced pathways related to short-chain fatty acid production. Obesity is associated with altered gut microbiota composition and function. However, the variability across studies regarding population characteristics, dietary pattern, and sequencing techniques limits the comparability of findings. Future research should prioritize standardized methodologies and confounding factors to elucidate the role of the gut microbiome in obesity.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Obesity/microbiology/metabolism
Bacteria/classification

@article {pmid41173369,
year = {2025},
author = {Goerdten, J and Rattner, J and Merdas, M and Achaintre, D and Yuan, L and Russo, P and Veidebaum, T and Molnár, D and Lissner, L and De Henauw, S and Moreno, LA and Aleksandrova, K and Foraita, R and Nöthlings, U and Keski-Rahkonen, P and Floegel, A},
title = {Reproducibility and sources of variation of urinary biomarkers of food intake of fruits, vegetables and chocolate in European children and adolescents.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.10.039},
pmid = {41173369},
issn = {1541-6100},
abstract = {BACKGROUND: Biomarkers of food intake (BFI) may improve dietary assessment. Thereby, a key concern is their reproducibility over time. In epidemiological studies this is important to accurately estimate habitual food intake, and consequent disease risk associations.

OBJECTIVE: We aimed to assess the reproducibility of twelve urinary metabolites linked to food intake and to investigate potential sources of their variation.

METHODS: The analyses are based on previously identified urinary metabolites associated with dietary intake of fruits, vegetables, and chocolate in the large-scale European IDEFICS/I.Family study. Metabolites were measured in 1,788 urine samples from 599 children at study baseline (2007/2008, n=597), at the first follow-up (2009/2010, n=596), and the third follow-up (2013/2014, n=595) using high-resolution liquid chromatography-mass spectrometry. Unadjusted and adjusted intra-class correlation coefficients (ICC) were calculated for 2-year and 4-year intervals. To identify sources of biomarker variability, various factors, including dietary intake, were analysed. The amount of variance explained by each factor was quantified using the partial coefficient of determination (R[2]).

RESULTS: The median ICCs were 0.27 (range: 0.11; 0.54) and 0.28 (range: 0.15; 0.51) over 2- and 4-years interval, respectively. Individual factors explained a median of 17% (range: 9.8%; 42.4%) of the variance for the 2-year interval and 14.6% (range: 8.3%; 43.8%) for the 4-year interval. Country of residence explained the largest proportion of variance (median 5% for the 2-year interval; 4.5% for the 4-year interval). Dietary intake explained only a variation of 0.7% (0.0%; 1.5%) and 0.6% (0.0%; 1.1%) for the 2- and 4-year interval, respectively.

CONCLUSION: The reproducibility of urinary metabolites was poor to moderate over the 2- to 4- year periods, and only part of the variability could be explained by the studied factors. Future studies should explore shorter time intervals and other sources of variation e.g., the influence of the gut microbiome and genetic factors.},
}

@article {pmid41173282,
year = {2025},
author = {Fu, Z and Li, W and Qiu, H and Romero-Freire, A and He, E},
title = {Critical role of crosstalk through the gut-liver and gut-kidney axes in mediating organ-specific toxicity induced by foodborne and waterborne rare earth elements.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {387},
number = {},
pages = {127327},
doi = {10.1016/j.envpol.2025.127327},
pmid = {41173282},
issn = {1873-6424},
abstract = {The escalating contamination of rare earth elements (REEs) in agricultural soils and rivers from intensive mining activities necessitates urgent investigation into their potential health risks. This study systematically compared the organ-specific toxicological effects of foodborne versus waterborne REE exposure in murine model, focusing on toxicity mechanisms mediated by the gut-liver and gut-kidney axes crosstalk. Elevated REE concentrations were detected in both liver and kidney tissues, as well as feces following exposure, with accumulation dependent on exposure level and duration, indicating that REEs can accumulate in mice despite existing excretion mechanisms. Histopathological analysis and immunofluorescence staining revealed that tissue damage related to inflammation and oxidative stress in the liver and kidney was caused by REE exposure, supported by altered metabolite profiles. Both foodborne and waterborne REEs disrupted hepatic metabolism related to amino acids and arachidonic acid, driving inflammation and oxidative stress. Whereas waterborne REEs preferentially impaired renal tryptophan and riboflavin metabolism associated with oxidative stress. Notably, both pathways disturbed the urea cycle in target organs, impacting nitrogen metabolism. Furthermore, REE exposure triggered a significant shift in intestinal flora composition, characterized by an elevated Firmicutes/Bacteroidota ratio. Correlation network analysis indicated significant crosstalk within the gut-kidney axis (p < 0.01), underscoring the critical role of gut microbiota in mediating REE toxicity. While the gut-liver axis exhibits comparatively weaker interactions. Overall, our study offers new insights into the distinct toxic action mechanisms of REEs through varied exposure patterns and highlights the gut microbiota as a key modulator of host health outcomes.},
}

@article {pmid41172985,
year = {2025},
author = {Padhi, P and Abdalla, A and Schneider, B and Backes, N and Otto, AA and Scheibe, IJ and Thomas, JP and Khadse, G and Samidurai, M and Jochmans, AK and George, A and Zenitsky, G and Jin, H and Anantharam, V and Kanthasamy, A and Mishra, A and Allenspach, K and Mochel, J and Phillips, GJ and Kanthasamy, AG},
title = {Bioengineered gut bacterium synthesizing levodopa alleviates motor deficits in models of Parkinson's disease.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.10.005},
pmid = {41172985},
issn = {1934-6069},
abstract = {L-3,4-Dihydroxyphenylalanine (L-DOPA), synthesized from L-tyrosine, is a direct precursor to dopamine. L-DOPA is the gold-standard treatment for Parkinson's disease (PD), given orally alongside decarboxylase inhibitors (e.g., benserazide) to enhance bioavailability. However, its chronic daily pulsatile-like delivery is associated with complications. Herein, we show the construction and in vivo efficacy of a programmable, titratable, genetically engineered E. coli Nissle 1917 system (EcNL-DOPA) that continuously synthesizes L-DOPA from L-tyrosine for systemic distribution. Oral administration of EcNL-DOPA with benserazide maintains therapeutic plasma L-DOPA concentrations and increases brain dopamine levels. EcNL-DOPA improves motor performance and limits depressive-like behaviors without adverse side effects in healthy mice, Parkinsonian mice, and canine models. Simulated physiological models from pharmacokinetic and pharmacodynamic studies in canines demonstrate the translational feasibility of this biotherapeutic system for potential human studies. This work lays the groundwork for EcNL-DOPA as a continuous, non-invasive microbial drug delivery platform for PD and chronic neurological diseases.},
}

@article {pmid41172954,
year = {2025},
author = {Suri, H and Suri, H and Nagda, N and Misra, T and Vuppu, S},
title = {Current perspectives on the human skin microbiome: Functional insights and strategies for therapeutic modulation.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {193},
number = {},
pages = {118655},
doi = {10.1016/j.biopha.2025.118655},
pmid = {41172954},
issn = {1950-6007},
abstract = {Human skin is inhabited by commensal microbiota comprising bacteria, fungi, viruses, and demodex mites. The skin microbiome is associated with several vital functions for the host, such as maintaining barrier integrity, modulating lipid homeostasis, eliminating pathogens, and stimulating the immune reactions. However, alterations in the composition of the skin microbiome are often found to be linked with inflammatory dermatological conditions like atopic dermatitis, psoriasis, acne vulgaris, rosacea, and wound-associated infections. These conditions can be diagnosed using culture-dependent and advanced culture-independent analyses, including multi-omics platforms and high-throughput sequencing technologies. Developments in microbiome research and biotechnology have catalysed initiatives to modify the skin microbiota as a therapeutic intervention. Current strategies encompass precision medicine utilising biomarkers, transplantation of complete microbial consortia, application of specific commensal microbes, bacteriophage therapy, use of pre- and probiotic metabolites, as well as sanitizers and antibiotics. This study consolidates existing knowledge regarding the composition and functional roles of the skin microbiome, investigates dysbiosis in skin pathologies, and examines potential microbiome-targeted therapeutic interventions. The study intends to address the challenges and future directions related to the clinical implementation of microbiome-targeted approaches, encompassing the regulatory aspects necessary to guarantee the efficacy and safety of innovative diagnostic and therapeutic applications.},
}

@article {pmid41172807,
year = {2025},
author = {Huang, KC and Lin, CY and Chuang, PY and Yang, TY and Tsai, YH and Li, YY and Chang, SF},
title = {Microbiota diversity and its influence on diabetic osteoporosis development.},
journal = {Biochemical and biophysical research communications},
volume = {790},
number = {},
pages = {152884},
doi = {10.1016/j.bbrc.2025.152884},
pmid = {41172807},
issn = {1090-2104},
abstract = {Diabetic osteoporosis represents a form of secondary osteoporosis whereby diabetes, particularly through chronic hyperglycemia, compromises bone quality and elevates fracture risk. Recent studies using type II diabetes mellitus (T2DM) rat models induced by a high-fat diet (HFD) and low-dose streptozotocin (STZ) have revealed both gut microbiota dysbiosis and osteoporotic bone changes. However, the mechanisms by which the gut microbiota contributes to diabetic osteoporosis remain poorly understood. This study aimed to elucidate the underlying mechanisms of diabetic osteoporosis through microbiome profiling and pathway enrichment analysis. A male T2DM rat model was established via HFD feeding and STZ injection. Bone structural integrity was assessed using micro-computed tomography, while gut microbiota composition was analyzed via 16 S rRNA gene pyrosequencing and subsequent bioinformatic processing. The results showed that T2DM rats exhibited significantly elevated levels of proinflammatory cytokines, which were negatively correlated with bone density and bone turnover markers. Microbiota diversity analysis revealed a decrease in beneficial bacterial taxa, including Lactobacillus, Romboutsia, Turicibacter, and Clostridia UCG-014, alongside an increase in potentially pathogenic Enterococcus, despite a modest increase in other beneficial genera such as Parabacteroidetes, Intestinomonas, and Faecalibaculum. Functional enrichment analysis indicated impaired short-chain fatty acid (SCFA) metabolism, specifically reduced propanoate and butanoate pathway, and enhanced tryptophan metabolism, both of which were associated with decreased bone mass. These findings suggest that microbiota-driven alterations in SCFA production contribute to systemic inflammation and bone loss. Identification of key microbial metabolites and pathways may guide the development of microbiome-targeted therapies to improve metabolic and skeletal health in diabetic populations.},
}

@article {pmid41172523,
year = {2025},
author = {Matishov, G and Rudoy, D and Tkacheva, I and Prazdnova, E and Neidorf, A and Kulikov, M and Nedina, N},
title = {Prospects of the BFT development for utilization of heterotrophic microbiome as a feed raw material source and maintenance of optimal parameters of the cultivation environment.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {85},
number = {},
pages = {e295017},
doi = {10.1590/1519-6984.295017},
pmid = {41172523},
issn = {1678-4375},
mesh = {*Microbiota/physiology ; *Aquaculture/methods ; *Animal Feed ; *Sewage/microbiology ; *Bioreactors/microbiology ; Heterotrophic Processes ; Animals ; },
abstract = {The need of the aquaculture development intensification is related with the growing demand of the world community for quality food products produced with minimal environmental impact. The trend of implementing industries that contribute to the achievement of sustainable development of mankind implies the development of new environmentally friendly technologies. The introduction of the biofloc system in aquaculture implies not only an increase in the production profitability due to effective water treatment in cultivation pools, but also the possibility to use the formed activated sludge flocs as raw material for feed additives. However, the formation of the BFT system microbiome is accompanied by significant changes in the species composition of the microbial community. The technology efficiency is largely related to the possibility of microbiome community management, so the study of species composition, quantitative characteristics and biological features of the BFT system components is of great interest. The dynamics of microbiome development, its influence on marketable qualities and morphophysiological characteristics of hydrobionts, as well as the biochemical features of floc raw materials, are investigated comprehensively.},
}

*Microbiota/physiology
*Aquaculture/methods
*Animal Feed
*Sewage/microbiology
*Bioreactors/microbiology
Heterotrophic Processes
Animals

@article {pmid41172500,
year = {2025},
author = {Silva, RM and Petean, GBF and Pannuti, CM and Souza, NV and Silva-Sousa, YTC and Gavini, G and Duarte, MAH and Estrela, C and Bueno, M and Mazzi-Chaves, JF and Paula-Silva, FWG and Sipert, C and Basso, F and Damião Sousa-Neto, M},
title = {Advances in clinical and translational research in endodontics: A comprehensive overview.},
journal = {Brazilian dental journal},
volume = {36},
number = {},
pages = {e236723},
pmid = {41172500},
issn = {1806-4760},
mesh = {Humans ; *Translational Research, Biomedical ; *Endodontics/trends ; },
abstract = {Clinical and translational research play a decisive role in advancing evidence-based endodontics by bridging basic science with clinical applications. This narrative review provides a comprehensive overview of the current state and advances in clinical and translational research in Endodontics, addressing methodological foundations, diagnostic challenges, and emerging technologies. It highlights the importance of well-designed randomized controlled trials, robust outcome definitions, and the inclusion of patient-reported outcome measures. The integration of advanced imaging, particularly cone-beam computed tomography, has significantly improved diagnostic accuracy and treatment monitoring. Molecular biology techniques, including polymerase chain reaction and biomarker profiling, have expanded the understanding of endodontic microbiome, immune responses, and host factors related to treatment outcomes. Despite these advances, persistent limitations include diagnostic imprecision, lack of standardized criteria, and underutilization of biomarkers and omics data in clinical practice. The rise of precision dentistry, propelled by genomics, bioinformatics, and artificial intelligence, holds the potential to revolutionize endodontic care through personalized diagnostic and therapeutic strategies. Bridging existing gaps will require rigorous study designs, coordinated multicenter efforts, and the effective integration of molecular diagnostics, all of which are critical to advancing endodontic science and optimizing patient outcomes. Likewise, the full potential of translational science can be harnessed to reshape the future of endodontics.},
}

Humans
*Translational Research, Biomedical
*Endodontics/trends

@article {pmid41172333,
year = {2025},
author = {Athreya, GS and Czuppon, P and Gokhale, CS},
title = {The Evolution of Dependence and Cohesion in Incipient Endosymbioses.},
journal = {The American naturalist},
volume = {206},
number = {5},
pages = {435-451},
doi = {10.1086/737588},
pmid = {41172333},
issn = {1537-5323},
mesh = {*Symbiosis ; *Biological Evolution ; Models, Biological ; Animals ; Reproduction ; },
abstract = {AbstractEukaryogenesis is the prototypical example of an egalitarian evolutionary transition in individuality, and endosymbiosis, more generally, is central to the origins of many complex biological systems. Why do only some symbioses undergo such a transition, and how does the host-symbiont relationship change during this process? Here, we characterize endosymbiosis by two emergent collective-level properties: host and symbiont survival as a collective ("mutual dependence") and the level of synchronized reproduction ("reproductive cohesion"). Using adaptive dynamics, we study the evolution of the traits underlying these properties. First, by adding a carrying capacity for the collective population-a realism omitted in previous models-we find novel reasons why complete dependence or cohesion might not evolve, thus providing further theoretical support for the rarity of transitions in individuality. Second, our model suggests that asymmetries in evolutionary outcomes of hosts and symbionts can be explained by a difference in their population growth parameters, coupled with their shared fate when in a collective. Last, we show that during the early stages of an endosymbiosis, even if investments in dependence and cohesion are uncorrelated, mutual dependence arises faster than reproductive cohesion. Our results hence shed light on three aspects of endosymbiosis: coevolution between the host and symbiont, coevolution between dependence and cohesion, and ultimately the opportunity to undergo an evolutionary transition. Connecting to ecological factors, this work uncovers fundamental properties of endosymbioses, providing a clear way forward for theoretical and empirical investigations.},
}

*Symbiosis
*Biological Evolution
Models, Biological
Animals
Reproduction

@article {pmid41172301,
year = {2025},
author = {Wang, Y and Le Roy, CI and Li, J and Han, S and Liu, Z and Lahiry, A and Sahu, H and Li, Q and Dong, J and Mondragon, A and Samuel, TM and Cai, W},
title = {Efficacy of a Ready-to-Feed Starter Liquid Infant Formula Containing 2-Fucosyllactose and Lacto-N-Neotetraose in Chinese Infants: Protocol for a Double Blind, Randomized Controlled Trial.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e66489},
doi = {10.2196/66489},
pmid = {41172301},
issn = {1929-0748},
mesh = {Humans ; *Infant Formula/chemistry ; Double-Blind Method ; *Trisaccharides/administration & dosage/pharmacology ; Infant ; *Oligosaccharides/administration & dosage/pharmacology ; Gastrointestinal Microbiome/drug effects ; China ; Infant, Newborn ; Female ; Male ; Milk, Human/chemistry ; Bifidobacterium ; Randomized Controlled Trials as Topic ; Quality of Life ; Feces/microbiology ; Breast Feeding ; East Asian People ; },
abstract = {BACKGROUND: Bioactive compounds, such as human milk oligosaccharides (HMOs), impact the development of the intestinal microbiome and immune maturation in early life. They have been shown to result in positive benefits, including improved gut health, reduced frequency of infections, and age-appropriate growth when added to infant formula. However, data supporting the added value of including these HMOs in early-stage infant formula is currently lacking among Chinese infants.

OBJECTIVE: In this double-blind randomized controlled trial including a nonrandomized reference breastfed group, we will test the efficacy of ready-to-feed infant formula containing 2 HMOs (2-fucosyllactose and lacto-N-neotetraose) on Bifidobacteria abundance, gut microbiome, gut and immune health, growth, and quality of life.

METHODS: Healthy infants will be enrolled between 3 and 14 days after birth at 5 sites in China and randomized to either the experimental group (fed ready-to-feed infant formula containing 2 HMOs) or the control group (fed the same ready-to-feed infant formula without the 2 HMOs), using a dynamic allocation algorithm with double blinding. Infants will receive trial formula until age 6 months and will be followed up until age 12 months. The breastfed group will serve as a reference. The primary end point will be Bifidobacteria abundance in fecal samples at 3 months, measured via quantitative polymerase chain reaction. Secondary end points will include fecal microbiome (including taxonomy, diversity, functionality, and metabolites), fecal markers of immune health, gastrointestinal tolerance, stooling patterns, immune competence (overall state of the immune system), sleep quality, growth, quality of life, medication use, and physician-reported adverse events. A 2-sided test at the 5% significance level will be used for statistical testing.

RESULTS: The study received ethical approval in March 2024 and will be completed by the end of 2026, which will be followed by a publication in a peer-reviewed journal.

CONCLUSIONS: The Starter Liquid Infant Formula Trial (STARLIT) will be one of the first to assess the efficacy of these 2 HMOs among Chinese infants on gut and immune health, in addition to clinically relevant outcomes such as quality of life, growth, and adverse events. This study should help to demonstrate that an increase in the growth of beneficial Bifidobacteria in response to intake of 2-fucosyllactose and lacto-N-neotetraose may have a broader impact on overall gut microbiome composition and infant gut and immune health.

TRIAL REGISTRATION: ClinicalTrials.gov NCT06361719; https://clinicaltrials.gov/study/NCT06361719.

PRR1-10.2196/66489.},
}

Humans
*Infant Formula/chemistry
Double-Blind Method
*Trisaccharides/administration & dosage/pharmacology
Infant
*Oligosaccharides/administration & dosage/pharmacology
Gastrointestinal Microbiome/drug effects
China
Infant, Newborn
Female
Male
Milk, Human/chemistry
Bifidobacterium
Randomized Controlled Trials as Topic
Quality of Life
Feces/microbiology
Breast Feeding
East Asian People

@article {pmid41171541,
year = {2025},
author = {Joseph, JS and Selvamani, SB and Thiruvengadam, V and Ramasamy, GG and Subramanian, S and Menon, G and Sivakumar, G and Manjunath, C},
title = {Gut microbiota profiling of Apis cerana indica across biodiversity hotspots in the Western Ghats, India.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {35},
pmid = {41171541},
issn = {1573-4978},
mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; },
abstract = {BACKGROUND: The gut microbiome of honey bees plays a crucial role in regulating key physiological traits and metabolic processes, including digestion, detoxification, nutrient assimilation, development and immunity. However, information on the gut bacterial diversity of Apis cerana indica bee populations in India remains limited. This study aims to address this critical knowledge gap in Western Ghats, India with outcomes that may provide valuable insights for improving beekeeping practices in the region.

METHODS AND RESULTS: To fill this gap, we investigated and characterized the gut bacteriome of A. cerana indica collected from two ecologically distinct regions within the Western Ghats. We employed a combination of next-generation sequencing (NGS) using the Oxford Nanopore platform and traditional culture-based methods targeting the 16S rRNA gene to analyze the microbial communities. Our results revealed that the gut bacterial communities of foraging A. cerana indica bees from both locations displayed unique and overlapping microbiome profiles. A total of 225 bacterial species across 30 bacterial orders were identified via 16S rRNA amplicon sequencing, with 92 species shared between the two sites. Prominent symbiotic bacterial groups included Gammaproteobacteria, Betaproteobacteria, Flavobacteria, Actinobacteria, Firmicutes, Proteobacteria, and Actinomycetota. Notably, core bee-associated symbionts exhibited a negative correlation with pathogenic bacterial taxa.

CONCLUSION: These findings offer valuable insights into the ecological and functional roles of the gut microbiome in A. cerana indica, a native honeybee species of the Western Ghats. The presence of shared bacterial species across regions suggests their potential significance in formulating conservation strategies for indigenous bee populations.},
}

Bees/microbiology
Animals
*Gastrointestinal Microbiome/genetics
India
RNA, Ribosomal, 16S/genetics
Biodiversity
Bacteria/genetics/classification
High-Throughput Nucleotide Sequencing/methods
Phylogeny

@article {pmid41171386,
year = {2025},
author = {Singh, S and Kriti, M and Sharma, P and Pal, N and Sarma, DK and Verma, V and Tiwari, RR and Kumar, M},
title = {From Gut to Reproductive Health: Exploring Microbiome Interactions and Future Interventions.},
journal = {Reproductive sciences (Thousand Oaks, Calif.)},
volume = {},
number = {},
pages = {},
pmid = {41171386},
issn = {1933-7205},
abstract = {Recent advances in microbiome research have illuminated the complex bidirectional interactions between gut health and reproductive well-being. Understanding the gut microbiome's influence on the reproductive system and vice versa reveals how both of them can affect hormone production, immune function, and ultimately overall reproductive health. Dysbiosis, an imbalance in the gut microbial community, has been linked with a range of reproductive issues, including decreased sperm count and motility, erectile dysfunction, polycystic ovary syndrome (PCOS), endometriosis, infertility, and adverse pregnancy outcomes. This review critically evaluates emerging therapeutic interventions aimed at restoring microbial balance and enhancing reproductive health, such as use of prebiotics, probiotics, bacteriophage therapy, and fecal microbiota transplantation (FMT). By exploring the intricate interplay between gut microbiota and reproductive health, this review also emphasizes the need for integrated approaches in research and clinical practice to develop effective microbiome-based therapies for better reproductive health outcomes.},
}

@article {pmid41171303,
year = {2025},
author = {Shi, J and Zhang, R and Zhang, L and Wang, Y and Xu, Y and Wang, Y and Raghavan, V and Wang, J},
title = {Urban Allergic Diseases Are Exacerbated by Adverse Environmental Factors.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c09233},
pmid = {41171303},
issn = {1520-5851},
abstract = {Allergic disease prevalence differs between urban and rural populations. We aimed to evaluate the relationships between environmental and dietary factors and allergic diseases in both urban and rural settings. The results showed that the alarming increase in the incidence and severity of allergic diseases coincided with environmental and lifestyle changes, such as global warming, extreme weather and dietary modifications. Higher greenhouse gas emissions, consumption of fast food and fried meat, use of pesticides, and less exposure to pets, greenery, and environmental microbes are associated with increased rates of urban allergic diseases. The living environment influenced the microbiota of rural and urban children. Changes in environments and lifestyles influence the commensal gut, skin, respiratory, and nasal microbiomes and their human hosts, contributing to the rising incidence of allergic diseases.},
}

@article {pmid41171140,
year = {2025},
author = {Zhang, Z and Zhao, H and Wang, T},
title = {PRIME: a database for 16S rRNA microbiome data with phenotypic reference and comprehensive metadata.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1057},
pmid = {41171140},
issn = {1362-4962},
support = {12222111//National Natural Science Foundation of China/ ; 12331009//National Natural Science Foundation of China/ ; 12571306//National Natural Science Foundation of China/ ; //Fundamental Research Funds for the Central Universities/ ; //Shanghai Jiao Tong University/ ; //National Natural Science Foundation of China/ ; },
abstract = {PRIME (Phenotypic Reference for Integrated Microbiome Enrichment) is a curated and standardized database of human microbiome 16S rRNA amplicon sequencing data, designed to facilitate cross-study analysis, reproducibility, and phenotype-driven discovery. PRIME aggregates 53 449 samples from 111 public studies, covering 93 body sites and 101 phenotypic categories, with detailed harmonization of sample-level metadata such as disease status, demographics, body sites, sequencing protocols, and experimental design. Each sample includes taxonomic abundance profiles generated via a consistent pipeline using both SILVA (138.2) and Greengenes2 (2024.09) reference databases, with results reported at multiple taxonomic levels as observed abundances (read counts) and relative abundances (proportions). A major strength of PRIME is its extensive manual curation, which standardizes phenotypic and contextual metadata across studies, enabling precise querying and robust phenotype-based comparisons. Users can interactively explore the database through a modern web interface, filter and visualize data by metadata fields, and download customized subsets. Programmatic access is supported via RESTful APIs and R package. PRIME aims to advance microbiome data integration and is continuously updated to incorporate new studies and features. The database is freely available at https://primedb.sjtu.edu.cn.},
}

@article {pmid41171125,
year = {2025},
author = {Kuhn, M and Schmidt, TSB and Ferretti, P and Głazek, A and Robbani, SM and Akanni, W and Fullam, A and Schudoma, C and Cetin, E and Hassan, M and Noack, K and Schwarz, A and Thielemann, R and Thomas, L and von Stetten, M and Alves, R and Iyappan, A and Kartal, E and Kel, I and Keller, MI and Maistrenko, O and Mankowski, A and Nishijima, S and Podlesny, D and Schiller, J and Schulz, S and Van Rossum, T and Bork, P},
title = {Metalog: curated and harmonised contextual data for global metagenomics samples.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1118},
pmid = {41171125},
issn = {1362-4962},
support = {668031//Horizon 2020/ ; ERC-AdG-669830/ERC_/European Research Council/International ; 101059915//European Union's Horizon Europe research and innovation programme/ ; NNF15OC0016692//MicrobLiver/ ; //Novo Nordisk Foundation/ ; //Deutsche Forschungsgemeinschaft/ ; 460129525//German Research Foundation/ ; //Ministry of Science/ ; //MWK/ ; //German Federal Ministry of Research, Technology and Space/ ; //European Molecular Biology Laboratory/ ; },
abstract = {Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data is deposited in public databases, the associated contextual data is often not complete and needs to be retrieved from primary publications. This lack of access to sample-level metadata like clinical data or in situ observations impedes cross-study comparisons and meta-analyses. We therefore created the Metalog database, a repository of manually curated metadata for metagenomics samples across the globe. It contains 80 423 samples from humans (including 66 527 of the gut microbiome), 10 744 animal samples, 5547 ocean water samples, and 23 455 samples from other environmental habitats such as soil, sediment, or fresh water. Samples have been consistently annotated for a set of habitat-specific core features, such as demographics, disease status, and medication for humans; host species and captivity status for animals; and filter sizes and salinity for marine samples. Additionally, all original metadata is provided in tabular form, simplifying focused studies e.g. into nutrient concentrations. Pre-computed taxonomic profiles facilitate rapid data exploration, while links to the SPIRE database enable genome-based analyses. The database is freely available for browsing and download at https://metalog.embl.de/.},
}

@article {pmid41171124,
year = {2025},
author = {Lv, J and Ma, S and Ma, C and Liu, F and Duan, X and Huang, X and Geng, Q and Liu, F and Li, G and Li, Y and Wang, J and Li, C and Zheng, H and Zhang, Y and Sun, Z and Wang, J and Fan, G and Huang, S and Zhang, L and Bao, Z and Wang, S},
title = {Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1098},
pmid = {41171124},
issn = {1362-4962},
support = {2024YFC2816000//National Key Research and Development Program of China/ ; LSKJ202202804//Marine S&T Fund of Shandong Province for Laoshan Laboratory/ ; 2025B1111180001//Guangdong Provincial Key Areas R&D Program Project/ ; SOLZSKY2025013//Hainan Province Science and Technology Special Fund/ ; 32573498//Natural Science Foundation of China/ ; 32222085//Natural Science Foundation of China/ ; QDLYY-2024011//Blue Seed Industry Science and Technology Innovation Project/ ; GZB20250215//Postdoctoral Fellowship Program of CPSF/ ; },
abstract = {Multi-omics analyses have significantly advanced the understanding of complex marine microbial communities and their interactions. Despite notable progress from recent large-scale ocean meta-analysis efforts, the effective integration and accessibility of these diverse datasets remain challenging. To address this, we introduce Ocean-M (http://om.qnlm.ac), a comprehensive and publicly accessible platform for marine microbial multi-omics data integration, analysis, and visualization. Ocean-M provides a systematic view of 54 083 high-quality metagenome-assembled genomes, including genome assembly statistics, genome clustering, gene annotation, and interactive tools for global-scale taxonomic profiling. The platform also incorporates microbial community networks, host-microbiome interactions, and environmental DNA datasets to support an integrated ecological framework for studying microbial interactions and ecosystem functions. Additionally, Ocean-M enables large-scale mining of ecologically and biotechnologically important genes, with curated catalogs of 151 798 biosynthetic gene clusters, 52 699 antibiotic resistance genes, and millions of carbohydrate-active enzymes and plastic-active enzymes. By combining multi-omics data with environmental metadata, Ocean-M serves as a valuable resource for advancing marine microbial ecology, global biogeography, and functional gene discovery.},
}

@article {pmid41171074,
year = {2025},
author = {Zhou, Y and Wang, Y and Xiao, B and Wang, S and Zhang, Z and Wang, X and Liu, B and Yang, Y and Wang, C and Zhou, C and Liao, M and Song, F and Luo, H},
title = {Predicting age from binarized human oral microbial data combined with an ensemble of classifiers.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0118225},
doi = {10.1128/msystems.01182-25},
pmid = {41171074},
issn = {2379-5077},
abstract = {It is well established that the composition of the human microbiome changes with age; however, limited research has explored the association between the oral microbiome and aging, as well as its potential for age prediction. In this study, we investigated the correlation between the oral microbiome and age by analyzing samples from 150 individuals across a wide age range (6-78 years). The observed species richness and Chao1 index significantly increased with age. Permutational multivariate analysis of variance (PERMANOVA), using both Bray-Curtis and Jaccard distances, identified age as a major factor influencing microbial variation. After a comprehensive comparison of four different oral microbiome data processing approaches, we then developed an ensemble model based on binarized oral microbial data, incorporating an eXtreme Gradient Boosting (XGBoost) algorithm with 32 classifiers. This ensemble model achieved a mean absolute error (MAE) of 7.20 years in the independent validation set (n = 15) and 4.33 years in the 20-59 age subgroup (n = 12), significantly outperforming traditional models. When the sample size increased to 2,550, the MAE in the independent validation set (n = 255) was reduced to 4.80 years, with the 20-59 age subgroup (n = 232) achieving an MAE of 3.76 years, highlighting its generalizability and robustness. Additionally, compared to the previously published model for age prediction based on oral microbiome, our model demonstrated significantly superior performance. These findings support the potential of integrating binarized microbial data with ensemble modeling as a promising direction for human age prediction based on the microbiome.IMPORTANCEPERMANOVA analysis with Jaccard distances revealed age as a major determinant of variation in microbial composition, highlighting the potential of binarized oral microbial data as a novel predictor for human age prediction. Furthermore, we developed an ensemble model combining an XGBoost algorithm and 32 classifiers to predict age from binarized oral microbial data. The model achieved an MAE of 7.20 years in the independent validation set (n = 15) and 4.33 years in the 20-59 age subgroup (n = 12). When applied to predict age in 2,550 samples from previous studies, the ensemble model outperformed the prior model, achieving an MAE of 4.44 years compared to the previous model's 4.94 years. These findings demonstrate that binarized oral microbial data, along with the ensemble model we developed, can effectively predict human age and provide a solid foundation for future age-related research.},
}

@article {pmid41168692,
year = {2025},
author = {Mo, X and Shi, S and Siddique, KHM and Li, Y and Zhang, Z and Zhang, M},
title = {Community interactions and functions drive bacteriome assembly in soil-plant continua of fragile estuarine wetland.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1477},
pmid = {41168692},
issn = {1471-2229},
support = {2022YFF1301004//Ministry of Science and Technology of the People's Republic of China/ ; },
abstract = {UNLABELLED: Restoration of degraded estuarine wetlands relies heavily on rhizosphere bacterial communities that support vegetation colonization and persistence. However, the mechanisms driving microbiome assembly across soil–plant continua in these fragile ecosystems remain poorly understood. Here, we examined plant traits, soil physicochemical properties, and α-diversity and community structure in rhizosphere and non-rhizosphere soils of two dominant species (Suaeda salsa and Phragmites australis) in a degraded estuary in China. We further assessed bacteriome assembly processes, β-diversity, and the relative influence of abiotic and biotic factors. Bacterial community structure differed significantly between the two plant continua, though diversity did not. Across both rhizosphere and non-rhizosphere soils, bacteriome assembly was governed predominantly by heterogeneous selection. Within this deterministic framework, intrinsic biotic factors—including keystone taxa, metabolic functions, and host plants—exerted stronger effects on community assembly than abiotic drivers. Moreover, available phosphorus facilitated this assembly pattern through indirect pathways. These findings highlight the pivotal role of biotic interactions in shaping bacteriomes and maintaining functional stability in fragile estuarine ecosystems, with implications for guiding ecological restoration.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-07341-9.},
}

@article {pmid41171001,
year = {2025},
author = {Smolkova, D and Rusin, M and Dobrowolska-Iwanek, J and Woźniakiewicz, M and Lavicka, J},
title = {Sensitive Profiling of Human Milk Oligosaccharides in Human Colostrum and Breast Milk by Capillary Electrophoresis-Mass Spectrometry.},
journal = {Journal of separation science},
volume = {48},
number = {11},
pages = {e70309},
doi = {10.1002/jssc.70309},
pmid = {41171001},
issn = {1615-9314},
mesh = {Humans ; *Milk, Human/chemistry ; *Colostrum/chemistry ; *Oligosaccharides/analysis ; Electrophoresis, Capillary ; Mass Spectrometry ; Female ; },
abstract = {Human milk oligosaccharides are pivotal for shaping the infant gut microbiome and immune development, yet their structural diversity hampers routine identification and quantification. We report an optimized capillary electrophoresis-mass spectrometry workflow that enables sensitive, isomer‑selective profiling of 10 biologically relevant human milk oligosaccharides in colostrum and early‑lactation breast milk. Human milk oligosaccharides were first neutralized to stabilize sialic acids and derivatized with Girard's reagent P, introducing a permanent positive charge to enhance electrophoretic resolution and electrospray ionization efficiency. Separation in a linear‑polyacrylamide‑coated capillary (0.25 M formic acid, 30 kV) and mass spectrometry detection with a nanoCEasy interface achieved baseline resolution of all targets except positional isomers lacto-N-difucohexaose I/II. Incorporation of Girard's reagent P‑labeled maltoheptaose as an internal standard improved migration time precision to < 0.5% RSD and reduced peak‑area repeatability to 9%-25% RSD. Limits of detection were 0.8-290 ng/mL, corresponding to fg-pg on‑column amounts and outperforming precedent APTS-based CE/LIF methodologies. Application to colostrum and milk samples from a single donor (1-3 months postpartum) revealed pronounced variation. Colostrum was dominated by 2'‑fucosyllactose and fucosylated lacto-N-fucopentaose isomers, whereas sialylated human milk oligosaccharides were present in smaller amounts. Longitudinally, 2'‑fucosyllactose remained the most abundant species, while lacto-N-fucopentaose and lacto-N-neotetraose/lacto-N-tetraose diminished markedly by Month 3. The presented capillary electrophoresis-mass spectrometry platform delivers reasonably fast (< 70 min), high‑sensitivity human milk oligosaccharide fingerprinting from minimal sample volumes and is readily adaptable to large‑cohort studies, offering new opportunities to elucidate the nutritional dynamics of the maternal milk glycome during lactation.},
}

Humans
*Milk, Human/chemistry
*Colostrum/chemistry
*Oligosaccharides/analysis
Electrophoresis, Capillary
Mass Spectrometry
Female

@article {pmid41170939,
year = {2025},
author = {Blondin-Brosseau, M and Zhang, W and Gravel, C and Harlow, J and Li, X and Nasheri, N},
title = {Survival of influenza virus H1N1 and murine norovirus in raw milk cheeses.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0188125},
doi = {10.1128/aem.01881-25},
pmid = {41170939},
issn = {1098-5336},
abstract = {The spillover of highly pathogenic avian influenza (HPAI) to dairy cattle and its presence at high titers in raw milk has created a concern that consumption of dairy products made from unpasteurized milk could result in human exposure. We examined whether H1N1, as a surrogate for HPAI viruses, and murine norovirus (MNV), as a surrogate for unenveloped enteric viruses, can survive the cheese-making process by making cream cheese-style and feta-style cheeses from artificially inoculated raw milk. We used the modified ISO 15216 method for viral extraction, which has a limit of detection of 3.0-3.7 log for infectious H1N1 in soft cheeses. Infectious H1N1 virus was detected in the curd from both types of cheeses and in the whey from cream cheese but not in the whey from feta cheese. Infectious MNV particles were detected in the curd and in the whey for both types of cheeses. To study the effect of salt, pH, aging, and microbiome of various unpasteurized milk cheeses on viral survival, we artificially inoculated different commercial unpasteurized milk cheeses with 7 log PFU of H1N1 and 6 log PFU of MNV and examined viral survival over an 8 week period at 4°C. We observed that H1N1 survived for 8 weeks, with an average of 2.6, 2.75, and 4.0 log reductions on cheddar, washed rind firm cheese, and semisoft brie-like cheese, respectively (P < 0.001). The level of infectious H1N1 fell below the limit of detection in cream cheese after 2 weeks of inoculation. It is noteworthy that the sensory qualities of soft and semisoft cheeses deteriorated in 2 weeks, but the sensory qualities of firm cheeses did not change drastically, demonstrating that, as expected, they endure the aging process better than the soft and semisoft cheeses. Furthermore, the limit of detection for soft cheeses is approximately 1 log lower compared to firm cheeses, and the extraction method has a lower efficiency for soft cheeses compared to firm cheeses. MNV survived in firm cheeses for 8 weeks with only 1 log reduction on cheddar cheese and 2 log reductions on the washed rind firm cheese (P < 0.05). The data obtained in this study could help with the risk assessment of dairy products made from unpasteurized milk.IMPORTANCEThe rapid spread of H5N1 viruses among dairy cattle in the United States and the viral shedding at high titers raised concern regarding the safety of dairy products, specifically cheeses made with unpasteurized milk. In this study, we demonstrated that murine norovirus and influenza virus can survive the cheese-making and aging process. Therefore, it is recommended that milk contaminated with viruses be heat-treated to ensure safety.},
}

@article {pmid41170737,
year = {2026},
author = {Zhang, R and Zhang, L and Tian, B and Wang, Y and Kang, X and Zheng, J},
title = {The gut‑bone‑cartilage triad: Microbial regulation of the Wnt/β‑catenin signaling pathway in osteoarthritis joint remodeling (Review).},
journal = {Molecular medicine reports},
volume = {33},
number = {1},
pages = {},
doi = {10.3892/mmr.2025.13733},
pmid = {41170737},
issn = {1791-3004},
mesh = {Humans ; *Osteoarthritis/metabolism/microbiology/pathology ; *Wnt Signaling Pathway ; *Gastrointestinal Microbiome ; Animals ; *Cartilage, Articular/metabolism/pathology ; *Bone Remodeling ; *Bone and Bones/metabolism ; },
abstract = {Osteoarthritis (OA) is a prevalent chronic joint disorder with a notable global health burden, characterized by articular cartilage degeneration, abnormal bone remodeling and synovial inflammation. Traditional treatments mainly focus on symptom management rather than addressing the underlying disease mechanisms. The gut microbiome serves a potential role in OA through the gut‑bone‑cartilage axis. Notably, the gut microbiome and its metabolites can influence bone and cartilage homeostasis, and the Wnt/β‑catenin signaling pathway has been implicated in OA pathogenesis. The present study comprehensively reviews the emerging evidence supporting the gut‑bone‑cartilage axis in OA and the role of microbial regulation of Wnt/β‑catenin signaling in joint remodeling. The current understanding of the influence of the gut microbiome on OA pathogenesis is summarized, discussing the mechanisms underlying the gut‑bone‑cartilage axis and exploring the therapeutic potential of targeting this axis. Future research should focus on developing targeted therapies that modulate the gut microbiome and the Wnt/β‑catenin pathway, as well as exploring the potential of gene editing and carrier technologies for OA treatment.},
}

Humans
*Osteoarthritis/metabolism/microbiology/pathology
*Wnt Signaling Pathway
*Gastrointestinal Microbiome
Animals
*Cartilage, Articular/metabolism/pathology
*Bone Remodeling
*Bone and Bones/metabolism

@article {pmid41170399,
year = {2025},
author = {Hasanthi, M and Chotikachinda, R and Medagoda, N and Lee, KJ},
title = {Exogenous protease supplementation in high- and low-fishmeal diets for Pacific white shrimp (Penaeus vannamei): Comparative effect on growth, immunity, nutrient digestibility and gut health.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {22},
number = {},
pages = {36-49},
pmid = {41170399},
issn = {2405-6383},
abstract = {The present study evaluated the effects of exogenous protease supplementation in low- and high-fishmeal (FM) diets on growth performance, feed utilization, innate immunity, digestive enzyme activity, nutrient digestibility, gut microbiota and intestinal morphology of Pacific white shrimp (Penaeus vannamei). A 2 × 3 factorial experiment was designed with two dietary FM levels (200 g/kg, positive control [PC]; and 100 g/kg, negative control [NC]) and three protease levels (0, 400 and 800 mg/kg) to obtain six experimental diets designated as PC, PC400, PC800, NC, NC400, and NC800. Six replicate groups of 30 shrimp (initial weight 0.30 ± 0.01 g) were fed the diets for 8 wk. Protease supplementation significantly improved (P < 0.001) growth performance and feed utilization efficiency in both high- and low-FM diets. Innate immunity and antioxidant enzyme activities were significantly enhanced (P < 0.001) with increasing FM and protease levels. Furthermore, the inclusion of protease in low-FM diets significantly increased (P < 0.001) total hemocyte count and phagocytic, phenoloxidase, lysozyme and superoxide dismutase activities, reaching levels comparable to the PC group. Increasing FM and protease levels significantly upregulated (P < 0.001) the expression of proPO, crustin, TGF-β, Lv IKK-β and TLR3 genes, while downregulating TNF-α. The inclusion of protease in the low FM diet significantly increased (P < 0.05) digestive enzyme activities, intestinal villi length, whole-body amino acid composition and nutrient digestibility to the levels comparable to the PC group. The relative abundance of heterotrophic marine bacteria (P < 0.001), Gram-positive bacteria (P = 0.034) and Lactobacilli spp. (P < 0.001) in the gut significantly increased (P < 0.05) with increasing protease levels, while an inverse relationship was observed for Vibrio spp. (P < 0.001). These results demonstrated that protease supplementation in either the high- or low-FM diets could improve shrimp growth, feed utilization efficiency, immunity, nutrient digestibility, intestinal morphology and gut microbiome. Notably, supplementing the low-FM diet with 800 mg/kg protease improved shrimp performance, reaching levels comparable to those obtained with the PC diet.},
}

@article {pmid41170114,
year = {2025},
author = {Sharma, E and Thind, S and Ohri, T and Goyal, R and Dhawan, R and Singh, J and Krishna, S and Sangha, R},
title = {The crippling grip of antimicrobial resistance in dentistry: A review.},
journal = {Bioinformation},
volume = {21},
number = {7},
pages = {1871-1874},
pmid = {41170114},
issn = {0973-2063},
abstract = {A primary challenge for dentists is maintaining or restoring a balanced oral microbiome, as it plays a significant role in determining oral health and disease states. However, oral diseases such as gingivitis, dental caries, periodontitis and peri-implantitis can occur when pathogenic microbes settle in the oral cavity and become part of the oral biofilm. There are several preventative and therapeutic strategies available today, but the majority of them are centered on antibiotics. Antibiotic stewardship in dentistry might be a helpful strategy to maximize and prevent inappropriate or even needless antibiotic usage, marking a step towards precision medicine, given the current context of antimicrobial resistance (AMR). Additionally, efforts are being made to discover novel, efficient treatments that can take the place of antibiotics.},
}

@article {pmid41169518,
year = {2025},
author = {Drovetski, SV and Shearn-Bochsler, VI and Hofmeister, EK and Karouna-Renier, NK and Dusek, RJ},
title = {A short-term sublethal oral exposure to microcystin-LR disrupts cecal microbiome homeostasis in mallard.},
journal = {Frontiers in toxicology},
volume = {7},
number = {},
pages = {1634241},
pmid = {41169518},
issn = {2673-3080},
abstract = {INTRODUCTION: The frequency of cyanobacterial blooms seems to have increased globally in recent decades due to human induced eutrophication and climate change. Cyanobacterial blooms can produce several groups of toxins, among which microcystin-LR (MC-LR) is one of the most abundant. Effects of MC-LR on avian microbiome have not been studied and studies in laboratory murines have been limited to metabarcoding of prokaryotes.

METHODS: Using RNA shotgun sequencing, we compared the richness and composition of metabolically active prokaryotes, expressed virulence factors, antimicrobial resistance genes, metabolic pathways, Gene Ontology terms, enzymes, and proteins in mallards (Anas platyrhynchos) that were orally exposed to a sublethal dose of MC-LR for one week and unexposed birds.

RESULTS: Richness and composition of all compared features did not differ between exposed and control birds and none were differentially expressed between exposure groups. However, richness and/or composition of all features except virulence factors and Carbohydrate Active enzymes had multiple-fold greater dispersion in exposed birds than in controls. This effect was especially pronounced in expressed metabolic (MetaCyc) pathways.

DISCUSSION: Our results suggest that MC-LR exposure had a stochastic (rather than deterministic) effect on cecal microbiota, especially its function. Observed disturbance of the microbiota homeostasis is consistent with the Anna Karenina Principle. This principle has been documented in a wide range of eukaryotes using primarily microbial community metabarcoding. Although stochastic disturbance of microbiota function has been hypothesized, our study seems to be the first to demonstrate this in an experimental study.},
}

@article {pmid41169482,
year = {2025},
author = {Cao, F and Yi, W and Wu, M and Gao, A and Kang, T and Hou, X},
title = {Characteristics of the gut microbiome of asymptomatic hyperuricemia.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1557225},
pmid = {41169482},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Hyperuricemia/microbiology ; Male ; Female ; Middle Aged ; Uric Acid/blood ; Adult ; Case-Control Studies ; Feces/microbiology ; Asymptomatic Diseases ; Biomarkers/blood ; Aged ; },
abstract = {PURPOSE: Asymptomatic hyperuricemia(AH) is characterized by elevated blood uric acid levels without symptoms,posing risks like gout, kidney stones, and cardiovascular diseases. This study aims to investigate the role of the gut microbiota in uric acid metabolism in AH.

METHODS: Clinical data from 30 AH patients and 30 healthy controls were collected. Fecal microbiota genomic DNA was extracted, PCR amplified, library constructed, and sequenced. Bioinformatics and statistical analyses were conducted to study the gut microbiota of the two groups.

RESULTS: The AH group exhibited significantly elevated levels of body mass index (BMI), Triglycerides (TG), Total Cholesterol (TC), as along with a history of smoking, hypertension, and fatty liver disease compared to the healthy group (P < 0.05). The overall richness and ecological diversity of gut microbiota in the AH group decreased, with differences in the distribution at the phylum and genus levels compared to the healthy group. Uric acid demonstrated significant correlations with various gut microbiota (e.g., Granulicatella), suggesting their potential as biomarkers for AH. Despite limitations such as a small sample size and lack of long-term follow-up, our findings provide new insights for the early diagnosis and personalized treatment of AH. Looking ahead, these discoveries may advance the clinical management of AH and the exploration of associated biomarkers.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Hyperuricemia/microbiology
Male
Female
Middle Aged
Uric Acid/blood
Adult
Case-Control Studies
Feces/microbiology
Asymptomatic Diseases
Biomarkers/blood
Aged

@article {pmid41169397,
year = {2025},
author = {Hu, X and Li, B and Li, Y and Liang, Y and Huang, T},
title = {Communication between gut microbiota-derived metabolites and the tumor microenvironment.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1649438},
pmid = {41169397},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Tumor Microenvironment/immunology ; *Neoplasms/metabolism/immunology/therapy/microbiology ; Animals ; Immunotherapy/methods ; },
abstract = {The gut microbiota has been increasingly recognized as a critical player in maintaining human health and influencing disease development. The tumor microenvironment (TME) is pivotal in tumor development and progression, comprising immune cells, stromal elements, extracellular matrix components, and cytokines. Recent studies have highlighted the promising potential of gut microbiota-derived metabolites (e.g., short-chain fatty acids, bile acids, polyamines, and tryptophan derivatives) to reshape the TME in various ways, generating significant interest for the development of novel therapeutic strategies. Beyond their established effects on traditional cancer treatments, emerging evidence suggests that microbiome-based interventions can substantially enhance cancer immunotherapy. However, the variable role of gut microbiota in modulating therapeutic responses complicates the prediction of clinical outcomes. Therefore, understanding the crosstalk between the gut microbiota and the TME is crucial and holds promise for the development of personalized and comprehensive cancer management strategies. This review aims to summarize the reciprocal regulatory mechanisms between gut microbiota-derived metabolites and the TME, and to explore how these interactions can be leveraged to improve cancer immunotherapy.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Tumor Microenvironment/immunology
*Neoplasms/metabolism/immunology/therapy/microbiology
Animals
Immunotherapy/methods