@article {pmid41314292,
year = {2025},
author = {Anand, R and Sahil, R and Jain, M and Maurya, GK and Kharat, AS},
title = {Plant-based diet as a precursor to human gut diversity.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.11.020},
pmid = {41314292},
issn = {1541-6100},
abstract = {The gut microbiome significantly influences human health with dietary patterns, a key factor that modulates the structure and function of microbiome consortia. Plant-based diets (PBDs), including vegan and vegetarian, are linked to positive alterations in gut microbiota by stimulating the bacterial growth necessary for producing short-chain fatty acids. These microbial alterations help reduce inflammation, enhance gut barrier integrity, and improve metabolic health. However, not all PBDs offer beneficial effects. Recent findings highlighted that raw or minimally processed foods may transmit plant and soil-derived microbes, such as Enterobacter hormaechei, Citrobacter freundii, Raoultella ornithinolytica, and Klebsiella pneumonia into the human gut, raising concern about opportunistic infections. Although PBDs benefit in lowering the risk of chronic diseases such as obesity, diabetes, and inflammatory bowel disease, proper dietary planning is necessary to prevent potential nutrient deficiencies. Upcoming research should explore personalized nutrition, long-term microbiome shifts, and microbial transplants to improve gut health through PBDs.},
}

@article {pmid41314088,
year = {2025},
author = {Majzoub, M and Thomas, T and Willcox, M and Coroneo, M and Ozkan, J},
title = {Exploring the potential for microbial transfer from exhaled breath to the ocular surface: a comparative analysis of respiratory and ocular microbiota.},
journal = {Contact lens & anterior eye : the journal of the British Contact Lens Association},
volume = {49},
number = {1},
pages = {102581},
doi = {10.1016/j.clae.2025.102581},
pmid = {41314088},
issn = {1476-5411},
abstract = {PURPOSE: Respiratory microbes typically enter the body via the nose and mouth, but transmission through the ocular surface-nasolacrimal duct route remains poorly understood. This study investigated the microbiota of exhaled breath, conjunctiva, and anterior nares in healthy individuals to assess the potential for microbial transfer from exhalations to the ocular surface.

DESIGN: Cross-sectional, single-center observational study.

METHODS: Exhalation, conjunctival, and nasal samples were collected from 20 participants. Exhaled breath samples were obtained by having participants read a standardized script for three minutes in front of a sterile agar plate positioned 15 cm from the mouth. Sterile phosphate-buffered saline was applied to the agar surface and a sterile cell scraper was used to collect the sample. Conjunctival and nasal samples were collected using sterile flocked swabs. All samples were stored at - 80 °C. Microbial DNA was extracted, followed by PCR amplification and paired-end 16S rRNA gene sequencing on the Illumina MiSeq platform.

RESULTS: The cohort included 20 participants (8 female, 12 male; mean age 41.9 ± 9.2 years). Significant differences were found in microbial richness (P < 0.0001), evenness (P < 0.01), and bacterial community structure (P < 0.001) across sites. While 9 % of amplicon sequencing variants (ASVs) were shared across all sites, only 1 % were shared between exhalations and the conjunctiva. The anterior nares shared more ASVs with both the conjunctiva (8 %) and exhalations (20 %).

CONCLUSIONS: Minimal microbial overlap between exhaled breath and the conjunctiva suggests that in healthy adults, under specific low-intensity conditions tested, direct transmission to the ocular surface appears minimal.},
}

@article {pmid41314076,
year = {2025},
author = {Md Ali, SA and Saito, S and Nishiyama, M and Phung, LD and Watanabe, T},
title = {Composted sewage sludge reshapes soil resistome connectivity and enhances antibiotic resistance gene dissemination in paddy fields.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181049},
doi = {10.1016/j.scitotenv.2025.181049},
pmid = {41314076},
issn = {1879-1026},
abstract = {The reuse of organic waste streams, such as composted sewage sludge (CSS), provides agronomic benefits, but also represents a critical pathway for the environmental dissemination of antibiotic resistance genes (ARGs). The consequences of CSS application for soil resistome dynamics and microbial ecology remain insufficiently understood. Here, we investigated paddy soils in Tsuruoka, Japan, under three fertilization treatments: CSS, chemical fertilizer (CF), and their combination (CSS + CF). Quantitative PCR targeted total bacterial (16S rRNA), fecal indicators (E. coli, Enterococcus spp.), mobile genetic element (MGE) (inlt1), and five ARGs (sul1, blaTEM, blaCTX-M Groups 1, 2, and 9). CSS amended soils showed elevated levels of intI1, sul1, and blaTEM in 2023, with blaTEM persisting into 2024. Although both E. coli and Enterococcus spp. showed weak correlations with ARGs, only Enterococcus spp. (ρ = 0.37, p < 0.05) showed statistically significant associations with intI1. Network analysis demonstrated that CSS fostered a highly interconnected resistome with sul1 emerging as a central hub linking multiple bacterial families. In contrast, CF maintained a sparse modular structure while CSS + CF generated an intermediate network. Collectively, these results demonstrate that CSS amplifies the potential for ARG dissemination by fostering a highly connected resistome, whereas co-application with chemical fertilizers partially disrupts this connectivity, thereby reducing dissemination risk in the soil environment. Our findings provide field-based evidence of the environmental impacts of waste-derived fertilization and underscore the need for integrated fertilization strategies and ARG surveillance to promote sustainable soil management and safeguard environmental health.},
}

@article {pmid41314069,
year = {2025},
author = {Kumari, SP and Hooda, S and Diwan, P and Gupta, RK},
title = {Seasonal variations and functional insights into the urban air microbiome across public transit environments at railway stations in Delhi, India.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181062},
doi = {10.1016/j.scitotenv.2025.181062},
pmid = {41314069},
issn = {1879-1026},
abstract = {Airborne microbial communities play an underappreciated yet critical role in shaping urban environmental health, particularly in densely crowded public transit systems. This study aimed to explore the taxonomic and functional landscape of airborne bacteria, highlighting the seasonal disparities across summer and autumn seasons, in the public transit air (railway stations) of Delhi, a populated megacity characterized by extreme pollution levels and one of the world's busiest railway networks. Metagenomic analyses revealed distinct seasonal signatures in microbial community composition and diversity. Alpha diversity was higher during autumn, though not statistically significant, while beta diversity differed significantly between seasons. LEfSe analysis identified season-specific indicator taxa, including Moraxella, Barrientosiimonas, Methylobacterium, for autumn and Stutzerimonas, Caulobacter, Pseudomonas for summer, representing a mix of opportunistic pathogens and environmentally significant taxa. Correlation networks highlighted distinct seasonal clustering patterns. Resistome and virulome profiling revealed the presence of different resistance gene classes and virulence factor categories in abundance. Correlation networks uncovered significant associations between specific genes and bacterial genera, suggesting ecological partitioning in gene carriage. Temperature and air quality index explained a part of the variance observed in the taxonomic and functional dynamics. Metagenome-assembled genomes captured seasonally distinct taxa, and biosynthetic gene cluster screening identified 317 gene clusters, including terpene, RiPP-like, and hserlactone clusters. The findings underscore the ecological complexity and public health relevance of airborne bacteria and raise concerns about their potential role in microbial transmission and long-term respiratory health risks. These insights are crucial for public health surveillance, urban air quality management, and guiding future investigations into the microbial safety of urban environments.},
}

@article {pmid41314010,
year = {2025},
author = {Liu, L and Sun, T and Ji, C and Li, F and Wu, H},
title = {DBDPE induces more persistent disturbances than BDE-209 in Crassostrea gigas: Gut microbiome-modulated physiological responses.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {290},
number = {},
pages = {107655},
doi = {10.1016/j.aquatox.2025.107655},
pmid = {41314010},
issn = {1879-1514},
abstract = {Decabromodiphenyl ether (BDE-209) and its alternative, decabromodiphenyl ethane (DBDPE), are brominated flame retardants (BFRs) globally distributed in marine environments, posing risks to marine organisms. The gut microbiome not only degrades BFRs but also undergoes BFR-induced compositional and host-microbe co-metabolic changes. In this study, Pacific oysters (Crassostrea gigas) were exposed to 1 and 100 μg l[-1] of BDE-209/DBDPE for 28 days, followed by a 14-day depuration period. The higher bioaccumulation potential of DBDPE compared to BDE-209 might be attributed to its greater hydrophobicity, along with gut damage caused by pathogen proliferation. Alterations in the gut microbiome and metabolome induced by both BFR-exposure were associated with immunity and energy supply. Compared to BDE-209, DBDPE exposure induced more severe oxidative stress. Additionally, metabolomic analysis suggested that DBDPE has the potential to cause cell membrane damage. Notably, adverse effects, such as pathogen proliferation, persisted in DBDPE-exposed groups during depuration, which challenges its safer-alternative status. During depuration, functional remodeling in BFR-exposed oysters occurred through alterations in metabolism and genetic information processing in the gut microbiome, as well as alterations in purine metabolism, ABC transporters, and glycerophospholipid metabolism within the host (the latter being exclusive to the DBDPE-exposed groups). Despite its higher initial bioaccumulation, the higher elimination efficiency of DBDPE was facilitated by the activation of host repair program characterized by Verrucomicrobiota-mediated gut barrier restoration and glycerophospholipid metabolism-supported membrane remodeling. Correlation network analysis indicated that the adverse effects of high-concentration BFRs might be mediated by the gut microbiome, specifically through indole derivatives that may have upregulated the invertebrate form of AhR. Additionally, in the high-dose DBDPE-exposed group, a correlation between IAA and CAT suggested a potential link between microbial metabolism and the host's antioxidant system. This study provides comprehensive insights into gut microbiome and metabolome responses to BDE-209 and DBDPE, elucidating recovery mechanisms and the mediating role of gut microbiome in BFR-induced adverse effects in oysters.},
}

@article {pmid41313993,
year = {2025},
author = {Zheng, Y and Crowther, TW and Qin, Y and Lei, J and Xu, M and Xu, Y and Chu, H and Wu, Q and Shi, Y},
title = {Liquor fermentation industry reshapes soil microbiomes and drives CO2 emissions via microbial dispersal.},
journal = {Journal of environmental management},
volume = {396},
number = {},
pages = {128135},
doi = {10.1016/j.jenvman.2025.128135},
pmid = {41313993},
issn = {1095-8630},
abstract = {The rapid expansion of industrial fermentation has raised concerns about its environmental impacts, particularly regarding microbial dispersal from production facilities into adjacent terrestrial ecosystems; however, the ecological and functional consequences of microbial introductions originating from fermentation facilities remain poorly elucidated. We studied eight Chinese liquor fermentation facilities spanning 26°-47°N and 83°-124°E, covering the major geographical range of the industry. Using large-scale soil metagenomics, in situ CO2 flux measurements, and microcosm experiments, we demonstrate that industrial fermentation significantly alters local soil microbial communities and enhances carbon decomposition potential. The results showed that soil carbon decomposition genes increased 13.6 % around fermentation facilities. Biologically, the fermentation process at the facilities introduced microorganisms into soil, such as Actinobacteria, whose abundance increased by 2.8 %. These microorganisms directly increased the abundance of carbon decomposition genes in the soil, while Actinobacteria also enhance soil carbon decomposition capacity by reducing microbial α diversity. Abiotically, the soil total carbon increased by 3-89 % around facilities, thereby enriching carbon decomposition genes. These soil microbial activities changed by fermentation facilities lead to an increase in soil CO2 emissions. Our study provides the first evidence that industrial fermentation facilities inadvertently modify soil microbial community and function. These findings establish a critical link between fermented food production systems and terrestrial carbon emissions, with important implications for sustainable fermentation practices and climate-smart industrial planning.},
}

@article {pmid41313960,
year = {2025},
author = {Ogbanga, N and Nelson, A and Smith, D and Somiari, R and Procopio, N},
title = {Oral microbiomes as forensic markers of origin and migration: Insights from an underrepresented population, Nigeria.},
journal = {Forensic science international. Genetics},
volume = {82},
number = {},
pages = {103395},
doi = {10.1016/j.fsigen.2025.103395},
pmid = {41313960},
issn = {1878-0326},
abstract = {The oral microbiome is shaped by environmental and host-associated factors, suggesting its utility for human profiling in forensics, particularly as an indicator of geographic origin and human migration. Using high-throughput sequencing and machine learning models, the predictive ability of the oral microbiome was assessed to determine the country of origin of the donors, using samples of individuals across 6 countries. The impact of migration on the predictive ability of the oral microbiome was also assessed through a longitudinal study of Nigerian migrants over a six-month period following migration. By analysing the oral microbiome at various time points during this timeframe, this study explores the influence of migration on the oral microbiome to provide insights into its applicability in forensic investigations. Our findings demonstrate that distinct microbial profiles correlate with the six geographic regions assessed in this study. Furthermore, the longitudinal sampling of Nigerian migrants revealed initial shifts in their microbiome profile, followed by a recovery to the original microbiome profile of Nigerian locals, observed after six months. These results highlight the forensic potential of the oral microbiome for geographic origin attribution, in migration tracking, and for providing intelligence information useful for forensic purposes.},
}

@article {pmid41313833,
year = {2025},
author = {Li, P and Shi, Y and Zhao, Y and Lu, X and Duan, J and Yang, Q and Xu, Y and Li, X and Dong, C and Wang, Z and Shen, Q},
title = {Trichoderma bio-organic fertilizer modulates the rhizosphere microbiome and Bacillus-assisted plant hormone regulation to promote pear rootstock growth.},
journal = {Microbiological research},
volume = {304},
number = {},
pages = {128400},
doi = {10.1016/j.micres.2025.128400},
pmid = {41313833},
issn = {1618-0623},
abstract = {Growth of container-grown Pyrus calleryana is often containered in heavy clay soils. Trichoderma-based bio-organic fertilizer (BOF) can improve seedling performance, yet how BOF mobilizes microbiome-hormone interactions under such conditions remains unclear. Here, we conducted a pot experiment with three treatments- water control (CK), 10 % (v/v) BOF and 20 % (v/v) BOF-under controlled conditions to assess plant growth, root hormone profiles, and rhizosphere communities. With 20 % BOF, seedling height, root length and root biomass increased (up to +131 %, +160 % and +165 %), bacterial diversity rose, and Firmicutes/Actinobacteria were enriched with an 8.3-fold increase of Bacillus. The ferment filtrates supported growth of the isolated Bacillus. Across treatments, Bacillus abundance correlated positively with indole-3-acetic acid (IAA) and isopentenyladenine (IP) and negatively with abscisic acid (ABA) (P < 0.05). Consistently, co-inoculation of Trichoderma and Bacillus increased IAA/IP and reduced ABA (P < 0.05), yielding stronger growth responses than single inoculations. These findings outline a BOF-mediated path in which Trichoderma-guided microbiome restructuring, together with a Trichoderma-responsive Bacillus, rebalances IAA/IP/ABA and promotes pear rootstock growth.},
}

@article {pmid41313610,
year = {2025},
author = {Butcher, J and Gosse, JT and Gobin, J and Ravel-Chapuis, A and Jasmin, BJ and Stintzi, A},
title = {Dystrophic Skeletal Muscle Phenotypes Can Be Horizontally Transferred via Fecal Microbiome Transplantations.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {23},
pages = {e71281},
doi = {10.1096/fj.202502999R},
pmid = {41313610},
issn = {1530-6860},
support = {OGI-149//Genome Canada (GC)/ ; Project 13440//MDECEC | Ontario Ministry of Research and Innovation (MRI)/ ; //Defeat Duchenne Canada (Vaincre Duchenne Canada)/ ; },
mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; Mice ; Mice, Inbred mdx ; *Muscle, Skeletal/pathology/microbiology/metabolism ; *Muscular Dystrophy, Duchenne/therapy/microbiology/pathology ; Mice, Inbred C57BL ; Phenotype ; *Muscular Dystrophy, Animal/microbiology/therapy ; *Gastrointestinal Microbiome ; Male ; },
abstract = {Duchenne muscular dystrophy (DMD) has no cure and accounts for > 80% of muscular dystrophy cases around the world. DMD patients experience severe muscle degeneration that continues until death and also suffer from gastrointestinal complications that undoubtedly impact their microbiotas. It is unclear whether dystrophic microbiotas simply reflect the disease or whether microbes are directly involved in muscle phenotypes. Here, we sought to determine the microbiota's causal role in promoting dystrophic muscles by performing intra/inter-genotype fecal microbiota transplantations (FMT) between wildtype and mdx mice; assessing FMT's impact on muscles and microbiotas over 9 weeks. Transplanting mdx microbiotas into wildtype mice induced an mdx-like muscle phenotype while the inverse improved muscle features. We identified several taxa differentially abundant between wildtype mice receiving either wildtype or mdx FMT, highlighting their potential role in muscle health. Our results highlight the active role microbes have in impacting muscle health through both beneficial and detrimental mechanisms. Accordingly, microbes represent unexploited therapeutic targets for improving health outcomes in muscular dystrophies.},
}

Animals
*Fecal Microbiota Transplantation/methods
Mice
Mice, Inbred mdx
*Muscle, Skeletal/pathology/microbiology/metabolism
*Muscular Dystrophy, Duchenne/therapy/microbiology/pathology
Mice, Inbred C57BL
Phenotype
*Muscular Dystrophy, Animal/microbiology/therapy
*Gastrointestinal Microbiome
Male

@article {pmid41313537,
year = {2025},
author = {Vishwakarma, RK and Gautam, P and Sahu, M and Nath, G and Yadav, BS},
title = {Gut Microbiome in Obesity: A Narrative Review of Mechanisms, Interventions, and Future Directions.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41313537},
issn = {1867-1314},
abstract = {Obesity has reached pandemic levels worldwide and is increasingly recognized as a multifactorial condition beyond excess caloric intake and sedentary lifestyle. Accumulating evidence emphasizes that the gut microbiota (GM), primarily composed of Firmicutes and Bacteroidetes, plays a crucial role in regulating energy balance, immune response, and host metabolism. Gut dysbiosis, characterized by reduced microbial diversity and altered phylum-level composition and shifts toward commonly observed higher Firmicutes-to-Bacteroidetes ratios (although this finding is inconsistent across studies), contributes to enhanced energy harvest, systemic inflammation, and metabolic dysfunction. Key mechanisms involve GM production of short-chain fatty acids (SCFAs) and modulation of hormonal signals, including leptin, ghrelin, insulin, GLP-1, and PYY, alongside interactions via the gut-brain axis. These pathways link microbial composition to appetite regulation, fat storage, and energy balance. Emerging microbiome-targeted therapies, such as probiotics, prebiotics, dietary modulation (e.g., fiber-rich diets), fecal microbiota transplantation, and bacteriophage therapy, show promise in restoring GM balance, promoting weight loss, and improving metabolic health, though results vary and require further validation. Despite advances in metagenomics and metabolomics, gaps persist in establishing causality and long-term efficacy. The integration of GM data with host genetics, diet, and environmental factors through systems biology has the potential to facilitate personalized management of obesity. This review synthesizes the GM's role in obesity pathogenesis and hormonal regulation, highlighting therapeutic potential and research directions for microbiota-based prevention and treatment.},
}

@article {pmid41313534,
year = {2025},
author = {Calabrese, F and Pasta, A and Formisano, E and Marabotto, E and Furnari, M and Pisciotta, L and Zentilin, P and Giannini, EG and Bodini, G},
title = {Diet in Inflammatory Bowel Diseases: Efficacy, Tolerability, and Microbiome Effects Toward Personalized Management.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10620-025-09590-y},
pmid = {41313534},
issn = {1573-2568},
abstract = {INTRODUCTION: Inflammatory bowel disease (IBD) is increasingly recognized as a condition in which diet is not only a trigger for symptoms but also a potential tool for disease modulation. Mounting evidence links dietary patterns and specific nutrients to intestinal inflammation, microbiome composition, and mucosal repair, opening new avenues for personalized therapy.

DIET INTERVENTIONS: Exclusive and partial enteral nutrition remain among the most effective nonpharmacologic strategies in Crohn's disease, while emerging data support the Mediterranean diet, specific carbohydrate diet, and low Fermentable Oligo-, Di-, Mono-saccharides And Polyols (FODMAP) approaches for symptom relief and quality-of-life improvement.

GAPS AND FUTURE DIRECTIONS: Nevertheless, evidence is often heterogeneous, with variability in dietary protocols, endpoints, and patient populations, making firm recommendations challenging. Adherence and long-term sustainability remain major barriers, underscoring the need for realistic, patient-centered approaches. By integrating current findings with clinical practice, diet can evolve from supportive care to a central component of multidisciplinary IBD management-if guided by robust evidence and tailored to individual needs. As research continues to refine the role of specific foods, nutrients, and patterns, dietary therapy holds promise not only to complement pharmacologic treatments but also to address the broader nutritional and metabolic needs of patients living with IBD.},
}

@article {pmid41313179,
year = {2025},
author = {Williams, G and Ahmad, H and Sutherland, S and Haycocks, J and Benedict, S and Hart, AJ and Doherty, HH and Sullivan, R and Alao, M and Ma, X and Xu, Q and Bryant, J and Glinkowska, M and Banks, P and Moynihan, P and Milner, MT and Moradigaravand, D and Banzhaf, M},
title = {High-throughput chemical genomic screening: a step-by-step workflow from plate to phenotype.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0088525},
doi = {10.1128/msystems.00885-25},
pmid = {41313179},
issn = {2379-5077},
abstract = {High-throughput chemical genomics uses phenotypic profiling of strain libraries under defined chemical and environmental conditions to identify gene functions. This approach enables the mapping of biological pathways and can potentially highlight drug targets. Chemical genomic data sets have been springboards for numerous hypothesis-driven research projects, with direct implications for antimicrobial resistance and clinical outcomes. High-throughput phenotypic profiles are valuable tools for enriching microbial sequence data with functional annotations and benefiting the broader scientific community. This work provides a step-by-step guide for conducting chemical genomics screens from start to finish.IMPORTANCEChemical genomic screening is a powerful systems biology approach for linking gene function to phenotype under diverse chemical and environmental stressors. However, its broader use in microbial research has been limited by the lack of standardized, reproducible workflows. Our study introduces a scalable, end-to-end protocol that integrates experimental, imaging, and computational steps into a cohesive framework for high-throughput screening across a range of microbial species. This enables researchers to generate consistent, high-quality phenotypic data suitable for large-scale analyses. The protocol supports systematic exploration of gene-environment interactions, microbial stress responses, and antimicrobial resistance. Its adaptability and troubleshooting guidance make it especially useful for groups working in microbiome research, synthetic biology, and microbial community studies. By bridging benchwork and computational analysis, this workflow expands the technical toolkit available to microbial systems biologists. Our work contributes to the development of robust methods for functional genomics and supports the core mission of mSystems to advance microbial systems biology.},
}

@article {pmid41313023,
year = {2025},
author = {Adam, D and Bensaada, D and Stulanovic, N and Focant, J-F and Stefanuto, P-H and Rigali, S},
title = {Comparative volatilomics identifies ubiquitous sulfur compounds inhibiting the fungal pathogen Rasamsonia argillacea.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0266625},
doi = {10.1128/spectrum.02666-25},
pmid = {41313023},
issn = {2165-0497},
abstract = {UNLABELLED: Members of the phylum Actinomycetota, particularly Streptomyces species, are prolific producers of bioactive metabolites, and bioprospecting in unique environments may uncover novel species producing previously undescribed antifungal compounds. In previous work, Streptomyces strains isolated from cave moonmilk deposits completely inhibited the growth of Rasamsonia argillacea, an emerging fungal pathogen associated with chronic granulomatous disease (CGD) and cystic fibrosis (CF). Cross-streak and bipartite Petri dish assays revealed that R. argillacea inhibition occurred specifically when bacteria were cultivated on Mueller-Hinton agar (MHA) and was mediated by volatile compounds rather than diffusible metabolites. This antifungal effect was not strain specific, as it was reproduced by phylogenetically diverse bacteria grown on MHA, suggesting the involvement of ubiquitous volatile molecules. Similar inhibitory effects were observed on MHA against other fungi and yeasts relevant to CGD and CF, supporting the hypothesis that these volatiles are broadly toxic rather than species-specific. To identify candidate ubiquitous antifungal VCs, we conducted comparative volatilomics of two phylogenetically distant bacterial strains that consistently inhibited fungal growth. Among the 143 VCs detected, only dimethyl trisulfide (DMTS) and dimethyl disulfide (DMDS) showed consistent presence in both bacterial volatilomes, with significantly increased production under conditions that promoted fungal inhibition. Exposure assays with pure compounds confirmed that both DMDS and DMTS strongly inhibited R. argillacea growth, with DMTS exhibiting greater potency. Our findings position these ubiquitous sulfur compounds as valuable models for exploring novel agents against human pathogens.

IMPORTANCE: Our findings suggest that antifungal activity against human pathogens may arise from common metabolic pathways shared across diverse microbes rather than from unique biosynthetic systems. Because dimethyl disulfide and dimethyl trisulfide can also be generated through microbial and dietary sulfur metabolism, it is plausible that the human microbiome may produce similar volatiles depending on diet composition, particularly following consumption of sulfur-rich foods. This study, therefore, underscores the critical influence of culture conditions on revealing bioactive volatile production and opens intriguing perspectives on the ecological and physiological roles of ubiquitous microbial metabolites in regulating fungal colonization and microbiome-host interactions.},
}

@article {pmid41313018,
year = {2025},
author = {Wang, K and Wang, H and Zhao, Z and Shen, X and Zhao, J and Zhang, H},
title = {Bifidobacterium animalis subsp. lactis Probio-M8 enhances chondroitin efficacy for knee osteoarthritis in postmenopausal women via the gut-joint axis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0086225},
doi = {10.1128/msystems.00862-25},
pmid = {41313018},
issn = {2379-5077},
abstract = {UNLABELLED: Knee osteoarthritis (KOA) is a chronic joint disease marked by cartilage degradation and inflammation. Probiotics exhibit anti-inflammatory properties and may influence the gut-joint axis. Thus, a 4-month human trial was conducted to assess the adjunctive effects of Bifidobacterium animalis subsp. lactis Probio-M8 on KOA in postmenopausal women. Sixty-five KOA patients were randomly allocated to the probiotic group (n = 37; Probio-M8 and chondroitin sulfate) or placebo group (n = 28; placebo and chondroitin sulfate). Following a 3-month intervention, participants from both groups entered a 1-month observation without probiotic supplementation. Our findings revealed that Probio-M8 co-administration significantly reduced Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) scores at months 1, 3, and 4 compared to the placebo group (P < 0.001). The probiotic group showed a significant decrease in serum IFN-γ and increases in IL-4 and IL-10 (P < 0.05). Fecal metagenome analysis showed significant changes in the gut microbiota of the probiotic group, with increases in potentially beneficial species, including Agathobaculum butyriciproducens, Bacteroides stercoris, B. animalis, Roseburia hominis, and Ruminococcus bromii, while Dorea formicigenerans decreased (P < 0.05). Changes in B. animalis were strongly associated with WOMAC scores. The gut metabolic potential analysis showed elevated levels of N-oleoylethanolamine and decreased levels of cholesterol and hypoxanthine in probiotic receivers (P < 0.05). Metabolite analysis revealed post-interventional alternations in fecal prostaglandin E2, stearic acid, cholic acid, chenodeoxycholic acid, xanthine, testosterone, and serum bile acids (P < 0.05). Collectively, Probio-M8 enhances the effectiveness of chondroitin sulfate in KOA management through modulating the gut-joint axis, potentially via regulating multiple inflammatory pathways.

IMPORTANCE: The pathogenesis of knee osteoarthritis (KOA) and its phenotypic expression have been associated with the human gut microbiota. Our study demonstrated that the co-administration of Probio-M8 with chondroitin sulfate significantly alleviates KOA symptoms. This probiotic intervention enhances therapeutic efficacy through modulation of the gut microbiota and associated metabolic pathways, reducing inflammation and improving clinical outcomes. Our results underscore the potential of probiotic-driven therapies as an adjunctive treatment strategy and underscore the importance of the gut-joint axis in KOA management.},
}

@article {pmid41313013,
year = {2025},
author = {Babb, PL and Akhund-Zade, J and Spacek, D and Brick, K and Christians, FC and Portnoy, V and Tsai, M-S and Jarman, KH and Bercovici, S and Vilfan, ID and Blauwkamp, TA},
title = {In-matrix library preparation for metagenomic sequencing of microbial cell-free DNA.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0094425},
doi = {10.1128/jcm.00944-25},
pmid = {41313013},
issn = {1098-660X},
abstract = {Metagenomic sequencing of microbial cell-free DNA (mcfDNA) enables comprehensive identification and quantification of diverse pathogens from blood and other biofluids. This approach enables minimally invasive diagnosis of deep-seated infectious disease, provides culture-free identification of antimicrobial resistance, and powers the discovery of novel microbial biomarkers for disease. However, widespread implementation of this approach is limited by lengthy and complex workflows, high host background cfDNA leading to high sequencing costs, and prevalent environmental DNA contamination risks. Addressing these barriers is critical for scalable deployment in both centralized and decentralized settings. To overcome these limitations, we developed Karius Helion-4 Chemistry (Helion-4), an in-matrix (DNA extraction-free) sample-to-DNA sequencing library workflow, to serve as a platform for mcfDNA sequencing applications in infectious disease, microbiome analyses, and disease biomarker discovery. We compared Helion-4 to two widely used metagenomic extraction-based sequencing workflows, as well as to the prior Karius chemistry platform (Digital Culture-3), using 36 clinical plasma specimens. Helion-4 enables end-to-end sequencing library construction for up to 96 samples in 5.25-6.1 h, including setup and final quality control evaluation, with 2.25 h of hands-on time when using automated liquid handling robots. Compared to the other methods, Helion-4 recovered 58-fold to 817-fold more endogenous mcfDNA per volume of plasma, while simultaneously demonstrating 1.8-fold to 6-fold lower exogenous background DNA contamination, likely due to the absence of DNA extraction. The fraction of mcfDNA reads among total reads was enriched by 60-fold to 164-fold for Helion-4 compared to current state-of-the-art methods, significantly lowering sequencing costs required for applications built on the Helion-4 platform vs other platforms. Collectively, these advances enable routine processing of small specimen volumes and provide a simple, efficient, and scalable approach for mcfDNA sequencing applications.IMPORTANCEMetagenomic sequencing of microbial cell-free DNA (mcfDNA) enables the identification and quantification of diverse pathogens from blood and other biofluids, providing minimally invasive and rapid diagnosis of deep-seated infectious disease. However, widespread implementation of this approach is limited by complex workflows, high sequencing costs, and prevalent contamination risks. Karius Helion-4 Chemistry, the first in-matrix (DNA extraction-free) sample-to-DNA sequencing library workflow, overcomes these limitations. Compared to the other methods, Helion-4 is faster, cleaner, and more sensitive. Helion-4 recovered up to 817-fold more endogenous mcfDNA per volume of plasma, while simultaneously demonstrating up to sixfold lower exogenous background DNA contamination. The fraction of mcfDNA reads among total reads was enriched by up to 164-fold for Helion-4, lowering sequencing costs. These advances by Helion-4 technology enable a simple, efficient, and scalable approach for mcfDNA sequencing applications and bring us closer to widespread, high-resolution, and real-time microbial profiling across diverse healthcare settings.},
}

@article {pmid41313007,
year = {2025},
author = {Fletcher, JR and Hansen, LA and Hoyser, JR and Hanna, AE and Martinez, R and Freeman, CD and Thorns, NT and Penningroth, MR and Villarreal, AR and Vogt, GA and Tyler, MA and Hines, KM and Hunter, RC},
title = {Commensal-derived short-chain fatty acids disrupt lipid membrane homeostasis in Staphylococcus aureus.},
journal = {mBio},
volume = {},
number = {},
pages = {e0139225},
doi = {10.1128/mbio.01392-25},
pmid = {41313007},
issn = {2150-7511},
abstract = {The role of commensal anaerobic bacteria in chronic respiratory infections is unclear, yet they can exist in abundances comparable to canonical pathogens in vivo. Their contributions to the metabolic landscape of the host environment may influence pathogen behavior by competing for nutrients and creating inhospitable conditions via toxic metabolites. Here, we show that the anaerobe-derived short-chain fatty acids (SCFAs) propionate and butyrate negatively affect Staphylococcus aureus physiology by disrupting branched-chain fatty acid (BCFA) metabolism. In turn, alterations to BCFA abundance impair S. aureus growth, compromise membrane integrity, diminish expression of the accessory gene regulator quorum-sensing system, and increase sensitivity to membrane-targeting antimicrobials. Disrupted BCFA metabolism also reduced S. aureus fitness in competition with Pseudomonas aeruginosa, suggesting that airway microbiome composition and the metabolites they exchange can directly impact pathogen succession over time. The pleiotropic effects of SCFAs on S. aureus fitness and their ubiquity as metabolites in the human host also suggest that they may be effective as adjuvants to traditional antimicrobial agents when used in combination.IMPORTANCEStaphylococcus aureus is a primary pathogen of chronic airway disease yet is also found in the upper airways of 30%-50% of the population to no obvious detriment. Thus, identifying the host and/or microbial factors that tip the balance between its commensal and pathogenic states may be key to its control. Here, we reveal that short-chain fatty acids produced by commensal microbiota promote a marked remodeling of the S. aureus lipid membrane that, in turn, sensitizes the pathogen to antimicrobials, disrupts accessory gene regulator quorum signaling, and reduces its competitive fitness. Altogether, these data suggest that co-colonizing microbiota and the metabolites they exchange with S. aureus may be key players in the microbial ecology of airway disease.},
}

@article {pmid41312997,
year = {2025},
author = {Castaneda, A and Indugu, N and Challa, K and Narayan, K and Johnson, A and Stefanovski, D and Webb, T and Zhao, X and Pitta, D},
title = {Investigating the antimethanogenic effects of selected nitro-compounds on methane production, rumen fermentation, and methanogenic archaea in vitro.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0103325},
doi = {10.1128/aem.01033-25},
pmid = {41312997},
issn = {1098-5336},
abstract = {Enteric methane emissions (EME) cause adverse environmental effects and energy losses to the host. Given the potent antimethanogenic effects of the nitro compounds (NC) ethyl-nitroacetate (ENA), ethyl-2-nitropropionate (ENP), and nitrate (NO3[-]), we hypothesized that they could effectively mitigate EME. Phase 1 determined dose responses of each NC, identified optimal doses, and evaluated their effects on gaseous composition, rumen fermentation, and bacterial-archaea populations. ENA and ENP tested at 8 and 16 mM inhibited CH4 production by 100%, whereas NO3[-] tested at 12 and 24 mM reduced CH4 production by 72%. However, the amount of spared H2 differed among NC, revealing differential effects on fermentation pathways. ENA increased propionate and butyrate concentrations at the expense of acetate, whereas ENP slightly reduced acetate and modestly increased propionate at 24 h post-incubation. NO3[-] acted as an alternative H2 sink without changing fermentation end products. The overall methanogenic community was not altered, but each NC differentially reduced the abundance of Methanobrevibacter ruminantium M1, Methanosphaera stadtmanae, and the methanogenic archaeon ISO4-H5. ENA greatly altered the bacterial profiles, followed by ENP and NO3[-]. Phase 2 investigated the impact of NC (0-1.25 mM) on M. stadtmanae cultures at 24 and 48 h post-incubation. The findings aligned with phase 1, confirming reduced CH4 production and H2 flux dynamics. ENA and ENP inhibited M. stadtmanae growth and CH4 production at all tested doses, whereas NO3[-] was effective at concentrations above 0.75 mM. These results highlight distinct mechanisms for CH4 mitigation, warranting further studies on additional methanogenic species to refine mitigation strategies.IMPORTANCEEME signify detrimental environmental impacts and constitutes an energy loss for the host. ENA, ENP, and NO3[-] showed distinct antimethanogenic effects, resulting in varied impacts on gas composition, rumen fermentation, and bacterial-archaea populations. ENA exerted the strongest and most direct inhibitory effect on methanogenesis, leading to notable changes in H2 and VFA accumulations and archaeal populations. Although ENP completely inhibited CH4 production, it resulted in low H2 accumulations, suggesting an indirect effect and a dose-dependent modulation of fermentation pathways. NO3[-] produced a moderate reduction in CH4 output by diverting H2 toward NH3 production while maintaining fermentation stability. M. stadtmanae cultures verified that ENA, ENP, and NO3[-] have distinct mechanisms of action, thereby affecting methanogenesis differently. These findings highlight the potential of nitro-compounds for CH4 reduction, underscoring the need for in vivo validation alongside detailed multi-omics analyses to fully understand their effects on rumen microbiota and metabolic networks.},
}

@article {pmid41312988,
year = {2025},
author = {Schluter, J and Jogia, W and Matheis, F and Ebina, W and Sullivan, AP and Gordon, K and Cruz, EFdl and Victory-Hays, ME and Heinly, MJ and Diefenbach, CS and Kang, UJ and Peled, JU and Foster, KR and Levitt, A and McLaughlin, E},
title = {A retrospectively registered pilot randomized controlled trial of postbiotic administration during antibiotic treatment increases microbiome diversity and enriches health-associated taxa.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0039025},
doi = {10.1128/iai.00390-25},
pmid = {41312988},
issn = {1098-5522},
abstract = {Antibiotic-induced microbiome injury, defined as a reduction of ecological diversity and obligate anaerobe taxa, is associated with negative health outcomes in hospitalized patients, and healthy individuals who received antibiotics in the past are at higher risk for autoimmune diseases. Postbiotics contain mixtures of bacterial fermentation metabolites and bacterial cell wall components that have the potential to modulate microbial communities. Yet, it is unknown if a fermentation-derived postbiotic can reduce antibiotic-induced microbiome injury. Here, we present the results from a single-center, randomized placebo-controlled trial involving 32 patients who received an oral, fermentation-derived postbiotic alongside oral antibiotic and probiotic therapy for non-gastrointestinal (GI) infections. At the end of the antibiotic course, patients receiving the postbiotic (n = 16) had significantly higher fecal bacterial alpha diversity (+40%, inverse Simpson index) compared to the placebo group (n = 16), and the treatment was well-tolerated. Analysis of 157 longitudinal fecal samples revealed that this increased diversity was driven by enrichment of health-associated taxa, notably obligate anaerobic Firmicutes, particularly Lachnospiraceae. In contrast, Escherichia/Shigella species, often linked to pathogenicity and antibiotic resistance, were reduced in postbiotic-treated patients at the end of antibiotic treatment and remained lower up to 10 days later. Our findings suggest that postbiotic co-administration during antibiotic therapy may augment health-associated gut microbiome composition and mitigate antibiotic-induced microbiome injury.Trial registration ISRCTN30327931 retrospectively registered.},
}

@article {pmid41312680,
year = {2025},
author = {Koike, Y and Morisaki, H and Motooka, D and Matsumoto, M and Takenaka, M and Murota, H},
title = {Postauricular Skin Mycobiome Profiles in Atopic Dermatitis Treated With Dupilumab or Cyclosporine A: A Descriptive Case Series.},
journal = {The Journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1346-8138.70083},
pmid = {41312680},
issn = {1346-8138},
support = {//Leading Medical Research Core Unit, Life Science Innovation, Nagasaki University Graduate School of Biomedical Sciences/ ; 25K11567//Japan Society for the Promotion of Science/ ; JP256f0137009//Japan Agency for Medical Research and Development/ ; },
abstract = {Atopic dermatitis (AD) essentially exhibits dysbiosis of skin fungal microbiome, mycobiome, characterized by depletion of Malassezia. The effects of recent systemic therapies for AD on skin mycobiome were not understood enough. We examined changes of skin mycobiome before and after systemic treatments with anti-IL-4Rα antibody (dupilumab: DUP) and calcineurin inhibitor (cyclosporine, CyA). Swab samples from postauricular areas in 19 AD patients treated with dupilumab (n = 13) and cyclosporine (n = 6) were collected before and 4-8 weeks after starting each treatment. Fungal DNA was amplified from the samples and sequenced with ITS1 metagenomic analysis, and taxonomic classification was performed. Fungi belonging to total 89 genera were detected. The share of the fungus was most occupied by Malassezia (81.3%), followed by Aspergillus (3.7%), and Trametes (1.1%) before DUP and CyA treatment, and occupied by Malassezia (87.3%), followed by Aspergillus (1.9%), and Candida (1.7%) after treatment. Three AD patients whose ratio of Malassezia in the skin mycobiome was under 50%, showed an exploratory increase of Malassezia after treatments (before 17.3%, after 67%). Analysis of the Malassezia species revealed an increase in M. restricta (before 70.5%, after 79.5%) and a decrease in M. globosa (before 23.9%, after 16.1%). No consistent patterns distinguishing DUP and CyA were observed. Systemic treatment with DUP and CyA was associated with shifts toward higher Malassezia abundance and modulation between M. restricta and M. globosa. These findings are exploratory and require validation in larger controlled studies.},
}

@article {pmid41312613,
year = {2025},
author = {Zuccotti, G and Calcaterra, V},
title = {The role of sex steroids in the human gut microbiome.},
journal = {Current opinion in pediatrics},
volume = {},
number = {},
pages = {},
pmid = {41312613},
issn = {1531-698X},
abstract = {PURPOSE OF REVIEW: Sex steroid hormones and the gut microbiome are increasingly recognized as bidirectionally interacting regulators of growth, metabolism, and endocrine maturation. While most research has focused on adults, accumulating evidence indicates that these interactions are established early in life and influence pubertal timing, metabolic homeostasis, and neuroendocrine development. This review synthesizes current human evidence on microbiome-sex steroid relationships across childhood and adolescence, highlighting mechanistic insights and clinical implications for pediatric endocrinology.

RECENT FINDINGS: Gut microbes modulate steroid hormone metabolism through enzymatic deconjugation and enterohepatic circulation, while pubertal hormonal shifts reciprocally influence microbial diversity and function. Early-life dysbiosis linked to antibiotics, diet, or obesity may alter hypothalamic-pituitary-gonadal activity. Microbial metabolites such as short-chain fatty acids, bile acids, and tryptophan derivatives regulate immune, metabolic, and neuroendocrine pathways, affecting growth and insulin sensitivity. Disruptions of this microbiome-hormone axis are implicated in pubertal timing disorders, metabolic dysfunction, polycystic ovary syndrome (PCOS), and inflammatory intestinal diseases, whereas fiber-rich diets and probiotics may help restore balance.

SUMMARY: The microbiome-sex steroid axis constitutes a fundamental component of pediatric endocrine development. Understanding this bidirectional relationship provides a framework for microbiome-informed strategies aimed at preventing and managing pubertal, metabolic, and neuroendocrine disorders during childhood and adolescence.},
}

@article {pmid41312383,
year = {2025},
author = {Miao, Z and Long, J and Huang, B and Yan, D and Wang, A},
title = {Roseburia hominis enriched by baicalin reverses the non-response to metformin via upregulating linolenic acid metabolism.},
journal = {iScience},
volume = {28},
number = {11},
pages = {113892},
pmid = {41312383},
issn = {2589-0042},
abstract = {Metformin is the most commonly used hypoglycemic drug for patients with type 2 diabetes (T2D), but about 30% of patients show non-response potentially linked to gut microbiota imbalance. Although baicalin exhibits potent gut microbiota-modulating activity, its role in reversing metformin non-response remains unclear. Here, we recruited patients with T2D who were non-responders to metformin treatment and collected their fecal samples to construct a humanized mouse model via fecal microbial transplantation. We found that baicalin combined with metformin improved the abnormal glucose tolerance in non-response mice, in which Roseburia hominis was considerably enriched. Mechanically, baicalin combined with metformin activated the AMP-activated protein kinase (AMPK)/acetyl-CoA carboxylase (ACC)/carnitine palmitoyl transferase 1 (CPT1) pathway, and its enriched R. hominis promoted linolenic acid metabolism, thus reversing the non-response to metformin. Besides, the efficacy of R. hominis in reversing the non-response of metformin was dependent on phospholipase A2 (linolenic acid metabolism key enzyme). Our findings provide feasibility strategies for the metformin treatment of non-responsive patients.},
}

@article {pmid41311995,
year = {2025},
author = {Lu, Q and Liu, P and Huang, G and Liu, L and Ge, Y and Wang, J and Hou, H and Wang, Y},
title = {Explainable multiomic screening for suboptimal health status in young adults: 3PM-guided innovation is envisaged.},
journal = {The EPMA journal},
volume = {16},
number = {4},
pages = {725-737},
pmid = {41311995},
issn = {1878-5077},
abstract = {OBJECTIVE: Suboptimal health status (SHS) is a reversible predisease stage and represents a key "window of opportunity" for predictive, preventive, and personalized medicine (3PM/PPPM). However, current screening methods still rely mainly on subjective questionnaires and lack objective, interpretable, and actionable tools for timely intervention. We aimed to develop an exploratory prototype system that combines multiomic signals with explainable artificial intelligence to apply 3PM in young adults.

METHODS AND RESULTS: Transcriptomic, metabolomic, and gut microbiome data from 30 SHS patients and 35 healthy controls were analyzed. Seven machine learning algorithms were compared, with elastic net selected for its balance of accuracy, stability, and interpretability. Calibration and decision curve analyses were performed to test robustness and clinical utility. Shapley additive explanations (SHAP) were applied for both global and individual interpretations. The multiomic elastic net prototype achieved high and stable discrimination (accuracy 0.941, ROC-AUC 0.999), with strong calibration and net benefit. Beyond statistical performance, the system identified biologically plausible and modifiable molecular targets-such as reduced vitamin K and elevated glycerophosphocholine-that are directly amenable to preventive strategies. SHAP further provided individual-level profiles, revealing the specific biological drivers of SHS risk for each participant and offering a template for personalized recommendations.

CONCLUSIONS: This study proposes an innovative 3PM-guided prototype system for predicting suboptimal health status on the basis of multiomics data. We suggest embedding this tool into preventive healthcare to enable early risk prediction, applying personalized interventions to delay or reverse the progression of SHS, and providing individualized follow-up to support long-term health management. From a public health perspective, this approach may substantially reduce the future burden of chronic diseases by addressing risks at a reversible stage.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13167-025-00426-3.},
}

@article {pmid41311994,
year = {2025},
author = {Bajinka, O and Jallow, L and Zhang, Y and Feng, X and Zhan, X and Li, N},
title = {The use of predictive, preventive, and personalized medical approaches to optimize hypertension management.},
journal = {The EPMA journal},
volume = {16},
number = {4},
pages = {785-804},
pmid = {41311994},
issn = {1878-5077},
abstract = {BACKGROUND: Hypertension, a major modifiable risk factor for cardiovascular disease, exhibits significant heterogeneity due to genetic, metabolic, and environmental influences. Traditional one-size-fits-all management is inadequate, necessitating predictive, preventive, and personalized medicine (3PM) approaches.

STUDY OBJECTIVE: This review critically evaluates 3PM's application in hypertension, focusing on leveraging biomarkers, artificial intelligence (AI), and digital health for risk stratification, early intervention, and tailored therapies.

KEY DISCUSSION: The 3PM framework leverages AI-driven integration of multi-omics, retinal imaging like ViT models, and hemodynamic profiling for risk prediction and treatment response forecasting; genetic profiling such as MTHFR, UMOD variants, urinary proteomics (CKD273 classifier), and microbiome-guided nutrition for early intervention; and pharmacogenomics, digital phenotyping like smartphone-guided dosing, and novel therapies such as aprocitentan and finerenone for personalized efficacy. Specific findings include aprocitentan reducing systolic BP by -15.3 mmHg in resistant hypertension, UMOD-guided torasemide use lowering BP by 8.5 mmHg in carriers, and microbiome-based nutrition reducing systolic BP by 14% in hyperglycemic patients. Key challenges include limited biomarker validation, "black box" AI algorithms, high costs, interoperability gaps, and equity barriers.

CONCLUSION: 3PM transforms hypertension management by enabling proactive, individualized care. However, rigorous validation, affordable diagnostics, pragmatic trials, and equitable access are essential to bridge translational gaps and achieve personalized cardiology's full potential.},
}

@article {pmid41311979,
year = {2025},
author = {Wang, P and Liang, J and Liu, F},
title = {Beyond antibiotics: advances in photothermal strategies for oral infections.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1637941},
pmid = {41311979},
issn = {2296-4185},
abstract = {The rising prevalence of antibiotic resistance necessitates innovative alternatives for managing polymicrobial oral infections. Photothermal therapy (PTT) emerges as a revolutionary approach that transcends conventional antimicrobial limitations by leveraging near-infrared (NIR)-activated photothermal agents to generate localized hyperthermia, enabling precise biofilm eradication while circumventing systemic drug resistance. The modality capitalizes on the anatomical accessibility of oral tissues and the optical transparency of dental structures, allowing spatiotemporal control over pathogenic niches from superficial caries biofilms to deep periodontal pockets. Recent advances in nanoplatform engineering have unlocked multifunctional PTT systems capable of synergizing thermal ablation with immunomodulation, biofilm matrix penetration, and even tissue regeneration, addressing the dual challenges of microbial persistence and host inflammatory damage. However, clinical translation remains hindered by unresolved technical barriers, including optimal thermal dosage calibration, lesion-specific material design, and long-term biosafety assessment. This review systematically dissects cutting-edge photothermal strategies across the oral infectious spectrum (dental caries, endodontic infections, periodontitis, and peri-implantitis) while critically evaluating their mechanistic innovations in overcoming antibiotic limitations. We further propose a roadmap for next-generation smart PTT systems integrating stimulus-responsive materials and microbiome-aware therapeutic paradigms to achieve personalized oral infection management.},
}

@article {pmid41311774,
year = {2025},
author = {Alshalhoob, HB and Almagushi, NA and Alanazi, RS and Alghuyaythat, WK and AlQifari, HS and Alfaqeh, AH and Sanguf, MA and Asiree, RH and Alajroush, N},
title = {Efficacy and Safety of Seawater Therapy Versus Non-pharmacological Interventions for Atopic Dermatitis: A Systematic Review.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e95450},
pmid = {41311774},
issn = {2168-8184},
abstract = {Marine water-based topical creams have been proposed as non-pharmacologic treatments for atopic dermatitis (AD), leveraging their mineralized nature to control inflammation, restore the skin barrier, and inhibit microbial colonization. However, their clinical efficacy and safety remain insufficiently characterized in existing observational and controlled studies. This systematic review aims to evaluate the effectiveness and safety of seawater and marine mineral-based therapies for patients with AD. A systematic review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidance. Randomized controlled trials and observational studies that investigated seawater or marine mineral-based treatments for AD were included. Seven databases were searched from April 2025 to September 10, 2025, using comprehensive Boolean and MeSH-based strategies. Extracted data included study design, intervention details, validated severity scores such as the Scoring Atopic Dermatitis (SCORAD) index, microbial colonization data, and adverse event profiles. Risk of bias was assessed with Risk of Bias (RoB) 2.0 and Risk Of Bias In Non-randomized Studies - of Interventions (ROBINS-I) tools. No review protocol was registered. Quantitative analysis of the 10 included studies demonstrated mean SCORAD improvements ranging from 26% to 55% in intervention groups. One trial reported a reduction from 45±4 to 7±1 in SCORAD, and another observed a 46±7.71% reduction with corticosteroids compared with 26±9.4% with thermal balneotherapy (therapeutic bathing in mineral water; p<0.03). Dead Sea climatotherapy (treatment in the unique climatic and mineral environment of the Dead Sea) and synchronous balneophototherapy (combined mineral water bathing with ultraviolet light therapy) consistently outperformed comparators in reducing severity scores. Qualitative findings revealed improvements in stratum corneum hydration, transepidermal water loss (TEWL, a measure of skin barrier integrity), and microbial composition, with marked reductions in Staphylococcus aureus colonization and enhanced microbial diversity. Adverse events were minimal and mild. In conclusion, seawater therapy demonstrated moderate clinical effectiveness in reducing AD severity and enhancing skin barrier function, with a favorable safety profile. These findings underscore the need to standardize treatment protocols and conduct larger trials to confirm long-term efficacy and reproducibility.},
}

@article {pmid41311719,
year = {2025},
author = {Hussain, A and Saeed, H and Islam, S and Sahu, PS and Shrivastava, AK},
title = {Editorial: Emerging mechanisms of host-pathogen interactions and immune responses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1730702},
pmid = {41311719},
issn = {2235-2988},
}

@article {pmid41311502,
year = {2025},
author = {Sun, G and Zhao, S and Huang, H and Guan, W and Wang, X and Zhang, H and Zhang, M and Hou, D and Xu, C and Chai, R},
title = {Integrated gut microbiome and metabolomics analysis reveals microbial-metabolic cross-talk in allergic rhinitis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1652915},
pmid = {41311502},
issn = {1664-302X},
abstract = {BACKGROUND: Emerging evidence indicates a link between gut dysbiosis and allergic rhinitis (AR) pathogenesis. Nevertheless, the mechanistic role of gut microbiota in AR progression requires further characterization. To address this, we employed an integrated multi-omics strategy to delineate gut microbial composition and metabolic signatures in AR patients.

METHODS: Fecal specimens from 23 AR patients and 15 matched healthy controls (total n = 38) were subjected to 16S rRNA gene sequencing to assess bacterial community structure, alongside untargeted metabolomic profiling of microbial metabolites. Spearman's rank correlation analysis was applied to evaluate microbiota-metabolite interactions.

RESULTS: Allergic rhinitis patients exhibited altered gut microbial community structure (beta diversity, P < 0.05) with depletion of SCFA-producing genera such as Faecalibacterium and enrichment of pro-inflammatory taxa like Fusobacterium. Metabolomic profiling identified significant disturbances in pathways including pantothenate and CoA biosynthesis, glycolysis, and pyruvate metabolism. Key discriminatory metabolites included maltol and 4-coumaric acid. Integrative analysis revealed significant correlations between specific bacteria and metabolites, such as Faecalibacterium with D-phenyllactic acid (ρ = 0.515, q = 0.046).

CONCLUSION: Our findings demonstrate that AR is associated with gut dysbiosis and metabolic dysfunction, highlighting the role of microbial-derived metabolites in immune regulation via the gut-nose axis. These insights support the potential for microbiota-targeted therapeutic strategies in AR management.},
}

@article {pmid41311501,
year = {2025},
author = {Wu, Q and Hu, S and Wang, Y and Wu, Y and Zhao, Y and Niu, L and Zhou, X and Shen, L and Liu, Y and Chen, Y and Gan, M and Zhu, L},
title = {Age-related gut microbiota succession in Neijiang pigs: insights for precision feeding and productivity.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1698169},
pmid = {41311501},
issn = {1664-302X},
abstract = {OBJECTIVE: To characterize age-related gut microbiota succession in Neijiang pigs and translate these dynamics into actionable insights for precision feeding and productivity improvement.

METHODS: Growth data from 0 to 180 days (n = 16, 780 weight records) were fitted with three non-linear models to determine the optimal growth curve and partition physiological stages. Fresh feces were collected at 25, 70, 110, and 150 days (n = 6/stage). 16S rRNA V3-V4 amplicon sequencing was used to profile microbiota composition and diversity; PICRUSt2 was employed to predict metagenome functions against the KEGG database.

RESULTS: The Gompertz model best described growth (R [2] = 0.996) with an inflection point at 84.2 days (25.9 kg). Microbial alpha-diversity (Shannon, Chao1) increased with age and plateaued after 110 days. Firmicutes and Bacteroidota dominated (>90% relative abundance), whereas Spirochaetota and Euryarchaeota expanded significantly in finishing pigs. LEfSe identified 45 stage-specific biomarkers: Prevotella_9, Collinsella and Blautia characterized suckling-weaning stages; Faecalibacterium and Clostridium_sensu_stricto_1 peaked at 70 days; Lactobacillus was dominant at 110 days; Treponema, Streptococcus and Bacteroides defined the 150-day microbiome. Functional prediction revealed a metabolic shift from basal biosynthesis and DNA repair in early life toward enhanced ABC transporters, bacterial motility proteins, oxidative phosphorylation and methane metabolism in finishing pigs.

CONCLUSION: Our data provide a temporal blueprint of gut microbiota maturation that mirrors host nutrient requirements across growth phases. These microbial indicators and functional signatures can guide stage-specific dietary formulations and microbiota-targeted interventions to improve feed efficiency, reduce environmental emissions and enhance the productivity of indigenous pig breeds.},
}

@article {pmid41311499,
year = {2025},
author = {Wang, J and Su, W and Chen, Q and Zhou, J and Wang, X and Jiang, R and Li, J and Xing, P},
title = {Microbiome-metabolome dysbiosis of bronchoalveolar lavage fluid of lung cancer patients.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1669172},
pmid = {41311499},
issn = {1664-302X},
abstract = {BACKGROUND: Recent studies indicate that microorganisms significantly influence lung cancer pathogenesis. This research explores the variations in microbiota and metabolites in the lower respiratory tract between lung cancer patients and individuals with benign pulmonary lesions to identify potential diagnostic biomarkers.

METHODS: Two hundred eight patients undergoing bronchoscopy at Tianjin Cancer Institute & Hospital and Tianjin Chest Hospital from October 2022 to October 2023 were screened. Ninety-five bronchoalveolar lavage fluid (BALF) was collected for metagenomic sequencing and untargeted metabolomic analysis. Comparisons of microbial diversity, taxonomic composition, and metabolite profiles were conducted between groups with lung cancer and benign lung conditions.

RESULTS: The cohort comprised 70 patients with lung cancer and 25 with benign lung lesions. Patients with lung cancer showed significantly reduced β-diversity (p = 0.005). Predominant microbes in lung cancer cases included Streptococcus, Haemophilus influenzae, and Veillonella parvula. A microbial-based diagnostic model differentiated lung cancer from benign lesions with an AUC of 0.931 (95%CI: 0.916-0.946). Metabolites increased in lung cancer were Citric acid, N-Acetylneuraminic acid, Oxoglutaric acid, and Neopterin, whereas L-Tryptophan, Uridine, 3-Hydroxybutyric acid decreased. The KEGG pathways suggest a significant link between microbial presence and both tumorigenesis and progression.

CONCLUSION: Specific microbial patterns in the lower respiratory tract of lung cancer patients could assist in the auxiliary diagnosis of the disease. The notably altered microorganisms and metabolites in the BALF from lung cancer patients, as opposed to those with benign conditions, correlate with cancer initiation and advancement.},
}

@article {pmid41311489,
year = {2025},
author = {Ahmed, W and Shakeel, Q and Ji, G},
title = {Editorial: Microbial regulation of plant immunity: mechanisms and applications.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1721914},
pmid = {41311489},
issn = {1664-302X},
}

@article {pmid41311301,
year = {2025},
author = {Zhang, Z and Liu, H and Du, X and Xu, Y and Wen, J},
title = {The antimicrobial action of apigenin against Phytophthora sojae and its recruitment effect on biocontrol agents in soybean rhizosphere.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70381},
pmid = {41311301},
issn = {1526-4998},
support = {32071637//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Plants release many kinds of metabolites in the rhizosphere, which recruit both pathogenic agents and beneficial microbes (improve plant growth or resist pathogens). Phytophthora sojae is a notorious plant pathogenic oomycete which causes the destructive Phytophthora root and stem rot (PRR) of soybean. However, it is not clear which beneficial biogenic metabolites are released from the resistant soybean that recruit beneficial microbes to defend Phytophthora sojae. We compared the rhizosphere components of a pair of soybean near-isogenic lines the susceptible Williams (W) and the resistant Williams82 (W82) pre-inoculation and post-inoculation with Phytophthora sojae, and analyzed the impact of the pathogen on plant rhizosphere composition. It is expected to screen the beneficial metabolites and microbes controlling PRR from the differential components of the resistant soybeans.

RESULTS: Rhizosphere soil of W82 and W post Phytophthora sojae inoculation had stronger inhibition effects on Phytophthora sojae infection to soybean than that of W82 and W. But there was no significant difference in α-diversity of rhizosphere microbiome between soybean pre-inoculation and post-inoculation. Some specialists in W82 rhizosphere induced by Phytophthora sojae, such as metabolites apigenin, and microbes Bacillus sporothermodurans had great inhibition effects on PRR. PRR incidence of apigenin treatment (41.3%) and Bacillus sporothermodurans (48%) treatment were significantly lower than control (equal volume of sterilized water with LB medium) (53-54%). Apigenin had the strongest inhibition effect on the mycelial growth of Phytophthora sojae among these metabolites and it was extremely related to the microbiome construction and the population of Bacillus in the rhizosphere.

CONCLUSION: Apigenin in the rhizosphere inhibits Phytophthora sojae directly and participates in the microbiome assembling in the rhizosphere and mediating the recruitment of Bacillus sporothermodurans to help soybean to resist PRR. © 2025 Society of Chemical Industry.},
}

@article {pmid41311178,
year = {2025},
author = {Adilijiang, Y and Sui, M and Ku'erban, A and Li, F and Liao, Q},
title = {[Effect and mechanism of digital cobalt-chromium alloy porcelain crowns and zirconia all-ceramic crowns restoration on periodontal health of patients with tooth defects].},
journal = {Shanghai kou qiang yi xue = Shanghai journal of stomatology},
volume = {34},
number = {5},
pages = {496-503},
pmid = {41311178},
issn = {1006-7248},
mesh = {Humans ; *Zirconium ; *Crowns ; *Dental Porcelain ; Male ; *Chromium Alloys ; Female ; Adult ; Middle Aged ; Periodontal Index ; Gingival Crevicular Fluid ; Ceramics ; },
abstract = {PURPOSE: To investigate the impact and underlying mechanisms of digital cobalt-chromium alloy porcelain crowns and zirconia all-ceramic crowns restoration on periodontal health in patients with tooth defects.

METHODS: A total of 26 patients with tooth defects who were treated in the Second People's Hospital of Kashi Region from March to June 2024 were selected and randomly divided into cobalt-chromium alloy ceramic crown group (n=13) and zirconia all-ceramic crown group (n=13). After 6 months of restoration, the periodontal health status of the two groups was evaluated, including gingival index, gingival bleeding index, plaque index, caries loss index and loss of clinical attachment. In addition, clinical plaque samples from patients were collected for 16S rRNA sequencing and data analysis to compare the characteristics of different flora in the two groups of samples. The samples of gingival crevicular fluid were collected and proteomic analysis was used to screen the differentially expressed proteins, and the biological process and functional pathway of their enrichment were discussed.

RESULTS: After 6 months of restoration, the gingival index, plaque index, and caries loss and repair index in the zirconia all-ceramic crown group were significantly lower than those in the cobalt-chromium porcelain crown group (P＜0.05). Although there was no significant difference in the α-diversity indexes of the plaque samples between the two groups, significant differences were observed in the microbial composition: Scardovia, Granulicatella, and Eikenella were significantly enriched in the zirconia all-ceramic crown group, while Peptococcus and Treponema were enriched in the cobalt-chromium porcelain crown group. In addition, a total of 105 differentially expressed proteins were identified by proteomic analysis, and these differentially expressed proteins were significantly enriched in metabolic related biological processes and functional pathways such as fatty acid metabolism and amino acid metabolism.

CONCLUSIONS: Zirconia all-ceramic crowns are superior to cobalt-chromium alloy porcelain crowns in terms of periodontal health for patients with dental defects, with less detrimental impact on oral microbiome, suggesting that zirconia crowns have a high clinical application value. The discovery of differential bacteria and differential expressed proteins provides potential biomarkers for early prediction of periodontal diseases and the development of personalized treatment plans.},
}

Humans
*Zirconium
*Crowns
*Dental Porcelain
Male
*Chromium Alloys
Female
Adult
Middle Aged
Periodontal Index
Gingival Crevicular Fluid
Ceramics

@article {pmid41311160,
year = {2025},
author = {Amin, H and Bertelsen, RJ and Cramer, C and Jögi, NO and Thorarinsdottir, H and Schlünssen, V and Benediktsdóttir, B and Janson, C and Gislason, T},
title = {Airborne Microbial Signatures of Sleep Apnea Risk: Enrichment of Human-Associated and Loss of Environmental Taxa.},
journal = {Journal of sleep research},
volume = {},
number = {},
pages = {e70257},
doi = {10.1111/jsr.70257},
pmid = {41311160},
issn = {1365-2869},
support = {804199//H2020 European Research Council/ ; },
abstract = {Sleep disorders such as obstructive sleep apnea (OSA) may be influenced by environmental exposures, yet the contribution of indoor microbial communities is not well understood. In this study, we examined whether the composition and load of airborne bacteria in bedrooms were associated with the Multivariable Apnea Prediction (MAP) index, a validated indicator of OSA risk. Bedroom air was sampled using electrostatic dust fall collectors in five Nordic centres participating in ECRHS III. Dust was analysed for bacterial load, endotoxin levels, and microbial composition using qPCR, LAL assay, and 16S rRNA sequencing. Associations between microbial exposures and MAP index were assessed using linear regression and categorical MAP cutoffs (≥ 0.5 and ≥ 0.7) adjusting for environmental factors. Bacterial community composition differed significantly between MAP groups, and participants with MAP ≥ 0.7 showed higher bacterial loads. However, alpha diversity and endotoxin levels did not vary by MAP category. A total of 35 bacterial genera were associated with MAP scores; taxa enriched in individuals with higher MAP values were primarily anaerobic and human-associated, whereas negatively associated genera were mostly aerobic and environmental. These findings suggest that the bedroom microbiome may carry a distinct microbial signature related to elevated OSA risk, potentially reflecting or contributing to sleep-disordered breathing.},
}

@article {pmid41310913,
year = {2025},
author = {Ramesh, A and Subbarayan, R and Srinivasan, D and Balakrishnan, R and Shrestha, R and Chauhan, A},
title = {Infectious Triggers and Immune Dynamics in Guillain-Barré Syndrome: Revisiting Campylobacter jejuni and the Silent Role of Haemophilus influenzae.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70177},
doi = {10.1002/mbo3.70177},
pmid = {41310913},
issn = {2045-8827},
support = {//The authors received no specific funding for this work./ ; },
mesh = {*Guillain-Barre Syndrome/immunology/microbiology/therapy/etiology ; Humans ; *Campylobacter jejuni/immunology/pathogenicity ; *Campylobacter Infections/immunology/complications/microbiology ; *Haemophilus influenzae/immunology/pathogenicity ; *Haemophilus Infections/immunology/complications/microbiology ; Lipopolysaccharides/immunology ; Molecular Mimicry ; },
abstract = {Guillain-Barré Syndrome (GBS) is a rapidly progressing immune-mediated neuropathy that remains the leading cause of acute flaccid paralysis worldwide. A substantial proportion of GBS cases are precipitated by infectious agents, most notably Campylobacter jejuni and Haemophilus influenzae, which initiate pathogenic autoimmunity via molecular mimicry. This narrative review aimed to synthesize current evidence on the microbial triggers of GBS and elucidate the immune mechanisms linking infection to neuropathic damage. We discuss the evolving landscape of GBS pathogenesis, emphasizing the roles of ganglioside-like lipooligosaccharide (LOS), host genetic predisposition, and dysregulated immune responses. The clinical heterogeneity of GBS subtypes, including axonal and demyelinating variants, was analyzed in relation to serotype-specific antibody profiles that inform the diagnosis and prognosis. Current therapeutic interventions, including intravenous immunoglobulin and plasma exchange, are critically assessed alongside experimental strategies, such as monoclonal antibody therapies, microbiome modulation, and LOS-targeted vaccines. This review highlights microbial surveillance and precision immunotherapy in the management of GBS. Collectively, this study underscores the central role of microbiological insights in redefining the prevention, diagnosis, and treatment of this complex neuroimmune disorder.},
}

*Guillain-Barre Syndrome/immunology/microbiology/therapy/etiology
Humans
*Campylobacter jejuni/immunology/pathogenicity
*Campylobacter Infections/immunology/complications/microbiology
*Haemophilus influenzae/immunology/pathogenicity
*Haemophilus Infections/immunology/complications/microbiology
Lipopolysaccharides/immunology
Molecular Mimicry

@article {pmid41310832,
year = {2025},
author = {Hoque, MM and Noorian, P and Espinoza-Vergara, G and To, J and Leo, D and Chari, P and Weber, G and Pryor, J and Duggin, IG and Lee, BB and Rice, SA and McDougald, D},
title = {Prediction of symptomatic and asymptomatic bacteriuria in spinal cord injury patients using machine learning.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {246},
pmid = {41310832},
issn = {2049-2618},
mesh = {Humans ; *Bacteriuria/diagnosis/microbiology ; *Spinal Cord Injuries/complications/microbiology ; *Machine Learning ; Female ; Male ; Adult ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; Urinary Tract Infections/microbiology/diagnosis ; Urinary Catheters/microbiology ; Aged ; },
abstract = {BACKGROUND: Individuals with spinal cord injuries (SCI) frequently rely on urinary catheters to drain urine from the bladder, making them susceptible to asymptomatic and symptomatic catheter-associated bacteriuria and urinary tract infections (UTI). Current identification of these conditions lacks precision, leading to inappropriate antibiotic use, which promotes selection for drug-resistant bacteria. Since infection often leads to dysbiosis in the microbiome and correlates with health status, this study aimed to develop a machine learning-based diagnostic framework to predict potential UTI by monitoring urine and/or catheter microbiome data, thereby minimising unnecessary antibiotic use and improving patient health.

RESULTS: Microbial communities in 609 samples (309 catheter and 300 urine) with asymptomatic and symptomatic bacteriuria status were analysed using 16S rRNA gene sequencing from 27 participants over 18 months. Microbial community compositions were significantly different between asymptomatic and symptomatic bacteriuria, suggesting microbial community signatures have potential application as a diagnostic tool. A significant decrease in local (alpha) diversity was noted in symptomatic bacteriuria compared to the asymptomatic bacteriuria (P < 0.01). Beta diversity measured in weighted unifrac also showed a significant difference (P < 0.05) between groups. Supervised machine learning models were trained on amplicon sequence variant (ASVs) counts and bacterial taxonomic abundances (Taxa) to classify symptomatic and asymptomatic bacteriuria with a repeated tenfold and leave-one-out participant (LOPO) type of cross-validation approaches. Combining urine and catheter microbiome data improved the model performance during repeated tenfold cross-validation, yielding a mean area under the receiver operating characteristic curve (AUROC) of 0.95 (95% CI 93-0.97) and 0.83 (95% CI 0.79-0.89) for ASVs and taxonomic features in the independent held-out test set, respectively. The LOPO cross-validation yielded a mean AUROC of 0.87 (95% CI 0.85-0.89) and 0.79 (95% CI 0.77-0.82) for ASVs and taxa features, respectively. These results suggest the potential of microbiome features in differentiating symptomatic and asymptomatic bacteriuria states.

CONCLUSIONS: Our findings demonstrate that signatures within catheter and urine microbiota could serve as tools to monitor the health status of SCI patients. Establishing a classification system based on these microbial signatures could equip physicians with alternative management strategies, potentially reducing UTI episodes and associated hospital costs, thus significantly improving patient quality of life while mitigating the impact of drug-resistant UTI. Video Abstract.},
}

Humans
*Bacteriuria/diagnosis/microbiology
*Spinal Cord Injuries/complications/microbiology
*Machine Learning
Female
Male
Adult
RNA, Ribosomal, 16S/genetics
Middle Aged
Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
Urinary Tract Infections/microbiology/diagnosis
Urinary Catheters/microbiology
Aged

@article {pmid41310812,
year = {2025},
author = {Tanca, A and Schallert, K and Grenga, L and Peters, SL and Abbondio, M and De Diego, L and Deledda, MA and Haange, SB and Miotello, G and Sáenz, JS and Wolf, M and Bastida, F and Devos, S and Hernandez-Raquet, G and Seifert, J and Wilmes, P and Van Den Bossche, T and Kunath, BJ and Heyer, R and Jehmlich, N and Benndorf, D and Hettich, RL and Armengaud, J and Uzzau, S},
title = {Critical Assessment of MetaProteome Investigation 2 (CAMPI-2): multi-laboratory assessment of sample processing methods to stabilize fecal microbiome for functional analysis.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {245},
pmid = {41310812},
issn = {2049-2618},
support = {ANR-20-CE34-0012//Agence Nationale de la Recherche/ ; ANR-24-INBS-0015//France2030 program - INBS ProFI/ ; 21023526-DeepMicro//Région Occitanie/ ; 863664//European Research Council, Horizon 2020 research and innovation program, EU/ ; 1286824N//Research Foundation Flanders/ ; BM/16965254//Luxembourg National Research Found, INTER Mobility program/ ; PON04a2_00557//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; },
mesh = {*Feces/microbiology/chemistry ; *Specimen Handling/methods ; Humans ; *Proteomics/methods ; *Gastrointestinal Microbiome ; *Proteome/analysis ; Bacteria/classification/genetics/isolation & purification ; Laboratories ; },
abstract = {BACKGROUND: Fecal samples are widely used as a proxy for studying gut microbiome composition in both human and animal research. Fecal metaproteomics provides valuable insights by tracking changes in the relative abundance of microbial taxa and their protein functions. To ensure reliable results, it is crucial to minimize alterations in the metaproteome occurring from sample collection to protein extraction. Therefore, employing effective stabilization methods is essential to preserve the integrity of the fecal metaproteome from sample collection to laboratory analysis, particularly over long distances or when rapid freezing options are not readily available. In line with these needs, the second edition of the Critical Assessment of MetaProteome Investigation (CAMPI-2) was specifically focused on testing sample stabilization protocols to be applied before metaproteomic analysis.

RESULTS: This collaborative multicenter study assessed the ability of five different stabilization methods, based on two commercial devices and three specific reagents (acetone, lithium dodecyl sulfate, and an RNAlater-like buffer), respectively, to stabilize the fecal metaproteome during room-temperature storage (14 days) and shipment to mass spectrometry facilities. The five methods were tested simultaneously by eight different laboratories across Europe, using aliquots from the same fecal sample. After protein extraction and digestion, duplicate aliquots of the resulting peptides were analyzed independently by two mass spectrometry facilities at distinct international locations. Analysis of the mass spectrometric data using two different search engines revealed that the fecal metaproteome profile differed considerably depending on the stabilization method used in terms of richness, alpha and beta diversity, reproducibility, and quantitative distribution of main taxa and functions. Although each method showed unique strengths and weaknesses, a commercial swab-based device stood out for its remarkable reproducibility and ranked highest for most of the metrics measured.

CONCLUSIONS: CAMPI-2 allowed a robust evaluation of five different methods for preserving fecal metaproteome samples. The present investigation provides useful data for the design of metaproteomics and multi-omics studies where fecal sampling cannot be immediately followed by long-term storage at - 80 °C. Further optimization of the tested protocols is necessary to improve stabilization efficiency and control bias in the taxonomic and functional profile of the gut microbiome. Video Abstract.},
}

*Feces/microbiology/chemistry
*Specimen Handling/methods
Humans
*Proteomics/methods
*Gastrointestinal Microbiome
*Proteome/analysis
Bacteria/classification/genetics/isolation & purification
Laboratories

@article {pmid41310806,
year = {2025},
author = {Utkina, I and Fan, Y and Willing, BP and Parkinson, J},
title = {Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {248},
pmid = {41310806},
issn = {2049-2618},
support = {RGPIN-2019-06852//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Metagenome ; *Bacteroides/metabolism/genetics/classification ; *Bacteria/classification/metabolism/genetics ; Fatty Acids, Volatile/metabolism ; Escherichia coli/metabolism/genetics ; },
abstract = {BACKGROUND: Members of the Bacteroidales, particularly Bacteroides species, with their ability to degrade dietary fibers and liberate otherwise unavailable substrates, exert a substantial influence on the microbiome of the lower intestine. However, our understanding of how this influence translates to the metabolic interactions that support community structure remains limited. In this study, we apply constraint-based modeling to investigate metabolic interactions in chicken cecal communities categorized by the presence or absence of Bacteroides.

RESULTS: From metagenomic datasets previously generated from 33 chicken ceca, we constructed 237 metagenome-assembled genomes. Metabolic modeling of communities built from these genomes generated profiles of short-chain fatty acids largely consistent with experimental assays and confirmed the role of B. fragilis as a metabolic hub, central to the production of metabolites consumed by other taxa. In its absence, communities undergo significant functional reconfiguration, with metabolic roles typically fulfilled by B. fragilis assumed by multiple taxa. Beyond B. fragilis, we found Escherichia coli and Lactobacillus crispatus also mediate influential metabolic roles, which vary in the presence or absence of B. fragilis. Notably, the microbiome's compensatory adaptations in the absence of B. fragilis produced metabolic alterations resembling those previously associated with inflammatory bowel disease in humans, including energy deficiency, increased lactate production, and altered amino acid metabolism.

CONCLUSIONS: This work demonstrates the potential of using the chicken cecal microbiome as a model system for investigating the complex metabolic interactions and key contributions that drive community dynamics in the gut. Our model-based predictions offer insights into how keystone taxa like B. fragilis may shape the metabolic landscape and functional organization of microbial communities. The observed metabolic adaptations in the absence of B. fragilis share metabolic similarities with profiles seen in dysbiotic states in humans and underscore the translational relevance of these insights for understanding gut health across different host systems. Video Abstract.},
}

Animals
*Chickens/microbiology
*Cecum/microbiology
*Gastrointestinal Microbiome
Metagenomics/methods
Metagenome
*Bacteroides/metabolism/genetics/classification
*Bacteria/classification/metabolism/genetics
Fatty Acids, Volatile/metabolism
Escherichia coli/metabolism/genetics

@article {pmid41310786,
year = {2025},
author = {Guilherme Pereira, C and Edwards, JA and Khasanova, A and Carlson, A and Brisson, V and Schaefer, E and Glavina Del Rio, T and Tringe, S and Vogel, JP and Des Marais, DL and Juenger, TE and Mueller, UG},
title = {Breeding of microbiomes conferring salt tolerance to plants.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {244},
pmid = {41310786},
issn = {2049-2618},
support = {DE-SC0021126//U.S. Department of Energy/ ; #1573//Joint Genome Institute/ ; },
mesh = {*Microbiota/genetics ; *Salt Tolerance/genetics ; RNA, Ribosomal, 16S/genetics ; *Brachypodium/microbiology/physiology/genetics ; Plant Leaves/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Plant Roots/microbiology ; Aluminum/metabolism ; *Plant Breeding ; Sodium/metabolism ; },
abstract = {BACKGROUND: Microbiome breeding through host-mediated selection is a technique to artificially select for microbiomes conferring beneficial properties to plants. Using a systematic selection protocol that maximises the heritability of microbiome effects, transmission fidelity, and microbiome stability through multiple selection cycles, we previously developed root-associated microbial communities conferring sodium and aluminium tolerance to Brachypodium distachyon, a model for cereal crops. Here, we explore the physiological mechanisms underlying our selected microbiomes' effect on plant fitness and analyse how our selection protocol shaped the composition and structure of these microbiomes. We analysed the effects of our selected microbiomes on plant fitness and tissue-nutrient concentration, then used 16S rRNA amplicon sequencing to examine microbial community composition and co-occurrence network patterns.

RESULTS: Our sodium-selected microbiomes reduced leaf sodium concentration by ~ 50%, whereas the aluminium-selected microbiomes had no effect on leaf-tissue nutrient concentration, suggesting different mechanisms underlying the microbiome-mediated stress tolerance. By testing the selected microbiomes in a cross-fostering experiment, we show that our artificially selected microbiomes attained (a) ecological robustness contributing to transplantability (i.e. inheritance) of microbiome-encoded effects between plants; and (b) network features identifying key bacteria promoting salt-stress tolerance.

CONCLUSIONS: Combined, these findings elucidate critical mechanisms underlying host-mediated artificial selection as a framework to breed microbiomes with targeted benefits for plants under salt stresses, with significant implications for sustainable agriculture. Video Abstract.},
}

*Microbiota/genetics
*Salt Tolerance/genetics
RNA, Ribosomal, 16S/genetics
*Brachypodium/microbiology/physiology/genetics
Plant Leaves/microbiology
*Bacteria/genetics/classification/isolation & purification
Plant Roots/microbiology
Aluminum/metabolism
*Plant Breeding
Sodium/metabolism

@article {pmid41310771,
year = {2025},
author = {Joshi, H and Bernard, B and Lemley, C and Wang, Z and Fan, P},
title = {Unveiling the rumen-microbiome-brain circuit: a unique dimension of gut-brain axis in ruminants.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {159},
pmid = {41310771},
issn = {1674-9782},
support = {2024-67015-42622//National Institute of Food and Agriculture/ ; },
abstract = {Gut-brain communication via the peripheral neural network is vital for regulating local digestive function and systemic physiology. Gut microbiota, which produces a wide array of neuroactive compounds, is a critical modulator in this bidirectional dialog. Perturbations in the gut microbiota have been implicated in neurological disorders such as depression and stress. Distinct from humans and other monogastric animals, ruminants possess a unique, microbially dense gastrointestinal compartment, the rumen, that facilitates the digestion of fibrous plant materials. These ruminal microbes are likely key contributors to rumen-brain crosstalk. Unlike certain microbe-derived neuroactive compounds produced in the hindgut that are minimally absorbed and primarily excreted in feces, those generated in rumen can reach the small intestine, where they are largely absorbed and affect central nervous system through systemic regulation in addition to the vagal pathway. Notably, emerging evidence suggests that rumen microbiota dysbiosis under stress is associated with abnormal behavior, altered hormonal and neurotransmitter levels. In this review, we introduce the concept of the rumen-microbiome-brain axis by comparing the anatomical structures and microbial characteristics of the intestine and the rumen, emphasizing the neuroactive potential of rumen microbiome and underlying mechanisms. Advances in this frontier hold tremendous promise to reveal a novel dimension of the gut-microbiome-brain axis, providing transformative opportunities to improve ruminant welfare, productivity, and agricultural sustainability.},
}

@article {pmid41310740,
year = {2025},
author = {Li, X and Zhang, Y and Chen, X and Zhang, Y and Khan, O and Xu, L},
title = {Gut microbiota variation drives differential performance in leaf beetles across host plants.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02278-5},
pmid = {41310740},
issn = {2049-2618},
support = {32370523//National Natural Science Foundation of China,China/ ; },
abstract = {BACKGROUND: Host plant significantly influences herbivorous insect fitness, while plant-mediated gut microbiota are recognized as a key determinant of insect performance. However, to what extent the differential performance of herbivorous insects on various plants is attributed to plant properties versus plant-mediated gut microbiota remains less clear.

RESULTS: Here, we initially observed that the leaf beetle Plagiodera versicolora preferred and exhibited superior performance on Salix babylonica compared with three other host plants. Intriguingly, eliminating larval gut microbiota abolished this preference-performance relationship, resulting in the loss of superior performance on S. babylonica. Further analysis of the larval gut microbiota revealed that Rosenbergiella nectarea was significantly enriched in S. babylonica-fed larvae and positively correlated with larval performance. Reintroduction of R. nectarea, but not two other gut commensal bacteria, restored the superior performance of germ-free (GF) larvae fed S. babylonica. Transcriptomic analysis linked this growth promotion to enhanced nutritional metabolism and developmental signaling. Integrated metabolomic and transcriptomic analyses further identified eight candidate genes underlying the observed effects. Notably, knockdown of either PvABCG1 or PvABCG5 recapitulated the microbiota-depleted phenotype, whereas reintroduction of R. nectarea into GF larvae only fully rescued PvABCG5 knockdown-induced growth retardation. Concurrently, R. nectarea supplementation increased the expression of key 20E synthesis genes (PvSPO, PvPHM, PvSHD), suggesting promotion of larval development may occur via a PvABCG5-mediated cholesterol-to-20E synthesis pathway.

CONCLUSIONS: Collectively, our results suggest that host plant-induced differential performance in herbivorous insects largely depends on their gut microbiota, suggesting a crucial role of the gut microbiome in herbivore host preference and the "preference-performance" relationship. Video Abstract.},
}

@article {pmid41310506,
year = {2025},
author = {Deng, Q and Tang, M and Gao, J and Liang, P},
title = {Association between gut microbiota dysbiosis and perioperative neurocognitive disorder and postoperative complications after valve replacement surgery: a prospective cohort study.},
journal = {BMC anesthesiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12871-025-03521-0},
pmid = {41310506},
issn = {1471-2253},
abstract = {BACKGROUND: To explore the relationship between gut microbiota disorder and perioperative neurocognitive disorder (PND) and postoperative complications after valve replacement.

METHODS: This prospective cohort study involved the patients above 50 years old undergoing elective heart valve replacement surgery. Postoperatively, the cognitive status on the first day without sedation after extubation was assessed. The microbial composition of the feces discharged for the first time after surgery was analyzed, and clinical symptoms of significant disruption in gastrointestinal microbiome within 7 days postoperatively were recorded. Patients with positive microbial results or clinical symptoms were categorized into the intestinal microbial disruption group, while the rest were the normal group. Subsequent analyses were conducted after propensity score matching for age, education duration, and gender between different microbial groups.

RESULTS: The final inclusion comprised 194 patients, In the PND group, patients had a significantly higher average age(P=0.002) comprising with normal group. Patients in the gut microbiota disturbance group had a higher average age compared to the normal group (P=0.005), with a significantly increased likelihood of developing PND (P=0.001) and other postoperative complications(P=0.008). After propensity score matching, establishing a matched queue consisting of 74 patient pairs, the incidence of PND in the flora disturbance group was 28.4% (21/74), higher than the normal group's 13.5% (10/74) (P=0.026).

CONCLUSIONS: The incidence of cognitive dysfunction and gut microbiota disorder after cardiac surgery is high, especially in elderly patients. Gastrointestinal microbiome dysbiosis is significantly associated with PND and other postoperative complications. Gastrointestinal microbiome dysbiosis is a risk factor for both PND and other postoperative complications.},
}

@article {pmid41310366,
year = {2025},
author = {Chen, J and Li, Y and Tang, S and Jin, W and Yan, R},
title = {Gut microbial β-glucuronidases and their role in the microbiome-metabolite axis in colorectal cancer.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10660},
pmid = {41310366},
issn = {2041-1723},
support = {MYRG-GRG2023-00241-ICMS-UMDF//Universidade de Macau (University of Macau)/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism/pathology ; *Gastrointestinal Microbiome/physiology ; HCT116 Cells ; *Glucuronidase/metabolism/genetics/chemistry ; Female ; Male ; Biomarkers, Tumor/metabolism ; Middle Aged ; },
abstract = {Colorectal cancer (CRC) development involves microbial and metabolic dysbiosis, with gut microbial β-glucuronidases (gmGUSs) potentially impacting carcinogenesis through de-glucuronidation of diverse important molecules. Here, we identify 550 gmGUSs from a public cohort, employing 114 alignment references, three structural domains, and seven conserved residues. Stage-specific shifts include enrichment of mini-Loop2 (a category defined by two active site-adjacent loop regions) and species-level gmGUS dysregulation (e.g., Bacteroides cellulosilyticus) in CRC. GUS biomarkers display modest efficacy in classifying CRC and adenoma patients from controls, though with limited generalizability, and in predicting CRC outcomes (AUCs > 0.8). Taxonomic and metabolic association analyses highlight microbe-gmGUS-metabolite (MGM) axis perturbations, including increased Alistipes and Fusobacterium, enriched mucin and flavonoid degraders, as well as amino acid and vitamin metabolism alterations linked to CRC progression. In vitro enzyme assays show that the identified gmGUSs possess differential substrate activities. Furthermore, RNA-seq of HCT116 cells co-cultured with BC.G3 (one of the differential gmGUSs from B. cellulosilyticus) reveals upregulation of RNA transcription, DNA replication, and protein folding, shedding preliminary light on its potential effects in CRC progression. Here, we define disturbance of MGM axis in colorectal tumorigenesis and offer potential early diagnostic biomarkers and therapeutic targets for CRC.},
}

Humans
*Colorectal Neoplasms/microbiology/metabolism/pathology
*Gastrointestinal Microbiome/physiology
HCT116 Cells
*Glucuronidase/metabolism/genetics/chemistry
Female
Male
Biomarkers, Tumor/metabolism
Middle Aged

@article {pmid41310268,
year = {2025},
author = {Fazeli, SA and Soleimani Samarkhazan, H},
title = {Metabolic Memory Following Metabolic Bariatric Surgery: Mechanisms, Clinical Implications, and Strategies for Long-Term Success.},
journal = {Obesity surgery},
volume = {},
number = {},
pages = {},
pmid = {41310268},
issn = {1708-0428},
abstract = {Metabolic bariatric surgery (MBS) treats severe obesity, but long-term benefits are often lost to weight regain and metabolic relapse driven by persistent molecular imprints. This narrative review synthesizes recent evidence and examines epigenetic, inflammatory, mitochondrial, and microbiota mechanisms underlying metabolic memory after MBS. Key imprints include altered adipose transcriptomes (e.g., lower IGF1 and GPX3), persistent NLRP3 inflammasome activation, and gut dysbiosis with variable, individual patterns. We highlight how these mechanisms drive clinical outcomes such as type 2 diabetes recurrence and residual cardiovascular risk, with tissue-specific epigenetic retention slowing renal and cardiac recovery. We evaluate evidence-based strategies to counteract or modulate metabolic memory. These include the strategic selection of bariatric procedure, preoperative metabolic optimization, Mediterranean diets rich in polyphenols, GLP-1/GIP co-agonists, senolytics (e.g., dasatinib + quercetin), and autologous fecal microbiome transplantation. Emerging preclinical approaches like CRISPR-dCas9 epigenetic editing and exploratory strategies like vagal neuromodulation show theoretical promise in targeting obesogenic memory pathways but remain far from clinical application. The review underscores the need for longitudinal multi-omics cohorts and metabolic memory biomarkers (e.g., PPARGC1A methylation, CCL25) to enable personalized interventions. By targeting metabolic memory proactively, MBS can evolve from weight-loss procedure to a durable reset of metabolic set points. However, it is crucial to acknowledge that many proposed strategies are derived from preliminary studies with limited sample sizes and follow-up, necessitating further validation in large-scale trials.},
}

@article {pmid41310118,
year = {2025},
author = {Donnelly, CG and Peng, S and Pflieger, L and Manfredi, J and Coleman, M and Rappaport, N and Price, ND and Finno, CJ},
title = {Bile acids segregate metabolic syndrome in a cohort of 100 deeply phenotyped horses.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1711},
pmid = {41310118},
issn = {2399-3642},
support = {D21EQ-050//Morris Animal Foundation (MAF)/ ; },
mesh = {Animals ; *Metabolic Syndrome/veterinary/blood/metabolism ; Horses ; *Bile Acids and Salts/metabolism/blood ; *Horse Diseases/blood/metabolism ; Phenotype ; Male ; Female ; },
abstract = {Metabolic syndrome (MetS)-encompassing obesity, insulin resistance, dyslipidemia, and hypertension-is prevalent in both humans and horses, offering a unique opportunity to explore shared pathophysiological mechanisms across species in a controlled model organism. In this first report from the Pioneer 100 Horse Health Project (P100HHP), we conducted a longitudinal, multi-omic analysis of 108 deeply phenotyped horses to interrogate individual health trajectories for precision insights into MetS. We identified two primary metabotypes: one characterized by elevated unsaturated triglycerides (TGs) and the other by increased levels of primary bile acids (BAs), notably taurocholic acid and taurochenodeoxycholic acid. Horses with higher circulating levels of taurocholic acid had significantly higher plasma insulin concentrations, especially after an oral sugar challenge (P = 0.01), indicating that specific BAs are associated with hyperinsulinemia-a key phenotype of MetS. Metabolomic signatures predicted body condition score (relative adiposity) with high performance, underscoring their potential for precision diagnostics. Seasonal variations influenced BA levels and were associated with shifts in the fecal microbiota, particularly in Clostridium and Proteobacteria populations. Additionally, we observed an inverse relationship between genetic diversity-measured by runs of homozygosity-and insulin levels, suggesting a genetic component to MetS susceptibility. Our findings demonstrate the power of deep phenotyping and multi-omic approaches to effectively delineate MetS subtypes in horses, highlighting the pivotal roles of bile acids and the microbiome in MetS pathogenesis. These insights not only advance the understanding of equine MetS but also establish the horse as a valuable translational model for human MetS, with potential implications for targeted diagnostics and therapeutics in both veterinary and human medicine.},
}

Animals
*Metabolic Syndrome/veterinary/blood/metabolism
Horses
*Bile Acids and Salts/metabolism/blood
*Horse Diseases/blood/metabolism
Phenotype
Male
Female

@article {pmid41309890,
year = {2025},
author = {Kuzmichenko, P and Fedorov, D and Galeeva, J and Postoeva, A and Krieger, E and Kudryavtsev, A and Pavlenko, A and Vvedensky, A and Starikova, E and Govorun, V and Ilina, E},
title = {Comparing alignment and de-novo approaches for gut microbiota metagenomic data analysis reveals differences in taxonomic resolution and novel functional insights.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {42423},
pmid = {41309890},
issn = {2045-2322},
support = {100217/WT_/Wellcome Trust/United Kingdom ; 075-15-2025-530//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Metagenomics/methods ; Feces/microbiology ; Metagenome ; Male ; *Bacteria/genetics/classification ; Female ; Adult ; },
abstract = {Microbiome annotation based on metagenomic data is primarily conducted using two global approaches: alignment-based approach (AL) and de novo approach (DN). This study aimed to evaluate the limitations of each approach, explore correlations between their results, and assess the equivalence of findings derived from different methodologies when analyzing the same dataset. Shotgun metagenomic sequencing data from 346 fecal samples, collected longitudinally within individuals in Arkhangelsk, Northwestern Russia, were analyzed. Each of the 173 participants provided two samples, one during 2015-2017 and another in 2022. The alterations in the microbiota associated with BMI served as a critical variable for facilitating the comparisons between the AL and DN. Exploratory analyses, including PERMANOVA, alpha diversity and beta diversity, revealed no significant differences between the two approaches. However, differential abundance analysis based on the AL yielded more statistically significant results, with the DN producing only a subset of these findings. An analysis of the metagenome-assembled genomes (MAGs) of bacteria that were differentially abundant revealed that one group of MAGs of Alistipes onderdonkii encodes the enzyme 2,5-diketo-D-gluconate reductase A. Using AL and DN together offers complementary functional insights, as the methods produce partially overlapping results. The novel enzyme finding suggests a potential role in metabolic pathways and underscores the value of integrative metagenomic analysis.},
}

*Gastrointestinal Microbiome/genetics
Humans
*Metagenomics/methods
Feces/microbiology
Metagenome
Male
*Bacteria/genetics/classification
Female
Adult

@article {pmid41309385,
year = {2025},
author = {Lee, I and Kim, SH and Lee, MJ and Oh, A and Lee, YK and Lee, KJ and Kim, BS},
title = {Strain-Level Differences of Bifidobacterium breve in the Gut Microbiome between Infants with and without Atopic Dermatitis: Insights from Genome Analysis and Immune Assays.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2509032},
doi = {10.4014/jmb.2509.09032},
pmid = {41309385},
issn = {1738-8872},
mesh = {Humans ; *Dermatitis, Atopic/microbiology/immunology ; *Gastrointestinal Microbiome/genetics ; *Bifidobacterium breve/genetics/isolation & purification/classification/immunology ; Infant ; Feces/microbiology ; Genome, Bacterial ; Probiotics ; Whole Genome Sequencing ; Phylogeny ; Female ; Male ; },
abstract = {Bifidobacterium breve is recognized as a probiotic with immune-enhancing properties. However, our previous studies revealed that this species is present at a higher relative abundance in the gut microbiome of infants with atopic dermatitis (AD). The potential functions of B. breve in the gut microbiome may vary at the strain level between infants with and without AD (non-AD). In this study, B. breve strains were isolated from the feces of infants with and without AD and analyzed whole genome sequencing and immune assay to identify strain level differences between AD and non-AD groups. Three B. breve strains were isolated from the feces of infants with AD (MHL_0001), in remission (MHL_0043), and non-AD infants (MHL_0062). The genomes of these isolates were compared to available complete genomes of B. breve strains. While the three isolates exhibited high overall genome similarity, differences in the sequence homology of immune related genes were observed between the AD strain (MHL_0001) and non-AD strain (MHL_0062). Immune assays further revealed marked differences in the anti-inflammatory effects between MHL_0001 and MHL_0062. These findings suggest that probiotic bacteria such as B. breve may adapt within the gut in response to host immune and physiological conditions. Moreover, the presence of B. breve in the gut microbiome does not necessarily guarantee beneficial effects for the host. Therefore, strain-level analysis is crucial to accurately determine the functional roles and impact of probiotic bacteria.},
}

Humans
*Dermatitis, Atopic/microbiology/immunology
*Gastrointestinal Microbiome/genetics
*Bifidobacterium breve/genetics/isolation & purification/classification/immunology
Infant
Feces/microbiology
Genome, Bacterial
Probiotics
Whole Genome Sequencing
Phylogeny
Female
Male

@article {pmid41309379,
year = {2025},
author = {Kim, H and Jeon, HJ and Jeong, HM and Bang, WY and Lee, HB and Lee, KS and Moon, JS and Kwon, H and Lee, J and Yang, J and Jung, YH},
title = {Modulation of the Gut Microbiome and Metabolomes by Fermentation Using a Probiotic Complex in a Dysbiosis-Associated Fecal Model.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2506014},
doi = {10.4014/jmb.2506.06014},
pmid = {41309379},
issn = {1738-8872},
mesh = {*Probiotics/pharmacology ; *Dysbiosis/microbiology/therapy ; *Gastrointestinal Microbiome/drug effects ; Humans ; Fermentation ; *Feces/microbiology ; *Metabolome ; Inflammatory Bowel Diseases/microbiology ; Bifidobacterium/metabolism ; Lactobacillus/metabolism ; Bacteria/classification/genetics/metabolism/isolation & purification ; Streptococcus/metabolism ; },
abstract = {Inflammatory bowel disease (IBD), affecting up to 0.5% of the global population, is frequently associated with gut microbiota dysbiosis and metabolic imbalances, which contribute to chronic constipation and abdominal discomfort. This study investigated the modulatory effects of an eight-strain probiotic complex comprising Lactobacillus, Bifidobacterium, and Streptococcus species on the gut microbiome and metabolome using an in vitro fecal fermentation model derived from a single IBD patient with dysbiosis. Metagenomic analysis demonstrated that increased abundance of beneficial bacteria, such as Lacticaseibacillus rhamnosus, while suppressing opportunistic pathogens, such as Escherichia coli and Enterococcus faecium. Metabolomic profiling further revealed significant alterations in metabolite levels that may help alleviate gut dysbiosis-related symptoms. These included increases in 3-hydroxybutyric acid, ascorbic acid, cadaverine, L-hydroxyproline, and N-acetylornithine and decreases in lysine and 3-aminoalanine. Given the single-donor design and the use of technical replicates, findings are presented as preliminary and descriptive rather than confirmatory. Collectively, these findings support the potential of probiotic fermentation to modulate microbial composition and metabolic output in a dysbiosis-associated context.},
}

*Probiotics/pharmacology
*Dysbiosis/microbiology/therapy
*Gastrointestinal Microbiome/drug effects
Humans
Fermentation
*Feces/microbiology
*Metabolome
Inflammatory Bowel Diseases/microbiology
Bifidobacterium/metabolism
Lactobacillus/metabolism
Bacteria/classification/genetics/metabolism/isolation & purification
Streptococcus/metabolism

@article {pmid41309364,
year = {2025},
author = {Joung, JY and Cheon, S and Song, JG and Han, C and So, JS and Moon, JK and Kim, HW and Kim, SH},
title = {Limosilactobacillus fermentum 2L Ameliorates Chronic Stress-Induced Neuroinflammation through Gut-Brain Axis Modulation in Mice.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2509035},
doi = {10.4014/jmb.2509.09035},
pmid = {41309364},
issn = {1738-8872},
mesh = {Animals ; Mice ; *Probiotics/pharmacology ; *Limosilactobacillus fermentum/physiology ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Male ; *Neuroinflammatory Diseases/therapy ; *Stress, Psychological ; Humans ; HT29 Cells ; *Brain/metabolism ; Disease Models, Animal ; *Brain-Gut Axis ; Hippocampus/metabolism ; Corticosterone/blood ; Anxiety ; Brain-Derived Neurotrophic Factor/metabolism ; Hypothalamo-Hypophyseal System ; },
abstract = {Chronic stress contributes to neuroinflammation and psychiatric disorders through gut-brain axis dysregulation. This study investigated the therapeutic potential of Limosilactobacillus fermentum 2L in ameliorating stress-induced neuroinflammation using an unpredictable chronic mild stress (UCMS) model. Five L. fermentum strains were screened for probiotic properties, with strain 2L selected based on superior acid and bile tolerance, cellular adhesion, and antioxidant activity. C57BL/6J mice underwent 7-week UCMS with concurrent 10-weeks of 2L treatment (10[9] CFU/day). Behavioral assessments, histological analysis, qRT-PCR, Western blotting, and gut microbiome analysis were performed. Strain 2L demonstrated superior gastrointestinal survival and anti-inflammatory properties in LPS-challenged HT-29 cells. In UCMS mice, 2L treatment significantly ameliorated anxiety- and depression-like behaviors, preserved hippocampal neuronal morphology, and normalized hypothalamic-pituitary-adrenal (HPA) axis dysfunction by reducing elevated corticosterone levels (155.9 ± 17.2 to 121.3 ± 3.1 ng/ml, p < 0.001). Molecular analysis revealed restored hippocampal BDNF expression, normalized serotonin receptors (HTR1A, 5HT7R), and attenuated stress-activated MAPK pathways (ERK1/2, JNK1/2). Treatment restored intestinal barrier integrity through tight junction protein upregulation and reduced pro-inflammatory cytokine expression. Microbiome analysis showed successful Limosilactobacillus colonization with restoration of beneficial bacteria (Faecalibaculum, Akkermansia) and normalization of stress-elevated Prevotella. L. fermentum 2L provides multifaceted neuroprotection through gut-brain axis modulation, involving microbiota restoration, intestinal barrier strengthening, HPA axis normalization, and enhanced neuroplasticity. These findings support the therapeutic potential of targeted probiotic interventions for stress-related neuropsychiatric disorders.},
}

Animals
Mice
*Probiotics/pharmacology
*Limosilactobacillus fermentum/physiology
Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
Male
*Neuroinflammatory Diseases/therapy
*Stress, Psychological
Humans
HT29 Cells
*Brain/metabolism
Disease Models, Animal
*Brain-Gut Axis
Hippocampus/metabolism
Corticosterone/blood
Anxiety
Brain-Derived Neurotrophic Factor/metabolism
Hypothalamo-Hypophyseal System

@article {pmid41309232,
year = {2025},
author = {Trần, TA and Lee, HY and Choi, HW},
title = {Metabolite-mediated mechanisms linking the urinary microbiome to bladder cancer.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {11},
pages = {e2509001},
doi = {10.71150/jm.2509001},
pmid = {41309232},
issn = {1976-3794},
support = {RS-2023-00221182//National Research Foundation of Korea/ ; RS-2025-00515944//National Research Foundation of Korea/ ; //Korea University/ ; },
mesh = {Humans ; *Urinary Bladder Neoplasms/microbiology/pathology/metabolism ; *Microbiota ; Dysbiosis/microbiology ; Bacteria/metabolism/genetics/classification ; *Urinary Tract/microbiology ; Animals ; },
abstract = {Bladder cancer is the most common malignancy of the urinary tract and is a major health burden globally. Recent advances in microbiome research have revealed that the urinary tract harbors a resident microbial community, overturning the long-held belief in its sterility. Increasing evidence suggests that microbial dysbiosis and microbially derived metabolites contribute to bladder cancer carcinogenesis, progression, and therapeutic responses. Distinct microbial signatures have been observed in bladder cancer patients, with notable differences across disease stages and between primary and recurrent cases. Mechanistic studies have demonstrated that microbe-associated metabolites and toxins can drive DNA damage, chronic inflammation, extracellular matrix remodeling, and epithelial-mesenchymal transition. In addition, biofilm formation allows bacteria to evade immune responses and promotes persistent inflammation, creating a tumor-permissive niche. Beyond pathogenesis, microbial activity also influences therapeutic outcomes; for instance, some microbial pathways can inactivate frontline chemotherapy, while others generate metabolites with anti-tumor properties. Collectively, these patterns define a microbiota-metabolite-immunity axis, presenting opportunities for precision oncology. Targeting microbial pathways, profiling urinary microbiota, and harnessing beneficial metabolites offer promising advancements in biomarker discovery, prognostic refinement, and the development of novel therapeutic strategies for bladder cancer.},
}

Humans
*Urinary Bladder Neoplasms/microbiology/pathology/metabolism
*Microbiota
Dysbiosis/microbiology
Bacteria/metabolism/genetics/classification
*Urinary Tract/microbiology
Animals

@article {pmid41308639,
year = {2025},
author = {Kvitne, KE and Allaband, C and Onuora, JC and Perry, D and Zuffa, S and Patel, L and Charron-Lamoureux, V and Mohanty, I and Sejane, K and Patan, A and Mahmud, AA and Ahmed, T and Bassani, DG and González, A and Hamer, DH and Haque, R and Ho, B and Hossain, MI and Islam, MS and McDonald, D and Pell, LG and Qamar, H and Roth, DE and Saha, S and Shah, PS and Siddiqui, MM and Sarker, SA and Sultana, S and Thomas, S and Burnett, LA and Tsunoda, SM and Bode, L and Dorrestein, PC and Knight, R},
title = {Environmental and maternal imprints on infant gut metabolic development.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.11.002},
pmid = {41308639},
issn = {1934-6069},
abstract = {Early life is a critical period for immune and metabolic development, but these patterns remain underexplored in populations from low- and middle-income countries. Here, we profile the microbiome and metabolome of 55 Bangladeshi mother-infant dyads over the first 6 months of life. Importantly, we observe an increase in microbially derived bile amidates and N-acyl lipids with age in conjunction with reads matching the bile salt hydrolase/transferase (bsh) gene. Although microbial source tracking confirms maternal fecal seeding, a substantial environmental contribution is also highlighted. Differences in infant fecal metabolic profiles are associated with delivery mode, maternal milk composition, household assets, and household-level water treatment. Cesarean section (C-section) delivery and untreated drinking water are linked to transient metabolic differences, including increases in bile amidates, N-acyl lipids, and other host-microbe co-metabolic products, including acylcarnitines. Multi-omics analysis reveals specific microbial-metabolite relationships, highlighting how early environmental and maternal living circumstances influence gut metabolic development through the microbiome.},
}

@article {pmid41308638,
year = {2025},
author = {Liu, H and Shen, J and Zhang, Z and Wang, J and Zhang, C and Zheng, L and Ni, H and Hong, L and Zhang, J and Xue, D and Chen, J and Yu, Q and Qu, Z and Ma, Y and Si, T and Zheng, L and Wang, S and Jiang, C and Li, Y and Wang, K and Dai, L},
title = {Exploring functional insights into the human gut microbiome via the structural proteome.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.11.001},
pmid = {41308638},
issn = {1934-6069},
abstract = {The human gut microbiome contains numerous proteins whose functions remain elusive yet are pivotal to host health. Sequence-based methods often falter when attempting to infer functions within this microbial proteome due to evolutionary divergence. To address this challenge, we develop the Human Gut Microbial Protein Structure Database, which incorporates ∼2.7 million predicted protein structures. Our findings reveal that structural analogy enhances the annotation of phage proteins. We detail the structural diversification of phage endolysins and confirm their potential in eliminating gut pathobionts. Furthermore, our structure-guided approach is effective in the identification of microbial-host isozymes. By employing structural alignments, we identify previously unrecognized bacterial enzymes involved in melatonin biosynthesis. Finally, we present an alignment-free method, dense enzyme retrieval, based on structure-encoded protein language models for ultrafast and sensitive detection of remote homologs. Our research underscores the value of computational structural genomics in elucidating the functional landscape of the human gut microbiome.},
}

@article {pmid41308172,
year = {2025},
author = {Binet, MT and Batley, GE and Stauber, JL and Kumar, A and Lu, HC and Ashbolt, NJ},
title = {An approach for deriving water quality guideline values for antimicrobials that integrates ecotoxicity and antimicrobial resistance endpoints.},
journal = {Integrated environmental assessment and management},
volume = {},
number = {},
pages = {},
doi = {10.1093/inteam/vjaf176},
pmid = {41308172},
issn = {1551-3793},
abstract = {Antimicrobials pose ecological risks in aquatic environments, particularly to cyanobacteria, aquatic plants and green algae, and with the potential to disrupt microbiomes upon which all biota rely. Beyond direct toxicity, these chemicals also contribute to the emergence and spread of antimicrobial resistance, posing risks to human, animal (including wildlife) and plant crop health, particularly through wastewater discharges and water reuse. Despite these concerns, Australia and New Zealand currently lack environmental water quality guideline values for antimicrobials. Furthermore, existing guideline value derivation frameworks for this region do not consider environmental endpoints to protect against antimicrobial resistance. This study critically reviews international approaches to estimating antimicrobial hazards to identify possible improvements for use in Australia and New Zealand. Through a co-design process with stakeholders across the water sector, a method for deriving guideline values using species sensitivity distributions was developed that integrates both traditional toxicity and antimicrobial resistance endpoints. Critically, the approach includes microbiome data, essential for capturing the impacts of antimicrobials on complex aquatic microbial communities. A case study with ciprofloxacin demonstrated that combining microbiome and single-species data in species sensitivity distributions provides a scientifically robust and data-efficient approach for developing environmental guideline values for antimicrobials. The framework may also have applicability to other contaminants known to influence antimicrobial resistance, such as other pharmaceuticals, metals, pesticides and microplastics. We also identified critical gaps that remain barriers to implementing antimicrobial resistance-inclusive frameworks for deriving water quality guideline values applicable to Australia and New Zealand.},
}

@article {pmid41279399,
year = {2025},
author = {Akresi, JE and Van Thanh Do, T and Cui, Z and Shanmugam, NRS and Moraïs, S and Mizrahi, I and Bayer, EA and Auchtung, J and Yin, Y},
title = {Mucinolysome in gut microbiomes of farm animals and humans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41279399},
issn = {2692-8205},
abstract = {Mucins are glycoproteins that create a protective barrier protecting host tissues from microbial pathogens and are instrumental for host health. Here, we provide evidence that mucin glycan degradation in the gut can be mediated by mucinolysomes, defined as extracellular multi-enzyme complexes specializing in mucin glycan degradation. We computationally predicted the presence of mucinolysomes across 63 metagenome-assembled genomes (MAGs) and two isolated genomes of anaerobic Limousia bacteria, including seven MAGs from human samples of six countries. All 65 genomes were found to display core mucinolysome components, consisting of 3~6 scaffoldins (containing up to 12 cohesin modules) and up to 22 dockerin-containing mucin glycan-degrading CAZymes (carbohydrate active enzymes). The organization of mucinolysomes allows the assembly of up to 24 CAZymes in the same complex. We validated that a cultivated Limousia strain ET540 from chicken cecum can support growth on mucins as its sole carbon source, triggering the expression of most mucinolysome-related genes, including both scaffoldins and CAZymes. We also modeled the assembly of proteins into a multi-enzyme complex by predicting the cohesin-dockerin interactions among most of the mucinolysome proteins using AlphaFold3. While mucinolysosome-encoding Limousia have low abundance in different animal hosts, their abundance and prevalence are higher in farm animals than in humans, highlighting a potentially important role in livestock gut ecosystems. Our findings reveal a novel mechanism of mucin glycan degradation and provide a framework to explore microbial contributions to gut health and host-microbe interactions across species.},
}

@article {pmid41134734,
year = {2025},
author = {Shaikh, FA and Nemeth, LE and Schmidhauser, CR and Nemeth, ZH},
title = {The Value of Baseline Intact Parathyroid Hormone in Vitamin D Supplementation for Early Multiple Sclerosis.},
journal = {Medical principles and practice : international journal of the Kuwait University, Health Science Centre},
volume = {},
number = {},
pages = {1-2},
doi = {10.1159/000548988},
pmid = {41134734},
issn = {1423-0151},
}

@article {pmid41308014,
year = {2025},
author = {Barat, B and Ghosh, K and Kulkarni, B and Banerjee, P and Ghosh, K},
title = {Enteric microbiome and obesity: a multidimensional narrative review.},
journal = {Microbial genomics},
volume = {11},
number = {11},
pages = {},
doi = {10.1099/mgen.0.001562},
pmid = {41308014},
issn = {2057-5858},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Obesity/microbiology ; Probiotics ; Animals ; },
abstract = {Obesity (henceforth called the pathologic condition) is a global epidemic affecting nearly 20% of adults worldwide and transcends genetic, ethnic and civilizational barriers in this era of globalization. Various ways of stemming the progress of the disease have been considered. One significant finding in this condition is an altered enteric microbiome. This review elucidates multiple mechanisms by which an altered enteric microbiome may contribute to the pathologic condition. Key roles include the microbiome's ability to process dietary roughage into absorbable nutrients, modulate intestinal physiology, enhance nutrient absorption and influence the endocrine function of adipose tissue and the liver to regulate appetite and hunger. The gut microbiome also interacts with the entero-insular axis, optimizing food utilization, and communicates with the central nervous system to alter appetite, satiety and food-seeking behaviour. Additional mechanisms include immunomodulation, chronic inflammation, epigenetic regulation and the production of vitamins and antioxidants. Promising therapeutic avenues, including engineering beneficial gut bacteria, developing targeted probiotic formulations and designing specialized food programmes can help combat this pathologic condition and potentially provide effective, non-invasive strategies to address this widespread condition.},
}

Humans
*Gastrointestinal Microbiome
*Obesity/microbiology
Probiotics
Animals

@article {pmid41307551,
year = {2025},
author = {Tamura, T and Ohsugi, Y and Katagiri, S and Kusano, A and Handa, T and Lin, P and Liu, A and Toyoshima, K and Takagi, S and Shiwaku, H and Sugihara, G and Takahashi, H},
title = {Oral Microbiota Associated With Cognitive Impairment in Schizophrenia: Composition and PICRUSt2-Predicted Functional Pathways.},
journal = {Schizophrenia bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1093/schbul/sbaf212},
pmid = {41307551},
issn = {1745-1701},
support = {24K18736//KAKENHI JP/ ; 24K12944//KAKENHI JP/ ; 24K02619//KAKENHI JP/ ; //Ministry of Education, Culture, Sports, Science and Technology of Japan/ ; //Enomoto Mental Health Association/ ; },
abstract = {BACKGROUND AND HYPOTHESIS: Cognitive impairment is a core disabling feature of schizophrenia (SZ). Changes in gut microbiota have been linked to cognitive dysfunction in SZ; however, changes in the oral microbiota in relation to immune dysregulation have only been recently reported, and their relevance to cognition remains unclear. The objective of this study was to explore the relationship between oral microbiota alterations and cognitive impairment in patients with SZ and to evaluate potential mediating mechanisms, including neuroinflammation and microbial functions.

STUDY DESIGN: In this cross-sectional study, we recruited 68 patients with SZ and 32 healthy controls (HC). Cognitive function was assessed using the Wechsler Adult Intelligence Scale-Fourth Edition. Oral microbiota composition was characterized by 16S rRNA gene sequencing, and microbial functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) based on the 16S profiles. Neuroinflammation was assessed using peripheral kynurenine (KYN) pathway activity as a proxy.

STUDY RESULTS: The patients with SZ exhibited significantly lower oral microbiota alpha diversity (driven by reduced evenness) and showed greater cognitive impairment and differences in the KYN pathway markers (neuroinflammation proxies) compared to HC. They also showed shifts in specific bacterial genera and the PICRUSt2-predicted functional pathways. Importantly, the oral microbiota alterations were significantly associated with cognitive impairment. Exploratory mediation analysis suggested that several pathways, including glycan biosynthesis and metabolism, may play a role in this association. In contrast, KYN pathway markers showed no significant association.

CONCLUSIONS: Our findings show an association between the oral microbiota alpha diversity and cognitive impairment in SZ, with the PICRUSt2-predicted functional pathways potentially implicated.},
}

@article {pmid41307322,
year = {2025},
author = {Baima, G and Dabdoub, S and Thumbigere-Math, V and Ribaldone, DG and Caviglia, GP and Tenori, L and Fantato, L and Vignoli, A and Romandini, M and Ferrocino, I and Aimetti, M},
title = {Multi-Omics Signatures of Periodontitis and Periodontal Therapy on the Oral and Gut Microbiome.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70055},
pmid = {41307322},
issn = {1600-0765},
support = {CUP B83C22004800006//Next Generation EU/ ; DM 1557 11.10.2022//Next Generation EU/ ; Prot. P2022YEX5R//Next Generation EU Program and the Italian Ministry of University and Research/ ; },
abstract = {AIM: To characterize the impact of periodontitis and of Steps I-II of periodontal therapy on microbiome composition, function, and metabolic output across the oral and gut environments.

METHODS: A multi-omics analysis was performed on saliva and stool samples collected from 50 systemically healthy individuals with and without Stage III-IV periodontitis. For participants with periodontitis, samples were analyzed both at baseline and 3 months after Steps I-II of periodontal therapy. High-throughput whole metagenome sequencing was used to profile microbial taxa and functional genes, NMR-based metabolomics profiled host-microbial metabolites. Single-omic differential abundance analysis between healthy samples and periodontitis samples was performed with MaAsLin2, while analysis between pre- and post-treatment was conducted with timeOmics. Variable selection and subsequent supervised multivariate analysis to determine group-separating markers utilized multi-level sparse Partial Least Squares Discriminant Analysis (sPLS-DA) through mixOmics. KEGG pathway enrichment was analyzed using clusterProfiler, whereas multi-omic data integration was performed with multi-block Partial Least Squares regression analysis.

RESULTS: Periodontitis was associated with significant compositional and functional changes in both saliva and stool, with increased abundance of pathobionts and loss of health-associated taxa in both niches. A subset of species was shared across oral and gut habitats, with detectable differences across clinical groups. As functional potential, periodontitis enriched microbial pro-inflammatory pathways (lipopolysaccharide biosynthesis, bacterial motility) and depleted beneficial short-chain fatty acid (SCFA)- and vitamin-producing functions. Metabolomic profiles revealed reduced SCFAs and amino acids in periodontitis, with elevated pro-inflammatory metabolites (succinate, trimethylamine) in both saliva and stool. Following therapy, microbial communities and their metabolic output partially reverted toward health-associated profiles, particularly in saliva. Stool samples showed subtler but consistent shifts, including a decrease in some typically oral species and decreased succinate and methylamine and restoration of amino acid and SCFA-related metabolites.

CONCLUSIONS: Periodontitis is associated with coordinated microbial and metabolic signatures across the oral and gut environments. Non-surgical periodontal therapy promotes partial ecological restoration in both niches, supporting the view of oral health as a modifiable target for influencing systemic microbial homeostasis.

TRIAL REGISTRATION: ClinicalTrials.gov identification number: NCT04826926.},
}

@article {pmid41307148,
year = {2025},
author = {Mclaughlin, MS and Yurgel, SN and Abbasi, PA and Ali, S},
title = {Changes in Environmental Conditions Differentially Affect the Bacterial Microbiome Communities in Different Apple Fruit Tissues.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70225},
doi = {10.1111/1758-2229.70225},
pmid = {41307148},
issn = {1758-2229},
support = {J-003004//Agriculture and Agri-Food Canada/ ; J-002516//Agriculture and Agri-Food Canada/ ; J-002861//Agriculture and Agri-Food Canada/ ; //Nova Scotia Fruit Gorwer Association/ ; 2090-21600-040-00D//USDA/ ; },
mesh = {*Malus/microbiology ; *Microbiota ; *Fruit/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Seasons ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The maintenance and manipulation of the beneficial plant microbiome is a new frontier in ecofriendly disease management, particularly during post-harvest storage. However, the fruit microbiome is highly variable and can be influenced by both biotic and abiotic factors. A comprehensive understanding of how these factors influence microbial communities is necessary in order to unlock the microbiome for sustainable disease management. In this study, we demonstrate the impacts of the growing season and management strategy on the composition and structure of the bacterial microbiome of 'Honeycrisp' apples at harvest from seven different orchards in the Atlantic Maritime Ecozone, over the course of two growing seasons. We show that the bacterial communities associated with core and peel tissues respond differently to changes in external environmental conditions, underscoring the need to include multiple tissue types in future fruit microbiome research. Finally, we characterize the microbial cooperation networks of apple core and peel tissues and identify key microbial taxa influencing these networks.},
}

*Malus/microbiology
*Microbiota
*Fruit/microbiology
*Bacteria/classification/genetics/isolation & purification
Seasons
RNA, Ribosomal, 16S/genetics

@article {pmid41307098,
year = {2025},
author = {Pangga, GM and Bamford, S and Richmond, A and Corcionivoschi, N and Ijaz, UZ and Gundogdu, O},
title = {The Transgenerational Link: Breeder Gut Microbiota and Broiler Progeny Development.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70174},
doi = {10.1002/mbo3.70174},
pmid = {41307098},
issn = {2045-8827},
support = {//This work was supported by the Biotechnology and Biological Sciences Research Council (grant number BB/T008709/1)./ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Chickens/microbiology/growth & development ; Female ; Reproduction ; },
abstract = {The gut microbiome of breeder hens plays a pivotal role in reproductive efficiency, egg quality, and progeny development. Its composition is shaped by host factors such as age and genetics, as well as environmental influences, including diet and management practices. Importantly, the breeder gut microbiome is not only dynamic but also responsive to targeted interventions that can enhance intestinal health, metabolic function, and laying performance. Vertical transmission of maternal microbes through the cloaca and egg components provides offspring with a foundational microbial community, with the yolk sac serving as a critical reservoir for early colonisers that influence gut maturation, immunity, and growth. Emerging evidence further demonstrates that maternal nutritional strategies can programme the gut microbiota of progeny and intestinal development, highlighting the breeder microbiome as both a determinant and mediator of transgenerational performance. These insights underscore the potential of microbiome-focused approaches to improve reproductive success and sustainability in poultry production.},
}

Animals
*Gastrointestinal Microbiome
*Chickens/microbiology/growth & development
Female
Reproduction

@article {pmid41306971,
year = {2025},
author = {Han, T and Zhang, Y and Zheng, G and Guo, Y},
title = {From pathogenic mechanisms to therapeutic perspectives: a review of gut microbiota and intestinal mucosal immunity in inflammatory bowel disease.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1704651},
pmid = {41306971},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Immunity, Mucosal ; *Intestinal Mucosa/immunology/microbiology ; *Inflammatory Bowel Diseases/therapy/immunology/microbiology/etiology ; Animals ; Dysbiosis/immunology ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; },
abstract = {Inflammatory bowel diseases (IBDs), which comprises Crohn's disease (CD) and ulcerative colitis (UC), is a multifactorial disorder with an as-yet undetermined etiology, with its global incidence rising rapidly, particularly in developing and Western countries. Although the exact etiology remains unclear, recent research implicates genetic predisposition, environmental factors, gut microbiota, and immune responses in the pathogenesis of IBD. Notably, dysbiosis of the gut microbiota-characterized by a reduction in the abundance and diversity of specific bacterial genera-has been suggested as a potential trigger for the onset of IBD, accompanying with dysregulated intestinal mucosal immunity involving in immune cells and nonimmune cells. Understanding and restoring the imbalanced gut microbiota, as well as identifying key bacterial species involved in IBD, are critical for elucidating disease mechanisms and developing therapeutic strategies. In this review, we explore the role of gut microbiota and intestinal mucosal immunity in the pathogenesis of IBD and offers insights into microbiota-centered therapeutic interventions, including probiotics, fecal microbiota transplantation, and microbial metabolites, that aim to modulate the gut microbiota for the treatment of IBD.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Immunity, Mucosal
*Intestinal Mucosa/immunology/microbiology
*Inflammatory Bowel Diseases/therapy/immunology/microbiology/etiology
Animals
Dysbiosis/immunology
Fecal Microbiota Transplantation
Probiotics/therapeutic use

@article {pmid41306925,
year = {2025},
author = {Corr, S and Lowe, C and Vos, M},
title = {Reciprocal transplantation experiments reveal local adaptation of seaweed-associated bacteria.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf205},
pmid = {41306925},
issn = {2730-6151},
abstract = {Seaweed microbiomes are diverse and frequently species-specific. By actively attracting and repelling settling bacteria through exuded metabolites, seaweeds are thought to exert a strong selective pressure on their microbiomes. However, to what degree seaweed-associated bacteria are adapted to their host has received little attention. Here, we retrieve cultivable seaweed bacterial communities from Palmaria palmata (Dulse) and Fucus serratus (Serrated Wrack) and use reciprocal transplant experiments to test whether bacterial isolates have the greatest fitness on their host seaweed species. We used agar derived from host seaweed extracts for bacterial isolation, which was found to be superior to a generic marine agar formulation based on both 16S rRNA gene amplicon alpha- and beta-diversity comparisons to uncultured samples. We then demonstrate that bacterial isolates from both seaweed species exhibit higher fitness in media derived from their native host compared to a non-native host. Although epibacterial fitness varied between hosts, bacterial isolates on average outperformed non-native counterparts in their native environment. By integrating amplicon sequencing with laboratory experiments, we demonstrate that bacteria are locally adapted to their seaweed host species. These findings contribute to the growing body of research exploring the evolutionary and ecological drivers that shape bacterial communities, with implications for ecosystem management, disease control, and microbial biotechnology.},
}

@article {pmid41306772,
year = {2025},
author = {Wu, J and Wu, L and Liu, R and Xuan, L and Qian, J and Fang, C and Wang, H and Guo, J and Du, L and Miao, Y and Liu, B and Liu, Y and Tang, G},
title = {Fabrication of Single-Bacterium Microgel with Gas-Shearing Strategy for Precision Probiotic Delivery in IBD Therapy.},
journal = {Research (Washington, D.C.)},
volume = {8},
number = {},
pages = {0955},
pmid = {41306772},
issn = {2639-5274},
abstract = {The human gut microbiome is essential for maintaining health, as it substantially impacts immune regulation and overall balance within the body. Accordingly, disruptions in this microbial community are associated with various diseases. Probiotics offer a promising solution, but their effectiveness is often hampered by challenges related to gastrointestinal delivery. To overcome the issue of probiotic survival in the gastrointestinal system, researchers have explored various encapsulation techniques. However, traditional coarse encapsulation techniques lack precision and effective targeting, limiting the delivery of viable organisms to the colon. Current methods face challenges such as inadequate particle size control, leakage, and poor survival in complex gastrointestinal environments. This research introduces a novel approach for encapsulating individual bacteria to create single-bacterium microgels, utilizing gas-shearing technology to enhance the survival and targeting capabilities of probiotics. This approach also demonstrates the capability to coat multiple microbial species, including bacteria and fungi, while ensuring good biocompatibility and mechanical support. Focusing on Escherichia coli Nissle 1917, we demonstrate that this method significantly improves therapeutic efficacy in treating inflammatory bowel disease compared to unencapsulated strains. Our results suggest that gas-shearing encapsulation represents a promising strategy for the fabrication of single-bacterium microgels, facilitating the development of effective probiotic therapies with potential applications in both biomedical and nutraceutical fields.},
}

@article {pmid41306540,
year = {2025},
author = {Cordi, CV and Hurley, JM},
title = {The Link Between Circadian Disruption and Alzheimer's Disease and Related Dementias: Insights from Peripheral Inflammation.},
journal = {Current opinion in physiology},
volume = {46},
number = {},
pages = {},
pmid = {41306540},
issn = {2468-8673},
abstract = {Circadian rhythms are essential for maintaining physiological homeostasis, influencing biological processes from the sleep-wake cycle to metabolism and immune responses. Disruption of these rhythms is increasingly linked to the pathogenesis of Alzheimer's Disease and Related Dementias (ADRDs), conditions characterized by cognitive decline and neuropsychiatric symptoms through various pathways including increases in inflammation. While many studies link the effects of circadian disruption on neuroinflammation to ADRDs, this review explores the potential link between the circadian disruption of peripheral inflammation and ADRDs. We discuss the evidence of how circadian misalignment can exacerbate neuroinflammation through the activation of the peripheral immune system. We further examine the role of peripheral factors such as insulin dysregulation, melatonin levels, and gut microbiome imbalances in amplifying these peripheral inflammatory responses. These data underscore the significance of circadian regulation in maintaining immune homeostasis, highlighting potential therapeutic avenues for mitigating ADRDs through the restoration of circadian integrity.},
}

@article {pmid41306408,
year = {2025},
author = {Vijendra, A and Kunkle, C and Jordan, J and Erickson, A and Osei-Karikari, K and Ratley, G and Myles, IA},
title = {Molecular connections between inflammation and social determinants of health.},
journal = {Frontiers in epidemiology},
volume = {5},
number = {},
pages = {1683955},
pmid = {41306408},
issn = {2674-1199},
abstract = {Chronic inflammatory diseases such as autoimmune disorders, cancer, cardiovascular diseases and neurodegenerative disorders are a significant cause of morbidity and mortality in the industrialized world. Socioeconomically disadvantaged communities bear a disproportionately high burden of these inflammatory diseases. This review synthesizes evidence linking various domains of the Social Determinants of Health (SDoH)-economic stability, education access and quality, healthcare access and quality, neighborhood and built environment, and social and community context-to inflammatory pathways and mechanisms. Across domains, biological mechanisms such as cytokine dysregulation, toll-like receptor (TLR) activation, hypothalamic-pituitary-adrenal (HPA) axis alterations and gut microbiome disruption act together to sustain proinflammatory states that drive adverse health outcomes in marginalized communities. Although causality is obscured by interrelated determinants, identifying inflammation as a shared pathway between various determinants highlights the need for structural interventions to reduce chronic disease burden.},
}

@article {pmid41306340,
year = {2025},
author = {Kim, H and Kim, HL and Boo, M and Choi, H and Han, J and Nam, S and Kang, SJ and Kim, JK and Han, Y and Jung, JH and Kim, W and Kim, KI and Um, JY and Park, J and Otterbein, LE and Kim, HI and Ko, SG},
title = {Herbal Combination of Angelica gigas, Zingiber officinale, and Aconitum carmichaeli Alleviates High Fat Diet-Induced Non-Alcoholic Fatty Liver Disease in Mice Through NRF2-Mediated Regulation of Adipogenesis and Non-Shivering Thermogenesis.},
journal = {Food science & nutrition},
volume = {13},
number = {12},
pages = {e71199},
pmid = {41306340},
issn = {2048-7177},
abstract = {Obesity is a complex metabolic disorder characterized by excessive fat accumulation and is closely associated with non-alcoholic fatty liver disease (NAFLD), a condition that increases the risk of metabolic complications such as insulin resistance, type 2 diabetes, and cardiovascular diseases. JI017 is a recently optimized multi-herbal formula composed of Angelica gigas, Zingiber officinale , and processed Aconitum carmichaeli. Clinical records of these three herbs indicate their potentially synergistic anti-obesity effects. This study was conducted to verify the effects of JI017 in an animal model of obesity-associated NAFLD. The effect of JI017 on glucose metabolism, white adipose tissue (WAT) adipogenesis, brown adipose tissue (BAT) thermogenesis, liver oxidative stress, and gut microbiota composition was assessed. The results showed that JI017 improved glucose sensitivity, reduced WAT mass by suppressing PPARγ and C/EBPα expression, and increased BAT thermogenesis through upregulation of UCP1 and PGC-1α. Additionally, JI017 reduced liver oxidative stress by increasing HO-1 and NRF2 expression and modulated the gut microbiota by restoring the Firmicutes/Bacteroidetes ratio. These findings on the multi-targeted effects of JI017 suggest its potential as a promising therapeutic approach for metabolic diseases including NAFLD.},
}

@article {pmid41306277,
year = {2025},
author = {Peng, Y and Ma, L and Zhou, H and Li, J and Wang, J},
title = {1DCNN-BiLSTM-transformer hypertension risk prediction model based on APW.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1714654},
pmid = {41306277},
issn = {1664-302X},
abstract = {INTRODUCTION: Hypertension has a multifactorial etiology. Recent studies have revealed a link between hypertension and gut microbiota dysbiosis. Pulse wave analysis holds significant clinical value for hypertension risk assessment. While research on deep learning models utilizing photoplethysmography (PPG) for hypertension classification has advanced, limitations persist. PPG offers limited richness and accuracy for characterizing blood pressure-related pathological information. In contrast, Arterial Pressure Waveform (APW) provides richer pathological information and exhibit stronger correlations with clinically interpretable features. However, deep learning research using APW for hypertension classification remains limited, as existing studies focus primarily on local feature extraction and neglect global temporal dynamics.

METHODS: To address these challenges, we propose a novel 1D-CNN-BiLSTM-Transformer architecture for hypertension risk assessment based on APW, where the 1D-CNN module extracts waveform morphology features from signals within individual pressure segments, the BiLSTM module models long-range temporal dependencies from signals within each segment, and the Transformer module explicitly captures nonlinear interaction from signals across different pressure segments through multi-head self-attention mechanisms.

RESULTS: We use the multi-channel APW database from the Population Health Data Archive (PHDA), containing hypertensive and non-hypertensive cases with APW signals acquired from six traditional Chinese medicine points (left-cun, left-guan, left-chi, right-cun, right-guan, and right-chi) to evaluate the model's performance. The model outperforms the current state-of-the-art methods in accuracy, precision, recall, and F1 score across all six points.

CONCLUSION: The proposed model enhances classification performance. The physiologically driven interpretable analysis demonstrates that APW can reflect pathophysiological features associated with gut microbiota dysbiosis. The model-driven interpretable analysis offers a decision-making basis for clinical diagnosis.},
}

@article {pmid41306171,
year = {2025},
author = {Ng, MK and Jacofsky, DJ and Barsoum, WK and Mont, MA},
title = {Human Health Applications of Calcium Montmorillonite Clay: A Systems-Based Review.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e95449},
pmid = {41306171},
issn = {2168-8184},
abstract = {Calcium montmorillonite (CMM) clay is a naturally occurring mineral with a longstanding history in medical applications, now receiving increased scientific attention for its broad therapeutic potential. Known for its ability to bind a range of harmful substances, including bacterial toxins, heavy metals, mycotoxins, and inflammatory mediators, it exerts its effects without systemic absorption, acting locally within the gastrointestinal tract or at the skin surface. This narrative review synthesizes current clinical and preclinical evidence on the human health applications of calcium montmorillonite, with focused sections on the gastrointestinal/metabolic, dermatologic, immune, and musculoskeletal systems. The gastrointestinal section covers its documented role in treating pediatric diarrhea, radiation enteritis, and dietary toxin exposure. In dermatology, the clay has been incorporated into topical preparations for acne, rashes, and wound care, supported by both laboratory data and real-world use. Hepatic and metabolic studies suggest that it may reduce liver fat accumulation, improve glucose metabolism, and modulate the gut microbiome, particularly in models of non-alcoholic fatty liver disease and obesity. Additional sections explore its potential relevance in renal toxin clearance, immune regulation, mucosal healing, and surgical recovery. Across these systems, calcium montmorillonite has demonstrated a strong safety profile, with minimal nutrient interaction and no evidence of systemic toxicity when properly sourced and used in appropriate contexts. With growing access to carefully studied, pharmaceutical-grade formulations, CMM may offer safe and consistent benefits across clinical and preventive care settings.},
}

@article {pmid41305918,
year = {2025},
author = {Shao-Yu, Y and Niu, D and Chen, J and Li, WY and Wang, X and Meng, QW and Song, WJ and Yang, YG and Wang, H and Li, RR and Li, BY and Zhang, LG and Hu, CJ and Xu, LF and Wang, HH and Zhang, L and Liang, CZ and Du, HX},
title = {Antibiotic cocktail-induced changes in gut microbiota drive alteration of bile acid metabolism to restrain Th17 differentiation through the FXR-NLRP3 axis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2582944},
doi = {10.1080/19490976.2025.2582944},
pmid = {41305918},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Th17 Cells/drug effects/immunology/cytology ; Male ; *Bile Acids and Salts/metabolism ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; Mice ; *NLR Family, Pyrin Domain-Containing 3 Protein/metabolism/genetics ; Humans ; *Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Mice, Inbred C57BL ; Cell Differentiation/drug effects ; Fecal Microbiota Transplantation ; *Prostatitis/immunology/microbiology/drug therapy ; Disease Models, Animal ; Interleukin-17 ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Antibiotics influence both gut microbial composition and immune regulation, but the detailed mechanisms are still undefined. Shifts in the microbiome caused by antibiotic exposure can modulate immune activity through various pathways. Therefore, we aimed to explore how antibiotics affect immune-inflammation by regulating Th17 cells through the gut microbiota of mice with experimental autoimmune prostatitis (EAP). Antibiotic-driven shifts in gut microbial communities and metabolite profiling in EAP mice were performed by integrating 16S rRNA sequencing with mass spectrometry-driven metabolomic analysis. Antibiotic cocktail (ABX) therapy mitigated EAP, modified the gut microbiome composition, and influenced bile acid metabolism. Fecal microbiota transplantation (FMT) using microbiota from ABX-treated feces into EAP mice effectively altered gut microbiome composition and alleviated disease symptoms, indicating that microbiome intervention reduces autoimmune inflammation and decreases deoxycholic acid (DCA) in mice. Subsequent experiments demonstrated that DCA suppresses farnesol X receptor (FXR) expression which can inhibit the NLRP3‒ IL17A axis, thus promoting Th17 cell development and exacerbating inflammatory cell infiltration of the prostate. Our initial clinical examination of patients with prostatitis and antibiotic treatment indicated that bile acid metabolism and Th17 cell development are affected by antibiotic therapy. This work revealed that antibiotic-induced gut microbiota dysbiosis decreases the bile acid metabolite DCA, further restraining Th17 cell differentiation via the FXR‒NLRP3 axis to alleviate autoimmune prostatitis. Our results reveal new perspectives regarding the interconnected dynamics of antibiotics, gut microbiota, bile acid metabolism, and immune regulation, with potential relevance for therapies targeting immune-mediated diseases.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Th17 Cells/drug effects/immunology/cytology
Male
*Bile Acids and Salts/metabolism
*Anti-Bacterial Agents/pharmacology/administration & dosage
Mice
*NLR Family, Pyrin Domain-Containing 3 Protein/metabolism/genetics
Humans
*Receptors, Cytoplasmic and Nuclear/metabolism/genetics
Mice, Inbred C57BL
Cell Differentiation/drug effects
Fecal Microbiota Transplantation
*Prostatitis/immunology/microbiology/drug therapy
Disease Models, Animal
Interleukin-17
RNA, Ribosomal, 16S/genetics

@article {pmid41305672,
year = {2025},
author = {Arishi, RA and Cheema, AS and McEachran, JL and Gridneva, Z and Furst, A and Roman, A and Bode, L and Lai, CT and Payne, MS and Geddes, DT and Stinson, LF},
title = {Development of the Breastfed Infant Oral Microbiome Is Associated with Concentrations and Intakes of Human Milk Oligosaccharides.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223622},
pmid = {41305672},
issn = {2072-6643},
mesh = {Humans ; *Milk, Human/chemistry ; *Oligosaccharides/administration & dosage/analysis ; Infant ; *Breast Feeding ; Female ; *Microbiota ; *Mouth/microbiology ; Male ; RNA, Ribosomal, 16S/genetics ; Adult ; },
abstract = {Background/Objectives: Human milk oligosaccharides (HMOs) are bioactive carbohydrates abundant in human milk that shape the infant gut microbiome, yet their influence on the oral microbiome remains poorly understood. This study investigated associations between HMO concentrations and infant HMO intakes and the composition of the oral microbiome in predominantly (n = 2) and exclusively (n = 54) breastfed infants. Methods: We profiled infant oral samples collected at 2 months of age using full-length 16S rRNA gene sequencing, alongside paired milk HMO analyses from 56 mother-infant dyads from the Western Australian BLOSOM cohort. Daily HMO intakes were calculated using 24 h milk intake data. Results: Concentrations of human milk 3FL and LNFPIII were negatively associated with infant oral Shannon diversity (p = 0.027) and richness (p = 0.037), respectively. LNFPII concentration and daily intake were linked to increased abundance of Neisseria subflava (both p = 0.025), while daily intakes of DFLNT and DFLNH were positively associated with Streptococcus parasanguinis (p = 0.028 and p = 0.040). Notably, the associations observed for daily HMO intakes were modest in effect size. Conclusions: These findings demonstrate a statistically significant but biologically limited effect of HMOs on the development of the infant oral microbiome. By clarifying how specific components of human milk shape early microbial development, this work provides mechanistic insights relevant to nutritional and supportive interventions that promote breastfeeding success.},
}

Humans
*Milk, Human/chemistry
*Oligosaccharides/administration & dosage/analysis
Infant
*Breast Feeding
Female
*Microbiota
*Mouth/microbiology
Male
RNA, Ribosomal, 16S/genetics
Adult

@article {pmid41305652,
year = {2025},
author = {Dargenio, VN and Sgarro, N and Grasta, G and Begucci, M and Castellaneta, SP and Dargenio, C and Paulucci, L and Francavilla, R and Cristofori, F},
title = {Hidden Hunger in Pediatric Obesity: Redefining Malnutrition Through Macronutrient Quality and Micronutrient Deficiency.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223601},
pmid = {41305652},
issn = {2072-6643},
mesh = {Humans ; *Micronutrients/deficiency ; Child ; *Pediatric Obesity/complications/physiopathology ; Gastrointestinal Microbiome ; *Nutrients/deficiency ; *Malnutrition/etiology ; *Hunger ; Inflammation ; Diet ; Biomarkers ; },
abstract = {Background: Pediatric obesity exemplifies the paradox of energy excess coexisting with nutritional inadequacy. Despite high caloric intake, children with obesity often display deficiencies in essential macro- and micronutrients that impair growth, metabolic regulation, and long-term health. This review critically examines the mechanisms underlying malnutrition in pediatric obesity, emphasizing the interplay between dietary quality, inflammation, microbiota alterations, and biomarker profiles, and identifies research gaps limiting precision nutrition approaches. Methods: A comprehensive narrative review of studies addressing macro- and micronutrient intake, metabolic and inflammatory biomarkers, and gut microbiota-host interactions in pediatric obesity was conducted. Evidence from both clinical and experimental models was integrated to evaluate mechanistic pathways, diagnostic criteria, and preventive strategies. Results: Obesity-related malnutrition arises from poor dietary quality, systemic inflammation, and microbiota dysbiosis, leading to impaired nutrient utilization and metabolic dysfunction. Deficiencies in vitamin D, calcium, iron, magnesium, and B vitamins are common and often coexist with macronutrient imbalances. Diets rich in saturated fats and refined carbohydrates exacerbate inflammation and metabolic risk, whereas plant-based proteins, unsaturated fats, and fiber support metabolic resilience. Precision nutrition and biomarker-guided monitoring show promise but require validation in pediatric cohorts. Evidence on microbiota modulation and nutrient-gene interactions remains inconsistent, reflecting methodological heterogeneity. Conclusions: Malnutrition in pediatric obesity should be recognized as a distinct clinical phenotype characterized by qualitative nutrient deficiency within a state of energy surplus. Addressing this paradox demands harmonized diagnostic criteria, longitudinal biomarker surveillance, and individualized dietary strategies informed by genetics and microbiome profiling. Multilevel interventions, linking clinical practice, policy, and food system reform, are essential to prevent lifelong metabolic complications and promote healthy growth trajectories.},
}

Humans
*Micronutrients/deficiency
Child
*Pediatric Obesity/complications/physiopathology
Gastrointestinal Microbiome
*Nutrients/deficiency
*Malnutrition/etiology
*Hunger
Inflammation
Diet
Biomarkers

@article {pmid41305634,
year = {2025},
author = {Blady, K and Pomianowski, B and Strugała, M and Smółka, L and Kursa, K and Stanek, A},
title = {Vitamin D in Atopic Dermatitis: Role in Disease and Skin Microbiome.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223584},
pmid = {41305634},
issn = {2072-6643},
mesh = {Humans ; *Vitamin D/metabolism/pharmacology ; *Dermatitis, Atopic/microbiology/immunology/drug therapy ; *Skin/microbiology/immunology/drug effects ; *Microbiota/drug effects ; Animals ; Skin Microbiome ; },
abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disorder associated with immune dysregulation, skin barrier dysfunction, and microbial dysbiosis characterized by Staphylococcus aureus overcolonization and reduced bacterial diversity. Beyond its classical role in calcium homeostasis, Vitamin D (VD) influences skin immunity and microbial composition. This review summarizes current knowledge on VD metabolism, its immunological pathways in AD, and its interactions with the skin microbiome. Recent evidence positions the skin as an active immunological organ rather than a passive barrier. Commensal bacteria such as Staphylococcus epidermidis not only inhibit pathogens by producing bacteriocins and modulins but also generate ceramides and short-chain fatty acids (SCFAs) that stabilize the lipid barrier. Moreover, dermal fibroblasts and preadipocytes produce antimicrobial peptides, while resident γδ T cells release growth factors like fibroblast growth factor 7 (FGF7), linking host defense with tissue regeneration. VD modulates AD by suppressing T helper 2 cells/T helper 17 cell responses, enhancing regulatory T cell development, inducing antimicrobial peptides, and strengthening skin and gut barrier integrity. Its interaction with the microbiome and pathways such as SCFA and aryl hydrocarbon receptor (AhR) signaling supports its potential as an adjunctive therapy in AD management. Evidence from mechanistic studies and animal models suggests that VD supplementation may modulate inflammation and microbial diversity. Clinical implications, therapeutic perspectives, and future research directions highlight the potential of VD as a therapeutic adjunct in AD management.},
}

Humans
*Vitamin D/metabolism/pharmacology
*Dermatitis, Atopic/microbiology/immunology/drug therapy
*Skin/microbiology/immunology/drug effects
*Microbiota/drug effects
Animals
Skin Microbiome

@article {pmid41305619,
year = {2025},
author = {Tanjung, C and Shibata, R and Fikri, B and Prawitasari, T and Zainuddin, AA and Juliaty, A and Yullyana, DS and Sundjaya, T and Kuswanto, H and Clarensia, J and Shimojo, N and Koletzko, B and Ohno, H and Massi, N},
title = {Longitudinal Microbiome and Metabolome Shifts After Successful Intervention in Impending Stunting in Indonesian Infants.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223570},
pmid = {41305619},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Infant ; Indonesia ; *Growth Disorders/microbiology/prevention & control ; *Metabolome ; Male ; Female ; Feces/microbiology ; Dietary Supplements ; Longitudinal Studies ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification ; },
abstract = {Background/Objectives: Stunting and weight faltering (WF) remain pressing public health challenges in low- and middle-income countries, with long-term consequences for child growth, development, and survival. While the role of gut health in early growth is increasingly recognized, evidence on how the gut microbiome and metabolome respond to nutritional interventions in WF infants is scarce. This study explored gut microbiome and metabolome changes in Indonesian infants aged 6-12 months who overcame WF following a one-month intervention. Methods: Infants were assigned to either a Nutritional Advice (NA) group or a Nutritional Advice plus Oral Nutritional Supplements (NAONS) group. Stool samples were collected before and after the intervention for microbiome (16S rRNA sequencing) and metabolome (LC-MS) analysis. Results: Significant shifts in gut microbial composition (beta diversity) and species richness (Chao1 index) were observed in both groups, suggesting enhanced microbial diversity and gut resilience. Within-group analysis revealed increases in beneficial genera such as Faecalibacterium and Peptostreptococcus, and a reduction in pro-inflammatory Fusobacterium in the NA group. The NAONS group showed a notable decrease in Proteus, a potentially pathogenic genus. Between-group comparisons indicated higher abundances of Lactococcus and Leuconostoc in the NAONS group, likely reflecting the influence of milk protein-rich supplements on microbial colonization, favoring lactic acid bacteria over SCFA-producing taxa, leading to better gut health. Metabolome analysis revealed significant changes in the NA group, increases in metabolites like Threonine, Tryptophan, and Xylose pointed to improved energy metabolism and gut health, while a decrease in Oxalic Acid suggested better metabolic efficiency. In contrast, the NAONS group, while benefiting from rapid weight gain, displayed a distinct metabolic profile influenced by high milk protein intake. No significant correlations were found between microbiome and metabolome changes, highlighting the complexity of gut-host interactions, suggesting that the interventions led to independent shifts in the aforementioned profiles. Conclusions: Overall, the findings suggest that nutritional interventions may enhance gut health and support recovery from weight faltering, providing insights into strategies that may contribute to restoring healthy growth trajectories and preventing stunting by modulating gut health.},
}

Humans
*Gastrointestinal Microbiome/physiology
Infant
Indonesia
*Growth Disorders/microbiology/prevention & control
*Metabolome
Male
Female
Feces/microbiology
Dietary Supplements
Longitudinal Studies
RNA, Ribosomal, 16S/genetics
Bacteria/classification

@article {pmid41305616,
year = {2025},
author = {Dale, HF and Kolby, M and Valeur, J},
title = {Ultra-Processed Food Consumption and Irritable Bowel Syndrome: Current Evidence and Clinical Implications.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223567},
pmid = {41305616},
issn = {2072-6643},
mesh = {Humans ; *Irritable Bowel Syndrome/etiology/epidemiology ; Gastrointestinal Microbiome ; *Fast Foods/adverse effects ; *Diet/adverse effects ; *Food Handling ; Food, Processed ; },
abstract = {Irritable bowel syndrome (IBS) is a prevalent disorder of gut-brain interaction (DGBI) with an adverse impact on quality of life. The global consumption of ultra-processed foods (UPF) is rapidly increasing, and UPF intake has recently been linked to a wide range of metabolic and chronic diseases. The potential role of UPF consumption in the onset and symptom generation of IBS is emerging but remains unclear. This narrative review synthesizes epidemiological evidence on the association between UPF consumption and IBS, integrates mechanistic insights from experimental and clinical studies and suggests clinical implications based on the current state of knowledge. Observational studies suggest that higher UPF intake may be associated with increased risk of IBS, although the evidence base is limited and subject to methodological challenges. Mechanistic studies indicate that additives including emulsifiers and non-nutritive sweeteners can alter pathways relevant to IBS symptom generation, such as gut microbiota composition, impair intestinal barrier function and trigger low-grade inflammation. Current evidence supports a possible link between UPF consumption and IBS. Increasing overall dietary quality and reducing UPF intake are promising complementary strategies to established dietary interventions. Future intervention trials may provide insights into relevant biological mechanisms, particularly if such changes co-occur with symptom improvement.},
}

Humans
*Irritable Bowel Syndrome/etiology/epidemiology
Gastrointestinal Microbiome
*Fast Foods/adverse effects
*Diet/adverse effects
*Food Handling
Food, Processed

@article {pmid41305603,
year = {2025},
author = {He, Y and Peng, K and Tan, J and Hao, Y and Zhang, S and Gao, C and Li, L},
title = {Short-Chain Fatty Acids and Colorectal Cancer: A Systematic Review and Integrative Bayesian Meta-Analysis of Microbiome-Metabolome Interactions and Intervention Efficacy.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223552},
pmid = {41305603},
issn = {2072-6643},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism/ethnology/prevention & control ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome/physiology ; Bayes Theorem ; *Metabolome ; Female ; Adenoma/microbiology ; },
abstract = {Objective: Existing studies on short-chain fatty acids (SCFAs) and colorectal cancer (CRC) yield contradictory conclusions and are limited to single ethnic groups or sample types. This study aimed to (1) quantify associations between total SCFAs/subtypes (acetate, propionate, butyrate) and CRC/advanced colorectal adenoma (A-CRA) risks; (2) identify modifiers (ethnicity, sample type, intervention); and (3) clarify SCFA-gut microbiota interaction mechanisms via integrative Bayesian meta-analysis and multi-ancestry data integration. Methods: We systematically searched PubMed, Embase, Cochrane Library, and Web of Science (inception to September 2025) using keywords: "Short-chain fatty acids", "SCFAs", "Colorectal cancer", "CRC", "Gut microbiota", "Dietary fiber", and "High-amylose maize starch butyrate". Eligible studies included 14 peer-reviewed original studies (7 observational, cohort/case-control/cross-sectional; 7 RCTs) covering Europeans, Asians, and African Americans. Inclusion criteria: Quantitative SCFA data (total/≥3 subtypes), clear ethnic grouping, reported CRC/A-CRA risks or intervention outcomes. Exclusion criteria: Reviews, animal/in vitro studies, incomplete data, low-quality studies (Newcastle-Ottawa Scale [NOS] <6 for observational; high Cochrane risk for RCTs), or limited populations (single gender/rare genetics). A Bayesian hierarchical random-effects model quantified effect sizes (Odds Ratio [OR]/Mean Difference [MD], 95% credible intervals [CrI]), with heterogeneity analyzed via multi-ancestry stratification, intervention efficacy, and microbiota interaction analyses (Preferred Reporting Items for Systematic Reviews and Meta-Analyses [PRISMA] 2020; International Prospective Register of Systematic Reviews [PROSPERO]: CRD420251157250). Results: Total SCFAs were negatively associated with CRC (OR = 0.78, 95% CrI: 0.65-0.92) and A-CRA (OR = 0.72, 95% CrI: 0.59-0.87), with butyrate showing the strongest protective effect (CRC: OR = 0.63, 95% CrI: 0.51-0.77). Ethnic heterogeneity was significant: Europeans had the strongest protection (OR = 0.71), Asians had weaker protection (OR = 0.86), and African Americans had the lowest fecal SCFA levels and the highest CRC risk. Fecal SCFAs showed a stronger CRC association than serum/plasma SCFAs (OR = 0.73 vs. 0.85). High-Amylose Maize Starch Butyrate (HAMSB) outperformed traditional fiber in increasing fecal butyrate (MD = 4.2 mmol/L vs. 2.8 mmol/L), and high butyrate-producing bacteria (Clostridium, Roseburia) enhanced SCFA protection (OR = 0.52 in high-abundance groups). Conclusions: SCFAs (especially butyrate) protect against CRC and precancerous lesions, with effects modulated by ethnicity, sample type, and gut microbiota. High-Amylose Maize Starch Butyrate is a priority intervention for high-risk populations (e.g., familial adenomatous polyposis, FAP), and differentiated strategies are needed: 25-30 g/d dietary fiber for Europeans, 20-25 g/d for Asians, and probiotics (Clostridium) for African Americans. Future Perspectives: Expand data on underrepresented groups (African Americans, Latinos), unify SCFA detection methods, and conduct long-term RCTs to validate intervention efficacy and "genetics-microbiota-metabolism" crosstalk-critical for CRC precision prevention.},
}

Humans
*Colorectal Neoplasms/microbiology/metabolism/ethnology/prevention & control
*Fatty Acids, Volatile/metabolism
*Gastrointestinal Microbiome/physiology
Bayes Theorem
*Metabolome
Female
Adenoma/microbiology

@article {pmid41305578,
year = {2025},
author = {Rehner, J and Gund, M and Becker, SL and Hannig, M and Rupf, S and Schattenberg, JM and Keller, A and The Imagine Consortium, and Molano, LG and Keller, V},
title = {Joint Bacterial Traces in the Gut and Oral Cavity of Obesity Patients Provide Evidence for Saliva as a Rich Microbial Biomarker Source.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223527},
pmid = {41305578},
issn = {2072-6643},
support = {469073465//DFG/ ; },
mesh = {Humans ; *Saliva/microbiology ; *Obesity/microbiology ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Mouth/microbiology ; Male ; Female ; Biomarkers/analysis ; Middle Aged ; Adult ; Dental Plaque/microbiology ; *Bacteria/isolation & purification/classification/genetics ; Metagenome ; },
abstract = {Background: The human microbiome holds promise for identifying biomarkers and therapeutic targets. In obesity, interactions between oral and gut communities are increasingly implicated and end in organ injury. Methods: From the IMAGINE study, we analyzed 418 shotgun metagenomes from three specimen types (dental plaque (n = 143; 65 non-obese, 78 obese), saliva (n = 166; 75 non-obese, 91 obese), and stool (n = 109; 57 non-obese, 52 obese)) to compare site-specific microbial shifts between obese (BMI > 30 kg/m[2]) and non-obese individuals. Differential abundance was assessed with ANCOM-BC; effect sizes were summarized as Cohen's d. Results: Across all samples, we detected 240 bacterial species in plaque, 229 in saliva, and 231 in stool, with 46 species present across all three sites. Absolute effect sizes were significantly larger in plaque (mean |d| = 0.26) and saliva (0.25) than in stool (0.21; p = 9 × 10[-3]). Several taxa showed an opposite directionality between oral and gut sites, including Streptococcus salivarius and Bifidobacterium longum, indicating site-specific associations. Notably, Actinomyces sp. and Streptococcus sp. exhibited promising effect sizes as diagnostic markers. Conclusions: The oral and gut microbiomes capture complementary obesity-related signals, with stronger shifts observed in oral sites. We suggest that integrating oral and gut profiling could enhance diagnostic and therapeutic strategies in obesity.},
}

Humans
*Saliva/microbiology
*Obesity/microbiology
*Gastrointestinal Microbiome
Feces/microbiology
*Mouth/microbiology
Male
Female
Biomarkers/analysis
Middle Aged
Adult
Dental Plaque/microbiology
*Bacteria/isolation & purification/classification/genetics
Metagenome

@article {pmid41305571,
year = {2025},
author = {Verstegen, REM and Zuurveld, M and Thijssen, S and de Bruijn, MJW and van Ark, I and Diks, MAP and Garssen, J and Folkerts, G and Kostadinova, AI and Hendriks, RW and Willemsen, LEM},
title = {A Specific Ratio of Dietary Short-Chain and Long-Chain Fructo-Oligosaccharides Shifts the Immune Response Away from Type 2 in a Murine Model for House Dust Mite-Induced Asthma.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223520},
pmid = {41305571},
issn = {2072-6643},
support = {10.1.19.001//Health Holland/ ; 10.1.19.001//Lung Foundation Netherlands/ ; },
mesh = {Animals ; *Asthma/immunology/microbiology ; *Oligosaccharides/administration & dosage/pharmacology ; *Pyroglyphidae/immunology ; Mice, Inbred BALB C ; Disease Models, Animal ; Gastrointestinal Microbiome/drug effects ; Mice ; Fatty Acids, Volatile ; Female ; Dietary Supplements ; Lung/immunology ; Feces/microbiology ; Bronchoalveolar Lavage Fluid ; Dietary Fiber/administration & dosage ; Th2 Cells/immunology ; },
abstract = {Background/Objectives: The gut microbiome has an important role in immune regulation, and dietary interventions that support a balanced microbiota may help to prevent the development of allergic asthma. Dietary fibers can beneficially affect the intestinal microbiome, but due to the diversity of fiber types, the effects differ. In this study, we investigate the preventive effects of two mixes of short-chain and long-chain (1:1 and 9:1 ratio) fructo-oligosaccharides (FOS) in a mouse model of house dust mite (HDM)-induced allergic asthma. Methods: BALB/c mice received FOS-supplemented (1% w/w) diets before and during intranasal exposures to HDM. Endpoint airway hyperreactivity measurements were performed, followed by the collection of bronchoalveolar lavage fluid (BALF), lung, serum and cecum content. Fecal microbiome composition was determined by DNA sequencing and short-chain fatty acid (SCFA) levels were determined in the cecum, serum and lung. Results: Fecal microbiome analyses revealed an increased abundance of Prevotellaceae after FOS1:1 supplementation in HDM-allergic mice. Additionally, FOS1:1 protected against an HDM-induced increase in basal airway resistance. Both FOS1:1 and FOS9:1 restored the systemic acetate levels in HDM-allergic mice. The two FOS supplementations did not affect HDM-induced inflammatory cell influx in the BALF. However, FOS1:1 increased the frequency of Th1-cells and prevented an HDM-induced increase in the Th2/Th1 balance. Upon ex vivo restimulation with HDM, lung cell suspensions of FOS1:1-fed mice produced less type 2-related cytokines compared to control-supplemented mice, and FOS9:1 followed a similar pattern. Conclusions: Specific short-chain and long-chain FOS ratios differentially affect the microbiome and immune system in a mouse model with HDM-induced allergic airway inflammation. Dietary supplementation with FOS1:1 shifts the immune response away from type 2, suggesting that dietary fibers like FOS1:1 may contribute as a part of a broader strategy to modulate HDM-induced allergic asthma.},
}

Animals
*Asthma/immunology/microbiology
*Oligosaccharides/administration & dosage/pharmacology
*Pyroglyphidae/immunology
Mice, Inbred BALB C
Disease Models, Animal
Gastrointestinal Microbiome/drug effects
Mice
Fatty Acids, Volatile
Female
Dietary Supplements
Lung/immunology
Feces/microbiology
Bronchoalveolar Lavage Fluid
Dietary Fiber/administration & dosage
Th2 Cells/immunology

@article {pmid41305568,
year = {2025},
author = {Liu, C and Zhao, Y and Li, J and Gao, S and Cao, J and Jing, N and Han, X and He, H and Liang, W and Wang, N},
title = {Limosilactobacillus fermentum IOB802 Protects Against Blue Light-Induced Retinopathy via Gut Microbiota Modulation.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223517},
pmid = {41305568},
issn = {2072-6643},
support = {No. 202228040//Jinan Innovation Team Project/ ; No.24ZYCGSY00390//Tianjin Science and Technology Achievement Transfer and Transformation Project/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Limosilactobacillus fermentum ; *Light/adverse effects ; *Retinal Diseases/prevention & control/etiology/microbiology ; Humans ; *Probiotics/pharmacology ; Cell Line ; Male ; Mice, Inbred C57BL ; Retina/radiation effects ; Lactobacillus plantarum ; Cytokines/metabolism ; Antioxidants/metabolism ; Disease Models, Animal ; Blue Light ; },
abstract = {BACKGROUND: Blue light-induced retinal photodamage represents a growing public health concern globally. Lactic acid bacteria and their bioactive metabolites represent a promising therapeutic strategy for mitigating such damage.

METHODS: This study evaluated the protective efficacy of Limosilactobacillus fermentum IOB802 and Lactobacillus plantarum subsp. plantarum IOB602 against blue light-induced retinal injury using both in vitro and in vivo models.

RESULTS: In ARPE-19 cells exposed to blue light, treatment with postbiotics from IOB802 and IOB602 significantly restored cell viability (p < 0.05), enhanced antioxidant enzyme activities (GSH-Px, SOD, and CAT, p < 0.05), and reduced inflammatory cytokine levels (IL-6, IL-1β, TNF-α, and VEGF, p < 0.05). Subsequent validation in a murine blue light-induced retinal damage model demonstrated that IOB802 notably preserved retinal architecture, upregulated antioxidant defenses, and promoted the expression of tight junction proteins. Mechanistically, IOB802 suppressed inflammation by inhibiting the phosphorylation of the IκBα/NF-κB pathway. Through 16S rDNA sequencing and short-chain fatty acid (SCFA) profiling, IOB802 was further shown to restore gut microbial diversity, increase beneficial bacteria, including Lachnospiraceae, Rikenellaceae, and Bacteroidaceae (p < 0.05), and elevate concentrations of key SCFAs (butyrate, acetate, and propionate; p < 0.05), underscoring the role of the gut-retina axis in mediating retinal protection.

CONCLUSIONS: In summary, IOB802 and its postbiotics alleviate blue light-induced retinopathy through antioxidative, anti-inflammatory, and microbiota-modulating mechanisms, offering novel insights into microbiome-based interventions for retinal diseases.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Limosilactobacillus fermentum
*Light/adverse effects
*Retinal Diseases/prevention & control/etiology/microbiology
Humans
*Probiotics/pharmacology
Cell Line
Male
Mice, Inbred C57BL
Retina/radiation effects
Lactobacillus plantarum
Cytokines/metabolism
Antioxidants/metabolism
Disease Models, Animal
Blue Light

@article {pmid41305378,
year = {2025},
author = {Lee, SJ and Seong, J and Lee, JA and Lee, Y and Kim, JH and Ahn, JY and Ku, NS and Choi, JY and Yeom, JS and Jeong, SJ},
title = {Respiratory Microbiome of Carbapenem-Resistant Acinetobacter baumannii Ventilator-Associated Pneumonia: A Pilot Study from the Republic of Korea.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/pathogens14111141},
pmid = {41305378},
issn = {2076-0817},
mesh = {Humans ; *Pneumonia, Ventilator-Associated/microbiology/mortality ; *Acinetobacter baumannii/drug effects/genetics/isolation & purification ; Male ; *Carbapenems/pharmacology ; Female ; Republic of Korea ; Pilot Projects ; Middle Aged ; Aged ; *Microbiota ; *Acinetobacter Infections/microbiology/mortality ; RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; Intensive Care Units ; Prognosis ; },
abstract = {Ventilator-associated pneumonia (VAP) is one of the most common hospital-acquired infections. Several studies have explored the potential role of the lung microbiome as a biomarker for identifying and predicting the prognosis of VAP. However, research on the respiratory microbiome in individuals with VAP caused by carbapenem-resistant Acinetobacter baumannii (CRAB) remains limited. Therefore, we aimed to analyze the respiratory microbiome of patients with CRAB VAP. Respiratory specimens were collected from patients who developed CRAB VAP. Microbiome diversity and composition were analyzed using 16S rRNA gene pyrosequencing. Patients were categorized into two groups based on mortality outcomes: intensive care unit (ICU) mortality or 28-day mortality after ICU discharge. Twenty patients with CRAB VAP were enrolled, including nine in the mortality group. No significant differences were observed in α-diversity indices between the study groups. However, multivariable Firth's logistic regression revealed a significant association between a relative abundance of the Enterococcus genus ≥ 1% and mortality outcomes (odds ratio: 0.06; 95% confidence interval: 0.00-0.771; p = 0.029). This study characterized the respiratory microbiome of patients with CRAB VAP and highlighted the potential role of microbiome analysis in predicting disease prognosis. Further studies with larger sample sizes are warranted to validate these findings.},
}

Humans
*Pneumonia, Ventilator-Associated/microbiology/mortality
*Acinetobacter baumannii/drug effects/genetics/isolation & purification
Male
*Carbapenems/pharmacology
Female
Republic of Korea
Pilot Projects
Middle Aged
Aged
*Microbiota
*Acinetobacter Infections/microbiology/mortality
RNA, Ribosomal, 16S/genetics
Anti-Bacterial Agents/pharmacology
Intensive Care Units
Prognosis

@article {pmid41305374,
year = {2025},
author = {Zhou, J and Fu, Z and Gao, Y and An, C and Zhang, Z and Zhong, X and Tian, L and Yang, X and Zhang, J and Zhang, Q and Wang, D and Li, N},
title = {Gut Microbiotas, Plasma Metabolites, and Autism Spectrum Disorder: A Bidirectional Mendelian Randomization Analysis.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/pathogens14111137},
pmid = {41305374},
issn = {2076-0817},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Autism Spectrum Disorder/microbiology/genetics/blood ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; Linkage Disequilibrium ; Metabolome ; Male ; Female ; },
abstract = {Background: Previous studies have indicated that the gut microbiome and plasma metabolites play key roles in autism spectrum disorder (ASD), but their causal relationships remain unclear. Linkage disequilibrium score regression (LDSC) and Mendelian randomization (MR) are powerful tools for assessing genetic causality. This study uses LDSC and MR to investigate the genetic links between the gut microbiome and ASD and explore the mediating role of plasma metabolites. Methods: To explore the genetic relationships between the gut microbiome, plasma metabolites, and ASD, we obtained summary statistics from large-scale genome-wide association studies (GWAS). Gut microbiome data came from a MiBioGen consortium meta-analysis (N = 18,340), ASD data from the Danish Psychiatric Central Research Register (DPCRR) (N = 18,382), and plasma metabolite data from the Canadian Longitudinal Study of Aging (CLSA) (N = 8299). We applied LDSC and bidirectional MR to analyze the genetic associations between the gut microbiome and ASD and plasma metabolites and ASD. Mediation MR was used to assess the mediating role of plasma metabolites in the gut microbiome-ASD relationship. Results: LDSC analysis revealed significant genetic correlations between the gut microbiota Lachnospiraceae NK4A136 group and Sellimonas with ASD. Moreover, bidirectional MR demonstrated causal effects of five gut microbial genera on ASD risk, as indicated by inverse variance weighted (IVW) methods. Similarly, we identified 49 plasma metabolites that exhibited genetic correlations with ASD, and 58 metabolites had causal effects on ASD in MR analysis. Mediation analysis revealed that specific bacteria, Ruminiclostridium5, reduce the occurrence of ASD through metabolites Delta-CEHC and Docosadioate (C22-DC). Furthermore, Ruminococcaceae UCG005 and Sutterella modulate ASD by inhibiting Serotonin and N-acetyl-L-glutamine, respectively. Conclusions: This study provides evidence of a causal relationship between the gut microbiome and ASD, with plasma metabolites acting as a potential mediator. Our findings offer new insights into the causal mechanisms linking the gut microbiome and ASD and provide a theoretical foundation for microbiome-based therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Autism Spectrum Disorder/microbiology/genetics/blood
Mendelian Randomization Analysis
Genome-Wide Association Study
Linkage Disequilibrium
Metabolome
Male
Female

@article {pmid41305349,
year = {2025},
author = {Ruden, DM},
title = {The Human Archaeome: Commensals, Opportunists, or Emerging Pathogens?.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/pathogens14111111},
pmid = {41305349},
issn = {2076-0817},
support = {5P42ES030991-07/NH/NIH HHS/United States ; 5P30ES036084-06/NH/NIH HHS/United States ; },
mesh = {Humans ; *Archaea/physiology/pathogenicity/classification ; *Microbiota ; *Symbiosis ; },
abstract = {Archaea, one of the three domains of life, are increasingly recognized as consistent, though often underappreciated, members of the human microbiome, yet their roles in health and disease remain poorly understood. Unlike bacteria, no archaeal species have been conclusively identified as primary mammalian pathogens, but their widespread presence across diverse body sites suggests potential indirect contributions to host physiology and pathology. Current evidence is synthesized on archaeal diversity and habitat specificity across multiple human-associated sites, encompassing the gastrointestinal, aerodigestive, and urogenital tracts as well as the skin. Methanogens dominate the lower gastrointestinal tract (LGT), where they influence fermentation dynamics and methane production, while members of the class Nitrososphaeria are prevalent on the skin and upper aerodigestive tract (UAT), reflecting ecological specialization. Variability in archaeal composition across niches highlights possible links to disease processes: methanogens have been associated with irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), obesity, and colorectal cancer (CRC); Methanobrevibacter oralis is enriched in periodontal disease; and archaea have been detected in the lungs of cystic fibrosis patients. Although archaea lack canonical bacterial virulence factors, they may contribute indirectly through metabolic cross-feeding, immune modulation, synergy in polymicrobial infections, and alteration of host-microbiome network dynamics. This review explores the emerging concept of the human "archaeome", evaluates current evidence for archaeal involvement in disease, and highlights emerging technologies, such as bacteria-MERFISH and multi-omics profiling, that enable translational applications including microbiome diagnostics, therapeutic targeting, and microbiome engineering.},
}

Humans
*Archaea/physiology/pathogenicity/classification
*Microbiota
*Symbiosis

@article {pmid41304681,
year = {2025},
author = {Zhou, X and Zhu, X and Fan, X and Huang, X and Ma, H and Cheema, HN and Zhang, K and Zheng, S},
title = {Exogenous Plant Growth-Promoting Rhizobacteria Enhance the Promoting Effect of Polyaspartic Acid on Potato Growth by Improving Rhizosphere Nutrient Availability and Reshaping Microbial Community.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/plants14223530},
pmid = {41304681},
issn = {2223-7747},
support = {2021YFYZ0005 and 2021YFYZ0019//the Sichuan Provincial Science and Technology Program Breeding Research Project/ ; sccxtd-2025-09//the National Modern Agricultural Industry Technology System Sichuan Tuber Crops Innovation Team Project/ ; SNSBJKJJHXM2024001//the Innovation and Application of Key Technologies for Green and Sustainable Yield Increase in New Potato Varieties/ ; 2522229017//the Key Technologies for Enhancing Potato Yield in Red Revolutionary Base Areas Training Program/ ; },
abstract = {Polyaspartic acid (PASP), a biodegradable and eco-friendly fertilizer synergist that shows potential to enhance nutrient use efficiency in agricultural systems, has its integrative role with rhizosphere microorganisms remain insufficiently explored. This study integrated outdoor pot experiments, soil biochemical analysis, and microbiome sequencing to investigate the effects of co-application of PASP and the plant growth-promoting rhizobacterium (PGPR) Enterobacter asburiae S13 on potato growth, with four treatments set up including blank control (CK), sole application of PASP (S0P1), sole inoculation of PGPR (S1P0), and co-application of PASP and PGPR (S1P1), and 25 pots per treatment as replicates. The results showed that, compared with the S0P1 treatment, the S1P1 treatment significantly increased plant height (9.59%), stem diameter (28.39%), root length (38.61%), as well as root and shoot biomass (21.26% and 25.17%, respectively) (ANOVA, Duncan's test, p < 0.05). It also enhanced ammonium nitrogen (40.00%), nitrate nitrogen (57.70%), available potassium (47.56%), and urease activity in the rhizosphere soil (ANOVA, Duncan's test, p < 0.05). 16S rRNA sequencing revealed that the S1P1 treatment enriched beneficial taxa such as Paucibacter and Massilia, while suppressing competitive genera such as Duganella and Pedobacter. Redundancy analysis (RDA) indicated that available potassium and ammonium nitrogen were the key factors shaping the microbial community structure. In conclusion, combining PASP with PGPR synergistically improves soil nutrient availability and reshapes the rhizosphere microbiome, resulting in enhanced potato growth, thus demonstrating its potential as a dual-function biostimulant for eco-efficient and sustainable potato production systems.},
}

@article {pmid41304632,
year = {2025},
author = {Wang, B and Meng, F and Cheng, T and Niu, J and Rao, D and Han, Z and Zhang, W and Zhang, Z},
title = {Comprehensive Responses of Physiology and Rhizosphere Microbiome to Saline-Alkaline Stress in Soybean Seedlings with Different Tolerances.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/plants14223480},
pmid = {41304632},
issn = {2223-7747},
support = {2023YFD2300100//National Key Research and Development Program of China/ ; CARS-04-PS15//China Agriculture Research System/ ; JLARS-2025030101//Jilin Agriculture Research System/ ; },
abstract = {Soil salinization severely threatens global crop production. Understanding the relationship between crop saline-alkaline tolerance physiology and the rhizosphere microbiome, and leveraging beneficial microorganisms to enhance crop stress resistance, holds importance for sustainable agricultural development. This study investigated the physiological and rhizosphere microbial responses of two soybean cultivars with different saline-alkaline tolerance to stress. Under saline-alkaline conditions, the tolerant cultivar exhibited superior physiological performance, including higher chlorophyll content, photosynthetic efficiency, and elevated activities of antioxidant enzymes (SOD, POD, and CAT), alongside reduced oxidative damage (MDA) and greater biomass accumulation. Combined metagenomic and physiological analyses revealed significant correlations of Bradyrhizobium and Solirubrobacter with key physiological indicators, including dry weight, PIABS, φpo, and MDA. The tolerant cultivar selectively enriched distinct marker microbes, such as Bradyrhizobium sp. and Bradyrhizobium liaoningense, in its rhizosphere. We conclude that the tolerant cultivar exhibits strong intrinsic physiological resistance. This resistance is further enhanced by a beneficially assembled rhizosphere microbiome, while the host plant's physiology remains the dominant factor.},
}

@article {pmid41304557,
year = {2025},
author = {Huang, S and Li, H and Wei, J and Zhou, H and Tang, Y and Gui, Y and Zhu, K},
title = {Drought-Driven Rhizosphere Microbiome and Metabolome Remodeling in Wild vs. Cultivated Saccharum arundinaceum.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/plants14223407},
pmid = {41304557},
issn = {2223-7747},
support = {2023GXNSFBA026223, 2023GXNSFBA026194//Natural Science Foundation of Guangxi/ ; GuikeAA24206005-4, GuikeAA24206006, GuikeAA23073001-1-22//Science and Technology Major Key Project of Guangxi Province/ ; 32160486, 32201766//National Natural Science Foundation of China/ ; CARS-17//China Agriculture Research System/ ; },
abstract = {Sugarcane is highly sensitive to the variations in soil moisture content capacity, and upregulated water stress efficiency restricts its development and crop output. Rhizospheric microbes and metabolites play key roles to mitigate the adverse effects of abiotic stresses, i.e., drought stress. The drought-tolerant wild sugarcane relative, Saccharum arundinaceum Retz., remains poorly characterized with respect to its rhizosphere microbial community dynamics under water limitation. To address this, we analyzed drought-associated shifts in the rhizosphere microbiome and metabolome by comparing native plants from a long-term arid habitat in Guangxi, China, with plants from an irrigated cultivation environment. We analyzed the effects of agronomic traits, soil properties, enzyme activities, and 16S rRNA sequencing and untargeted metabolomics to characterize microbial communities and metabolites, with correlation analyses. Results demonstrated that wild plants possessed thicker stems, higher proline levels, and increased antioxidant enzyme activity. Their rhizospheres were enriched with Actinobacteria, Proteobacteria, and Chloroflexi, which exhibited upregulated urease and acid phosphatase activities. Metabolites linked to phosphotransferase systems and sugar metabolisms were also more abundant. Positive correlations between these microbes, metabolites, and drought traits reveal site-specific microbial-metabolic modules that confer drought resilience, providing valuable insights for sugarcane breeding programs.},
}

@article {pmid41304481,
year = {2025},
author = {Zhou, R and Zhu, M and Chen, M},
title = {Gut Microbiota Dysbiosis and Toxic Metabolite Pathways Linked to Childhood Obesity in Eastern China.},
journal = {Toxics},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/toxics13110929},
pmid = {41304481},
issn = {2305-6304},
support = {82273668//National Natural Science Foundation of China/ ; 82574133//National Natural Science Foundation of China/ ; 25KJA330002//Key Natural Science Foundation of the Jiangsu Higher Education Institutions of China/ ; NA//Excellent Young Backbone Teachers of "Qinglan Project" of Colleges and Universities in Jiangsu Province/ ; NA//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
abstract = {Childhood obesity is a newly emerging public health and an emerging concern in environmental health in rapidly urbanized areas of China. This preliminary study investigated the gut microbiome composition and toxic metabolite pathways of school-aged children in Nanjing. Using 16S rRNA sequencing and PICRUSt2-based functional predictions, we observed significant microbial structural changes between the normal weight group and the overweight/obese group, although α diversity was similar. Overweight and obese children exhibited a markedly higher Firmicutes/Bacteroidetes ratio as well as an enrichment of genera such as Subdoligranulum, Ruminococcus, and Lachnospira, indicating increased energy harvesting and inflammation. Functionally, the downregulation of tryptophan metabolism in obese children suggests a reduction in anti-inflammatory indole and an increase in the production of pro-inflammatory kynurenine. In contrast, the upregulation of thiamine metabolism may be linked to enhanced carbohydrate utilization and lipid biosynthetic activity. Our toxicology network analysis and molecular docking experiments suggest that AhR and thiamine-related metabolic enzymes are targets of tryptophan and thiamine metabolism, respectively, and that PPARG is also a potential molecular target mediating thiamine metabolism in childhood obesity. These findings highlight the environment-microbiome-host axis as a potential pathway for metabolic toxicity in childhood obesity. Further studies are needed to validate these toxicological mechanisms and identify microbial biomarkers for early intervention.},
}

@article {pmid41304326,
year = {2025},
author = {Liu, Y and He, P and Liu, D and Song, Y and Jia, C and Wang, D and Jin, Q and Song, G and Wei, Q},
title = {Analysis of Gut Microbial Communities and Functions in Passer ammodendri Under Two Extreme Environments.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112642},
pmid = {41304326},
issn = {2076-2607},
support = {2021YFC2302002, 2022YFC2602200, 2022YFC2602301//the National Key Research and Development Project/ ; },
abstract = {The gut microbiome regulates multiple physiological processes of the host and plays a significant role in the adaptation of wild animal hosts to extreme environments. The saxaul sparrow (Passer ammodendri) is a typical bird species found in the northwest of China, characterized by its strong adaptability to extreme environments. Studying it can help reveal the microbial adaptation mechanisms of the host to extreme environments. Therefore, we conducted a comparative analysis of the intestinal microbial community characteristics and functions of the saxaul sparrow in high-altitude (Pamir Plateau) and desert (Tazhong Town) habitats in Xinjiang. The results of full-length 16S rRNA sequencing and species annotation indicated that the bacterial species composition (relative abundance > 0.1%) of the intestinal microbiota community of the saxaul sparrow was Candidatus Arthromitus sp. SFB rat Yit, Escherichia coli, Enterococcus faecium, Enterococcus faecalis, and Klebsiella pneumoniae, in sequence. In addition, Lysinibacillus sphaericus is a unique strain specific to the Tazhong group, while Stenotrophomonas maltophilia has a much higher abundance in the Tazhong group than in the Pamir Plateau group. It is worth noting that both groups of samples contain potential opportunistic pathogenic bacteria, such as Escherichia coli and Klebsiella pneumoniae. The Shannon index of the Pamir Plateau group was lower than that of the Tazhong Town group (p = 0.0026), indicating that the intestinal microbial diversity of the Pamir Plateau group was lower than that of the Tazhong Town group. However, there was no significant difference in the ACE index between the two groups and it was not statistically significant (p > 0.05). The Beta diversity analysis revealed that the distance between the two groups of samples was considerable (p = 0.001), indicating a significant separation. The functional annotation results indicated that the Pamir Plateau group exhibited enhanced capabilities in carbohydrate metabolism, energy metabolism, and DNA damage repair, while the Tazhong Town group demonstrated enhanced lipid metabolism and detoxification abilities. These findings will help reveal the possible impact of the living environment on the composition and function of the intestinal microbiota of the saxaul sparrow, fill the gap in comparative studies of the intestinal microbiota characteristics of the saxaul sparrow in two extreme environments, and provide new theoretical support for subsequent related research.},
}

@article {pmid41304325,
year = {2025},
author = {Garzon, A and Portillo-Gonzalez, R and Habing, G and Weimer, BC and Schlesener, C and Silva-Del-Rio, N and Karle, BM and Miramontes, C and Pereira, RV},
title = {Co-Occurrence Patterns of Bacterial Communities and Resistance Genes: A Comprehensive Multi-Pen Fecal Microbiome and Resistome Study in Dairy Farms.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112641},
pmid = {41304325},
issn = {2076-2607},
support = {2018-68003-27466//USDA National Institute of Food and Agriculture/ ; },
abstract = {Antimicrobial resistance (AMR) poses a critical public health threat, with rising multidrug resistance cases compromising treatment effectiveness. Knowledge about the resistome in dairy production systems remains limited, particularly regarding lactating cows. This study investigated the microbiome and resistome across the hospital, fresh, and mid-lactation pens on 18 conventional dairy farms in California and Ohio using shotgun metagenomic sequencing of pooled fecal samples. Pooled fecal pat samples were collected as part of a larger field study using a quasi-experimental design that assigned farms to the training intervention group (six per state) or the control group (three per state). For the training intervention group, farm worker(s), identified as having the task of diagnosing and treating adult cows on the farm, participated in a training program on antimicrobial stewardship practices. Pooled fecal samples (n = 7) were collected at enrollment and 3 months after the intervention was completed on each participating farm (n = 18). A total of 10,221 bacterial species and 345 AMR genes conferring resistance to 22 antimicrobial classes were identified. The hospital pen exhibited a higher AMR gene diversity compared to fresh and mid-lactation pens (p < 0.05). Several AMR genes showed bimodal distribution, suggesting complex transmission mechanisms. Network analysis revealed distinct gene correlation profiles across pens, with the hospital pen showing fewer gene interactions. Our findings suggest that farm-level antimicrobial drug use may not be the sole or primary driver of resistome composition in pooled fecal samples from dairy cattle, highlighting the need to investigate other factors influencing AMR dynamics in livestock systems.},
}

@article {pmid41304317,
year = {2025},
author = {Zhang, Y and Feng, D and Huo, J and Xu, J and Wang, Y and Liu, Q and Bai, W and Liu, Q and Zhang, Y},
title = {Cultivar-Dependent Differences in Agronomic Characteristics, Nutritional Value, Fermentation Quality, and Bacteriome Profile of Whole-Plant Sorghum Silage.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112634},
pmid = {41304317},
issn = {2076-2607},
support = {CARS-06-14.5-A30//the National Millet Sorghum Industrial Technology System/ ; 32202703//the national natural science foundation of China/ ; },
abstract = {Forage scarcity in semi-arid regions necessitates the identification of optimal sorghum cultivars for high-quality silage production. This study systematically evaluated varietal differences in agronomic characteristics, nutritive value, fermentation quality, and bacterial community structure of whole-plant sorghum silage. A completely randomized design was implemented with four sorghum cultivars representative of semi-arid northwestern China: Liaotian1 (LT1), Jinnuo3 (JN3), Jinza2001 (JZ2001), and Jinza1531 (JZ1531). Five quadrats per cultivar in experimental fields were randomly designated as biological replicates for silage production. The plants were harvested at the dough stage, chopped, and ensiled in laboratory-scale silos (n = 20, 4 cultivars × 5 replicates) for 120 days. Analyses included agronomic measurements, chemical composition, fermentation parameters, microbial plate enumeration, and bacterial community profiling via 16S rRNA gene amplicon sequencing of the V3-V4 hypervariable region. The results showed that cultivar significantly influenced (p < 0.01) all agronomic traits and most nutritional parameters. The forage-type cultivar LT1 showed the highest biomass yield but the lowest nutritional quality, with higher neutral detergent fiber (47.77% vs. 29.21-32.35%; p < 0.05) and lower starch (10.94% vs. 18.10-24.30%; p < 0.05) contents as well as higher dry matter losses (1.39% vs. 0.91-1.23%; p < 0.05) than grain-type cultivars. In contrast, the grain-type cultivar JN3 exhibited balanced yield-quality traits with the highest (p < 0.05) starch (24.30%) and crude protein (7.50%) contents. Most fermentation parameters differed significantly (p < 0.01) among cultivars, with JN3 showing elevated ammonia-nitrogen (0.24 g/kg) but within acceptable ranges. Microbial diversity analysis revealed cultivar-driven differences in bacterial communities, with JN3 enriched in Leuconostoc and early-colonizing taxa (p < 0.05 and LDA Score > 4). It is concluded that the grain-type cultivar JN3 is the most suitable cultivar for whole-plant sorghum silage production in water-limited regions due to its optimal yield-quality balance. The findings underscore the importance of integrated cultivar evaluation and suggest the potential of targeted microbial inoculants for enhancing silage quality.},
}

@article {pmid41304316,
year = {2025},
author = {Hu, P and Carr, AN and Parlov, M and Swift, D and Tiesman, JP and Ramji, N and Schoch, JJ and Teufel, AG},
title = {Metagenomics Investigation on Baby Diaper Area Microbiome and Its Association with Skin pH and Dermatitis in the Diapered Area.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112632},
pmid = {41304316},
issn = {2076-2607},
abstract = {Dermatitis in the diapered area (DDA) is the most common skin condition in infants and can cause significant pain and discomfort, leading to disturbed sleep, changes in temperament, and heightened concern and anxiety for caregivers. This study investigates the relationship between skin pH, microbiome composition, and DDA severity in 158 infants from China, the US, and Germany, focusing on the buttocks, perianal, and thigh regions. Significant variations in DNA biomass and microbiota profiles were noted. Escherichia coli and Veillonella atypica were linked to higher rash scores and elevated skin pH, while Bifidobacterium longum showed a negative correlation with buttocks pH and rash severity but not with perianal rash. Correlation patterns emerged for other species, like Enterococcus faecalis, between perianal and buttocks rashes. Functional analysis identified key categories, including lipid and fatty acid metabolism, cofactor, amino acid, and carbohydrate metabolism, homeostasis and osmolarity stress, and microbial virulence and oxidative stress response, which are vital for skin health, DDA, and pH regulation in infants. These findings underscore the importance of maintaining a mildly acidic skin pH and minimizing fecal and urine residues for optimal infant skin health, suggesting that microbiota significantly influence DDA development, and provide insights for future preventive strategies and therapeutic interventions.},
}

@article {pmid41304309,
year = {2025},
author = {Paoli, JE and Thongthum, T and Bassett, M and Beardsley, J and Tagliamonte, MS and Cash, MN and Spertus Newman, J and Smith, LM and Anderson, BD and Salemi, M and Subramaniam, K and von Fricken, ME and Braun de Torrez, E and Mathis, V and Mavian, CN},
title = {Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112625},
pmid = {41304309},
issn = {2076-2607},
support = {Department of Pathology EPIG RAS 2021-2022//University of Florida/ ; Florida Informatics Institute SEED 2022-2023//University of Florida/ ; Biodiversity Institute SEED 2022-2023//University of Florida/ ; },
abstract = {Florida's bat virome remains poorly characterized despite the state's high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like virus 2 (HVLV2) genome from T. brasiliensis feces, a finding consistent with an arthropod-derived dietary signal rather than active bat infection. An Alphacoronavirus (AlphaCoV) was detected in two M. austroriparius specimens, including one with a putative co-infection involving an Astrovirus (AstV), the first detection of AstV in Florida bats to date. Parallel profiling of the M. austroriparius gut microbiome highlighted compositional differences in the co-infected individual relative to AlphaCoV-only and virus-negative bats, suggestive of potential associations between viral detection and gut microbial shifts. Our study expands the known viral diversity in Florida bat populations, and demonstrates how metagenomics can simultaneously illuminate host diet, viral exposure, and gut microbial ecology. This approach provides a scalable framework for monitoring how diet, microbiome composition, and environmental pressures shape the bat virome, and inform conservation and zoonotic risk assessments.},
}

@article {pmid41304301,
year = {2025},
author = {Martinez, A and St-Pierre, B},
title = {Metagenomic Identification and Characterization of Novel Vitamin B12 Synthesizers from the Rumen of Beef Cattle Fed High-Lipid Inclusion Diets.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112617},
pmid = {41304301},
issn = {2076-2607},
support = {SD00H866-26//South Dakota State University Agricultural Experiment Station Hatch funds (USDA National In-stitute of Food and Agriculture)/ ; },
abstract = {Beef production in intensive systems requires optimal nutrition to maximize growth and profitability. While triglycerides contain twice the energy per unit weight compared to polysaccharides, they are not nearly as commonly used as a supplemental source of energy compared to starch, largely in part due to their negative effects on rumen physiology when their inclusion levels are too high. To gain further insights into the response of rumen microbial communities to elevated dietary lipid levels, we took advantage of rumen samples collected as part of a previously published study that tested high inclusion (4% and 8%) of tallow or linseed oil in beef cattle as part of a 5 × 5 Latin square design, with corn used as a base dietary ingredient. Using a 16S rRNA gene-based profiling approach, two uncharacterized candidate rumen bacterial Operational Taxonomic Units (OTUs), referred to as Bt-995 and Bt-1367, were found to be in higher abundance in rumen samples collected from steers when they were fed diets with higher inclusion of linseed oil. Using a metagenomics approach to assemble contigs corresponding to genomic regions of these OTUs, various predicted metabolic functions were found to be shared. Consistent with the dietary treatments of the original animal study, functions associated with starch utilization and triglyceride metabolism were identified. Unexpectedly, however, contig sets from both OTUs also encoded genes predicted to be involved in vitamin B12 biosynthesis, as well as ethanolamine utilization, a function that is dependent on vitamin B12 as a co-factor. Together, these results indicate that vitamin B12-related functions may provide an advantage to rumen bacteria under conditions of high dietary triglyceride inclusion.},
}

@article {pmid41304278,
year = {2025},
author = {Qiao, T and Zhu, Z},
title = {Multi-Kingdom Gut Microbiome Interaction Characteristics Predict Immune Checkpoint Inhibitor Efficacy Across Pan-Cancer Cohorts.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112595},
pmid = {41304278},
issn = {2076-2607},
support = {2025A04J5264//Guangzhou Basic and Applied Basic Research Project/ ; 2023A1515010744//Guangdong Basic and Applied Basic Research Foundation/ ; },
abstract = {An increasing number of studies have confirmed that the gut microbiota, especially bacteria, is closely related to the efficacy of immune checkpoint inhibitor (ICI) therapy. However, the effectiveness of multi-kingdom microbiota and their interactions in predicting the therapeutic effect of ICI therapy remains uncertain. We integrated extensive gut metagenomic databases, including 1712 samples of 10 cohorts from 7 countries worldwide, to conduct rigorous differential analysis and co-occurrence network analysis targeting multi-kingdom microbiota (bacteria, fungi, archaea, and virus). We ultimately identified two subtypes (C1 and C2) by employing a weighted similarity network fusion (WSNF) method. Subtype C2 exhibited higher microbial diversity, better treatment response, and improved prognosis compared to subtype C1. Notably, subtype C2 was associated with higher abundance of beneficial genera such as Bacteroides and Kluyveromyces, while subtype C1 contained potentially detrimental taxa like Malassezia. A multi-kingdom model incorporating 32 genera demonstrated superior predictive accuracy for ICI therapy efficacy compared to single-kingdom models. Co-occurrence network analysis revealed a more robust and interconnected microbiome in subtype C2, suggesting a stable gut environment correlates with effective ICI therapy efficacy. This study highlights the potential of a multi-kingdom signature in predicting the efficacy of ICI therapy, offering a novel perspective for personalized therapy in oncology.},
}

@article {pmid41304268,
year = {2025},
author = {Bednarska, NG and Reitlo, LS and Beisvag, V and Stensvold, D and Haberg, AK},
title = {Microbial Signatures Mapping of High and Normal Blood Glucose Participants in the Generation 100 Study.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112582},
pmid = {41304268},
issn = {2076-2607},
abstract = {Intestinal dysbiosis has been linked to metabolic disorders, including insulin resistance and type 2 diabetes mellitus (T2DM). T2DM typically follows a prediabetic stage, during which insulin resistance develops. During the early stages of T2DM, its development can be corrected, thus potentially preventing or delaying the onset of the disease. This secondary, exploratory, cross-sectional comparison study aimed to contrast the gut microbiome of individuals with elevated fasting blood glucose to that of individuals with glucose levels within the normal range. This study involved 65 older adults (ages 76-83 years) enrolled from the randomized controlled trial entitled the "Generation 100 Study", all of whom consented to provide their gut microbiome samples. We employed a high-throughput sequencing of the bacterial 16S rRNA gene to obtain metagenomic microbial profiles for all participants. These profiles were then correlated with clinical measures. Overall, microbial alpha diversity was significantly reduced in the high glucose group. We have also observed distinct patterns of microbial beta diversity between high and normal glucose groups. At the phylum level, we found that Synergistes, Elusimicobia, Euryarchaeota, Verrucomicrobia, and Proteobacteria were all significantly decreased in participants with high blood glucose. Additionally, P. copri (ASV 909561) was significantly elevated (10-fold increase) in the high glucose groups, suggesting that it may serve as an early T2DM marker. In contrast to prior reports on the Fusobacterium genus, we found that it was significantly increased in the normal glucose group, with a significant 151-fold increase compared to the high glucose group. Directly linking gut microbiota profiles with clinical indicators such as fasting blood glucose and T2DM diagnosis allows the identification of specific microbial features associated with glucose dysregulation, providing preliminary population-level evidence to guide future translational research. Our results indicate significant changes in the microbiome that may provide valuable insights for early intervention in pre-diabetic states.},
}

@article {pmid41304266,
year = {2025},
author = {Santoyo, G},
title = {Advances in the Plant Microbiome: Rhizosphere, Endosphere, and Phyllosphere.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112581},
pmid = {41304266},
issn = {2076-2607},
abstract = {The continuous growth of the global human population demands sustainable production systems that move away from synthetic fertilizers, pesticides, and other agrochemicals, which pose serious toxicological, environmental, and public health risks [...].},
}

@article {pmid41304258,
year = {2025},
author = {Viana, J and Ferro, T and Pitschieller, R and Machado, V and Su, N and Mendes, JJ and Botelho, J},
title = {Neutrophils at the Crossroads of Oral Microbiome Dysbiosis and Periodontal Disease.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112573},
pmid = {41304258},
issn = {2076-2607},
support = {10.54499/UIDB/04585/2020//FCT/ ; },
abstract = {Neutrophils are the most abundant circulating leukocytes and essential components of innate immunity. Through mechanisms such as phagocytosis, reactive oxygen species (ROS) production, degranulation, and neutrophil extracellular trap (NET) formation, they play a crucial role in host defense. However, dysregulated neutrophil responses are linked to chronic inflammatory conditions, including periodontitis. This review summarizes current evidence on neutrophil biology in periodontal health and disease, focusing on functional mechanisms, recruitment pathways, the influence of dysbiosis, and their potential as biomarkers and therapeutic targets. Neutrophils display a dual role in periodontal tissues: while protecting against microbial invasion, their excessive or impaired activity contributes to tissue destruction. Altered chemotaxis, defective phagocytosis, and uncontrolled NET release perpetuate inflammation and alveolar bone loss. Neutrophil-derived enzymes, including myeloperoxidase, elastase, and matrix metalloproteinases, emerge as promising biomarkers for early diagnosis. In parallel, therapeutic strategies targeting oxidative stress, NET regulation, or neutrophil hyperactivity are being explored to preserve periodontal tissues. Neutrophils are central players in periodontal pathophysiology. Understanding their regulation and interaction with the oral microbiome may enable the development of novel diagnostic and therapeutic approaches, ultimately improving periodontal disease management.},
}

@article {pmid41304256,
year = {2025},
author = {Mateescu, DM and Ilie, AC and Cotet, I and Guse, C and Muresan, CO and Pah, AM and Badalica-Petrescu, M and Iurciuc, S and Craciun, ML and Avram, A and Margan, MM and Enache, A},
title = {Gut Microbiome Dysbiosis in COVID-19: A Systematic Review and Meta-Analysis of Diversity Indices, Taxa Alterations, and Mortality Risk.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112570},
pmid = {41304256},
issn = {2076-2607},
support = {"Victor Babes" University of Medicine and Pharmacy Timisoara//"Victor Babes" University of Medicine and Pharmacy Timisoara/ ; },
abstract = {COVID-19 is associated with gut microbiome alterations that may influence disease outcomes through immune and inflammatory pathways. This systematic review and meta-analysis evaluated global evidence on gut dysbiosis in COVID-19. We searched PubMed/MEDLINE, Embase, Web of Science, Scopus, and Cochrane Library up to 5 October 2025 (PROSPERO CRD420251160970). Alpha-diversity indices and microbial taxa log-fold changes (logFC) were analyzed using random-effects models. The pooled standardized mean difference (SMD) for the Shannon index was -0.69 (95% CI -0.84 to -0.54; I[2] = 42%), confirming reduced microbial diversity. Faecalibacterium prausnitzii showed a significant pooled depletion (logFC = -1.24; 95% CI -1.68 to -0.80; k = 10; I[2] = 74%), while Enterococcus spp. was increased (logFC = 1.45; 95% CI 1.12-1.78). Egger's test did not suggest publication bias (p = 0.32). Gut dysbiosis was consistently associated with reduced microbial diversity and enrichment of pathogenic taxa, correlating with increased disease severity and mortality (HR = 1.67). These findings highlight the potential of microbiome profiling as a prognostic tool in COVID-19, although clinical translation requires further validation.},
}

@article {pmid41304252,
year = {2025},
author = {Ramírez-López, M and Bautista-Cruz, A and Toledo-López, A and Aquino-Bolaños, T},
title = {Rhizospheric and Endophytic Plant Growth-Promoting Bacteria Associated with Coffea arabica L. and Coffea canephora Pierre ex Froehner: A Review of Their Agronomic Potential.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112567},
pmid = {41304252},
issn = {2076-2607},
support = {SIP-20240857and SIP-20252379//Instituto Politécnico Nacional/ ; },
abstract = {Plant growth-promoting bacteria (PGPB) associated with Coffea arabica L. and Coffea canephora Pierre ex Froehner offer a viable strategy to reduce synthetic inputs and enhance resilience in coffee agroecosystems. This review synthesizes evidence from the past decade on rhizosphere-associated and endophytic taxa, their plant growth-promotion and biocontrol mechanisms and the resulting agronomic outcomes. A compartment-specific core microbiome is reported, in the rhizosphere of both hosts, in which Bacillus and Pseudomonas consistently dominate. Within endophytic communities, Bacillus predominates across tissues (roots, leaves and seeds), whereas accompanying genera are host- and tissue-specific. In C. arabica, endophytes frequently include Pseudomonas in roots and leaves. In C. canephora, root endophytes recurrently include Burkholderia, Kitasatospora and Rahnella, while seed endophytes are enriched for Curtobacterium. Functionally, coffee-associated PGPB solubilize phosphate; fix atmospheric nitrogen via biological nitrogen fixation; produce auxins; synthesize siderophores; and express 1-aminocyclopropane-1-carboxylate deaminase. Indirect benefits include the production of antifungal and nematicidal metabolites, secretion of hydrolytic enzymes and elicitation of induced systemic resistance. Under greenhouse conditions, inoculation with PGPB commonly improves germination, shoot and root biomass, nutrient uptake and tolerance to drought or nutrient limitation. Notable biocontrol activity against fungal phytopathogens and plant-parasitic nematodes has also been documented. Key priorities for translation to practice should include (i) multi-site, multi-season field trials to quantify performance, persistence and economic returns; (ii) strain-resolved omics to link taxa to functions expressed within the plant host; (iii) improved bioformulations compatible with farm management and (iv) rationally designed consortia aligned with production goals and biosafety frameworks.},
}

@article {pmid41304248,
year = {2025},
author = {Chen, F and He, X and Liu, Q and Gao, F and Zeng, C and Li, D},
title = {Bio-Organic Fertilizer Modulates the Rhizosphere Microbiome to Enhance Sugarcane Growth and Suppress Smut Disease.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112563},
pmid = {41304248},
issn = {2076-2607},
support = {2023YFD1902802//National Key Research and Development Program of China/ ; },
abstract = {Sugarcane smut, caused by the fungal pathogen Sporisorium scitamineum, leads to significant economic losses in the global sugarcane industry. Bio-organic fertilizers (BF) offer a promising and sustainable strategy to mitigate smut incidence and enhance sugarcane growth. While the application of BF is known to modulate root exudates and rhizosphere microbial community structure, thereby promoting disease resistance, the precise mechanisms underpinning BF-mediated suppression of sugarcane smut remain largely unclear. This study investigated the microbiological mechanisms of smut suppression using a pot experiment, comparing a novel BF treatment (composted substrate enriched with Bacillus subtilis, Bacillus altitudinis, Bacillus cereus, Trichoderma harzianum, and Trichoderma longibrachiatum, biochar, and calcium carbonate) with a control receiving only conventional organic fertilizer. BF application significantly increased plant height (by 95.2%), dry weight (137.5%), fresh weight (253.3%), and sugar content (43.1%) relative to the control. Furthermore, the BF treatment enhanced catalase activity by 167.8% and peroxidase activity by 102.3% in sugarcane leaves, while the control effectiveness against the incidence of smut disease reached 88.0%. Analysis of the rhizosphere microbiome revealed that BF application significantly altered microbial alpha- and beta-diversity. Specifically, the BF treatment notably enriched beneficial genera such as Pseudomonas and Meyerozyma. Beta-diversity analysis revealed distinct microbial community structures in BF-treated rhizosphere soil compared to the control. Correlation and random forest analyses identified Pseudomonas and Meyerozyma as key taxa that were positively associated with sugarcane growth parameters and negatively correlated with smut incidence. These findings elucidate the dual role of this novel BF in enhancing sugarcane growth and suppressing smut incidence through the strategic reshaping of the rhizosphere microbiome.},
}

@article {pmid41304231,
year = {2025},
author = {Fadiji, AE and Adeniji, A and Lanrewaju, AA and Adedayo, AA and Chukwuneme, CF and Nwachukwu, BC and Aderibigbe, J and Omomowo, IO},
title = {Key Challenges in Plant Microbiome Research in the Next Decade.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112546},
pmid = {41304231},
issn = {2076-2607},
abstract = {The plant microbiome is pivotal to sustainable agriculture and global food security, yet some challenges hinder fully harnessing it for field-scale impact. These challenges span measurement and integration, ecological predictability and translation across environments and seasons. Key obstacles include technical challenges, notably overcoming the limits of current sequencing for low-abundance taxa and whole-community coverage, integrating multi-omics data to uncover functional traits, addressing spatiotemporal variability in microbial dynamics, deciphering the interplay between plant genotypes and microbial communities, and enforcing standardized controls, metadata, depth targets and reproducible workflows. The rise of synthetic biology, omics tools, and artificial intelligence offers promising avenues for engineering plant-microbe interactions, yet their adoption requires regulatory, ethical, and scalability issues alongside clear economic viability for end-users and explicit accounting for evolutionary dynamics, including microbial adaptation and horizontal gene transfer to ensure durability. Furthermore, there is a need to translate research findings into field-ready applications that are validated across various soils, genotypes, and climates, while ensuring that advances benefit diverse regions through global, interdisciplinary collaboration, fair access, and benefit-sharing. Therefore, this review synthesizes current barriers and promising experimental and computational strategies to advance plant microbiome research. Consequently, a roadmap for fostering resilient, climate-smart, and resource-efficient agricultural systems focused on benchmarked, field-validated workflows is proposed.},
}

@article {pmid41304229,
year = {2025},
author = {Watanabe, K and Yanagi, U},
title = {Comparison of QIIME1 and QIIME2 for Analyzing Fungal Samples from Various Built Environments.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112545},
pmid = {41304229},
issn = {2076-2607},
support = {21ek0410055//Japan Agency for Medical Research and Development/ ; 22ek0410097//Japan Agency for Medical Research and Development/ ; 21LA1005//Ministry of Health Labour and Welfare/ ; 21LA1501//Ministry of Health Labour and Welfare/ ; },
abstract = {This study evaluates the differences between bioinformatics pipelines by analyzing samples collected from various built environments. Previous comparative studies of microbial community analysis pipelines have largely focused on bacterial communities, mock communities, or soil fungi, often with small sample sizes, and have not specifically targeted built environments. Our results highlight key differences between OTU (QIIME1) and ASV (QIIME2) analyses. OTU analysis clusters OTUs at 97% similarity and tends to show higher diversity values in diversity analyses. Regarding abundantly detected fungi, OTU analysis identified more genera than ASV analysis. However, the OTU method has a high rate of false positives and false negatives, indicating low error-removal capability and suggesting that many fungal genera may have been detected. Therefore, a combined approach using OTU analysis combined with ASV analysis allows for both the comprehensive detection of dominant taxa and the inclusion of rare species. Overall, our findings emphasize that the choice of pipeline significantly influences the composition of the observed fungal community in built environments. Careful consideration of both OTU and ASV strategies can enhance the reliability and completeness of fungal metabarcoding studies, particularly when studying complex indoor microbial communities.},
}

@article {pmid41304219,
year = {2025},
author = {Cui, J and Tang, L and Li, Z and Wang, S and Zhou, J and Yan, H and Wang, X},
title = {Active Factors in the Adult Pig Colon: Microbial Transplantation Versus Supplementation with Metabolites in Weaned Piglets.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112533},
pmid = {41304219},
issn = {2076-2607},
support = {No. 2022YFD1300402//the Key Program of the National Natural Science Foundation of China/ ; No. 32202715//National Natural Science Foundation of China/ ; No. 23DAA00403//the National Natural Science Foundation of China/ ; No. 2023B10564001//the Double first-class discipline promotion project under grant/ ; },
abstract = {The adult pig intestinal microbiota boosts piglet intestinal and microbiome development, thereby improving growth. However, the functional bacteria, metabolites, and their region-specific intestinal roles remain to be characterized. Administration of adult colon microbiota (CM; devoid of metabolites) to piglets promoted intestinal development post-weaning, as indicated by increased intestinal mucosal weight, villus-to-crypt ratio of the ileum (p < 0.05), and stimulated mucin secretion (p < 0.05). This effect was potentially mediated by modulating beneficial microbiota, including ASV50_Prevotella 7, ASV52_Prevotella 1, and ASV81_Coprococcus 1. Adult colon-derived microbiota was found to preferentially colonize the piglet colon, supported by significantly higher bacterial loads in colonic contents. Piglets receiving adult colon supernatant (CS; without bacterial cells) showed improved feed efficiency (FE; p < 0.05), with numerically higher body weight (BW) and average daily gain (ADG) compared to the control (CON) group. Additionally, CS transplantation (CST) promoted intestinal development, potentially by modulating abundances of beneficial bacteria species, including ASV95_Turicibacter, and ASV109_Ruminococcaceae, which correlated with increased production of antioxidant and anti-inflammatory chemicals, including protocatechuic acid (PCA, p < 0.01). Adult colon-derived microbiota and metabolites enhanced intestinal development in piglets. CS supplementation improved growth and immunity, mitigating post-weaning stress potentially through enriching growth-linked bacteria (e.g., Turicibacter and Ruminococcaceae) and metabolites production (e.g., prephenate and PCA). These findings highlight these functional microbiota and metabolites as promising direct-fed microbial or metabolite additives for piglet growth and intestinal health post-weaning.},
}