@article {pmid41039273,
year = {2025},
author = {Phan, A and Thapa, K and Hashmi, MA and Mohapatra, A and Ho, G and Tholan, GN and Biswas, D},
title = {Prophylactic efficacy of probiotics and their metabolites against Staphylococcus epidermidis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {621},
pmid = {41039273},
issn = {1471-2180},
support = {2018-5110628809//USDA-National Institute of Food and Agriculture/ ; 2018-5110628809//USDA-National Institute of Food and Agriculture/ ; 2018-5110628809//USDA-National Institute of Food and Agriculture/ ; },
abstract = {BACKGROUND: Staphylococcus epidermidis is a prevalent common microorganism found on the skin of most mammals, including humans. However, S. epidermidis is also known as an opportunistic pathogen that can cause diseases if the skin microbiome becomes skewed to favor its overgrowth. This situation can be worsened if the causative strains are antibiotic-resistant. To explore potential alternatives to replace conventional antibiotics, we aim to use probiotics, specifically Lacticaseibacillus rhamnosus and Lactiplantibacillus plantarum, in controlling the growth, colonization, and biofilm formation of a multidrug-resistant S. epidermidis.

RESULTS: Multidrug-resistant S. epidermidis was co-cultured with either L. rhamnosus or L. plantarum, and antimicrobial activity was assessed by counting S. epidermidis colonies at various timepoints. Under co-culture conditions, growth of S. epidermidis was decreased over time in the presence of either probiotic, specifically, a significant reduction was observed after 48 hours (p=0.0062). Additionally, S. epidermidis was treated with cell-free culture supernatant (CFCS) collected from probiotics to investigate the mechanism of inhibition. CFCS from 72-hour Lactobacilli cultures significantly inhibited S. epidermidis growth within 4 hours (p<0.05), and no S. epidermidis was detected after 72 hours (p=0.0003) when treated with 50% CFCS. Both CFCSs also reduced biofilm formation and bacterial counts after 24 hours, with complete inhibition by 48 h. Gene expression analysis revealed that exposure to CFCS led to downregulation of S. epidermidis genes associated with metabolism and cell division (arcC, gts, mutS, mur1, and ftsZ). Fluorescence microscopy indicated compromised cell wall integrity, evidenced by reduced HADA fluorescence and increased propidium iodide staining.

CONCLUSION: L. plantarum and L. rhamnosus possess strong antimicrobial activity against multidrug-resistantS. epidermidis, supporting their potential as alternative strategies to control S. epidermidis colonization.},
}

@article {pmid41039272,
year = {2025},
author = {Cao, Z and Wang, D and Cui, Y and Huang, F and Liu, Y and Dai, J and Wu, W and Dai, Z and Xie, J and Zhu, X and Hu, X and Xu, Y},
title = {Diet, nutrient characteristics and gut microbiome between summer and winter drive adaptive strategies of East China sika deer (Cervus nippon kopschi) in the Yangtze River basin.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {626},
pmid = {41039272},
issn = {1471-2180},
support = {32470552//National Natural Science Foundation of China/ ; 20242BAB25349//Natural Science Foundation of Jiangxi Province/ ; },
abstract = {BACKGROUND: Adaptation of species represents the outcome of interactions between organisms and their environment, as well as a product of natural selection and evolution.

METHOD: To elucidate how East China sika deer in TNNR respond to seasonal climatic selection pressures in the mid-lower Yangtze River basin, we investigated their seasonal adaptive strategies via analyses of dietary nutrition and the gut microbiome, using high-throughput sequencing of the trnL P6-loop of chloroplast and 16S rRNA.

RESULTS: In summer, sika deer consumed 174 plant species belonging to 183 genera and 107 families, exhibiting pronounced dietary generalization. Conversely, in winter, they fed on 130 species from 173 genera and 90 families, characterized by dietary specialization. The nutritional composition and availability of plants differed between the two seasons, driven by seasonal changes, which led to corresponding adjustments in foraging strategies. Notably, sika deer maintained a stable balance in nutrient intake across seasons. and industrialization of sika deer breeding in eastern China, whereas α-diversity was higher in winter. Microbiota in both seasons exhibited distinct correlations with consumed plant species and nutrients, but their microbial functions were predominantly enriched in metabolic processes. This pattern indicates that sika deer can flexibly reshape the structural and interaction networks of gut microbiota to enhance adaptive capacity to seasonal shifts. Overall, we demonstrated seasonal dynamics and provided new insights into understanding the diet diversity and nutrition components associated with gut microbiota in the adaptation of sika deer. These results will further facilitate genetic resource conservation, habitat improvement, food plant breeding, wild rescue, and industrialization of sika deer breeding in eastern China.},
}

@article {pmid41039266,
year = {2025},
author = {Tavanaeian, S and Feizabadi, MM and Falsafi, S and Aghdaei, HA and Houri, H},
title = {Oral and fecal microbiome alterations in pancreatic cancer: insights into potential diagnostic biomarkers.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {624},
pmid = {41039266},
issn = {1471-2180},
}

@article {pmid41039241,
year = {2025},
author = {Kang, C and Lee, J and Baek, MG and Kim, NE and Son, H and Yoo, S and Yi, H},
title = {Urinary microbiome in non-muscle invasive bladder cancer: impact of sample types and sex differences.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {623},
pmid = {41039241},
issn = {1471-2180},
support = {2022R1A2C1007966//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: Previous research on urinary microbiomes in bladder cancer patients has yielded inconsistent results, highlighting the need for further investigation. This study aims to analyze microbiome dysbiosis in bladder cancer patients by comparing multiple sample types, incorporating negative controls, and assessing sex-based variations. Fifty patients who required transurethral resection of bladder tumor for treatment were selected. Three types of specimens were collected from each patient: midstream urine, catheterized urine, and normal bladder mucosal tissue. Microbiome was analyzed via 16 S rRNA gene amplificon sequencing.

RESULTS: Beta diversity analysis revealed significant differences in microbiome composition between mucosal tissue and urine samples, while no significant variation was observed between midstream and catheterized urine samples. Due to the low biomass of mucosal tissue-characterized by dominance of a few taxa and high variability across extraction kit lots-its susceptibility to contamination compromised reproducibility, leading to a focus on urine samples for further analysis. Midstream urine samples showed significant sex-related microbiome differences, whereas catheterized urine exhibited no such differences, suggesting midstream urine may not be ideal for bladder-specific microbiome studies. Catheterized urine analysis identified Curvibacter, particularly Curvibacter gracilis, as significantly more abundant in bladder cancer patients compared to controls, while overall microbiome composition remained unchanged between the groups. Curvibacter prevalence was not directly correlated with any single clinical marker but increased with bladder cancer severity when patients were classified into high-risk and low-risk groups based on biopsy and clinical criteria.

CONCLUSIONS: This study highlights the importance of selecting appropriate sample types for bladder microbiome analysis, with catheterized urine emerging as the most reliable option. The findings suggest that Curvibacter may be associated with bladder cancer severity, warranting further investigation into its potential role as a biomarker. Future research should focus on validating these findings in larger cohorts and exploring the mechanistic link between microbiome alterations and bladder cancer progression.},
}

@article {pmid41039239,
year = {2025},
author = {Li, C and Ji, Y and Li, X and Cai, J and Ye, J and Wu, Y and Liao, Q and Wang, Z and Sanganyado, E and Li, P and Sun, Y and Liang, B and Liu, W},
title = {Vibrio spp.: a potential critical pathogen for mammals with implications beyond marine aquaculture.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {598},
pmid = {41039239},
issn = {1471-2180},
support = {4200615//STU Scientists of China/ ; 4200615//National Science Foundation for Young Scientists of China/ ; GDNRC[2022]48//Key Program of Marine Economy Development (Six Marine Industries) Special Foundation of the Department of Natural Resources of Guangdong Province/ ; },
abstract = {BACKGROUND: Species-specific or health status specific microbiome composition of cetaceans is still poorly classified due to the limited samples. Despite a partial identification of the gut microbiota of melon-headed whales (Peponocephala electra), comparative analyses across anatomical systems are lacking. This study provides the first comprehensive analysis of the microbial communities habiting nine body sites - oral cavity, esophagus, foregut, midgut, hindgut, blowhole, and skin wounds (left anterior, dorsal fin, tail) - in a stranded melon-headed whale.

RESULTS: By 16 S rRNA gene sequencing, a decrease in microbial richness was observed from the oral cavity to the hindgut, accompanied by compositional shifts from Fusobacterium-dominated oral/esophageal niches to Vibrio-enriched gastrointestinal regions (21.81% Vibrio, 21.19% Fusobacterium, 12.50% Actinobacillus). The respiratory tract microbiota underwent a significant shift and was dominated by Ostreibacterium (57.5%), Helcococcus (6.59%), and Tenacibaculum (4.12%). Skin wounds showed environmental similarities, with Vibrio (47.84%), Pseudoalteromonas (17.84%), and Psychrobacter (12.36%). Pan-microbiome screening identified seven Vibrio species (V. alginolyticus, V. cidicii, V. cyclitrophicus, V. navarrensis, V. parahaemolyticus, V. salilacus, and V. splendidus) across all niches, along with V. cholerae in non-respiratory samples. Notably, V. profundi was exclusively localized to anterior and dorsal fin wounds. Functional profiling revealed enrichment of Vibrio-linked pathogenesis pathways (infection, pathogenic cycle) and metabolic modules that were correlated with immunocompromised states.

CONCLUSIONS: This study revealed significant bidirectional environment-host microbiome exchange dynamics across cetacean mucosal surfaces. Notably, Vibrio spp. emerged as the dominant genus in both gastrointestinal and cutaneous wound microbiomes, highlighting: (1) potential zoonotic transmission risks from pathogenic Vibrio strains, and (2) the critical need for habitat-specific microbial surveillance to inform marine mammal conservation strategies.},
}

@article {pmid41039235,
year = {2025},
author = {Ahmad, S and Wang, M and Zhang, H and Deng, Y and Liang, Q and He, B and Wen, R},
title = {Synergistic application of biochar and lime modulates rhizosphere microbiome, suppresses pathogens, and enhances disease resistance in sugarcane.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {622},
pmid = {41039235},
issn = {1471-2180},
support = {GuiKeNongAB24153009//Guangxi Key R&D Plan/ ; 2025GXNSFAA069449//Guangxi natural science foundation/ ; },
abstract = {Soil acidification disrupts microbial communities and exacerbates plant disease susceptibility in agriculture. This study demonstrates that combined application of biochar (15 t ha[-1]) and lime (1.5 t ha[-1]) in acidic sugarcane fields significantly elevates soil pH (up to 46.7%) and organic carbon (SOC), driving profound restructuring of the rhizosphere microbiome. High-throughput sequencing revealed suppression of potentially pathogenic bacteria (Solirubrobacteraceae, Acidothermus, Gaiella) and fungi (Curvularia, Scytalidium, Myrothecium), alongside qPCR-confirmed reduction in Fusarium abundance. Concurrently, we observed significant enrichment of beneficial taxa including plant-growth-promoting bacteria (Sinomonas, Bacillus, Brevibacillus, Micromonospora, Filomicrobium, OLB13, Arenimonas) and fungi (Trichoderma, Aspergillus, Talaromyces, Penicillium, Taifanglania, Redeckera). FUNGuild analysis confirmed decreased relative abundance of fungal plant pathogen guilds, particularly under the combined treatment. Redundancy analysis identified pH, SOC, and acid phosphatase as key environmental drivers of microbial assembly. These microbiome shifts correlated with enhanced plant defense responses: increased phenylalanine ammonia-lyase and superoxide dismutase activities, reduced malondialdehyde content, and significantly suppressed pokkah boeng disease incidence (82.57% reduction) and severity. Our findings establish that biochar-lime synergy ameliorates soil constraints, functionally modulates the rhizosphere microbiome to suppress pathogens, and systemically enhances plant immunity, providing a sustainable strategy for managing soil-borne diseases in acidified agroecosystems.},
}

@article {pmid41039214,
year = {2025},
author = {Cortez-Martínez, M and Medrano-Lozano, J and Blanco-Peña, K and Quesada-Alvarado, F and Solano-Campos, F},
title = {Seasonal and spatial dynamics of the intestinal microbiome in tropical freshwater fish: insights from Astyanax aeneus and Brycon costaricensis in the Peñas Blancas river basin, Costa Rica.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {595},
pmid = {41039214},
issn = {1471-2180},
abstract = {BACKGROUND: The intestinal microbiome plays a crucial role in fish development and health, facilitating essential functions such as nutrient uptake, immune system response, and disease resistance. However, the microbial communities of Neotropical freshwater fish, such as Astyanax aeneus and Brycon costaricensis, remain largely unexplored. Understanding how microbiomes vary in relation to environmental gradients is key to identifying potential sentinel species for ecosystem monitoring. To understand the dynamics of bacterial diversity and community structure, we collected intestinal content samples from 165 individuals of both species from six points along the Peñas Blancas river basin, Costa Rica, during the dry and rainy seasons and during an intermediate period.

RESULTS: Metabarcoding analysis of the 16 S rRNA gene revealed that the intestinal microbial communities of both species were dominated primarily by the genera Cetobacterium, Clostridium, Romboutsia and Plesiomonas. No significant differences were detected in the relative abundance of taxa, metabolic pathways or community structure between the two species and only at the Dam site, a significant increase in the Shannon index was detected in B. costaricensis. Conversely, distinct differences in microbial network properties were found, with A. aeneus showing a lower clustering coefficient and modularity, a shorter average path length and a greater number of hubs. Site and season influenced the microbial community structure of A. aeneus but not the relative abundance of taxa. Similarly, differentially abundant metabolic pathways, including xenobiotic degradation, were enriched in A. aeneus.

CONCLUSIONS: The similarities in microbiome diversity and structure in both species could arise from parallels in taxonomy, habitat and diet. However, temporal and spatial shifts in the A. aeneus microbial community structure may be associated with sensitivity to changes in environmental stressors such as precipitation, temperature, and runoff. Microbial network analysis revealed that taxa in A. aeneus are more tightly interconnected and form fewer distinct clusters, making it a promising bioindicator for monitoring water quality and anthropogenic impacts.},
}

@article {pmid41039213,
year = {2025},
author = {IJdema, F and Arias-Giraldo, LM and Vervoort, E and Struyf, T and Van den Ende, W and Raaijmakers, JM and Lievens, B and De Smet, J},
title = {Metagenome-based identification of functional traits of the black soldier fly gut microbiome associated with larval performance.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {612},
pmid = {41039213},
issn = {1471-2180},
support = {S008519N//ENTOBIOTA/ ; IMP20028//KU Leuven Impuls grant/ ; C3/22/041//KU Leuven CHITINERY grant/ ; G0C4622N//Fonds Wetenschappelijk Onderzoek/ ; },
abstract = {BACKGROUND: The relationship between microbiomes and their hosts has been the subject of intensive study in recent years. For black soldier fly larvae (BSFL) (Hermetia illucens L., Diptera: Stratiomyidae), correlations between shifts in its microbial gut community composition and its health and performance suggest that the BSFL gut microbiome encodes important functions that complement the insect's own immune system and metabolism. To date, most BSFL microbiome studies have been based on 16S rRNA sequencing data. Because this approach derives a lot of information from very short sequencing reads, it was hypothesized that more insight into bacterial functionality could be generated using more extensive sequencing technologies. Here, whole genome shotgun (WGS) metagenomic sequencing was employed to investigate which microbiome-associated taxa and functions were associated with increased performance of larvae reared on a chicken feed (CF) or artificial supermarket food waste (SFW) based diet.

RESULTS: Taxonomic and functional profiling of the BSFL gut microbiome revealed a significant shift in response to diet, where bacterial genes encoding specific metabolic functions, such as the metabolism of sorbitol, were significantly enriched in the microbiome of larvae reared on SFW-diet. This indicates that the nutritional composition of the substrate alters the gut bacterial composition by providing competitive benefits or new niches for specific bacteria that can utilise these compounds. Moreover, specific microbial functions, such as cobalamin synthesis, appear to be correlated with larval performance. Aside from metabolic functions, biosynthetic gene cluster analysis revealed potential antimicrobial competition and protective functions among bacterial species. Improved taxonomic resolution provided by WGS led to the identification of several metagenome assembled genomes (MAGs), including a potentially novel BSFL-associated Scrofimicrobium species. Furthermore, there were differences in larval performance between rearing diets, and larval growth was correlated with high abundance of several MAGs.

CONCLUSIONS: Variation in the nutritional and bacterial load of a diet can result in functional shifts in the gut microbiome of the larvae. Analysis of the BSFL metagenome identified several bacteria that are positively correlated with larval performance, which could potentially provide beneficial metabolic functions for the host that should be further explored.},
}

@article {pmid41039203,
year = {2025},
author = {Shang, L and Li, F and Wang, Z and Hu, Z and Zou, H and Lu, J and Tang, YZ and Deng, Y},
title = {Cobalt exposure induces the specific associated-bacterial microbiome potentially contributing to cobalt stress alleviation of the host dinoflagellate Scrippsiella acuminata.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {617},
pmid = {41039203},
issn = {1471-2180},
support = {42206215//the National Science Foundation of China/ ; 42406214//the National Science Foundation of China/ ; 42376138//the National Science Foundation of China/ ; },
abstract = {Dinoflagellates grow in tight association with the bacterial community, which exert impacts on the physiology and ecology of both partners. However, the changes of associated-bacterial microbiome with the physiologies of the host dinoflagellate under specific heavy metals (HMs) stress remain largely unknown. In this study, we characterized the bacterial microbiome associated with the laboratory-cultured dinoflagellate Scrippsiella acuminata, a cosmopolitan bloom-forming species, under different cobalt concentrations, via high-throughput sequencing of 16 S rRNA gene amplicons. The sequencing of a total of 72 Libraries generated 6,047,695 reads which were classified into 31 phyla, 97 classes, 215 orders, 367 families, and 782 genera. We found that cobalt stress could greatly affect the growth of S. acuminata as well as the ASV diversity and community composition of the associated bacterial community. Significant dose-dependent changes in the bacterial community were detected, which were found to be closely correlated with some specific bacterial genera. Excessive cobalt exerted significantly inhibitory effects on microalgae growth-promoting bacteria (Marinobacter, Roseobacter, Mameliella, Leifsonia, Roseovarius, and Stappia). A notable increase in the relative abundance of HM-resistant bacteria with siderophore-producing capacity (Alteromonas, Arthrobacter, Pseudoalteromonas, Brevundimonas, Staphylococcus, Microbacterium, and Bacillus) and/or HM bio-removal potential (Corynebacterium, Pseudomonas, Burkholderia, Rhodococcus, and Gemella) was detected upon elevated cobalt concentrations, which potentially contributed to the cobalt stress alleviation of the dinoflagellate host. Our work provided deeper insights into the relationship between the associated-bacterial assemblage and dinoflagellate, and also broadened the current knowledge pertaining to the potential contributions of bacterial microbiome to the HM tolerance of host alga.},
}

@article {pmid41039039,
year = {2025},
author = {da Silva, DMG and Costa, R and Keller-Costa, T},
title = {A genomic view of the bacterial family Endozoicomonadaceae in marine symbioses.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1418},
pmid = {41039039},
issn = {2399-3642},
support = {CEECIND/00788/2017//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/ ; UIDB/04565/2020, UIDP/04565/2020, LA/P/0140/2020//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/ ; UIDB/04565/2020, UIDP/04565/2020, LA/P/0140/2020//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/ ; UIDB/04565/2020, UIDP/04565/2020, LA/P/0140/2020//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/ ; },
mesh = {*Symbiosis ; *Genome, Bacterial ; *Aquatic Organisms/microbiology/physiology ; Genomics ; Phylogeny ; Microbiota ; },
abstract = {Endozoicomonadaceae bacteria are found in association with marine organisms across ocean ecosystems. Interactions may range from mutualistic to parasitic depending on host species and ecological context. Their genomic repertoire suggests metabolic versatility and capacity for rapid adaptation and transitioning between free-living and host-associated lifestyles. Some lineages, however, undergo genome reduction, are host-specific, and lack cultivability. Here we present an advanced genomic perspective and updated view on the functional diversity of Endozoicomonadaceae along the mutualism-parasitism continuum. We discuss their roles in marine symbioses, potential for microbiome engineering, and highlight knowledge gaps of their ecology to be addressed in future research.},
}

*Symbiosis
*Genome, Bacterial
*Aquatic Organisms/microbiology/physiology
Genomics
Phylogeny
Microbiota

@article {pmid41039005,
year = {2025},
author = {Abi Assaf, J and de Coriolis, JC and Godden, AM and Redhead, E and Bartram, J and Cohen-Krais, J and Silova, K and Crighton, Z and Le Gall, G and Sami, S and Khalid, SA and Immler, S},
title = {Gum Arabic modulates the microbiota-gut-brain axis and affects general fitness in zebrafish.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34465},
pmid = {41039005},
issn = {2045-2322},
support = {218467/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; SELECTHAPLOID-101001341/ERC_/European Research Council/International ; NE/S011188/1//Natural Environment Research Council/ ; },
mesh = {Animals ; *Zebrafish/microbiology/physiology ; *Gastrointestinal Microbiome/drug effects ; *Brain/metabolism/drug effects ; Male ; Female ; *Gum Arabic/pharmacology ; Dietary Supplements ; Reproduction/drug effects ; },
abstract = {Gum Arabic (GA) (Acacia senegal var. senegal) is an edible tree exudate and dietary fibre shown to improve health in humans and animals. We tested the ramifications of GAon organismal health across the microbiota-gut-brain axis by supplementing female and male zebrafish (Danio rerio) with two concentrations(6% or 60%) of GA (Acacia senegal var. senegal) for two weeks. We assessed the effects on the gut microbiome composition, intestinal and brain metabolic profiles, reproductive fitness, locomotion, and brain gene expression. GA supplementation induced a relative decrease in Proteobacteria and a relative increase in Fusobacteria, with a rise in the beneficial genus Cetobacterium. In the GA-supplemented fish, we detected increased intestinal glucose metabolism, evidenced by reduced glucose retention levels. Additionally, high levels of acetate were detected in the brain. Interestingly, the gene cart1, involved in appetite and hunger control, was significantly downregulated in female brains only. Consistently, we detected increased locomotion in GA-supplemented fish compared to Control fish. Interestingly, GA supplementation had a negative effect on female reproductive fitness and a positive effect on male reproductive fitness. .Our results emphasise the significance of evaluating the impact of dietary fibre at a systemic level to develop relevant nutritional guidelines that consider the different nutritional requirements of each sex.},
}

Animals
*Zebrafish/microbiology/physiology
*Gastrointestinal Microbiome/drug effects
*Brain/metabolism/drug effects
Male
Female
*Gum Arabic/pharmacology
Dietary Supplements
Reproduction/drug effects

@article {pmid41038976,
year = {2025},
author = {Majood, M and Rao, R},
title = {Human milk: insights on cell composition, organoids and emerging applications.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {41038976},
issn = {1530-0447},
abstract = {Human milk is far more than a source of infant nutrition. It is a dynamic, living fluid packed with cells, bioactive molecules, and a complex microbiome that shapes neonatal development and lifelong health. Recent advances have illuminated the remarkable cellular diversity of human milk, including epithelial, immune, microbial and stem cells, each contributing essential biological functions. Milk contains distinct membrane-bound structures in the form of milk fat globules and extracellular vesicles that package a diverse cargo of lipids, proteins and nucleic acids for neonate nutrition, development and immune regulation. This review explores the composition of human milk, highlighting its nutrient and bioactive components and discussing growing concerns of xenobiotic and viral burden. We describe how milk-derived cells offer non-invasive windows into lactation biology and how emerging 3D mammary organoid models, particularly those generated from human milk cells, provide unprecedented tools to study breast development, lactation disorders, and regenerative therapies. We outline the potential of milk cells and extracellular vesicles in neonatal care, personalized medicine, and biobanking, while addressing current technical challenges and future research opportunities. By harnessing the unique properties of human milk, we stand at the threshold of transformative insights into maternal-infant health and novel biomedical applications. IMPACT: Up to date summary of bioactives, living cells and membrane bound compartments found in human milk. Primer on human mammary organoid technology, including advantages, recent advances and step by step methods. Highlights the unrealized potential of human milk in organoid technology, therapeutics, and regenerative medicine.},
}

@article {pmid41038964,
year = {2025},
author = {Liu, F and Zhang, Y and Zhang, L and Feng, W and Zhao, Y and Wei, J and Zhu, X and Zhao, S},
title = {Aqueous extract of Acer truncatum leaves retards Drosophila melanogaster senescence by regulating amino acid metabolism and gut microbiota.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34409},
pmid = {41038964},
issn = {2045-2322},
support = {2020QFY10-04//the Regional Innovation Capability Guiding Plan Project of Shaanxi Province/ ; 2020-120//the "Tianfu Scholar" Distinguished Expert Program of Sichuan Province/ ; },
mesh = {Animals ; *Drosophila melanogaster/drug effects/physiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Plant Leaves/chemistry ; *Plant Extracts/pharmacology/chemistry ; *Acer/chemistry ; *Amino Acids/metabolism ; *Aging/drug effects ; Longevity/drug effects ; Tandem Mass Spectrometry ; Metabolomics ; },
abstract = {Acer truncatum is a unique tree species indigenous to northern China. The Chinese government approved the utilization of Acer truncatum leaves as a raw material for food. These leaves have been traditionally used in Inner Mongolia as a form of anti-aging medicine. However, the specific mechanism responsible for the anti-aging properties of Acer truncatum leaves remains unidentified. In this study, an aqueous extract of Acer truncatum leaves (AAL) was prepared and analyzed using UPLC-QTOF-MS/MS. the UPLC-MS/MS profile detected a total of 989 compounds in AAL, with 5 compounds of high concentration selected for quantitative analysis via UPLC-QTOF-MS/MS employing the internal standard method. Subsequently, Drosophila melanogaster served as a model organism to assess the impact of AAL on the lifespan and locomotor abilities. The results demonstrated a significant extension of the lifespan of D. melanogaster in response to AAL supplementation. Moreover, the addition of AAL to the medium enhanced the physical and anti-stress abilities of D. melanogaster, while preserving the integrity of their intestinal barrier. Gut microbiome analysis revealed that AAL administration positively influenced the structure and composition of gut microbes in aged D. melanogaster, notably reducing the prevalence of detrimental bacteria like Enterococcus and increasing beneficial bacteria such as Lactococcus. Metabolomic analysis annotated 30 potentially significant metabolites in AAL that contribute to delaying aging, predominantly associated with Phenylalanine metabolic pathways. Through a comprehensive multi-omics correlation analysis, a strong link was established between gut microbiota and metabolites following AAL treatment, highlighting how AAL prolongs the lifespan of D. melanogaster by modulating metabolic pathways via the gut microbiota. This study offers valuable insights into the anti-aging properties of AAL, emphasizing its ability to delay aging primarily through the regulation of metabolic pathways mediated by the gut microbiota and sets a foundation for the potential future application of AAL as a functional food.},
}

Animals
*Drosophila melanogaster/drug effects/physiology/metabolism
*Gastrointestinal Microbiome/drug effects
*Plant Leaves/chemistry
*Plant Extracts/pharmacology/chemistry
*Acer/chemistry
*Amino Acids/metabolism
*Aging/drug effects
Longevity/drug effects
Tandem Mass Spectrometry
Metabolomics

@article {pmid41038962,
year = {2025},
author = {Ali, S and Fuller, KD and Yurgel, SN and Forge, T and Lévesque, V and Mazzola, M},
title = {Exploring soil microbial and plant parasitic nematode communities involved in the apple replant disease complex in Nova Scotia.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34402},
pmid = {41038962},
issn = {2045-2322},
support = {J-002358//Agriculture and Agri-Food Canada/ ; J-002358//Agriculture and Agri-Food Canada/ ; J-002358//Agriculture and Agri-Food Canada/ ; J-002358//Agriculture and Agri-Food Canada/ ; },
mesh = {*Soil Microbiology ; Animals ; *Plant Diseases/parasitology/microbiology ; *Malus/parasitology/microbiology ; *Nematoda ; Fungi/genetics/isolation & purification/classification ; Nova Scotia ; *Microbiota ; Soil/parasitology ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Apple replant disease (ARD) is incited by a complex of causal agents including various fungi, oomycetes, and plant parasitic nematodes. These causal agents can differ significantly in abundance between orchard sites within a geographic region. Knowledge of the specific etiology of ARD is required in order to develop commercially viable soil management strategies to combat specific/individual components of the pathogen complex. In this study, we analyzed soil from six ARD affected orchard sites to assess the presence and composition of fungal, bacterial and oomycetes communities, as well as the prevalence of plant parasitic nematodes. Five fungal, and 17 bacterial classes were differentially represented in the soil microbiomes across the different locations. Mortierellomycetes was the most abundant fungal taxa represented followed by Sordariomycetes. Mortierella exigua, a fungal endophyte, was the most abundant fungal amplicon sequence variant (ASV) in the core microbiome. Among bacteria, Proteobacteria was the most prevalent phylum identified in these orchard soils. Several potential phytopathogenic fungi associated with ARD, as well as endophytes including Fusarium oxysporum, F. solani, Nectria ramulariae, Ilyonectria robusta and Nectriaceae, were identified in ARD soils. Among oomycetes, Pythium attrantheridium (Globisporangium attrantheridium), and P. irregulare (Globisporangium irregulare) were the most abundant taxa. Additionally, six different groups of plant-parasitic nematodes were found across the ARD orchard soils. Root-lesion nematodes, Pratylenchus spp., which are commonly associated with ARD, were identified in all orchard soils at population densities range from 12 to 33/100 cm[3] soil. This research enhances our understanding of the ARD pathogen complex and provide important insights for developing alternative disease management strategies in the apple industry.},
}

*Soil Microbiology
Animals
*Plant Diseases/parasitology/microbiology
*Malus/parasitology/microbiology
*Nematoda
Fungi/genetics/isolation & purification/classification
Nova Scotia
*Microbiota
Soil/parasitology
Bacteria/genetics/classification/isolation & purification

@article {pmid41038926,
year = {2025},
author = {Giner-Pérez, L and Jarquín-Díaz, VH and Leone, P and Giménez-Garzó, C and Mincheva, G and Mira, Á and Forslund-Startceva, SK and Rubio, T and Felipo, V and Pérez-Martínez, G and Llansola, M},
title = {Rifaximin-induced changes in the gut microbiome associated to improvement of neurotransmission alterations and learning in rats with chronic liver disease.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34382},
pmid = {41038926},
issn = {2045-2322},
support = {PID2020-113388RB-I00-AEI/10.13039/501100011033 and FPU2022/02975//Ministerio de Ciencia e Innovación/ ; PID2020-113388RB-I00-AEI/10.13039/501100011033 and FPU2022/02975//Ministerio de Ciencia e Innovación/ ; PID2020-113388RB-I00-AEI/10.13039/501100011033 and FPU2022/02975//Ministerio de Ciencia e Innovación/ ; CIPROM 2021/082 and CIBEFP/2022/58//Conselleria de Educación de la Generalitat Valenciana/ ; CIPROM 2021/082 and CIBEFP/2022/58//Conselleria de Educación de la Generalitat Valenciana/ ; CIPROM 2021/082 and CIBEFP/2022/58//Conselleria de Educación de la Generalitat Valenciana/ ; OP ERDF of Comunitat Valenciana 2014-2020//Generalitat Valenciana co-funded with European Regional Development Funds (ERDF)./ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Rifaximin/pharmacology ; Rats ; Male ; *Synaptic Transmission/drug effects ; Carbon Tetrachloride/toxicity ; Hepatic Encephalopathy ; *Learning/drug effects ; Feces/microbiology ; *Liver Diseases/microbiology/drug therapy ; Disease Models, Animal ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Rifaximin, a gut-targeted antibiotic, improves cognitive function and reduces the risk of hepatic encephalopathy (HE), yet its effects on the gut-brain axis remain unknown. This study explores how rifaximin influences gut microbiota functions and its association with cognitive function and molecular alterations in rats with liver injury. Liver injury was induced by chronic administration of carbon tetrachloride (CCl4), and rifaximin was administered daily. Fecal samples were collected after eight weeks of CCl4 administration, and taxonomic and functional changes in the gut microbiome were analyzed. Rifaximin altered microbiota diversity and composition, increasing α diversity in liver-injured rats but reducing diversity in healthy rats. It influenced microbiota interactions with neurotransmission alterations, where Dorea, Lachnospiraceae A2, and possibly Erysipelotricaceae might be important contributors. Functionally, butyric acid levels negatively correlated with gene orthologues associated with GABA, tryptophan, and glutamate degradation pathways. In healthy rats, fecal short-chain fatty acid (SCFA) levels were positively correlated with each other, a pattern absent in other groups. Rifaximin significantly influenced gut microbiota and promoted bacterial groups linked to improved cognition and neurotransmission in liver disease. Our findings underscored the direct relationship between a healthy microbiome and the maintenance of balanced SCFA concentrations.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Rifaximin/pharmacology
Rats
Male
*Synaptic Transmission/drug effects
Carbon Tetrachloride/toxicity
Hepatic Encephalopathy
*Learning/drug effects
Feces/microbiology
*Liver Diseases/microbiology/drug therapy
Disease Models, Animal
Anti-Bacterial Agents/pharmacology

@article {pmid41038906,
year = {2025},
author = {Yang, I and He, X and Jeon, J and Claussen, H and Arthur, R and Cushenan, P and Weaver, SR and Luo, R and Black, M and Shannahan, J and Wright, C},
title = {The impact of vaping behavior on functional changes within the subgingival microbiome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34374},
pmid = {41038906},
issn = {2045-2322},
support = {1R56DE031814-01/DE/NIDCR NIH HHS/United States ; 1R56DE031814-01/DE/NIDCR NIH HHS/United States ; 1R56DE031814-01/DE/NIDCR NIH HHS/United States ; 1R56DE031814-01/DE/NIDCR NIH HHS/United States ; 1R56DE031814-01/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Vaping/adverse effects ; *Microbiota/drug effects ; Female ; Male ; Adult ; Electronic Nicotine Delivery Systems ; Volatile Organic Compounds/analysis ; Young Adult ; Adolescent ; Saliva/microbiology ; *Gingiva/microbiology ; Periodontal Diseases/microbiology/etiology ; },
abstract = {The use of Electronic Nicotine Delivery Systems (ENDS), or vaping devices, has raised concerns about their potential impact on oral health, particularly periodontal disease. While traditional smoking is a well-established risk factor for periodontal disease, the biological and microbial effects of ENDS use are less well understood. Our study examined how vaping and vaping behaviors influence the subgingival plaque microbiome and the associated metabolic pathways that may contribute to oral disease. We enrolled 70 healthy adults aged 18-35, including 48 regular ENDS users and 22 non-vaping controls. ENDS users were categorized by puffing behavior into low, medium, and high flow groups using a validated topography device. All participants underwent periodontal screening and provided saliva and subgingival plaque samples. To evaluate exposure profiles, ENDS users also submitted their personal devices for emissions testing, and volatile organic compounds (VOCs) were collected and analyzed using gas chromatography-mass spectrometry and high-performance liquid chromatography. Compared to non-vapers, ENDS users demonstrated distinct shifts in their oral microbiome, with reductions in beneficial taxa and increased bacteria associated with inflammation and periodontal disease. These changes were more pronounced in high-puff volume users, who also exhibited lower microbial diversity. Functional profiling revealed vaping-associated enrichment of pathways related to lipid metabolism, inflammation, and xenobiotic degradation. Untargeted salivary metabolomics identified metabolic disruptions consistent with these functional shifts. Integrative network analyses incorporating VOC measurements demonstrated correlations between microbial composition, puff volume, and metabolic disruptions, particularly in lipid-regulated and inflammatory pathways. To our knowledge, this is one of the first studies to integrate vaping behavior, oral microbiome profiling, salivary metabolomics, and VOC emissions analysis in a human cohort. These findings suggest ENDS use, especially at higher intensities, may disrupt oral microbial and metabolic homeostasis through both biological and chemical pathways potentially enhancing periodontal disease risk. These patterns point to potential biological and chemical pathways of concern, warranting further investigation and informing public health priorities.},
}

Humans
*Vaping/adverse effects
*Microbiota/drug effects
Female
Male
Adult
Electronic Nicotine Delivery Systems
Volatile Organic Compounds/analysis
Young Adult
Adolescent
Saliva/microbiology
*Gingiva/microbiology
Periodontal Diseases/microbiology/etiology

@article {pmid41038688,
year = {2025},
author = {Paz, HES and Stolf, CS and Bao, K and Monteiro, MF and Carvalho, LM and Silbereisen, A and Belibasakis, GN and Casarin, RCV and Bostanci, N},
title = {The Subgingival Host-Microbial Landscape in Mothers With Periodontitis and Their At-Risk Offspring.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70045},
pmid = {41038688},
issn = {1600-051X},
support = {2019/09740-3//São Paulo Research Foundation (FAPESP)/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brasil (CAPES)/ ; 88887.717561/2022-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brasil (CAPES)/ ; FoUI-966140//Steering Group KI/Region Stockholm for Dental Research (SOF)/ ; FoUI-978687//Steering Group KI/Region Stockholm for Dental Research (SOF)/ ; },
abstract = {AIM: To evaluate the subgingival proteome and microbiome of mothers with periodontitis and their offspring, thereby assessing signatures of periodontal diseases.

METHODS: Forty participants in four groups were included: mothers with periodontitis and their offspring, as well as periodontally healthy mothers and their offspring. Periodontal clinical parameters were assessed. Gingival crevicular fluid (GCF) and subgingival biofilm were collected from the same sites. Proteome from GCF was investigated by liquid chromatography-tandem mass spectrometry with data-independent acquisition (DIA-PASEF). Bacterial DNA from subgingival biofilms was sequenced using the 16S rRNA gene for taxonomy assignment.

RESULTS: Overall, 6147 bacterial and human proteins (≥ 2 peptides) were quantified. Despite the absence of attachment loss, the offspring of mothers with periodontitis presented with similar proteotypes as their mothers, characterised by up-regulation of inflammatory response cascades and down-regulation of epithelial barrier proteins. They also displayed higher colonisation patterns by periodontopathogens while presenting with increased expression of bacterial virulence proteins compared with controls.

CONCLUSION: The study showed that the maternal periodontal microbiome and proteome associate with those of the offspring and relate to maternal periodontal status. These early ecological events may potentially promote offspring's susceptibility to dysbiosis and may predispose them to periodontitis.},
}

@article {pmid41038565,
year = {2025},
author = {Habiba, U and Noor, M and Kayani, MUR and Huang, L},
title = {Horizontal gene transfers differentially shape the functional potential of the infant gut metagenome.},
journal = {Life sciences},
volume = {},
number = {},
pages = {124006},
doi = {10.1016/j.lfs.2025.124006},
pmid = {41038565},
issn = {1879-0631},
abstract = {Horizontal gene transfer (HGT) is a major driver of microbial evolution, influencing the metabolic potential of microbial communities. Despite its significance, the consequences of HGT in shaping the microbial metabolic potential remain poorly understood, particularly in complex environments such as the human gut. This study aimed to assess the impact of HGT in infant gut microbiome from Caesarean section (CSD) and vaginal delivery (VD) groups during the first year of life. At Month 0, CSD infants exhibited a higher number of HGT events than VD infants. However, the numbers converged around Month 2 and remained comparable until Month 9, with no significant differences between groups (p > 0.05). HGT in VD was primarily driven by Coprococcus catus and Ruminococcus sp_5_1_39BFAA, while in CSD, Salmonella enterica and Klebsiella pneumoniae were dominant donors and acceptors. Functional analysis revealed that HGT in VD enriched genes related to carbohydrate metabolism and immune responses, whereas CSD was enriched for metabolic processes and biofilm formation. Additionally, HGT events were associated with Neonatal Intensive Care Unit Admission and diet transitions. These results suggest that HGT events in the VD and CSD groups differently shape the functional potential of the infant gut microbiome, with possible health implications that require further investigation. However, experimental validation is needed to establish a causal link.},
}

@article {pmid41038555,
year = {2025},
author = {Guo, C and Zhang, S and Zhang, H and Chen, L and Gao, S and Xu, M and Shi, H and Zhu, J},
title = {Per- and Polyfluoroalkyl Substances (PFAS) Disrupt Gut Microbiome Composition and Metabolism in Metabolic Syndrome: Evidence from a Host-Free In Vitro Colonic Model.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127189},
doi = {10.1016/j.envpol.2025.127189},
pmid = {41038555},
issn = {1873-6424},
abstract = {Metabolic syndrome (MetS) is a global health concern linked to metabolic abnormalities and increased risk of type 2 diabetes and cardiovascular disease. Recent studies suggest that exposure to per- and polyfluoroalkyl substances (PFAS) may contribute to MetS through alterations in gut microbiota and metabolism, but the underlying mechanisms remain unclear. This study aimed to investigate the effects of PFAS exposure on gut microbiota composition and metabolism in MetS using a three-stage, automated, computer-controlled in vitro Human Colonic Model (HCM) system. We introduced PFAS exposure to the gut microbiome in vitro at two concentrations (100 ng/mL and 1000 ng/mL) and analyzed microbial community structure using microbiome analysis, while changes in gut microbial metabolism were assessed through targeted and untargeted metabolomics. Our results showed that PFAS exposure significantly altered gut microbiota composition, with notable changes in key genera such as Morganella and Bilophila. Metabolomics analysis revealed an increase in short-chain fatty acid (SCFA) production at 1000 ng/mL of PFAS exposure, as well as significant alterations in other metabolites, including decreased acetophenone and taurocholic acid in both concentrations. These findings suggest that PFAS exposure may disrupt gut microbiota homeostasis and contribute to metabolic disturbances associated with MetS. This study highlights the need for further investigation into the mechanisms underlying PFAS-induced alterations in gut microbiota and their potential impact on human health.},
}

@article {pmid41038411,
year = {2025},
author = {Taoum, C and Devaux, A and Rouanet, P and Colombo, PE and Boucher, D and Bonnet, M},
title = {Gut microbiota and chemoradiotherapy response in rectal cancer: biomarker opportunities.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {104974},
doi = {10.1016/j.critrevonc.2025.104974},
pmid = {41038411},
issn = {1879-0461},
abstract = {The gut microbiota is increasingly recognized as a key factor in rectal carcinogenesis. This review synthesizes current clinical and preclinical evidence linking specific microbial signatures, such as Fusobacterium nucleatum, Duodenibacillus massiliensis and colibactin-producing Escherichia coli (CoPEC) to chemoradiotherapy (CRT) treatment efficacy and resistance. Microbiota-driven mechanisms include immune modulation, inflammation, and drug metabolism. We highlight emerging microbial biomarkers and therapeutic strategies such as antibiotics, probiotics, and fecal microbiota transplantation. Integrating microbiome profiling into clinical workflows could refine patient stratification and enhance CRT efficacy in rectal cancer. Ongoing clinical trials aim to validate these associations and establish robust microbial biomarkers for CRT response prediction in rectal cancer.},
}

@article {pmid41038408,
year = {2025},
author = {Meng, L and Xie, H and Duan, X and Liang, X and Tang, X and Luo, H and Xiao, X and Li, Z},
title = {Temporal shifts and cross-site relationships of oral, gut, and vaginal microbiota during the third trimester of pregnancy.},
journal = {Genomics},
volume = {},
number = {},
pages = {111123},
doi = {10.1016/j.ygeno.2025.111123},
pmid = {41038408},
issn = {1089-8646},
abstract = {BACKGROUND: The maternal microbiome during pregnancy influences maternal and neonatal health, yet its dynamics and cross-site relationships in the third trimester remain unclear.

METHODS: Oral, fecal, and vaginal samples were collected from 22 healthy pregnant women and analyzed using 16S rRNA gene sequencing.

RESULTS: As pregnancy progressed, gut microbial richness significantly increased, while vaginal richness significantly declined. Source tracking showed that the majority of microbes originated from their respective niches, although low-level cross-site contributions were also observed. Correlation-based network analysis revealed complex associations among microbial communities across sites. The oral microbiome exhibited distinct relative contributions and network relationships to the gut and vaginal microbiomes. Moreover, some low-abundance genera (relative abundance <1 %) played a critical role in maintaining ecological balance compared to high-abundance genera.

CONCLUSIONS: This study demonstrates dynamic, site-specific microbial changes and highlights potential microbial connections across body sites during late pregnancy, offering new ecological insights relevant to maternal-fetal health.},
}

@article {pmid41038354,
year = {2025},
author = {Qing, Z and Haibei, H and Hanxue, Y and Juan, S},
title = {Mitigation of tetracycline resistance genes in silage through targeted lactic acid bacteria inoculation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133416},
doi = {10.1016/j.biortech.2025.133416},
pmid = {41038354},
issn = {1873-2976},
abstract = {The dissemination of antibiotic resistance genes (ARGs) in silage ecosystems poses a critical challenge to ecological stability and public health security. This investigation focuses on tetracycline resistance genes (TRGs), the most prevalent subtype of ARGs in silage, employing a targeted selection strategy for lactic acid bacteria (LAB) inoculants. From 226 isolated LAB strains, four candidates (LP1-3: Lactiplantibacillus plantarum; LC1: Lacticaseibacillus paracasei) demonstrating superior growth kinetics (OD600 > 1.6 within 24 h) and rapid acidification capacity (pH < 3.9 within 24 h) were selected. Strains LP3 and LC1 exhibited minimal intrinsic TRGs content. These four strains reduced (p < 0.001) pH, ammonia-N concentration, and coliform bacterial counts of stylo silage. Metagenomic analysis revealed that strains LP1-3 promoted Lactiplantibacillus dominance (0.709-0.975 vs. 0.379-0.509 in the control), while LC1 enhanced Lacticaseibacillus abundance (0.449-0.612 vs. 0.002-0.013 in the control). Ensiling process downregulated 367 and upregulated 227 ARGs. Inoculation with the four LAB strains further enhanced the suppression of ARGs. Among the top 30 TRGs, 22 were reduced by strains LP1-3 and 20 by LC1. Quantitative PCR results showed that strains LP1-3 decreased (p < 0.05) the contents of tetA and tetG during 30 days fermentation. Among the TRGs increased, tetA(60), tetB(58), tet(T) were positively correlated with Lactiplantibacillus spp., tetA(58), tetB(60), tetA(46), tetB(46), tet(43) were significantly correlated with Lacticaseibacillus spp. (R > 0.4, p < 0.001). In conclusion, the fermentation process induced substantial ARGs profile modifications, LAB-mediated microbiome engineering enables TRGs suppression, providing a scientific foundation for precision silage management strategies targeting antimicrobial resistance mitigation.},
}

@article {pmid41038332,
year = {2025},
author = {Zhang, Y and Liu, Y and Wei, Y and Ren, Z and Jin, YH and Li, G},
title = {The role of rare ginsenosides in the prevention and treatment of liver diseases.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {120666},
doi = {10.1016/j.jep.2025.120666},
pmid = {41038332},
issn = {1872-7573},
abstract = {Ginseng (Panax ginseng C. A. Mey.) is a traditional herb that occupies a very important position in traditional Chinese medicine (TCM). Many references have recorded the traditional application methods of ginseng and improve the effects of liver-blood insufficiency and chronic liver injury. Modern studies have found that rare ginsenosides are the key to their role and have therapeutic effects on a variety of liver diseases, further verifying their traditional applications.

AIM OF THIS REVIEW: This article reviews recent research advances on the structure, origin and pharmacological effects of rare ginsenosides to evaluate the preventive and therapeutic effects of rare ginsenosides on different types of liver diseases.

MATERIALS AND METHODS: This article utilized keywords like "Rare ginsenosides", "Source", "Drug-induced liver injury", "Metabolic dysfunction-associated fatty liver disease", "Liver fibrosis", "Hepatocellular carcinoma", and "Therapeutic interventions" to gather research on rare ginsenosides related to liver diseases from databases such as PubMed, Web of Science, and CNKI, up to February 2025. The collected information was then summarized and analyzed.

RESULTS: The structural characterization and preparation process of rare ginsenosides were clarified. In terms of pharmacological activities, rare ginsenosides possess a variety of activities, including anti-inflammatory, antioxidant, anti-tumor and immunomodulatory. In addition, rare ginsenosides showed protective effects against liver diseases through various mechanisms. However, their clinical application remains limited due to low content, poor water solubility, low oral bioavailability, and unclear mechanisms. Future efforts will accelerate translation through fermentation optimization, nanocarriers, structural modification, and microbiome research.

CONCLUSION: The multiple pharmacological activities of rare ginsenosides make them candidates for the treatment of various liver diseases and provide a broader direction for exploring the Chinese medicine treatment of liver diseases.},
}

@article {pmid41037885,
year = {2025},
author = {Goo, D and Lee, DJ and Kim, Y and Kim, WK},
title = {The effects of dietary levels of corn distillers dried grains with solubles and supplementation of valine and isoleucine on growth performance, intestinal health, and cecal microbiome in Ross 708.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {105910},
doi = {10.1016/j.psj.2025.105910},
pmid = {41037885},
issn = {1525-3171},
abstract = {The current study was conducted to investigate the effects of additional valine and isoleucine in a high corn distillers dried grains with solubles (DDGS) diet on growth performance, intestinal health, and cecal microbiome in broilers. A total of 800 0-d-old male Ross 708 were allocated into 5 dietary treatments with 8 replicates. The five diet groups were as follows: 1) corn-soybean meal (SBM)-based control (CON) group; 2) 15 % DDGS (15D) group (replacing corn and SBM with 15 % DDGS); 3) 15D + additional valine and isoleucine to have the same leucine:valine and leucine:isoleucine ratios as the CON group (15DB); 4) 30 % DDGS (30D) group; and 5) 30D + additional valine and isoleucine to have the same leucine:valine and leucine:isoleucine ratios as the CON group (30DB). The reduction in growth performance, carcass weight, breast muscle, and lean weight was intensified with increasing dietary DDGS levels. The 15DB group showed similar body weight gain (BWG) and carcass weight compared to the CON group. The 30DB group showed significant differences in phylum- and family-level cecal bacterial diversities compared to the 30D group but did not create significant growth improvement. No significant differences were observed in growth performance, carcass weight, body composition, intestinal morphology, jejunal gene expression levels, and alpha and beta diversity of cecal microbiota between the 15D and 15DB, and 30D and 30DB groups. Additional valine and isoleucine did not show consistent improvements in intestinal health and growth performance in DDGS-supplemented diets. The effect of additional valine and isoleucine varied depending on how much corn and SBM was replaced with DDGS in the diet, which may have been affected by additional factors other than intestinal health. In conclusion, additional valine and isoleucine may play a role in growth and muscle deposition but not have significant impact on the intestinal health in broiler diets that replaced corn and SBM with high levels of DDGS.},
}

@article {pmid41037883,
year = {2025},
author = {Park, JW and Kim, H and Choi, SA and Lee, HK and Shin, DH},
title = {Effects of patulin on quail muscle cells and the potential for microbiome-mediated recovery.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {105872},
doi = {10.1016/j.psj.2025.105872},
pmid = {41037883},
issn = {1525-3171},
abstract = {Mycotoxins pose a significant threat to livestock health and productivity by compromising immunity and inducing various toxicities. This study investigated the potential of specific Bacillus strains to mitigate mycotoxin-induced muscle damage in poultry cells. We treated quail muscle clone 7 (QM7) muscle cells with patulin, a common mycotoxin, to induce cellular injury. Subsequently, the damaged QM7 cells were treated with the candidate microbial strains, B. subtilis and B. velezensis. Our findings revealed that patulin treatment elevated stress-inducible gene expression and apoptosis markers, concurrently disrupting normal myoblast differentiation, as evidenced by altered expression patterns of Paired Box 7 (PAX7) and Myogenic Differentiation 1 (MyoD) and impaired myotube formation. Notably, treatment with the Bacillus strains significantly reduced these negative effects, reducing stress and apoptosis indicators while promoting a different pattern of myotube development. Although the exact mechanism of muscle recovery warrants further functional assessment, our results highlight the potential of B. subtilis and B. velezensis as agents for mitigating mycotoxin-induced damage in poultry, and offer novel strategies for enhancing animal health and agricultural sustainability.},
}

@article {pmid41037658,
year = {2025},
author = {Sun, W and Ma, L and Feng, X and Fan, Y and Cai, Y and Li, X},
title = {Efficacy of gut microbiota-based therapy for autism Spectrum Disorder and attention Deficit Hyperactivity Disorder: a systematic review and meta-analysis.},
journal = {Psychology, health & medicine},
volume = {},
number = {},
pages = {1-25},
doi = {10.1080/13548506.2025.2565181},
pmid = {41037658},
issn = {1465-3966},
abstract = {The gut-brain axis is an emerging therapeutic target for neurodevelopmental conditions such as Autism Spectrum Disorder (ASD) and Attention Deficit Hyperactivity Disorder (ADHD). However, the overall efficacy of gut microbiome-based interventions remains unclear. This systematic review and meta-analysis, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines, aimed to synthesize the evidence on these interventions. Fifteen randomized controlled trials (RCTs) were identified from 1,080 records across PubMed, Embase, Web of Science, Cochrane, PsycInfo, MEDLINE, and ClinicalTrials.gov through August 2024. Interventions included probiotics, prebiotics, dietary changes, and fecal transplants. Using random-effects models, pooled analysis showed a small but significant overall benefit of gut microbiota-based interventions (Standardized Mean Difference, SMD = -0.12; 95% Confidence Interval, CI: -0.19 to -0.04), with low heterogeneity (I[2] = 5.9%). Effects differed by disorder: ADHD demonstrated greater improvement (SMD = -0.24; 95% CI: -0.42 to -0.06; I[2] = 50.4%) compared to ASD (SMD = -0.05; 95% CI: -0.15 to 0.04; I[2] = 0%). Duration-specific effects emerged: 8-week interventions showed significant outcomes (SMD = -0.32; 95% CI: -0.58 to -0.06), while shorter or longer durations lacked significance. Acceptability analysis from eight studies revealed comparable dropout rates between intervention and control groups (ASD: Risk Ratio, RR = 1.002; ADHD: RR = 0.943), with no serious adverse events reported. Subgroup analyses identified participant age, diagnosis type, and geographic location as heterogeneity sources. Despite methodological limitations and small sample sizes, findings suggest gut microbiome modulation may offer a safe adjunctive therapy, particularly for ADHD, with optimal effects emerging at 8 weeks. The gut-brain axis appears promising for neurodevelopmental disorders, but current evidence remains preliminary. Future research should prioritize large-scale RCTs with standardized protocols, mechanistic investigations, and long-term follow-up to establish clinical guidelines and clarify biological pathways. Findings underscore the need to tailor interventions to specific disorders and optimize treatment duration.},
}

@article {pmid41037624,
year = {2025},
author = {Tsai, HH and Tang, Y and Jiang, L and Xu, X and Dénervaud Tendon, V and Pang, J and Jia, Y and Wippel, K and Vacheron, J and Keel, C and Andersen, TG and Geldner, N and Zhou, F},
title = {Localized glutamine leakage drives the spatial structure of root microbial colonization.},
journal = {Science (New York, N.Y.)},
volume = {390},
number = {6768},
pages = {eadu4235},
doi = {10.1126/science.adu4235},
pmid = {41037624},
issn = {1095-9203},
mesh = {*Plant Roots/microbiology/metabolism ; *Glutamine/metabolism ; Rhizosphere ; *Arabidopsis/microbiology/metabolism ; *Microbiota ; *Plant Exudates/metabolism ; Chemotaxis ; },
abstract = {Plant roots release exudates to encourage microbiome assembly, which influences the function and stress resilience of plants. How specific exudates drive spatial colonization patterns remains largely unknown. In this study, we demonstrate that endodermal Casparian strips-forming the root's extracellular diffusion barrier-restrict nutrient leakage into the rhizosphere, coinciding with and controlling spatial colonization patterns of rhizobacteria. We find that vasculature-derived glutamine leakage is a major bacterial chemoattractant and enhancer of proliferation, defining a previously unknown pathway for root exudate formation. Bacteria defective in amino acid chemoperception display reduced attraction toward leakage sites, and roots with Casparian strip defects display bacterial overproliferation, dependent on bacterial capacity for amino acid metabolization. Associated chronic immune stimulation suggests that endodermal nutrient restriction is crucial for regulating microbial colonization and assembly, limiting excessive proliferation that could compromise plant health.},
}

*Plant Roots/microbiology/metabolism
*Glutamine/metabolism
Rhizosphere
*Arabidopsis/microbiology/metabolism
*Microbiota
*Plant Exudates/metabolism
Chemotaxis

@article {pmid41037233,
year = {2025},
author = {Yamada, M and Kubo, M and Kaneshiro, K and Kai, M and Morisaki, T and Hayashi, S and Ochiai, Y and Sato, Y and Mizoguchi, K and Takao, Y and Arimura, A and Nakamura, M},
title = {Characterization of gut microbiota dysbiosis in breast cancer patients.},
journal = {Breast cancer (Tokyo, Japan)},
volume = {},
number = {},
pages = {},
pmid = {41037233},
issn = {1880-4233},
support = {JP21K19532//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: While lifestyle factors are known to be associated with breast cancer development, the potential role of the gut microbiome, which is influenced by lifestyle, as a risk factor is not well understood. We conducted a comparative analysis of the intestinal microbiota between healthy individuals and breast cancer patients to investigate the potential impact of gut microbiome composition on breast cancer development. This study aimed to explore the role of intestinal microbial communities in breast cancer pathogenesis.

METHODS: We conducted a comparative analysis of fecal 16S rRNA amplicon sequencing data from 100 individuals in the general population and 79 breast cancer patients. We investigated the differences between the two groups in terms of relative abundance, absolute quantity, diversity, and functionality of the gut microbiota.

RESULTS: Breast cancer groups showed higher levels of Firmicutes and lower levels of Bacteroidota at the phylum level, and an increase in Fusobacteriota was found in the human epidermal growth factor receptor 2 (HER2)-negative breast cancer group. Additionally, certain genera were more or less common in breast cancer groups at the genus level. The study also indicated lower gut microbiota diversity and loss of heterogeneity in breast cancer groups and reduced functional genes and pathways.

CONCLUSION: Compared to the general population, breast cancer patients exhibited a distinct dysbiosis in their gut microbiota. Further investigation is warranted to determine if this dysbiotic state, linked to a predicted downregulation of functional pathways critical for homeostasis, plays a role in breast cancer development.},
}

@article {pmid41037094,
year = {2025},
author = {Wadop, YN and Bernal, R and Njamnshi, WY and Satizabal, CL and Beiser, A and Ruiz, A and Njamnshi, AK and Vasan, RS and Seshadri, S and Himali, JJ and Fongang, B},
title = {Altered gut microbiota mediates the association between APOE genotype and amyloid-β accumulation in middle-aged adults.},
journal = {Journal of neurology},
volume = {272},
number = {10},
pages = {670},
pmid = {41037094},
issn = {1432-1459},
support = {AG059421/AG/NIA NIH HHS/United States ; AG054076/AG/NIA NIH HHS/United States ; AG049607/AG/NIA NIH HHS/United States ; AG033090/AG/NIA NIH HHS/United States ; AG066524/AG/NIA NIH HHS/United States ; P30 AG066546/AG/NIA NIH HHS/United States ; 5P30AG059305-03/AG/NIA NIH HHS/United States ; RF1 AG061729A1/AG/NIA NIH HHS/United States ; 5U01AG052409-04/AG/NIA NIH HHS/United States ; UG3AG090675)/AG/NIA NIH HHS/United States ; NINDS (NS017950/AG/NIA NIH HHS/United States ; UF1NS125513/AG/NIA NIH HHS/United States ; K01NS126489/AG/NIA NIH HHS/United States ; P30AG066546//South Texas Alzheimer's Disease Research Center/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Middle Aged ; *Amyloid beta-Peptides/metabolism ; *Apolipoprotein E4/genetics ; *Apolipoproteins E/genetics ; *Dysbiosis/metabolism/microbiology/genetics ; *Alzheimer Disease/genetics/metabolism/microbiology ; Aged ; Genotype ; *Brain/metabolism ; },
abstract = {BACKGROUND: The apolipoprotein E (APOE) ε4 allele is the strongest genetic risk factor for Alzheimer's disease, yet the mechanisms linking APOE to amyloid-β (Aβ) pathology remain incompletely understood. Emerging evidence suggests that the gut microbiome may modulate neurodegeneration; however, its role as a mediator in the APOE-Aβ relationship remains unclear.

OBJECTIVE: Evaluate whether specific microbial taxa mediate APOE-related effects on brain Aβ burden in a population-based study.

METHODS: This study involved 227 participants from the Framingham Heart Study with stool 16S rRNA sequencing and carbon-11 Pittsburgh Compound-B imaging for Aβ collected at the third examination (2016-2019). Associations between gut microbiota and global/regional Aβ deposition were assessed using multivariable models. We stratified participants by APOE ε4 status and conducted mediation analysis to evaluate whether specific taxa mediated APOE-related effects on Aβ. Microbial functional potential was inferred to examine enrichment of metabolic pathways.

RESULTS: Higher Aβ burden was significantly associated with the depletion of protective genera (e.g., Faecalibacterium, Ruminococcus, Butyricicoccus) and the enrichment of pro-inflammatory taxa (e.g., Alistipes, Bacteroides) and Barnesiella. These associations were more pronounced in APOE ε4 carriers, who exhibited a broader spectrum of microbial dysbiosis. Mediation analysis showed that Ruminococcus, Butyricicoccus, Clostridium, and Christensenellaceae collectively mediated ~ 0.3-0.4% of the effect of APOE ε4 on global Aβ burden. Functional profiling revealed a reduced abundance of microbial genes involved in key metabolic pathways among individuals with higher Aβ levels.

CONCLUSION: Gut microbiome composition mediates the deleterious effect of APOE ε4 on cerebral amyloid deposition, suggesting that microbiome-targeted interventions may mitigate APOE-related risk.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
Female
Middle Aged
*Amyloid beta-Peptides/metabolism
*Apolipoprotein E4/genetics
*Apolipoproteins E/genetics
*Dysbiosis/metabolism/microbiology/genetics
*Alzheimer Disease/genetics/metabolism/microbiology
Aged
Genotype
*Brain/metabolism

@article {pmid41037066,
year = {2025},
author = {Scott, CM and Holman, DB and Gzyl, KE and Ibe, A and Taheri, AE},
title = {Production Systems and Age Influence Fecal Mycobiota Diversity and Composition in Swine.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {104},
pmid = {41037066},
issn = {1432-184X},
mesh = {Animals ; *Feces/microbiology ; Swine/microbiology ; *Fungi/classification/genetics/isolation & purification ; *Animal Husbandry/methods ; *Gastrointestinal Microbiome ; *Mycobiome ; Biodiversity ; DNA, Fungal/genetics ; Age Factors ; Female ; },
abstract = {The gut microbiome is an important factor in animal health and can be influenced by factors such as age, diet, stress, environmental conditions, and farming practices. Bacterial communities of the gut microbiome in many species have been extensively studied, but research on the fungal microbiota remains limited and underrepresented in the literature. The objective of this study was to characterize the fecal mycobiota of swine raised under two different production systems: outdoor pasture-based or conventional indoor systems. Fecal samples from nursery, growing-finishing, and sow pigs from both farming systems were collected, and the mycobiota was profiled using PCR amplification and sequencing of the universal fungal internal transcribed spacer 1 (ITS1) region. A significant difference in fungal community structure was observed between the conventionally raised and pasture-raised pigs, as well as among all three production phases. Four species, Arthrographis kalrae, Enterocarpus grenotii, Pseudallescheria angusta, and Sagenomella oligospora, were differentially abundant between the two farms, all of which had higher relative abundance in the pasture-raised pigs. Additionally, pasture-raised pigs hosted a more diverse fungal community with higher species richness in their gastrointestinal tract. In summary, farming practices and pig age influenced the pig fecal mycobiota.},
}

Animals
*Feces/microbiology
Swine/microbiology
*Fungi/classification/genetics/isolation & purification
*Animal Husbandry/methods
*Gastrointestinal Microbiome
*Mycobiome
Biodiversity
DNA, Fungal/genetics
Age Factors
Female

@article {pmid41036865,
year = {2025},
author = {Smith, S and Ciesielski, M and Clerkin, T and Ben-Horin, T and Noble, RT},
title = {Farmed oyster mortality follows consistent Vibrio community reorganization.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0107825},
doi = {10.1128/msystems.01078-25},
pmid = {41036865},
issn = {2379-5077},
abstract = {Mortality events in marine bivalves cause substantial economic losses in aquaculture, yet the microbial dynamics underlying these events remain poorly characterized. Here, we investigated succession patterns in oyster-associated Vibrio communities during mortality events by sampling eastern oysters (Crassostrea virginica) at a North Carolina commercial farm that has experienced repeated, unexplained mortality events. Through whole-genome sequencing of 110 Vibrio isolates from 26 oysters sampled across mortality events in two consecutive years, we identified six conserved phylogenetic clades with distinct temporal associations. Vibrio mediterranei and a clade of resident vibrios consistently dominated the initial cultured community at the onset of mortality. However, V. mediterranei was absent as mortality progressed, coinciding with increased abundance of V. harveyi, V. alginolyticus, V. diabolicus, and V. agarivorans. Comparative genomic analysis revealed that initial isolates were enriched in pathways associated with host colonization and complex carbon metabolism, while isolates from elevated mortality showed enrichment in virulence mechanisms and adaptation to degraded host tissues. Temporal separation between genetically distinct clades suggests microbial competition shapes community assembly during mortality events that ultimately reached >85% mortality in both years. This predictable succession from commensal to potentially pathogenic Vibrio species provides genome-level insight into microbial community dynamics during oyster mortality. The consistent loss of V. mediterranei prior to severe mortality suggests this species could serve as a bioindicator for early warning systems to mitigate economic losses in shellfish aquaculture.IMPORTANCEMortality events in aquaculture systems represent complex host-microbe-environment interactions that challenge our ability to predict and prevent disease. By characterizing succession patterns in oyster-associated Vibrio communities at whole-genome resolution, we reveal a consistent transition from metabolically versatile species associated with healthy oysters to functionally distinct Vibrio taxa enriched in virulence factors and tissue degradation pathways as mortality progresses. This genome-level evidence for predictable community reorganization suggests that monitoring commensal Vibrio populations, particularly the presence or absence of Vibrio mediterranei, could provide earlier warning of impending disease compared to tracking only known pathogens. This shift in monitoring approach could advance aquaculture disease management while expanding our fundamental understanding of how microbial community transitions contribute to host health and disease progression.},
}

@article {pmid41036846,
year = {2025},
author = {Schlievert, PM and Brennan, PE and Klem, RE and Reardan, DT},
title = {Antifungal, antibacterial, and anti-inflammatory activity of glycerol dithionomonolaurate, an analog of glycerol monolaurate.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0031825},
doi = {10.1128/msphere.00318-25},
pmid = {41036846},
issn = {2379-5042},
abstract = {UNLABELLED: Glycerol dithionomonolaurate (NB2) is an analog of the natural antimicrobial compound glycerol monolaurate (GML) with enhanced antimicrobial activity. The advantage of NB2 over GML is the presence of a dithionate to greatly reduce microbial cleavage through glycerol ester hydrolases, such as Staphylococcus aureus lipase. NB2 exhibited antimicrobial activity against Candida fungal species, including Candida auris, with comparable minimum bactericidal concentration (MBC) and minimum inhibitory concentration (MIC) of 50-100 µg/mL compared to 250-500 µg/mL for GML. NB2 exhibited a broad range of antibacterial activity including both gram-positive and gram-negative organisms, while sparing normal microbiome lactobacilli. When 10[8] C. auris and 10[9] S. aureus were incubated on Todd Hewitt agar plates in the presence of two times the MBC for NB2, no resistant colonies grew, likely the result of the large number of antimicrobial targets inhibited. Like GML, NB2 inhibited exotoxin production at non-antibacterial concentrations. NB2 exhibited anti-staphylococcal activity when tested topically on a dermatitis skin model on rabbits. NB2 inhibited the production of chemokines (interleukin-8 and macrophage inflammatory protein-3α) by human vaginal epithelial cells, suggesting anti-inflammatory activity. Unlike clear GML solutions, NB2 was pale yellow. The absorption spectrum of NB2 was not sufficient to raise Food and Drug Administration concerns over phototoxicity. Collectively, the data suggest that NB2 could become a useful topical agent for the prevention of both fungal and bacterial infections as a dual-active anti-infective, killing microbes and reducing harmful inflammation, such as seen in atopic dermatitis.

IMPORTANCE: Fungi and many bacteria commonly develop resistance to antimicrobial agents or have inherent resistance. Many microbes initiate infections through the skin and mucous membranes, in part by producing toxins and causing harmful inflammation. We describe a novel topical antimicrobial agent, glycerol dithionomonolaurate (NB2), effective against Candida and a wide range of gram-positive and gram-negative bacteria; the compound did not kill normal microbiome lactobacilli. NB2 is likely to have many microbial targets for killing, suggesting resistance to the molecule may not develop. At sub-antibacterial concentrations, glycerol dithionomonolaurate inhibited exotoxin production by Staphylococcus aureus. The molecule was not inactivated by staphylococcal lipase. Glycerol dithionomonolaurate effectively treated S. aureus dermatitis in a rabbit skin model and reduced chemokine production by human epithelial cells. Glycerol dithionomonolaurate may prove useful to treat many types of skin and mucous membrane infections by both antimicrobial and anti-inflammatory activities, such as in atopic dermatitis.},
}

@article {pmid41036840,
year = {2025},
author = {Diaz, B and Krishna, R and Schoeniger, JS and Mageeney, CM},
title = {Exploring phage-host interactions in Burkholderia cepacia complex bacterium to reveal host factors and phage resistance genes using CRISPRi functional genomics and transcriptomics.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0193625},
doi = {10.1128/spectrum.01936-25},
pmid = {41036840},
issn = {2165-0497},
abstract = {Complex interactions of bacteriophages with their bacterial hosts determine phage host range and infectivity. While phage defense systems and host factors have been identified in model bacteria, they remain challenging to predict in non-model bacteria. In this paper, we integrate functional genomics and transcriptomics to investigate phage-host interactions, revealing active phage resistance and host factor genes in Burkholderia cenocepacia K56-2. Burkholderia cepacia complex species are commonly found in soil and are opportunistic pathogens in immunocompromised patients. We studied infection of B. cenocepacia K56-2 with Bcep176, a temperate phage isolated from Burkholderia multivorans. A genome-wide dCas9 knockdown library targeting B. cenocepacia K56-2 was constructed, and a pooled infection experiment identified 63 novel genes or operons coding for candidate host factors or phage resistance genes. The activities of a subset of candidate host factor and resistance genes were validated via single-gene knockdowns. Transcriptomics of B. cenocepacia K56-2 during Bcep176 infection revealed that expression of genes coding for host factor and resistance candidates identified in this screen was significantly altered during infection by 4 h post-infection. Identifying which bacterial genes are involved in phage infection is important to understand the ecological niches of B. cenocepacia and its phages, and for designing phage therapies.IMPORTANCEBurkholderia cepacia complex bacteria are opportunistic pathogens inherently resistant to antibiotics, and phage therapy is a promising alternative treatment for chronically infected patients. Burkholderia bacteria are also ubiquitous in soil microbiomes. To develop improved phage therapies for pathogenic Burkholderia bacteria, or engineer phages for applications, such as microbiome editing, it's essential to know the bacterial host factors required by the phage to kill bacteria, as well as how the bacteria prevent phage infection. This work identified 65 genes involved in phage-host interactions in Burkholderia cenocepacia K56-2 and tracked their expression during infection. These findings establish a knowledge base to select and engineer phages infecting or transducing Burkholderia bacteria.},
}

@article {pmid41036443,
year = {2025},
author = {Pang, A and Pu, S and Pan, Y and Huang, N and Li, D},
title = {Short-chain fatty acids from gut microbiota restore Th17/Treg balance in rheumatoid arthritis: Mechanisms and therapeutic potential.},
journal = {Journal of translational autoimmunity},
volume = {11},
number = {},
pages = {100316},
pmid = {41036443},
issn = {2589-9090},
abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune disorder characterized by synovial inflammation and joint destruction. Dysregulation of the Th17/Treg balance is a key immunological hallmark of RA. Emerging evidence highlights the critical role of gut microbiota-derived short-chain fatty acids (SCFAs) in maintaining immune homeostasis. This review systematically elucidates how SCFAs modulate the Th17/Treg equilibrium through three synergistic mechanisms: (1) metabolic reprogramming via AMPK/mTOR signaling, (2) epigenetic regulation by inhibiting HDAC, and (3) modulation of cytokine cascades. We integrate preclinical and clinical evidence showing that SCFAs reduce synovial inflammation by suppressing NLRP3 inflammasome activation, resulting in a 70 % decrease in IL-1β levels, while enhancing Treg suppressive function with a threefold increase in IL-10. Notably, butyrate exhibits circadian fluctuations that negatively correlate with morning stiffness severity (r = -0.82, p < 0.01), suggesting novel chronotherapeutic opportunities. Therapeutically, we evaluate promising microbiota-targeted strategies including high-fiber diets (which increase butyrate levels by 240 % and reduce Disease Activity Score 28 (DAS28) by 1.8 points), engineered nanoparticle delivery systems (achieving 89 % colonic retention), probiotic interventions (Bifidobacterium-mediated reduction of CCR9-positive Th17 cells), and precision combination therapies (showing a 40 % greater efficacy than monotherapy). Our work establishes a comprehensive translational roadmap, spanning molecular insights to clinical applications. We propose microbiome-guided personalized medicine as a paradigm shift in RA management, supported by the first systematic integration of multi-omics methods-metabolomics, single-cell sequencing, and spatial transcriptomics-to decode the gut-joint axis and identify actionable therapeutic targets for this refractory autoimmune condition.},
}

@article {pmid41036398,
year = {2025},
author = {Halane, H and McDowell, T and Dhaubhadel, S},
title = {Temporal sampling of root exudates using coated blade-SPME for decoding plant-pathogen interactions.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1616881},
pmid = {41036398},
issn = {1664-462X},
abstract = {Root exudates shape the rhizosphere and mediate plant-microbe interactions, yet traditional sampling techniques often disturb the natural environment. Here, we present the use of coated blade-solid-phase microextraction (CB-SPME) method for passive, non-invasive in situ temporal metabolomic profiling of pea (Pisum sativum) root exudates during infection by the soil-borne pathogen Aphanomyces euteiches. In comparison to previously established extraction techniques, CB-SPME delivered lower absolute recovery but superior reproducibility while maintaining sensitivity. This non-destructive approach preserves rhizosphere integrity, enabling continuous monitoring of dynamic metabolite fluctuations and offers new insights into how root exudate influences plant-microbiome interactions.},
}

@article {pmid41036226,
year = {2025},
author = {Li, T and Lu, Y and Yu, F and Zhong, Q and Meng, Y and Feng, Y and Hu, Y and Tian, X and Li, T and Shi, R},
title = {Aerobic exercise modalities on gut microbiome and skeletal muscle quality in ovariectomized mice.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1634934},
pmid = {41036226},
issn = {2235-2988},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Muscle, Skeletal/physiology ; Female ; Ovariectomy ; Mice, Inbred C57BL ; *Physical Conditioning, Animal ; RNA, Ribosomal, 16S/genetics ; Estrogens/blood ; Mice ; DNA, Ribosomal/chemistry/genetics ; Estradiol/blood ; Aromatase/metabolism ; Sequence Analysis, DNA ; },
abstract = {OBJECTIVE: This study aimed to investigate the effects of aerobic exercise on skeletal muscle quality, gut microbiota composition, and estrogen levels in ovariectomized (OVX) mice, and to elucidate the potential underlying mechanisms, thereby providing experimental evidence for exercise intervention in postmenopausal women.

METHODS: Adult female C57BL/6J mice were randomly assigned to four groups (n = 6 per group): Sham, OVX, Sham+ET, and OVX+ET. After 6 weeks of recovery, the exercise groups received 8 weeks of treadmill training. Muscle morphology, function, and protein metabolism pathways were assessed using histology, grip tests, and Western blotting. Aromatase and estrogen levels were evaluated by immunofluorescence and ELISA. Gut microbiota composition was analyzed via 16S rRNA sequencing and correlated with muscle function.

RESULTS: Eight weeks of aerobic exercise significantly improved skeletal muscle mass, fiber cross-sectional area, and grip strength in OVX mice, and reduced fatigue index compared to OVX controls. Immunofluorescence revealed increased aromatase expression and intramuscular E2 levels following exercise, with no significant difference in serum estradiol. Western blot analysis indicated activation of the Akt/mTOR/p-S6 pathway and inhibition of FOXO3-mediated protein degradation. 16S rRNA sequencing showed that exercise increased α-diversity (Shannon and Simpson indices) and altered microbial community structure, as shown by distinct clustering in PCoA plots. At the genus level, exercise modulated the relative abundance of several bacterial taxa. Spearman correlation analysis demonstrated that microbial diversity indices were positively associated with lean mass and fatigue resistance.

CONCLUSION: Aerobic exercise significantly improves muscle mass and function in ovariectomized mice, potentially through a combined mechanism involving regulation of protein metabolism, enhancement of local estrogen synthesis, and modulation of gut microbiota composition.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Muscle, Skeletal/physiology
Female
Ovariectomy
Mice, Inbred C57BL
*Physical Conditioning, Animal
RNA, Ribosomal, 16S/genetics
Estrogens/blood
Mice
DNA, Ribosomal/chemistry/genetics
Estradiol/blood
Aromatase/metabolism
Sequence Analysis, DNA

@article {pmid41036149,
year = {2025},
author = {Huang, Z and Kaur Sekhon, V and Sadeghian, R and Vaida, ML and Jo, C and McCormick, BA and Ward, DV and Bucci, V and Haran, JP},
title = {ADAM-1: An AI Reasoning and Bioinformatics Model for Alzheimer's Disease Detection and Microbiome-Clinical Data Integration.},
journal = {IEEE access : practical innovations, open solutions},
volume = {13},
number = {},
pages = {145953-145967},
pmid = {41036149},
issn = {2169-3536},
abstract = {Alzheimer's Disease Analysis Model Generation 1 (ADAM-1) is a multi-agent reasoning large language model (LLM) framework designed to integrate and analyze multimodal data, including microbiome profiles, clinical datasets, and external knowledge bases, to enhance the understanding and classification of Alzheimer's disease (AD). By leveraging the agentic system with LLM, ADAM-1 produces insights from diverse data sources and contextualizes the findings with literature-driven evidence. A comparative evaluation with XGBoost revealed a significantly improved mean F1 score and significantly reduced variance for ADAM-1, highlighting its robustness and consistency, particularly when utilizing human biological data. Although currently tailored for binary classification tasks with two data modalities, future iterations will aim to incorporate additional data types, such as neuroimaging and peripheral biomarkers, and expand them to predict disease progression, thereby broadening ADAM-1's scalability and applicability in AD research and diagnostic applications.},
}

@article {pmid41035896,
year = {2025},
author = {Bautista, J and Echeverría, CE and Maldonado-Noboa, I and Ojeda-Mosquera, S and Hidalgo-Tinoco, C and López-Cortés, A},
title = {The human microbiome in clinical translation: from bench to bedside.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1632435},
pmid = {41035896},
issn = {1664-302X},
abstract = {The human microbiome, once regarded as a passive passenger, is now recognized as a dynamic and essential determinant of human physiology, shaping immunity, metabolism, neurodevelopment, and therapeutic responsiveness across the lifespan. Advances in multi-omic technologies, experimental models, and computational approaches have revealed mechanistic insights into how microbial communities modulate host systems across diverse body sites, including the gut, skin, lungs, oral cavity, and reproductive tract. The clinical translation of this knowledge has begun to redefine early-life programming, cardiometabolic regulation, immune homeostasis, neuropsychiatric resilience, and cancer therapy response. Innovative strategies such as phage therapy, live biotherapeutics, precision nutrition, and microbiota transplantation illustrate the therapeutic potential of harnessing microbial functions to prevent or treat disease. In parallel, large-scale initiatives cataloging the microbiome of underexplored niches, such as the vagina and skin, are advancing health equity by broadening representation in microbial reference datasets. Yet significant challenges persist, including interindividual variability, incomplete functional annotation of microbial "dark matter," and the absence of validated biomarkers. Addressing these gaps requires standardized methodologies, harmonized regulatory frameworks, and longitudinal studies across diverse populations. This review outlines the progress and remaining hurdles in translating microbiome science into clinical practice and concludes that the microbiome now stands at the forefront of a paradigm shift, transforming concepts of disease etiology, therapeutic design, and the future of individualized medicine.},
}

@article {pmid41035891,
year = {2025},
author = {Lawore, DC and Jena, S and Berard, AR and Birse, K and Lamont, A and Mackelprang, RD and Noel-Romas, L and Perner, M and Hou, X and Irungu, E and Mugo, N and Knodel, S and Muwonge, TR and Katabira, E and Hughes, SM and Levy, C and Calienes, FL and Hladik, F and Lingappa, JR and Burgener, AD and Green, LN and Brubaker, DK},
title = {Computational microbiome pharmacology analysis elucidates the anti-cancer potential of vaginal microbes and metabolites.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1602217},
pmid = {41035891},
issn = {1664-302X},
abstract = {The vaginal microbiome's role in risk, progression, and treatment of female cancers has been widely explored. Yet, there remains a need to develop methods to understand the interaction of microbiome factors with host cells and to characterize their potential therapeutic functions. To address this challenge, we developed a systems biology framework we term the Pharmacobiome for microbiome pharmacology analysis. The Pharmacobiome framework evaluates similarities between microbes, microbial byproducts, and known drugs based on their impact on host transcriptomic cellular signatures. Here, we apply our framework to characterization of the Anti-Gynecologic Cancer Vaginal Pharmacobiome. Using published vaginal microbiome multi-omics data from the Partners PrEP clinical trial, we constructed vaginal epithelial gene signatures associated with each profiled vaginal microbe and metabolite. We compared these microbiome-associated host gene signatures to post-drug perturbation host gene signatures related to 35 FDA-approved anti-cancer drugs from the Library of Integrated Network-based Cellular Signatures database to identify vaginal microbes and metabolites with high statistical and functional similarity to these drugs. We found that select lactobacilli particularly L. crispatus and their metabolites, such as taurine, can regulate host gene expression in ways similar to certain anti-cancer drugs. Additionally, we experimentally tested our model prediction that taurine, a metabolite produced by L. crispatus, kills cancerous breast and endometrial cancer cells. Our study shows that the Pharmacobiome is a robust framework for characterizing the anti-cancer therapeutic potential of vaginal microbiome factors with generalizability to other cancers, microbiomes, and diseases.},
}

@article {pmid41035890,
year = {2025},
author = {Giner-Pérez, L and Gallego, JJ and Gimènez-Garzó, C and Batallas, D and Jarquín-Díaz, VH and Casanova-Ferrer, F and Fiorillo, A and Urios, A and Martínez-Medina, JN and López-Gramaje, A and Arenas, YM and Escudero-García, D and Benlloch, S and Salvador, A and Felipo, V and Forslund-Startceva, SK and Pérez Martínez, G and Montoliu, C},
title = {The analysis of the gut microbiome during liver disease progression led to the identification of biomarkers for related mild cognitive impairment.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1670512},
pmid = {41035890},
issn = {1664-302X},
abstract = {INTRODUCTION: Although it is well established that liver disease is associated with alterations in the gut microbiome (GM), the mechanisms linking these microbial changes to the progression of liver disease-and more critically, to its related cognitive impairment-remain poorly understood. Therefore, to define biomarkers for the early and advanced phases of these conditions, it is necessary to gain insight into changes in the GM throughout the evolution of the disease, particularly regarding the early onset of cognitive decline.

METHODS: The GM taxonomy and function profiles were defined, data were collected for dietary intake, fecal short-chain fatty acids (SCFA), cognitive status, quality of life and biochemical and immunological blood parameters of patients belonging to different stages of liver disease (MASLD and cirrhosis) and cognitive function.

RESULTS: This study showed: 1) the fibrosis stage severity (F1 to F4) in liver disease was associated with reduced GM diversity independently of cognitive status and with a decline in beneficial autochthonous bacteria; 2) Streptococcus mutans and Allisonella histaminiformans could serve as potential biomarkers for NAFLD-associated mild cognitive impairment; 3) bacterial metabolic functions involved in sugar degradation and the breakdown of tryptophan and glutamate were downregulated and linked to CXCL13 plasma levels and neuroinflammation; 4) correlations between SCFA concentrations disappeared with liver disease and cognitive impairment.

CONCLUSION: In this context, maintaining a balanced production of fecal SCFA is more important than individual concentrations. The downregulation of specific microbial metabolic pathways, along with the presence of certain bacterial species, holds promise as early-stage biomarkers and highlights the potential of microbiome-targeted strategies for monitoring and managing liver-related cognitive impairment.},
}

@article {pmid41035886,
year = {2025},
author = {Tayyab, M and Zhao, Y and Zhang, Y},
title = {Microbiome engineering to enhance disease resistance in aquaculture: current strategies and future directions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1625265},
pmid = {41035886},
issn = {1664-302X},
abstract = {Aquaculture, a cornerstone of global food security, faces critical threats from disease outbreaks, antimicrobial resistance, and ecological disruption. Through a narrative analysis of over 160 studies, this review synthesizes advances in microbiome engineering-a sustainable approach to enhancing disease resistance in aquatic animals-addressing key gaps: the inconsistent efficacy of conventional probiotics and prebiotics under field conditions, and the need for climate-resilient solutions. Critically, we highlight the emergence of precision microbiome engineering as a transformative paradigm. We integrate findings from genomics, metabolomics, clustered regularly interspaced short palindromic repeats, and artificial intelligence to identify microbial strategies that enhance host resilience. Genomic and multi-omics methods reveal health-associated microbes and metabolites, such as Vibrio-dominated dysbiosis markers in shrimp and butyrate-mediated immunity. Guided by these biomarkers, we describe precision-tailored probiotics-host-derived or genome-edited Bacillus subtilis strains whose adhesion factors, metabolic outputs (e.g., butyrate, bacteriocins), and heat stress tolerance are matched to the target species' gut niche. These are combined with complementary prebiotics (e.g., chitosan oligosaccharides) and synbiotics (e.g., Lactiplantibacillus plantarum plus king oyster mushroom extracts) that suppress pathogens through competitive exclusion and immune modulation. Ecologically rational innovations-interventions explicitly grounded in ecological theory (niche complementarity, K-selection) to stabilize resource-efficient microbiomes-such as fecal microbiota transplantation and synthetic consortia, demonstrate further disease control potential. Our synthesis reveals that translating microbiome engineering from laboratory to farm requires overcoming host-microbiome compatibility challenges and ecological risks. Policy alignment with the United Nations Sustainable Development Goals-Zero Hunger (Sustainable Development Goal 2), Climate Action (Sustainable Development Goal 13), and Life Below Water (Sustainable Development Goal 14)-is critical for sustainable adoption.},
}

@article {pmid41035851,
year = {2025},
author = {Wang, W and Tang, B and Yuan, S and Luan, H and Qi, T and Chen, J},
title = {Plasma metabolites mediate the causal relationship between gut microbiota and erectile dysfunction: insights from Mendelian randomization study.},
journal = {Sexual medicine},
volume = {13},
number = {5},
pages = {qfaf076},
pmid = {41035851},
issn = {2050-1161},
abstract = {BACKGROUND: While the relationship between gut microbiota and erectile dysfunction (ED) has been reported, the specific pathways involved remain unclear.

AIM: This study aims to investigate the causal relationship between gut microbiota and ED, and to identify the potential role of plasma metabolites as mediators.

METHODS: Utilizing aggregated genome-wide association study (GWAS) data, a comprehensive two-sample Mendelian randomization (MR) analysis was performed involving 196 gut microbiota taxa, 1400 plasma metabolites and ED. Causal relationships between gut microbiota, plasma metabolites and ED were explored. In addition, mediation analysis was applied to identify the pathway from gut microbiota to ED mediated by plasma metabolites.

OUTCOMES: This study reveals that plasma metabolites act as mediators regulating the influence of gut microbiota on ED.

RESULTS: MR analysis identified causal relationships between six gut microbial taxa and ED, with Butyrivibrio increasing the risk of ED, while Alistipes, Prevotella 9, Dialister, Marvinbryantia, and LachnospiraceaeUCG010 exhibited protective effects. Additionally, 45 plasma metabolites demonstrated causal associations with ED. Finally, mediation analysis revealed four mediation relationships. Sensitivity analysis indicated no heterogeneity or pleiotropy in this study.

CLINICAL IMPLICATIONS: Modulating gut microbiota or targeting specific metabolites may offer new therapeutic approaches for ED, highlighting the potential for microbiome-based interventions.

STRENGTHS AND LIMITATIONS: The MR approach and large-scale GWAS data provide robust causal evidence, but the findings are limited by their focus on European populations and lack of experimental validation. Further studies are needed to confirm these mechanisms in diverse cohorts and functional models.

CONCLUSION: This study establishes a causal link between gut microbiota, plasma metabolites, and ED, identifying specific microbial taxa and metabolites as key contributors to ED risk. The mediating role of plasma metabolites highlights potential therapeutic strategies, such as probiotics or dietary interventions targeting harmful metabolites.},
}

@article {pmid41035682,
year = {2025},
author = {Jin, S and Wijerathne, CUB and Siow, YL and O, K},
title = {Disruption of the transsulfuration pathway by acute kidney injury causes intestinal damage.},
journal = {iScience},
volume = {28},
number = {10},
pages = {113511},
pmid = {41035682},
issn = {2589-0042},
abstract = {Acute kidney injury (AKI) impairs intestinal function through oxidative stress. The transsulfuration pathway is essential for sulfur amino acid metabolism and antioxidant defense through glutathione biosynthesis. This study investigated how AKI caused intestinal injury and the mechanisms involved. AKI was induced in Sprague-Dawley rats through kidney ischemia (45 min)-reperfusion (24 h). AKI decreased intestinal glutathione (antioxidant) levels and compromised intestinal barrier function. Glutathione biosynthesis in mammals requires cysteine made through the reverse transsulfuration pathway, catalyzed by cystathionine beta-synthase (CBS) and cystathionine gamma-lyase (CSE). AKI decreased the expression of these enzymes in intestinal epithelium. AKI also altered gut microbiota composition and the expression of bacterial enzymes in the forward transsulfuration pathway, which could disrupt intestinal antioxidant defense. The inhibition of this pathway in gut epithelial cells reduced glutathione levels and tight junction protein expression. These results suggest that the disruption of the transsulfuration pathway impairs antioxidant defense, leading to intestinal barrier damage and dysbiosis in AKI.},
}

@article {pmid41035679,
year = {2025},
author = {Hagihara, M and Yamashita, M and Ariyoshi, T and Minemura, A and Yoshida, C and Higashi, S and Oka, K and Takahashi, M and Ota, A and Maenaka, A and Iwasaki, K and Hirai, J and Shibata, Y and Umemura, T and Mori, T and Kato, H and Asai, N and Mikamo, H},
title = {Clostridium butyricum-altered lung microbiome is associated with enhanced anti-influenza effects via G-protein-coupled receptor120.},
journal = {iScience},
volume = {28},
number = {10},
pages = {113502},
pmid = {41035679},
issn = {2589-0042},
abstract = {We previously reported that orally administered Clostridium butyricum enhances anti-influenza virus effects through the interferon-λ upregulation in mice lungs; however, the precise mechanism remains unclear. Orally administered C. butyricum promotes the proliferation of Bifidobacterium species in the lung microbiome, and this enhances C. butyricum induced anti-influenza effects. Among the Bifidobacterium species, B. longum effectively enhanced the sensitivity of the lung epithelial cells to long-chain fatty acids through the G-protein-coupled receptor120 upregulation. Oral administration of C. butyricum altered long-chain fatty acid metabolism and promoted interferon-λ production through G-protein-coupled receptor120. We hypothesized that these effects enhance anti-influenza virus responses through interferon-λ upregulation via collaboration between long-chain fatty acid metabolism alterations and the lung microbiome moderation. This study identified a gut-lung axis mechanism and provides insights into viral respiratory infection treatment and prophylaxis.},
}

@article {pmid41035652,
year = {2025},
author = {Kalopedis, EA and Zorgani, A and Zinovkin, DA and Barri, M and Wood, CD and Pranjol, MZI},
title = {Leveraging the role of the microbiome in endometriosis: novel non-invasive and therapeutic approaches.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1631522},
pmid = {41035652},
issn = {1664-3224},
mesh = {Humans ; *Endometriosis/therapy/microbiology/immunology/diagnosis/metabolism/etiology ; Female ; *Gastrointestinal Microbiome/immunology ; Dysbiosis/therapy/immunology/microbiology ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Animals ; Lactobacillus ; Biomarkers ; },
abstract = {Endometriosis (EMS) is an oestrogen-dependent condition characterised by ectopic endometrial-like tissue growth with a chronic and inflammatory nature leading to severe symptoms and reduced quality of life. Emerging evidence implicates gut microbiome dysbiosis in EMS pathogenesis, driving chronic inflammation, immune dysfunction, and altered bacterial taxa within patient gut microbiome. This review examines the intricate relationship between gut dysbiosis and EMS, with a focus on immunomodulatory mechanisms and the downstream consequences of the bacterial contamination theory. It evaluates recent findings regarding microbial imbalances and microbial diversity, pinpointing gaps in current research that mandate further understanding. For example, while microbial markers like Lactobacillus depletion and elevated Escherichia coli have been observed in patients, their diagnostic potential remains poorly defined. Additionally, it addresses the broader implications of EMS, including its physical, mental and healthcare burdens. Simultaneously, critiquing current drawbacks in diagnostic and therapeutic strategies such as their invasiveness and limited efficacy. The review further evaluates novel microbiome-based strategies namely Lactobacillus-based probiotics and faecal microbiota transplantation (FMT), assessing their potential in modulating immune responses and alleviating EMS symptoms while considering associated challenges. Lastly, it highlights the emerging role of metabolomics in identifying non-invasive and diagnostic biomarkers like short-chain fatty acids (SCFAs), implicated in the interplay between microbial metabolites and immune signalling pathways in EMS.},
}

Humans
*Endometriosis/therapy/microbiology/immunology/diagnosis/metabolism/etiology
Female
*Gastrointestinal Microbiome/immunology
Dysbiosis/therapy/immunology/microbiology
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Animals
Lactobacillus
Biomarkers

@article {pmid41035504,
year = {2025},
author = {Olaguez-Gonzalez, JM and Chairez, I and Breton-Deval, L and Alfaro-Ponce, M},
title = {In-silico assessment of dynamic symbiotic microbial interactions in a reduced microbiota related to the autism spectrum disorder symptoms.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {4078-4088},
pmid = {41035504},
issn = {2001-0370},
abstract = {The gut microbiota plays a crucial role in human health, with growing evidence linking its composition to the development of Autism Spectrum Disorder. However, inconsistencies in previous studies have hindered the identification of a definitive microbial signature associated with Autism Spectrum Disorder. Machine learning models have emerged as powerful tools for analyzing microbiome data, yet their interpretability remains limited. In this study, we integrate in silico simulations with machine learning predictions to explore microbial interactions under different dietary conditions and provide biological context to features of the intestinal microbiota that are linked to Autism Spectrum Disorder. This study employs constraint-based modeling to simulate metabolic exchanges among key bacterial taxa in order to assess their ecological relationships. Findings reveal that high-fiber diets foster mutualistic and balanced interactions, whereas Western-style diets promote competitive and parasitic dynamics, potentially contributing to gut dysbiosis in Autism Spectrum Disorder. In addition, the presence of oxygen (a factor associated with colonocyte permeability, a pathological condition of the colon) significantly alters microbial interactions, influencing metabolic dependencies and the overall structure of the community. This integrative approach enhances the interpretability of machine learning-based Autism Spectrum Disorder classifiers, bridging computational predictions with mechanistic insights. By identifying diet-dependent microbial interactions, our study highlights potential dietary interventions to modulate the composition of the gut microbiota in Autism Spectrum Disorder. These findings underscore the value of combining in silico modeling and machine learning for unraveling complex microbiome-host relationships and improving Autism Spectrum Disorder biomarker identification.},
}

@article {pmid41035378,
year = {2025},
author = {Zhang, Q and Cui, J and Hou, Y and Guo, L and Li, H and Zhou, G and Wang, X and Zhu, B and Shi, K and Zhang, Y and Bi, Y and Li, Y and Sun, L and Feng, Y and Yuan, J and Wang, X},
title = {Alterations in Gut Microbiota and Metabolism in Cirrhotic Portal Hypertension: Implications for Disease Progression.},
journal = {Alimentary pharmacology & therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.70392},
pmid = {41035378},
issn = {1365-2036},
support = {7232272//the Beijing Municipal Natural Science Foundation/ ; BJZYYB-2023-06//the Beijing Traditional Chinese Medicine Technology Development Fund Project/ ; 81774234//the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Although gut microbiota has been implicated in various liver disorders, its relationship with cirrhotic portal hypertension (CPH) remains unclear.

AIMS: To investigate the structural and functional alterations of gut microbiota in patients with CPH and the potential role of these alterations in the progression of CPH.

METHODS: We collected faecal samples from 35 patients with CPH and 71 patients without CPH (controls) to conduct microbiome and metabolomic analyses. Gut microbes, faecal metabolites and their functional pathways associated with CPH were identified using multiple bioinformatics approaches. To understand the role of gut microbiota in the pathogenesis of CPH, we carried out faecal microbiota transplantation, CPH-characteristic bacterial transplantation and antibacterial experiments in mice.

RESULTS: Microbial diversity was diminished, and gut microbial structures were altered in patients with CPH compared to the controls, primarily manifested as increased abundance of lipopolysaccharide-producing bacteria and decreased abundance of anti-inflammatory bacteria. This dysbiosis of gut microbiota was accompanied by changes in the faecal metabolome, particularly in arginine biosynthesis and nitric oxide production. Transplantation of gut microbiota from CPH patients, as well as the transplantation of CPH-associated bacteria Veillonella nakazawae, was found to exacerbate CPH progression in mice. Antibiotic treatment significantly alleviated the CPH progression induced by N-dimethylnitrosamine in mice.

CONCLUSIONS: Our study reveals that gut microbiota dysbiosis is implicated in CPH progression, potentially providing new avenues for microbiome-based treatment for CPH.},
}

@article {pmid41035209,
year = {2025},
author = {Gong, Y and Kramer, EM and Liao, IT and Roy, R},
title = {Nectar, the original cocktail: an introduction to a Virtual Issue.},
journal = {The New phytologist},
volume = {248},
number = {3},
pages = {1101-1104},
doi = {10.1111/nph.70585},
pmid = {41035209},
issn = {1469-8137},
}

@article {pmid41035107,
year = {2025},
author = {Kawano, K and Kawabe, K and Sano, Y and Hori, T and Kihara, M and Kikuchi, Y and Itoh, H},
title = {Wild gut microbiome suppresses the potentially opportunistic pathogen Aeromonas in medaka under domesticated rearing conditions.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {98},
pmid = {41035107},
issn = {2524-4671},
support = {JP15K21660//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: The gut microbiome plays a crucial role in the metabolic health and pathogen resistance of various host animals. It is also well established that external environmental factors can influence the gut microbiome, leading to differences in its composition. However, the functional implications of these differences remain poorly understood. This study examined the gut microbiome of medaka (Oryzias latipes species complex) by comparing domesticated and wild populations, with the aim of gaining insights into the functional significance of their specific characteristics, particularly those of the wild-type microbiome.

RESULTS: For the comparative analysis of the gut microbiome, 48 domesticated and 122 wild medaka were collected from multiple laboratories, pet stores and streams across Japan. The results showed that wild medaka exhibited significantly higher gut microbiome diversity, with a broader range of bacterial members. In contrast, the gut microbiome of domesticated medaka harbored lower microbial diversity and was consistently dominated by Aeromonas, a typical opportunistic pathogen in fish. Additionally, 88.6% of Aeromonas isolates from domesticated medaka exhibited haemolytic activity. Moreover, a domesticated rearing experiment with wild populations showed no proliferation or dominance of Aeromonas in their gut, as observed in domesticated medaka. A further rearing experiment revealed that pre-exposing antibiotic-treated medaka to sediments from their natural habitats prevented Aeromonas colonisation, even when reared under domesticated conditions.

CONCLUSIONS: These findings suggest that the habitat-derived wild gut microbiome can inhibit Aeromonas proliferation in domesticated fish, highlighting its potential to mitigate opportunistic diseases in aquaculture.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00462-4.},
}

@article {pmid41035034,
year = {2025},
author = {Shimogama, T and Tahara, T and Shijimaya, T and Yamazaki, J and Kobayashi, S and Nakamura, N and Takahashi, Y and Tomiyama, T and Honzawa, Y and Fukui, T and Naganuma, M},
title = {Gastric microbiome in gastric cancer sequence depicts diverse microbial structures associated with cancer risk and prognosis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1039},
pmid = {41035034},
issn = {1479-5876},
support = {22K08089//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Stomach Neoplasms/microbiology/pathology/genetics ; Prognosis ; Female ; Male ; Middle Aged ; Risk Factors ; DNA Methylation/genetics ; Mutation/genetics ; Gastric Mucosa/microbiology/pathology ; *Gastrointestinal Microbiome ; Aged ; *Microbiota ; Tumor Suppressor Protein p53/genetics ; *Stomach/microbiology ; },
abstract = {OBJECTIVE: Increasing evidence indicated substantial involvement of non-Helicobacter pylori microbiota in gastric tumorigenesis. We aimed to elucidate detailed relationship of microbiome dynamics between two different steps in gastric cancer (GC) such as cancer initiation and progression, and assessed their associations with clinicopathological and molecular changes.

METHODS: We systemically characterized gastric microbiome during GC initiation and progression using 944 biopsies from primary GC, non-cancerous gastric mucosa from both GC and non-cancer subjects. The association between specific microbial characteristics and GC risk, prognosis and molecular changes such as TP53 mutation, DNA methylation and telomere shortening were also evaluated.

RESULTS: Microbial α-diversity in the gastric mucosa was decreased in relation to the GC occurrence, while it increased in primary GC tissue. Such paradoxical change was also observed in specific groups of bacteria during GC occurrence and its progression. GC risk-related microbiome was associated with differentiated GC, severe intestinal metaplasia, associated DNA methylation and telomere shortening, while GC tissue-specific microbiome was associated with more aggressive features of GC and TP53 mutation status.

CONCLUSIONS: Our findings suggested the different role of non-Helicobacter pylori microbiota in GC initiation and progression steps.},
}

Humans
*Stomach Neoplasms/microbiology/pathology/genetics
Prognosis
Female
Male
Middle Aged
Risk Factors
DNA Methylation/genetics
Mutation/genetics
Gastric Mucosa/microbiology/pathology
*Gastrointestinal Microbiome
Aged
*Microbiota
Tumor Suppressor Protein p53/genetics
*Stomach/microbiology

@article {pmid41035022,
year = {2025},
author = {Durif, C and Denis, S and Lemoine, N and Deschamps, C and Uriot, O and Brun, M and Guillou, D and Blanquet-Diot, S},
title = {A new in vitro model of the adult pig colon microbiome: application to the study of feed ingredients.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {100},
pmid = {41035022},
issn = {2524-4671},
abstract = {BACKGROUND: There is an intricate relationship between pig nutrition and gut microbiome. For technical, cost and societal reasons, in vitro gut models can be advantageously used as an alternative to in vivo experiments to perform mechanistic studies on the interactions between gut microbes and nutrients. In this context, the aim of the present study was to develop a new in vitro model of the healthy adult pig colon integrating both luminal and mucosal microenvironments. The model was further used to evaluate feed ingredients (lactose and lactose + sucrose). Gut Microbiota composition and metabolic activities were followed by 16S Metabarcoding and short chain fatty acid (SCFA) / gas measurement, respectively. Then, the effect of the both feedstuffs on skatole production, responsible for boar taint in male pigs, was also investigated.

RESULTS: Based on in vivo data, the new MPigut-IVM was set-up to reproduce the main physicochemical (pH, transit time, self-maintained anaerobiosis), nutritional (composition of ileal effluents, bile salts) and microbial (lumen and mucus-associated microbiota) parameters of the large intestine in healthy adult pigs. The model was validated through in vitro-in vivo comparisons regarding SCFA concentrations and bacterial profiles at the phylum and family levels. Lactose and lactose + sucrose had no significant impact on SCFAs but increased gas production (P < 0.01 with lactose). Both sugars, particularly lactose + sucrose, tended to reduce skatole concentrations while increasing indole levels (P > 0.05). This was associated to a slight reduction of the numbers of skatole-producing bacteria Olsenella scatoligenes (P > 0.05). Both feed ingredients induced a decrease in bacterial α-diversity (P < 0.05).

CONCLUSION: Despite obvious limitations such as lack of host interactions, the adult MPigut-IVM represents a powerful platform for Microbiome studies in the pig colonic environment. In Line with the 3R regulations, this in vitro model can be useful to perform preliminary screening of innovative feed strategies to improve pig health and help to elucidate their mechanisms of action in relation with gut microbiota, taking into account inter-individual variabilities.},
}

@article {pmid41034963,
year = {2025},
author = {Lewis, ZJ and Scott, A and Madden, C and Vik, D and Zayed, AA and Smith, GJ and Justice, SS and Rudinsky, A and Hokamp, J and Hale, VL},
title = {Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {199},
pmid = {41034963},
issn = {2049-2618},
support = {Canine Intramural Grant//College of Veterinary Medicine, Ohio State University/ ; DBI 20222070//National Science Foundation/ ; 1K08ES034821-01A1/NH/NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; Animals ; Dogs ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Humans ; Metagenome ; *Microbiota/genetics ; DNA, Bacterial/genetics ; *Urinary Tract/microbiology ; *Urine/microbiology ; Gastrointestinal Microbiome/genetics ; },
abstract = {BACKGROUND: The gut microbiome has emerged as a clear player in health and disease, in part by mediating host response to environment and lifestyle. The urobiome (microbiota of the urinary tract) likely functions similarly. However, efforts to characterize the urobiome and assess its functional potential have been limited due to technical challenges including low microbial biomass and high host cell shedding in urine. Here, to begin addressing these challenges, we evaluate urine sample volume (100 ml-5 mL) and host DNA depletion methods and their effects on urobiome profiles in healthy dogs, which are a robust large animal model for the human urobiome. We collected urine from seven dogs and fractionated samples into aliquots. One set of samples was spiked with host (canine) cells to model a biologically relevant host cell burden in urine. Samples then underwent DNA extraction followed by 16S rRNA gene and shotgun metagenomic sequencing. We then assembled metagenome-assembled genomes (MAGs) and compared microbial composition and diversity across groups. We tested six methods of DNA extraction: QIAamp BiOstic Bacteremia (no host depletion), QIAamp DNA Microbiome, Molzym MolYsis, NEBNext Microbiome DNA Enrichment, Zymo HostZERO, and propidium monoazide.

RESULTS: In relation to urine sample volume, ≥ 3.0 mL resulted in the most consistent urobiome profiling. In relation to host depletion, individual (dog) but not extraction method drove overall differences in microbial composition. DNA Microbiome yielded the greatest microbial diversity in 16S rRNA sequencing data and shotgun metagenomic sequencing data and maximized MAG recovery while effectively depleting host DNA in host-spiked urine samples. As proof-of-principle, we then mined MAGs for select metabolic functions including central metabolism pathways and environmental chemical degradation.

CONCLUSIONS: Our findings provide guidelines for studying the urobiome in relation to sample volume and host depletion and lay the foundation for future evaluation of urobiome function in relation to health and disease. Video Abstract.},
}

*Metagenomics/methods
Animals
Dogs
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Humans
Metagenome
*Microbiota/genetics
DNA, Bacterial/genetics
*Urinary Tract/microbiology
*Urine/microbiology
Gastrointestinal Microbiome/genetics

@article {pmid41034842,
year = {2025},
author = {Areloegbe, SE and Abugu, IA and Ajadi, IO and Aturamu, A and Ajadi, MB and Atuma, CL and Akintayo, CO and Omoruyi, GO and Onyekweli, SO and Badejogbin, OC and Amusa, OA and Adelekan, OE and Ajayi, K and Oyewole, PA and Olaniyi, KS},
title = {Probiotics mitigates ovarian angiogenic disturbance in letrozole-induced PCOS.},
journal = {BMC complementary medicine and therapies},
volume = {25},
number = {1},
pages = {346},
pmid = {41034842},
issn = {2662-7671},
mesh = {Animals ; Female ; Letrozole ; *Probiotics/pharmacology ; *Polycystic Ovary Syndrome/chemically induced/drug therapy ; Rats, Wistar ; Rats ; *Ovary/blood supply/drug effects ; Disease Models, Animal ; Vascular Endothelial Growth Factor A/metabolism ; *Neovascularization, Pathologic ; },
abstract = {BACKGROUND: Among metabolic/endocrine diseases affecting women in the reproductive years, polycystic ovarian syndrome (PCOS) is well documented as the leading cause of female infertility and several complications including dyslipidemia, cardiomorbidities, among others. Vascular endothelial growth factor (VEGF) is a proangiogenic marker which plays crucial roles in endothelial dysfunction, including ovarian dysfunction. Probiotics are gut microbiome that regulate metabolic health via epigenetic modulation of histone. Nevertheless, the present study was designed to investigate the beneficial effect of probiotics on aberrant ovarian angiogenesis in a PCOS rat model.

MATERIALS AND METHODS: Eight-week-old female Wistar rats were divided into four groups (n = 5). The administration of 1 mg/kg (p.o) letrozole for three weeks induced PCOS. thereafter the animals were treated with 3 × 10[9] CFU (p.o) from probiotics for six weeks.

RESULTS: The rats that received letrozole exhibited obesity, ovarian weight gain, hyperandrogenism, hypoestrogenism, and multiple ovarian cysts and demonstrated an increased level of anti-Mullerian hormone. Animals in this group also demonstrated ovarian triglyceride accumulation, inflammation, lipid peroxidation, elevated corticosterone as a parameter that show metabolic stress and elevated angiogenic factor (VEGF). Also, a decreased level of antioxidant defense (NrF2), and HIF-1a and a significant decrease in mitofusin 2 (Mfn2) was observed while histone deacetylase 2 (HDAC2) was significantly elevated when compared to the control group. Interestingly, treatment with probiotics significantly reversed these ovarian metabolic, biochemical and morphological changes.

CONCLUSION: Collectively, the present result suggests that probiotics ameliorates aberrant ovarian angiogenesis with subsequent improvement of ovarian function in PCOS model. This beneficial effect of probiotics is accompanied by modulation of Mfn2 and suppression of HDAC2.},
}

Animals
Female
Letrozole
*Probiotics/pharmacology
*Polycystic Ovary Syndrome/chemically induced/drug therapy
Rats, Wistar
Rats
*Ovary/blood supply/drug effects
Disease Models, Animal
Vascular Endothelial Growth Factor A/metabolism
*Neovascularization, Pathologic

@article {pmid41034730,
year = {2025},
author = {Selvaraj, VK and Patel, JS and Hui, JPM and Zhang, J and Berrué, F and Prithiviraj, B},
title = {Ascophyllum nodosum based plant biostimulant shapes the bacterial community in the rhizosphere of corn.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1263},
pmid = {41034730},
issn = {1471-2229},
mesh = {*Zea mays/microbiology/drug effects ; *Rhizosphere ; Plant Roots/microbiology ; *Ascophyllum/chemistry ; Pseudomonas/drug effects/physiology/genetics ; *Microbiota/drug effects ; Soil Microbiology ; *Plant Exudates/pharmacology ; },
abstract = {BACKGROUND: Plant biostimulants are an emerging class of agricultural inputs known to enhance plant growth and improve their tolerance to abiotic stress. While biostimulants are widely used, their mechanisms of action remain poorly understood. This study investigates the effects of an Ascophyllum nodosum-based biostimulant (ANE) on the rhizosphere bacterial communities of corn (Zea mays).

RESULTS: Root exudates from ANE root-treated plants promoted the swarming motility of Pseudomonas protegens (CHA0), a plant growth-promoting rhizobacterium. Gene expression analysis showed that root exudates from 0.01% ANE-treated plants up-regulated P. protegens CHA0 genes associated with chemotaxis (cheW, cheV), pyoverdine (pvdS), pyrrolnitrin (prnD), and hydrogen cyanide (hcnA) biosynthesis compared to controls. ANE also significantly altered rhizosphere microbiome composition, increasing the abundance of genera such as Chryseolinea, Pseudoxanthomonas, Novosphingobium, Quadrisphaera, Turneriella, and Kitasatospora. Liquid chromatography-high resolution mass spectrometry (LC-HRMS) and partial least squares-discriminant analysis (PLS-DA) revealed distinct chemical profiles in the root extracts of ANE-treated plants. Specifically, ANE increased the concentrations of benzoxazinoids, including 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) and 6-methoxybenzoxazolinone (MBOA) in maize roots by approximately 1.4-fold and 1.76-fold, respectively.

CONCLUSION: Overall, these findings suggest that ANE modifies the rhizosphere microbiome by influencing the chemical composition of both root tissue and root exudates.},
}

*Zea mays/microbiology/drug effects
*Rhizosphere
Plant Roots/microbiology
*Ascophyllum/chemistry
Pseudomonas/drug effects/physiology/genetics
*Microbiota/drug effects
Soil Microbiology
*Plant Exudates/pharmacology

@article {pmid41034705,
year = {2025},
author = {Bruscadin, JJ and Cardoso, TF and Conteville, LC and da Silva, JV and Ibelli, AMG and Pena, GAC and Porto, T and de Oliveira, PSN and Andrade, BGN and Zerlotini, A and Regitano, LCA},
title = {HolomiRA: a reproducible pipeline for miRNA binding site prediction in microbial genomes.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {236},
pmid = {41034705},
issn = {1471-2105},
support = {2022/06281-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2019/04089-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2019/04089-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 456191/2014-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {*MicroRNAs/metabolism/genetics ; Binding Sites ; *Software ; Humans ; Animals ; *Computational Biology/methods ; Cattle ; *Genome, Microbial ; *Genome, Bacterial ; },
abstract = {BACKGROUND: Small RNAs, such as microRNAs (miRNAs), are candidates for mediating communication between the host and its microbiota, regulating bacterial gene expression and influencing microbiome functions and dynamics. Here, we introduce HolomiRA (Holobiome miRNA Affinity Predictor), a computational pipeline developed to predict target sites for host miRNAs in microbiome genomes. HolomiRA operates within a Snakemake workflow, processes microbial genomic sequences in FASTA format using freely available bioinformatics software and incorporates built-in data processing methods. The pipeline begins by annotating protein-coding sequences from microbial genomes using Prokka. It then identifies candidate regions, evaluates them for potential host miRNA binding sites and the accessibility of these target sites using RNAHybrid and RNAup software. The predicted results that meet the quality filter parameters are further summarized and used to perform a functional analysis of the affected genes using SUPER-FOCUS software.

RESULTS: In this paper, we demonstrate the use of the HolomiRA pipeline by applying it to publicly available metagenome-assembled genomes obtained from human feces, as well as from bovine feces and ruminal content. This approach enables the prediction of bacterial genes and biological pathways within microbiomes that could be influenced by host miRNAs. It also allows for the identification of shared or unique miRNAs, target genes, and taxonomies across phenotypes, environments, or host species.

CONCLUSIONS: HolomiRA is a practical and user-friendly pipeline designed as a hypothesis-generating tool to support the prediction of host miRNA binding sites in prokaryotic genomes, providing insights into host-microbiota communication mediated by miRNA regulation. HolomiRA is publicly available on GitHub: https://github.com/JBruscadin/HolomiRA .},
}

*MicroRNAs/metabolism/genetics
Binding Sites
*Software
Humans
Animals
*Computational Biology/methods
Cattle
*Genome, Microbial
*Genome, Bacterial

@article {pmid41034666,
year = {2025},
author = {},
title = {Gut microbiota keeps watch over future egg cells.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41034666},
issn = {1476-4687},
}

@article {pmid41034647,
year = {2025},
author = {Salas, AA and Stewart, CJ and Young, GR},
title = {Early gut microbiome composition of very preterm infants randomised to receive human milk volumes of 60 ml/kg/day or more within the first 36 hours after birth.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {41034647},
issn = {1530-0447},
abstract = {BACKGROUND: Early and increased exposure to human milk combined with minimal exposure to parenteral nutrition could reduce hospitalisation costs, improve postnatal growth, and influence the diversity of the gut microbiome.

METHODS: Faecal samples from very preterm infants randomised to receive either 60 to 80 ml/kg/day (intervention group) or 20 to 30 ml/kg/day (control group) of human milk within the first 36 h after birth were collected at approximately postnatal day 14. After trial completion, samples were analysed by 16S rRNA gene sequencing to determine early differences in the gut microbiome between the randomisation groups using adjusted models.

RESULTS: We analysed faecal samples from 95 infants with a median gestational age of 31 weeks (mean birthweight: 1487 g). In adjusted analyses, taxonomic richness and Shannon alpha diversity were not significantly higher in the intervention group. No significant differences in microbial diversity composition between samples (i.e., beta diversity) were found. Four distinctive de novo community clusters were identified during the trial, but they did not differ according to randomisation groups.

CONCLUSION: Early and increased exposure to human milk shortly after birth does not appear to increase the richness and diversity of the gut microbiome by postnatal day 14 in very preterm infants.

TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT04337710 IMPACT: In very preterm infants, early and increased exposure to human milk and its bioactive components did not alter gut microbiome richness or diversity by postnatal day 14. Randomisation strengthens microbiome analyses by limiting confounding in human milk feeding trials.},
}

@article {pmid41000896,
year = {2025},
author = {Dillard, BA and Sanders, JG and Husain, AP and Yule, KM and Moeller, AH},
title = {Isolation by distance promotes strain diversification in the wild mouse gut microbiota.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41000896},
issn = {2692-8205},
abstract = {Bacterial species within the mammalian gut microbiota exhibit considerable strain diversity associated with both geography and host genetic ancestry. However, because geography and host ancestry are typically confounded, disentangling their contributions to the diversification of gut bacterial strains has remained challenging. Here, we show through joint profiling of gut bacterial and mitochondrial genomes from wild-living populations of deer mice (Peromyscus maniculatus) sampled across the United States that isolation by distance (IBD) drives gut bacterial strain diversification independently of the effects of host ancestry. Analyses revealed significant IBD in 27 predominant gut bacterial species, including members of the Muribaculaceae and Lachnospiraceae, but limited evidence for co-inheritance of gut bacterial genomes with mitochondria during the diversification of extant mouse populations. Gut bacterial species capable of forming spores exhibited reduced IBD independently of phylogenetic history, indicating that adaptations facilitating bacterial dispersal can mitigate the geographic structuring of strain diversity. These results show that the diversification of gut bacterial strains within rodent species has been mediated by geographic separation of host populations rather than host genealogical divergence.},
}

@article {pmid41034629,
year = {2025},
author = {Brown, JL and Johnston, W and Butcher, MC and Burleigh, M and Ramage, G},
title = {The butterfly effect: collateral damage and impacts of antimicrobial strategies on the oral microbiome.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {84},
pmid = {41034629},
issn = {2731-8745},
support = {BB/V509541/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/V509541/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {The oral cavity is a complex environment hosting diverse microbial biofilms on different surfaces, all immersed in saliva that enables recolonisation and spread. These microbial populations fluctuate with diet, hygiene, antimicrobials, and disease. While biofilm control measures aim to protect health, they may cause unintended effects, including antimicrobial resistance (AMR). Persistent resistant microbes reshape oral and systemic niches through ecological disruption and genetic adaptation, which may negatively impact human health.},
}

@article {pmid41034550,
year = {2025},
author = {Low, JM and Gupta, A and Toh, R and Lim, SL and Chan, SY and Swarup, S and Lee, LY},
title = {Vertical Transmission of Gut Dysbiosis From Mothers With Gestational Diabetes to Infants.},
journal = {Journal of diabetes},
volume = {17},
number = {10},
pages = {e70148},
doi = {10.1111/1753-0407.70148},
pmid = {41034550},
issn = {1753-0407},
support = {NUS DBS R-154-Rb77-133//National University of Singapore (NUS)'s Institute for Health Innovation & Technology (iHealthtech)/ ; NUHSRO/2020/077/MSC/02/SB//NUS Medicine Synthetic Biology Translational Research Program/ ; NCSP2.0/2023/PVO/LJM//NUHS Clinician Scientist program, Singapore/ ; MOH-RTF23jan-0004/MOH-001381-00//National Medical Research Council (NMRC), Singapore, Research Training Fellowship/ ; },
abstract = {BACKGROUND: Vertical transmission of microbes from a mother's gut to their offspring plays a crucial role in the genesis of the early life gut microbiome. Gestational Diabetes Mellitus (GDM) is the commonest metabolic disorder during pregnancy, which has adverse short- and long-term effects on both maternal and infant health. We aimed to capture the GDM-associated biosignatures in infants' gut microbiome from birth to the first 6 weeks of life.

METHODS: 53 GDM mother-infant dyads and 16 healthy mother-infant dyads were recruited. We performed targeted 16S rRNA gene amplicon sequencing on stool samples. Various statistical analyses were performed to understand the changes in the microbiome profile of infants and identify GDM-associated bacterial biomarkers in mothers and their transfer to infants.

RESULTS: GDM altered the gut microbiome of pregnant women as compared to healthy counterparts (PERMANOVA, p.adjusted < 0.05), with predominance of bacterial members associated with insulin resistance, proinflammatory conditions, and other metabolic processes. Infants born to GDM mothers have distinctive early life microbiome (meconium and six weeks stools) compared to infants born to control mothers (PERMANOVA, p.adjusted < 0.05). We also identified the presence of various GDM-associated microbial signatures such as Blautia and Collinsella in both meconium and one-month-old stool samples of infants born to GDM mothers.

CONCLUSION: This study provides a better understanding of the impact of GDM on the seeding of a specific set of microbes during the early life colonization event in the infant gut that increases the risk of inflammatory and metabolic diseases in the future.},
}

@article {pmid41034461,
year = {2025},
author = {Łętocha, A and Michalczyk, A and Bielecka, E and Kantyka, T and Miastkowska, M and Sikora, E},
title = {Skin microbiome friendly topical formulations containing probiotic - loaded alginate microspheres: in vitro studies.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34246},
pmid = {41034461},
issn = {2045-2322},
}

@article {pmid41033907,
year = {2025},
author = {Embleton, ND and van den Akker, CHP and Alshaikh, BN},
title = {Probiotic supplementation - does it prevent or cause neonatal sepsis?.},
journal = {Seminars in fetal & neonatal medicine},
volume = {},
number = {},
pages = {101668},
doi = {10.1016/j.siny.2025.101668},
pmid = {41033907},
issn = {1878-0946},
abstract = {Probiotic supplementation in preterm infants is one of the most extensively studied interventions in neonatal medicine, with over 50 randomised controlled trials. This paper examines the relationship between probiotic supplementation and late onset sepsis (LOS), considering mechanistic pathways, clinical evidence, and safety profile. Multiple systematic reviews and meta-analyses consistently show that probiotics reduce necrotising enterocolitis (NEC) incidence and all-cause mortality in preterm infants, establishing them as one of the most beneficial interventions in neonatology. Current evidence suggests modest effects on LOS, with Cochrane systematic reviews reporting relative risk 0.89 (95 % CI 0.82-0.97) but with low certainty. Mechanisms supporting LOS reduction include competitive pathogen exclusion, enhanced epithelial barrier function, improved immune responses, and reduced time to full enteral feeding with decreased intravenous access requirements. The safety profile of probiotics is reassuring, with serious adverse events being exceptionally rare. Probiotic-induced sepsis probably occurs in less than 0.5 % of treated infants, representing a very low risk that must be weighed against the likely substantial benefits for NEC and mortality reduction. Product contamination and other quality issues exist but appear manageable with appropriate quality control. Given the robust evidence for NEC and mortality reduction, probiotics represent a valuable intervention for preterm infants but may have limited, if any impact on sepsis. While their specific role in LOS prevention and impacts on the resistome requires further investigation, the overall benefit-risk profile strongly favors their use. Future research will further refine understanding of optimal strain selection and implementation strategies for maximizing clinical benefits while maintaining safety.},
}

@article {pmid41033906,
year = {2025},
author = {Ommert, I and Mägi, CA and Lilliesköld, S and Blomqvist, YT and Axelin, A and Linnér, A},
title = {The role of parents to prevent infections in the neonatal intensive care unit.},
journal = {Seminars in fetal & neonatal medicine},
volume = {},
number = {},
pages = {101669},
doi = {10.1016/j.siny.2025.101669},
pmid = {41033906},
issn = {1878-0946},
abstract = {Late onset sepsis is a major cause of morbidity and mortality in the neonatal intensive care unit, and it is frequently acquired from the environment. Infant- and family-centered developmental care, which involves skin-to-skin contact, breastfeeding and continuous parental participation in the care, is an effective infection prevention strategy. Kangaroo mother care, including skin-to-skin contact supports the development of a diverse skin microbiome, distinct from that of the hospital environment. Breastmilk further contributes to infection prevention and immune system development through multiple mechanisms. Parental involvement may improve the safety and quality of care delivery by hospital staff. In summary, parents play an important role in infection prevention in the neonatal intensive care unit. The risks of not including parents in the care of their infants should be further considered both in research and clinical practice.},
}

@article {pmid41033689,
year = {2025},
author = {Li, K and Li, T and Liu, Y and Zou, B and Geng, G and Xu, Y and Liu, J and Wang, Y},
title = {Decoding Rhizosphere Synergies: Pseudomonas and Bacillus Enhance Microbiome-Mediated Suppression of Rhizoctonia solani in Sugar Beet.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-05-25-0159-R},
pmid = {41033689},
issn = {0031-949X},
abstract = {Sugar beet is a crucial sugar crop with substantial economic and nutritional value. The occurrence of damping-off disease severely impacts sugar beet quality and yield. Here, we successfully isolated two endophytes from sugar beet, and it follow as Bacillus albus SB-3 and Pseudomonas chlororaphis SB-35, via morphological observation and molecular identification. Both SB-3 and SB-35 exhibited nitrogen-fixing and potassium mobilization capabilities, with SB-35 demonstrating additional traits including phosphate solubilization, potassium mobilization. SB-3 and SB-35 promoted the growth of sugar beet, resulting in increased biomass, and improved soil available nutrient. Besides, SB-3 and SB-35 had also extracellular protease activities and inhibited the mycelium growth of Rhizoctonia solani. In independent pot experiments, SB-3 and SB-35 exhibited significantly controlling the damping-off of seedlings for sugar beet. Further analysis indicated that SB-3 and SB-35 may alter microbial community structure, reducing the abundance of Rhizoctonia solani, promoting the recruitment of beneficial microorganisms, such as Hypocrea, Peziza, and Talaromyces, to occupy ecological niches, thereby reducing the numbers of pathogen. The two bacterial strains modulated the diversity and community structure of rhizosphere microorganisms, suggesting a microbiome-mediated mechanism underlying their host-beneficial effects. This study advances our understanding of harnessing endophytes to enhance sugar beet productivity and suppressing sugar beet damping-off caused by Rhizoctonia solani.},
}

@article {pmid41033626,
year = {2025},
author = {Kong, F and Guan, DX and Lu, L and Lu, S and Xu, J and Wang, H},
title = {Multi-element amendment reshaped rhizosphere microbiome: A microbially driven Fe/Mn/S synergistic action for Cd immobilization.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122985},
doi = {10.1016/j.envres.2025.122985},
pmid = {41033626},
issn = {1096-0953},
abstract = {Cadmium (Cd) contamination in soils threatens rice safety, necessitating effective remediation strategies. While the silicon-calcium-magnesium amendment (FSY) is known to reduce Cd bioavailability, its precise microbial mechanisms remain underexplored. This study integrated metagenomics and machine learning to investigate FSY's impact on the rice rhizosphere microbiome and to elucidate the biological drivers of Cd immobilization. FSY application and rice growth stage were the core factors that significantly reshaped bacterial and archaeal community structures, shifting archaeal community assembly toward deterministic processes, while the fungal community remained relatively stable. Co-occurrence network analysis revealed that FSY enhanced the complexity and stability of microbial interactions, strengthening the roles of key functional taxa. Crucially, functional profiling showed that FSY significantly upregulated genes related to multi-barrier systems: (1) iron/manganese oxidation (e.g., feoB) associated with iron-manganese plaque (IP) formation; (2) sulfate reduction (e.g., dsrA) linked to cadmium sulfide (CdS) precipitation; and (3) microbial Cd resistance (e.g., the czcA gene). Machine learning identified 14 core species, including key taxa in Campylobacterota and Thermoproteota, as the pivotal drivers of synergistic Fe/Mn/S-Cd interaction. These findings substantiated the microbially driven Fe/Mn/S synergistic model for Cd immobilization through three interconnected mechanisms: enhanced microbially mediated mineral fixation (IP thickening and CdS precipitation), and strengthened community-level Cd resistance. This research provided a deep mechanistic understanding of how chemical amendments induced microbial functions to mitigate heavy metal risks, thereby offering a scientifically-grounded strategy for remediation and safe use of Cd-contaminated field.},
}

@article {pmid41033577,
year = {2025},
author = {Dai, X and Chen, Y and Fang, S},
title = {Impact of Fidaxomicin on the Microbiome in Pediatric Clostridioides Difficile Infection: Proposal of a Microbiota-Sparing Metric.},
journal = {The Journal of pediatrics},
volume = {},
number = {},
pages = {114842},
doi = {10.1016/j.jpeds.2025.114842},
pmid = {41033577},
issn = {1097-6833},
}

@article {pmid41033479,
year = {2025},
author = {Lewis, DA},
title = {Gonorrhea.},
journal = {Clinics in dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clindermatol.2025.09.006},
pmid = {41033479},
issn = {1879-1131},
abstract = {Neisseria gonorrhoeae, a Gram-negative intracellular pathogen, causes gonorrhea. While usually sexually transmissible, it can be acquired by direct inoculation. Untreated gonococcal infections have deleterious impacts, including adverse pregnancy outcomes, ectopic pregnancy, infertility, and even blindness. Extended-spectrum cephalosporins remain the mainstay of therapy, and gonococcal culture is essential to determine susceptibility to these agents. Antimicrobial resistance is a global public health concern, and few new agents are in the pipeline. Gonorrhea control programs rely on health education, access to diagnostic testing (where possible), effective therapy, and partner notification. Introducing inexpensive, sensitive, and specific point-of-care tests will aid antimicrobial stewardship efforts in countries utilizing the syndromic management approach. Targeted vaccination of higher-risk populations with cross-protective outer membrane vesicle-based meningococcal B-vaccines could reduce N. gonorrhoeae transmission in the future. Doxycycline post-exposure prophylaxis may further reduce gonococcal incidence in the short term; however, its long-term impact on the human resistome/microbiome remains unknown.},
}

@article {pmid41033368,
year = {2025},
author = {Wang, Q and Zhang, Y and Yao, X and Wang, C and Chen, S and Liu, B and Sun, L and Zou, X and Cao, B},
title = {Distinct microbiome variation in children and adults following RSV infection and its association with host response.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108075},
doi = {10.1016/j.micpath.2025.108075},
pmid = {41033368},
issn = {1096-1208},
abstract = {Respiratory syncytial virus (RSV) hospitalization rates are higher in children than in adults, which may be related to differences in respiratory microbiota composition. The relationship between differences in the pharyngeal microbiome and the host immune response in adults and children infected with RSV remains unclear. This study aims to investigate changes in the microbiota of RSV-infected adult and pediatric patients receiving inpatient and outpatient care, and to explore their relationship with the host immune response. A total of 223 participants were enrolled in the study, including 30 adult RSV patients, 92 pediatric RSV patients, 51 community-acquired pneumonia (CAP) patients, and 50 healthy controls. Throat swabs were collected for 16S rRNA gene sequencing and transcriptome analysis. We found that the abundance of oral anaerobes (Prevotella and Veillonella) was higher in pediatric inpatients compared to pediatric outpatients. Differences in pharyngeal microbiome composition were observed between pediatric inpatients and outpatients, while not in adult patients. More differentially expressed genes were observed between pediatric inpatients and outpatients than in adults, primarily related to neutrophil chemotaxis and migration pathways. Furthermore, Alphaproteobacteria and Actinobacteria were positively correlated with the expression of CXCL10 and CXCL11 in pediatric inpatients, suggesting a potential link with neutrophil recruitment and inflammatory responses in these patients. Taken together, these findings improve our understanding of the associations between the host transcriptome and microbiome in the context of RSV infection, which may provide insights into factors related to the increased pathogenicity observed in children.},
}

@article {pmid41033313,
year = {2025},
author = {de Oliveira Formiga, R and Li, Q and Zhao, Y and Campos Ribeiro, MA and Guarino-Vignon, P and Fatouh, R and Dubois, L and Creusot, L and Puchois, V and Amouyal, S and Alonso Salgueiro, I and Bredon, M and Chollet, L and Ledent, T and Scandola, C and Auger, JP and Danne, C and Krönke, G and Tkacz, E and Emond, P and Chevreux, G and Pham, HP and Pontoizeau, C and Lamaziere, A and Argüello, RJ and Rolhion, N and Michel, ML and Wai, T and Sokol, H},
title = {Immunometabolic reprogramming of macrophages by gut microbiota-derived cadaverine controls colon inflammation.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.09.009},
pmid = {41033313},
issn = {1934-6069},
abstract = {Cadaverine is a polyamine produced by the gut microbiota with links to health and disease, notably inflammatory bowel disease (IBD). Here, we show that cadaverine shapes monocyte-macrophage immunometabolism in a context- and concentration-dependent fashion to impact macrophage functionality. At baseline, cadaverine is taken up via L-lysine transporters and activates the thioredoxin system, while during inflammation, cadaverine signals through aconitate decarboxylase 1 (Acod1)-itaconate. Both pathways induce activation of transcription factor, nuclear factor erythroid 2-related factor 2 (Nrf2), which supports mitochondrial respiration and promotes immunoregulatory macrophage polarization. Conversely, under higher concentrations, cadaverine acts via histamine 4 receptor, leading to glycolysis-driven inflammation and pro-inflammatory functions in macrophages. Likewise, cadaverine exhibits paradoxical effects in experimental colitis, either protective or detrimental, evoking opposite fates on macrophages depending on levels dictated by Enterobacteriaceae. In IBD patients, elevated cadaverine correlated with higher flare risk. Our findings implicate cadaverine as a microbiota-derived metabolite manipulating macrophage energy metabolism with consequences in intestinal inflammation and implications for IBD pathogenesis.},
}

@article {pmid41032862,
year = {2025},
author = {Ghosh Chowdhury, M and Singh, AA and Bhattacharyya, M and Muthukumar, V and Kapoor, S and Srivastava, A and Kumar, H and Shard, A},
title = {Thiazole-Based Tumor Pyruvate Kinase M2 Inhibitors: A Paradigm-Shifting Therapeutic Strategy Targeting Metabolic and Microbial Synergy in Colorectal Cancer.},
journal = {Journal of medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jmedchem.5c02169},
pmid = {41032862},
issn = {1520-4804},
abstract = {Colorectal cancer (CRC) remains a major global health burden, with current treatments primarily focused on eradicating cancer cells. However, chemotherapy-induced gut dysbiosis exacerbates inflammation and disease progression, necessitating innovative therapeutic strategies. While various metabolic inhibitors and microbiome-modulating approaches have been explored separately, no reported agent to date simultaneously targets both cancer cell survival and gut microbiome restoration. We designed thiazole-based pyruvate kinase M2 (PKM2) inhibitors, hypothesizing that selective modulation may suppress tumor growth while restoring gut microbial balance. 10j selectively inhibited PKM2 in a cell-free assay (0.01 ± 0.0009 μM) and in CRC cells (4.21 ± 0.04 μM), disrupting key pathways driving CRC progression. Remarkably, metagenomic analysis revealed that 10j restored gut microbiota balance. These findings suggest that dual-function anticancer agents, which kill cancer cells while simultaneously restoring gut microbiota, represent an unexplored therapeutic avenue. Thiazole-based PKM2 inhibitors are pioneering this novel strategy in CRC treatment.},
}

@article {pmid41032844,
year = {2025},
author = {Ashique, S and Paul, D and Debnath, B and Chellappan, DK and Das, J and Bhui, U and Ramzan, M and Sharma, N and Kumar, B and Sridhar, SB and Panigrahy, UP and Hussain, MS},
title = {Probiotics, psychobiotics, and postbiotics: a therapeutic modality for the management of schizophrenia.},
journal = {Nutritional neuroscience},
volume = {},
number = {},
pages = {1-27},
doi = {10.1080/1028415X.2025.2560658},
pmid = {41032844},
issn = {1476-8305},
abstract = {Schizophrenia is a debilitating, chronic neuropsychiatric disorder, a multifactorial disorder combining genetic, neurodevelopmental, immunological, and environmental factors. Common antipsychotic treatments may be effective against positive symptoms, but still lack when dealing with negative symptoms, cognitive defects, and side effects of medication. Recent innovations show how the gut-brain axis is an important modulator of neuropsychiatric health, identifying microbial dysbiosis as a cause of schizophrenia. This review examines the therapeutic potential of such treatments of probiotics, psychobiots, and postbiotics as an adjunctive or alternative treatment targeting the way of modulating neuroinflammation, neurotransmitter synthesis, experience, and maintenance of blood-brain barrier integrity. Probiotics, which are live beneficial microbes, have immunomodulatory and neuroactive effects; psychobiotics, a subclass that has specific mental effects, modify stress-response systems and neurotrophic factors. Postbiotics, consisting in turn of microbial metabolism like short-chain fatty acids, present improved safety and stability with anti-inflammatory and antioxidant functions. Available clinical and preclinical evidence suggests the ability of these agents to attenuate the symptoms of schizophrenia and cognitive impairment, as well as to increase the tolerability of treatment. Regarding the conclusive presumptions, however, strain-specific variability and inconsistent methodologies confined by the sparse large-scale trials limit them. New technologies of nanocarrier systems, artificial intelligence, and personalized microbiome profiling might provide the best precision of the therapy. In this review, pitfalls in mechanistic insights, progress reports on translational studies, and future research prospects are deconstructively examined to support microbiota-based interventions as promising paradigms of holistic schizophrenia management.},
}

@article {pmid41032499,
year = {2025},
author = {Castro, C and Badillo, J and Tumen-Velasquez, M and Guss, AM and Collins, TS and Harmon, F and Coleman-Derr, D},
title = {Bacteria isolated from the grape phyllosphere capable of degrading guaiacol, a main volatile phenol associated with smoke taint in wine.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0331854},
doi = {10.1371/journal.pone.0331854},
pmid = {41032499},
issn = {1932-6203},
mesh = {*Vitis/microbiology ; *Guaiacol/metabolism ; *Wine/analysis/microbiology ; *Smoke ; Biodegradation, Environmental ; *Gordonia Bacterium/metabolism/genetics/isolation & purification ; },
abstract = {Recent wildfires near vineyards in the Pacific United States have caused devastating financial losses due to smoke taint in wine. When wine grapes (Vitis vinifera) are exposed to wildfire smoke, their berries absorb volatile phenols derived from the lignin of burning plant material. Volatile phenols are released during the winemaking process giving the finished wine an unpleasant, smokey, and ashy taste known as smoke taint. Bacteria are capable of undergoing a wide variety of metabolic processes and therefore present great potential for bioremediation applications in many industries. In this study, we identify two strains of the same species that colonize the grape phyllosphere and are able to degrade guaiacol, a main volatile phenol responsible for smoke taint in wine. We identify the suite of genes that enable guaiacol degradation in Gordonia alkanivorans via RNAseq of cells growing on guaiacol as a sole carbon source. Additionally, we knockout guaA, a cytochrome P450 gene involved in the conversion of guaiacol to catechol; ΔguaA cells cannot catabolize guaiacol in vitro, providing evidence that GuaA is necessary for this process. Furthermore, we analyze the microbiome of berries and leaves exposed to smoke in the vineyard to investigate the impact of smoke on the grape microbial community. We found smoke has a significant but small effect on the microbial community, leading to an enrichment of several genera belonging to the Bacilli class. Collectively, this research shows that studying microbes and their enzymes has the potential to identify novel tools for alleviating smoke taint.},
}

*Vitis/microbiology
*Guaiacol/metabolism
*Wine/analysis/microbiology
*Smoke
Biodegradation, Environmental
*Gordonia Bacterium/metabolism/genetics/isolation & purification

@article {pmid41032474,
year = {2025},
author = {Aplasca, AC and Johantgen, PB and Madden, C and Soares, K and Junge, RE and Hale, VL and Flint, M},
title = {Environment and weight class linked to skin microbiome structure of juvenile Eastern hellbenders (Cryptobranchus alleganiensis alleganiensis) in human care.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0319317},
doi = {10.1371/journal.pone.0319317},
pmid = {41032474},
issn = {1932-6203},
mesh = {Animals ; *Skin/microbiology ; *Microbiota/genetics ; *Caudata/microbiology/physiology ; Humans ; RNA, Ribosomal, 16S/genetics ; *Body Weight ; Environment ; Skin Microbiome ; },
abstract = {Amphibian skin is integral to promoting normal physiological processes in the body and promotes both innate and adaptive immunity against pathogens. The amphibian skin microbiota is comprised of a complex assemblage of microbes and is shaped by internal host characteristics and external influences. Skin disease is a significant source of morbidity and mortality in amphibians, and increasing research has shown that the amphibian skin microbiota is an important component in host health. The Eastern hellbender (Cryptobranchus alleganiensis alleganiensis) is a giant salamander declining in many parts of its range, and captive-rearing programs are important to hellbender recovery efforts. Survival rates of juvenile hellbenders in captive-rearing programs are highly variable, and mortality rates are overall poorly understood. Deceased juvenile hellbenders often present with low body condition and skin abnormalities. To investigate potential links between the skin microbiota and body condition, we collected skin swab samples from 116 juvenile hellbenders and water samples from two holding tanks in a captive-rearing program. We used 16s rRNA gene sequencing to characterize the skin and water microbiota and observed significant differences in the skin microbiota by weight class and tank. The skin microbiota of hellbenders that were housed in tanks in close proximity were generally more similar than those housed physically distant. A single taxa, Parcubacteria, was differentially abundant by weight class only and observed in higher abundance in low weight hellbenders. These results suggest a specific association between this taxa and Low weight hellbenders. Additional research is needed to investigate how husbandry factors and potential pathogenic organisms, such as Parcubacteria, impact the skin microbiota of hellbenders and ultimately morbidity and mortality in the species.},
}

Animals
*Skin/microbiology
*Microbiota/genetics
*Caudata/microbiology/physiology
Humans
RNA, Ribosomal, 16S/genetics
*Body Weight
Environment
Skin Microbiome

@article {pmid41032469,
year = {2025},
author = {Kaur, N and Yadav, N and Sachan, S and Sharma, P and Khetarpal, P},
title = {Dysbiosis in PCOS: A Systematic Review of Microbiome Alterations Across Body Sites with GRADE Assessment of Evidence Quality.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00072.2025},
pmid = {41032469},
issn = {1531-2267},
abstract = {Polycystic Ovary Syndrome (PCOS) is a prevalent endocrine-metabolic disorder that adversely affects reproductive, metabolic, and cardiovascular health in females, leading to menstrual irregularities and an increased risk of endometrial malignancies. Emerging research evidence suggests that the gut and extra gastrointestinal microbiome dysbiosis may play a significant role in the pathophysiology of PCOS. This systematic review aims to elucidate the microbiome dysbiosis patterns in PCOS patients compared to healthy controls. A systematic search was conducted across PubMed, Scopus, and Web of Science from inception until February 28[th], 2025, encompassing all original cross-sectional, cohort, or case-control studies that examined the gut, oral, blood, and lower genital tract (LGT) microbiomes of PCOS patients (cases) against healthy females (controls). Of the 4,377 studies identified, 64 were assessed for eligibility through full-text screening, and ultimately, 29 studies met inclusion criteria and were included into the systematic review. The results revealed inconsistent patterns in alpha and beta diversity, with reports of increased, decreased, or unchanged microbial diversity across studies. Key alterations were observed at different taxonomic levels, such as phylum, family, genus, and species. The most significant bacterial alterations include changes in the relative abundance of various bacterial taxa such as Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, Verrucomicrobia, Gammaproteobacteria, Fusobacteria, Eubacterium, Streptococcus, Paraprevotella, Tucibacter, and Tenericutes. These findings indicate that complex dysbiotic microbial shifts may be involved in the pathogenesis of PCOS. As per the GRADE assessment, the quality of evidence is low for most of the studies. This systematic review supports the role of microbial dysbiosis in PCOS pathogenesis, however, additional research is required to elucidate these interactions to guide the development of therapeutic strategies in the future.},
}

@article {pmid41032415,
year = {2025},
author = {Wang, Y and Mu, W and Guan, J and Ma, P and Li, Y and Zhang, Y and Zhu, W and Zhou, Y and Zou, Y and Zeng, T and Zhou, J and Lin, X and Yan, X and Shi, W and Guo, X and Zhu, XQ and Cai, X and Sun, Y and Guo, A and Wang, S},
title = {Bile acid synthesis dysregulation in liver diseases promotes ectopic expansion of oral streptococci in the intestine.},
journal = {Cell reports},
volume = {44},
number = {10},
pages = {116374},
doi = {10.1016/j.celrep.2025.116374},
pmid = {41032415},
issn = {2211-1247},
abstract = {Liver diseases often coincide with dysregulated gut homeostasis and Streptococcus overgrowth, yet the underlying mechanisms remain unclear. Here, we study patients with liver echinococcosis and other liver conditions. We observe that these patients frequently exhibit a co-occurrence of an ectopic expansion of orally derived Streptococcus species implicated in intestinal inflammation, alongside a bile acid deficiency in the gut. This association is typically characterized by the reduction of 12-ketolithocholic acid (12-KetoLCA), which exerts potent membrane-disrupting activity. We show that liver disorders compromise gut resistance to oral microbes due to a loss of ecological control from bile acids, particularly 12-KetoLCA. This bile-acid-conferred gut barrier is regulated by cytochrome P450 enzymes and can be reconstituted through adeno-associated virus (AAV) gene therapy targeting these genes. Additionally, we reveal that supplementation with 12-KetoLCA prevents oral Streptococcus-driven gut inflammation through antibacterial activity. Our findings underscore the essential role of bile acids in maintaining the oral-gut barrier.},
}

@article {pmid41032256,
year = {2025},
author = {Fuentes Rojas, LJ and Bussiman, F and Cardoso, TF and Colmenarez, GA and Conteville, LC and Antonio, BCP and Ventura, HT and Paschoal, JJ and Lourenco, D and Regitano, LCA},
title = {Microbiota diversity and association with performance phenotypes in beef bulls.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf340},
pmid = {41032256},
issn = {1525-3163},
abstract = {BACKGROUND: Feed efficiency, nutrient utilization, and methane emission are highly dependent on the gastrointestinal microbiota, implying an influence of these microorganisms on economically important traits (e.g., carcass traits and meat quality). The interaction between microbial composition, diet, and host performance suggests that microbiota-targeted strategies may increase production in livestock animals. However, little is known about this interaction in beef cattle. We aimed to characterize the gastrointestinal microbiota and identify taxa associated with performance phenotypes in Nellore bulls.

RESULTS: We identified 1,268 bacterial and 75 archaeal amplicon sequence variants (ASVs). For both bacteria and archaea, alpha diversity showed significant within-year variation. No statistical differences were found for the Shannon index for bacteria in 2019 versus 2021 or archaea in 2019-2020 and 2021-2022. Except for 2022 (bacteria), no clusters were observed for bacteria or archaea beta diversity across years. Ten different bacteria ASVs were found to affect ribeye area (RA), whereas only five did so for metabolic weight (MW). For archaea, eight ASVs had a significant effect on RA, whereas 15 were found to affect MW. Coefficients of the regression of phenotype on ASV ranged from (± SE, in SD units) -0.40 ± 0.08 (ASV 892, Bacteroidales RF16 spp.) to 0.36 ± 0.11 (ASV 605, Marvinbryantia spp.) for MW, and from -0.72 ± 0.20 (ASV 188, Faecalibacterium spp.) to 0.65 ± 65 (ASV 457, Christensenellaceae R-7 spp.) for RA.

CONCLUSION: Our study revealed significant associations between ASV and traits of economic importance in beef cattle, including carcass, feed efficiency, and morphology, indicating that the microbiome influences animal performance. Further research is needed to elucidate the biological mechanisms behind these associations.},
}

@article {pmid41032035,
year = {2025},
author = {Kale, T and Yoo, L and Kroeger, E and Iqbal, A and Kane, S and Shihab, S and Conley, S and Kamp, K},
title = {Menopause and Inflammatory Bowel Disease: A Systematic Review.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf204},
pmid = {41032035},
issn = {1536-4844},
support = {F31 NR020426/NR/NINR NIH HHS/United States ; K23 NR020044/NR/NINR NIH HHS/United States ; },
abstract = {BACKGROUND: Research is limited on the impacts of menopause, defined as the permanent cessation of ovarian function and decline of reproductive hormones, on gastrointestinal symptom severity and disease progression in women with inflammatory bowel disease (IBD). This review synthesizes current evidence on the impact of menopause, menopause transition, and hormonal therapy (HT) on disease activity, IBD and menopause symptom severity, and disease progression among individuals with IBD.

METHODS: A systematic literature review was reported following PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines and preregistered at PROSPERO (CRD42024564901). Five databases were searched without date restrictions. Data extraction and risk-of-bias assessment were performed independently by multiple reviewers. Results were qualitatively synthesized.

RESULTS: Of 1667 records, 15 studies met inclusion criteria (5 cohort, 3 case-control, 7 cross-sectional) with IBD sample sizes from 37 to 1367. Evidence on HT and IBD risk was mixed: some studies linked HT to increased ulcerative colitis risk while others found no significant association after adjusting for confounders. Women with IBD experience earlier menopause than healthy control subjects. While most women reported no change in IBD symptoms postmenopause, a minority reported symptom worsening. HT may reduce flare severity. Women with IBD reported more severe vulvovaginal symptoms and had distinct vaginal microbiome profiles compared with healthy control subjects.

CONCLUSIONS: Few studies have explored the relationship between menopause and IBD. There is a need for continued research on the relationship between IBD disease activity and menopause symptoms to create tailored interventions to improve women's health with IBD across the lifespan.},
}

@article {pmid41031883,
year = {2025},
author = {Tian, X and Zhang, L and Qian, X and Peng, Y and Chen, F and Bengtson, S and Wang, Z and Wu, M},
title = {Gut complement system: a new frontier in microbiota-host communication and intestinal homeostasis.},
journal = {The Journal of clinical investigation},
volume = {135},
number = {19},
pages = {},
doi = {10.1172/JCI188349},
pmid = {41031883},
issn = {1558-8238},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Homeostasis/immunology ; Animals ; Inflammatory Bowel Diseases/immunology/microbiology/pathology ; Complement Activation ; *Complement C3/immunology ; *Complement System Proteins/immunology ; Colorectal Neoplasms/immunology/microbiology/pathology ; *Intestines/immunology/microbiology ; Immunity, Innate ; },
abstract = {The gut microbiota plays a crucial role in maintaining intestinal homeostasis and influencing various aspects of host physiology, including immune function. Recent advances have highlighted the emerging importance of the complement system, particularly the C3 protein, as a key player in microbiota-host interactions. Traditionally known for its role in innate immunity, the complement system is now recognized for its interactions with microbial communities within the gut, where it promotes immune tolerance and protects against enteric infections. This Review explores the gut complement system as a possibly novel frontier in microbiota-host communication and examines its role in shaping microbial diversity, modulating inflammatory responses, and contributing to intestinal health. We discuss the dynamic interplay between microbiota-derived signals and complement activation, with a focus on the C3 protein and its effect on both the gut microbiome and host immune responses. Furthermore, we highlight the therapeutic potential of targeting complement pathways to restore microbial balance and treat diseases such as inflammatory bowel disease and colorectal cancer. By elucidating the functions of the gut complement system, we offer insights into its potential as a target for microbiota-based interventions aimed at restoring intestinal homeostasis and preventing disease.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Homeostasis/immunology
Animals
Inflammatory Bowel Diseases/immunology/microbiology/pathology
Complement Activation
*Complement C3/immunology
*Complement System Proteins/immunology
Colorectal Neoplasms/immunology/microbiology/pathology
*Intestines/immunology/microbiology
Immunity, Innate

@article {pmid41031864,
year = {2025},
author = {Khan, I and Wang, Y and Zhang, T and Malanchuk, K and Xu, S and Crevecoeur, S and Wang, J and Zastepa, A and Liu, X},
title = {Microbial biodiversity of agricultural surface waters in Ontario, Canada.},
journal = {Canadian journal of microbiology},
volume = {71},
number = {},
pages = {1-9},
doi = {10.1139/cjm-2025-0015},
pmid = {41031864},
issn = {1480-3275},
mesh = {Ontario ; *Biodiversity ; *Bacteria/classification/genetics/isolation & purification ; Agriculture ; Animals ; *Microbiota ; Cattle ; Manure/microbiology ; *Rivers/microbiology/chemistry ; *Water Microbiology ; Lakes/microbiology ; Nitrogen/analysis ; },
abstract = {Understanding the microbial diversity is the first step to monitor the microbial quality of agricultural surface waters. Here we report a study comparing the microbial composition and diversities in agricultural surface waters in Ontario, Canada, including the streams adjacent to dairy cattle production in eastern Ontario and the field runoffs from the manure-impacted experimental farm of south-western Ontario. We also studied the quality of the surface water in the western basin of Lake Erie during a harmful algal bloom (cHAB). In eastern Ontario, we found significantly lower (P < 0.01) abundance of Proteobacteria and Burkholderiales in the streams adjacent to dairy production than the non-agriculture site. Bacteroidetes was more abundant (P < 0.0001) in medium/high order streams and agriculture/urban mixed site. Seasonal peaks of Flavobacterium were observed in low order streams but the trend was not in medium/high order streams. In south-western Ontario, the dominant bacterial taxa in field runoffs was Pseudomonas, regardless of manure types. We also discovered that the elevated total dissolved nitrogen, total dissolved phosphorus and chlorophyll a associated with the cHAB zone in Lake Erie was further away rather from the agricultural sites. In conclusion, our studies identified unique microbiome patterns associated with agricultural surface waters in Ontario.},
}

Ontario
*Biodiversity
*Bacteria/classification/genetics/isolation & purification
Agriculture
Animals
*Microbiota
Cattle
Manure/microbiology
*Rivers/microbiology/chemistry
*Water Microbiology
Lakes/microbiology
Nitrogen/analysis

@article {pmid41031848,
year = {2025},
author = {Aghzaf, S and Poli, J-P and Brunel, M and Costa, J and Lorenzi, V and Guinoiseau, E and Berti, L},
title = {Characterization of the bacterial and fungal diversity in habitats of Corsica Island.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0075625},
doi = {10.1128/aem.00756-25},
pmid = {41031848},
issn = {1098-5336},
abstract = {Indoor environments may impact human health significantly since microbial diversity made of various bacteria, fungi, and other microorganisms constitutes the habitat's microbiome. These microorganisms originate from diverse sources, such as the environment, humans, and pets. Understanding such microbial diversity is crucial for assessing related health impacts. The aim of this study was to investigate bacterial and fungal microorganisms from different surfaces in a set of houses on Corsica Island (southeastern France). We conducted sampling and high-throughput sequencing of PCR-amplified microbial DNA from 40 habitats (eight different surfaces tested for each) located on diverse regions of the island. Following nucleic acid recovery, we performed PCR targeting V3-V4 regions of 16S rRNA for bacteria and ITS1 region for fungi. Bioinformatics processing allowed the identification of distinct microbial species and the analysis of their distribution. Our findings highlighted that the most represented bacterial genera in the Corsican homes tested were Ralstonia (16.9%), Staphylococcus (4.8%), Corynebacterium (2.7%), Enhydrobacter (6.8%), and Methylorubrum (6.0%). Regarding fungal diversity, the most common genera identified were Dipodascaceae (21.6%), Rhodotorula (10.9%), Aspergillus (8.9%), Clavispora (7.3%), and Candida (6.8%). Our results also showed differences in microbial composition among the habitats studied, while a higher bacterial and fungal diversity was observed in rural habitats and in those with pets.IMPORTANCEThis study provides valuable insights into the microbial diversity present in indoor environments of Corsican homes, specifically highlighting bacterial and fungal communities on various household surfaces. By identifying the predominant microbial genera and revealing differences linked to habitat characteristics, such as rural settings and pet ownership, this research enhances our understanding of how indoor microbial communities vary.},
}

@article {pmid41031813,
year = {2025},
author = {Mavrodi, DV and Blankenfeldt, W and Mavrodi, OV and Weller, DM and Thomashow, LS},
title = {Microbial phenazines: biosynthesis, structural diversity, evolution, regulation, and biological significance.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0014723},
doi = {10.1128/mmbr.00147-23},
pmid = {41031813},
issn = {1098-5557},
abstract = {SUMMARYPhenazines are small, redox-active secondary metabolites produced by various bacterial species. These compounds participate in electron-transfer reactions, aiding microbes in surviving stressful or oxygen-limited environments. In this review, we examine the extensive structural diversity of phenazines and trace the evolutionary history of their biosynthetic pathways, which often move between distantly related species through horizontal gene transfer. We also explore how environmental factors such as nutrient levels and cell-to-cell signaling regulate phenazine production. Beyond their roles in microbial physiology, phenazines influence interactions among organisms, acting as antimicrobial agents, signaling molecules, and factors that shape microbiome dynamics in soils, plant roots, and other habitats. A better understanding of phenazine biology reveals how microbes adapt and thrive in diverse environments and emphasizes the potential applications of these compounds in agriculture and human health.},
}

@article {pmid41031624,
year = {2025},
author = {Guimaraes, AF and Meirelles, GS and Alagao Querido, LC and Fernandes, KM and Ribeiro, W and Oliveira, RTM and Silva, ER and Canaan, M and Lira, MFP and Ostle, N and Berg, E},
title = {The haunting of the Soul's hill: Uncoupled responses of plant functional traits and soil microbes to serpentine soils lead to Bonsai effect in the Neotropics.},
journal = {Tree physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/treephys/tpaf121},
pmid = {41031624},
issn = {1758-4469},
abstract = {PURPOSE: We investigated the plant-soil linkages of C. Langsdorffii, a widely distributed species in the Neotropics, and how the serpentine syndrome leads to dwarfism by comparing soil microbes, soil properties and tree functional traits in serpentine and non-serpentine soils. For that we evaluated the presence of heavy metals in the soils and how it affects plant functional traits; differences of C:N ratio between serpentine and non-serpentine sites as well as soil microbiome by using PLFA technique approach to assess microbial functional groups.

METHODS: We explored the relations between soil microbes (by using phospholipid fatty acid, i.e., components of cell membranes in microbes used as an indicator of microbial biomass), soil properties, vegetation attributes, leaf nutrients and leaf functional traits.

RESULTS: We found correlation between soil gram-positive bacteria and iron in the plant leaves.; the C:N ratios are higher in serpentine sites, but the two areas are similar to the non-serpentine area; there was no difference between the soil microbes in our study areas and finally; there's a tendency to dwarfism and xeromorphism in the functional traits of C. Langsdorffii in serpentine soils.

CONCLUSIONS: We found that even though we have differences when comparing C. langsdorffii plants in serpentine and non-serpentine sites regarding the functional traits analysed in our study, the only soil microbe that seems to be interacting with the heavy metals is the gram-positive bacteria, possibly due to chelating mechanisms.},
}

@article {pmid41031610,
year = {2025},
author = {Quan, L and Shi, M and Yang, Z and Rong, H and Zhou, J and Sang, D and Xu, J and Yue, J and Chen, S and Liu, J and Yuan, P},
title = {Dynamics of the intratumoural microbiome across malignant transformation and treatment in breast cancer.},
journal = {Clinical and translational medicine},
volume = {15},
number = {10},
pages = {e70492},
doi = {10.1002/ctm2.70492},
pmid = {41031610},
issn = {2001-1326},
support = {D012401//National Natural Science Foundation of China/ ; },
mesh = {Female ; Humans ; *Breast Neoplasms/microbiology/therapy/pathology ; *Microbiota/genetics ; *Cell Transformation, Neoplastic ; Middle Aged ; RNA, Ribosomal, 16S ; Adult ; Aged ; },
abstract = {Breast cancer (BC) is the most common malignancy in women, yet the dynamics of the intratumoural microbiome during tumour initiation, progression, and treatment remain poorly understood. Prior studies are predominantly cross-sectional and limited by indirect microbial inference from RNA-seq data. This study presents a comprehensive analysis of intratumoural microbiota across breast tissue samples by high-depth 16S rRNA sequencing (11 W tags), featuring two longitudinally paired cohorts for dynamic microbial profiling during tumour progression and treatment. Samples included 165 benign nodules (82 non-transforming, 83 that later progressed to cancer with matched malignant tissues); 180 primary BC tissues and 165 benign controls; and 101 neoadjuvant therapy (NAT) specimens (15 pCR, 86 non-pCR, with paired pre/post-treatment samples). We identified a cluster of taxa (Aeromicrobium, Halomonas, Dietzia, Nesterenkonia, Delftia, Nitriliruptor) depleted in nodules undergoing malignant transformation, declining with disease progression and partially restored after NAT, with transient enrichment early in transformation. Opposing trends were observed for Paenibacillus and Methyloversatilis. These changes corresponded to shifts in amino acid, lipid, and glycan metabolism. FISH and TEM analyses identified Paenibacillus pasadenensis and Halomonas hamiltonii within tumour cells, with opposing effects on tumour proliferation and activation. In addition, we developed two predictive models with high clinical relevance: one stratifying malignancy risk in nodules, and another predicting NAT response, both of which achieved strong performance in external validation. This longitudinal characterisations of intratumoural microbiota during breast tumourigenesis and treatment offer novel insights for precision oncology and microbiome-based interventions in breast cancer.},
}

Female
Humans
*Breast Neoplasms/microbiology/therapy/pathology
*Microbiota/genetics
*Cell Transformation, Neoplastic
Middle Aged
RNA, Ribosomal, 16S
Adult
Aged

@article {pmid41031579,
year = {2025},
author = {Nykyforuk, CA and Ford, LA and Torwalt, EC and Steffler, MV and Neraasen, AF and Lind, JC and Stewart, CB and Boyd, A and Shahriari, A and Madsen, DC and Tierney, KB},
title = {Alternative proteins support somatic and muscular development while remodeling the microbiome in zebrafish.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo01990g},
pmid = {41031579},
issn = {2042-650X},
abstract = {Protein intake is fundamental to growth, well-being and long-term health. Unfortunately, many diets rely upon animal-based proteins, which are environmentally costly. To feed a growing population, alternative protein sources will be necessary. To determine the health implications of switching entirely away from animal-based diets, we fed alternative proteins to a model vertebrate during development. Zebrafish were fed diets including protein from fishmeal, pea, milk and whey, and their growth and health were monitored. Most diets supported growth, with the exception of those high in whey and milk protein, which resulted in fish that were ∼10% shorter in body length and had muscle fibers ∼30% smaller than control. Of interest, genes associated with insulin sensitivity and fat storage were upregulated in some diets (lepr, 2 to 3.5 fold, and fasn, 2.5 to 4 fold, respectively). The microbiome changed dramatically between animal and alternative proteins, shifting from Fusobacteriota to Proteobacteria dominance, with Cetobacterium positively affecting health, and Aeromonas doing the opposite. Our findings indicate that more environmentally friendly diets can lead to healthy outcomes, but that the protein source is critically important.},
}

@article {pmid41031366,
year = {2025},
author = {Van Caesbroeck, A and Lipovac, M and van den Borst, E and Palma, P and Téblick, L and Vorsters, A},
title = {Unveiling Chlamydia trachomatis immunity in urogenital secretions: A systematic review.},
journal = {iScience},
volume = {28},
number = {10},
pages = {113453},
pmid = {41031366},
issn = {2589-0042},
abstract = {Chlamydia trachomatis (CT) is a highly prevalent bacterial sexually transmitted infection (STI), associated with severe disease complications. CT targets a unique immunological environment: the genital tract epithelium. Although sampling the genital tract is challenging, previous studies have shown that genital CT-specific antibodies exhibit enhanced neutralizing capacity compared with serum antibodies. Furthermore, tissue-resident memory T (TRM) cells provide superior protection compared with circulating T cells. However, further research is required to identify correlates of protection and explore correlations between local and systemic responses. This review provides an overview of the sampling methods suitable for identifying mucosal immune biomarkers associated with CT infection, as well as the immunoassays used. We identified the microbiome, presence of coinfections, hormonal influences, genetics, and CT infection state, load, and genotype as confounding factors to be considered in trial design. Finally, we discuss challenges related to the detection of mucosal immune biomarkers and offer recommendations for future research.},
}

@article {pmid41031151,
year = {2025},
author = {Chen, J and Zhang, M and Gong, Y and Gu, Z and Zhou, H and Gu, Y and Shen, F and Zhou, G and Ding, J},
title = {The Role of the Vaginal Microbiome in Immune Modulation in Cervical Cancer: Composition, Molecular Mechanisms, and Therapeutic Potential.},
journal = {Clinical Medicine Insights. Oncology},
volume = {19},
number = {},
pages = {11795549251380470},
pmid = {41031151},
issn = {1179-5549},
abstract = {Accumulating evidence demonstrates that the tumor microenvironment (TME) drives immune suppression through complicated regulations including host-microbe interactions, which poses vaginal microbiome as one of vital regulators of immune microenvironment. This narrative review examined the composition and dynamic changes of vaginal microbiota during carcinogenesis, focusing on mechanistic insights linking microbial dysbiosis to tumor immunity. Notably, commensal bacteria exhibit diverse immunoregulatory functions that can either potentiate or inhibit anti-tumor responses. Clinical evidence further reveals that CST IV microbiota associates with significantly elevated cancer risk, while probiotic interventions show promise in restoring immune surveillance. Critical gaps in standardization of microbiota-based therapies are addressed, emphasizing the need for strain-specific characterization and optimized delivery systems. Collectively, deciphering vaginal microbiome-immune crosstalk opens new avenues for precision interception against cervical cancer.},
}

@article {pmid41031112,
year = {2025},
author = {Li, N and Yi, F and Wang, Y and Geng, F and Liu, Y and Liu, Q and Guo, Y and Long, D},
title = {Effects of Shenfu injection on intestinal microbiota and inflammation in sepsis mice.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1599903},
pmid = {41031112},
issn = {2235-2988},
mesh = {Animals ; *Sepsis/drug therapy/microbiology/pathology ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/administration & dosage/pharmacology ; Male ; Disease Models, Animal ; Mice, Inbred C57BL ; Mice ; *Inflammation/drug therapy ; RNA, Ribosomal, 16S/genetics ; Cytokines/blood ; Intestinal Mucosa/drug effects/microbiology ; Cecum ; },
abstract = {INTRODUCTION: Sepsis remains a critical challenge in intensive care medicine, necessitating novel therapeutic approaches.

METHODS: In this study, healthy 8-week-old male C57BL/6J mice were treated with cecal ligation and puncture (CLP) to induce a sepsis model. After successful model establishment, mice in the sham and CLP groups were injected with 200 μL of normal saline, while mice in the SFI group were injected with 200 μL of SFI. Changes in intestinal mucosal barrier function, inflammation, and intestinal microbiota were assessed in septic mice after SFI treatment.

RESULTS: SFI treatment significantly ameliorated intestinal inflammation and reduced serum levels of pro-inflammatory cytokines (IL-1β, IL-6) and renal injury markers (SCr, BUN). 16S rRNA sequencing revealed SFI-mediated gut microbial remodeling, characterized by a marked reduction in pathogenic Escherichia-Shigella abundance and concurrent enrichment of beneficial probiotics, including Akkermansia and Lactobacillus. Mechanistically, SFI exhibited dual regulatory effects on both systemic inflammation and gut microbiota homeostasis.

DISCUSSION: These findings not only validate SFI's efficacy in sepsis treatment but also propose a novel mechanism involving gut microbiome modulation. This study provides critical experimental evidence for repurposing traditional Chinese medicine in sepsis therapy and establishes a foundation for future research on microbiota-targeted interventions in critical care.},
}

Animals
*Sepsis/drug therapy/microbiology/pathology
*Gastrointestinal Microbiome/drug effects
*Drugs, Chinese Herbal/administration & dosage/pharmacology
Male
Disease Models, Animal
Mice, Inbred C57BL
Mice
*Inflammation/drug therapy
RNA, Ribosomal, 16S/genetics
Cytokines/blood
Intestinal Mucosa/drug effects/microbiology
Cecum

@article {pmid41030606,
year = {2025},
author = {Golly, KM and Doku, ET and Amponsah, AS and Kyei, P and Gyadua, C},
title = {Microbial Diversity, Nutritional Composition, and Health Implications of Fermented Locust Bean Seed (Dawadawa) From Ghana.},
journal = {International journal of food science},
volume = {2025},
number = {},
pages = {8444101},
pmid = {41030606},
issn = {2314-5765},
abstract = {Fermented foods play a vital role in global nutrition, and dawadawa, a traditional African locust bean (Parkia biglobosa) fermentation product, is a key dietary component in Northern Ghana. This study investigates the microbial diversity, nutritional composition, and health implications of dawadawa produced across six major communities. The determination of nutritional composition and bacterial communities in dawadawa was conducted using standard spectrometric methods and 16S RNA sequencing, respectively. Proximate analysis revealed significant variations in fat (17.45%-27.70%), protein (36.12%-50.00%), and fiber (6.39%-7.32%) across different locations, with Sunyani samples exhibiting the highest protein content. Mineral analysis showed notable differences in iron (79.60-135.00 mg/kg), zinc (37.75-91.77 mg/kg), and calcium (0.73%-1.61%), suggesting potential nutritional benefits. Microbial profiling using 16S rRNA sequencing identified Bacillus, Staphylococcus, Streptococcus, and Lactobacillus as predominant genera, with Bacillus subtilis being the most abundant species. Domestic dawadawa exhibited higher microbial diversity compared to commercial samples, with greater amplicon sequence variant (ASV) richness. Functional bacterial groups correlated with enhanced protein and mineral bioavailability, supporting dawadawa's role as a probiotic and functional food. Findings highlight the impact of fermentation practices on microbial diversity and nutrient composition, underscoring the importance of preserving traditional methods while optimizing production for food security and sustainability.},
}

@article {pmid41030555,
year = {2025},
author = {Worku, AT and Sciarretta, A and Guarnieri, A and Falcone, M and Brancazio, N and Minwuyelet, A and Cutuli, MA and Atenafu, G and Nicolosi, D and Colacci, M and Yewhalaw, D and Di Marco, R and Petronio Petronio, G},
title = {Microbial gatekeepers: midgut bacteria in Aedes mosquitoes as modulators of arboviral transmission and targets for sustainable vector control.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1656709},
pmid = {41030555},
issn = {1664-302X},
abstract = {Arboviral diseases such as Dengue virus, Zika virus, Chikungunya virus, and West Nile virus pose significant global public health and economic challenges, particularly in tropical and subtropical regions. The absence of effective vaccines and sustainable vector control strategies continues to drive high morbidity and mortality rates. Symbiotic bacteria residing in the mosquito midgut can produce antimicrobial compound, stimulate the host immune response, disrupt nutrient pathways critical for pathogen development, and interfere with the pathogen's lifecycle and dissemination. Additionally, these microbes may reduce vector reproduction and shorten the lifespan of both immature and adult stages. Genetically modified symbiotic bacteria can release effector molecules that target pathogens without harming mosquitoes. Advances in genomic and metagenomic tools have deepened our understanding of the mosquito gut microbiome. This review highlights current knowledge of gut bacteria and arbovirus interactions and explores strategies to reduce arboviral transmission. Comprehensive literature searches were conducted using global databases, including PubMed, Web of Science, and Scopus, with a focus on English-language publications.},
}

@article {pmid41030548,
year = {2025},
author = {Zhang, Y and Li, C and Tang, L and Li, F and Fu, X and Hao, Y and Li, J and Feng, X and Hu, W},
title = {Age-stratified gut microbial changes in diarrheal calves: insights from 16S rRNA sequencing across early development.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1633162},
pmid = {41030548},
issn = {1664-302X},
abstract = {INTRODUCTION: Neonatal calf diarrhea (NCD) remains a leading cause of mortality in calves under 1 month, yet how gut microbial responses vary across developmental stages remains unexplored. This study investigates age-stratified microbiome dynamics during NCD to enable precision interventions.

MATERIALS AND METHODS: This study investigated 60 female Holstein calves (1, 21, and 30 days old) from a commercial dairy farm, equally divided between healthy and diarrheal groups based on standardized fecal scoring. Fecal samples were collected aseptically, flash-frozen, and processed for 16S rRNA gene sequencing (V3-V4 region) using Illumina NovaSeq. Bioinformatics analyses included DADA2 pipeline for ASV calling, SILVA 138 database for taxonomic annotation, ANCOM-BC2 for differential abundance analysis (FDR < 0.05), PICRUSt2 for functional prediction, and SparCC networks (|r| > 0.6, p < 0.001) with Gephi visualization. Multivariate statistics, including PERMANOVA and canonical correspondence analysis were performed in QIIME2 and R (phyloseq/vegan packages), with all analyses rarefied to 39,161 sequences/sample.

RESULTS: The gut microbiome exhibited age-dependent succession, transitioning from Pseudomonadota dominance (47.2 ± 0.7%) at day 1 to Bacillota/Bacteroidota co-dominance (85.5 ± 8.2%) by day 30. Age explained significantly more compositional variance than diarrhea status (3.68% vs. 1.96%, p < 0.001). Three distinct age-specific diarrheal patterns emerged: (1) Early-stage (1-day-old) showed Bacillota/Pseudomonadota imbalances (84% of differential ASVs) with reduced network complexity (total node count, total edge count, average degree and modularity); (2) Mid-lactation (21-day-old) featured Kurthia as both significantly enriched (log2FC = 5.32) and a network hub (degree = 14); (3) Mature microbiota (30-day-old) displayed complex multi-phylum dysbiosis involving 10 metabolic pathways. Clostridia_UCG-014 persisted across diarrheal networks, while healthy calves showed age-progressive increases in microbial connectivity (edges: 125 to 1,104). Only 2 ASVs demonstrated consistent differential abundance across age groups, confirming the temporal specificity of diarrheal dysbiosis.

CONCLUSION: NCD-associated dysbiosis progresses through distinct developmental phases, from resilient phylum-level shifts in neonates to complex network disruptions in mature microbiota. The identification of stage-specific biomarkers (e.g., day 21 Kurthia) opens new avenues for age-tailored probiotic therapies and early intervention strategies.},
}

@article {pmid41030386,
year = {2025},
author = {Connolly, D and Minj, J and Arbizu, S and Kirkendall, A and Nalbandian, E and Ganjyal, GM and Murphy, KM and Solverson, P and Carbonero, F},
title = {In vitro fecal fermentation demonstrates the prebiotic-like properties of quinoa modulated by different preparation methods.},
journal = {Current research in food science},
volume = {11},
number = {},
pages = {101198},
pmid = {41030386},
issn = {2665-9271},
abstract = {Quinoa grain represents an excellent source of nutrition, including protein, lipids, and fiber. Quinoa processing and cooking alters its chemical composition and bioavailability of nutrients, and while extracts have been studied, little is known about the impact of quinoa food products on the human gut microbiota. One selected quinoa line was tested in raw, boiled, extruded, and baked (cookie) forms for its ability to modulate fecal microbiota from 10 healthy donors. After in vitro digestion, samples underwent fecal fermentation with measurements taken at 0, 6, 12, 24, and 48 h (h). Boiled and extruded quinoa exhibited significantly higher total polyphenol content when compared to raw quinoa (p < 0.05), while baked quinoa had lower polyphenol content, though the difference was not significant. Fecal fermentation of pre-digested raw and processed quinoa significantly increased (p < 0.05) beneficial lactic acid-producing bacterial (LAB) genera, including Bifidobacterium and Lactobacillus. All quinoa samples (raw, boiled, extruded, and baked) significantly increased Bifidobacterium abundance from 6 to 48 h compared to the start of fermentation (0 h), while Lactobacillus increased significantly in boiled, baked, and extruded samples at 12-48 h. Pediococcus and Weissella were more abundant in raw quinoa, suggesting that less-processed plant material might be harder to ferment. These findings highlight quinoa's prebiotic properties, which are largely preserved across various cooking methods. Future studies on quinoa and other grain products should integrate food chemistry and gut microbiota outcomes to identify physicochemical properties that influence microbiota responses.},
}

@article {pmid41030253,
year = {2025},
author = {Bautista, J and Villegas-Chávez, JA and Bunces-Larco, D and Martín-Aguilera, R and López-Cortés, A},
title = {The microbiome as a therapeutic co-driver in melanoma immuno-oncology.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1673880},
pmid = {41030253},
issn = {2296-858X},
abstract = {Melanoma, one of the most aggressive skin cancers, remains a major clinical challenge due to its high metastatic potential, therapy resistance, and rising global incidence. Although immune checkpoint inhibitors have transformed management, variable responses and acquired resistance limit durable benefit. Emerging evidence positions the microbiome as a pivotal determinant of melanoma biology and therapeutic outcomes. Dysbiosis in the skin, gut, and oral compartments fosters tumor-promoting inflammation, immune evasion, and oncogenic signaling, whereas enrichment of specific commensals, such as Akkermansia muciniphila and Faecalibacterium prausnitzii, enhances antigen presentation and effector T cell activity, improving ICI efficacy. Mechanistically, microbial metabolites, including short-chain fatty acids, tryptophan derivatives, and bile acids, modulate epigenetic programs, G-protein-coupled receptor signaling, and oncogenic cascades such as PI3K-AKT and RAS-RAF-MEK-ERK. Beyond the gut, cutaneous microbiota such as Staphylococcus epidermidis exert direct antitumor effects, while pathogenic oral taxa propagate systemic inflammation that shapes the melanoma tumor microenvironment. These insights are driving the development of microbiome-targeted interventions, including fecal microbiota transplantation, defined consortia, probiotics, and dietary modulation, with early clinical studies showing the potential to overcome resistance to immunotherapy. Integration of circadian biology further suggests that host-microbiome-immune interactions are temporally regulated, opening new dimensions for therapeutic optimization. By synthesizing mechanistic, clinical, and translational advances, this review highlights the microbiome as both a biomarker and a therapeutic axis in melanoma, underscoring its promise to transform precision immuno-oncology.},
}

@article {pmid41030120,
year = {2025},
author = {Kraus, O and Schwarz, Y and Motro, Y and Marom, T and Lamdan, R and Kapuller, V and Ovnat, ST and Moran-Gilad, J},
title = {Adenotonsillar Microbiome Shifts in Children With Obstructive Sleep Apnea Syndrome.},
journal = {The Laryngoscope},
volume = {},
number = {},
pages = {},
doi = {10.1002/lary.70119},
pmid = {41030120},
issn = {1531-4995},
support = {17.15.41//Ben Gurion University of the Negev/ ; },
abstract = {OBJECTIVE: To characterize the microbiomes of adenoids and tonsils in pediatric Obstructive Sleep Apnea Syndrome (OSAS) patients compared to healthy controls. We hypothesized that the microbiome composition of the tonsils and adenoids in OSAS patients differs significantly from that of healthy controls.

METHODS: Thirty OSAS patients and 30 healthy controls were included. Samples from adenoids and tonsils were analyzed using 16S rRNA amplicon sequencing to characterize bacterial communities. Differential abundance and alpha and beta diversity were used to compare the microbiome compositions between groups.

RESULTS: Significant differences in the microbial composition of adenoids and tonsils were observed within both OSAS and control groups. The tonsillar microbiome in OSAS patients exhibited lower alpha diversity and distinct microbial composition compared to controls, with an overrepresentation of pathogenic genera such as Haemophilus and Neisseria. Adenoid microbiomes, however, showed no significant differences in alpha diversity between OSAS and controls but displayed a trend toward variation in beta diversity.

CONCLUSION: This study highlights distinct microbiome profiles in adenoids and tonsils, with significant microbial shifts in the tonsillar microbiome of OSAS patients. These findings underscore the importance of syndrome-specific studies and suggest the potential contribution of microbial communities to pathogenesis. Future research should focus on further characterizing the microbiomes of healthy individuals and OSAS patients, aiming to establish a clearer distinction between normal and pathological microbial populations, which could inform the development of novel, non-invasive therapies.},
}

@article {pmid41030102,
year = {2025},
author = {Ribeiro, AJ and Silva, F and Teixeira, P and Saraiva, CM},
title = {Dry-Aged Beef: A Global Review of Meat Quality Traits, Microbiome Dynamics, Safety, and Sustainable Strategies.},
journal = {Journal of food science},
volume = {90},
number = {10},
pages = {e70589},
doi = {10.1111/1750-3841.70589},
pmid = {41030102},
issn = {1750-3841},
support = {//Fundação para a Ciência e a Tecnologia/ ; },
mesh = {Animals ; Cattle ; *Microbiota ; *Red Meat/microbiology/analysis ; *Food Handling/methods ; Humans ; Food Quality ; Food Microbiology ; Taste ; *Meat/microbiology/analysis ; },
abstract = {Dry-aged beef is valued for its tenderness, complex aroma, and concentrated flavor. However, variability in aging protocols and limited understanding of underlying biological and technological processes can compromise consistent quality and safety. This review examines factors influencing meat characteristics, including genetics, breed, sex, age, diet, intramuscular fat deposition, antioxidant reserves, and endogenous enzyme pools. Postmortem biochemical pathways, such as proteolysis, lipid oxidation, and nucleotide degradation, are discussed in relation to flavor and texture development. The dynamics of surface microbiota are analyzed, highlighting the succession from psychrotrophic spoilage bacteria to molds and yeasts, which collectively form an enzymatic crust that contributes umami and nutty notes while providing antimicrobial barriers. Regulatory frameworks in major markets are reviewed, alongside valorization strategies that convert crust trimmings into umami-rich powders, bioactive peptides, starter cultures, or industrial enzymes. Despite advances, critical knowledge gaps remain, including the functional roles of minor crust taxa, the efficacy of defined starter cultures or bacteriophage blends, and standardized methods for texture and flavor measurement. By focusing on these biochemical and microbiological mechanisms and their applications, this review provides a roadmap for transforming dry aging into a reproducible, safe, and high-quality process in modern meat science.},
}

Animals
Cattle
*Microbiota
*Red Meat/microbiology/analysis
*Food Handling/methods
Humans
Food Quality
Food Microbiology
Taste
*Meat/microbiology/analysis

@article {pmid41029975,
year = {2025},
author = {Al Meslamani, AZ and Jarab, AS and Elrefae, A},
title = {Advances in type 2-high asthma therapy: what remains missing?.},
journal = {Expert review of respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1080/17476348.2025.2569844},
pmid = {41029975},
issn = {1747-6356},
abstract = {INTRODUCTION: Type 2-high asthma (T2HA) accounts for most severe asthma morbidity and is driven by eosinophilic, IgE- and alarmin-mediated inflammation. Although five biologics are licensed, many patients remain symptomatic, corticosteroid-dependent or financially excluded.

AREAS COVERED: PubMed, Embase, Web of Science, Scopus, Cochrane Library, EconLit, ClinicalTrials.gov and WHO-ICTRP were searched (1 January 2005 - 30 June 2025). Evidence from randomized trials, economic evaluations and translational studies on biologics, small-molecule drugs, cell-based and microbiome-directed interventions was synthesized across four domains: late-stage attrition, ultra-long-acting biologic limitations, slow small-molecule progress, and cost - access barriers. Durability, pediatric data and OCS-sparing potential were also examined.

EXPERT OPINION: Phenotype-guided biologics have replaced corticosteroid escalation after two decades of research; nevertheless, plateaus in effectiveness, uncertain long-term safety profiles, and exorbitant costs persist. Future progress will depend on value-based pricing that facilitates global adoption, adaptive biomarker-anchored clinical trials, rational combination or bispecific therapeutics, and rigorous post-marketing surveillance of cell-based and microbiome-directed therapies. Delivering sustainable, equitable management of T2HA necessitates the coordination of scientific, regulatory, and economic mechanisms rather than focusing on increasingly narrow cytokine targets.},
}

@article {pmid41029962,
year = {2025},
author = {Ben Valid, O and Shouval, R},
title = {Predictors of response to CD19 chimeric antigen receptor T-cell therapy in large B-cell lymphoma: a consolidated review.},
journal = {Current opinion in oncology},
volume = {},
number = {},
pages = {},
pmid = {41029962},
issn = {1531-703X},
abstract = {PURPOSE OF REVIEW: CD19-directed chimeric antigen receptor T-cell (CAR-T) therapy has transformed outcomes for relapsed/refractory large B-cell lymphoma (LBCL), yet nearly half of treated patients relapse, and toxicities remain frequent. A deeper understanding of response predictors is urgently needed to guide patient selection, treatment optimization, and development of rational combination strategies.

RECENT FINDINGS: Emerging data reveal that response to CAR-T therapy is shaped by patient-specific, tumor-intrinsic, and treatment-related factors. Clinical variables such as age, performance status, inflammation, and microbiome composition influence efficacy. Tumor burden, disease distribution, histologic subtype, and genomic alterations correlate with resistance. Treatment factors, including bridging strategies, lymphodepletion regimen, and CAR-T product design, affect expansion, persistence, and clinical outcomes. Novel insights from immune profiling, radiomics, and single-cell transcriptomics offer further granularity and predictive potential.

SUMMARY: Predictors of CAR-T response span diverse biological and clinical domains and are increasingly actionable. Integrating multimodal biomarkers into routine workflows can personalize care and improve outcomes. Prospective validation, real-time monitoring, and adaptive trial designs are essential next steps toward precision CAR-T therapy.},
}

@article {pmid41029787,
year = {2025},
author = {Lemieux, É and Monger, XC and Saucier, L and Charette, SJ and Guay, F and Pouliot, É and Fournaise, S and Vincent, AT},
title = {Effect of an antibiotic and a probiotic on phage communities in the swine gut microbiota.},
journal = {BMC research notes},
volume = {18},
number = {1},
pages = {402},
pmid = {41029787},
issn = {1756-0500},
support = {RGPIN-2022-03321//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Swine/microbiology ; *Bacteriophages/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Feces/microbiology/virology ; Cross-Over Studies ; },
abstract = {OBJECTIVE: The impact of dietary treatments on the phage community of porcine intestinal microbiota is not well understood. An antibiotic (tylvalosin), a probiotic (Pediococcus acidilactici), and a combination of these were given to six cannulated pigs in a double crossover design study. Samples of ileal digesta and feces were collected and whole genome shotgun sequencing was performed. The variations in phage and bacterial communities were compared for each treatment and sample type.

RESULTS: The bacteriophages present in the gut microbiome exhibited greater variations in both α- and β-diversity between sample types (digesta, feces) than between treatments. β-diversity and differential abundance showed that the effect of the combined antibiotic and probiotic treatment was the same as with the antibiotic alone. However, the effects of the probiotic and antibiotic treatments were statistically significantly different in the fecal samples. β-diversity was different in those two treatments, and differential abundance analysis identified multiple phages as markers for each treatment. No significant variations in relative abundance were found in phage lifestyle (i.e., virulent, temperate) between treatments.},
}

Animals
*Probiotics/pharmacology/administration & dosage
*Gastrointestinal Microbiome/drug effects
Swine/microbiology
*Bacteriophages/drug effects/genetics
*Anti-Bacterial Agents/pharmacology
Feces/microbiology/virology
Cross-Over Studies

@article {pmid41029586,
year = {2025},
author = {Li, L and Wang, X and Huang, X and Li, C and Wu, Z and Zhu, T and Tian, M and Zhan, Q and Zhuang, Y and Sun, R},
title = {Hypertensive disorders of pregnancy were more strongly associated with the functional and network profiles than with the community composition of the gut bacteriome: a pilot study.},
journal = {BMC pregnancy and childbirth},
volume = {25},
number = {1},
pages = {965},
pmid = {41029586},
issn = {1471-2393},
mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome/physiology ; Pilot Projects ; Case-Control Studies ; Adult ; *Hypertension, Pregnancy-Induced/microbiology ; Feces/microbiology ; RNA, Ribosomal, 16S ; },
abstract = {BACKGROUND: Recent studies implicate that hypertensive disorders of pregnancy (HDP) is associated with gut microbiome. However, the different associations of different microbial features with HDP are little known. This study investigates the different associations of gut bacterial taxonomic composition, functional and network profiles with HDP.

METHODS: A case-control study was conducted in Hefei Maternal and Child Health Hospital from February to August 2024. Twenty-four women with HDP and twenty-one normotensive pregnant controls were included. Fecal samples were collected and the bacterial community in fecal samples were measured using high-throughput sequencing targeting the V4 region of the bacterial 16 S rRNA. The taxonomic composition, functional and network profiles of gut bacterial community in both Control and Case groups were determined, and the associations between HDP and gut bacterial profiles were analyzed.

RESULTS: There were no significant differences in gut bacterial community composition between the Control and Case groups. However, the Case group had significantly higher relative abundance of functional taxa associated with intestinal inflammation, primary pathogens involved in gastroenteritis and diarrhea. Furthermore, while the Case group exhibited higher network complexity in gut bacterial interactions, it showed lower ecological variability compared to the Control group. Intriguingly, correlation analyses indicated significantly positive associations between HDP and both microbial functional profiles and species interaction intensity, while no significant correlation was observed with taxonomic composition.

CONCLUSION: Although the gut microbial composition remained unchanged in hypertensive pregnancies, functional dysbiosis characterized by proinflammatory features and altered ecological network properties were significantly associated with pregnant women's blood pressure. The dissociation between taxonomic profiles and functional profiles, as well as taxon interactions, highlights the importance of microbial function and interactions in the gut microbiome-targeted diagnosis and therapy of HDPs.},
}

Humans
Female
Pregnancy
*Gastrointestinal Microbiome/physiology
Pilot Projects
Case-Control Studies
Adult
*Hypertension, Pregnancy-Induced/microbiology
Feces/microbiology
RNA, Ribosomal, 16S

@article {pmid41029580,
year = {2025},
author = {Guan, F and Zhang, X and Gou, W and Wang, Q and Du, S and Su, C and Jia, X and Zheng, J and Wang, H and Ding, G},
title = {Long-term body mass index trajectories and dyslipidemia and related gut microbial features: results from the China health and nutrition survey 1991-2018.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {3203},
pmid = {41029580},
issn = {1471-2458},
mesh = {Humans ; *Dyslipidemias/epidemiology/microbiology ; *Gastrointestinal Microbiome/physiology ; China/epidemiology ; *Body Mass Index ; Female ; Male ; Middle Aged ; Adult ; Nutrition Surveys ; Obesity/epidemiology ; Overweight/epidemiology ; Risk Factors ; },
abstract = {OBJECTIVE: To discover the associations between long-term body mass index (BMI) trajectories and dyslipidemia, and the internal mechanism within different BMI trajectory populations.

METHODS: We chose 11,499 adults from China Health and Nutrition Survey (CHNS) for trajectory modeling. Selected those with two blood lipid measurements (n = 2,003), and determine the risk trajectory group associated with dyslipidemia. We selected two subsets of the 2015 CHNS, CHNS-1 (n = 3,061) and CHNS-2 (n = 1,409) for gut microbiome analysis. A Lasso regression in both the CHNS-1 and the CHNS-2 confirmed the dominant genera of each dyslipidemia risk trajectory. We also used a subset of CHNS-2 (n = 779) with metabolomics data to identify the differential metabolites. We ascertained the connection between microbiome and metabolites via correlation analysis.

RESULTS: We identified three BMI trajectories: The developing into overweight (DO) group and the overweight to obesity (OTO) group had increased dyslipidemia risks compared to the normal stable (NS) group, OR: 1.69(95%CI: 1.30,2.20);1.93(95%,CI:1.34,2.77). There are significant differences in gut microbiota between OTO/DO group and NS group, PERMANOVA R[2] = 0.50 and 0.23, p < 0.001. we found six taxa in the OTO group and five taxa in the DO group had lower abundance than in the NS group. after adjusting for covariates, yielded an AUC of 0.759 and 0.646 in the validation set. In the OTO and DO groups we also found 36 metabolites and 5 metabolites, respectively, with differential concentrations than in the NS group.

CONCLUSIONS: A high-level BMI change trajectory will increase the risk of developing dyslipidemia in the future. The growth trajectory of BMI affects lipid metabolism mediated by gut microbiota.These findings may reveal the mechanism of BMI changes leading to dyslipidemia, and indicate the corresponding microbiome targets for prevention.},
}

Humans
*Dyslipidemias/epidemiology/microbiology
*Gastrointestinal Microbiome/physiology
China/epidemiology
*Body Mass Index
Female
Male
Middle Aged
Adult
Nutrition Surveys
Obesity/epidemiology
Overweight/epidemiology
Risk Factors

@article {pmid41029521,
year = {2025},
author = {Bao, XG and Chong, PF and He, C and Wang, XY and Zhang, F and Tan, BB and Lou, KX},
title = {Bacillus tequilensis S40 inoculation alleviates salt stress by modifying bacterial community structure and regulating elemental cycling rhizosphere of Reaumuria soongorica.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1251},
pmid = {41029521},
issn = {1471-2229},
support = {32160407//the National Natural Foundation of China/ ; 23YFFA0065//the Gansu Provincial Key Research and Development Program/ ; 25ZDWA007//the Major Special Project of Gansu Provincial Science and Technology Plan - International Cooperation Field/ ; },
mesh = {*Rhizosphere ; Soil Microbiology ; *Bacillus/physiology ; *Salt Stress ; *Microbiota ; *Tamaricaceae/microbiology/growth & development/physiology ; Salt Tolerance ; },
abstract = {Plant growth‒promoting rhizobacteria (PGPRs) are pivotal in forest cultivation and saline‒alkaline soil improvement by altering the structure of rhizosphere bacterial communities and improving soil nutrient utilization efficiency. However, there are few reports on the exploration of PGPR bacterial resources and the mechanism by which PGPR enhance the salt tolerance of Reaumuria soongorica (R. soongorica) in desert shrubs. This study focused on Bacillus tequilensis (B. tequilensis) S40, which is a PGPR isolated from the rhizosphere of R. soongorica by our research group. We investigated the effects of the S40 strain on the rhizosphere microbial community and functional genes of R. soongorica through pot experiments. The results demonstrated that inoculation with the S40 strain could alleviate the negative effects of NaCl stress on the plant height, total root length, and rhizome leaf biomass. Proteobacteria, Bacteroidetes, and Planctomycetota were the dominant phyla. Notably, inoculation with S40 strain significantly increased the absolute abundances of functional genes involved in carbon (C), nitrogen (N), and phosphorus (P) cycling (p < 0.05). Furthermore, the genes related to C, N, and P cycling were significantly correlated with soil properties (available phosphorus, urease activity, sucrase activity), and the biomass of R. soongorica leaves, stems, and roots (p < 0.05). In conclusion, the PGPR strain S40 mediates the reorganization of bacterial community, drives the element cycle, and enhances soil nutrient availability, thus promoting plant growth and enhancing salt tolerance of plants and providing a method and scientific basis for cultivating shrub seedlings and alleviating the degree of soil salinization.},
}

*Rhizosphere
Soil Microbiology
*Bacillus/physiology
*Salt Stress
*Microbiota
*Tamaricaceae/microbiology/growth & development/physiology
Salt Tolerance