@article {pmid41101342,
year = {2025},
author = {Niu, C and Zhang, J and Singh, H and Mostafa, MAO and Zhu, K and Farooq, U and Okolo, PI and Mushtaq, A and Daglilar, E and Alweis, R},
title = {Impact of Concomitant Proton Pump Inhibitor Use on the Efficacy of Immune Checkpoint Inhibitors Across Multiple Cancer Types.},
journal = {Journal of the National Comprehensive Cancer Network : JNCCN},
volume = {},
number = {},
pages = {1-7},
doi = {10.6004/jnccn.2025.7070},
pmid = {41101342},
issn = {1540-1413},
abstract = {BACKGROUND: Proton pump inhibitors (PPIs) are commonly prescribed medications that may influence the gut microbiome and impact the efficacy of immune checkpoint inhibitors (ICIs) in cancer treatment.

PATIENTS AND METHODS: We conducted a large retrospective cohort study using the TriNetX database, encompassing >35,621 patients with cancer treated with ICIs between January 2015 and June 2021. Patients were stratified into 2 cohorts: those receiving ICIs with concurrent PPI use and those without PPI use.

RESULTS: Concomitant PPI use was associated with significantly higher mortality rates in patients treated with PD-1 inhibitors across multiple cancer types, including melanoma (hazard ratio [HR], 1.889; 95% CI, 1.752-2.037); breast cancer (HR, 1.512; 95% CI, 1.345-1.701); urothelial carcinoma (HR, 1.406; 95% CI, 1.276-1.551); colorectal cancer (HR, 1.310; 95% CI, 1.187-1.445); hepatocellular carcinoma (HR, 1.413; 95% CI, 1.238-1.614); renal cancer (HR, 1.490; 95% CI, 1.375-1.614); Hodgkin lymphoma (HR, 1.646; 95% CI, 1.212-2.236); head and neck cancers (HR, 1.402; 95% CI, 1.259-1.561); and lung cancer (HR, 1.308; 95% CI, 1.184-1.445). Similar trends were observed with PD-L1 inhibitors, where PPI use correlated with increased mortality in melanoma (HR, 1.657; 95% CI, 1.049-2.617); breast cancer (HR, 1.584; 95% CI, 1.297-1.934); renal cancer (HR, 1.380; 95% CI, 1.059-1.799); and urothelial carcinoma. ICU admissions were more frequent among PPI users across different cancer types and ICI treatments.

CONCLUSIONS: This study underscores the potential risks associated with the concomitant use of PPIs and ICIs in cancer treatment. The findings suggest that careful consideration is necessary when prescribing PPIs to patients undergoing ICI therapy.},
}

@article {pmid41101029,
year = {2025},
author = {Ma, L and Liu, F and Zhou, M and Zhang, M and Zheng, J and Wang, Z and He, Z and Yan, Q and Wu, B and Wang, C and Shu, L},
title = {Amoebae contribute to the diversity and fate of antibiotic resistance genes in drinking water system.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109867},
doi = {10.1016/j.envint.2025.109867},
pmid = {41101029},
issn = {1873-6750},
abstract = {Free-living amoebae represent a significant eukaryotic group that thrives in drinking water systems, posing considerable risks to water quality due to their inherent pathogenicity and associations with various microorganisms. However, the symbiotic microbial profiles of different amoeba species and the impact of amoeba-bacteria interactions on the antibiotic resistome within drinking water systems remain poorly understood. In this study, we obtained 24 amoeba isolates from tap water, encompassing diverse phyla within the amoeba lineage. Through metagenome sequencing, we uncovered variations in symbiotic microbiome composition across different amoeba species and strains. Notably, amoebae acted as vectors for human pathogens, including bacteria and viruses. The majority of symbionts carried multiple antibiotic-resistance genes and virulence factors. Furthermore, dominant symbiotic species could be cultured independently, underscoring the critical role of amoebae in preserving and transmitting antibiotic-resistant opportunistic pathogens in drinking water systems. Disinfection experiments demonstrated highly diverse viability of amoebae and their protective capabilities for symbionts against chlorine disinfection. Our findings expand the germplasm bank for amoebae and symbiotic bacteria derived from tap water and emphasize the necessity for further research on amoeba-bacteria symbiosis to ensure drinking water quality and public health safety.},
}

@article {pmid41100899,
year = {2025},
author = {Gélinas, V and Paquet, VE and Paquet, MF and Vincent, AT and Charette, SJ},
title = {Phylogenetic and Genomic Insights of Flavobacterium Diversity in Quebec's Fish Farms.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0076},
pmid = {41100899},
issn = {1480-3275},
abstract = {The genus Flavobacterium constitutes a vast pool of microorganisms living in multiple environmental niches including fish pathogens and species in the fish microbiome. Veterinary reports have identified flavobacteria in fish from Quebec's fish farms, confirming their association with infections. However, these reports have not conducted in-depth characterization, and the diversity of non-pathogenic flavobacteria in Quebec remains unknown. This study is the first step in assessing the diversity of Flavobacterium in Quebec's fish farms, without focusing solely on pathogenic strains. Seventeen isolates were collected from different fish farms, from either the water or fish. Microbial species identification was performed using PCR genotyping of the gyrB gene, whole-genome sequencing, and phylogenetic analysis. Antimicrobial susceptibility tests for tetracycline and florfenicol, the two most commonly used antibiotics in Quebec aquaculture, along with predictive tools, were employed to assess resistance. This study revealed potential new species among the isolates. No known pathogenic species were detected, and all 17 isolates clustered within CIIIb or CIIIc, recently described phylogenetic clades of Flavobacterium found in various environments, and the majority showed resistance to antibiotics. This study highlights the expanding diversity of Flavobacterium, particularly among species associated with fish, and underscores the need for further research in Quebec.},
}

@article {pmid41100723,
year = {2025},
author = {Guan, WJ and Pan, CX and Martinez-Garcia, MA},
title = {The Upper Airway Microbiome in Bronchiectasis: Expanding the Landscape of Airway Dysbiosis.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.202508-2095ED},
pmid = {41100723},
issn = {1535-4970},
}

@article {pmid41100528,
year = {2025},
author = {Deschner, D and Hill, JE},
title = {Identification of genes that differentiate Mannheimia haemolytica genotypes 1 and 2 using a pangenome approach.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0325338},
doi = {10.1371/journal.pone.0325338},
pmid = {41100528},
issn = {1932-6203},
mesh = {*Mannheimia haemolytica/genetics/pathogenicity/classification ; Genotype ; *Genome, Bacterial ; Animals ; Cattle ; *Genes, Bacterial ; Bacterial Proteins/genetics ; },
abstract = {Mannheimia haemolytica is an opportunistic bacterial pathogen associated with the economically costly bovine respiratory disease. Two genotypes have been described, of which genotype 2 is more strongly associated with disease. Several previous studies have investigated the genomic differences between the genotypes and/or the major serotypes (1, 2 and 6) of M. haemolytica, however we still lack a clear basis for the greater disease association of genotype 2 (serotypes 1 and 6) and demonstrations of phenotypic differences are scarce. This work builds upon previous investigations to identify genes that differentiate the two genotypes with a particular focus on genes that may play a role in virulence and fitness in the respiratory tract microbiome. We identified 422 genotype differentiating genes in a collection of 206 unique M. haemolytica genomes (61 genotype 1, 145 genotype 2). Genotype differentiating genes included genotype-associated variants of a TonB-dependent siderophore receptor homolog, transferrin binding protein B, leukotoxin A, and IgA1 proteases. We also identified a genotype 1 associated lytic transglycosylase, and a genotype 2 specific highly immunogenic outer membrane lipoprotein. Genotype 2 genomes were significantly larger in size and contained more predicted protein coding genes than genotype 1 genomes. These results expand our knowledge of what differentiates the genotypes 1 and 2 of M. haemolytica and provides information that can be used as the basis for laboratory investigations of corresponding phenotypic differences.},
}

*Mannheimia haemolytica/genetics/pathogenicity/classification
Genotype
*Genome, Bacterial
Animals
Cattle
*Genes, Bacterial
Bacterial Proteins/genetics

@article {pmid41100520,
year = {2025},
author = {Stirnemann, EM and Sasse, J},
title = {How to harness the effects of exudates and microbes that support beneficial plant-plant interactions for sustainable agriculture.},
journal = {PLoS biology},
volume = {23},
number = {10},
pages = {e3003416},
doi = {10.1371/journal.pbio.3003416},
pmid = {41100520},
issn = {1545-7885},
mesh = {*Crops, Agricultural/microbiology/growth & development/metabolism ; *Agriculture/methods ; Plant Roots/microbiology/metabolism ; Rhizosphere ; *Plant Exudates/metabolism ; Microbiota/physiology ; Soil Microbiology ; *Plants/microbiology/metabolism ; },
abstract = {Root exudates, species-specific metabolites released by plants into the rhizosphere, shape plant nutrient uptake, plant-plant and plant-microbiome interactions. When optimized, such interactions boost the productivity of sustainable agricultural systems such as intercropping and crop rotation. However, why certain combinations of crops are beneficial and others are not, remains unclear. This Essay outlines how optimal crop combinations could be determined, focusing on the molecular interplay of crops and their microbial partners. With an advanced understanding of root exudation and its effects on microbes, new strategies for sustainable farming could be unlocked, reducing reliance on fertilizers and pesticides, and tackling challenges raised by a changing climate.},
}

*Crops, Agricultural/microbiology/growth & development/metabolism
*Agriculture/methods
Plant Roots/microbiology/metabolism
Rhizosphere
*Plant Exudates/metabolism
Microbiota/physiology
Soil Microbiology
*Plants/microbiology/metabolism

@article {pmid41100345,
year = {2025},
author = {Meunier, D and Corona-Torres, R and Boulton, K and Wu, Z and Ballantyne, M and Glendinning, L and Ahmad, AA and Borowska, D and Taylor, L and Vervelde, L and Del Pozo, J and Vasilogianni, M and Jaramillo-Ortiz, J and Sanchez-Arsuaga, G and Psifidi, A and Tomley, F and Watson, KA and McGrew, MJ and Stevens, MP and Blake, DP and Hume, DA},
title = {Interleukin 10 controls the balance between tolerance, pathogen elimination, and immunopathology in birds.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
doi = {10.7554/eLife.106252},
pmid = {41100345},
issn = {2050-084X},
support = {BB/P022049/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P021638/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 13393976//Cobb-Vantress/ ; 13302777//Roslin Institute/ ; BBS/E/D/20002174/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/RL/230002B/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Interleukin-10/genetics/metabolism/immunology ; *Chickens/immunology ; Salmonella typhimurium/immunology ; *Immune Tolerance ; Campylobacter jejuni/immunology ; Macrophages/immunology ; *Immunity, Mucosal ; Cecum/microbiology ; *Poultry Diseases/immunology/microbiology ; Campylobacter Infections/immunology/veterinary ; Gastrointestinal Microbiome ; },
abstract = {Effective mucosal immunity in the intestine involves a fine balance between tolerance of the microbiome, recognition, and elimination of pathogens, and inflammatory tissue injury. The anti-inflammatory cytokine IL10 regulates these processes in the intestines of mice and humans; the anti-inflammatory activity of IL10 is also conserved in birds. To determine the function of IL10 in avian mucosal immunity, we generated germ line modifications of the chicken IL10 locus to abolish or reduce IL10 expression. In vitro analysis of macrophage response to lipopolysaccharide confirmed the loss of IL10 protein expression, the lack of dosage compensation in heterozygotes, and prevention of autocrine inhibition of nitric oxide production in homozygous IL10 knockout macrophages. IL10-deficiency significantly altered the composition of the caecal microbiome, but unlike IL10-deficient mice and humans, IL10-deficient chickens did not exhibit spontaneous colitis. Following experimental challenge with Salmonella enterica serovar Typhimurium or Campylobacter jejuni in IL10-deficient chickens, enhanced clearance of the pathogens was associated with elevated transcription of pro-inflammatory genes and increased infiltration of inflammatory cells into gut mucosa. In IL10-deficient chickens challenged with the parasite Eimeria tenella, pathogen clearance was accelerated but caecal lesions were more severe and weight gain was compromised. Neither the heterozygous IL10 knockout nor a homozygous IL10 enhancer mutation had a major effect on pathogen clearance or inflammation in any of the challenge models. Our findings highlight the intrinsic compromise in mucosal immune response and have important implications for the development of strategies to combat avian and zoonotic pathogens in poultry.},
}

Animals
*Interleukin-10/genetics/metabolism/immunology
*Chickens/immunology
Salmonella typhimurium/immunology
*Immune Tolerance
Campylobacter jejuni/immunology
Macrophages/immunology
*Immunity, Mucosal
Cecum/microbiology
*Poultry Diseases/immunology/microbiology
Campylobacter Infections/immunology/veterinary
Gastrointestinal Microbiome

@article {pmid41100191,
year = {2025},
author = {Fernandes, ILB and Cantor, MC and Fonseca, A and Ganda, E and Felix, TL},
title = {The association of lung consolidation in beef × dairy cattle at weaning with feedlot growth performance, carcass characteristics, liver health, and liver microbiome diversity.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf358},
pmid = {41100191},
issn = {1525-3163},
abstract = {Bovine respiratory disease (BRD) is the costliest disease in the cattle industry and often compromises the immune system. The objective of this observational cohort study was to evaluate the impact of lung consolidation (LC) diagnosed at weaning (8 ± 2 wk of age) on feedlot growth performance, carcass characteristics, and liver health and microbiome in beef × dairy cattle. At 4 d post-weaning, LC was assessed by thoracic ultrasonography. The cattle (n = 139) either had ≥ 1 cm2 LC in at least one lung lobe and were BRD positive (35 calves; BRD) or did not (< 1 cm2) and were negative (104 calves; CONTROL). Cattle were moved to the feedlot at 353 ± 53 d of age where individual feed intake and body weights (BW) were recorded. Cattle were sent to slaughter when they reached a target final BW (steers = 680 kg and heifers = 635 kg). Liver scores and carcass data were collected. A subset (n = 29; 18 BRD cattle vs. 11 CONTROL cattle) had healthy liver tissue analyzed to investigate the association of LC at weaning with the liver microbiome diversity at slaughter. Only cattle with edible livers and no lung lesions were included in the microbiome analysis subset. Liver tissue samples were collected at slaughter and subsequently sequenced for microbiome analysis using an Illumina platform through targeted sequencing of the V4 region of the 16S rRNA gene. Mixed linear models were used to assess the effects of LC on growth performance and carcass characteristics with calf ranch, sex, and breed as fixed effects in the model. Generalized linear mixed models were used to assess the distributions of lung scores, liver scores, and quality grade at slaughter between LC and CONTROL cattle. To assess the effect of LC at weaning on the liver microbial communities at slaughter, the beta diversity (ADONIS) test was run, and the relative abundance of taxa is presented. There were no differences between BRD and CONTROL cattle for growth performance or most carcass traits (P > 0.05). However, the marbling score was greater (P = 0.05) in carcasses from CONTROL cattle (495 ± 7.82; LSM ± SEM) when compared with carcasses from BRD cattle (462 ± 13.84at 8 ± 2 wk of age. The beta diversity in the liver did not differ (P > 0.05) between BRD and CONTROL cattle. Staphylococcus was the most abundant genus among the liver samples, regardless of health status at weaning. A diagnosis of BRD by LC in beef × dairy cattle at weaning (57 ± 14 d of age) reduced marbling and impacted quality grade.},
}

@article {pmid41100183,
year = {2025},
author = {Miller, HE and Sasser, CN and Hernandez, MS and Legako, JF and Anderson, CJ and Schmitz-Esser, S and Ericsson, AC and Broadway, PR and Sanchez, NCB and Carroll, JA and Penn, MJC and Petry, AL},
title = {Fiber deprivation and insoluble corn-based fibrous co-products modulate gastrointestinal mucosa-associated microbiota, extracellular matrix remodeling, and intestinal morphology in growing pigs.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf360},
pmid = {41100183},
issn = {1525-3163},
abstract = {This study examined how insoluble corn-based fibrous coproducts (ICBF) affect gastrointestinal (GI) mucosal microbiota, gene expression, and intestinal morphology in growing pigs compared to fiber deprivation. Fifty-six gilts (26.7±2.5 kg BW), were randomly assigned to one of 7 semi-synthetic diets. Treatments included a fiber-deprived control [CTL;<1% insoluble dietary fiber (IDF)], and 6 diets where an ICBF replaced 30% of corn starch: dehulled degermed corn (DHDG; IDF=1.7%), ground corn (COR; IDF=4.7%), corn gluten meal (CGM; IDF=5.2%), dried distillers grains (DDGS; IDF=8.6%), high protein dried distillers grains (HP; IDF=13.5%), and corn bran (BRN; IDF=17.5%). Pigs were individually housed and limit-fed 2.4 times maintenance. On day 31, duodenum, jejunum, ileum, and colon tissues were collected. Microbial 16S rRNA sequencing of mucosal material, tissue transcriptomics, and histological analyses were conducted in various intestinal regions. Data were analyzed using mixed models with diet as a fixed effect and linear and quadratic contrasts to assess response IDF. A negative binomial model with FDR correction were used for operational taxonomic unit (OTU) analysis, and transcriptomics were evaluated with DESeq2 comparing ICBF sources to CTL (Q ≤ 0.05, |log2FC| ≥ 2). In the ileal mucosa, Shannon and Simpson diversity indices linearly increased with IDF%, while in the colon mucosa Chao1 and Shannon diversity responded quadratically (P<0.05). Among the top 100 most abundant OTUs, 60 and 86 differed in ileal and colonic mucosa, respectively (Q<0.05). In the ileum and colon pigs fed low-ICBF diets (CTL, DHDG) had increased abundance of OTUs containing opportunistic or potentially pathogenic species (e.g., Enterobacteriaceae, Campylobacter, Streptococcus). However, moderate-to-high ICBF diets, CGM, DDGS, and BRN, enriched mucosal-associated Lactobacillus, Bifidobacterium, and Akkermansia. In the duodenum and ileum, villous height had a positive quadratic relationship to increasing IDF, while the jejunum villous height linearly decreased (P<0.05). Gene expression profiles revealed that moderate-to-high ICBF (DDGS, HP, and BRN) upregulated genes associated with cell structure and extracellular matrix (ECM) remodeling (TPPP3, MUC5AC, SERPINA1). Fiber-deprivation upregulated genes associated with ECM degradation (MMP9, MMP12), and collagen formation (COL26A1). Thus, both fiber deprivation and excessive ICBF can disrupt mucosal microbial and host homeostasis.},
}

@article {pmid41099894,
year = {2025},
author = {Khumalo, NN and Obi, LU and Yusuf, AA and Adeleke, RA},
title = {Dietary modulation of gut microbiota and functional enzymes in savannah honey bees (Apis mellifera scutellata Lepeletier).},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {226},
pmid = {41099894},
issn = {1432-0614},
support = {PR_DAAD210907637972//National Research Foundation/ ; SRUG220326856//National Research Foundation/ ; },
mesh = {Animals ; Bees/microbiology/enzymology ; *Gastrointestinal Microbiome ; *Diet ; Pollen ; *Bacteria/classification/genetics/isolation & purification/enzymology ; Biodiversity ; Animal Feed/analysis ; },
abstract = {Honey bees gather pollen from flowering plants, using it as a vital protein source and, in turn, acquire pollen-associated microbes that interact with their existing gut microbiota. Despite their ecological importance, limited information exists regarding the gut microbiota of African savannah honey bees (Apis mellifera scutellata Lepeletier) and how diet and its associated microbial community influence this crucial internal ecosystem. This study aimed to investigate the differences in gut microbiota between wild honey bees collected during the flowering season and microbially depleted honey bees reared under semi-sterile conditions and fed various protein diets. To achieve this, freshly hatched worker bees were maintained in hoarding cages and assigned one of four protein diets: fresh sunflower pollen, casein, sterilised casein, or sterilised pollen. High-throughput DNA metabarcoding was then employed to compare the microbial composition of the honey bee gut across these groups. Our findings revealed that the gut of microbially depleted honey bees exhibited higher species diversity and richness. Conversely, the non-core gut microbial community predominated in wild bees and those fed the different protein diets. Specifically, Commensalibacter, Bartonella, and Bifidobacterium were the most dominant bacterial genera across all treatments. Interestingly, Gilliamella, a common core gut bacterium, was undetected, while Apibacter was exclusively found in wild honey bees. Furthermore, pollen-associated microbes such as Devosia and Pedobacter were identified solely in the gut of honey bees fed a pollen diet. Functional predictions of the gut microbial community also indicated the presence of key enzymes such as β-glucosidase, β-galactosidase, pyruvate dehydrogenase and phosphoglycerate mutase, which are crucial for enhancing nutrient absorption, digestion, and carbohydrate metabolism. These results underscore the intricate relationship between honey bees, microbes, and plants, offering valuable insights into how diet and its associated microbial communities could shape the gut microbiota of African honey bees. KEY POINTS: • The non-core gut microbiota dominates the African savannah honey bee • The type of diet influenced the microbial diversity and community abundance in the honey bee gut • Key enzymes involved in digestion, nutrition absorption, and carbohydrate metabolism were enhanced in the gut • Pollen-associated microbes found in the diet present potential avenues for probiotic development to improve honey bee health.},
}

Animals
Bees/microbiology/enzymology
*Gastrointestinal Microbiome
*Diet
Pollen
*Bacteria/classification/genetics/isolation & purification/enzymology
Biodiversity
Animal Feed/analysis

@article {pmid41099815,
year = {2025},
author = {Price, A and Mog, SYA and Dubach, J and Billington, C and Larsen, P},
title = {Microbiomes of 2024's Periodical Cicada Brood XIII Vary By Species and Location.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {105},
pmid = {41099815},
issn = {1432-184X},
support = {2216567 & 1912104//National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Microbiota ; *Hemiptera/microbiology ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; Illinois ; Male ; Female ; },
abstract = {The 17-year Periodical cicadas (Magicicada spp.) are long-lived insects that emerge in mass synchronized events after 17 years underground. Their survival and ecological success depend heavily on their microbiomes, which include obligate bacterial symbionts essential for nutrient acquisition, as well as occasional pathogens such as the behavior-altering fungus Massospora cicadina. While the periodical cicada lifecycle is well studied, little is known about how cicada microbiomes vary across species and environments during a single emergence event. During the 2024 emergence of Brood XIII in northern Illinois, 17-year cicadas were sampled from four ecologically distinct forest preserves. Cicadas were identified by species and sex; their microbiomes were assayed using 16S rRNA gene sequencing and tested for the presence of the fungal pathogen M. cicadina DNA in asymptomatic individuals. Sampling sites were characterized by plant community composition, historical disturbance, and potential presence of the antifungal compound juglone. Microbiome composition differed significantly by cicada species and site, but not by sex. The obligate symbionts Hodgkinia cicadicola and Sulcia muelleri dominated microbiome profiles, though other bacteria-including Pantoea agglomerans, a potential pheromone producer-were variably abundant. Cicada species distributions were non-random across sites and correlated with local plant diversity. M. cicadina DNA was detected in 23% of otherwise asymptomatic cicadas, with infection rates varying by location and negatively correlated with microbiome diversity. This study highlights complex interactions between cicada species, their microbial communities, and environmental variables such as plant diversity, soil chemistry, and land use history.},
}

Animals
*Microbiota
*Hemiptera/microbiology
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Symbiosis
Illinois
Male
Female

@article {pmid41099795,
year = {2025},
author = {Baars, IM and Mrázek, J and Kreisinger, J and Mikšík, I and Dietz, MW and Falcao Salles, J and Tieleman, BI and Gvoždíková Javůrková, V},
title = {Exploring the associations between preen oil bacterial, chemical and proteomic profiles of passerines.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {11},
pages = {173},
pmid = {41099795},
issn = {1572-9699},
support = {OCENW.KLEIN.541//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 14-16861P//Grantová Agentura České Republiky/ ; RVO: 68081766//Institutional Research Support of the Czech Academy of Sciences/ ; },
mesh = {Animals ; Proteomics ; Volatile Organic Compounds/metabolism/analysis ; *Bacteria/classification/metabolism/isolation & purification/genetics ; *Passeriformes/microbiology/metabolism ; *Proteome/analysis ; Bacteriocins/metabolism ; },
abstract = {Preen gland bacteria are thought to be the key producers of preen oil components such as chemosignalling molecules including volatile organic compounds (VOCs) and antimicrobial compounds including peptides and antimicrobial VOCs. However, data on the preen oil bacteriome and chemical composition are limited to a small subset of bird species, and the presence of antimicrobial peptides is largely unexplored. Here, we performed an exploratory study to characterize, for the first time, the preen oil chemical and proteomic profiles and to explore the possible contribution of the bacteriome to the production of preen oil VOCs and antimicrobial peptides (bacteriocins) in eight passerine species, each represented by a single individual. Preen oil bacteriome, chemical and proteomic profiles varied among birds. The bacterial profiles were dominated by the genera Streptococcus, Lactococcus, Corynebacterium and Cutibacterium. The chemical profiles mainly consisted of alcohols, ketones and carboxylic acids. The biological functions primarily associated with the proteomic profiles were proteolysis and response to oxidative stress. Although we were unable to explore a direct association between the bacteriome and chemical profiles, the preen oil contained bacteriocin- and VOC-producing bacterial genera capable of producing detected microbially-derived VOCs (mVOCs), the relative abundance of which varied between birds. Riparian species showed the highest chemical diversity and high abundances of putative preen oil mVOC-producing bacteria, which could suggest habitat-specific adaptations. This exploratory study may significantly contribute to the formulation of hypotheses on the potential role of host ecological factors in the variation of preen oil bacterial, chemical and proteomic profiles in passerines.},
}

Animals
Proteomics
Volatile Organic Compounds/metabolism/analysis
*Bacteria/classification/metabolism/isolation & purification/genetics
*Passeriformes/microbiology/metabolism
*Proteome/analysis
Bacteriocins/metabolism

@article {pmid41099783,
year = {2025},
author = {Alavian, F and Hajimohammadi, A},
title = {Interplay between gut Microbiome and glymphatic system in cognitive function and memory regulation.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {1038},
pmid = {41099783},
issn = {1573-4978},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Cognition/physiology ; *Glymphatic System/metabolism/physiology ; *Memory/physiology ; Animals ; Brain/metabolism ; Neurodegenerative Diseases/metabolism ; Dysbiosis ; Aquaporin 4/metabolism ; },
abstract = {The glymphatic system, a network of perivascular channels in the brain, clears toxins and metabolic products such as amyloid-β (Aβ), supporting cognitive function and preventing neurodegenerative diseases. The gut microbiome also affects brain health and cognitive functions by producing anti-inflammatory metabolites and neurotransmitters. In this narrative review study, recently published articles from reputable scientific databases were collected and analyzed. Characteristics related to the gut microbiome, its metabolites, and their impact on the glymphatic system and ultimately cognitive function were examined. These findings indicate that microbial metabolites such as short-chain fatty acids (SCFAs) and neurotransmitters such as serotonin and melatonin reduce brain inflammation and improve sleep quality and synaptic plasticity, which are essential for memory stabilization. Disruption of the gut microbiome (dysbiosis) leads to increased inflammation and dysfunction of the glymphatic system, resulting in the accumulation of toxic proteins and decreased cognitive function. Proper polarization of aquaporin-4 (AQP4), a water channel protein critical for fluid homeostasis in the brain, in astrocytes is essential for the effective functioning of this system, and its disruption is associated with diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). Understanding the interaction between the gut microbiome and the glymphatic system presents a new pathway for regulating memory and cognitive health, which could be an important target for the prevention and treatment of neurodegenerative diseases. Enhancing the gut microbiome through probiotics and a healthy diet may improve glymphatic system function and brain health, thereby preventing cognitive disorders.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Cognition/physiology
*Glymphatic System/metabolism/physiology
*Memory/physiology
Animals
Brain/metabolism
Neurodegenerative Diseases/metabolism
Dysbiosis
Aquaporin 4/metabolism

@article {pmid41099660,
year = {2025},
author = {Yang, X and Luo, H and Li, Q and Zhu, W and Fu, L and Chen, L and Li, X and Su, H and Zhang, L and Huang, Y},
title = {Gut Microbiota and SCFAs Mediate the Therapeutic Effects of Canagliflozin in PCOS by Promoting White Fat Browning.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {20},
pages = {e71138},
doi = {10.1096/fj.202502661R},
pmid = {41099660},
issn = {1530-6860},
support = {2024NSFSC1730//National Science Foundation project of Sichuan Province/ ; 2024LZXNYDJ101//Science and Technology Strategic Coopration Project of Luzhou-Southwest Medical University/ ; 2024SYF169//Science and Technology Strategic Cooperation Project of Luzhou Government - Southwest Medical University/ ; CYZZD24-12//Chengdu Medical College Technology Program/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Polycystic Ovary Syndrome/drug therapy/metabolism/microbiology ; Female ; Mice ; *Canagliflozin/pharmacology/therapeutic use ; *Fatty Acids, Volatile/metabolism ; *Adipose Tissue, White/metabolism/drug effects ; *Adipose Tissue, Brown/metabolism/drug effects ; Sodium-Glucose Transporter 2 Inhibitors/pharmacology ; Insulin Resistance ; Mice, Inbred C57BL ; },
abstract = {Polycystic ovary syndrome (PCOS) is a common endocrine disorder in women, characterized by hyperandrogenism and frequently accompanied by insulin resistance. Canagliflozin (Cana), a sodium-dependent glucose transporter 2 (SGLT2) inhibitor used to treat diabetes, significantly inhibits renal SGLT2 activity. Clinical studies indicate that SGLT2 inhibitors improve endocrine and reproductive disorders in PCOS patients; however, whether these benefits involve the gut microbiota remains unknown. A PCOS mouse model was established by subcutaneous administration of dehydroepiandrosterone (DHEA). Serum samples were collected for the quantification of sex hormones, insulin, and lipid profiles. Ovarian, adipose tissue, and intestinal samples were harvested for analyses including hematoxylin-eosin staining, immunohistochemistry, reverse transcription polymerase chain reaction, and Western blotting. Gut microbiota composition was assessed via 16S rDNA sequencing, and short-chain fatty acid (SCFA) concentrations in intestinal contents were measured by gas chromatography. Cana improves ovarian function in PCOS mice, addressing disrupted estrous cycles, abnormal ovarian morphology, and hormonal imbalances. Meanwhile, Cana also demonstrated positive effects on glucose tolerance, insulin sensitivity, and gut barrier function. These changes were accompanied by enhanced white fat browning and increased mitochondrial biogenesis. Mechanistically, these beneficial effects were associated with modulation of the gut microbiota and its metabolites SCFAs, and butyric acid add-on treatment could significantly ameliorate insulin resistance and reproductive dysfunction in a PCOS mouse. This study reveals that Cana contributes to WAT browning and gut microbiota homeostasis, indicating that its therapeutic effects on PCOS-related metabolic and reproductive dysfunction are partially driven by modulation of the gut microbiome.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Polycystic Ovary Syndrome/drug therapy/metabolism/microbiology
Female
Mice
*Canagliflozin/pharmacology/therapeutic use
*Fatty Acids, Volatile/metabolism
*Adipose Tissue, White/metabolism/drug effects
*Adipose Tissue, Brown/metabolism/drug effects
Sodium-Glucose Transporter 2 Inhibitors/pharmacology
Insulin Resistance
Mice, Inbred C57BL

@article {pmid41099535,
year = {2025},
author = {Rusanova, A and Mamontov, V and Ri, M and Meleshko, D and Trofimova, A and Fedorchuk, V and Ezhova, M and Finoshin, A and Lyupina, Y and Isaev, A and Sutormin, D},
title = {Taxonomically different symbiotic communities of sympatric Arctic sponge species show functional similarity with specialization at species level.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0114725},
doi = {10.1128/msystems.01147-25},
pmid = {41099535},
issn = {2379-5077},
abstract = {UNLABELLED: Marine sponges harbor diverse communities of associated organisms, including eukaryotes, viruses, and bacteria. Sponge-associated microbiomes contribute to the health of host organisms by defending them against invading bacteria and providing them with essential metabolites. Here, we describe the microbiomes of three sympatric species of cold-water marine sponges-Halichondria panicea, Halichondria sitiens, and Isodictya palmata-sampled at three time points over a period of 6 years in the White Sea. We identified the sponges as low microbial abundance species and detected stably associated bacteria that represent new taxa of sponge symbionts within Alpha- and Gammaproteobacteria. The sponges carried unique sets of unrelated species of symbiotic bacteria, illustrating the varying complexity of their microbiomes. At the community level, sponge-associated microbiomes shared common symbiotic features: they encoded multiple eukaryotic-like proteins, biosynthetic pathways and transporters of amino acids and vitamins essential for sponges. At the species level, however, different classes of eukaryotic-like proteins and pathways were distributed between dominant and minor symbionts, indicating specialization within microbiomes. Particularly, the taurine and sulfoacetate import and degradation pathways were associated exclusively with dominant symbionts in all three sponge species, suggesting that these pathways may represent symbiotic features. Our study indicates convergent evolution in the microbiomes of sympatric cold-water sponge species, as reflected by strong functional similarity despite the presence of distinct, taxonomically unrelated symbiotic communities.

IMPORTANCE: Sponges are regarded among the earliest multicellular organisms and the most ancient examples of animal-bacterial symbiosis. The study of host-microbe interactions in sponges has advanced rapidly due to the application of next-generation sequencing (NGS) technologies that help overcome the challenges of investigating their communities. However, many sponge species, particularly those from polar ecosystems, remain poorly characterized. Here, we demonstrate that three sympatric cold-water sponge species, including two analyzed for the first time, harbor distinct sets of bacterial symbionts, stably associated over 6 years. Using CORe contigs ITerative Expansion and Scaffolding, an algorithm developed in this study, we reconstructed high-quality symbiont genomes and revealed shared features indicative of convergent evolution toward symbiosis. Notably, we identified a potentially novel symbiotic feature-a gene cluster likely involved in sulfoacetate uptake and dissimilation. We also observed shifts in microbiome composition, associated with increasing water temperatures, raising concerns about the impact of global warming on cold-water ecosystems.},
}

@article {pmid41099524,
year = {2025},
author = {Day, AW and Hayes, E and Perez-Lozada, J and DiLeo, A and Blandino, K and Maguire, J and Kumamoto, CA},
title = {Candida albicans colonization modulates murine ethanol consumption and behavioral responses through elevation of serum prostaglandin E2 and impact on the striatal dopamine system.},
journal = {mBio},
volume = {},
number = {},
pages = {e0223925},
doi = {10.1128/mbio.02239-25},
pmid = {41099524},
issn = {2150-7511},
abstract = {UNLABELLED: Candida albicans is a commensal yeast that is a common component of the gastrointestinal (GI) microbiome of humans. C. albicans has been shown to bloom in the GI tract of individuals with alcohol use disorder (AUD) and can promote and increase the severity of alcoholic liver disease. However, the effects of C. albicans blooms on the host in the context of AUD or AUD-related phenotypes, such as ethanol preference, have been unstudied. In this work, we report a reduction in ethanol consumption and preference in mice colonized with C. albicans. C. albicans-colonized mice exhibited elevated levels of serum prostaglandin E2 (PGE2), and the reduced ethanol preference was reversed by injection with antagonists of PGE2 receptors. Furthermore, injection of mice with a PGE2 derivative decreased their ethanol preference. These results show that PGE2 acting on its receptors prostaglandin E receptor 1 (EP1) and prostaglandin E receptor 2 (EP2) drives reduced ethanol preference in C. albicans-colonized mice. We also showed altered transcription of dopamine receptors in the dorsal striatum of C. albicans-colonized mice and more rapid acquisition of ethanol-conditioned taste aversion, suggesting alterations to reinforcement or aversion learning. Finally, C. albicans-colonized mice were more susceptible to ethanol-induced motor coordination impairment, showing significant alterations to the behavioral effects of ethanol. This study identifies a member of the fungal microbiome that alters ethanol preference and demonstrates a role for PGE2 signaling in these phenotypes.

IMPORTANCE: Candida albicans is a commensal yeast that is found in the gut of most individuals. C. albicans has been shown to contribute to alcoholic liver disease. Outside of this, the impact of intestinal fungi on alcohol use disorder (AUD) had been unstudied. As AUD is a complex disorder characterized by high relapse rates and there are only three FDA-approved therapies for the maintenance of abstinence, it is important to study novel AUD contributors to find new therapeutic targets. Here, we show that an intestinal fungus, C. albicans, can alter mammalian ethanol consumption through an immune modulator, prostaglandin E2. The results highlight novel contributors to AUD-related phenotypes and further implicate the gut-brain axis in AUD. Future studies could lead to new therapeutic avenues for the treatment of AUD.},
}

@article {pmid41099510,
year = {2025},
author = {Wallace, BA and Varona, NS and Stiffler, AK and Vermeij, MJA and Silveira, C},
title = {High microbial diversity, functional redundancy, and prophage enrichment support the success of the yellow pencil coral, Madracis mirabilis, in Curaçao's coral reefs.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0120825},
doi = {10.1128/msystems.01208-25},
pmid = {41099510},
issn = {2379-5077},
abstract = {UNLABELLED: Coral reefs have undergone extensive coral loss and shifts in community composition worldwide. Despite this, some coral species appear naturally more resistant, such as Madracis mirabilis (herein Madracis). Madracis has emerged as the dominant hard coral in Curaçao, comprising 26% of coral cover in reefs that declined by 78% between 1973 and 2015. Although life history traits and competitive mechanisms contribute to Madracis's success, these factors alone may not fully explain it, as other species with similar traits have not shown comparable success. Here, we investigated the potential role of microbial communities in the success of Madracis on Curaçao reefs by leveraging a low-bias bacterial and viral enrichment method for metagenomic sequencing of coral samples, resulting in 77 unique bacterial metagenome-assembled genomes and 2,820 viral genomic sequences. Our analyses showed that Madracis-associated bacterial and viral communities are 12% and 20% richer than the communities of five sympatric coral species combined. The Madracis-associated bacterial community was dominated by Ruegeria and Sphingomonas, genera that have previously been associated with coral health, defense against pathogens, and bioremediation. These communities also displayed higher functional redundancy, which is often associated with ecological resilience. The viral community exhibited a 50% enrichment of proviruses relative to other corals. These proviruses had the genomic capacity to laterally transfer genes involved in antibiotic resistance, central metabolism, and oxidative stress responses, potentially enhancing the adaptive capacity of the Madracis microbiome and contributing to Madracis's success on Curaçao's reefs.

IMPORTANCE: Understanding why some coral species persist and thrive while most are in fast decline is critical. Madracis mirabilis is increasingly dominant on degraded reefs in Curaçao, yet the role of microbial communities in its success remains underexplored. This study highlights the potential role of Madracis-associated bacterial and viral communities in supporting coral resilience and competitive success. By identifying key microbial partners and viral genes that may enhance host stress tolerance and defense against pathogens, we broaden the understanding of how the coral holobiont contributes to species persistence under environmental stress. These insights are valuable for predicting key microbial community players in reef interactions and may inform microbiome-based strategies to support coral conservation and restoration.},
}

@article {pmid41099505,
year = {2025},
author = {Brubaker, L and McDonald, D and Putnam, S and Brennan, C and Fok, CS and Lewis, CE and Lowder, JL and Mueller, MG and Rickey, LM and Mueller, ER and Song, SJ and Rudser, K and Knight, R and Lukacz, ES and , },
title = {Bladder health and the urogenital microbiome in community-dwelling adult females.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0055825},
doi = {10.1128/msystems.00558-25},
pmid = {41099505},
issn = {2379-5077},
abstract = {UNLABELLED: Despite the established association with lower urinary tract symptoms, the relationship between a healthy bladder and the urogenital microbiome is unknown. This observational cohort study of 435 community-dwelling women examined bladder health and function using a validated instrument. Voided urine samples were self-collected, shipped to a repository, and underwent 16S rRNA amplicon sequencing. Two hundred seventy-four (56%) samples were retained following a limit-of-detection analysis for low biomass samples. A differential abundance analysis showed that Lactobacillus, the dominant genus, was associated with higher bladder function scores, but not global perception of bladder health, while Prevotella and Anerococcus were associated with lower scores. Associations between the female urogenital microbiome exist across the bladder health spectrum.

IMPORTANCE: There is increasing awareness that human microbiomes impact health and modulate certain health conditions. Recently, investigators developed a validated assessment of bladder health in adult women. This advance facilitated evaluation of the urogenital microbiome, across the adult lifespan and across the spectrum of bladder health in a population-based, observational study.},
}

@article {pmid41099502,
year = {2025},
author = {Serrador, D and Getz, LJ and Cao, KY and Campbell, JR and Kaul, R and Navarre, WW},
title = {Complete genome sequences of six Lactobacillus iners strains isolated from Kenyan women.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0075925},
doi = {10.1128/mra.00759-25},
pmid = {41099502},
issn = {2576-098X},
abstract = {Lactobacillus iners is one of the most common members of the vaginal microbiome, with a controversial role in vaginal health. Here, we present the complete genome sequences of six L. iners strains isolated from cervicovaginal secretions from women in Nairobi, Kenya.},
}

@article {pmid41099497,
year = {2025},
author = {Comstock, LE},
title = {Lessons from the model gut Bacteroidales Bacteroides fragilis and Bacteroides thetaiotaomicron and future opportunities.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0034625},
doi = {10.1128/jb.00346-25},
pmid = {41099497},
issn = {1098-5530},
abstract = {Bacteroidales is an order of bacteria that includes members that colonize the human gut, oral cavity, cow rumen, and other host-associated environments. Most humans become colonized with gut Bacteroidales species relatively soon after birth and later become colonized at high density with numerous diverse species. Bacteroidales strains often persist in the human gut for decades where they extensively evolve, acquiring point mutations, prophage, mobile plasmids, and integrative conjugal elements, making each person's gut Bacteroidales strains highly personalized. Much of what we have learned about basic biological properties of gut Bacteroidales comes from analyses of two species, Bacteroides fragilis and Bacteroides thetaiotaomicron, which were studied for different reasons. Three decades ago, there was only one human gut Bacteroidales genus recognized, the Bacteroides, into which all human gut Bacteroidales species were classified. Today, the human gut Bacteroidales number over 50 species with more than 14 genera and at least seven families. Studies of B. fragilis and B. thetaiotaomicron have provided a wealth of information of basic processes of these gut symbionts, many of which are generally applicable to other species of gut Bacteroidales. In this review, I provide a historical perspective as to why these two species have served as models, as well as some of the biological processes learned from studies of these two species. Finally, I discuss why present and future analyses of the gut Bacteroidales have expanded beyond these two model organisms.},
}

@article {pmid41099294,
year = {2025},
author = {Leonardi, A and Frizzo, R and Cavarzeran, F and Ozkan, J and Rosani, U},
title = {Ocular Microbiome in Dupilumab-Induced Ocular Surface Disease.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70104},
pmid = {41099294},
issn = {1398-9995},
}

@article {pmid41099014,
year = {2025},
author = {Vázquez-González, L and Peña-Reyes, C and Regueira-Iglesias, A and Balsa-Castro, C and Tomás, I and Carreira, MJ},
title = {EPheClass: ensemble-based phenotype classifier from 16S rRNA gene sequences.},
journal = {Frontiers in bioinformatics},
volume = {5},
number = {},
pages = {1514880},
pmid = {41099014},
issn = {2673-7647},
abstract = {One area of bioinformatics that is currently attracting particular interest is the classification of polymicrobial diseases using machine learning (ML), with data obtained from high-throughput amplicon sequencing of the 16S rRNA gene in human microbiome samples. The microbial dysbiosis underlying these types of diseases is particularly challenging to classify, as the data is highly dimensional, with potentially hundreds or even thousands of predictive features. In addition, the imbalance in the composition of the microbial community is highly heterogeneous across samples. In this paper, we propose a curated pipeline for binary phenotype classification based on a count table of 16S rRNA gene amplicons, which can be applied to any microbiome. To evaluate our proposal, raw 16S rRNA gene sequences from samples of healthy and periodontally affected oral microbiomes that met certain quality criteria were downloaded from public repositories. In the end, a total of 2,581 samples were analysed. In our approach, we first reduced the dimensionality of the data using feature selection methods. After tuning and evaluating different machine learning (ML) models and ensembles created using Dynamic Ensemble Selection (DES) techniques, we found that all DES models performed similarly and were more robust than individual models. Although the margin over other methods was minimal, DES-P achieved the highest AUC and was therefore selected as the representative technique in our analysis. When diagnosing periodontal disease with saliva samples, it achieved with only 13 features an F1 score of 0.913, a precision of 0.881, a recall (sensitivity) of 0.947, an accuracy of 0.929, and an AUC of 0.973. In addition, we used EPheClass to diagnose inflammatory bowel disease (IBD) and obtained better results than other works in the literature using the same dataset. We also evaluated its effectiveness in detecting antibiotic exposure, where it again demonstrated competitive results. This highlights the importance and generalisation aspect of our classification approach, which is applicable to different phenotypes, study niches, and sample types. The code is available at https://gitlab.citius.usc.es/lara.vazquez/epheclass.},
}

@article {pmid41098988,
year = {2025},
author = {Bautista, J and Fuentes-Yépez, MP and Adatty-Molina, J and López-Cortés, A},
title = {Microbial signatures in metastatic cancer.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1654792},
pmid = {41098988},
issn = {2296-858X},
abstract = {Metastasis remains the leading cause of cancer-related death, yet the biological determinants that enable tumor cells to disseminate and colonize distant organs are incompletely understood. Emerging evidence identifies the microbiome, not merely as a bystander, but as an active architect of the metastatic cascade. Microbial communities residing in the gut, mucosal barriers, and within tumors shape metastatic progression by modulating immune surveillance, stromal remodeling, oncogenic signaling, and therapy response. Intratumoral and even intracellular microbes regulate epithelial-mesenchymal transition, angiogenesis, and immune escape, while gut-derived metabolites condition pre-metastatic niches and alter systemic immunity. Technological advances in spatial transcriptomics, single-cell multi-omics, and metagenomics have revealed a spatially organized, functionally integrated microbial ecosystem within tumors, challenging long-held assumptions of sterility in cancer biology. This review synthesizes five converging dimensions of this paradigm: microbial interactions in the metastatic tumor microenvironment; microbiome-mediated immunoediting and metastatic escape; the role of intratumoral and intracellular bacteria in dissemination; spatial-multi-omic approaches to map microbial niches; and microbial biomarkers predictive of metastasis and therapy outcomes. Collectively, these findings recast the microbiome as a critical and targetable determinant of metastasis. Deciphering the tumor-microbe-host triad holds transformative potential for biomarker development, therapeutic innovation, and precision oncology.},
}

@article {pmid41098902,
year = {2025},
author = {Thakur, L and Thakur, S and Rani, V and Verma, S and Kushwaha, PP},
title = {Editorial: Understanding the role of microbiome in alteration of cellular metabolism and cancer development.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1686038},
doi = {10.3389/fcimb.2025.1686038},
pmid = {41098902},
issn = {2235-2988},
}

@article {pmid41098896,
year = {2025},
author = {Primm, TP and Cannon, SR and Karki, AB},
title = {Small worms big discoveries: Galleria mellonella as a model for Campylobacter jejuni infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1686074},
pmid = {41098896},
issn = {2235-2988},
mesh = {Animals ; *Campylobacter jejuni/pathogenicity/genetics ; *Disease Models, Animal ; *Campylobacter Infections/microbiology/immunology ; Larva/microbiology ; Virulence Factors/metabolism ; *Moths/microbiology/immunology ; Virulence ; Host-Pathogen Interactions ; Immunity, Innate ; Humans ; },
abstract = {Galleria mellonella larva have served as a simple, cost-effective model for studying innate immunity and Campylobacter jejuni infection. The model commonly employs an acute, high-dose septic infection via hemocoel injection, with observable endpoints of death and melanization. Studies using G. mellonella have provided insights into C. jejuni virulence factors, including the capsule, transcriptional regulators, outer membrane vesicles, and a T6SS. It has revealed signals for virulence, such as pancreatic amylase and growth temperature, and also allowed for comparisons between C. jejuni strains and across multiple species in the genus. Limitations include the use of high bacterial doses that may obscure the role of specific virulence factors, lack of accounting for larval size variations, and unclear connection to the human anaerobic, microbially-rich gut environment. Future development of this model could allow oral infections for exploring pathogen-microbiome interactions and further assessing mechanisms of this important pathogen.},
}

Animals
*Campylobacter jejuni/pathogenicity/genetics
*Disease Models, Animal
*Campylobacter Infections/microbiology/immunology
Larva/microbiology
Virulence Factors/metabolism
*Moths/microbiology/immunology
Virulence
Host-Pathogen Interactions
Immunity, Innate
Humans

@article {pmid41098822,
year = {2025},
author = {Pons Salom, A and Aspillaga, E and Catalán, IA and Viver, T and Signaroli, M and Sanllehi, J and Grau, A and Martorell-Barceló, M and Barcelo-Serra, M and Alós, J},
title = {Behavioural types correlate with the gut microbiome in juvenile wild and reared gilthead seabream.},
journal = {Royal Society open science},
volume = {12},
number = {10},
pages = {250100},
pmid = {41098822},
issn = {2054-5703},
abstract = {The gut microbiome influences host behaviour through the gut-brain axis (GBA), a bidirectional network of signalling pathways. Although the GBA has been well studied in humans and other mammals, its role in shaping individual behavioural variation in fish remains largely unexplored. In this study, standardized behavioural tests were conducted on 67 juvenile gilthead seabream (Sparus aurata), consisting of 30 wild and 37 reared individuals, across five major behavioural axes-boldness, aggressiveness, sociability, activity and exploration-to determine their behavioural types using linear mixed models. High levels of repeatability of behaviour and consistent behavioural types were observed along the five studied axes. Gut samples from contrasting behavioural types were analysed for diversity, composition and structure using 16S rRNA sequencing. Statistically significant correlations and differences were found between wild and reared groups in both behavioural types and gut microbiome characteristics. These findings provide novel evidence of associations between behavioural types and the gut microbiome in juvenile marine fish, suggesting that gut microbiome may play a role in modulating fish behaviour. While this relationship could involve GBA interactions, further research is needed to confirm such mechanisms. This work could have translational significance for understanding survival, recruitment and life-history evolution in the early life stages of wild fish, as well as improving conservation management of species in both aquaculture and their natural habitats.},
}

@article {pmid41098818,
year = {2025},
author = {Pfister, CA and Stanfield, E and Bogan, M and Weigel, BL and Volbrecht, S and Scorza, K},
title = {Foundational kelp species reveal links between host traits, the environment and the associated microbial community.},
journal = {Royal Society open science},
volume = {12},
number = {10},
pages = {250637},
pmid = {41098818},
issn = {2054-5703},
abstract = {Canopy kelp are foundational species in coastal ecosystems and host diverse bacterial communities. Here, we test the association between bull kelp (Nereocystis luetkeana) host traits, blade-associated bacterial taxa and seawater environmental features across nine sites spanning more than 200 km in Washington state. Traits related to kelp fitness, environmental features and microbial community structure differed geographically. Kelp carbon fixation and tissue nitrogen content were greater at outer coast locales, compared with more inland locales in central and south Puget Sound. Geographic differences in carbon fixation rates, tissue nitrogen and bulb diameter were positively correlated with seawater nutrients and negatively correlated with sea surface temperature. Bacterial taxa showed differentiation among sites, and blade-associated bacterial densities were higher at the outer coast site compared with the most inland site. Yet, 11 bacterial genera were present in at least 80% of the samples; these taxa probably serve as core members of the N. luetkeana microbiome and show both positive and negative correlations with host health and environmental features. We show that there are strong interrelationships between kelp traits, seawater features and bacterial community composition with implications for the health of this highly productive foundational species in coastal ecosystems.},
}

@article {pmid41098770,
year = {2025},
author = {Zhou, F and Wu, Y and Ren, B and Liu, Y and Luo, K and Li, Q and Huang, F and Peng, X and Li, Y and Su, Z and Li, J},
title = {Meta-omics reveals subgingival plaque reconstruction dynamics.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2569528},
pmid = {41098770},
issn = {2000-2297},
abstract = {BACKGROUND: The homeostasis of the subgingival microbiome is crucial for periodontal health, although the dynamics governing its community variation remain insufficiently studied. This study aims to investigate the dynamics of subgingival microbiota reassembly after disruption, focusing on core taxa, functions, and driving forces.

METHODS: 339 subgingival plaques in periodontally healthy states were collected before and after ultrasonic cleaning across 12 timepoints for 1 year. All samples underwent full-length 16S rRNA sequencing; 30 were selected for metagenomic sequencing.

RESULTS: Our findings revealed that disturbed subgingival microbiota underwent short-term disruptions but subsequently reverted to baseline, maintaining stability within a year. Homogeneous selection dominated assembly, driving convergent structure under consistent pressure. Such a recovery process was accompanied by key taxa increased sequentially: Pseudomonas fluorescens early, Haemophilus parainfluenzae mid-stage, and Capnocytophaga spp. late. Functionally, reconstruction began with energy metabolism, expanded via biofilm formation and LPS biosynthesis mid-stage, and involved late apoptosis and complex amino acid metabolism. Microbial interactions, including positive regulation from Veillonella HMT 780 to Fusobacterium HMT 248, internally drove community assembly.

CONCLUSION: Our study clarifies species and functional dynamics during subgingival microbiota reconstruction and maps time-directed networks among stage-specific bacteria, offering a theoretical basis for targeted microbiome regulation.},
}

@article {pmid41098769,
year = {2025},
author = {Li, Y and Xin, Y and Zong, W and Li, X},
title = {The role of oral microbiota in digestive system diseases: current advances and perspectives.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2566403},
pmid = {41098769},
issn = {2000-2297},
abstract = {The oral microbiota is intimately linked to human health and various disease states. With the advent of the Human Microbiome Project, our comprehension of the oral microbiota has substantially improved. This microbial community is not only associated with a range of oral diseases, such as dental caries and periodontal diseases, but also with numerous digestive disorders, as demonstrated by recent clinical studies. Specific bacteria residing in the oral cavity, such as Porphyromonas gingivalis, Fusobacterium species and Streptococcus species, have been shown to translocate to the gastrointestinal tract, thereby establishing a potential connection between the oral and gut microbiota. The transfer and ectopic colonization of oral microbiota within the gastrointestinal tract may contribute to both the onset and exacerbation of gastrointestinal diseases. Following the principles of dysregulation characteristics, mechanism research and innovative treatment, this paper systematically reviews the association between the oral microbiota and various digestive system diseases. This paper explores how specific oral microbiota drive digestive system diseases mechanisms and evaluates treatments including probiotics, prebiotics, fecal microbiota transplantation, and targeted antimicrobial therapies. By clarifying the oral-gut microbiota-disease link, it highlights oral microbiota monitoring as a promising tool for early detection, diagnosis, and therapy.},
}

@article {pmid41098533,
year = {2025},
author = {Sarghie, L and Istvan, P and Aparicio, R and Walker, DW and Tacutu, R and Surleac, M},
title = {Parkin overexpression modulates gut-microbiota composition during aging in Drosophila melanogaster.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1672083},
pmid = {41098533},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiota plays a key role in host health during aging, influencing metabolism, immune function, and lifespan. In older individuals, the microbial community often becomes less diverse and more unstable, which can contribute to chronic inflammation and increased disease risk. Parkin, an E3 ubiquitin ligase, is known to extend lifespan when overexpressed in Drosophila melanogaster, but it's still unclear whether it also influences the gut microbiota during aging and whether this might contribute to its longevity effects.

METHODS: To investigate this, we used an inducible genetic system to overexpress Parkin in adult D. melanogaster. Midguts were collected at four time points: days 10, 30, 45, and 60, and bacterial DNA was extracted for 16S rRNA amplicon sequencing to characterize microbiota composition and diversity. To assess the functional impact of these microbial communities, homogenates from Parkin-overexpressing and control flies were fed to germ-free wild-type recipients, followed by monitoring of lifespan and expression of antimicrobial peptides.

RESULTS AND DISCUSSION: Parkin overexpression resulted in age-dependent changes in gut microbiota composition and diversity. Community structure shifted significantly, with more pronounced differences observed in older flies. When fed to germ-free wild-type flies, homogenates from middle-aged and old control flies reduced the median lifespan. In contrast, the microbiome from Parkin-overexpressing flies was more similar to that of young flies. It did not reduce median lifespan and did not trigger the proinflammatory response seen with the control microbiome. Our findings suggest that Parkin promotes a gut microbial environment that is more balanced and less inflammatory, which may support healthier aging.

CONCLUSION: This study demonstrates that Parkin overexpression influences gut microbiota composition in a way that may be beneficial to host health during aging. The microbial communities associated with Parkin-overexpressing flies were not only distinct but also functionally advantageous, reducing immune activation and extending median lifespan in germ-free recipients. To our knowledge, this is the first study to use Parkin overexpression to explore potential Parkin-related changes in the gut microbial community, changes that were captured dynamically at four different stages of the D. melanogaster lifespan.},
}

@article {pmid41098531,
year = {2025},
author = {Juárez-Aragón, MC and Pantoja-Irys, JR and de la Rosa-Manzano, E and Garrido-Olvera, L and Mujica-Sánchez, H and Trejo-De León, CR and Vázquez-Lobo, A},
title = {Microbiome diversity across physicochemical gradient in low-medium enthalpy springs at the Sierra Madre Oriental eastern flank, northeastern Mexico.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1663000},
pmid = {41098531},
issn = {1664-302X},
abstract = {INTRODUCTION: Bacterial communities are fundamental to the functionality of thermal springs where they engage in essential processes such as the oxidation of sulfur, reduction of nitrates, carbon fixation, production of unique metabolites, and stabilization of microbial trophic networks. Northeastern Mexico presents a diverse array of thermal springs located within tropical karst systems situated among folded mountains and ancient inactive karstic regions. The geological complexity of these environments indicates a substantial potential for microbiome diversity; however, the composition and functional dynamics of microbial communities in these springs have not been thoroughly investigated.

METHODS: This study involved the collection of water samples from six hot springs, to characterize the planktonic microbiome using advanced metagenomic sequencing techniques. Additionally, we examined the relationship between microbial composition and physicochemical parameters.

RESULTS: Our analysis identified a total of 425 microbial species, which included 409 bacterial species, 13 eukaryotic organisms, and 3 archaeal taxa. The Ojo Caliente and Mainero Azufroso springs displayed the highest microbial diversity, whereas the Balneario El Bañito and Taninul springs exhibited the lowest. The Phyum Pseudomonadota was the predominant across the majority of springs, while Campylobacterota and Chlorobiota were specifically identified in the less diverse Balneario El Bañito and Taninul springs, respectively. A total of 30 indicator species were identified, predominantly in El Bañito and Potrero Prieto springs, emphasizing the distinctiveness of their microbial environments. Moreover, we found that electrical conductivity and bicarbonate concentration had a significant impact on the structure of this microbial communities.

DISCUSSION: This study highlights the ecological importance of these unique ecosystems in northeastern Mexico, with the Mainero Azufroso and Ojo Caliente springs identified as reservoirs of high microbial diversity.},
}

@article {pmid41098530,
year = {2025},
author = {Sharma, A and Andreani, NA and Keller, L and Herpertz-Dahlmann, B and Seitz, J and Baines, JF and Dempfle, A},
title = {Comparison of 16S ribosomal RNA hypervariable regions in microbiome studies of anorexia nervosa.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1665847},
pmid = {41098530},
issn = {1664-302X},
abstract = {INTRODUCTION: Short read sequencing of the 16S ribosomal RNA (rRNA) gene targeting specific hypervariable regions is widely employed to study the human gut microbiota. In these studies, the selection of particular 16S rRNA hypervariable regions is a crucial step. However, the results of such studies exhibit significant variability depending on the targeted hypervariable region.

METHODS: In this study, we systematically evaluated the performance of hypervariable regions V1V2 and V3V4 in a longitudinal gut microbiome study of adolescent patients with anorexia nervosa (AN) and matched controls.

RESULTS: The dominant genera, such as Bacteroides H, Faecalibacterium and Phocaeicola A 858004 were consistently detected in both hypervariable regions across timepoints. The within-sample longitudinal alpha diversity measures varied between the regions with the Chao1 index values being higher in the V1V2 region. The overall microbiome profiles based on beta diversity also differed between the regions. Bland-Altman analysis revealed a general lack of strong agreement between the two sequencing methods, except for a few taxa such as Faecalibacterium, Ruminococcus, Roseburia, Turicibacter and Anaerotruncus. While some results were similar across both hypervariable regions, most of the findings were sensitive to the chosen region.

CONCLUSION: This study underscores the importance of primer selection in microbiome studies of AN, as it can influence taxonomic resolution and diversity estimates along with downstream statistical analyses.},
}

@article {pmid41098272,
year = {2025},
author = {Kouser, M and Chaudhry, S and Sana, M},
title = {Exploring Insights Into Vaginal Microbiome Profiles in Relation to Intrauterine Insemination Success Rates.},
journal = {Cureus},
volume = {17},
number = {9},
pages = {e92244},
pmid = {41098272},
issn = {2168-8184},
abstract = {BACKGROUND: The vaginal microbiome has an essential role in female reproduction, especially during assisted reproduction treatments. The objective of the study was to examine vaginal microbiome profiles of women following intrauterine insemination (IUI) procedures and determine how they relate to clinical pregnancy outcomes.

MATERIALS AND METHODS: A prospective observational study was conducted on 100 women with IUI treatment. Before the procedure, vaginal swabs were taken and sequenced using the 16S rRNA gene to determine microbial community types. Based on microbiome profiles, patients were divided into Lactobacillus-dominant (n = 68) and non-Lactobacillus-dominant (n = 32) groups. Clinical pregnancy rates were compared between the two groups. SPSS Statistics version 26.0 (IBM Corp. Released 2019. IBM SPSS Statistics for Windows, Version 26.0. Armonk, NY: IBM Corp.) was used, with p < 0.05 considered statistically significant.

RESULTS: Overall, 68% of the participants had Lactobacillus-dominant vaginal microbiomes, whereas 32% had varied non-Lactobacillus profiles. The rate of clinical pregnancy was significantly improved in the Lactobacillus-dominant group compared to the non-dominant group, 26 (38.2%) vs. 4 (12.5%), p = 0.008. Logistic regression analysis revealed that the Lactobacillus-dominant profile was independently associated with the success of IUI (adjusted OR 3.85; 95% CI 1.28-11.58; p = 0.016). There were no significant differences in age, body mass index, and infertility duration between the two groups.

CONCLUSIONS: The success rates of IUI were significantly associated with vaginal microbiome composition, particularly the predominance of Lactobacillus. These results support that microbiome profiling may become a helpful technique to predict and enhance the success rates in fertility treatment.},
}

@article {pmid41098119,
year = {2025},
author = {Afzal, L and Dulai, AS and Khan, ZE and Nguyen, N and Afzal, N and Gunt, HB and Sivamani, RK},
title = {Open-Label, Prospective Study of a Prebiotic Gel Cream on Its Efficacy of Mild to Moderate Acne Management and Effects on the Functional Skin Microbiome.},
journal = {Journal of cosmetic dermatology},
volume = {24},
number = {10},
pages = {e70138},
doi = {10.1111/jocd.70138},
pmid = {41098119},
issn = {1473-2165},
support = {//Burt's Bees Inc/ ; },
mesh = {Humans ; *Acne Vulgaris/microbiology/drug therapy/diagnosis ; Female ; *Prebiotics/administration & dosage/adverse effects ; Male ; *Skin/microbiology/drug effects ; *Microbiota/drug effects ; Adult ; Young Adult ; Prospective Studies ; *Skin Cream/administration & dosage/adverse effects ; Treatment Outcome ; Gels ; Adolescent ; Severity of Illness Index ; Propionibacterium acnes/isolation & purification ; Skin Microbiome ; },
abstract = {BACKGROUND: Acne vulgaris is a chronic inflammatory condition, which is estimated to affect greater than 85% of the population. Acne is a multifactorial condition, which can be influenced by diet, environment, and the microbiome.

AIMS: The purpose of this clinical study is to assess the safety and effects of a prebiotic-containing gel cream on the skin microbiome of individuals with non-cystic acne-prone skin.

PATIENTS/METHODS: In this 7-week clinical trial, 30 eligible participants were recruited and enrolled from the Sacramento region. The study consisted of three visits: (1) screening; (2) week 0, baseline; (3) week 6. All participants received a standard non-comedogenic cleanser and a prebiotic-containing gel cream. The primary endpoint in this study was alteration in C. acnes abundance in mild to moderate non-cystic, acne-prone skin. The secondary endpoint in this study was functional gene analysis for skin barrier and skin inflammation-related genes from whole genome sequencing of the skin microbiome.

RESULTS: Acne lesions significantly reduced in non-inflammatory lesions, inflammatory lesions, and total lesions after treatment (-36.0%, -34.5%, and -35.9%, respectively). On the glabella, there was a 12.5 log2 fold increase in abundance of a healthy strain of C. acnes that is not associated with acne vulgaris. Furthermore, there was a wide range of functional bacterial genetic changes that may be associated with increased collagen and glutathione production. The gel cream was rated very well tolerated, and there were no adverse effects reported.

CONCLUSIONS: This prebiotic-containing gel cream can be an effective form of management for acne vulgaris by creating beneficial shifts in the skin microbiome.},
}

Humans
*Acne Vulgaris/microbiology/drug therapy/diagnosis
Female
*Prebiotics/administration & dosage/adverse effects
Male
*Skin/microbiology/drug effects
*Microbiota/drug effects
Adult
Young Adult
Prospective Studies
*Skin Cream/administration & dosage/adverse effects
Treatment Outcome
Gels
Adolescent
Severity of Illness Index
Propionibacterium acnes/isolation & purification
Skin Microbiome

@article {pmid41097974,
year = {2025},
author = {Zheng, P and Yu, C and Lyu, X and Wang, Q},
title = {[Multi-omics association among intestinal microbiome, metabolome, and histone H4 acetylation in children with asthma].},
journal = {Wei sheng yan jiu = Journal of hygiene research},
volume = {54},
number = {5},
pages = {784-804},
doi = {10.19813/j.cnki.weishengyanjiu.2025.05.012},
pmid = {41097974},
issn = {1000-8020},
mesh = {Humans ; *Asthma/microbiology/metabolism ; *Histones/metabolism ; *Gastrointestinal Microbiome ; Acetylation ; Child ; *Metabolome ; Male ; Female ; Feces/microbiology ; Metabolomics ; Multiomics ; },
abstract = {OBJECTIVE: To analyze the correlation between intestinal microbiome, metabolome and histone H4 acetylation level in children with asthma, and explore the mechanism that gut microbiome affects children with asthma.

METHODS: Histone H4 acetylation in induced sputum, 16S rRNA gene sequencing of gut microbiome, and untargeted fecal metabolomics were detected in asthmatic children and control children. Network method was used to analyze the correlation between characteristic gut microbes of asthma and histone H4 acetylation, Quantile g-computation(QGC)was used to analyze the effect of characteristic microbes on histone H4 acetylation, and the mediation model was used to analyze the mediating effect of metabolites in the process of gut microbes affecting histone H4 acetylation.

RESULTS: The mean A(optical density) value of histone H4 acetylation in sputum was 0.668±0.260 in asthmatic children(n=37), and 0.593±0.069 in control group(n=20). A total of 5 characteristic gut genera of children with asthma were significantly correlated with H4 acetylation level(adjusted P<0.05). QGC analysis showed that the 5 characteristic gut genera had a positive effect on the histone acetylation level of histone H4(P=0.001), and the A value of histone H4 acetylation increased by 0.124 for every 1 quantile increase in the relative abundance of characteristic gut genera(95%CI 0.058-0.190). By spearman analysis, 34 fecal metabolites were significantly correlated with the five characteristic gut genera and histone H4 acetylation levels. Prevotella was found have influenced the level of H4 acetylation through the mediating effect of N-delta-acetylornithine, phenethylamine, 2-hydroxy-3-methylvalerate, alpha-ketoglutaramate, gamma-glutamylglycine, and mevalonolactone.

CONCLUSION: The metabolites related with the characteristic gut bacteria in asthmatic children were associated with histone H4 acetylation, which suggested that the gut microbiome may induce childhood asthma by regulating epigenetic variation.},
}

Humans
*Asthma/microbiology/metabolism
*Histones/metabolism
*Gastrointestinal Microbiome
Acetylation
Child
*Metabolome
Male
Female
Feces/microbiology
Metabolomics
Multiomics

@article {pmid41097965,
year = {2025},
author = {Jia, X and Wang, H and Guan, F and Zhang, X and Su, C and Huang, F and Du, W and Zhang, J and Ouyang, Y and Bai, J and Wei, Y and Li, L and Zhang, B},
title = {[Association of gut microbiome and serum metabolite with dyslipidemia in Chinese adults of 4 provinces in 2018 and 2022].},
journal = {Wei sheng yan jiu = Journal of hygiene research},
volume = {54},
number = {5},
pages = {722-731},
doi = {10.19813/j.cnki.weishengyanjiu.2025.05.003},
pmid = {41097965},
issn = {1000-8020},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Dyslipidemias/microbiology/blood/epidemiology ; China/epidemiology ; Adult ; Male ; Female ; Middle Aged ; Feces/microbiology ; Lipids/blood ; },
abstract = {OBJECTIVE: To analyze the serum metabolites and gut microbiota associated with dyslipidemia in adult residents in China.

METHODS: The data were derived from the 2018 China Health and Nutrition Survey and the 2022 China Development and Nutrition Health Impact Cohort Survey, and adults(≥ 18 years) who participated in the two rounds of surveys and had completed serum metabolite and lipids data were selected. According to Chinese Guideline for Lipid Management(Primary Care Version 2024), subjects with at least one of hypertriglyceridemia, hypercholesterolemia, high LDL-C level or low HDL-C level were identified as dyslipidemia. Participants were divided into two groups: constant normal lipids(CNL) and occurred dyslipidemia(OD). Broadly targeted ultra-performance liquid chromatography-tandem mass spectrometry(UPLC-MS/MS) analysis was performed to measure serum metabolites and orthogonal partial least square discriminate analysis were used to identify different metabolites between groups. Fecal samples were collected and 16S rRNA sequencing was performed at baseline to analyze the α diversity of intestinal microbiota(Shannon and Simpson indexes), β diversity(Bray-curtis distance) and differential bacteria between groups. Spearman rank correlation was used to analyze the correlation between gut microbiota and serum metabolites.

RESULTS: A total of 1090 subjects were included during 2018-2022, of whom 226(20.7%) developed dyslipidemia at follow-up, and 864(79.3%) remained normal serum lipid levels. There were 49 differential metabolites identified between the CNL and OD groups, in which the metabolites with higher amount in the OD group was mainly lysophosphatidylcholine of glycerophospholipids. There was no significant difference in Shannon and Simpson indices between the two groups, and β diversity analysis showed that there were differences in the overall microbiota structure between the two groups. Both univariate and multivariate analyses identified eight different bacterial genera, and Veillonella, Faecalitalea, and Psychrobacter were the common differential bacteria, and the first two genera were relatively abundant in the OD group. Faecalitalea was negatively correlated with five lysophosphatidylcholine metabolites.

CONCLUSION: Serum metabolite levels of glycerophospholipids, gut Veillonella and Faecalitalea may be related to dyslipidemia in adults in China.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Dyslipidemias/microbiology/blood/epidemiology
China/epidemiology
Adult
Male
Female
Middle Aged
Feces/microbiology
Lipids/blood

@article {pmid41097963,
year = {2025},
author = {Guan, F and Huang, F and Zhang, X and Wang, L and Zhang, J and Jia, X and Du, W and Quyang, Y and Wang, H and Zhang, B},
title = {[Differential gut microbiota among adult residents of 15 provinces of China in 2018 and their relationship with blood lipids].},
journal = {Wei sheng yan jiu = Journal of hygiene research},
volume = {54},
number = {5},
pages = {707-714},
doi = {10.19813/j.cnki.weishengyanjiu.2025.05.001},
pmid = {41097963},
issn = {1000-8020},
mesh = {Humans ; *Gastrointestinal Microbiome ; China/epidemiology ; Adult ; *Lipids/blood ; Feces/microbiology ; *Inflammation/microbiology/blood ; Female ; Male ; Middle Aged ; Bacteria/classification/genetics/isolation & purification ; C-Reactive Protein/analysis ; },
abstract = {OBJECTIVE: To analyze the characteristics and differences of gut microbiota in adult residents of 15 provinces of China under different inflammation levels, and to analyze their correlation with blood lipid levels.

METHODS: A total of 4158 adult residents who participated in the 2018 China Health and Nutrition Survey and completed all the surveys were selected. Biochemical tests were performed on serum samples, and 16S amplicon sequencing was carried out on fecal samples. According to the ultra-sensitive C-reactive protein, the population was divided into a low inflammation group and a high inflammation group. The uniformity and richness of bacterial species and the overall distribution characteristics of bacterial communities between the two groups were analyzed through diversity analysis, and the differences in bacterial communities between the two groups were analyzed using linear discriminant analysis. Finally, the differences in bacterial communities between the groups were analyzed in association with the physiological and biochemical indicators of the population.

RESULTS: Compared with the low inflammation group, the bacterial diversity in the high inflammation group was lower, and there was a significant difference in the overall bacterial composition between the two groups(R~2=0.25%, P=0.01). Six genera were enriched in the samples of the low inflammation group, and four genera were enriched in the high inflammation group. Among them, Lactobacillus and Streptococcus were positively correlated with BMI, and Romboutsia was positively correlated with TC, LDL-C and HDL-C. Clostridium UCG-014, Ruminococcus and Faecalibacterium were positively correlated with TG.

CONCLUSION: The study found that there are differences in the overall structure and dominant bacteria of the gut microbiome in people with different inflammation levels, and the inflammatory response may have a certain impact on blood lipid levels through these dominant bacterial genera.},
}

Humans
*Gastrointestinal Microbiome
China/epidemiology
Adult
*Lipids/blood
Feces/microbiology
*Inflammation/microbiology/blood
Female
Male
Middle Aged
Bacteria/classification/genetics/isolation & purification
C-Reactive Protein/analysis

@article {pmid41097883,
year = {2025},
author = {Castenschiold, CDF and Mignani, C and Christiansen, S and Alsved, M and Ickes, L and Tesson, SVM and Löndahl, J and Bilde, M and Bataillon, T and Finster, K and Šantl-Temkiv, T},
title = {Atmospheric Biogenic Ice-Nucleating Particles Link to Microbial Communities in the Arctic Marine Environment in Western Greenland.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c03650},
pmid = {41097883},
issn = {1520-5851},
abstract = {Biogenic ice-nucleating particles (INPs) can significantly impact mixed-phase clouds by enhancing precipitation and reducing albedo. As Arctic sea ice diminishes, the exposure of open ocean may increase aerosolization rates of marine bioaerosols and INPs. We investigated INP concentrations and microbial communities in ambient marine air, sea bulk water (SBW), and sea surface microlayer (SML) along a transect from the Davis Strait to Baffin Bay. INP concentrations in SBW increased with latitude, regardless of the extent of terrestrial freshwater input. We further identified correlations between INP levels and abundances of specific microbial taxa, including Formosa, Lewinella, Micromonas, and Dino-Group-I-Clade-5, suggesting potential ice nucleation activity of these taxa. Air samples exhibited distinct microbiomes compared to seawater, indicating terrestrial contributions, but at the highest observed wind speeds (7-8 m/s), substantial contributions of the seawater microbiome were detected in the air. Elevated atmospheric INP concentrations at higher latitudes correlated with seawater INP levels, which was supported by laboratory sea spray experiments showing that INPs in SBW influenced aerosol INP levels. Our findings highlight the Arctic Ocean as a significant source of biogenic atmospheric INPs and enhance our understanding of marine microbes as contributors to biogenic INPs. By identification of potential ice nucleation active microbial taxa and examination of aerosolization processes, this study provides a framework for future research on Arctic marine-derived INPs and their atmospheric impact.},
}

@article {pmid41097858,
year = {2025},
author = {Chen, X and Tian, H and Han, L and Xu, W},
title = {Gut Microbiota Influences Meningioma Pathogenesis via Circulating Metabolites: A Two-Sample Mendelian Randomization Study.},
journal = {Brain and behavior},
volume = {15},
number = {10},
pages = {e70973},
doi = {10.1002/brb3.70973},
pmid = {41097858},
issn = {2162-3279},
support = {ZR2022QH335//Natural Science Foundation of Shandong Province/ ; 81902539//National Natural Science Foundation of China/ ; },
mesh = {*Meningioma/microbiology/metabolism/genetics ; Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Mendelian Randomization Analysis/methods ; *Meningeal Neoplasms/microbiology/metabolism/genetics ; Female ; },
abstract = {BACKGROUND: Meningiomas are common solitary intracranial tumors without any apparent risk factors. In light of the growing interest in gut microbiome-brain tumor interactions, this investigation sought to explore potential links between intestinal microbial communities and meningioma pathogenesis, while also exploring the potential mediating role of specific metabolites.

METHODS: To investigate potential causal links between intestinal microbial communities and meningioma development, we implemented a bidirectional two-sample Mendelian randomization (MR) approach examining 196 microbial taxa. Our analytical strategy incorporated a two-stage MR methodology to pinpoint potential mediating factors. Furthermore, we performed comprehensive mediation analyses to assess the degree to which particular metabolic intermediates might influence the observed microbiota-meningioma associations.

RESULTS: Eight distinct microbial taxa exhibited potential causal associations with meningioma development. Among the identified taxa, genus Lachnoclostridium (odds ratio [OR]: 0.60; 95% confidence interval [CI]: 0.41, 0.89; p = 0.010) and class Lentisphaeria (OR: 0.73; 95% CI: 0.57, 0.95; p = 0.017) were suggestively associated with a reduced risk of meningioma, whereas family Oxalobacteraceae (OR: 1.28; 95% CI: 1.04, 1.58; p = 0.018) suggested a positive association with the risk of meningioma. An exploratory mediation analysis suggested that the relationships between genus Lachnoclostridium, class Lentisphaeria, and family Oxalobacteraceae and meningioma were mediated by the histidine to pyruvate ratio, hydroxymalonate, and 1-linoleoylglycerol. Each of these accounted for 10.65%, 10.78%, and 11.82%, respectively.

CONCLUSION: This investigation provides preliminary evidence that intestinal microbial communities play a contributory role in meningioma pathogenesis, with circulating metabolites potentially serving as key intermediaries in this microbiota-meningioma axis.},
}

*Meningioma/microbiology/metabolism/genetics
Humans
*Gastrointestinal Microbiome/physiology/genetics
Mendelian Randomization Analysis/methods
*Meningeal Neoplasms/microbiology/metabolism/genetics
Female

@article {pmid41097775,
year = {2025},
author = {Jaye, K and Alsherbiny, MA and Chang, D and Li, CG and Bhuyan, DJ},
title = {Guardians in the Gut: Mechanistic Insights into a Hidden Ally Against Triple-Negative Breast Cancer.},
journal = {Cancers},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/cancers17193248},
pmid = {41097775},
issn = {2072-6694},
abstract = {The gut microbiome possesses a diverse range of biological properties that play a role in maintaining host health and preventing disease. Gut microbial metabolites, including short-chain fatty acids, natural purine nucleosides, ellagic acid derivatives, and tryptophan metabolites, have been observed to have complex and multifaceted roles in the gut and in wider body systems in the management of disease, including cancer. Triple-negative breast cancer is the most aggressive subtype of breast cancer, with restricted treatment options and poor prognoses. Recently, preclinical research has investigated the antiproliferative potential of gut microbial metabolites against this type of breast cancer with promising results. However, little is understood about the mechanisms of action and molecular pathways driving this antiproliferative potential. Understanding the complex mechanisms of action of gut microbial metabolites on triple-negative breast cancer will be instrumental in the investigation of the combined administration with standard chemotherapeutic drugs. To date, there is a paucity of research studies investigating the potential synergistic interactions between gut microbial metabolites and standard chemotherapeutic drugs. The identification of synergistic potential between these compounds may provide alternate and more effective therapeutic options in the treatment and management of triple-negative breast cancer. Further investigation into the mechanistic action of gut microbial metabolites against this breast cancer subtype may support the administration of more cost-effective treatment options for breast cancer, with an aim to reduce side effects associated with standard treatments. Additionally, future research will aim to identify more potent metabolite-drug combinations in the mitigation of triple-negative breast cancer progression and metastasis.},
}

@article {pmid41097753,
year = {2025},
author = {Łatkiewicz, T and Rasoul-Pelińska, K and Kułak, K and Tarkowski, R and Kułak, A and Puzio, I},
title = {Gynecological Cancer Oncobiome Systematic Review.},
journal = {Cancers},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/cancers17193227},
pmid = {41097753},
issn = {2072-6694},
abstract = {Objective: The primary objective of this systematic review is to present current knowledge about the oncobiome of gynecological cancers. Methods: Our systematic review contains data about the oncobiome of uterine corpus cancer, ovarian cancer and cervical cancer. Articles about other gynecological cancers were excluded. Results: A total of 72 articles were included in our systematic review. In uterine corpus cancer, cervical cancer and ovarian cancer, representatives of bacteria, fungi, viruses and parasites can be found. The oncobiome of ovarian cancer is connected with the oncobiome of head and neck cancers. Our systematic review proved that the human papilloma virus is connected with ovarian and cervical cancer. Gut dysbiosis can be used as a marker of ovarian cancer. In cervical cancer, we found the difference between the microbiota of healthy patients and patients with cervical cancer. Methylobacter, Robignitomaculum, Klebsiella, Micromonospora and Microbispora have an impact on overall survival. The microbiome of uterine corpus cancer is more differentiated than in cancer-free samples. Chronic endometrial inflammation has an impact on endometrial microbiome. Discussion: Treatment of gynecological cancers is changing permanently. Chemotherapy, as a systematic treatment, is being left in the past. Modern methods of therapy are addressed to specific genes. In the past, researchers claimed that tumors are sterile. However, the newest research indicates that malignancies were found to have genetic fragments of pathogens, which can be used as vectors for medications or as markers for the detection of a specific malignancy. Three most common gynecological cancers are as follows: endometrial cancer, ovarian cancer and cervical cancer. Each of these has their specific microbiome, which can be used for oncological treatment. These discoveries create possibilities for new, efficient methods of treatment. This systematic review analyzes publications about the composition of the gynecological tumor microenvironment, correlation between microbiomes of different organs, the female reproductive tract and the microbiome of the female reproductive tract during malignancy. Moreover, we provide information on the influence of some pathogens on the treatment.},
}

@article {pmid41097535,
year = {2025},
author = {Mulet, JM and Benito, P and Celdrán, M and Yenush, L and Porcel, R},
title = {Impact of Different Microbial Biostimulants and Salt Stress on the Endophytome of the Edible Part of Lettuce and Tomato Plants.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {19},
pages = {},
doi = {10.3390/foods14193366},
pmid = {41097535},
issn = {2304-8158},
support = {PAID-06-22//Universitat Politècnica de València/ ; MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia, Innovación y Universidades/ ; },
abstract = {The human gut microbiota plays a critical role in health throughout life. While fruits and vegetables are well-known sources of nutrients and prebiotics, recent studies suggest they may also contribute viable microorganisms to the gut microbiome, particularly when consumed raw. However, the impact of agricultural practices-such as the use of microbial biostimulants or exposure to salt stress-on the composition of the edible plant microbiome remains poorly understood. In this study, we performed a comprehensive metataxonomic analysis of the endophytic microbiome in the edible tissues (leaves or fruits) of lettuce (Lactuca sativa) and tomato (Solanum lycopersicum), cultivated under standard conditions with or without microbial biostimulants and salt stress. Our results show that microbial biostimulants-Priestia megaterium (PGPB) and Rhizophagus irregularis (AMF)-as well as moderate salt stress, significantly reshape the composition and diversity of endophytes in both crops. Notably, the PGPB and NaCl treatments enhanced the abundance of bacterial genera such as Pantoea, Stenotrophomonas, and Massilia, which are associated with plant health and may have probiotic potential. Salt stress also increased alpha-diversity indices and favored the presence of Firmicutes and Bacteroidota, phyla commonly linked to a healthy human gut microbiome. Agronomic inputs used in organic and conventional farming, such as microbial biostimulants or controlled salt exposure, may represent novel strategies to enhance the microbial quality of fresh produce and promote gut microbial diversity through diet.},
}

@article {pmid41097330,
year = {2025},
author = {Sikora, E and Łętocha, A and Michalczyk, A and Kozik, A},
title = {Encapsulation of Acid Whey in Alginate Microspheres for Application in Skin Microbiome-Friendly Topical Formulations: Optimization Through a Design of Experiments Approach.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {19},
pages = {},
doi = {10.3390/molecules30193907},
pmid = {41097330},
issn = {1420-3049},
mesh = {*Alginates/chemistry ; *Microspheres ; *Skin/microbiology ; *Microbiota/drug effects ; Probiotics/chemistry ; *Whey/chemistry ; Drug Compounding ; Emulsions ; Humans ; *Whey Proteins/chemistry ; Particle Size ; Cosmetics/chemistry ; Animals ; Skin Microbiome ; },
abstract = {Skin microbiome-friendly preparations are gaining increasing popularity in the cosmetics and pharmaceutical industries. Fermented plants, lysates, and heat-treated products are used as probiotic ingredients in cosmetics. This is due to the presence of Lactobacillus bacteria, such as acid or acid-rennet whey, which are natural probiotics that can positively impact the skin microbiome. However, due to technological difficulties, the direct use of whey as a cosmetic ingredient is limited. An optimized emulsification method was used to obtain alginate microspheres as carriers of whey. The process parameters were optimized using the Design of Experiments (DoEs) methodology. The effect of three key variables, including the type of probiotic raw material (whey from 1-cows, 2-goats, and 3-mixed), the alginate-to-raw material ratio (1-3%), and sonication time (0.5-1.5 min), on parameters such as encapsulation efficiency, bacterial survival, viscosity, and microspheres size was analyzed. The results obtained demonstrated that the optimal process parameters were the sonication time of 0.5 min and the alginate-to-whey mass ratio of 1.5% for all types of whey material studied. However, the most important factor influencing the properties and functionality of the microspheres was sonication time. The optimized whey-loaded microspheres were incorporated into a preservative-containing emulsion system, in which the viability of whey-derived bacteria was monitored over time. The whey encapsulation process effectively maintained the bacteria's probiotic properties, protecting their viability despite the presence of preservatives (at a level of 4.92 ± 0.9 log CFU/g after 30 days of formulation storage), thus confirming the feasibility of incorporating liquid whey into skincare formulations.},
}

*Alginates/chemistry
*Microspheres
*Skin/microbiology
*Microbiota/drug effects
Probiotics/chemistry
*Whey/chemistry
Drug Compounding
Emulsions
Humans
*Whey Proteins/chemistry
Particle Size
Cosmetics/chemistry
Animals
Skin Microbiome

@article {pmid41097290,
year = {2025},
author = {Zaborowska, M and Wyszkowska, J and Słaba, M and Borowik, A and Kucharski, J and Bernat, P},
title = {The Effect of Organic Materials on the Response of the Soil Microbiome to Bisphenol A.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {19},
pages = {},
doi = {10.3390/molecules30193868},
pmid = {41097290},
issn = {1420-3049},
support = {30.610.006-110//University of Warmia and Mazury in Olsztyn, Faculty of Agriculture and Forestry, Department of Soil Science and Microbiology/ ; NGR/319/2022//he Minister of Science under "the Regional Initiative of Excellence Program/ ; Rector's Scientific Grant - Edition II"//University of Warmia and Mazury in Olsztyn/ ; },
mesh = {*Soil Microbiology ; *Benzhydryl Compounds/pharmacology ; *Phenols/pharmacology ; *Microbiota/drug effects ; Soil/chemistry ; Bacteria/drug effects/genetics/classification ; *Soil Pollutants ; Fungi/drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Zea mays/growth & development ; Bisphenol A Compounds ; },
abstract = {In view of the increasing environmental pollution caused by bisphenol A (BPA), understanding its impact on the microbiological properties of soil, which play a key role in maintaining soil fertility and consequently ecosystem stability, is particularly important. Therefore, the aim of this study was to assess the sensitivity of the soil microbiome to this xenobiotic and to evaluate the potential of organic materials such as starch (St), grass compost (Co), and fermented bark (B) to restore the balance of soil cultivated with Zea mays. The negative effects of BPA on the abundance, diversity, and structure of bacterial and fungal communities in soil contaminated with 500 and 1000 mg kg[-1] d.m. of soil were confirmed. Changes in the phospholipid profile, including phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylglycerol (PG), and ergosterol (E), were also assessed. BPA applied at 1000 mg kg[-1] d.m. of soil inhibited the proliferation of organotrophic bacteria and actinomycetes, while stimulating fungal growth. This xenobiotic's impact is also reflected by a decrease in PC and PG levels in soil under BPA pressure. Through amplification of the V3-V4 16S rRNA region (for bacteria) and the ITS1 region (for fungi), the dominant bacterial phylum Proteobacteria was identified, with genera including Cellulosimicrobium, Caulobacter, Rhodanobacter, Sphingomonas, Mucilaginibacter, and Pseudomonas. Among fungi, Ascomycota dominated, primarily represented by the genus Penicillium. Of all the organic materials tested for mitigating BPA's negative effects, grass compost was identified as the most promising, not only restoring soil homeostasis but also enhancing the growth and development of Zea mays cultivated in BPA-contaminated soil.},
}

*Soil Microbiology
*Benzhydryl Compounds/pharmacology
*Phenols/pharmacology
*Microbiota/drug effects
Soil/chemistry
Bacteria/drug effects/genetics/classification
*Soil Pollutants
Fungi/drug effects/genetics
RNA, Ribosomal, 16S/genetics
Zea mays/growth & development
Bisphenol A Compounds

@article {pmid41097262,
year = {2025},
author = {Ebrahim, Z and Proost, S and Tito, RY and Raes, J and Glorieux, G and Moosa, MR and Blaauw, R},
title = {Correction: Ebrahim et al. The Effect of ß-Glucan Prebiotic on Kidney Function, Uremic Toxins and Gut Microbiome in Stage 3 to 5 Chronic Kidney Disease (CKD) Predialysis Participants: A Randomized Controlled Trial. Nutrients 2022, 14, 805.},
journal = {Nutrients},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/nu17193054},
pmid = {41097262},
issn = {2072-6643},
abstract = {After a thorough review of our data and methodology, we identified an issue related to assigning enterotypes to samples from "The Effect of ß-Glucan Prebiotic on Kidney Function, Uremic Toxins and Gut Microbiome in Stage 3 to 5 Chronic Kidney Disease (CKD) Predialysis Participants: A Randomized Controlled Trial" [...].},
}

@article {pmid41097233,
year = {2025},
author = {Karekezi, J and Kim, H and Dusabimana, T and Nugroho, TA and Ndahigwa, EN and So, YJ and Kim, J and Kim, TR and Sohn, M and Miao, J and Moon, Y and Park, SW},
title = {Lactiplantibacillus plantarum LM1001 Supplementation Attenuates Muscle Atrophy and Function Decline in Aged Mice.},
journal = {Nutrients},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/nu17193156},
pmid = {41097233},
issn = {2072-6643},
support = {RS-2023-00273563//National Research Foundation of Korea/ ; 2021R1A5A8029490//National Research Foundation of Korea/ ; Fund for Professors on Sabbatical Leave, 2025//Gyeongsang National University/ ; },
mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; Male ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Sarcopenia ; *Aging/physiology ; *Muscular Atrophy/prevention & control ; Mice ; Diet, High-Fat/adverse effects ; *Dietary Supplements ; *Lactobacillus plantarum ; Muscle, Skeletal/physiopathology ; Muscle Strength/drug effects ; Insulin-Like Growth Factor I/metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; },
abstract = {Background/Objectives: Aging and metabolic disorders are associated with a decline in muscle function, referred to as age-related sarcopenia. The underlying mechanisms of sarcopenia include cellular senescence, imbalanced protein homeostasis, accumulation of oxidative and inflammatory stressors, and mitochondrial dysfunction. Probiotic supplementation improves the gut microbiome and enhances muscle function via the gut-muscle axis. However, details of molecular mechanisms and the development of an appropriate treatment are under active investigation. Methods: We have examined the effects of Lactiplantibacillus plantarum LM1001, a probiotic that reportedly improves the digestibility of branched-chain amino acids in myocyte cultures, but exactly how it contributes to muscle structure and function remains unclear. Results: We show that aged mice (male C57BL6/J) fed a high-fat diet (HFD) exhibit weak muscle strength, as reflected by a reduction in grip strength. LM1001 supplementation increases muscle strength and restores myofibril size, which has been altered by HFD in aged mice. Expression of myogenic proteins is increased, while protein markers for muscle atrophy are downregulated by LM1001 treatment via the IGF-1/Akt/FoxO3a pathway. LM1001 improves gut microbiota that are altered in aged HFD-fed mice, by increasing their abundance in beneficial bacteria, and efficiently maintains the epithelial lining integrity of the large intestine. Conclusions: We conclude that LM1001 supplementation serves a beneficial role in patients suffering from sarcopenia and metabolic disorders, improving their muscle function, gut microbiota, and intestinal integrity.},
}

Animals
*Probiotics/pharmacology/administration & dosage
Male
Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
*Sarcopenia
*Aging/physiology
*Muscular Atrophy/prevention & control
Mice
Diet, High-Fat/adverse effects
*Dietary Supplements
*Lactobacillus plantarum
Muscle, Skeletal/physiopathology
Muscle Strength/drug effects
Insulin-Like Growth Factor I/metabolism
Proto-Oncogene Proteins c-akt/metabolism

@article {pmid41097227,
year = {2025},
author = {Mao, JS and Cui, HY and Zhou, XZ and Zhang, SW},
title = {Recent Progress in Exploring Dietary Nutrition and Dietary Patterns in Periodontitis with a Focus on SCFAs.},
journal = {Nutrients},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/nu17193150},
pmid = {41097227},
issn = {2072-6643},
support = {82401128//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Periodontitis/prevention & control/epidemiology/microbiology ; *Dietary Fiber/administration & dosage ; *Fatty Acids, Volatile/metabolism ; *Diet ; *Nutritional Status ; Diet, Mediterranean ; },
abstract = {Dietary patterns greatly affect periodontitis, a chronic inflammatory disease that compromises both dental and systemic health. According to the emerging evidence, periodontal risk is more strongly associated with the overall dietary quality, especially fiber density intake, than any one micronutrient. While the average intake in industrialized countries is only half of the recommended 30 g day[-1], high-fiber diets such as the Mediterranean diet, the Dietary Approaches to Stop Hypertension (DASH), and whole-food plant-based diets are consistently associated with a 20-40% lower periodontitis prevalence. Dietary fiber plays a central role in regulating immune responses, strengthening tissue barriers, improving metabolic homeostasis, and shaping a healthy microbiome through its microbial fermentation products: short-chain fatty acids (SCFAs). This makes it a biologically rational and clinical evidence-supported strategy for the prevention and management of periodontitis. Integrating high-fiber diet recommendations into routine periodontal care and public health policies could be a crucial step towards more comprehensive oral and systemic health management. This narrative review elaborates on the mechanistic, observational, and intervention data highlighting the role of dietary fiber, especially SCFAs, in periodontal health.},
}

Humans
*Periodontitis/prevention & control/epidemiology/microbiology
*Dietary Fiber/administration & dosage
*Fatty Acids, Volatile/metabolism
*Diet
*Nutritional Status
Diet, Mediterranean

@article {pmid41097199,
year = {2025},
author = {Dey, P},
title = {All That Glitters Ain't Gold: The Myths and Scientific Realities About the Gut Microbiota.},
journal = {Nutrients},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/nu17193121},
pmid = {41097199},
issn = {2072-6643},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Dysbiosis/microbiology ; Probiotics ; Diet ; Fecal Microbiota Transplantation ; },
abstract = {Gut microbial modulation through diet is central to human health and disease. Despite tremendous effort in understanding the impact of nutrients and drugs on the gut microbiota, and attempts to develop dietary strategies that facilitate gut-beneficial effects, several erroneous gut microbiota-associated concepts remain prevalent in popular belief. This article discusses widespread misconceptions about the gut microbiota, contrasting them with contemporary scientific facts. In this article, ten prevalent myths, including the obsolete 10:1 bacteria-to-human-cell ratio, the reductive categorization of microbes as 'good' or 'bad', and the discredited universal biomarker status of the Firmicutes/Bacteroidetes ratio in relation to metabolic diseases, have been debunked. Essential facts highlighting the context-dependency of the microbiome, considerable inter-individual heterogeneity, and dynamic reactivity to dietary changes are discussed. This questions the assumptions that increased diversity always signifies health, that probiotics are intrinsically safe, that fecal microbiota transplantation is a universal remedy, or that leaky gut syndrome constitutes a clearly defined diagnosis. It is highlighted that eubiosis and dysbiosis do not possess uniform criteria, and microbiome-drug interactions are extremely individualized. The gut microbiota operates as a dynamic, adaptive ecosystem, necessitating sophisticated, evidence-based methodologies for study and therapeutic application, transcending simplistic misconceptions in favor of tailored insights and therapies.},
}

*Gastrointestinal Microbiome/physiology
Humans
Dysbiosis/microbiology
Probiotics
Diet
Fecal Microbiota Transplantation

@article {pmid41097131,
year = {2025},
author = {Ochocińska, AM and Podstawka, I and Kępka, A and Waszkiewicz, N},
title = {Diet as a Modulator of Gut Microbiota May Reduce Alzheimer's Disease Risk.},
journal = {Nutrients},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/nu17193053},
pmid = {41097131},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Alzheimer Disease/prevention & control/microbiology ; Diet, Mediterranean ; Diet, Ketogenic ; Diet, Western/adverse effects ; Dysbiosis ; *Diet ; Risk Factors ; },
abstract = {The aging process, along with an inadequate diet and an inflammatory gut response resulting from dysbiosis, contributes to the pathogenesis of Alzheimer's disease (AD). Modifying the composition of the gut microbiota through appropriate pre/probiotic-rich diets may act as a preventive option for AD. The variety of functions performed by the gut microbiota makes this ecosystem one of the most important systems in the human body. The Mediterranean diet (MedDiet), the Dietary Approaches to Stop Hypertension (DASH), the Mediterranean-DASH Intervention for Neurodegenerative Delay diet (MIND), and the modified ketogenic-Mediterranean diet (MKD) positively affect the intestinal microflora and may reduce the risk of dementia. A ketogenic diet has a neuroprotective effect and improves cognitive function but leads to a significant decrease in the abundance and diversity of bacterial species in favor of harmful bacteria. A Western-style diet (Western diet, WD) rich in processed products, red meat, simple sugars, and saturated fatty acids has a negative impact on gut microbiota function, increasing the risk of AD. Our review supports the hypothesis that factors like a proper diet and a healthy gut microbiota have a positive impact on the prevention of neurodegenerative diseases, including AD. A thorough understanding of the role the microbiota plays in the proper functioning of the nervous system can aid in the prevention of AD by developing new dietary strategies and dietary lifestyles.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Alzheimer Disease/prevention & control/microbiology
Diet, Mediterranean
Diet, Ketogenic
Diet, Western/adverse effects
Dysbiosis
*Diet
Risk Factors

@article {pmid41097128,
year = {2025},
author = {Wu, Y and Chen, Q and Fan, R and Song, L and Wang, S and You, M and Cai, M and Li, Y and Xu, M},
title = {Association Between the Dietary Inflammatory Index and Life's Essential 8 in Older Adults Based on Gut Microbiota Profiles.},
journal = {Nutrients},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/nu17193050},
pmid = {41097128},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome ; Aged ; Male ; Female ; *Inflammation ; *Diet/adverse effects ; *Cardiovascular Diseases/prevention & control/etiology ; RNA, Ribosomal, 16S/genetics ; Aged, 80 and over ; Middle Aged ; },
abstract = {BACKGROUND/OBJECTIVES: As the global population ages, cardiovascular disease (CVD) emerges as a critical challenge for public health, with chronic inflammation identified as a key contributing risk factor. As a modifiable lifestyle factor, diet plays a critical role in the prevention of CVD. Given the established link between diet and inflammation, clarifying the relationship between dietary inflammatory potential and cardiovascular health (CVH) is of significant public health importance. This study aimed to evaluate the association between dietary inflammatory potential and CVH in an elderly population, and to explore the related role of the gut microbiota.

METHODS: Dietary inflammatory potential was quantified using the Dietary Inflammatory Index (DII), CVH was assessed by the American Heart Association's Life's Essential 8 (LE8) score, and gut microbiome analysis was profiled by 16S rRNA gene sequencing.

RESULTS: Results showed that higher DII scores, indicative of a pro-inflammatory dietary pattern, were significantly linked to reduced LE8 scores, suggesting an inverse association between dietary inflammatory potential and CVH. Based on the gut microbiome, participants with high CVH exhibited greater α diversity compared with those with low CVH, while both α and β diversity were higher in the anti-inflammatory diet group than in the pro-inflammatory diet group. These results indicate that anti-inflammatory diets may be associated with better CVH, possibly through the preservation of the ecological balance of the gut microbiota. Correlation analyses further pointed to several genera potentially associated with both dietary inflammatory potential and CVH. Functional predictions suggested that variation in dietary inflammatory potential could be linked to differences in microbial metabolic functions relevant to energy, lipid and glucose metabolism, and inflammatory processes.

CONCLUSIONS: In conclusion, this study provides novel evidence linking dietary inflammatory potential, gut microbiota, and CVH in older adults, and offers preliminary insights for dietary interventions and microbiota-targeted strategies in CVD prevention.},
}

Humans
*Gastrointestinal Microbiome
Aged
Male
Female
*Inflammation
*Diet/adverse effects
*Cardiovascular Diseases/prevention & control/etiology
RNA, Ribosomal, 16S/genetics
Aged, 80 and over
Middle Aged

@article {pmid41097077,
year = {2025},
author = {So, MT and Ullah, A and Waris, A and Alhumaydhi, FA},
title = {The Etiological Role of Impaired Neurogenesis in Schizophrenia: Interactions with Inflammatory, Microbiome and Hormonal Signaling.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199814},
pmid = {41097077},
issn = {1422-0067},
support = {QUAPC-2025//Deanship of Graduate Studies and Scientific Research at Qassim University for financial support (QU-APC-2025)./ ; },
mesh = {Humans ; *Schizophrenia/etiology/metabolism/pathology/microbiology ; *Neurogenesis ; Signal Transduction ; Animals ; *Microbiota ; Inflammation/metabolism ; },
abstract = {Schizophrenia is a prevailing yet severely debilitating psychiatric disorder characterized by a convoluted etiology. Although antipsychotics have been available for over half a century, they primarily mitigate symptoms rather than providing definitive care. This limitation suggests that the neurotransmitter systems targeted by these medications are not the root cause of the disorder. Ongoing research seeks to elucidate the cellular, molecular, and circuitry pathways that contribute to the development of schizophrenia. Unfortunately, its precise pathogenesis remains incompletely understood. Accumulating evidence implicates dysregulated neurogenesis and aberrant neurodevelopmental processes as key contributors to disease progression. Recent advances in proteomics and imaging technology have facilitated the emergence of novel models of schizophrenia, emphasizing the roles of neuroinflammation, sex steroids, and cortisol. This paper aims to organize and map the intercorrelations and potential causal effects between various mechanistic models to gain deeper insight on how these mechanisms contribute to the cause, risks, and symptoms of the disorder. Furthermore, we discuss the potential therapeutic strategies that target these pathological pathways. Elucidating these mechanisms may ultimately advance our understanding of schizophrenia's etiological foundations and guide the development of curative interventions.},
}

Humans
*Schizophrenia/etiology/metabolism/pathology/microbiology
*Neurogenesis
Signal Transduction
Animals
*Microbiota
Inflammation/metabolism

@article {pmid41097043,
year = {2025},
author = {Chernevskaya, E and Sorokina, E and Polyakov, P and Gorshkov, K and Kovaleva, N and Zakharchenko, V and Beloborodova, N},
title = {Evaluation and Modulation of Gut Microbiome Dysfunction in Chronically Critically Ill Patients: A Prospective Pilot Study.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199778},
pmid = {41097043},
issn = {1422-0067},
mesh = {Humans ; *Critical Illness/therapy ; *Gastrointestinal Microbiome/drug effects ; Pilot Projects ; Male ; Female ; Prospective Studies ; Middle Aged ; Aged ; Anti-Bacterial Agents/therapeutic use ; Chronic Disease ; Adult ; },
abstract = {Assessing gut microbiota disturbances for subsequent modulation remains a challenge. This study aims to evaluate the safety and efficacy of a microbiota-oriented strategy in treating patients with chronic critical illness (CCI). This single-center prospective study included chronically critically ill patients, stratified into three groups by severity of microbiota dysfunction. Three different microbiota modulation regimens including metabiotics, enteral, and anaerobic-safe systemic antibiotics were applied subsequently. Forty-three patients with chronic critical illness were included. Mild microbiota dysfunction was present in 49% patients, moderate in 19% and severe in 32%. Monitoring of biomarkers for 14 days confirmed the safety of reducing the pharmacological load in mild to moderate microbiota dysfunction. The microbiota-oriented strategy demonstrated improvements in neurological condition, a decrease in inflammation, and normalization of several hematological and biochemical parameters, without contributing to the activation of opportunistic microorganisms in the intestinal microbiota. The incidence of pneumonia in patients with CCI was reduced significantly during the 28-day observation period. The results of the pilot study suggest the potential benefits of a microbiota-oriented strategy in preventing nosocomial pneumonia in CCI patients.},
}

Humans
*Critical Illness/therapy
*Gastrointestinal Microbiome/drug effects
Pilot Projects
Male
Female
Prospective Studies
Middle Aged
Aged
Anti-Bacterial Agents/therapeutic use
Chronic Disease
Adult

@article {pmid41097031,
year = {2025},
author = {Chen, Y and Han, L and Ye, T and Xie, C},
title = {Research Progress on Diseases and Pests of Chrysanthemum (2015-2025).},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199767},
pmid = {41097031},
issn = {1422-0067},
support = {CSTB2024TIAD-LUX0004//Basic Research and Key Technology Integration and Application of Functional Flowers/ ; 2024LYXZ024//Basic Research and Key Technology Integration and Application of Functional Flowers/ ; 2024YFD1600900//National Key R&D Program of China/ ; },
mesh = {*Chrysanthemum/genetics/parasitology/microbiology/virology ; *Plant Diseases/microbiology/parasitology/genetics ; Animals ; Disease Resistance/genetics ; Pest Control, Biological ; },
abstract = {Chrysanthemum morifolium Ramat. is a major ornamental crop that suffers from diverse fungal, bacterial, viral, and insect pests, causing significant yield and quality losses. Between 2015 and 2025, rapid progress in molecular biology, genomics, and ecological regulation has advanced both fundamental research and applied control strategies. Multi-locus sequencing, multiplex PCR, and next-generation sequencing refined the identification of fungal and bacterial pathogens, while functional studies of WRKY, MYB, and NAC transcription factors revealed key resistance modules. Hormone-mediated signaling pathways, particularly those of salicylic acid, jasmonic acid, and abscisic acid, were shown to play central roles in host defense. Despite these advances, durable genetic resistance against bacterial pathogens and broad-spectrum defense against viruses remains limited. Novel technologies, including virus-free propagation, RNA interference, and spray-induced gene silencing, have shown promising outcomes. For insect pests, studies clarified the damage and virus-vectoring roles of aphids and thrips, and resistance traits linked to trichomes, terpenoids, and lignin have been identified. Biocontrol agents such as Trichoderma spp., Bacillus spp., predatory mites, and entomopathogenic fungi have also demonstrated efficacy. Future efforts should integrate molecular breeding, genome editing, RNA-based tools, and microbiome management to achieve sustainable chrysanthemum protection.},
}

*Chrysanthemum/genetics/parasitology/microbiology/virology
*Plant Diseases/microbiology/parasitology/genetics
Animals
Disease Resistance/genetics
Pest Control, Biological

@article {pmid41097012,
year = {2025},
author = {Yu, H and Niu, X and Niu, B and Lei, P and Xu, N and Yang, S and Yu, Q and Li, G and Wang, L},
title = {Liver-Targeted Scutellarin Nanoemulsion Alleviates Fibrosis with Ancillary Modulation of the Gut-Liver Microbiota.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199746},
pmid = {41097012},
issn = {1422-0067},
support = {2021-I2M-1-070; 2023-I2M-2-006//CAMS Innovation Fund for Medical Sciences/ ; },
mesh = {*Apigenin/pharmacology/administration & dosage/chemistry ; Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Glucuronates/pharmacology/administration & dosage/chemistry ; *Liver Cirrhosis/drug therapy/pathology/metabolism/microbiology ; Emulsions/chemistry ; *Liver/drug effects/microbiology/metabolism/pathology ; Hepatic Stellate Cells/drug effects/metabolism ; Male ; Mice, Inbred C57BL ; *Nanoparticles/chemistry ; Humans ; Disease Models, Animal ; Transforming Growth Factor beta1/metabolism ; },
abstract = {Liver fibrosis, a progressive condition with limited pharmacotherapies, poses a global health challenge. Scutellarin (SCU), a flavonoid derived from Erigeron breviscapus, has demonstrated anti-fibrotic activity and modulates gut microbiota. Emerging evidence suggests that SCU may also influence the hepatic microbiome. However, its clinical utility is constrained by poor water solubility and low oral bioavailability. Here, we developed an SCU-loaded nanoemulsion (SCE) to enhance solubility and liver-targeted delivery. In vitro, SCE increased SCU uptake in hepatic stellate cells (HSCs) and significantly inhibited TGF-β1-induced fibrogenesis. In a bile duct ligation (BDL) mouse model, oral administration of SCE improved hepatic SCU accumulation and produced superior anti-fibrotic efficacy. SCE treatment attenuated fibrosis and collagen deposition in the liver and improved liver function markers. Mechanistic investigations using 16S rRNA sequencing revealed that SCU treatment was associated with beneficial microbiota changes, although its main therapeutic effects were achieved through enhanced hepatic targeting. Notably, the SCE formulation was well-tolerated, showing no significant toxicity in vitro or in vivo. In conclusion, the SCU-loaded nanoemulsion achieved enhanced hepatic delivery of SCU and exerted potent anti-fibrotic effects via multiple mechanisms, including direct suppression of fibrogenesis and ancillary modulation of the gut-liver microbiome, offering a promising therapeutic strategy for liver fibrosis.},
}

*Apigenin/pharmacology/administration & dosage/chemistry
Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Glucuronates/pharmacology/administration & dosage/chemistry
*Liver Cirrhosis/drug therapy/pathology/metabolism/microbiology
Emulsions/chemistry
*Liver/drug effects/microbiology/metabolism/pathology
Hepatic Stellate Cells/drug effects/metabolism
Male
Mice, Inbred C57BL
*Nanoparticles/chemistry
Humans
Disease Models, Animal
Transforming Growth Factor beta1/metabolism

@article {pmid41096928,
year = {2025},
author = {Yang, B and Wu, J and Hou, X and Bai, T and Liu, S},
title = {Memory in Misfire: The Gut Microbiome-Trained Immunity Circuit in Inflammatory Bowel Diseases.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199663},
pmid = {41096928},
issn = {1422-0067},
support = {2022YFC2504005//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Inflammatory Bowel Diseases/immunology/microbiology/therapy ; Animals ; *Immunologic Memory ; Immunity, Innate ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Trained Immunity ; },
abstract = {Inflammatory bowel disease (IBD) demonstrates chronic relapsing inflammation extending beyond adaptive immunity dysfunction. "Trained immunity"-the reprogramming of innate immune memory in myeloid cells and hematopoietic progenitors-maintains intestinal inflammation; however, the mechanism by which gut microbiome orchestration determines protective versus pathological outcomes remains unclear. Microbial metabolites demonstrate context-dependent dual effects along the gut-bone marrow axis. Short-chain fatty acids typically induce tolerogenic immune memory, whereas metabolites like succinate and polyamines exhibit dual roles: promoting inflammation in certain contexts while enhancing barrier integrity in others, influenced by cell-specific receptors and microenvironmental factors. Interventions include precision probiotics and postbiotics delivering specific metabolites, fecal microbiota transplantation addressing dysbiotic trained immunity, targeted metabolite supplementation, and pharmacologic reprogramming of pathological myeloid training states. Patient stratification based on microbiome composition and host genetics enhances therapeutic precision. Future research requires integration of non-coding RNAs regulating trained immunity, microbiome-immune-neuronal axis interactions, and host genetic variants modulating microbiome-immunity crosstalk. Priorities include developing companion diagnostics, establishing regulatory frameworks for microbiome therapeutics, and defining mechanistic switches for personalized interventions.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Inflammatory Bowel Diseases/immunology/microbiology/therapy
Animals
*Immunologic Memory
Immunity, Innate
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Trained Immunity

@article {pmid41096907,
year = {2025},
author = {Murillo-Cancho, AF and Lozano-Paniagua, D and Nievas-Soriano, BJ},
title = {Dietary and Pharmacological Modulation of Aging-Related Metabolic Pathways: Molecular Insights, Clinical Evidence, and a Translational Model.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199643},
pmid = {41096907},
issn = {1422-0067},
mesh = {Humans ; *Aging/metabolism/drug effects ; *Caloric Restriction ; *Metabolic Networks and Pathways/drug effects ; Animals ; Longevity ; Fasting ; Translational Research, Biomedical ; *Diet ; },
abstract = {Advances in geroscience suggest that aging is modulated by molecular pathways that are amenable to dietary and pharmacological intervention. We conducted an integrative critical review of caloric restriction (CR), intermittent fasting (IF), and caloric restriction mimetics (CR-mimetics) to compare shared mechanisms, clinical evidence, limitations, and translational potential. Across modalities, CR and IF consistently activate AMP-activated protein kinase and sirtuins, inhibit mTOR (mechanistic target of rapamycin) signaling, and enhance autophagy, aligning with improvements in insulin sensitivity, lipid profile, low-grade inflammation, and selected epigenetic aging measures in humans. CR-mimetics, such as metformin, resveratrol, rapamycin, and spermidine, partially reproduce these effects; however, long-term safety and efficacy in healthy populations remain incompletely defined. Methodological constraints-short trial duration, selective samples, intermediate (nonclinical) endpoints, and limited adherence monitoring-impede definitive conclusions on hard outcomes (frailty, disability, hospitalization, mortality). We propose the Active Management of Aging and Longevity (AMAL) model, a three-level biomarker-guided framework that integrates personalized diet, chrono-nutrition, exercise, and the selective use of CR-mimetics, along with digital monitoring and decision support. AMAL emphasizes epigenetic clocks, multi-omics profiling, inflammatory and microbiome metrics, and adaptive protocols to enhance adherence and clinical relevance. Overall, CR, IF, and CR mimetics constitute promising, complementary strategies to modulate biological aging; rigorous long-term trials with standardized biomarkers and clinically meaningful endpoints are needed to enable their scalable implementation.},
}

Humans
*Aging/metabolism/drug effects
*Caloric Restriction
*Metabolic Networks and Pathways/drug effects
Animals
Longevity
Fasting
Translational Research, Biomedical
*Diet

@article {pmid41096891,
year = {2025},
author = {Sheikh, MY and Younus, MF and Shergill, A and Hasan, MN},
title = {Diet and Lifestyle Interventions in Metabolic Dysfunction-Associated Fatty Liver Disease: A Comprehensive Review.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199625},
pmid = {41096891},
issn = {1422-0067},
mesh = {Humans ; *Life Style ; Insulin Resistance ; Exercise ; *Diet ; *Fatty Liver/metabolism/therapy ; Gastrointestinal Microbiome ; *Non-alcoholic Fatty Liver Disease ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) and its progressive form, metabolic dysfunction-associated steatohepatitis (MASH), have become the leading causes of chronic liver disease worldwide, with increasing rates of cirrhosis, hepatocellular carcinoma, and cardiovascular complications. Pathogenesis involves a complex interplay of dietary excess, sedentary lifestyle, insulin resistance, adipose tissue dysfunction, and alterations in the gut microbiome, which collectively lead to hepatocellular stress, inflammation, and fibrogenesis. Despite ongoing advances in pharmacotherapy, lifestyle intervention remains the cornerstone of management. Evidence shows that sustained weight loss of ≥5% reduces hepatic steatosis, ≥7% improves necroinflammation, and ≥10% stabilizes or reverses fibrosis. Dietary strategies, including Mediterranean-style patterns, high-protein approaches, and intermittent fasting, have been shown to be effective in improving insulin sensitivity and reducing intrahepatic triglycerides. Exercise interventions, focusing on both aerobic fitness and resistance training, enhance metabolic flexibility and combat sarcopenia, thereby improving hepatic and systemic outcomes. Equally important are behavioral support, digital health tools, and multidisciplinary approaches that enhance adherence and address barriers such as socioeconomic disparities, limited access, and patient engagement issues. Personalized nutrition plans, integrating physical activity, and ongoing support for behavioral change are essential for long-term disease management. This review synthesizes current evidence on the roles of macronutrients, micronutrients, dietary quality, physical activity, and adjunctive behavioral strategies in managing MASLD. By translating mechanistic insights into practical, evidence-based recommendations, we aim to provide clinicians, dietitians, and exercise professionals with effective frameworks to slow disease progression and improve outcomes across diverse patient populations.},
}

Humans
*Life Style
Insulin Resistance
Exercise
*Diet
*Fatty Liver/metabolism/therapy
Gastrointestinal Microbiome
*Non-alcoholic Fatty Liver Disease

@article {pmid41096858,
year = {2025},
author = {Liang, Y and Zhao, Y and Fasano, A and Su, CW},
title = {Gut Permeability and Microbiota in Parkinson's Disease: Mechanistic Insights and Experimental Therapeutic Strategies.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199593},
pmid = {41096858},
issn = {1422-0067},
support = {1R21AI144738-24/NH/NIH HHS/United States ; },
mesh = {Humans ; *Parkinson Disease/microbiology/therapy/metabolism ; *Gastrointestinal Microbiome/physiology ; Animals ; Permeability ; alpha-Synuclein/metabolism ; Blood-Brain Barrier/metabolism ; },
abstract = {Globally, Parkinson's disease (PD) is the neurodegenerative condition with the most rapidly increasing prevalence, and a growing body of evidence associates its pathology with impairments in the gut-brain axis. Traditionally viewed as a disease marked by the loss of dopaminergic neurons, emerging evidence emphasizes that chronic neuroinflammation is a driver of neurodegeneration, with gut-originating inflammation playing a crucial role. Increased intestinal permeability, often called "leaky gut," allows harmful substances, toxins, and misfolded α-synuclein into the systemic circulation, potentially exacerbating neuroinflammation and spreading α-synuclein pathology to the brain through the vagus nerve or compromised blood-brain barrier (BBB). This review synthesizes current insights into the relationship between gut health and PD, emphasizing the importance of gut permeability in disrupting intestinal barrier function. This paper highlights innovative therapeutic approaches, particularly personalized therapies involving gut microbiome engineering, as promising strategies for restoring gut integrity and improving neurological outcomes. Modulating specific gut bacteria to enhance the synthesis of certain metabolites, notably short-chain fatty acids (SCFAs), represents a promising strategy for reducing inflammatory responses and decelerating neurodegeneration in Parkinson's disease.},
}

Humans
*Parkinson Disease/microbiology/therapy/metabolism
*Gastrointestinal Microbiome/physiology
Animals
Permeability
alpha-Synuclein/metabolism
Blood-Brain Barrier/metabolism

@article {pmid41096808,
year = {2025},
author = {Queirós, C and Lisboa, C and Magina, S},
title = {Unveiling the Microbiome's Role in Hidradenitis Suppurativa: A Comprehensive Review of Pathogenetic Mechanisms.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199542},
pmid = {41096808},
issn = {1422-0067},
mesh = {Humans ; *Hidradenitis Suppurativa/microbiology/pathology/etiology ; Dysbiosis/microbiology ; *Microbiota ; *Gastrointestinal Microbiome ; Skin/microbiology ; },
abstract = {Hidradenitis suppurativa (HS) is a chronic, recurrent, and highly debilitating inflammatory disorder of the pilosebaceous unit. Its pathogenesis is considered multifactorial, involving genetic, environmental, hormonal, lifestyle, and microbiome-related factors. The microbiota, defined as the collection of microorganisms, their genomes, and their interactions within a given environment, colonizes multiple sites of the healthy human body, which include the skin and gut, where it contributes to the maintenance of homeostasis. In HS, both skin and gut microbiota exhibit disruptions in composition and diversity, a state referred to as dysbiosis. Alterations in the expression of antimicrobial peptides in HS further implicate the microbiome in disease pathophysiology. In addition, chronic inflammation, bacterial biofilm formation, and dysbiosis are thought to contribute to the severity and recurrence of HS. Although the precise role of dysbiosis in HS pathogenesis remains unclear, several studies have demonstrated a reduction in cutaneous microbial diversity in HS patients, distinguished by an increased abundance of anaerobic and opportunistic bacteria and a reduction in commensal species. The intestinal microbiome has been even less thoroughly investigated, but available evidence suggests decreased overall diversity and richness, with enrichment of pro-inflammatory and depletion of anti-inflammatory bacterial taxa. This review aims to provide an overview of the current knowledge regarding the role of the microbiome in HS, with the goal of informing the direction of future research, including the potential utility of the microbiome as a biomarker for diagnosis and severity stratification in HS.},
}

Humans
*Hidradenitis Suppurativa/microbiology/pathology/etiology
Dysbiosis/microbiology
*Microbiota
*Gastrointestinal Microbiome
Skin/microbiology

@article {pmid41096729,
year = {2025},
author = {Chen, JC and Hsu, MH and Hu, SW and Lin, YY},
title = {Exploring the Diagnostic and Predictive Value of Oral Microbiome in Esophageal Cancer: A Systematic Review and Meta-Analysis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199457},
pmid = {41096729},
issn = {1422-0067},
support = {113-2813-C-040-065-B//National Science and Technology Council (NSTC), Taiwan/ ; },
mesh = {Humans ; *Esophageal Neoplasms/diagnosis/microbiology ; *Microbiota ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Esophageal Squamous Cell Carcinoma/microbiology/diagnosis ; },
abstract = {The research interest in the oral microbiome's role in esophageal cancer is growing, yet a comprehensive synthesis of available evidence is still lacking. This study aimed to explore the effects of oral microbiome on the development of esophageal cancer through a systematic review of existing literature retrieved from the Embase, PubMed, and Web of Science databases. Eighteen studies published between 2015 and 2024 were obtained, involving 1191 cases and 1403 controls, mostly using oral saliva samples and 16S rRNA gene sequencing. Findings on alpha-diversity were inconsistent, while most studies reported significant beta-diversity differences between cases and controls. Notably, several investigations on esophageal squamous cell carcinoma showed higher levels of Prevotella, Porphyromonas, and Fusobacterium, while two studies on esophageal adenocarcinoma reported elevated levels of Actinomyces species. A fixed-effect meta-analysis of two studies showed that individuals with specific oral microbial signatures had significantly higher odds of developing esophageal squamous cell carcinoma (OR = 9.50; 95% CI: 5.89-15.29). Quality assessments highlighted methodological strengths but noted variability in group comparability and local applicability. These results reveal the potential of oral microbiome shift as an early detection biomarker and for developing personalized strategies in treating esophageal cancer, meriting further clinical investigation.},
}

Humans
*Esophageal Neoplasms/diagnosis/microbiology
*Microbiota
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics
Saliva/microbiology
Esophageal Squamous Cell Carcinoma/microbiology/diagnosis

@article {pmid41096709,
year = {2025},
author = {Więckowska, M and Szelenberger, R and Poplawski, T and Bijak, M and Gorniak, L and Stela, M and Cichon, N},
title = {Gut as a Target of Ochratoxin A: Toxicological Insights and the Role of Microbiota.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199438},
pmid = {41096709},
issn = {1422-0067},
mesh = {*Ochratoxins/toxicity ; *Gastrointestinal Microbiome/drug effects ; Humans ; Animals ; Intestinal Mucosa/drug effects/microbiology/metabolism ; Dysbiosis/microbiology/chemically induced ; *Gastrointestinal Tract/microbiology/drug effects ; },
abstract = {Ochratoxin A (OTA) is a widespread foodborne mycotoxin that poses significant risks to both human and animal health. Upon ingestion, the gastrointestinal tract (GIT) becomes the main site of exposure, where OTA interacts directly with the intestinal epithelium and resident microbiota. Research indicates that OTA disrupts the integrity of the intestinal barrier and alters its permeability. Moreover, OTA undergoes transport and partial metabolism within the intestine before being excreted. Detoxification pathways for OTA include enzymatic degradation and adsorption by microorganisms. Notably, OTA has profound toxic effects on the gut ecosystem; it can alter the relative abundance of bacterial taxa by reducing beneficial populations and promoting opportunistic or pathogenic strains. These changes contribute to an imbalance in the microbiota, impairing host metabolic and immune functions. This dysbiosis is characterized by disrupted microbial homeostasis and impaired communication between the host and its gut microbiome. This review highlights the dual role of the intestine as both a target and a modulator of OTA toxicity. It emphasizes the importance of gut microbiota in mediating the toxicological outcomes of OTA and explores microbiome-based strategies as potential avenues for detoxification.},
}

*Ochratoxins/toxicity
*Gastrointestinal Microbiome/drug effects
Humans
Animals
Intestinal Mucosa/drug effects/microbiology/metabolism
Dysbiosis/microbiology/chemically induced
*Gastrointestinal Tract/microbiology/drug effects

@article {pmid41096656,
year = {2025},
author = {Van den Abbeele, P and Poppe, J and Baudot, A and Vu, LD},
title = {Triacetin and a Mushroom Blend Restore Butyrate Production by IBS Microbiomes Ex Vivo, Thus Promoting Barrier Integrity.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199388},
pmid = {41096656},
issn = {1422-0067},
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/metabolism/drug therapy ; *Gastrointestinal Microbiome/drug effects ; *Butyrates/metabolism ; Male ; Female ; Adult ; Middle Aged ; Caco-2 Cells ; *Agaricales/chemistry ; Fatty Acids, Volatile/metabolism ; Intestinal Mucosa/metabolism/drug effects/microbiology ; Dysbiosis/microbiology ; Fermentation ; },
abstract = {Irritable Bowel Syndrome (IBS) is a common gastrointestinal disorder, characterized by abdominal pain, altered bowel habits (diarrhea and/or constipation) and a dysbiosis of the gut microbiome. This dysbiosis is difficult to restore via fiber supplementation, which typically promotes gas production, potentially worsening IBS symptoms. We therefore studied how two novel products, triacetin (TA; REBiome™) and a mushroom blend (MB; Hōlistiq™), modulate the microbiome of IBS subjects (n = 8) using the ex vivo SIFR[®] (Systemic Intestinal Fermentation Research) technology combined with a co-culture of epithelial/immune (Caco-2/THP-1) cells. First, the IBS microbiomes revealed large interpersonal variability and an IBS-associated dysbiosis. TA increased the beneficial metabolites acetate and butyrate (~Anaerobutyricum soehngenii, Mediterraneibacter_A butyricigenes, Faecalibacterium prausnitzii). Moreover, MB stimulated a wide range of gut microbes and additionally promoted propionate. Despite more strongly increasing total short-chain fatty acid (SCFA) levels, TA induced significantly less gas production than MB. Mechanistically, acetate with TA was derived from hydrolysis, a process that indeed does not induce gas production. Notably, both TA and MB enhanced gut barrier integrity (transepithelial electrical TEER), which is related to lower symptom severity in IBS patients. Overall, our findings highlight the product-specific microbiome modulation and potential of MB, TA or combinations thereof as dietary interventions for managing IBS symptom severity.},
}

Humans
*Irritable Bowel Syndrome/microbiology/metabolism/drug therapy
*Gastrointestinal Microbiome/drug effects
*Butyrates/metabolism
Male
Female
Adult
Middle Aged
Caco-2 Cells
*Agaricales/chemistry
Fatty Acids, Volatile/metabolism
Intestinal Mucosa/metabolism/drug effects/microbiology
Dysbiosis/microbiology
Fermentation

@article {pmid41096628,
year = {2025},
author = {Yagi, S and Fukui, H and Shiraishi, T and Kaku, K and Wakita, M and Takagi, Y and Ikenouchi, M and Sato, T and Kawai, M and Yokoyama, Y and Takagawa, T and Tomita, T and Kitaoka, S and Shinzaki, S},
title = {Effect of Chronic Social Defeat Stress on the Small-Intestinal Environment, Including the Gut Flora, Immune System, and Mucosal Barrier Integrity.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199359},
pmid = {41096628},
issn = {1422-0067},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Stress, Psychological/immunology/microbiology/metabolism ; Mice ; *Intestinal Mucosa/metabolism/immunology/microbiology ; Male ; *Intestine, Small/microbiology/metabolism/immunology ; Mice, Inbred C57BL ; Tight Junction Proteins/metabolism ; *Social Defeat ; Cytokines/metabolism ; Permeability ; *Immune System ; Mice, Inbred ICR ; },
abstract = {Psychological stress is deeply involved in the pathophysiology of gastrointestinal diseases. We investigated the effect of psychological stress on the small-intestinal environment, including gut flora, immune system, and mucosal integrity in mice subjected to chronic social defeat stress (CSDS). CSDS mice were established by exposing a C57BL/6N mouse to an ICR aggressor mouse. Stool samples were obtained to investigate its properties and the gut microbiome profile. Using small-intestinal tissues, the expression of cytokines, antimicrobial peptides, and tight junction proteins (TJPs) were examined by real-time RT-PCR and immunohistochemistry. Small-intestinal permeability was evaluated by transepithelial electrical resistance assay. For stool properties, mean Bristol scale score and fecal water content were significantly lower in the CSDS group. Pseudomonadota and Patescibacteria were significantly more abundant in the stools from CSDS mice. Among TJPs and antimicrobial peptides, the expression of Occludin, Claudin-4, and Regenerating gene IIIγ was significantly decreased in the small intestine epithelium of CSDS mice. The small-intestinal permeability was significantly increased in CSDS mice. Lipopolysaccharide immunoreactivity, the number of macrophages, and proinflammatory IL-1β expression were significantly increased in the small intestine of CSDS mice. These findings suggest that psychological stress is associated with mucosal barrier dysfunction and microinflammation in small-intestinal tissues.},
}

Animals
*Gastrointestinal Microbiome
*Stress, Psychological/immunology/microbiology/metabolism
Mice
*Intestinal Mucosa/metabolism/immunology/microbiology
Male
*Intestine, Small/microbiology/metabolism/immunology
Mice, Inbred C57BL
Tight Junction Proteins/metabolism
*Social Defeat
Cytokines/metabolism
Permeability
*Immune System
Mice, Inbred ICR

@article {pmid41096606,
year = {2025},
author = {Grefhorst, A and Kleemann, AS and Havik, S and Troise, AD and De Pascale, S and Scaloni, A and Nieuwdorp, M and Bui, TPN},
title = {Intestinal Myo-Inositol Metabolism and Metabolic Effects of Myo-Inositol Utilizing Anaerostipes rhamnosivorans in Mice.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199340},
pmid = {41096606},
issn = {1422-0067},
support = {09150162210057//NWO/ ; },
mesh = {Animals ; *Inositol/metabolism ; Mice ; Gastrointestinal Microbiome ; Fatty Acids, Volatile/metabolism ; Diet, High-Fat/adverse effects ; Male ; *Clostridiales/metabolism ; Cecum/metabolism ; Mice, Inbred C57BL ; Prebiotics/administration & dosage ; Intestines/microbiology ; },
abstract = {The gut microbiome is strongly implicated in the development of obesity and type 2 diabetes mellitus (T2DM). A recent study demonstrated that 6-week oral supplementation of Anaerostipes rhamnosivorans (ARHAM) combined with the prebiotic myo-inositol (MI) reduced fasting glucose levels in mice. In the present study, we investigated the effects of a 13-week ARHAM-MI supplementation in high-fat diet-fed mice and examined the metabolic fate of MI, including its microbial conversion into short-chain fatty acids (SCFAs), using [13]C-MI and stable isotope tracers in the cecum, portal vein, and peripheral blood. The results showed that the ARHAM-MI group gained less weight than the MI-only and placebo groups. Analysis of intestinal mRNA and stable isotope tracing revealed that MI is primarily absorbed in the upper gastrointestinal tract, whereas microbial conversion to SCFAs predominantly occurs in the cecum and is enhanced by ARHAM. ARHAM-MI mice also showed increased cecal Gpr43 mRNA expression, indicating enhanced SCFA-mediated signaling. Notably, SCFAs derived from MI displayed distinct distribution patterns: [13]C-butyrate was detected exclusively in the cecum, [13]C-propionate was present in the cecum and portal vein, whereas [13]C-acetate was the only SCFA detected in peripheral blood. Collectively, ARHAM-MI co-supplementation confers modest metabolic benefits in high-fat diet-fed mice, underscoring the need to optimize the dosage and administration frequency of ARHAM-MI to enhance its therapeutic efficacy.},
}

Animals
*Inositol/metabolism
Mice
Gastrointestinal Microbiome
Fatty Acids, Volatile/metabolism
Diet, High-Fat/adverse effects
Male
*Clostridiales/metabolism
Cecum/metabolism
Mice, Inbred C57BL
Prebiotics/administration & dosage
Intestines/microbiology

@article {pmid41096588,
year = {2025},
author = {Alghamdi, AK and Rawat, A and Alzayed, W and Parween, S and Nagarajan, AP and Saad, MM and Hirt, H},
title = {Mangrove-Derived Endophytic Bacteria Enhance Growth, Yield, and Stress Resilience in Rice.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199317},
pmid = {41096588},
issn = {1422-0067},
support = {BAS/1/1062-01-01//KAUST/ ; },
mesh = {*Oryza/growth & development/microbiology/genetics/physiology ; *Endophytes/physiology ; *Stress, Physiological ; Plant Roots/microbiology/growth & development ; *Bacteria ; Salt Tolerance ; Gene Expression Regulation, Plant ; Salinity ; Arabidopsis/growth & development/microbiology/genetics ; },
abstract = {Global climate change increasingly challenges agriculture with flooding and salinity. Among strategies to enhance crop resilience to these stresses, we tested several endophytic bacterial strains from mangroves, which are permanently exposed to flooding and high salinity. We show several strains that can enhance flooding and salinity tolerance in Arabidopsis and rice plants. Two strains and their combination massively enhanced the growth and yield of Oryza sativa cv. Nipponbare under both soil and hydroponic growth conditions with and without salt treatment. The bacteria-induced transcriptome changes in O. sativa roots, particularly related to ABA-signaling and lignin and suberin deposition in root tissues, explain the altered responses of colonized rice plants to hypoxic and saline stress conditions. Importantly, bacterially colonized rice plants exhibited enhanced yield and improved grain quality. These results show that microbes can be a powerful tool for enhancing the yield and resilience of rice to hypoxic and saline stress conditions.},
}

*Oryza/growth & development/microbiology/genetics/physiology
*Endophytes/physiology
*Stress, Physiological
Plant Roots/microbiology/growth & development
*Bacteria
Salt Tolerance
Gene Expression Regulation, Plant
Salinity
Arabidopsis/growth & development/microbiology/genetics

@article {pmid41096559,
year = {2025},
author = {Poluektova, EU and Stavrovskaya, A and Pavlova, A and Yunes, R and Marsova, M and Koshenko, T and Illarioshkin, S and Danilenko, V},
title = {Gut Microbiome as a Source of Probiotic Drugs for Parkinson's Disease.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199290},
pmid = {41096559},
issn = {1422-0067},
support = {075-15-2024-638//Ministry of Science and Higher Education of the Russian Federation for major scientific projects in priority areas of scientific and technological development/ ; },
mesh = {*Parkinson Disease/microbiology/therapy/drug therapy ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/therapeutic use ; Animals ; },
abstract = {Parkinson's disease (PD) is a progressive, irreversible neurodegenerative disorder characterized by motor impairments and a wide spectrum of non-motor symptoms, including gastrointestinal dysfunction, sleep disturbances, depression, and cognitive decline. These manifestations arise from disturbances across multiple systems-gastrointestinal, neuroendocrine, immune, enteric, and central nervous systems. Alterations in the gut microbiota may play a causal role in PD onset and frequently accompany disease progression. The gut-brain axis, particularly the vagus nerve, is increasingly recognized as a key communication pathway whose dysregulation contributes to systemic dysfunction and the breakdown of homeostasis, ultimately driving PD pathology. Currently, there is no cure for PD, and existing treatments primarily target symptom relief. Effective management of PD requires a comprehensive approach that integrates multiple pharmacologically active agents aimed at restoring impaired organ functions and, when possible, neutralizing toxic factors that accelerate disease progression. One promising therapeutic avenue lies in functional gut bacteria, which form the basis for developing live biotherapeutic products, postbiotics, and bacterial vesicles. In this review, we summarize current data on the effects of probiotics in PD, drawing on both animal models and clinical studies. We highlight the role of probiotics in modulating PD pathophysiology and discuss their potential as adjunctive therapeutic agents. To provide a broader perspective, we also include sections describing the clinical manifestations of PD, gut microbiota alterations associated with the disease, and the role of artificial intelligence, particularly machine learning, in constructing functional models of PD.},
}

*Parkinson Disease/microbiology/therapy/drug therapy
Humans
*Gastrointestinal Microbiome/drug effects
*Probiotics/therapeutic use
Animals

@article {pmid41096524,
year = {2025},
author = {Yu, Q and Li, N and Bao, P and Huang, C and Zheng, Q and Wang, T and Ma, C and Deng, J and Jiang, F and Jia, J and Yan, P},
title = {Microbiota-Metabolite-Host Crosstalk Mediates the Impact of Dietary Energy Levels on Colonic Homeostasis in High-Altitude Ruminants.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/ani15192929},
pmid = {41096524},
issn = {2076-2615},
support = {KS20240//Pamir Yak Breed Improvement and Innovation Application Project/ ; TCYC-TP2023//Xinjiang Tianchi Talent Research Program/ ; TZYC-TP2023//Tingzhou Talent Research Program/ ; 2022KJ137 and ZR2023MC164//Shandong Natural Science Foundation/ ; },
abstract = {The colon plays a crucial role in energy metabolism and intestinal health of ruminants during various physiological stages. Plateau ruminants have long been subjected to extreme environments characterized by hypoxia, cold, and nutritional scarcity, which makes their dependence on energy metabolism particularly pronounced. However, existing research on the regulatory effects of dietary energy levels on the colonic function of plateau ruminants is still quite limited. This study involved 60 healthy male Pamir yaks with consistent body conditions, which were randomly divided into three groups: a low-energy diet group (YG, Neg 1.53 MJ/kg), a medium-energy diet group (QG, Neg 2.12 MJ/kg), and a high-energy diet group (RG, Neg 2.69 MJ/kg). Each yak was provided with 5 kg of mixed feed daily over a 170-day feeding trial. The results indicated that a high-energy diet enhanced growth performance in yaks (p < 0.05). However, it also induced local colonic inflammation, decreased levels of immune factors (IgA, IgG, and IL-10), and increased the abundance of potentially pathogenic bacteria, such as Klebsiella and Campylobacter (p < 0.05). Conversely, a medium-energy diet fostered the proliferation of beneficial bacteria such as Bradymonadales, Parabacteroides, and Mogibacterium (p < 0.05), and preserved immune homeostasis. Additionally, multi-omics analysis revealed that the QG group was significantly enriched in key metabolic pathways, including pyruvate metabolism and glycine, serine, and threonine metabolism and panto-thenate and CoA biosynthesis pathways, among others (p < 0.05), demonstrating a synergistic regulatory effect among the microbiome, metabolism, and host. In summary, a moderate-energy diet can promote the proliferation of beneficial bacteria in the extreme environment of the plateau. By regulating pathways such as Amino acid, Nucleotide, and Lipid metabolism, it coordinates the expression of key host genes and metabolite levels, effectively balancing immune signals and energy metabolism. This interaction establishes a beneficial microbial-metabolism-host pattern that supports colon health.},
}

@article {pmid41096509,
year = {2025},
author = {Abrams, AN and Kuehn, LA and Keele, JW and Gonda, MG and McDaneld, TG},
title = {Evaluation of Nasal Microbial Communities of Beef Calves During Pre-Weaning Outbreak of Bovine Respiratory Disease.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/ani15192914},
pmid = {41096509},
issn = {2076-2615},
support = {3040-31000-100-00D//Agricultural Research Service - Plains Area/ ; },
abstract = {Bovine respiratory disease complex (BRDC) is a leading cause of morbidity and mortality in pre-weaned calves, yet the role of commensal nasal microbiota in outbreak severity remains poorly understood. This study characterized nasal bacterial communities during two BRDC outbreaks of differing severity (moderate vs. severe) and at ~30 days post-treatment. Nasal swabs were collected from calves and analyzed using 16S rRNA gene sequencing (V1-V3 regions, Illumina MiSeq) and quantitative PCR targeting three major BRDC pathogens. Microbial community profiles differed between outbreak groups and across timepoints. Calves in the severe outbreak group exhibited lower microbial diversity compared to those in the moderate outbreak. In both groups, diversity significantly increased from outbreak to post-treatment. At the time of disease, nasal communities were dominated by the genera Mycoplasmopsis, Mesomycoplasma, and Caviibacter, with qPCR confirming Mycoplasma bovirhinis as the predominant species. These findings indicate that BRDC outbreaks in pre-weaned calves are associated with reduced microbial diversity and the dominance of pathogenic Mycoplasma species, with recovery characterized by greater bacterial diversity. Shifts in nasal microbiome composition between outbreak and post-treatment may reflect pathogen-driven disruption during disease and subsequent microbial community rebalancing.},
}

@article {pmid41096480,
year = {2025},
author = {Moroni, F and Naya-Català, F and Terova, G and Domingo-Bretón, R and Calduch-Giner, JÀ and Pérez-Sánchez, J},
title = {One Function, Many Faces: Functional Convergence in the Gut Microbiomes of European Marine and Freshwater Fish Unveiled by Bayesian Network Meta-Analysis.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/ani15192885},
pmid = {41096480},
issn = {2076-2615},
support = {871108//TNA program (PID24876) within H2020 AQUAEXCEL3.0 project (871108)/ ; PID2023-146990OB-I00//Spanish MCIU project BreamHOLOBIONT (PID2023-146990OB-I00)/ ; },
abstract = {Intestinal microbiota populations are constantly shaped by both intrinsic and extrinsic factors, including diet, environment, and host genetics. As a result, understanding how to assess, monitor, and exploit microbiome-host interplay remains an active area of investigation, especially in aquaculture. In this study, we analyzed the taxonomic structure and functional potential of the intestinal microbiota of European sea bass and rainbow trout, incorporating gilthead sea bream as a final reference. The results showed that the identified core microbiota (40 taxa for sea bass and 20 for trout) held a central role in community organization, despite taxonomic variability, and exhibited a predominant number of positive connections (>60% for both species) with the rest of the microbial community in a Bayesian network. From a functional perspective, core-associated bacterial clusters (75% for sea bass and 81% for sea bream) accounted for the majority of predicted metabolic pathways (core contribution: >75% in sea bass and >87% in trout), particularly those involved in carbohydrate, amino acid, and vitamin metabolism. Comparative analysis across ecological phenotypes highlighted distinct microbial biomarkers, with genera such as Vibrio, Pseudoalteromonas, and Paracoccus enriched in saltwater species (Dicentrarchus labrax and Sparus aurata) and Mycoplasma and Clostridium in freshwater (Oncorhynchus mykiss). Overall, this study underscores the value of integrating taxonomic, functional, and network-based approaches as practical tools to monitor intestinal health status, assess welfare, and guide the development of more sustainable production strategies in aquaculture.},
}

@article {pmid41096444,
year = {2025},
author = {Okonkwo, UN and Smit, CJ and Egbu, CF},
title = {Mechanistic Insights into the Physiological and Meat Quality Responses of Broiler Chickens Fed Incremental Turmeric Rhizome Meal.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/ani15192849},
pmid = {41096444},
issn = {2076-2615},
support = {2016/2017/TETFund/29//Tertiary Education Trust Fund of Nigeria/ ; },
abstract = {Natural products, such as turmeric rhizome meal (TRM), may hold the key to a sustainable solution to antimicrobial resistance rise and antibiotic prohibition in food-producing animals. This study evaluated the effects of dietary TRM at 0 (CON), 0.3 (TRM3), 0.6 (TRM6), and 0.9 g/kg (TRM9) on growth, nutrient digestibility, immunity, gut function, nutrient transport biomarkers, microbiome, and meat quality in 280 one-day-old male Ross 308 chicks over a 42-day feeding trial. Birds fed TRM indicated higher body weight gain and lower feed conversion ratio (p < 0.05). The TRM groups promoted higher (p = 0.001) serum immunoglobulin Y, immunoglobulin M, and interleukin-10 compared to the CON. Birds fed CON had higher interleukin-2 (p = 0.025), interleukin-6 (p = 0.027), and TNF-α (p = 0.008) levels compared to the TRM groups. Lactobacillus counts in jejunal villi and crypts were higher in the TRM groups than in the CON (p < 0.05). Dietary TRM increased electrogenic glucose and lysine transport, accompanied by up-regulation of claudin-5, zonula occludens 1, and mucin-2 expression (p < 0.05). In breast muscle, TRM fortification reduced malondialdehyde levels (p < 0.05) while increasing long-chain polyunsaturated fatty acids (p < 0.05). Thus, TRM is a potent, residue-free phytobiotic alternative to conventional antibiotic growth promoters in poultry systems.},
}

@article {pmid41096368,
year = {2025},
author = {Ma, W and Yang, L and Jing, Y and Mo, Q and Song, Q and Wang, C and Zhu, M},
title = {Dynamic Changes in the Crop Milk and Salivary Microbiota of Breeding Pigeons During the Raising Brooding Period.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/ani15192772},
pmid = {41096368},
issn = {2076-2615},
support = {2023YFD1302004//the National Key R&D Program of China/ ; 19211162//the Livestock and Poultry Breeds Project of Ministry of Agriculture and Rural Affairs/ ; 2024LZGC020//the Key R&D Program of Shandong Province/ ; 2024LZGC002//the Key R&D Program of Shandong Province/ ; },
abstract = {The microbiota within crop milk not only participates in the physiological regulation of parent pigeons but also promotes the healthy growth of squabs. Consequently, microbial sequencing of both crop milk and the saliva through which it passes is essential to elucidate microbial changes in both compartments during the raising brooding period. This study sampled crop milk and saliva of Mimas at three distinct time points corresponding to Days 1, 4, and 7 of raising brooding, and collected samples from three pairs of healthy breeding pigeons with similar body weights at each time point. The results demonstrated that α diversity increased in both the crop milk and salivary microbiota over time, surpassing the levels observed at the initial secretion stage. Compared to R1, the Simpson index of the salivary microbiome was significantly higher at R7 (p < 0.05). Ligilactobacillus constituted the most abundant genus in crop milk, whereas saliva harbored a greater diversity of potentially pathogenic bacteria. Phylogenetic analysis revealed a close evolutionary relationship between Ligilactobacillus and Enterococcus in crop milk, suggesting potential functional synergy. Furthermore, functional prediction indicated that ABC transporter-related genes presented the lowest expression in the crop milk microbiota during its peak secretion period. Notably, Pearson correlation analysis revealed a significant negative correlation between Ligilactobacillus abundance in crop milk and Psittacicella abundance in saliva. In summary, the crop milk and salivary microbiota exhibit distinct temporal dynamics, and their specific microbial compositions and functions can provide new research directions for the healthy breeding of squabs.},
}

@article {pmid41095775,
year = {2025},
author = {Tatarciuc, D and Curca, FR and Virvescu, DI and Butnaru, OM and Goriuc, A and Bida, S and Luchian, I and Surlari, Z and Scurtu, M and Ursu, RG and Budala, DG},
title = {Alzheimer's Disease and Oral Health from Clinical Challenges to Interdisciplinary Care: A Narrative Review.},
journal = {Journal of clinical medicine},
volume = {14},
number = {19},
pages = {},
doi = {10.3390/jcm14196696},
pmid = {41095775},
issn = {2077-0383},
abstract = {The link between oral health and Alzheimer's disease (AD) has gained increasing attention in recent years. Emerging evidence suggests that this association is bidirectional, involving both biological mechanisms and behavioral consequences that reinforce one another over time. Literature Review: A narrative synthesis of systematic reviews, meta-analyses, and scoping reviews published between January 2010 and March 2024 was conducted. Searching was performed in four electronic databases (PubMed, Scopus, the Web of Science, and the Cochrane Library), using a combination of MeSH terms and free-text keywords related to dementia and oral health. Inclusion criteria targeted human studies published in English with full-text access and a clear focus on the interplay between oral status and Alzheimer's disease. Results: The reviewed literature indicates that periodontal disease, tooth loss, and oral microbiome alterations may contribute to neuroinflammation and cognitive decline, potentially influencing the onset and progression of AD. Conversely, Alzheimer's disease negatively affects oral health through impaired self-care, reduced motor coordination, salivary changes, and altered pain perception. Conclusions: By mapping out these interconnections, the findings support a shift in perspective; oral health should be considered a relevant factor in both the prevention and management of Alzheimer's disease. Dentistry and neurology must move closer together in clinical practice, particularly in the care of older adults. Promoting oral health is not just about preserving teeth; it may be part of preserving cognitive function and quality of life.},
}

@article {pmid41095773,
year = {2025},
author = {Suárez-Cortés, M and Juan-Pérez, A and Molina-Rodríguez, A and Araújo de Castro, J and Castaño-Molina, MÁ and Fernández-Ruiz, VE and Jiménez-Méndez, A and Martínez Pérez-Munar, P and Rico-Chazarra, S and Ramos-Molina, B and Sánchez-Solís, M and Blanco-Carnero, JE and Ruiz-Alcaraz, AJ and Núñez-Sánchez, MÁ},
title = {Dynamics of the Epigenome, Microbiome, and Metabolome in Relation to Early Adiposity in the Maternal-Infant Axis: Protocol for a Prospective, Observational Pilot Study in the Spanish NEMO Cohort.},
journal = {Journal of clinical medicine},
volume = {14},
number = {19},
pages = {},
doi = {10.3390/jcm14196694},
pmid = {41095773},
issn = {2077-0383},
support = {22080/JLI/22//Fundación Séneca - Agencia de Ciencia y Tecnología de la Región de Murcia/ ; CP23/00051//Instituto de Salud Carlos III/ ; },
abstract = {Background: Childhood obesity has reached epidemic levels in developed countries and is an emerging concern in developing regions. Children with excess weight are more likely to maintain this condition over time into adulthood and face a higher risk of developing metabolic disorders such as type 2 diabetes, hypertension, metabolic dysfunction-associated liver disease, and dyslipidemia. Early identification of obesity risk is, therefore, a key public health challenge. Methods: This is an observational, prospective, single-center cohort pilot study in 66 mother-infant dyads recruited at the Gynecology and Obstetrics Service of the Virgen de la Arrixaca University Hospital (Murcia, Spain). The primary objective is to identify early-life, non-invasive biomarkers associated with increased adiposity by integrating multi-omics approaches and analyzing maternal-infant interactions. Pregnant women will be enrolled during the third trimester and will undergo a baseline visit at 38 weeks of gestation for clinical and anthropometric assessment. Buccal swabs and fecal samples will be collected at baseline and in the peripartum period for epigenetic (DNA methylation), metagenomic, and metabolomic analyses. Infants will be evaluated at birth and followed at 6 months, 1 year, 2 years, and 3 years. Each visit will include detailed anthropometric measurements, along with collection of buccal swabs and fecal samples for multi-omics profiling. Conclusions: This multidisciplinary study aims to assess how maternal factors influence infant epigenetic and microbial patterns, and their relation to adiposity development. Early identification of such biomarkers may guide personalized prevention strategies and reduce the long-term burden of obesity-related comorbidities.},
}

@article {pmid41095223,
year = {2025},
author = {Wu, C and Sun, Q and Wang, W},
title = {Effects of Biochar Combined with Nitrogen Fertilizer Application on Pepper Yield, Quality and Rhizosphere Soil Microbial Community Diversity.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {19},
pages = {},
doi = {10.3390/plants14193082},
pmid = {41095223},
issn = {2223-7747},
support = {Jilin Province in 2024 three district talent support plan project.//Jilin Province in 2024 three district talent support plan project./ ; },
abstract = {In agricultural systems, excessive application of nitrogen fertilizer often leads to low nitrogen use efficiency and environmental pollution. In order to solve this problem, we studied the synergistic effect of biochar and nitrogen fertilizer on pepper yield, quality and rhizosphere soil health. This study was conducted under a temperate continental monsoon climate in Changchun, China. Using 'Jinfu 803' pepper (Capsicum annuum L.) as the test material, biochar was prepared from corn straw under oxygen-limited conditions at 500 °C. the comprehensive effects of the combined application of biochar (0, 0.7% soil mass ratio) and nitrogen fertilizer (0, 75, 375, 675 kg/hm[2] pure nitrogen) on pepper yield, fruit quality, rhizosphere soil physicochemical properties, and microbial community structure were studied. Redundancy analysis (RDA), high-throughput sequencing, and multivariate statistical methods were used to analyze the association patterns between soil environmental factors and microbial functional groups. The results showed that the combined application of biochar and nitrogen fertilizer significantly improved soil porosity (increased by 12.3-28.6%) and nutrient content, increased yield, and improved quality, among which the treatment of 0.7% biochar combined with 375 kg/hm[2] nitrogen fertilizer (B1N2) had the best effect. Under this treatment, the pepper yield reached 24,854.1 kg/hm[2], which was 42.35% higher than that of the control (B0N0). Notably, the nitrogen partial factor productivity (PFPN) of the B1N2 treatment (66.3 kg/kg) was significantly higher than that of the corresponding treatment without biochar and was not significantly lower than that of the high-nitrogen B1N3 treatment. The contents of soluble sugar and vitamin C in fruits increased by 51.18% and 39.16%, respectively. Redundancy analysis (RDA) revealed that the bacterial community structure was primarily shaped by soil pH, organic matter, and porosity, while the fungal community was predominantly influenced by alkaline hydrolyzable nitrogen and total nitrogen. Furthermore, the B1N2 treatment specifically enriched key functional microbial taxa, such as Chloroflexi (involved in carbon cycling) and Mortierellomycota (phosphate-solubilizing), which showed significant positive correlations with improved soil properties. In conclusion, B1N2 is the optimal treatment combination as it improves soil physical conditions, increases nutrient content, optimizes microbial community structure, and enhances pepper yield and quality.},
}

@article {pmid41095116,
year = {2025},
author = {Navarro, BB and Machado, MJ and Figueira, A},
title = {Nitrogen Use Efficiency in Agriculture: Integrating Biotechnology, Microbiology, and Novel Delivery Systems for Sustainable Agriculture.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {19},
pages = {},
doi = {10.3390/plants14192974},
pmid = {41095116},
issn = {2223-7747},
support = {140619/2022-4//National Council for Scientific and Technological Development/ ; 140991/2022-0//National Council for Scientific and Technological Development/ ; 88887.615059/2021-00//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; 001//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; 310645/2021-2//National Council for Scientific and Technological Development/ ; },
abstract = {Nitrogen (N) is the primary macronutrient that supports global agriculture. The Haber-Bosch process revolutionized the use of synthetic N fertilizers, enabling significant increases in crop yield. However, N losses from fertilization led to negative impacts on the environment. Improving crops' N use efficiency (NUE) has been constrained by the limited understanding of N uptake and assimilation mechanisms, and the role of plant-microbe interactions. Among biological approaches, N fixation by cover crops and rhizobia symbioses represents a cornerstone strategy for improving NUE. The adoption of plant growth-promoting bacteria and arbuscular mycorrhizal fungi may enhance N acquisition by increasing root surface, modulating phytohormone levels, and facilitating nutrient transfer. Advances in plant molecular biology have identified key players and regulators of NUE (enzymes, transporters, and N-responsive transcription factors), which enhance N uptake and assimilation. Emerging biotechnological strategies include de novo domestication by genome editing of crop wild relatives to combine NUE traits and stress resilience back into domesticated cultivars. Additionally, novel fertilizers with controlled nutrient release and microbe-mediated nutrient mobilization, hold promise for synchronizing N availability with plant demand, reducing losses, and increasing NUE. Together, these strategies form a multidimensional framework to enhance NUE, mitigate environmental impacts, and facilitate the transition towards more sustainable agricultural systems.},
}

@article {pmid41095098,
year = {2025},
author = {Much, DG and Saran, A and Merini, LJ and Vangronsveld, J and Thijs, S},
title = {Evaluating the Capability of Epipremnum aureum and Its Associated Phylloplane Microbiome to Capture Indoor Particulate Matter Bound Lead.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {19},
pages = {},
doi = {10.3390/plants14192956},
pmid = {41095098},
issn = {2223-7747},
support = {BOF-BILA N°8546//Hasselt University/ ; },
abstract = {In this study we evaluated over a 1-year period, the ability of Epipremnum aureum leaves to collect particulate matter (PM)-bound Pb from an indoor environment. Using Illumina MiSeq, we investigated the changes in the phylloplane microbiome connected with the accumulation of this pollutant. Plants were placed in a shooting room, where PM release from each shot was recorded, along with PM2.5 and PM10 sequestration and leaf element enrichment by ICP. Additionally, black carbon (BC) sequestration was determined, and SEM-EDX was performed on leaves after 12 months of exposure. Our results indicated that ambient air pollution shapes microbial leaf communities by affecting their diversity. At the order level, Pseudomonadales, along with Micrococcales, appeared (at a low relative abundance) after exposure to indoor PM-bound Pb air pollution. This study provides a unique comparison of Epipremnum aureum air filtration performance between a standard office environment and a firearm shooting range. The air filtration approach holds promise for reducing indoor air pollution, but more knowledge about the underlying mechanisms supporting genera capable of coping with airborne pollutants is still required.},
}

@article {pmid41094699,
year = {2025},
author = {Serrana, JM and Dessirier, B and Nascimento, FJA and Broman, E and Posselt, M},
title = {Microbial hydrocarbon degradation potential of the Baltic Sea ecosystem.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {204},
pmid = {41094699},
issn = {2049-2618},
support = {Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; },
mesh = {*Hydrocarbons/metabolism ; Biodegradation, Environmental ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Ecosystem ; Metagenome ; Petroleum/metabolism ; Microbiota ; Metagenomics/methods ; *Water Pollutants, Chemical/metabolism ; Oceans and Seas ; },
abstract = {BACKGROUND: The Baltic Sea receives petroleum hydrocarbons from various point sources. The degradation of these contaminants in the environment is typically facilitated by a variety of microorganisms that possess a range of genes and metabolic functions related to the degradation of various hydrocarbon substrates. However, our understanding of natural attenuation and the microbial capacity to degrade these contaminants within the Baltic Sea ecosystem remains limited. In this study, we compiled metagenomes from the benthic and pelagic ecosystems across the Baltic Sea to identify microorganisms and characterize their genes and metabolic functions involved in the degradation of hydrocarbon compounds.

RESULTS: Known hydrocarbon-degrading phyla, i.e., Pseudomonadota, Myxococcota A, Actinomycetota, and Desulfobacterota, were identified within the Baltic Sea metagenome-assembled genomes (MAGs). Notably, 80% of the MAGs exhibited multiple hydrocarbon degradation gene annotations (> 10 reads per kilobase million). Aerobic degradation was the predominant pathway for hydrocarbon degradation across environmental samples. Hydrocarbon degradation gene abundances varied among samples and Baltic Sea subbasins, with long-chain alkanes and dibenzothiophene compounds being the preferred substrates. Species richness and diversity of both benthic and pelagic microorganisms positively correlated with hydrocarbon degradation gene diversity, with the pelagic ecosystem exhibiting significantly higher richness and diversity compared to the benthic ecosystem. Additionally, the composition of the hydrocarbon degradation genes across the Baltic Sea subbasins was influenced by oil spill history, with areas that experienced higher spill volumes showing lower microbial diversity, suggesting potential enrichment of specific hydrocarbon degraders. Among the environmental factors assessed, depth played a significant role in shaping the composition of genes involved in hydrocarbon degradation within the Baltic Sea.

CONCLUSIONS: Using metagenomics, we profiled the native microorganisms associated with hydrocarbon degradation in the Baltic Sea. This knowledge will aid in understanding the natural capacities of microbial communities, potentially linked to the natural attenuation of hydrocarbon pollutants in the area. Insights into microbial degradation potential can enhance predictions of petroleum pollutant persistence and accumulation, support mitigation strategies for marine pollution, and reveal the ecological resilience of native microbial communities in marine ecosystems. Video Abstract.},
}

*Hydrocarbons/metabolism
Biodegradation, Environmental
*Seawater/microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
Ecosystem
Metagenome
Petroleum/metabolism
Microbiota
Metagenomics/methods
*Water Pollutants, Chemical/metabolism
Oceans and Seas

@article {pmid41094562,
year = {2025},
author = {Vijay, A and Simpson, L and Tooley, M and Turley, S and Kouraki, A and Kelly, A and Menni, C and Armstrong, J and Jones, S and Valdes, AM},
title = {The anti-inflammatory effects of three different dietary supplement interventions.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1081},
pmid = {41094562},
issn = {1479-5876},
support = {MR/Y010175/1/MRC_/Medical Research Council/United Kingdom ; MR/W026813/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *Dietary Supplements ; Male ; Female ; *Anti-Inflammatory Agents/pharmacology/therapeutic use ; Inflammation/blood ; Biomarkers/blood ; Fatty Acids, Omega-3/pharmacology ; Middle Aged ; Adult ; Inulin/pharmacology ; Prebiotics ; },
abstract = {BACKGROUND: Understanding how diet influences inflammation requires identifying specific dietary components responsible for anti-inflammatory effects. This study examined the impact of six-week supplementation with a single-source prebiotic fibre (inulin), omega-3, or a synbiotic (fermented kefir + prebiotic fibre mix) on a broad range of inflammatory markers.

METHODS: Serum inflammatory proteins were profiled using the Olink 96 inflammation panel in a 6-week intervention. Participants received one of the following: synbiotic (n = 20; 170 ml kefir + 10 g prebiotic), omega 3 (n = 33; 500 mg/day), inulin fibre (n = 31; 20 g/day), or no supplementation (n = 20 control). Changes from baseline and between groups were analysed using parametric methods and effect sizes (Cohen's d). FDR-adjusted p < 0.05 was considered significant.

RESULTS: All three dietary interventions significantly reduced inflammatory markers versus control. TNF-α decreased with omega-3 (d= - 0.618, 95% CI -0.73 to -0.09, p = 0.01) and inulin fibre (d=-1.012, 95% CI -0.71 to -0.20, p = 0.001). The synbiotic group showed broader and larger reductions, including IL-6 (d=-0.882,95% CI -1.36 to -0.17, p = 0.01), IFN-γ (d=-0.940, 95% CI -2.03 to -0.31, p = 0.009), SIRT2 (d=-1.505, 95% CI -1.30 to -0.51, p < 0.0001), 4EBP1 (d=-1.384, 95% CI -1.43 to -0.32, p = 0.0004), CCL23 (d=-1.356, 95% CI -1.40 to -0.48, p = 0.0002), and mucosal cytokines CCL25 (d=-1.137, 95% CI -0.90 to -0.23, p = 0.001) and CCL28 (d=-1.006, 95% CI -0.80 to -0.16, p = 0.003). Increases in serum butyrate correlated with reductions in IL-6 following the synbiotic intervention.

CONCLUSIONS: All interventions reduced systemic inflammation, but the synbiotic produced broader and stronger effects, targeting proteins linked to immune and metabolic function. While gut microbiome profiling was not included in this study, it is planned in future work to clarify how synbiotics may influence host-microbiome interactions and inflammatory regulation.

TRIAL REGISTRATION: Trial registration Clinicaltrials.gov NCT06480812. Registered 28th June 2024 Retrospectively registered https//clinicaltrials.gov/study/NCT06480812.},
}

Humans
*Dietary Supplements
Male
Female
*Anti-Inflammatory Agents/pharmacology/therapeutic use
Inflammation/blood
Biomarkers/blood
Fatty Acids, Omega-3/pharmacology
Middle Aged
Adult
Inulin/pharmacology
Prebiotics

@article {pmid41094180,
year = {2025},
author = {Li, X and Zhu, J and Zhi, Y and Zheng, L and Guo, Z and Lu, X and Yu, Z and Jia, R},
title = {Dose-dependent zinc application modulates cadmium accumulation in wheat via rhizosphere metabolites and bacterial community.},
journal = {Environmental geochemistry and health},
volume = {47},
number = {11},
pages = {501},
pmid = {41094180},
issn = {1573-2983},
support = {232300421246//Natural Science Foundation of Henan Province/ ; YLK202507//Henan Province Science and Technology Promoting Forestry Project/ ; },
mesh = {*Triticum/metabolism/microbiology ; *Cadmium/metabolism/analysis ; *Rhizosphere ; *Zinc/pharmacology ; *Soil Pollutants/metabolism/analysis ; Soil Microbiology ; *Bacteria/metabolism/genetics/drug effects ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Zinc (Zn) application in appropriate dose effectively reduces cadmium (Cd) accumulation in wheat plants, but the mechanisms by which different Zn rates regulate Cd accumulation via rhizosphere processes remain unclear. Using the pot experiments and multi-omics analyses, this study examined how low (75 mg/kg) and high (150 mg/kg) Zn application rates influence wheat Cd accumulation. Low Zn application reduced grain Cd content by 38.7% and total plant Cd accumulation by 25.0%, along with a 5.2% decrease in DTPA-extractable Cd concentration in rhizosphere soil. Metabolomic and 16S rRNA sequencing showed that low Zn application decreased several key organic and amino acids and enriched Cd-immobilizing bacteria (Azospirillum and Rhodobacter), thereby reducing Cd bioavailability in the rhizosphere. Spearman correlation analysis indicated that low Zn application regulated the abundance of Cd-related bacteria by altering specific organic acids in the wheat rhizosphere. In contrast, high Zn application increased Cd accumulation, raising rhizosphere DTPA-extractable Cd concentration by 22.6%, likely because excessive Zn transformed iron-manganese oxide-Cd into exchangeable-Cd, despite reducing the abundance of rhizosphere organic and amino acids. These findings clarify distinct rhizosphere mechanisms driving Cd accumulation under varying Zn rates, providing a theoretical basis for optimizing Zn fertilization to mitigate Cd contamination in wheat production.},
}

*Triticum/metabolism/microbiology
*Cadmium/metabolism/analysis
*Rhizosphere
*Zinc/pharmacology
*Soil Pollutants/metabolism/analysis
Soil Microbiology
*Bacteria/metabolism/genetics/drug effects
RNA, Ribosomal, 16S/genetics

@article {pmid41094150,
year = {2025},
author = {Zhang, Y and Bhosle, A and Bae, S and Eckenrode, K and Huang, X and Tang, J and Lavrentovich, D and Awad, L and Hua, J and Wang, Y and Morgan, XC and Li, B and Krueger, A and Garrett, WS and Franzosa, EA and Huttenhower, C},
title = {Predicting functions of uncharacterized gene products from microbial communities.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41094150},
issn = {1546-1696},
support = {R24DK110499//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; U19AI110820//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; },
abstract = {The majority of genes in microbial communities remain uncharacterized. Here we develop a method to infer putative function for microbial proteins at scale by assessing community-wide multiomics data. We predict high-confidence functions for >443,000 protein families (~82.3% previously uncharacterized), including >27,000 protein families with weak homology to known proteins and >6,000 protein families without homology. These were drawn from 1,595 gut metagenomes and 800 metatranscriptomes from the Integrative Human Microbiome Project (HMP2/iHMP). Integrating additional information such as sequence similarity, genomic proximity and domain-domain interactions improves performance of the method. Our method's implementation, FUGAsseM, is generalizable and predicts protein function in both well-studied and undercharacterized communities. FUGAsseM achieves similar levels of accuracy in the context of microbial communities when compared to state-of-the-art approaches designed for application to single organisms while simultaneously providing much greater breadth of coverage. This initial study expands the functional landscape of the human gut microbiome and allows for exploration of microbial proteins in undercharacterized communities.},
}

@article {pmid41094135,
year = {2025},
author = {Dahlman, S and Avellaneda-Franco, L and Rutten, EL and Gulliver, EL and Solari, S and Chonwerawong, M and Kett, C and Subedi, D and Young, RB and Campbell, N and Gould, JA and Bell, JD and Docherty, CAH and Turkington, CJR and Nezam-Abadi, N and Grasis, JA and Lyras, D and Edwards, RA and Forster, SC and Barr, JJ},
title = {Isolation, engineering and ecology of temperate phages from the human gut.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41094135},
issn = {1476-4687},
abstract = {Large-scale metagenomic and data-mining efforts have revealed an expansive diversity of bacteriophages (phages) within the human gut[1-3]. However, functional understanding of phage-host interactions within this complex environment is limited, largely due to a lack of cultured isolates available for experimental validation. Here we characterize 134 inducible prophages originating from 252 human gut bacterial isolates using 10 different induction conditions to expand the experimentally validated temperate phage-host pairs originating from the human gut. Importantly, only 18% of computationally predicted prophages could be induced in pure cultures. Moreover, we construct a 78-member synthetic microbiome that, when co-cultured in the presence of human colonic cells (Caco2), led to the induction of 35% phage species. Using cultured isolates, we demonstrate that human host-associated cellular products may act as induction agents, providing a possible link between gastrointestinal cell lysis and temperate phage populations[4,5]. We provide key insights into prophage diversity and genetics, including a genetic pathway for domestication, finding that polylysogeny was common and resulted in coordinated prophage induction, and that differential induction can be influenced by divergent prophage integration sites. More broadly, our study highlights the importance of culture-based techniques, alongside experimental validation, genomics and computational prediction, to understand the biology and function of temperate phages in the human gut microbiome. These culture-based approaches will enable applications across synthetic biology, biotechnology and microbiome fields.},
}

@article {pmid41093983,
year = {2025},
author = {Zhang, J and Sekela, JJ and Hutchinson, LE and Yang, J and Sellers, RS and Bhatt, AP and Redinbo, MR},
title = {Sex-dependent responses in mice to indomethacin-induced organ injury and gut microbiome-targeted alleviation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36025},
pmid = {41093983},
issn = {2045-2322},
support = {NIH R35 award GM152079/NH/NIH HHS/United States ; },
mesh = {Animals ; *Indomethacin/adverse effects/toxicity ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred C57BL ; *Anti-Inflammatory Agents, Non-Steroidal/adverse effects/toxicity ; Sex Factors ; Spleen/drug effects/pathology ; Liver/drug effects/pathology ; Colon/drug effects/pathology ; RNA, Ribosomal, 16S/genetics ; Glucuronidase/antagonists & inhibitors/metabolism ; Sex Characteristics ; },
abstract = {Nonsteroidal anti-inflammatory drugs (NSAIDs) are used widely but produce gastrointestinal (GI) toxicities in both short- and long-term users. Previous studies have shown that the intestinal microbiota play an important role in gut damage and that gut microbial β-glucuronidase (GUS) inhibitors can alleviate NSAID-induced injury in male mice by blocking the GI reactivation of NSAID-glucuronides. Here, in both male and female C57BL/6 mice, we examine the effects of indomethacin alone and with the GUS inhibitor UNC10201652. Oral delivery of 5 mg/kg body weight indomethacin over 5 days decreased body weight, induced colonic and hepatic inflammatory cytokine gene expression, and enlarged the spleens of both male and female mice. However, sex-specific inflammatory responses to indomethacin were observed, with males demonstrating more colonic injury while females presented greater splenic and hepatic toxic responses. Females also showed a unique indomethacin-induced bloom of fecal Verrucomicrobia as measured by 16S rRNA metagenomic sequencing. UNC10201652 alleviated aspects of these indomethacin-induced toxicities, including features of the male-specific colonic damage and the female-specific compositional changes and spleen and liver toxicities. Thus, GI and non-GI tissues in male and female mice respond distinctly to indomethacin-induced damage. These findings advance our understanding of how sex impacts systemic responses to xenobiotic exposure and may lead to improved therapeutic outcomes with these widely used drugs.},
}

Animals
*Indomethacin/adverse effects/toxicity
Female
Male
*Gastrointestinal Microbiome/drug effects
Mice
Mice, Inbred C57BL
*Anti-Inflammatory Agents, Non-Steroidal/adverse effects/toxicity
Sex Factors
Spleen/drug effects/pathology
Liver/drug effects/pathology
Colon/drug effects/pathology
RNA, Ribosomal, 16S/genetics
Glucuronidase/antagonists & inhibitors/metabolism
Sex Characteristics

@article {pmid41093938,
year = {2025},
author = {Chen, Y and Jiang, Y and Li, Z and Zhu, M and Akimana, AG and Wang, K and Zhou, K and Zhang, X and Ji, X and Chen, M},
title = {The effect of phytoestrogens and PAHs on endometriosis and the involvement of gut microbiota, inflammation, and molecular targets.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36027},
pmid = {41093938},
issn = {2045-2322},
support = {2023YFC2705700//China National Key Research & Development (R&D) Plan/ ; 82273668//Natural Science Foundation of China/ ; },
mesh = {Humans ; Female ; *Endometriosis/metabolism/chemically induced/etiology/epidemiology/pathology ; *Phytoestrogens/adverse effects/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Polycyclic Aromatic Hydrocarbons/adverse effects/toxicity ; *Inflammation/chemically induced/metabolism ; Adult ; Endocrine Disruptors/adverse effects ; Biomarkers ; Middle Aged ; },
abstract = {Endometriosis is a common estrogen-dependent inflammatory disease, yet its complex etiology is not fully understood. Endocrine Disrupting Chemicals (EDCs) exposure disrupts human reproduction, but studies on mixed EDCs and endometriosis risk are Limited. The study Analyzed 2,644 women, assessing 12 phthalates, 8 polycyclic aromatic hydrocarbons, And 6 phytoestrogens in a representative US population. Various statistical models (generalized linear model, partial least squares discriminant analysis, weighted quantile sum, quantile g-computation, restricted cubic spline) were used to explore the link between EDC exposure and endometriosis risk, with mediating effects of lipid metabolism and inflammatory biomarkers examined. Biological mechanisms were identified through an integrated strategy involving target analysis of key chemicals and endometriosis intersections, network establishment, pathway analysis, and target validation. Various statistical models revealed that the gut microbiota metabolite enterolactone (ENL) was negatively associated with endometriosis, while the PAH metabolite 1-Hydroxyphenanthrene (1-OHPHE) was positively associated. Mediation analysis showed that uric acid (UA) and ferritin (Fer) were associated with mediating pathways in the relationships between ENL And decreased risk, And 1-OHPHE and increased risk, respectively. Network and target analysis indicated that ENL affects risk via ESR1, while 1-OHPHE disturbs it through GRB2. ENL can bind to XDH, inhibiting UA production. ENL supplementation may mitigate PAH-induced risks through the PI3K-Akt pathway. In conclusion, higher ENL levels were associated with reduced endometriosis risk, while 1-OHPHE was associated with increased prevalence. Inflammatory mediators UA And Fer demonstrated potential mediating associations in these relationships. ENL levels may be associated with attenuation of 1-OHPHE associations with endometriosis, potentially through gut microbiota-related pathways. These findings emphasize the role of environmental and microbiome interactions in modulating endometriosis risk.},
}

Humans
Female
*Endometriosis/metabolism/chemically induced/etiology/epidemiology/pathology
*Phytoestrogens/adverse effects/toxicity
*Gastrointestinal Microbiome/drug effects
*Polycyclic Aromatic Hydrocarbons/adverse effects/toxicity
*Inflammation/chemically induced/metabolism
Adult
Endocrine Disruptors/adverse effects
Biomarkers
Middle Aged

@article {pmid41093806,
year = {2025},
author = {Wang, W and Zhang, L and Zhou, Y},
title = {Causal effects of gut microbiota on diabetic kidney disease: insights from 16S rRNA sequencing and bidirectional Mendelian randomization.},
journal = {Renal failure},
volume = {47},
number = {1},
pages = {2566381},
doi = {10.1080/0886022X.2025.2566381},
pmid = {41093806},
issn = {1525-6049},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; *Diabetic Nephropathies/microbiology/etiology ; Female ; Mendelian Randomization Analysis ; *Dysbiosis/microbiology/complications ; Feces/microbiology ; Aged ; *Diabetes Mellitus, Type 2/complications ; Disease Progression ; Adult ; },
abstract = {Dysbiosis of the gut microbiome plays a critical role in diabetic kidney disease (DKD) development and progression. We stratified 46 type 2 DKD patients from Ruijin Hospital into early or advanced DKD groups in this cross-sectional study. Fecal samples underwent 16S rRNA sequencing. Statistical analyses (t-tests, Chi-square, GLMs) and MR were performed using SPSS and R. We found that advanced DKD patients exhibited distinct gut microbiota profiles, with LEfSe analysis showing higher Butyricimonas, Fusicatenibacter, and Barnesiella and lower Allisonella compared to early DKD, while DKD-susceptible individuals had elevated Fusobacterium and reduced Allisonella and Eubacterium. GLMs linked Barnesiella, Streptococcus, Fusobacterium to DKD susceptibility (p < 0.05), and Slackia and Eubacterium to early/resistant DKD. MR analysis demonstrated causality: Barnesiella (OR: 2.382), Butyricimonas (OR: 1.278), Desulfovibrio (OR: 2.518), and Hemophilus (OR: 1.622) worsened DKD, whereas Slackia and Allisonella protected against eGFR decline (p < 0.05). Reverse MR revealed the bidirectional effects-severe DKD increased Ruminococcus2 but suppressed Allisonella and Akkermansia (p < 0.05), underscoring microbiota-DKD interplay. Sensitivity analyses (MR-Egger, weighted median, leave-one-out) confirmed the robustness and directionality of these causal effects. In conclusion, 10 key bacterial genera were causally linked to DKD progression and susceptibility, including harmful (Barnesiella, Butyricimonas, Desulfovibrio, Hemophilus, Bacteroides, Streptococcus, Ruminococcus2) and protective taxa (Slackia, Allisonella, Akkermansia). These genera serve as novel biomarkers for early detection and risk stratification, and as potential therapeutic targets for microbiota-modulating interventions to mitigate DKD progression. The bidirectional microbiota-DKD interplay further underscores the promise of targeting gut dysbiosis in DKD precision management.},
}

Humans
*Gastrointestinal Microbiome/genetics
Male
Middle Aged
RNA, Ribosomal, 16S/genetics
Cross-Sectional Studies
*Diabetic Nephropathies/microbiology/etiology
Female
Mendelian Randomization Analysis
*Dysbiosis/microbiology/complications
Feces/microbiology
Aged
*Diabetes Mellitus, Type 2/complications
Disease Progression
Adult

@article {pmid41093739,
year = {2025},
author = {Li, S and Montini, F and Song, A and Willocq, V and Chan, E and Shamah, R and Weiner, M and Glanz, BI and Weiner, HL and Cox, LM},
title = {Alterations of the nasal and oral microbiota in multiple sclerosis.},
journal = {EBioMedicine},
volume = {},
number = {},
pages = {105959},
doi = {10.1016/j.ebiom.2025.105959},
pmid = {41093739},
issn = {2352-3964},
abstract = {BACKGROUND: While changes in the gut microbiota have been reported in multiple sclerosis (MS), little is known about the nasal and oral microbiota, which are important modulators of the mucosal immune system. The gingival microbiota can drive systemic inflammation, the pharyngeal microbiota can lead to autoimmune-mediated neurologic diseases, and altered nasal bacterial toxigenic genes are reported in active MS.

METHODS: We investigated nasal, gingival, and oropharyngeal microbiota from 69 MS to 40 healthy control subjects by 16S rRNA sequencing and identified site-specific microbiota differences in both the nasal and oral microbiota related to relapsing and progressive MS. We identified microbes associated with MS diagnosis, disease progression, disease modifying therapy, smoking, and anatomical site using linear regression analysis while controlling for confounding factors and subject demographics.

FINDINGS: We identified site-specific microbiota differences in both the nasal and oral microbiota related to relapsing and progressive MS. Using baseline microbiota samples and clinical outcomes over time, we identified potential beneficial microbes, including Dolosigranulum pigrum in the nasal microbiota and Prevotella sp. in the oral microbiota, as well as potential detrimental Streptococcus sp. in the oral microbiota.

INTERPRETATION: Taken together, our data suggest that nasal and oral microbiota are altered in MS, are linked to the disease course and provide an avenue to better understand MS pathogenesis and treatment.

FUNDING: This work was supported by the Nancy Davis Race to Erase MS Young Investigator Award (LMC), NIH/NINDS R01NS087226 (HLW), Water Cove Charitable Foundation (HLW), and the Clara E. and John H. Ware Jr. Foundation (HLW, LMC).},
}

@article {pmid41093280,
year = {2025},
author = {Bowen, MR and Agblemanyo, FE and Persad, PM and Wozniak, AS and Biddle, JF},
title = {Influence of Seasonal Succession on Microbiological and Physiochemical Composition in Shallow Estuarine Sediments.},
journal = {Environmental microbiology},
volume = {27},
number = {10},
pages = {e70194},
doi = {10.1111/1462-2920.70194},
pmid = {41093280},
issn = {1462-2920},
support = {//University of Delaware/ ; 2051069//National Science Foundation/ ; 2123368//National Science Foundation/ ; //Nancy Targett Graduate Fellowship/ ; },
mesh = {*Geologic Sediments/microbiology/chemistry ; Seasons ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota ; Estuaries ; Temperature ; DNA, Bacterial/genetics ; Phylogeny ; },
abstract = {Marine sediments harbour diverse microbial populations, but with increasing depth, these microbes are thought to have low activity due to depleted electron acceptors and lack of new organic matter after burial. However, physiochemical changes in environmental parameters could impact the metabolic activity of microbes in marine sediments. We performed seasonal sampling of shallow sediments to examine changes in population and abundance in relation to physiochemical changes over the year. We used amplicon sequencing, quantitative PCR and geochemistry to assess seasonal abundance of microbial populations at 3 depths (12-14, 38-40 and 48-50 cm) in shallow coastal sediments. 16S rRNA amplicon sequencing showed the sediment microbiome consists of common sediment taxa with minor seasonal variation. However, bacterial gene counts of 16S rRNA genes were highest in summer (2.50 × 10[12] genes/g of sediment) and lowest in spring (1.64 × 10[11] genes/g sediment). We observed differences in sediment temperature at depth across seasons (Summer 28°C-25.5°C; Winter 8.7°C-6.3°C) and correlated changes in dissolved organic matter composition that are not typically reported for this environment. We conclude deeper microbial populations in shallow sediments may experience seasonal abundance shifts resulting in a more variable subsurface community than initially presumed in the literature.},
}

*Geologic Sediments/microbiology/chemistry
Seasons
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
*Microbiota
Estuaries
Temperature
DNA, Bacterial/genetics
Phylogeny

@article {pmid41093258,
year = {2025},
author = {Gastaldo-Jordan, I and Villalba-Pita, C and Martínez-Raga, J and Sanz, Y and Medina-Rodríguez, EM},
title = {ARE CONVENTIONAL ANTIDEPRESSANTS ENOUGH? THE GUT MICROBIOME AND NANOCARRIER-BASED DELIVERY SYSTEMS AS FUTURE PROSPECTS FOR DEPRESSION TREATMENT.},
journal = {Neuroscience and biobehavioral reviews},
volume = {},
number = {},
pages = {106421},
doi = {10.1016/j.neubiorev.2025.106421},
pmid = {41093258},
issn = {1873-7528},
abstract = {Depression is the leading cause of disability worldwide and thus a major contributor to the economic burden of disease. In addition to genetic and epigenetic factors, sustained psychological stress linked to modern lifestyles (often characterized by high social expectations, elevated workload and increasing financial needs) may trigger psychiatric diseases such as depression. The effective treatment of this psychiatric condition represents one of the major challenges of our time, due to its skyrocketing increase in prevalence. While conventional antidepressants often provide low response rates and have frequent adverse effects, emerging research is revealing novel and more efficient therapeutic approaches. Notably, the bacteria that populates our intestinal tract, also known as the gut microbiota, is highly susceptible to stress and other factors associated with depression. Therefore, gut microbiota-targeting interventions based on lifestyle modifications or direct supplementation with biotherapeutic agents are being proposed as monotherapy or as adjuvants to conventional treatments. In addition, novel delivery systems, such as nanocarriers, for current antidepressants are being explored to improve drug bioavailability and therapeutic efficiency. This review summarizes the role of the gut microbiota in the pathogenesis of depression and its link with current antidepressant treatments. Furthermore, it explores how strategies like nanoparticle-based delivery systems are paving the way for the next generation of treatments.},
}

@article {pmid41093171,
year = {2025},
author = {Yang, L and Xu, W and Wang, X and Huang, S and Liu, J},
title = {Multiscale crosstalk between oral-gut microbiome and brain structure.},
journal = {Journal of affective disorders},
volume = {393},
number = {Pt B},
pages = {120420},
doi = {10.1016/j.jad.2025.120420},
pmid = {41093171},
issn = {1573-2517},
abstract = {BACKGROUND: Brain macrostructural variations reflect deterioration due to disease and comprehensive profiling of the associated digestive tract microbiome signature advances mechanistic understanding.

METHODS: Here, employing genome-wide association study(GWAS) data from MiBioGen consortium, Danish ADDITION-PRO cohort, and United Kingdom Biobank(UKB), through bidirectional Mendelian randomization(MR) analyses, we analyzed the associations between 239 microbiota(196 gut microbiota and 43 salivary microbiota) and 283 imaging-derived phenotypes(IDPs) of brain structure measures, involving gray matter volume (GMV), orientation dispersion index (ODI), volume fraction of intracellular water (ICVF), and volume fraction of the isotropic diffusion compartment (ISOVF). Ultimately, keyword co-occurrence was conducted by bibliometric analysis to summarize the research realm of "microbiome-brain".

RESULTS: After Bonferroni correction, in forward MR results, we identified 123 associations between 50 microbiota and 92 IDP measures, with Parvula species, unknown-Streptococcus species, and Neisseria genus showing the most associations. The brain regions that showed the most MR relationships with microbiota were posterior division of the right middle temporal gyrus, left cerebral peduncle, left cingulum hippocampus, and splenium of corpus callosum. However, in inverse MR results, merely 8 associations were discovered between IDPs and microbiota. Furthermore, bibliometric outcome indicated that depression was the most studied disease in "microbiome-brain" research.

CONCLUSIONS: In summary, this study generates a comprehensive atlas mapping the patterns of association between microbiota and brain structure, highlighting their potential value for studying brain disorders.},
}

@article {pmid41093142,
year = {2025},
author = {Marizzoni, M and Mombelli, E and Alboni, S and Rosa, M and Moretti, DV and Mirabelli, P and Coppola, L and Luongo, D and Salamone, D and Saleri, S and Piazza, F and Begni, V and Salvatore, M and Frisoni, GB and Cattaneo, A},
title = {Microbiota-gut-brain axis dysregulation in Alzheimer's disease and its modulation through probiotic supplementation.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106138},
doi = {10.1016/j.bbi.2025.106138},
pmid = {41093142},
issn = {1090-2139},
abstract = {BACKGROUND: The microbiota-gut-brain axis (MGBA) has been implicated in the pathophysiology of Alzheimer's Disease (AD).Probiotics reduced the progression of ADin different mouse models, possibly through MGBA modulation, but human data are still limited.

OBJECTIVE: Here, we evaluated whether differences in the gut microbiome (GM), pro-inflammatory markers and other MGBA mediators were associated with probable AD (pAD). We also assessed the impact of a 12-week probiotic treatment on MGBA.

METHODS: Forty-five pAD patients and 47 healthy subjects (HC) were recruited at IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli of Brescia (Italy). An uncontrolled clinical investigation was performed to test the effects of 12-week probiotic supplementation in the pAD group. Fecal microbiota composition, intestinal and blood inflammatory markers, and microbiota-related metabolites were assessed before supplementation in all participants and after only in pAD.

RESULTS: pAD patients showed intestinal inflammation, an altered GM profile, blood changes in the tryptophan metabolism, and reduced glutamate levels compared with HC (p-value < 0.049). Probiotic supplementation partially modulated these alterations, determining a reduction in several pro-inflammatory mediators, and an increase of GM-related protective factors, such as butyrate (p-value < 0.040) in pAD.

CONCLUSIONS: These findings confirmed the presence of MGBA alterations in AD and suggested a potential beneficial effect of probiotic supplementation through modulation of GM functionality rather than composition. Further research is required to confirm these results and their clinical relevance.},
}

@article {pmid41093108,
year = {2025},
author = {Chandel, N and Patel, P and Somvanshi, PR and Verma, AK and Thakur, V},
title = {Inverse association between serum vitamin B12 level and abundance of potential B12-producing gut microbes in Indian children.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.10.021},
pmid = {41093108},
issn = {1541-6100},
abstract = {BACKGROUND: The human gut microbiome is a natural source of essential micronutrients like B-vitamins, which are utilized by both the host and other community members. The prevalence and abundance of known B-vitamin producers and B-vitamin biosynthesis pathways have already been reported in gut microbiome cohorts of a few countries including India.

OBJECTIVE: To test whether the presence of B-vitamin producers/biosynthetic pathways associates with serum B-vitamin levels, taking B12 as a case example.

METHODS: Fecal samples were collected from non-deficient (serum B12 level > 210 pg/mL, n=29) and B12 deficient (serum B12 level < 210 pg/mL, n=30) children from a tribal region of central India. Whole metagenomic DNA was extracted, sequenced, and analyzed for taxonomic profiling and diversity comparisons. Differentially abundant taxa between two groups were identified. The prevalence and abundance of potential B12 producers were compared, and their association with serum B12 level was established.

RESULTS: A comparison of within-sample diversity between the two groups didn't show any difference; however, between-sample diversity was significantly less in the B12 deficient group. Differential abundance testing also showed different microbiome structure in the B12 deficient group, where a higher abundance of B12 transporter-carrying Bacteroides thetaiotaomicron, a few pathogenic species, and ten known B12 producers was observed. Potential B12 producers were also significantly prevalent and abundant in the deficient group. Their cumulative abundance was also significantly higher in the deficient group and showed a negative association with serum B12 levels.

CONCLUSION: A higher abundance of potential B12 producers in the deficient group suggested an adaptive mechanism by the gut microbiome to meet the community's B12 requirements, by selectively promoting the growth of B12 producers, but causality remains to be proved.},
}

@article {pmid41093074,
year = {2025},
author = {Brake, J and Banerjee, R},
title = {Power and Poison: The intersections of H2S and O2 metabolism.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {110810},
doi = {10.1016/j.jbc.2025.110810},
pmid = {41093074},
issn = {1083-351X},
abstract = {The metabolic interaction between hydrogen sulfide (H2S) and O2 exemplifies the interplay between chemical power and poison at the electron transport chain as these gases influence the conversion of nutrient energy to cellular currency. H2S is a product of mammalian and microbial metabolism and is both an inorganic nutrient and a respiratory poison. In its former role, H2S transfers its reducing power to coenzyme Q as it is oxidized by sulfide quinone oxidoreductase in the inner mitochondrial membrane. As a respiratory poison, H2S inhibits complex IV and profoundly influences intracellular O2 levels with pleiotropic effects on hypoxia sensing and signaling, and on cellular metabolism, glimpses of which are only just beginning to emerge. The high concentration of luminal sulfide in the lower gut combined with the steep radial O2 gradient, ranging from a virtually anoxic lumen to a highly vascular lamina propria, raises many questions about how the interaction between these gases plays out with local and long-range impacts on biology. Their interaction is equally germane in other hypoxic tissues where endogenous H2S production and/or constitutively low sulfide oxidation capacity could potentially dial up O2 availability. Importantly, H2S oxidation can prevail even when its concentration rises to levels that poison complex IV, and is enabled by rerouting electrons through complex II, using fumarate as a terminal electron acceptor. Methodological advancements that support the quantitative analysis of in vivo models will be critical for broadening our understanding of the metabolic and physiological import of the O2-H2S interplay.},
}

@article {pmid41093067,
year = {2025},
author = {Wakelin, SA and Armstrong, C and Ganasamurthy, S and Wigley, K and Mercier, C},
title = {Comparison of primer sets for short-read NGS-based characterisation of oomycete communities.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107293},
doi = {10.1016/j.mimet.2025.107293},
pmid = {41093067},
issn = {1872-8359},
abstract = {Oomycetes have diverse ecological roles spanning threats to food security to vital contributors in nutrient cycling and biological control. Despite their importance, they are often overlooked in environmental microbiome studies. We evaluated several primer sets for their ability to characterize oomycete communities in eDNA samples. The ITS1/3oo primer set performed best among those evaluated in our single-protocol eDNA survey, returning high oomycete richness and broader taxonomic coverage; we note this reflects performance under our experimental conditions rather than an absolute, universally optimal primer. For broader eukarya coverage, the 18S rRNA primer set from the Earth Microbiome Programme outperformed the COI-based primers tested. Although these broad-coverage primer sets detected a wide range of oomycetes, their performance in oomycete-specific coverage was not as strong as oomycete-targeted primer sets. Evaluation of the primer sets were undertaken using eDNA samples collected from soil in which Kunzea robusta (kānuka; Myrtaceae), and Phormium tenax (harakeke; Asphodelaceae) were cultivated. An average of 52 and 54 oomycete ASVs, respectively, were associated with the rhizosphere of these plants, spanning Haptoglossa, Alanopsis, Aphanomyces, Achyla, Pythium, Phytopythium, Globiosporangium, Phytophthora, Myzocytiopsis, Eurychasma and Lagendum lineages. Based on evaluation of a range of oomycete targeting primers on real-world samples, we are able to provide recommendations for primer sets that maximise oomycete detection and provide the best balance of specificity and coverage for eDNA-based community profiling. These primers can be used to capture the diversity and ecological roles of oomycetes in natural and managed ecosystems, enabling more accurate assessments of their impact on plant health, soil and nutrient dynamics, as well as deepening our understanding of the diversity and distribution of this understudied clade of microbial life.},
}

@article {pmid41093042,
year = {2025},
author = {Noordzij, HT and Wortel, MT and Heintz-Buschart, A and Petrikonyte, P and de Muinck, EJ and Trosvik, P},
title = {Assembly-based analysis of the infant gut microbiome reveals novel ubiquitous plasmids.},
journal = {Plasmid},
volume = {134},
number = {},
pages = {102761},
doi = {10.1016/j.plasmid.2025.102761},
pmid = {41093042},
issn = {1095-9890},
abstract = {Little is known about the role of mobile genetic elements in natural ecosystems such as the infant gut microbiome. Here, we conduct the most comprehensive longitudinal study of the infant plasmidome to date by analyzing monthly fecal samples from 12 infants from birth to one year of age. We employ an assembly-based bioinformatic pipeline for the reconstruction and identification of full-length plasmids, including a novel approach for assigning putative plasmid hosts. We then investigated plasmid content and dynamics in the infant gut microbiome. After assembly and identification, we identified 620 unique circular plasmids in the infant cohort, including a number of novel sequences. Independent assembly of the same plasmids in several samples and infants helped corroborate the authenticity of the plasmids. Among the observed plasmids was the recently described ubiquitous and abundant Bacteroides plasmid pBI143. Overall, the genus Bacteroides had the highest plasmid carriage, while the highest plasmid diversity was observed in Clostridium, including 5 previously unknown widespread plasmids. Lastly, we leveraged the longitudinal nature of our dataset to investigate contemporaneous correlations between temporal variations in plasmid abundances and species dynamics. This enabled us to link co-residing plasmids and tightly linked plasmid-taxon pairs within each infant. These insights into plasmid ecology help us understand determinants driving plasmid distribution in complex microbial communities.},
}

@article {pmid41092978,
year = {2025},
author = {Alverdy, JC},
title = {Comment on "Gut microbiome and metabolome profiling in obesity reveals an association between the effectiveness of sleeve gastrectomy and the composition and function of the gut microbiome".},
journal = {Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract},
volume = {},
number = {},
pages = {102255},
doi = {10.1016/j.gassur.2025.102255},
pmid = {41092978},
issn = {1873-4626},
}

@article {pmid41092847,
year = {2025},
author = {Zhang, Y and Su, K and Munir, F and Wang, W and Liang, X and Wang, J and Hua, J and Ma, W},
title = {Gut microbiome metagenomics in diarrheic and healthy Simmental cattle from Ningxia Province, China.},
journal = {Research in veterinary science},
volume = {197},
number = {},
pages = {105922},
doi = {10.1016/j.rvsc.2025.105922},
pmid = {41092847},
issn = {1532-2661},
abstract = {INTRODUCTION: The gut microbiome plays a crucial role in health and disease. This study aims to investigate the composition, characteristics, and functional diversity of the intestinal microbiome by performing metagenomic sequencing on fecal samples from diarrheic and healthy Simmental cattle.

RESULTS: This study compared the gut microbiome differences between two groups of Simmental cattle (5 diarrheic and 20 healthy) in Ningxia province, China. Metagenomic analysis revealed higher microbial heterogeneity in the diarrheic group, likely reflecting pathogen-driven ecological disruption, whereas the healthy group was dominated by butyrate-producing and fiber-degrading bacteria, maintaining intestinal homeostasis. Antibiotic resistance gene analysis detected glycopeptide resistance genes in both groups, but the healthy group also carried aminoglycoside/tetracycline resistance genes and poxtA. KEGG pathway analysis showed that the diarrheic group was enriched in purine synthesis-related pathways, while the healthy group exhibited dominant metabolic pathways such as glutamine synthase. Virulence factor analysis indicated that the diarrheic group had higher abundances of capsular polysaccharides and type IV secretion systems, potentially promoting bacterial colonization and immune evasion. In summary, diarrheic cattle harbored a gut microbiome dominated by opportunistic pathogens, accompanied by metabolic dysregulation and antimicrobial resistance risks, whereas healthy cattle maintained a microbial community rich in short-chain fatty acid producers. This study provides a theoretical foundation for gut microbiome modulation and antimicrobial resistance control in ruminants.

CONCLUSION: This study revealed distinct gut microbiome composition and function between diarrheic and healthy cattle through sequencing analysis. The findings offer insights for ruminant diarrhea management and provide a basis for developing more scientific antibiotic management strategies in animal husbandry.},
}

@article {pmid41092781,
year = {2025},
author = {Lai, JL and Gong, X and Fu, Q and Luo, XG},
title = {Mechanisms of uranium and cadmium Co-contamination on rhizosphere microecology and accumulation in sweet potato varieties.},
journal = {Journal of environmental radioactivity},
volume = {291},
number = {},
pages = {107832},
doi = {10.1016/j.jenvrad.2025.107832},
pmid = {41092781},
issn = {1879-1700},
abstract = {This study investigated rhizosphere microecological mechanisms driving interspecific variation in uranium (U) and cadmium (Cd) accumulation among sweet potato cultivars, informing low-accumulator selection strategies and Phyto management of contaminated soils. Employing two contrasting cultivars (high-accumulation purple sweet potato vs. low-accumulation Sushu No. 8), we conducted pot experiments to analyse photosynthetic responses, mineral nutrition dynamics, rhizosphere microbiome shifts, and soil metabolomic profiles under heavy metal stress. While exhibiting superior photosynthetic efficiency relative to Sushu 8, the purple cultivar demonstrated greater sensitivity to U + Cd co-stress, showing 4.68-13.05 % reductions in intercellular CO2 concentration (Ci), transpiration rate (Tr), and stomatal conductance (Gs). Notably, its roots accumulated 15.4 times higher Cd contamination indices (Pi_Cd) than Sushu 8, with significantly elevated bioconcentration factors (BCF) and transfer coefficients (TF) across all tissues. Heavy metal exposure reduced operational taxonomic units (OTUs) in the purple cultivar's rhizosphere microbiome but enhanced microbial diversity in Sushu 8. Metabolomic profiling revealed U/Cd-induced activation of galactose metabolism, ABC transporters, and pyrimidine metabolic pathways, with amino acid and nucleotide flux strongly correlating to microbial community dynamics. These findings demonstrate cultivar-specific heavy metal accumulation patterns are governed by rhizosphere processes involving mineral acquisition efficiency, microbiome configuration, and metabolic reprogramming, with high-accumulator microbiomes exhibiting greater environmental susceptibility.},
}

@article {pmid41092682,
year = {2025},
author = {Li, Y and Tang, L and He, Y and Li, Y and Yu, Q and Chen, X and Yin, Z and Zhen, D and Zhang, X and Yu, J},
title = {Skin microbiota, immune phenotypes, inflammatory response and hypertrophic scars: A Mendelian randomization study.},
journal = {Burns : journal of the International Society for Burn Injuries},
volume = {51},
number = {9},
pages = {107705},
doi = {10.1016/j.burns.2025.107705},
pmid = {41092682},
issn = {1879-1409},
abstract = {BACKGROUND: There is emerging evidence of a link between skin microbiota and Hypertrophic scars (HS), but the specific causal relationships and the role of immune responses are unclear.

METHODS: A genome-wide association study (GWAS) and Mendelian randomization (MR) analysis were used to explore the causal effects of skin microbiota, cytokines, and immune phenotypes on HS, with inverse variance weighting (IVW) as the main statistical method. Mediation analyses were also conducted to see if cytokines and immune phenotypes mediate the relationship between skin microbiota and HS.

RESULT: There were 4 positive and 4 negative causal effects between skin microbiota and HS. Five cytokines and 34 immune phenotypes were identified as having causal effects on HS. Additionally, 1 inflammatory factor and 5 immune phenotypes were significant mediators in 4 skin microbiota, while no significant mediators were found in the others.

CONCLUSION: The skin microbiome, immune phenotypes, and inflammatory response are causally linked to HS, with some acting as key mediators from skin microbiota to scars.},
}

@article {pmid41092679,
year = {2025},
author = {Zuali, L and Ralte, L and Zothanzama, J and Sailo, CV and Kumar, NS},
title = {Distinct oral microbiome profiles in substance users in the high-incidence Mizo tribal community, Northeast India.},
journal = {Archives of oral biology},
volume = {180},
number = {},
pages = {106418},
doi = {10.1016/j.archoralbio.2025.106418},
pmid = {41092679},
issn = {1879-1506},
abstract = {OBJECTIVES: To characterize the oral microbiome of substance users (primarily tobacco, alcohol, and opioids) compared to healthy controls in the high-incidence Mizo tribal community of Northeast India, and to examine their association with food and lifestyle habits.

METHODS: Saliva samples from 53 substance users and 35 healthy controls were subjected to 16S rRNA (V3-V4 region) sequencing. Alpha and beta diversity analyses, differential abundance testing, and microbial functional prediction were conducted. Statistical analyses were corrected for multiple comparisons using false discovery rate (FDR) adjustment where applicable. Associations with food and lifestyle habits were also examined.

RESULTS: Substance users exhibited significantly lower alpha diversity, and beta diversity analyses revealed distinct clustering between the two groups. Firmicutes_D, Actinobacteria, Rothia, and Streptococcus were more abundant in substance users, whereas Bacteroidota, Proteobacteria, Neisseria, and Prevotella were enriched in healthy controls. Functional predictions indicated upregulation of biofilm formation and xenobiotic degradation pathways in substance users. Exposure to Jhum cultivation, prenatal smoking, and consumption of fermented pork fat (saum) were correlated with microbial composition.

CONCLUSIONS: Substance use and associated environmental exposures were linked to oral microbiome dysbiosis. Certain bacterial taxa may serve as potential microbial biomarkers of substance use in this high-risk tribal population, warranting further investigation.},
}

@article {pmid41092573,
year = {2025},
author = {Ai, J and Zong, Y and Yang, X and Li, L and Zhou, H and Peng, S and He, H and Zhang, W and Hu, C and Wang, Q},
title = {Functional microbial communities in the hydrolysis-acidogenesis stage promote sludge viral inactivation under anaerobic digestion.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124751},
doi = {10.1016/j.watres.2025.124751},
pmid = {41092573},
issn = {1879-2448},
abstract = {The sludge produced in biological wastewater treatment enriches enormous viruses, and the pathogens inactivation is vitally important for protecting public and ecosystem health. Anaerobic digestion (AD) is an ideal bio-stabilization technology to reduce sludge volume and convert nutrients into valuable products, but the compositional variation and host-connections of viruses in sludge during AD process remains poorly explored. Herein, we reported differences in the viral and bacterial microbiomes of sludge subjected to three stages of hydrolysis, acidogenesis and methanogenesis in AD system. As results, the dominant identified viromes phylum associated with animal/plant as hosts were Nucleocytoviricota, Pisuviricota and Preplasmiviricota excepted for phages in AD system; and the metatranscriptome combined with key species-virus activity correlation analysis revealed these viral community inactivation was positively correlated to phyla of Bacillota, Actinobacteria Bacteroidetes and Proteobacteria. Thus, the enzymes of cellulase, proteases and lipases were possible key factors in viral inactivation, which would be increased by secreting of Bacillota and Actinomycetota in hydrolysis-acidogenesis stages, leading to higher virus inactivation via membrane proteins destruction; while enhanced activities of methanogens communities in methanogenesis stage completed and suppressed the Bacillota activities, resulted in viral genes replication and higher residual viral abundance in sludge. These findings gave more insights of relationships between functional microbiome and viral survival in sludge of AD process, and provided important scientific guidance in regulating microbial community structure of AD system to ensure the safe management of sludge in pandemic emergencies.},
}

@article {pmid41092484,
year = {2025},
author = {Zhou, W and Yang, Q and Guo, J and Li, S and Su, M and Leng, F and Rong, T and Shi, J and Gao, Y and Jiang, T and Xu, J and Li, Y},
title = {SMTdb: A comprehensive spatial meta-transcriptome resource in cancer.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf263},
pmid = {41092484},
issn = {1537-1719},
abstract = {Microorganisms have been detected in various tumors, and research on the tumor microbiome has received increasing attention. However, the investigation of the cancer microbiome at the spatial resolution level remains a challenging issue. The emergence of spatially resolved transcriptomics technology has enabled to map transcripts at the single-cell resolution in various cancer types. Here, we constructed a comprehensive spatial meta-transcriptome resource by manually curating 203 fresh frozen slices from 20 cancer types encompassing 334,253 spots and 1,908,646 cells. A spatial meta-transcriptome database (SMTdb, http://bio-bigdata.hrbmu.edu.cn/SMTdb/) was constructed to provide detailed insights into the abundance, distribution, and enriched tumor microenvironment (TME) regions of 1218 microbiota in spatial tissue slices. SMTdb enables to explore the vast interactive data of spatial distribution and expression of microbiota, provides host gene modules associated with certain microbiota, and contains data on the co-occurrence between the microbiota and immune cells within the TME. The atlas resource serves as a comprehensive and structured platform to investigate the interactions between microbial ecosystems and hosts in cancer.},
}