@article {pmid41360872,
year = {2025},
author = {Cheatham, SM and Rehman, Z and Arastonejad, M and Kane, R and Ahmad, N and Luffman, N and Harada, H and Zhang, Y and Tyc, KM and Gewirtz, DA and Akbarali, HI},
title = {Butyrate prevents chemotherapy-induced gastrointestinal toxicity and microbial dysbiosis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30385-8},
pmid = {41360872},
issn = {2045-2322},
support = {P30 DA033934/NH/NIH HHS/United States ; T32DA007927/NH/NIH HHS/United States ; P30CA016059/NH/NIH HHS/United States ; P30DA0339324/NH/NIH HHS/United States ; },
abstract = {Chemotherapy-induced gastrointestinal toxicity is a significant dose-limiting complication for cancer treatment. Disruption of the gastrointestinal (GI) epithelial barrier function by several chemotherapeutic agents results in development of mucositis and diarrhea. Thus, maintaining barrier integrity may be of therapeutic benefit. Recent studies have shown the beneficial effects of the microbial metabolite butyrate, a short chain fatty acid (SCFA), on epithelial barrier integrity. In this current study, we tested the effect of oral butyrate on irinotecan-induced gastrointestinal (GI) toxicity in mice. Irinotecan dose-dependently reduced body weight, increased fecal water content and increased gastrointestinal motility. Acetylcholine induced contractions were markedly increased in colons of irinotecan treated mice as were nicotine-induced inward currents in isolated ileum myenteric neurons. Loperamide reduced GI motility of irinotecan treated mice, however tolerance developed with chronic use, consistent with clinical findings of loperamide refractory diarrhea in patients. Oral butyrate improved epithelial permeability and prevented irinotecan-induced increase in β-glucuronidase activity in fecal samples. Irinotecan treatment produced a significant shift in the β diversity of the fecal microbiome that was mitigated by butyrate. The microbial dysbiosis was associated with increases in the mucin degrading bacteria Akkermansia muciniphilia and the hydrogen sulfide producing Desulfovibrio sp10575755 that was reduced with butyrate treatment.},
}

@article {pmid41360562,
year = {2026},
author = {He, Q and Li, X and Liu, C and Liu, Z and Zhou, S and Li, Y and Ma, T},
title = {Application and research progress of dietary fiber-based fat substitutes in food systems.},
journal = {Food research international (Ottawa, Ont.)},
volume = {223},
number = {Pt 2},
pages = {117876},
doi = {10.1016/j.foodres.2025.117876},
pmid = {41360562},
issn = {1873-7145},
mesh = {*Dietary Fiber/analysis ; *Fat Substitutes/chemistry ; Humans ; Emulsions ; Food Handling ; Nutritive Value ; Dietary Fats ; },
abstract = {The rising global burden of diet-related noncommunicable diseases has accelerated the development of low-fat foods that retain desirable sensory and functional properties. Dietary fibers, leveraging their unique water-holding capacity, gelling behavior, and tunable rheology, have emerged as versatile fat replacers across diverse food matrices. This review synthesizes recent advances in the design and application of dietary-fiber-based fat substitutes, categorizing them into two primary classes: Abbas et al. (2024) (1) fat-free mimetics (hydrogels and particulate systems) and (Akal, 2023 (2)) fat-based substitutes (fiber-stabilized emulsions, emulsion gels, and oleogels). Key strategies to enhance fiber functionality, including chemical, enzymatic, and physical modifications for hydrophobicity enhancement, and synergistic composites with proteins or lipids, are critically evaluated. Representative applications in meat products, dairy systems, baked goods, and spreads are analyzed, emphasizing improvements in texture, water/fat retention, oxidative stability, and nutritional profiles. Persistent challenges include replicating the crispness and melt behavior of full-fat analogs, ensuring the safety of modified fibers, balancing essential fatty acids and fat-soluble vitamins, and optimizing gastrointestinal tolerance. Future directions encompass multi-component mimetics (e.g., protein-fiber complexes and polysaccharide-lipid hybrids), sustainable modification technologies (enzymatic/physical treatments), and precision replacement strategies guided by nutritional genomics and microbiome science. Interdisciplinary collaboration and supportive policy frameworks will be pivotal in advancing dietary-fiber-based fat substitutes toward a new paradigm of 'healthy, palatable, and safe' low-fat foods.},
}

*Dietary Fiber/analysis
*Fat Substitutes/chemistry
Humans
Emulsions
Food Handling
Nutritive Value
Dietary Fats

@article {pmid41360553,
year = {2026},
author = {Du, S and Zhang, X and Zhang, M and Lin, T and Liu, B and Jing, M and Zhao, J and Chen, L},
title = {Comparative analysis of Tibetan human milk fat globule membrane proteins across lactation stages.},
journal = {Food research international (Ottawa, Ont.)},
volume = {223},
number = {Pt 2},
pages = {117862},
doi = {10.1016/j.foodres.2025.117862},
pmid = {41360553},
issn = {1873-7145},
mesh = {Humans ; *Milk, Human/chemistry ; *Glycoproteins/analysis/metabolism ; *Glycolipids/analysis/metabolism ; Female ; *Lipid Droplets ; *Lactation ; Colostrum/chemistry ; Proteomics/methods ; Infant ; Tibet ; *Membrane Proteins/analysis ; Feces/microbiology ; Adult ; Infant, Newborn ; Gastrointestinal Microbiome ; Milk Proteins/analysis ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Milk fat globule membrane (MFGM) proteins are significant nutrients contained in human milk. However, information on MFGM proteins in Tibetan human milk remains limited. This study analyzed and compared MFGM proteins in human colostrum (HC), human transitional milk (HT), and human mature milk (HM) from Tibetan lactating mothers using label-free quantitative proteomics. We identified 2977 proteins in HC, HT, and HM, of which 215 were differentially expressed proteins (DEPs). In addition, the uniquely expressed proteins (UEPs) in HC, HT, and HM were also identified. We used bioinformatics to analyze these DEPs and UEPs and revealed the relationships between MFGM proteins, as well as their functions and pathways of action. The 16S rRNA was conducted on infant fecal samples, which reveals correlations between human milk MFGM proteins and the infant gut microbiome. This study enhances the understanding of MFGM proteins in human milk and provides new insights for improving infant formulas and developing specific products, especially for populations in high-altitude regions.},
}

Humans
*Milk, Human/chemistry
*Glycoproteins/analysis/metabolism
*Glycolipids/analysis/metabolism
Female
*Lipid Droplets
*Lactation
Colostrum/chemistry
Proteomics/methods
Infant
Tibet
*Membrane Proteins/analysis
Feces/microbiology
Adult
Infant, Newborn
Gastrointestinal Microbiome
Milk Proteins/analysis
RNA, Ribosomal, 16S/genetics

@article {pmid41360535,
year = {2026},
author = {Wang, H and Luo, Y and Zhang, Y and Xiong, Y and Bian, G and Feng, B},
title = {Flavor quality during fermentation of the specialty product proso millet (Panicum miliaceum L.) thick wine: Insights from microbiome and metabolomics analyses.},
journal = {Food research international (Ottawa, Ont.)},
volume = {223},
number = {Pt 2},
pages = {117835},
doi = {10.1016/j.foodres.2025.117835},
pmid = {41360535},
issn = {1873-7145},
mesh = {*Fermentation ; *Wine/analysis/microbiology ; *Taste ; *Microbiota ; *Metabolomics/methods ; Odorants/analysis ; Lactobacillus/metabolism ; Volatile Organic Compounds/analysis ; Hydrogen-Ion Concentration ; Bacteria/metabolism/classification ; Lactic Acid/analysis ; },
abstract = {Proso millet (PM) thick wine is a fermented, health-promoting traditional Chinese rice wine; however, little is known about the succession and functional roles of microbiota during its fermentation. In this study, we examined the correlations between microbial communities, physicochemical properties, and flavor components during PM fermentation. The results showed that the decreasing pH and increasing total acid and lactic acid levels were associated with the metabolism of dominant bacteria, particularly Lactobacillus. The aroma of PM thick wine is characterized primarily by fruity, sweet, apple, and green, with terpenoids, esters, and aldehydes identified as the main volatile differential metabolites contributing to aroma during fermentation. In the early fermentation stages, Lactobacillus, Bacillus, and Enterobacter were the predominant bacterial genera, whereas Lactobacillus became dominant in the later stages as the microbial community shifted toward greater acid tolerance. Correlation analysis indicated that Lactobacillus promoted the production of terpenoids and acids, while the remaining nine dominant bacterial genera promoted aldehyde production in PM thick wine. These findings provide theoretical guidance for further studies on flavor regulation in PM thick wine at the microbial community level and via microbial augmentation.},
}

*Fermentation
*Wine/analysis/microbiology
*Taste
*Microbiota
*Metabolomics/methods
Odorants/analysis
Lactobacillus/metabolism
Volatile Organic Compounds/analysis
Hydrogen-Ion Concentration
Bacteria/metabolism/classification
Lactic Acid/analysis

@article {pmid41360533,
year = {2026},
author = {Chen, L and Yang, J and Wang, Y and Xiao, X and Zhang, H and Hou, X and Liu, D and Du, H},
title = {Artemisia argyi folium as a traditional and safe dietary additive ameliorates metabolic syndrome via gut microbiota and its metabolites.},
journal = {Food research international (Ottawa, Ont.)},
volume = {223},
number = {Pt 2},
pages = {117830},
doi = {10.1016/j.foodres.2025.117830},
pmid = {41360533},
issn = {1873-7145},
mesh = {*Artemisia/chemistry ; *Metabolic Syndrome/drug therapy ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Plant Extracts/pharmacology/chemistry ; Male ; Mice ; *Food Additives/pharmacology ; Polyphenols ; Plant Leaves/chemistry ; },
abstract = {Artemisia argyi, a globally recognized plant widely used in medicine and food, has become an important and popular food additive in Asia and other parts of the world. However, its edible safety has always been controversial. Herein, we aimed to evaluate the safety and health benefits of A. argyi as a dietary additive. Fresh and dried A. argyi water extracts (FAA and DAA, respectively) were prepared by simulating two processing methods for edible tender A. argyi. And chemical composition analysis showed that both FAA and DAA were rich in nutritional and functional components, including polysaccharides, proteins, and polyphenols. UHPLC-TQ-MS analysis showed that tender A. argyi mainly contained 11 polyphenol components (mainly flavonoids and phenolic acids). Then, an acute toxicity study, based on the maximum limit method, showed that single administrations of FAA and DAA at doses of 40 and 133 g/kg, respectively (crude drug dosage), induced no signs of poisoning and no mortality. In a sub-chronic toxicity study, FAA and DAA treated at 3.42 and 6.83 g/kg (crude drug dosage) induced no significant toxic reactions, hematological abnormalities, or impairments in organ structure and function. Serum metabolomic analysis revealed the presence of only 46 and 52 differential metabolites in the FAA and DAA groups, respectively. Functional enrichment analysis revealed that tender A. argyi did not induce toxicity by altering metabolism from an overall perspective; however, it may have induced beneficial effects by regulating lipid metabolism. Furthermore, dual consideration of chemical abundance and network pharmacological analyses indicated that eupatilin was the most promising active ingredient among the polyphenols for treating metabolic syndrome. In mice with metabolic syndrome, eupatilin reversed changes in body weight, reduced blood glucose levels, and improved dysregulated lipid metabolism and intestinal barrier damage. Mechanistically, the gut microbiome analysis showed 9 differential genera were significantly restored after eupatilin intervention. And metabolomic analysis showed that 4 key differential metabolites were identified from the feces of Eup-treated mice. In addition, integrated analysis revealed that eupatilin mainly promoted L-phenylalanine metabolism by increasing the abundance of Akkermansia and decreasing the abundance of Helicobacter and Rikenella. Briefly, these findings systematically elucidated the safety of tender A. argyi as a dietary additive and its health benefits in metabolic syndrome via gut microbiota and metabolites. Importantly, this study will provide essential scientific support for the dual application of A. argyi in medicine and nutrition.},
}

*Artemisia/chemistry
*Metabolic Syndrome/drug therapy
*Gastrointestinal Microbiome/drug effects
Animals
*Plant Extracts/pharmacology/chemistry
Male
Mice
*Food Additives/pharmacology
Polyphenols
Plant Leaves/chemistry

@article {pmid41360358,
year = {2025},
author = {Wang, N and Tang, Y},
title = {Rebalancing the inflammatory niche in allergic rhinitis ".},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {},
number = {},
pages = {120776},
doi = {10.1016/j.cca.2025.120776},
pmid = {41360358},
issn = {1873-3492},
abstract = {Allergic rhinitis (AR) may be driven in part by cross-talk between resident microbiota, microbe-derived small molecules, and tissue-resident group 2 innate lymphoid cells (ILC2s). In this review we focus on defined signaling axes by which Traditional Chinese Medicine (TCM) can influence that network: (1) microbially produced short-chain fatty acids (SCFAs), particularly butyrate, suppress ILC2 proliferation and type-2 cytokine output primarily via HDAC inhibition that downregulates the lineage transcription factor GATA3; receptor-dependent effects via the SCFA sensors FFAR3 (GPR41), FFAR2 (GPR43), and GPR109A (HCAR2) also occur in some cell types and tissues, and can engage β-arrestin/ERK or AMPK-linked pathways depending on cell context. In purified ILC2s, ex-vivo reductions in GATA3 and IL-13/IL-5 are observed at low micromolar to several hundred micromolar butyrate (human ILC2 ≈ 10 μM; murine ex-vivo ILC2 ≈ 200 μM), while viability is generally preserved below ~1 mM, indicating a physiologically plausible dose window for metabolite-driven modulation; (2) microbially modified secondary bile acids alter mucosal immune tone and epithelial function via FXR and TGR5 signaling; and (3) microbial tryptophan metabolites (indoles) act as aryl hydrocarbon receptor (AhR) ligands that preserve epithelial integrity and shape ILC3/ILC2 balance. We review preclinical and emerging clinical data suggesting that selected TCM formulas and phytochemicals (e.g., Gegen Qinlian Decoction, Astragalus polysaccharides, berberine, baicalin/baicalein, glycyrrhizin) are associated with (a) remodeling of gut and airway microbial communities and increases in SCFA or beneficial bile/indole pools in preclinical and some human studies, (b) measurable rises in systemic or luminal SCFAs in several models and limited human cohorts, and (c) direct attenuation of epithelial alarmin (TSLP/IL-33) signaling in cellular and animal models. Where human data exist, causality remains unproven and further mechanistic clinical investigation is required. Together these actions provide testable, mechanism-based routes to suppress ILC2 activation and restore mucosal homeostasis in AR. We explicitly link TCM-driven microbiome/metabolome changes to canonical molecular mediators (HDAC, GPR41/43, FXR/TGR5, AhR, TSLP/IL-33, HMGB1) to facilitate mechanistic trial design that measures taxa → metabolite → receptor/epithelial → ILC2 causal chains.},
}

@article {pmid41360332,
year = {2025},
author = {Yu, Y and Jin, Y and Zhou, Y and Cui, Z and Xin, Y and Liu, H and Zhao, J and Elsabahy, M and Su, M and Gao, H},
title = {Nanoprodrug targeting tumor-associated intracellular bacteria enhances colorectal cancer immunotherapy.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {114512},
doi = {10.1016/j.jconrel.2025.114512},
pmid = {41360332},
issn = {1873-4995},
abstract = {The tumor-associated intracellular microbiota influences cancer progression by fostering an immunosuppressive tumor microenvironment. Targeting pro-tumor intracellular bacteria may represent a promising strategy for cancer immunotherapy. Herein, we reveal that Fusobacterium nucleatum (F. nucleatum) is preferentially enriched within M2-polarized macrophages in both human colorectal cancer (CRC) specimens and cellular models. Notably, its intracellular presence correlates significantly with reduced CD8[+] T cell infiltration, highlighting its immunosuppressive function. To disarm this microbial shield, we develop infection-specific ciprofloxacin (CIP) prodrug nanoparticles (MTCP-NPs) conjugated to an M2 macrophage-targeting peptide (IL4Rpep-1) via a cathepsin B (CTSB)-cleavable linker (FRRG) to selectively kill intramacrophage F. nucleatum. MTCP-NPs undergo IL4 receptor-mediated endocytosis in F. nucleatum-infected macrophages, where intracellular CTSB triggers CIP release to eliminate F. nucleatum and suppress indoleamine 2,3-dioxygenase (IDO) secretion. In F. nucleatum-infected CRC models, MTCP-NPs clear intracellular bacteria, alleviate immunosuppression by downregulating IDO and reducing MDSCs to mobilize CD8[+] T cell immunity. Furthermore, this treatment modulates the gut microbiota by reprogramming tryptophan metabolism. When combined with anti-PD-L1 therapy, MTCP-NPs amplify anti-tumor efficacy and prolong survival while promoting the generation of memory-like T cells associated with sustained immune responses. This strategy establishes a unique microbiome-immunotherapy framework by targeting tumor-associated intracellular bacteria to unleash T cell responses.},
}

@article {pmid41360158,
year = {2025},
author = {Wang, D and Zeng, J},
title = {Microbiome analysis reveals the adverse effects of diarrhea on the gut microbiota of yaks.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108218},
doi = {10.1016/j.micpath.2025.108218},
pmid = {41360158},
issn = {1096-1208},
abstract = {Diarrhea exhibits a extremely high prevalence among yak calves, significantly affecting the development of the yak industry and resulting in substantial economic losses. Gut microbiota has been demonstrated to be closely related to various diseases, particularly gastrointestinal disorders. However, to date, no studies have specifically explored the relationship between diarrhea in yak calves and gut microbiota. Therefore, this study aims to characterize the alterations of gut microbiota in yak calves during diarrhea. Results indicated that the diversity and abundance of the gut bacterial community in diarrheic yak calves were significantly reduced. In contrast, the gut fungal community remains relatively stable during diarrhea, with no significant changes observed in its diversity and abundance. Although diarrhea does not affect the composition of the dominant phyla of intestinal bacteria and fungi, the abundance of some microbial taxa has experienced significant changes. Specifically, diarrhea resulted in a marked increase in 2 phyla and 14 genera, while a significant decrease was observed in 5 phyla and 137 genera in gut bacterial community. Additionally, 30 genera in the gut fungal community exhibited significant increases, whereas 12 genera demonstrated significant decreases during diarrhea. Notably, we also identified significant alterations in intestinal function during diarrhea, including cytoskeleton and carbohydrate transport, etc. Taken together, this research indicated that diarrhea significantly affects the gut microbiota in yak calves, with more pronounced changes observed in the gut bacterial community. Furthermore, this research also represents a crucial exploration of the composition and alterations of gut microbiota in diarrheic yak calves, which will help prevent and control diarrhea in yaks inhabiting high-altitude regions and promote the development of the yak industry.},
}

@article {pmid41359366,
year = {2025},
author = {Cheah, S and Burke, J and Bruinsma, FJ and Evans, M and Tsimiklis, H and Hodge, AM and Lynch, BM and Giles, GG and Sinha, R and Southey, MC and Milne, RL},
title = {Faecal sample collection for gut microbiome research in a prospective cohort: a pilot study within the Australian Breakthrough Cancer Study.},
journal = {Cancer research communications},
volume = {},
number = {},
pages = {},
doi = {10.1158/2767-9764.CRC-25-0445},
pmid = {41359366},
issn = {2767-9764},
abstract = {Large prospective analyses of human gut microbiome profiles are needed to elucidate the role of microbiome variation in the development of disease. We conducted a pilot study to assess the feasibility of home faecal sample collection within a cohort study. A subset of cohort study participants was randomly selected and randomised into four groups defined by faecal sample collection method and questionnaire components. Of 1,093 invited participants, 610 (56%) opted in and, of those, 88% returned a sample. Of those asked to provide a faecal sample via faecal occult blood test card (FOBT) and complete a short "day of sample" questionnaire (dosQ), 49% returned a sample. Sample return was comparable for participants additionally asked to provide a sample via ethanol tube (51%), complete a food frequency questionnaire (48%), or complete both additional activities (49%). Whole genome sequencing and metagenomic analysis on paired FOBT and ethanol samples showed that both collection methods provided sufficient quality and quantity of DNA for downstream metagenomic analyses and displayed highly concordant microbiome profiles. Home faecal sample collection for microbiome analysis is feasible in a large prospective cohort. Including additional components did not reduce the likelihood of participants completing all requested items.},
}

@article {pmid41359046,
year = {2025},
author = {Dalby, KL and Horsley, H and Spratt, D and Khasriya, R},
title = {The Vaginal Microbiome and Recurrent and Chronic Urinary Tract Infection.},
journal = {International urogynecology journal},
volume = {},
number = {},
pages = {},
pmid = {41359046},
issn = {1433-3023},
abstract = {INTRODUCTION AND HYPOTHESIS: The vaginal and urinary microbiomes are closely linked, yet the role of this relationship in recurrent and chronic urinary tract infections (UTIs) remains uncertain. Research into genitourinary ecology and UTI has largely focused on acute infections and reproductive age groups, leaving a gap in understanding the role of the microbiome in recurrent and chronic cases. This review is aimed at presenting that disruptions within vaginal microbiota contribute to UTI chronicity in menopausal women, highlighting the potential for microbiome-targeted interventions in this high-risk group.

METHODS: A comprehensive literature review was conducted, with search terms including cystitis, urogenital, antibiotic, infection, and bladder, vaginal microbiome, vaginal ecology, topical oestrogen, atrophy, genitourinary syndrome of menopause, vulvo-vaginal atrophy (VVA), bacterial vaginosis and lactobacillus. Relevant articles were screened, critiqued, and synthesised based on key themes.

RESULTS: Lactobacillus spp. appears to be the key component of a healthy vaginal microbiome. Decreased vaginal Lactobacillus abundance, seen with vaginal dysbioses and the menopause, correlates with an increased presence of urinary pathogens, increasing susceptibility to UTI. This review demonstrates that interventions to optimise vaginal ecology could reduce UTI burden. These approaches offer non-antibiotic treatment strategies, lowering antimicrobial resistance risk. However, studies frequently exclude those with chronic and recurrent infections, underscoring the necessity for more research targeting this group.

CONCLUSIONS: This review highlights the link between disrupted vaginal ecology and recurrent and chronic UTI, and the need for expanded research into microbiome-targeted treatments. A paucity of studies researching recurrent and chronic UTI cohorts limits the evidence base for clinical generalisation, meaning that more focussed studies are needed to improve understanding and clinical management.},
}

@article {pmid41359024,
year = {2025},
author = {Qian, K and Du, M and Tan, S and Ding, M and Song, M and Lu, M and Qi, C and Cheng, L and Zhang, X},
title = {gutMSNP: a comprehensive database for human gut microbial single-nucleotide polymorphisms.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1205},
pmid = {41359024},
issn = {1362-4962},
support = {62222104//National Natural Science Foundation of China/ ; 62172130//National Natural Science Foundation of China/ ; 62222104//National Natural Science Foundation of China/ ; },
abstract = {gutMSNP (https://bio-computing.hrbmu.edu.cn/gutMSNP/home) is a user-friendly database designed to provide a systematic and comprehensive resource for single-nucleotide polymorphisms (SNPs) in the human gut microbiome. Given that even a single SNP in gut microbial genomes can profoundly modulate microbial pathogenicity and thereby impact host health, a large-scale, standardized SNP repository is indispensable for elucidating microbial functions and the molecular mechanisms underpinning microbiota-driven disorders. The current release of gutMSNP includes: (i) 164 015 783 SNPs identified across human gut microbial genomes and categorized into three coverage confidence levels; (ii) 364 species-level and 8251 gene-level microbial records, each exhibiting phenotype-specific SNP distribution patterns; (iii) 8146 representative reference genomes of human gut microbes; and (iv) an online tool for capturing SNPs. The database enables users to search for SNPs in microbial species of interest along with detailed functional and positional annotations, explore phenotype-specific SNP distribution patterns in selected species and their associated genes, download reference genomes for downstream analyses, and detect as well as annotate SNPs in user-uploaded microbial genome files. With its massive SNP dataset, versatile query capabilities, and integrated analytical tools, gutMSNP will serve as a fundamental resource for SNP-based investigations in the human gut microbiome.},
}

@article {pmid41358834,
year = {2025},
author = {Zhang, Q and Wang, Y and Zhang, H and Xu, G and Xu, S and Yang, G},
title = {Blubber Thickening Driven by UCP1 Inactivation: Insights from a Cetacean-Like Transgenic Mouse Model.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70047},
pmid = {41358834},
issn = {1749-4877},
abstract = {Cetaceans possess thick blubber, a specialized adipose tissue essential for thermal insulation, a streamlined body form, energy storage, and buoyancy. However, the mechanisms that underpin this adaptation are not yet fully understood. Here, we found that uncoupling protein 1 (UCP1) of cetaceans has undergone significant evolutionary relaxation. A transgenic mouse model with cetacean-like UCP1 inactivation revealed a pronounced obesity phenotype, including expanded brown adipose tissue (BAT) and increased white adipose tissue (WAT) adipocyte hyperplasia. Histological, metabolic, and physiological assessments showed reduced lipolysis, impaired glucose metabolism, and upregulated lipid metabolism pathways in BAT. Additionally, gut microbiome analysis indicated an increased Firmicutes/Bacteroidetes ratio, suggesting enhanced energy absorption and weight gain. Comparison with traditional UCP1-KO mice further revealed that the unique mutations in cetacean UCP1 could be the molecular basis for observed fat accumulation phenotype. Our findings provide novel insights into the evolutionary mechanisms underlying blubber thickening in the secondary aquatic adaptation of cetaceans.},
}

@article {pmid41358730,
year = {2025},
author = {Yan, H and Zhang, Y and Zhang, Z and Zhao, Z and Zhang, L and Ju, F},
title = {Soil pH and nitrate shape deterministic assembly of microbial communities in agricultural soils via Nitrososphaeria.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0206725},
doi = {10.1128/aem.02067-25},
pmid = {41358730},
issn = {1098-5336},
abstract = {UNLABELLED: Understanding the assembly mechanisms of soil microbial communities is critical for maintaining nitrogen cycling in agricultural ecosystems, which underpins soil fertility and sustains crop productivity. While environmental filtering and biotic interactions shape these communities, our understanding of how functional taxa interact with soil properties across extensive agricultural landscapes remains limited. Here, we investigated the influence of environmental factors on the Chinese agricultural soil microbiome, integrating assessments of microbiota diversity, composition, and assembly process. The results indicated that soil pH and moisture were among the strongest abiotic factors explaining the agricultural soil microbiota compositional variation at a continental scale, surpassing the examined geographical and climatic effects. Stochastic processes dominated the assembly of microbial communities in large-scale agricultural soils, whereas the relative importance of deterministic processes increased with rising pH from acidic to alkaline soils. Phylogenetic turnover, as indicated by the beta nearest taxon index (βNTI), revealed determinism peaked under nitrogen-limited conditions but weakened with moderate precipitation, suggesting that both extreme aridity and rainfall amplify environmental filtering. We also found that divergent environmental preferences were displayed by ammonia-oxidizing microorganisms, including four archaeal genera belonging to the Nitrososphaeria class. Their significant correlations with βNTI as well as soil pH, nitrate, and moisture suggested that soil properties likely influenced prokaryotic community assembly primarily through modulating these functional taxa. This study highlights the vital role of ammonia-oxidizing-related soil properties in shaping the functional groups and assembly mechanisms of soil microbial communities, while enhancing our understanding of how ecological niche modifications by ammonia-oxidizers influence community interactions and nutrient dynamics in agricultural soils.

IMPORTANCE: Agricultural soil microbiomes are essential for element cycling, fertility maintenance, and crop productivity, yet how key functional taxa interact with environmental factors to shape community assembly remains poorly understood. In this transcontinental study spanning diverse vegetation types, we demonstrate that ammonia-oxidizing archaea mediate soil microbial community assembly in response to pH and nitrate levels, with evidence of nonlinear threshold effects driven by nitrate. These findings underscore the pivotal role of keystone taxa in structuring soil biodiversity and ecological functions. Our study offers valuable insights into microbially mediated carbon and nitrogen cycling under climate change and supports crop-specific soil management strategies for sustainable agriculture.},
}

@article {pmid41358671,
year = {2025},
author = {Ngwese, MM and Adegbite, BR and Zinsou, JF and Fitzstevens, JL and Schmidt, VT and Moure, PAN and Maloum, MN and Tyakht, AV and Huus, KE and Youngblut, ND and Kremsner, PG and Adegnika, AA and Ley, RE},
title = {Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2587966},
doi = {10.1080/19490976.2025.2587966},
pmid = {41358671},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Feces/parasitology/microbiology ; Animals ; Gabon/epidemiology ; Female ; Male ; Child ; *Helminthiasis/parasitology/epidemiology/microbiology ; Metagenomics ; *Helminths/isolation & purification/classification/genetics ; Child, Preschool ; Rural Population ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Ascaris lumbricoides/isolation & purification ; Strongyloides stercoralis/isolation & purification ; Necator americanus/isolation & purification ; Trichuris/isolation & purification ; Biodiversity ; },
abstract = {Soil-transmitted helminths (STH) are common in (sub)tropical regions and primarily affect impoverished populations. These parasites reside in the gut, where they interact with both the microbiota and host immunity. Clinical STH detection is laborious and often not performed within the context of gut microbiome studies. Here, we present a proof-of-concept study assessing whether fecal metagenome data could be used to assess STH infection, and to relate STH infection to microbiome features. We leveraged 310 gut metagenomes obtained from mother-child pairs in two different locations in Gabon: one rural and one semi-urban, and assessed the presence of four STH species (Ascaris lumbricoides, Strongyloides stercoralis, Trichuris trichiura, and Necator americanus) using qPCR. Sequence data were used to characterize the microbiomes and to detect these parasites. Metagenomic read mapping and genome coverage metrics closely matched qPCR detection patterns. Within-location analyses revealed that parasite species richness was associated with microbiome diversity and taxonomic composition, with the strongest associations observed in children from the rural site. Applying this approach to published data from five additional African cohorts identified context-specific parasite-microbiome associations, as well as a modest but reproducible association between microbiome alpha diversity and parasite infection. These findings highlight the potential of shotgun metagenomics for concurrent parasite detection and microbiome profiling across diverse geographic and demographic contexts.},
}

Humans
*Gastrointestinal Microbiome/genetics
Feces/parasitology/microbiology
Animals
Gabon/epidemiology
Female
Male
Child
*Helminthiasis/parasitology/epidemiology/microbiology
Metagenomics
*Helminths/isolation & purification/classification/genetics
Child, Preschool
Rural Population
Bacteria/classification/genetics/isolation & purification
Metagenome
Ascaris lumbricoides/isolation & purification
Strongyloides stercoralis/isolation & purification
Necator americanus/isolation & purification
Trichuris/isolation & purification
Biodiversity

@article {pmid41358650,
year = {2025},
author = {Lee, I and Kim, BS and Suk, KT and Lee, SS},
title = {Corrigendum to: Gut Microbiome-Based Strategies for the Control of Carbapenem-Resistant Enterobacteriaceae.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e35005},
doi = {10.4014/jmb.2025.3512.C01},
pmid = {41358650},
issn = {1738-8872},
}

@article {pmid41358462,
year = {2025},
author = {Nema, A and Dhar, D and Ramireddy, VSR and Priyam, K and Agarwal, S and Srivastava, SK},
title = {A Small Pill-Like Ingestible Microdevice for Site-Specific Microbiome Sampling in the Upper GI Tract.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e10289},
doi = {10.1002/smll.202510289},
pmid = {41358462},
issn = {1613-6829},
support = {IIRPSG-2024-01-00486//Indian Council of Medical Research/ ; },
abstract = {The gut microbiota varies along the length and cross-section of the gastrointestinal (GI) tract, influencing diseases. Direct sampling from the upper GI tract remains challenging due to anatomical constraints and low-volume genomic sequencing. Here, we report an ingestible, pill-like microdevice (7 × 2.7 mm) that enables in vivo microbiome and biomarker sampling in Sprague-Dawley rats - demonstrating, for the first time, successful autonomous pyloric transit of a microdevice via oral gavage. The device comprises an enteric-coated gelatin cap that protects it in gastric pH (1-1.5) and disintegrates at intestinal pH (3-5), allowing luminal fluid via an inlet connected to activation and sampling chambers. A polyacrylate hydrogel in the activation chamber swells to seal the inlet to prevent cross-contamination. In vivo studies (n = 5) confirmed successful pyloric transit in 4/5 rats without tissue injury or inflammation. Each retrieved device yielded 13.48 ± 4.66 ng genomic DNA, enabling 16S rRNA sequencing of site-specific microbiota distinct from fecal profiles. Concurrent detection of intestinal alkaline phosphatase (≈6.5 µg mL[-1]) confirmed dual microbiome-protein biomarker capability. We demonstrate species-level microbiota identification via nanopore sequencing using an orally ingestible platform technology for longitudinal gut microbiome profiling, paving way for studies in large animals and humans.},
}

@article {pmid41358163,
year = {2025},
author = {Schulte-Hillen, R and Giesler, JK and Mock, T and Belshaw, N and John, U and Harder, T and Kühne, N and Neuhaus, S and Wohlrab, S},
title = {Genotype and culture condition effects on single-cell diatom microbiomes: enhanced detection of low-abundance taxa with CRISPR-Cas9.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf194},
pmid = {41358163},
issn = {2730-6151},
abstract = {Primary production in aquatic systems is governed by interactions between microalgae and their associated bacteria. Most of our knowledge about algal microbiomes stems from natural mixed communities or isolated algal monocultures, which therefore does neither address the role of genotypic diversity among the algal host cells nor do they reveal how this host diversity impacts the assembly process of associated bacteria. To overcome this knowledge gap, we developed a single-cell 16S sequencing approach in combination with CRISPR-Cas9 guided depletion of host 16S contaminations from the chloroplast. The validity of this novel method was tested by comparing bacterial communities of 144 single-cells across three genotypes of the Arctic marine diatom Thalassiosira gravida grown under different environmental conditions. From these, 62 single-cells were additionally sequenced after CRISPR-Cas9 treatment. Due to the improved sequencing depth, bacterial richness associated with individual diatom cells was increased by up to 56%. By applying this CRISPR-Cas9 treatment we not only revealed intraspecific host-genotype associations but also low-abundance bacterial taxa that were not detected by standard 16S rRNA gene metabarcoding. Thus, the CRISPR-Cas9 assisted single-cell approach developed in this study advances our understanding on how the intraspecific diversity among algal hosts impacts the assembly process of their associated bacteria. This knowledge is essential to understand the co-evolution and adaptation of species in algal microbiomes.},
}

@article {pmid41358162,
year = {2025},
author = {Nicolas-Asselineau, L and Speth, DR and Zeller, LM and Woodcroft, BJ and Singleton, CM and Liu, L and Dueholm, MKD and Milucka, J},
title = {Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf209},
pmid = {41358162},
issn = {2730-6151},
abstract = {Effective wastewater treatment is of critical importance for preserving public health and protecting natural environments. Key processes in wastewater treatment, such as denitrification, are performed by a diverse community of prokaryotic and eukaryotic microbes. However, the diversity of the microbiome and the potential role of the different microbial taxa in some wastewater treatment plant setups is not fully understood. We aimed to investigate the presence and diversity of denitrifying bacteria of the candidate family Azoamicaceae that form obligate symbioses with protists in wastewater treatment plants. Our analyses showed that denitrifying endosymbionts belonging to the Ca. Azoamicus genus are present in 20%-50% of wastewater treatment plants worldwide. Time-resolved amplicon data from four Danish WWTPs showed high temporal fluctuations in the abundance and composition of the denitrifying endosymbiont community. Twelve high-quality metagenome-assembled genomes of denitrifying endosymbionts, four of which were circular, were recovered. Genome annotation showed that a newly described, globally widespread species, Ca. Azoamicus parvus, lacked a nitrous oxide reductase, suggesting that its denitrification pathway is incomplete. This observation further expands the diversity of metabolic potentials found in denitrifying endosymbionts and indicates a possible involvement of microbial eukaryote holobionts in wastewater ecosystem dynamics of nitrogen removal and greenhouse gas production.},
}

@article {pmid41358150,
year = {2025},
author = {Coufal, S and Zakostelska, ZJ and Thon, T and Roubalova, R and Kadleckova, D and Salakova, M and Tachezy, R and Hrncir, T and Kverka, M and Ticha, V and Pavelcova, M and Kleinova, P and Preiningerova, JL and Kovarova, I and Kreisinger, J and Tlaskalova-Hogenova, H and Havrdova, EK},
title = {Ocrelizumab transiently alters microbiota and modulates immune response depending on treatment outcome.},
journal = {iScience},
volume = {28},
number = {12},
pages = {113872},
pmid = {41358150},
issn = {2589-0042},
abstract = {Multiple sclerosis (MS) is an autoimmune disease characterized by central nervous system atrophy. Microbiota dysbiosis is implicated in MS pathogenesis and treatment outcomes. In our study, we observed microbiota changes already present in treatment-naïve individuals with clinically isolated syndrome, affecting both bacteria and viruses. Gut bacteria alterations were transient during the first 12 months of anti-CD20 therapy. After 12 months, responders showed increased gut microbiota alpha diversity approaching healthy control levels, while non-responders showed a significant decline. Key changes involved Parabacteroides spp., producers of short-chain fatty acids that support gut barrier function and have anti-inflammatory potential. We detected altered gut barrier biomarkers and antibodies against common commensals in MS patients, which were modulated by anti-CD20 treatment. Notably, lipopolysaccharide-binding protein and mannose-binding lectin decreased only in responders. These findings suggest that intestinal barrier damage contributes to immune responses linked to microbial translocation, MS pathogenesis, and treatment outcomes.},
}

@article {pmid41358148,
year = {2025},
author = {Liang, S and Huang, L and Ma, K and Wang, R and Ji, F and Shi, M and Piao, M and Liang, Z and Guo, R and Chen, R and Chen, C and Xie, L},
title = {Pediatric diarrhea management with probiotics supplementation: Results from a randomized controlled trial.},
journal = {iScience},
volume = {28},
number = {12},
pages = {113981},
pmid = {41358148},
issn = {2589-0042},
abstract = {Diarrhea remains a major cause of illness in children, and probiotics are often explored as adjunctive therapies. In this randomized, double-blind, placebo-controlled trial, 141 children aged 6 months to 6 years were assigned to receive either Limosilactobacillus reuteri FPHC2951, Bifidobacterium breve FPHC4024, or placebo alongside standard care for one month. Gut microbiota composition was analyzed before and after intervention using 16S rRNA gene sequencing. While all groups showed increased microbial α-diversity, greater enrichment of Limosilactobacillus and Bifidobacterium occurred in the probiotic groups. Clostridioides difficile levels declined across all groups. Among children receiving antibiotics, microbiota changes were notable only in the probiotic groups. However, no significant differences were observed in diarrhea duration or clinical symptoms between groups. These results suggest that probiotic supplementation can enhance gut microbial recovery during pediatric diarrhea and antibiotic exposure, although the added clinical benefits beyond standard care remain limited.},
}

@article {pmid41357544,
year = {2025},
author = {Firozpoor, J and Gardini, R and Escobar Huezo, ME and Eccard, JA},
title = {Rodent species composition in urban and forested areas in eastern Germany.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e143224},
pmid = {41357544},
issn = {1314-2828},
abstract = {BACKGROUND: Zoonoses are major concerns for public health and after the recent pandemic, have been under a global spotlight for their often unpredictable spread and rapid evolution. In particular, the relationship between wildlife biodiversity and zoonoses lies at the core of the challenges of disease dynamics in a changing world. To address the challenge of rodent-borne diseases, transmitted by rodents acting as hosts for various zoonoses and thriving in different environments, we focus on rodent species composition in European temperate forests and urban parks, where human-wildlife interactions are likely to occur. Using live-trapping, we describe rodent communities for integration into an eco-health framework.

NEW INFORMATION: The dataset introduced here is part of the European project BiodivERsA-BioRodDis (https://www6.inrae.fr/biodiversa-bioroddis), whose goal is to examine the connection between rodent biodiversity, the dynamics of rodent-borne diseases and temporal variations in a changing climate. We provide records of small mammals (Rodentia) captured from forested habitats, with different levels of urbanisation in northeast Germany, within the district of Potsdam (Brandenburg). The trapping took place between winter 2020 and spring 2022 at four different sites. All four sites were sampled in winter 2020, three were revisited in spring 2021 and two in autumn 2021 and spring 2022. This variation was mainly due to logistical constraints and low trapping success at some sites. Using live traps, we collected a total of 620 occurrence records of rodents, including the species Apodemus flavicollis, Apodemus agrarius, Myodes glareolus and Microtus arvalis. A subset of the captures (n = 264) was subsequently dissected for pathogen screening and gut microbiome characterisation, not reported here.},
}

@article {pmid41357037,
year = {2025},
author = {Syromyatnikov, MY and Burakova, IY and Smirnova, YD and Morozova, PD and Pogorelova, SV and Chirkin, EA and Tolkacheva, AA},
title = {Study of Akkermansia muciniphila Effect on the Gut Microbiome of Mice Under LPS-Induced Systemic Inflammation.},
journal = {International journal of inflammation},
volume = {2025},
number = {},
pages = {8695182},
pmid = {41357037},
issn = {2090-8040},
abstract = {Probiotics are strains of living bacteria and yeast that play an important role in regulating the gut microbiota and enhancing host immunity. In the last decade, the bacterial species Akkermansia muciniphila has attracted great interest due to its possible probiotic properties, which play an important role in human health. However, the mechanisms of action of A. muciniphila are still poorly understood. The effect of the A. muciniphila on the intestinal microbiome of model animals with systemic inflammation induced by lipopolysaccharide (LPS) is unexplored. This study aims to investigate the impact of A. muciniphila on the microbiological composition of the mouse gut under LPS-induced systemic inflammation using high-throughput sequencing. The study used a new generation sequencing method aimed at genome-wide sequencing of microorganisms, which makes it possible to study changes in the composition of the microbiome at the bacterial species level, as well as to identify the genes of the metabolic pathways of intestinal bacteria in the studied mice. Our analysis revealed statistically significant differences across all studied groups, with a notable predominance of members from the families Muribaculaceae, Rikenellaceae, and Oscillospiraceae. Consumption of A. muciniphila increased the alpha diversity of gut bacteria (Shannon index) in the context of induced inflammation. Evaluation of the effect of LPS and A. muciniphila on metabolic pathways showed statistically significant differences for the pathways of synthesis and degradation of amino acids, transforming folic acid, and synthesis of sugars. Genetic analysis showed that the probiotic bacterium A. muciniphila reduced the degree of negative effects of LPS on the mouse gut microbiome under systemic inflammation.},
}

@article {pmid41356942,
year = {2025},
author = {Alasbily, H and Mohamed, HH and Asheibi, A and Bazina, MS and Alkaseh, A and Ghaith, HM and Ali Fahmi, F},
title = {Probiotics in Periodontal Diseases: Mechanisms, Evidence Mapping, Limitations, and Future Directions.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e96042},
pmid = {41356942},
issn = {2168-8184},
abstract = {Periodontal disease represents a spectrum of inflammatory disorders that impact the teeth's supporting tissues. It is initiated by the buildup of microbial plaque and sustained by dysbiosis, an imbalance in the oral microbiome that causes tissue damage and disturbs host-microbe homeostasis. These diseases can range from reversible inflammation of the gingiva (gingivitis) to irreversible destruction of the periodontal apparatus (periodontitis). While scaling and root planing, with or without antimicrobials, can effectively reduce bacterial burden, mechanical debridement by itself may not restore microbial symbiosis and may allow disease-associated microbial populations to persist. Incomplete pathogen clearance from deep pockets, residual calculus, or inaccessible root surfaces frequently results in bacterial regrowth and disease progression. Probiotics have emerged as a possible alternative or supplement in periodontal therapy. Their possible benefits include microbial balance restoration in the oral cavity, as well as anti-inflammatory, immunomodulatory, and bone-preserving actions. Nonetheless, the strain-specific effects, dosage regimen, safety profile especially in certain patients and the absence of large-scale, long‑term randomized controlled trials to definitively establish their efficacy remain as concerns. This review discusses the mechanisms through which probiotics may influence periodontal diseases, systematically maps preclinical and clinical evidence, and highlights current limitations and future directions for their application in periodontal therapy.},
}

@article {pmid41356879,
year = {2025},
author = {Farhad, ME and Belal, I and Baana, M and Childs, C and Al-Rufayie, M},
title = {Biomarkers of Probiotic Therapy in Ulcerative Colitis: A Systematic Review of Mechanisms Underlying Remission.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e96126},
pmid = {41356879},
issn = {2168-8184},
abstract = {Ulcerative colitis (UC) is a chronic immune-mediated inflammatory bowel disease of unknown aetiology that affects the colon. Patients with UC typically exhibit dysbiosis - an altered gut microbiota profile compared with healthy individuals, who have a more diverse microbial community - suggesting that dysbiosis may be either a cause or a consequence of UC. Current therapeutics include aminosalicylates and steroids with anti-inflammatory and immunosuppressive properties; however, these treatments do not address dysbiosis and instead relieve symptoms. Antibiotics are sometimes used to exert selective pressure on the microbiota and eliminate Gram-negative bacteria, but they are associated with significant side effects, including diarrhoea, Clostridioides difficile infection, thrush, and peripheral neuropathy. Probiotics, live microorganisms that confer a health benefit on the host, represent a growing area of interest in the treatment of inflammatory bowel disease (IBD), with the potential to modulate the gut microbiota. Randomised controlled trials (RCTs) measuring biomarkers in patients with UC treated with probiotics were identified through searches of four databases. After screening against predefined inclusion and exclusion criteria, eligible studies were assessed for risk of bias. Thirteen RCTs were included, using interventions such as VSL#3 (Actial Nutrition Inc., Covington, Louisiana) and bifidobacteria-fermented milk (BFM), and measured biomarkers including cytokines over follow-up periods of up to one year. Pro-inflammatory signalling markers, such as nuclear factor-κB (NF-κB), were measured in two of 13 studies and showed significant reductions following probiotic therapy. Conversely, anti-inflammatory biomarkers such as interleukin-10 (IL-10) were significantly increased in all four studies that assessed them. These findings provide insights into the inflammatory pathways targeted by probiotics, including down-regulation of Toll-like receptor 2 (TLR2), leading to reduced pro-inflammatory cytokine production. Such results may inform the development of novel therapeutics targeting these pathways and support the use of biomarkers as objective indicators of disease activity or treatment response, in contrast to potentially biased clinical scores.},
}

@article {pmid41356810,
year = {2025},
author = {Akpınar, A and Markiewicz, LH and Harsa, HŞ and Paveljšek, D and Domínguez-Soberanes, J and Agirbasli, Z and Naziri, E and El Jalil, MH and Bouchaud, G and Salminen, S and Savary-Auzeloux, I and Humblot, C and Chassard, C and Pracer, S and Vergères, G and Karakaş-Budak, B},
title = {Efficacy of fermented foods for the prevention and treatment of bacterial vaginosis and vulvovaginal candidiasis.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1658988},
pmid = {41356810},
issn = {2296-861X},
abstract = {Vaginal function in healthy women is closely associated with a lactobacilli-dominated microbiome. Among the most common conditions arising from dysbiosis are bacterial vaginosis (BV) and vulvovaginal candidiasis (VVC). While the efficacy of oral probiotics for the treatment of BV and VVC is well documented, the role of consuming fermented foods remains underexplored. This systematic review aims to present a systematic evaluation of the potential role of fermented foods in the prevention and treatment of BV and VVC and establish the extant research gap between the realm of the clinical sciences and the field of food science and technology. For this purpose, under the guidance of COST Action CA20128-Promoting Innovation of Fermented Foods (PIMENTO), a systematic literature review was conducted in two phases. PubMed, Scopus, and Cochrane databases were used for Phase I to analyze articles on human trials and observational studies where the intervention/exposure involved oral consumption of fermented food. In Phase II, a two-step search strategy was employed: (i) identifying microorganisms with demonstrated clinical efficacy in managing BV and VVC, and (ii) reviewing food science literature where these strains are utilized for fermentation. It was observed that 87% of the food starter applications exploited only two of the 54 efficacious strains identified through clinical studies, namely Lactobacillus rhamnosus GG and Lactobacillus acidophilus LA-5. Findings underscore the potential of fermented foods as carriers for beneficial microorganisms and their relevance in supporting vaginal health. This review contributes to a deeper understanding of the interplay between nutritional consumption of viable probiotic strains and their importance in immunomodulation, highlighting the need for more integrated research efforts across disciplines. Future research aimed at filling this gap will enable informed clinical decisions and dietary recommendations.},
}

@article {pmid41356732,
year = {2025},
author = {Cai, L and Li, Y and Liu, Y and Ma, G and Zhang, Q and Li, X and Li, N},
title = {Endotracheal intubation-related oral mucosal membrane pressure injuries: a narrative review of biomechanical insights, biomaterial optimization, and intelligent monitoring.},
journal = {Frontiers in medical technology},
volume = {7},
number = {},
pages = {1667748},
pmid = {41356732},
issn = {2673-3129},
abstract = {OBJECTIVES: This article is a narrative review that synthesizes current evidence on orotracheal intubation-related oral mucosal membrane pressure injuries in intensive care unit (ICU) patients, focusing on mechanisms, risk factors, and prevention strategies. The review is intended to inform clinicians and researchers by integrating insights from intensive care, biomechanics, biomaterials, and oral microbiology.

METHODS: A comprehensive literature search was conducted in PubMed, Web of Science, Embase, and CNKI using the terms "orotracheal intubation", "oral mucosal injury", "device-related pressure injury", "biomechanics", "biomaterials" and "oral microbiome". Studies published between 2000 and 2025, including both clinical and experimental research, were considered without language restrictions.

RESULTS: Evidence indicates that vertical pressure, shear force, and friction from endotracheal tubes are key contributors to oral mucosal injury. Reported risk factors include advanced age, prolonged intubation, malnutrition, and inflammation. Preventive strategies have been explored in four domains: biomechanical modeling using finite element analysis, biomaterial optimization such as hydrogel and nanocoatings, regulation of the oral microecosystem through probiotics, and intelligent monitoring systems incorporating artificial intelligence and Internet of Things technologies.

CONCLUSIONS: Orotracheal intubation-related oral mucosal pressure injuries are multifactorial and preventable. This narrative review integrates biomechanical insights, optimized biomaterials, microbiome regulation, and intelligent monitoring into a multidimensional prevention framework. Such strategies may enhance early identification, reduce complications, and improve clinical outcomes in ICU patients.},
}

@article {pmid41356699,
year = {2025},
author = {Kim, SM and Praveen, Z and Kim, YH and Ko, JH and Choi, YS and Park, JY and Lee, JH and Choi, SW and Kim, MK},
title = {Functional profiling of the oral microbiome reveals microbial and oncogenic signatures in never-smoking female patients with oral squamous cell carcinoma.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2594842},
pmid = {41356699},
issn = {2000-2297},
abstract = {BACKGROUND: The pathogenesis of oral squamous cell carcinoma (OSCC) in never-smoking females remains poorly understood, as these patients lack traditional risk factors. This subgroup accounts for an increasing proportion of OSCC cases and may exhibit distinct tumor biology. Here, we investigated the association between the alterations in the salivary microbiome and OSCC in never-smoking female patients.

MATERIALS AND METHODS: Saliva samples from 72 never-smoking female patients with OSCC and 494 never-smoking healthy female controls were analyzed using 16S rRNA gene sequencing. Microbial community structure and function were compared using statistical analyses, machine learning algorithms, and pathway prediction with PICRUSt2.

RESULTS: Patients with OSCC exhibited significantly different microbial diversity and composition compared to controls. The genera Rhodococcus, Slackia, Lactobacillus, and Enterobacterales_g were enriched in the OSCC group, whereas Corynebacterium was more abundant in the Control group. These taxa were associated with oncogenic pathways, including PI3K-Akt signaling and nicotinate/nicotinamide metabolism. Functional inference also indicated enrichment of cancer-related orthologs such as LKB1, NFKB1, ITGAV, and TRAF4.

CONCLUSIONS: Salivary microbiome alterations, both taxonomic and functional, are associated with OSCC in never-smoking females. These findings suggest a potential microbial contribution to carcinogenesis in this unique patient population and offer novel insights into disease mechanisms.},
}

@article {pmid41356698,
year = {2025},
author = {Xu, Y and Leng, X and Liu, Q and Ji, Q and Li, J and Huang, X and Li, L and Lin, Y and Karlsson, I and Zhan, Y},
title = {The oral microbiome as mediators in the association between smoking and all-cause mortality.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2594296},
pmid = {41356698},
issn = {2000-2297},
abstract = {BACKGROUND: Smoking increases mortality risk and alters the oral microbiome, but its mediating role in the smoking-survival relationship remains unclear. This study examined whether oral microbiome diversity mediates the association between smoking and all-cause mortality.

METHODS: We included 8,223 participants from the National Health and Nutrition Examination Survey with linked mortality data through 2019. Oral microbiome diversity was assessed using alpha and beta diversity metrics. Associations between smoking, diversity, and mortality were assessed using Weibull Accelerated Failure Time models. Multivariable linear regression evaluated the relationship between smoking and oral microbiome diversity. Mediation analysis estimated the Natural Direct Effect (NDE) and Natural Indirect Effect (NIE). Sensitivity analyses assessed effect heterogeneity.

RESULTS: Among participants, 429 were deceased. Current smoking was associated with a 42.3% shorter survival time (TR = 0.577). Greater ln-transformed observed Operational Taxonomic Units (OTU) richness was associated with 33.2% longer survival time (TR = 1.332). Smoking was associated with survival time through NIE = 1.013 (95% CI: 1.003, 1.033) and NDE = 0.577 (95% CI: 0.474, 0.697). Sensitivity analyses supported the findings.

DISCUSSION: Oral microbiome diversity partially mediated the association between smoking and mortality. Although smoking shortened survival, its effect on increasing OTU richness modestly suppressed this risk. These results highlight a complex microbial pathway and support further investigation into species-level mechanisms and potential microbiome-targeted interventions.},
}

@article {pmid41356486,
year = {2025},
author = {Dedecius, D and Kolář, J and Martinů, J and Štefka, J and Nováková, E and Hypša, V},
title = {Generalist vs. specialist strategy shapes microbiomes in blood feeding parasite Polyplax serrata.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1720127},
pmid = {41356486},
issn = {1664-302X},
abstract = {Insects live in association with bacterial communities, collectively referred to as the microbiome. Microbiome composition varies widely across insect taxa and is shaped by multiple factors, including host phylogeny, environmental conditions, geographic distribution, and nutritional ecology. One hypothesis is that microbiome composition may also reflect whether the host adopts a generalist or specialist ecological strategy. We tested this hypothesis using the sucking louse Polyplax serrata, which offers several advantages as a model system. First, as permanent ectoparasites, lice inhabit a relatively stable and simplified environment, thereby minimizing potential confounding variables. Second, within P. serrata, two closely related lineages have been identified: one restricted to a single rodent host (Apodemus flavicollis), and the other exploiting two hosts (A. flavicollis and A. sylvaticus). We analyzed and compared microbiome structure in these two lineages using 16S rRNA gene amplicon sequencing. While alpha diversity did not differ between the lineages, beta diversity differed significantly, particularly in pairwise dissimilarities among individual samples. These results suggest that in P. serrata, host specialization strategy influences microbiome diversity, with the "generalist" lineage harboring more heterogeneous communities. This finding extends previous observations on ecological divergence between the two lineages, showing that closely related cryptic species with highly similar genomes, living sympatrically in the same environment, can rapidly evolve distinct life strategies that, in turn, shape both their genetic structure and their microbiomes.},
}

@article {pmid41356485,
year = {2025},
author = {Bai, B and Ma, J and Xu, W and Chen, X and Chen, X and Lv, C and Su, W and Li, Y and Sun, H and Zhang, B and Xiang, D and Li, Z and Wu, Y and Sun, J and Yin, M},
title = {Gut microbiota and colorectal cancer: mechanistic insights, diagnostic advances, and microbiome-based therapeutic strategies.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1699893},
pmid = {41356485},
issn = {1664-302X},
abstract = {Colorectal cancer (CRC) is closely linked to gut microbiota dysbiosis. We synthesize evidence that carcinogenic microbes promote CRC through chronic inflammation, bacterial genotoxins, and metabolic imbalance, highlighting key pathways involving Fusobacterium nucleatum, pks [+] Escherichia coli, and enterotoxigenic Bacteroides fragilis (ETBF). Building on these mechanisms, we propose a minimal diagnostic signature that integrates multi-omics with targeted qPCR, and a pathway-therapy-microbiome matching framework to guide individualized treatment. Probiotics, fecal microbiota transplantation (FMT), and bacteriophage therapy show promise as adjunctive strategies; however, standardization, safety monitoring, and regulatory readiness remain central hurdles. We advocate a three-step path to clinical implementation-stratified diagnosis, therapy matching, and longitudinal monitoring-supported by spatial multi-omics and AI-driven analytics. This approach aims to operationalize microbiome biology into deployable tools for risk stratification, treatment selection, and surveillance, advancing toward microbiome-informed precision oncology in CRC.},
}

@article {pmid41356481,
year = {2025},
author = {Rao, AV and Ghare, SS and Gautam, V and Hoffman, KL and Petrosino, J and So-Armah, K and Samet, JH and Patts, GJ and Cheng, DM and Blokhina, E and Krupitsky, EM and Lioznov, D and Zvartau, E and McClain, CJ and Tindle, H and Freiberg, MS and Barve, SS},
title = {Sex differences in beneficial and pathogenic bacteria in People With HIV (PWH) with a history of heavy alcohol drinking.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1632949},
pmid = {41356481},
issn = {1664-302X},
abstract = {BACKGROUND: HIV-1 infection and hazardous levels of alcohol consumption have been independently linked to gut dysbiosis affecting beneficial butyrate-producing bacteria. However, sex-based differences in the composition and function of gut microbiome of People With HIV (PWH) with a history of heavy alcohol drinking remain undetermined, which is the focus of this study.

METHODS: Cross-sectional study examining structural and functional features of the gut microbiome in PWH between men and women with a history of hazardous alcohol drinking recruited at St. Petersburg, Russia. 16S rDNA sequencing information was used for metataxonomic, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) and Linear Discriminant Analysis Effect Size (LEfSe) analyses. Group-wise comparisons were done using Mann-Whitney U-test. Further, linear and logistic regression models were used to evaluate the association between sex and measures of gut microbial dysbiosis and Firmicutes/Bacteroidota (F/B) ratio, respectively. Data were adjusted for confounding covariates particularly, HIV-viral load, Anti-retroviral Therapy (ART) and alcohol usage.

RESULTS: Metataxonomic analysis demonstrated that women depicted significantly higher microbial diversity (Operational Taxonomic Units, OTUs and Shannon Index), higher percent relative abundance (%RA) of Firmicutes, lower %RA of Bacteroidota and higher F/B ratio. Importantly, logistic regression revealed that women had twice the odds of having F/B ratio > 1. Notably, women demonstrated significantly higher %RA of butyrate-producing bacterial families, i.e., Lachnospiraceae, Oscillospiraceae, Rikenellaceae and Marinifilaceae and genera. Correspondingly, significantly greater expression of bacterial genes involved in butyrate synthesis in women was demonstrated by PICRUSt2 analysis. Additionally, women depicted lower %RA of pathobiont, Prevotellaceae particularly, Prevotella_9 genus.

CONCLUSION: Overall, we observed significant sex-based differences in the relative abundances of beneficial bacterial communities such as butyrate producers and potential pathogenic Prevotella community in the gut microbiome of PWH with a history of heavy alcohol consumption. The observed sex-based differences are clinically relevant and could inform therapeutic strategies with evidence-based probiotics.},
}

@article {pmid41356477,
year = {2025},
author = {Chakraborty, A and Roy, A and He, S and Castellano-Hinojosa, A and Asiegbu, FO and Coutinho, TA},
title = {Editorial: Forest microbiome: dynamics and interactions in the anthropocene era.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1729625},
pmid = {41356477},
issn = {1664-302X},
}

@article {pmid41356475,
year = {2025},
author = {Wang, L and Liu, W and Wang, L and Zhang, K and Li, D and Ji, J and Luo, J and Zhu, X and Cui, J and Gao, X},
title = {Cross-generational ripples: sublethal fipronil exposure alters Binodoxys communis microbiome without lethal consequences.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1637234},
pmid = {41356475},
issn = {1664-302X},
abstract = {INTRODUCTION: Fipronil, a broad-spectrum phenylpyrazole insecticide, demonstrates high efficacy against Aphis gossypii (cotton aphid). However, its potential effects on Binodoxys communis, a key natural enemy of A. gossypii, remain largely unexplored. This study comprehensively assessed the safety of fipronil for B. communis, with particular emphasis on sublethal effects and associated microbiome alterations.

METHODS: We evaluated the sublethal effects of fipronil on the development of B. communis across parental (F0) and offspring (F1) generations. Furthermore, the alterations in the microbial diversity and community structure of B. communis were analyzed using 16S rRNA sequencing. Functional prediction of the microbiota was performed via PICRUSt2.

RESULTS: Indirect fipronil exposure significantly prolonged larval development in the parental generation (F0, p = 0.017), while showing no statistically significant impact on the offspring generation (F1). 16S rRNA sequencing revealed apparent alterations in the microbial community. In adults, the dominant genus shifted from Akkermansia to Muribaculum after 1 h exposure, while the dominant phylum showed significantly reduced abundance after 3 d. In larvae, the major phylum (Proteobacteria) remained unchanged, but the major genus shifted from Brevitalea to Vicinamibacter. Functional prediction indicated that the predicted genes were predominantly enriched in metabolic pathways (75% of the functional repertoire).

DISCUSSION: These results suggest that fipronil exposure induces previously unrecognized sublethal effects on a key natural enemy insect, primarily by disrupting its symbiotic microbiota, which may play a major role in host metabolism. Our findings highlight the ecological risks of fipronil and emphasize the need for pesticide risk assessments that consider sublethal effects on beneficial insects and their microbiota.},
}

@article {pmid41356464,
year = {2025},
author = {Zhou, W and Huang, S and Huang, X},
title = {Editorial: Mutualistic and antagonistic interactions in the human oral microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1731807},
pmid = {41356464},
issn = {1664-302X},
}

@article {pmid41356350,
year = {2025},
author = {Adeosun, WB and Poswayo, SK and Parihar, SP and Loots, DT},
title = {The Functionality of the Cysteinyl Leukotriene Receptor 1 (CysLTR1) in the Lung by Metabolomics Analysis of Bronchoalveolar Lavage Fluid.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8052995/v1},
pmid = {41356350},
issn = {2693-5015},
abstract = {Introduction The cysteinyl leukotriene receptor 1 (CysLTR1) is known as a potent lipid mediator with a well-established role in inflammatory regulation and lung disease. While its involvement in immune cell recruitment has been previously reported, its broader impact on pulmonary metabolism remains poorly understood. Objectives The study aims to investigate the metabolic consequences of a CysLTR1 deletion in mice to elucidate its role in pulmonary metabolic homeostasis. Methods Bronchoalveolar lavage fluid (BALF) was collected from CysLTR1 knockout (KO) and wild-type (WT) mice and analysed using standardized untargeted gas chromatography-time-of-flight mass spectrometry (GC-TOFMS) metabolomics. Results Metabolomics analyses of the BALF collected from the CysLTR1 KO mice presented significantly reduced levels of glucose, glucosamine, and glyceric acid, indicating the role of the CysLTR in lung glucose uptake and consequently lung glycolysis and gluconeogenesis. This is further supported by reductions in myo-inositol and D-chiro-inositol, also supporting previous findings that this occurs due to insulin resistance. Consequential disruption of various glucose-dependent pathways, including the pentose phosphate pathway (reduced gluconic acid, sedoheptulose and xylose) and purine metabolism (reduced 1-methylinosine) indicates a consequential altered nucleotide turnover, and the significantly reduced concentrations of butanoic acid, decan-2-ol, and 1-hexadecanol, indicate changes to fatty acid metabolism in the lung, as a compensatory response to the initial glucose deficiency induced by the CysLTR1 KO. Lastly, the changes to mandelic acid, glutaric acid, tricarballylic acid, and decan-2-ol, furthermore, indicate the role of CysLTR1 in the composition/metabolism of the microbiome. Conclusion This study expands our knowledge on the role of CysLTR1 beyond its role in immune regulation, that may later serve towards a better understanding of CysLTR1 associated lung diseases and in the development of improved therapeutic strategies.},
}

@article {pmid41356328,
year = {2025},
author = {Mehravaran, S and Pop, M},
title = {Sequencing the ocular surface microbiome: a review of methodological practices and considerations.},
journal = {Frontiers in ophthalmology},
volume = {5},
number = {},
pages = {1660816},
pmid = {41356328},
issn = {2674-0826},
abstract = {PURPOSE: The human ocular surface microbiome (OSM) plays a vital role in ocular health, infection prevention, and immune modulation. However, use of sequencing technology for researching the OSM is challenged by low sample biomass, high sample variability, and methodological inconsistencies. This review systematically evaluates existing literature on OSM research, identifying methodological challenges and proposing standardization strategies to enhance data quality, comparability, and clinical relevance.

METHODS: A comprehensive analysis of peer-reviewed studies was conducted to assess methodologies used in sequencing-based OSM research, with focus on considerations in scope: sample size, selection, choice of eye, time frame, recruitment and enrollment criteria; sample collection and handling: sampling environment, topical anesthesia, sample collection tools and ocular region; sample preservation: temperature and use of buffers; and sample analysis: DNA extraction, quantification, and sequencing approach. Advantages and limitations of different approaches were identified, and best practices for standardization were explored.

RESULTS: This review identified substantial variations in sample collection and processing methodologies, many of which are known to impact OSM composition. However, the influence of certain approaches remains unclear. Additionally, large reporting gaps were observed, as many studies failed to describe critical methodological elements, including specific sample handling procedures and sequencing parameters.

CONCLUSIONS: While sequencing technologies offer valuable insights, our findings highlight the need for further investigation of different methodological approaches to determine best practices and establish standardized methodological protocols, as well as the need for standardized reporting protocols in OSM research. These standards are essential for enhancing data reliability and translating findings into clinical applications.},
}

@article {pmid41356285,
year = {2025},
author = {Karmazyn, M},
title = {Targeting Gut Microbiome Dysbiosis as a Potentially Effective Therapeutic Approach for the Treatment of Heart Failure.},
journal = {Reviews in cardiovascular medicine},
volume = {26},
number = {11},
pages = {47146},
pmid = {41356285},
issn = {2153-8174},
}

@article {pmid41356231,
year = {2025},
author = {Abou-Khalil, R},
title = {Nutritional Interventions for Enhancing Sleep Quality: The Role of Diet and Key Nutrients in Regulating Sleep Patterns and Disorders.},
journal = {Food science & nutrition},
volume = {13},
number = {12},
pages = {e71309},
pmid = {41356231},
issn = {2048-7177},
abstract = {Sleep disorders and poor sleep quality are increasingly recognized as global health concerns, with substantial consequences for mental and physical health. While pharmacological treatments are available, growing evidence suggests that nutritional interventions offer effective, sustainable alternatives for enhancing sleep quality. This review aims to synthesize current evidence on the impact of key nutrients, dietary patterns, bioactive compounds, and gut microbiome modulation on sleep regulation, and to explore emerging personalized nutrition approaches for managing sleep disorders. A comprehensive review of clinical trials, observational studies, and mechanistic research published over the past two decades was conducted. Key focus areas included sleep-supportive nutrients, dietary patterns (e.g., Mediterranean, ketogenic, plant-based diets), chrononutrition, gut-brain axis modulation, functional foods, and personalized nutrition strategies. Evidence supports the role of specific nutrients (e.g., magnesium, tryptophan, omega-3 fatty acids) and dietary patterns rich in anti-inflammatory and antioxidant compounds in improving sleep outcomes. Functional foods such as tart cherry juice and kiwifruit demonstrate potential benefits. The gut microbiome emerges as a significant regulator of sleep physiology, suggesting probiotics and prebiotics as novel interventions. Personalized nutrition approaches, incorporating genetic, metabolic, and lifestyle factors, offer promising individualized solutions. Nutritional interventions represent a promising, non-pharmacological strategy for improving sleep quality and managing sleep disorders. Future research should focus on personalized approaches and large-scale clinical trials to validate and refine these strategies for clinical practice.},
}

@article {pmid41355950,
year = {2026},
author = {Muhammad, S and Li, M and Jia, Q and Ijaz, M and Liang, S and Zeng, W and Chen, D and Zhang, Y and Du, X and Song, W and Guo, B},
title = {Advances in the engineering of living probiotics for cancer immunotherapy.},
journal = {Theranostics},
volume = {16},
number = {3},
pages = {1164-1226},
pmid = {41355950},
issn = {1838-7640},
mesh = {*Probiotics/administration & dosage/therapeutic use ; Humans ; *Neoplasms/therapy/immunology ; *Immunotherapy/methods ; Tumor Microenvironment/immunology ; Animals ; Bacteria/genetics ; Drug Delivery Systems/methods ; },
abstract = {The role of bacteria in tumor development has been increasingly recognized through advances in sequencing technologies, revealing their influence on the tumor microenvironment and immune system. Live bacterial therapy, known for its unique ability to target tumors, colonize cancerous tissues, and activate immune responses, is emerging as a novel approach to cancer treatment. To enhance the therapeutic efficacy and safety of this strategy, various engineering techniques have been developed to modify bacteria, enabling the creation of advanced bacteria-based drug delivery systems. Living probiotics can selectively colonize the tumor microenvironment, where they interact with immune cells to enhance antitumor responses. This review provides an overview of the complex relationship between bacteria and tumors and discusses engineering methods for bacterial modification, including physicochemical approaches and synthetic biology. It further highlights the applications of these strategies in enhancing cancer therapies. Finally, it examines the future opportunities for engineered bacteria in cancer therapy, focusing on the potential of combination therapies, personalized medicine, and the role of the microbiome in enhancing therapeutic outcomes. With ongoing advancements, engineered bacteria hold great promise for improving the efficacy and safety of cancer treatments, offering a new frontier in oncology.},
}

*Probiotics/administration & dosage/therapeutic use
Humans
*Neoplasms/therapy/immunology
*Immunotherapy/methods
Tumor Microenvironment/immunology
Animals
Bacteria/genetics
Drug Delivery Systems/methods

@article {pmid41355913,
year = {2025},
author = {Roganovic, J and Radosevic, M and Dordevic, A},
title = {Role of the gut microbiome in the development and prognosis of pediatric leukemia.},
journal = {World journal of clinical oncology},
volume = {16},
number = {11},
pages = {111419},
pmid = {41355913},
issn = {2218-4333},
abstract = {The gut microbiome plays a pivotal role in immune homeostasis and systemic inflammatory regulation, both of which are critically involved in the pathogenesis and progression of pediatric leukemias. Recent evidence reveals that children with leukemia often exhibit distinct gut microbiome profiles at diagnosis, marked by reduced microbial diversity and the enrichment of pro-inflammatory taxa such as Enterococcus and Streptococcus. This microbial dysbiosis may promote leukemogenesis by disrupting immune regulation and driving chronic inflammation. Chemotherapy significantly alters the gut microbiome, inducing dysbiosis characterized by a loss of beneficial commensals and the dominance of pathobionts. Specific microbial signatures, such as the enrichment of Bacteroides, correlate with reduced inflammation and improved prognosis, underscoring the gut microbiome's prognostic value. Emerging therapies, including dietary adjustments, probiotics, and fecal gut microbiome transplantation, aim to restore microbial balance and reduce treatment-related complications. Moreover, gut microbiome profiling shows potential for identifying biomarkers linked to leukemia predisposition, paving the way for early diagnosis and tailored preventive strategies. This mini-review explores recent advancements in understanding the influence of the gut microbiome on pediatric leukemias, emphasizing its role as both a therapeutic target and a prognostic biomarker. Integrating gut microbiome research into clinical practice may help optimize treatment outcomes and improve quality of life for children with leukemia.},
}

@article {pmid41355723,
year = {2025},
author = {Murphy, K and Gromisch, M and Connolly, J and Wang, T and McWalters, J and Atrio, J and Mahant, AM and Gera, S and Colanta, A and Cajigas, A and Kelly, L and Estrella, H and Gustafson, D and Minkoff, H and Anastos, K and Keller, MJ and Herold, BC},
title = {Impact of vaginal estradiol on the genitourinary syndrome of menopause, vaginal microbiome and mucosal immune mediators in women living with HIV.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciaf669},
pmid = {41355723},
issn = {1537-6591},
abstract = {BACKGROUND: Women with HIV (WWH) experience early onset menopause and symptoms may impact antiretroviral therapy (ART) adherence. Vaginal estradiol is safe and effective for treatment of the genitourinary syndrome of menopause (GSM) but has not been studied in WWH. The study objective was to test whether vaginal estradiol would improve GSM symptoms in menopausal WWH.

METHODS: Menopausal WWH were randomized 1:1 to 12-weeks of open-label vaginal estradiol (n=25) versus no treatment (n=26). Participants had at least one GSM vulvovaginal symptom in the month prior (dryness, itching, irritation, soreness, or dyspareunia) and clinical atrophy. The primary outcome was difference in mean symptom severity (scale 0-3) defined by the composite vaginal symptom index (VSI) between baseline and week 12. Changes in severity of participants' most bothersome symptom (MBS), vaginal maturation index (VMI), vaginal microbiome, and mucosal immune mediators were assessed. Results were compared by paired t-test or Wilcoxon signed rank tests; a mixed effect model examined differences in VSI improvement between groups.

RESULTS: Mean age was 59 years, 78% self-reported as Black, and all were on ART. Both groups had significant reductions in VSI, however the magnitude was significantly greater in the estradiol group (p<0.0001). Estradiol and younger age were associated with VSI improvement. VMI and MBS improved significantly only in the estradiol group. There were no significant changes in the microbiome or mucosal mediators.

CONCLUSIONS: The favorable response to estradiol suggests that treatment perhaps initiated earlier may be beneficial for GSM in WWH and should be studied in larger clinical trials.},
}

@article {pmid41355585,
year = {2026},
author = {Liu, Y and Wang, F and Zhou, Z and Xiao, Y and Zhang, Z and Lu, X and Yan, H and Yang, X and Lu, B},
title = {The Safety and Quality of Staple Root and Tuber Crops: A Review on Hazards, Detection Methods, and Mitigation Strategies.},
journal = {Comprehensive reviews in food science and food safety},
volume = {25},
number = {1},
pages = {e70353},
doi = {10.1111/1541-4337.70353},
pmid = {41355585},
issn = {1541-4337},
support = {//China Agriculture Research System of MOF and MARA/ ; //National Key Research and Development Program of China/ ; },
mesh = {*Plant Roots/chemistry ; *Crops, Agricultural/chemistry ; *Plant Tubers/chemistry ; *Food Safety ; Food Contamination/analysis/prevention & control ; Quality Control ; },
abstract = {Staple root and tuber crops (SRTCs), including potatoes, cassava, sweet potatoes, yams, and taros, play vital roles in global nutrition. However, they present significant safety hazards, which poses threats to human health, have garnered widespread public concern, and consequently constrain the further development and utilization of SRTCs. This review systematically examines recent advances in quality and safety control for SRTCs, with a particular focus on the progress and challenges in detection methods and mitigation strategies for the associated hazards. It further proposes the establishment of an integrated farm-to-fork quality control system for SRTCs. This review identifies shared hazard profiles (endogenous toxins, heavy metals, pesticides, mycotoxins, acrylamide, microplastics) across SRTCs and highlights key strategies for mitigation. Significant advancements in rapid detection technologies (sensors, immunoassays, spectral imaging) offer enhanced sensitivity and field applicability compared to traditional methods. Crucially, establishing an integrated farm-to-fork quality control system, incorporating genetic improvement, optimized cultivation/postharvest practices, and innovative processing, is essential for comprehensive hazard reduction. Future research priorities include multiomics approaches, rhizosphere microbiome engineering, and Industry 4.0 integration to further enhance SRTCs safety and utilization. Our work aims to enhance the safety and quality of SRTCs, thereby promoting their broader development and utilization.},
}

*Plant Roots/chemistry
*Crops, Agricultural/chemistry
*Plant Tubers/chemistry
*Food Safety
Food Contamination/analysis/prevention & control
Quality Control

@article {pmid41355544,
year = {2025},
author = {Chaudhary, V and Singh, AP and Sharma, H and Taumar, D},
title = {Next-Generation Probiotics in Allergy Therapy: Scientific Evidence and Clinical Applications.},
journal = {Anti-inflammatory & anti-allergy agents in medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715230407403251105101126},
pmid = {41355544},
issn = {1875-614X},
abstract = {The global increase in allergic diseases, such as atopic dermatitis, allergic rhinitis, asthma, and food allergies, has become a major public health issue. These diseases typically involve immune dysregulation, including a Th1/Th2 imbalance, increased IgE levels, regulatory T cell (Treg) dysfunction, and epithelial barrier dysfunction. New research has recognised an important role for the gut and mucosal microbiome in regulating immune responses and has prompted interest in the therapeutic utility of probiotics. Probiotics are live microbes that, when given in adequate amounts, confer health benefits, generally such as immunomodulation or restoration of gut barrier function. Traditional probiotics (i.e., Lactobacillus and Bifidobacterium species) reduce allergic inflammation through promotion of Treg differentiation, increases in antiinflammatory cytokines (e.g., IL-10), suppression of Th2 cytokines (e.g., IL-4), and modification of IFNγ. Traditional probiotics also support mucosal barrier function and restore microbial composition by producing short-chain fatty acids (SCFAs), like butyrate, which act directly on Gprotein- coupled receptors and histone deacetylases to suppress inflammation. Next-generation probiotics (NGPs), such as Akkermansia muciniphila, Faecalibacterium prausnitzii, Bacteroides fragilis, and some clusters of Clostridia, can provide more targeted effects. These NGPs can secrete anti-inflammatory metabolite compounds, such as polysaccharide A (PSA), which modulate dendritic cells and increase Treg activity, and can promote mucin production to improve gut barrier function. Overall, there are key issues with strain specificity, dose, safety in immunocompromised individuals, and possible regulatory classification issues. Future opportunities may include precision microbiome profiling, synthetic biology, and artificial intelligence-driven strain discovery to develop personalised approaches to allergy immunotherapy.},
}

@article {pmid41355462,
year = {2025},
author = {Morais-Almeida, M and Baptista-Pestana, R},
title = {Environmental factors influencing the microbiome in adult asthma: emerging mechanistic insights.},
journal = {Current opinion in allergy and clinical immunology},
volume = {},
number = {},
pages = {},
pmid = {41355462},
issn = {1473-6322},
abstract = {PURPOSE OF REVIEW: Asthma is a mosaic of phenotypes shaped by complex host-environment interactions. Among these, the microbiome has moved to a central determinant of disease expression, and airway and gut microbiome should be seen as active players in asthma pathophysiology. This review critically examines how environmental exposures, including pollution, drugs, diet, and climate, remodel microbial ecosystems, and reprogram immune responses in adults with asthma, with emphasis on clinical translation.

RECENT FINDINGS: Advances from multiomics, large-scale cohorts, and Mendelian randomization studies reinforce the concept of the gut-lung axis as a decisive modulator of asthma outcomes. Airway dysbiosis, often marked by Proteobacteria dominance, consistently correlates with poor asthma control, exacerbations, and steroid resistance. Environmental determinants of microbiome reshape erode immune tolerance. Microbial metabolites such as short-chain fatty acids act as molecular messengers capable of restoring epithelial and immune balance. These findings challenge the traditional inflammatory-centric view of asthma and demand broader mechanistic frameworks.

SUMMARY: The microbiome should be considered a central piece of the puzzle in asthma research. Precision medicine in adult asthma will remain aspirational unless microbiome-informed biomarkers and interventions are embraced. Robust interventional studies are urgently needed to translate this promise into practice.},
}

@article {pmid41355426,
year = {2026},
author = {Muhammad, A and Kong, X and Li, L and Khan, MHU and Jia, P and Miao, C and Zhang, Z},
title = {Melatonin Enhances Peanut Productivity by Enriching Root-Associated Nitrogen-Fixing Bacteria.},
journal = {Journal of pineal research},
volume = {78},
number = {1},
pages = {e70105},
doi = {10.1111/jpi.70105},
pmid = {41355426},
issn = {1600-079X},
support = {//This work was partially supported by the Key R&D and Promotion Projects of Henan Province (242102111094, 242102111148, 252102111077), the International Science and Technology Cooperation Project of Henan Province (242102521050), the Henan Province High-Talent Foreign Experts Introduction Plan (HNGD2024030), and the Henan Center of Outstanding Overseas Scientists (GZS2024018)./ ; },
mesh = {*Melatonin/pharmacology ; *Arachis/microbiology/drug effects/growth & development ; *Plant Roots/microbiology/drug effects ; *Nitrogen-Fixing Bacteria/drug effects ; Microbiota/drug effects ; Soil Microbiology ; Nitrogen Fixation/drug effects ; },
abstract = {Melatonin, a pleiotropic phytohormone, is widely recognized as a promising bio-stimulant, yet its integrative effects on root development, yield gain, and microbiome assembly in legumes remain underexplored. In this study, we investigated the effects of melatonin seed treatment across three peanut genotypes, focusing on plant productivity and the composition and structure of bacterial communities in root, rhizosphere, and bulk soil compartments. Melatonin treatment substantially improved root biomass, nodulation, nitrogen balance index, and yield-related traits, with the highest response observed in the genotype Xinbaihua 16. Amplicon sequencing revealed that melatonin induced distinct genotype and compartment specific shifts in bacterial community composition, with the root bacteria showing the increased remodeling, including a 45.9% increase in unique amplicon sequence variants (ASVs). Melatonin selectively enriched key Proteobacteria taxa such as Rhizobium, Sphingomonas, and Enterobacter hormaechei, known for their plant-growth promoting and biocontrol capabilities. Notably, melatonin-enriched taxa also included widely recognized nitrogen-fixing symbionts such as Pararhizobium and Ensifer, underscoring a direct link between melatonin-induced microbiome shifts and enhanced nitrogen acquisition capacity. Co-occurrence network analysis indicated that melatonin-treated roots harbored more complex bacterial networks, and Modules 3 and 4, dominated by melatonin-induced Proteobacteria, were strongly correlated with most plant traits. Collectively these findings highlight melatonin dual role as a bio-stimulant and microbiome modulator, promoting a functionally enriched and responsive bacteria that support enhanced plant performance. This study provides novel insights into the melatonin-mediated coordination of plant performance and bacterial assembly, offering a foundation for microbiome-informed crop improvement strategies.},
}

*Melatonin/pharmacology
*Arachis/microbiology/drug effects/growth & development
*Plant Roots/microbiology/drug effects
*Nitrogen-Fixing Bacteria/drug effects
Microbiota/drug effects
Soil Microbiology
Nitrogen Fixation/drug effects

@article {pmid41354993,
year = {2025},
author = {Zhang, W and Zhang, M and Xie, J and Huang, H and Schmitz-Esser, S and Li, W and Liu, H and Li, D},
title = {Dynamics of the gut microbiome and resistome in response to prophylactic antibiotic treatment in post-surgical giant pandas.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-25645-6},
pmid = {41354993},
issn = {2045-2322},
support = {2023NSFSC0011//Natural Science Foundation of Sichuan Province/ ; 2023NSFSC0011//Natural Science Foundation of Sichuan Province/ ; QD2023A46//Mianyang Teachers' College/ ; QD2023A46//Mianyang Teachers' College/ ; 2022 CPB-B09//the grants from the independent project of Chengdu Research Base of Giant Panda Breeding/ ; },
abstract = {For giant pandas, the ecological impact of prophylactic postoperative antibiotics on their gut microbial communities and resistome is not well characterized. Here, we assessed the impact of intravenous cefotaxime administration by analyzing longitudinal fecal samples from five giant pandas via 16 S rRNA sequencing (n = 304 samples) and shotgun metagenomics (n = 22 samples). 16 S-based analysis revealed that antibiotic exposure significantly altered bacterial community structure, resulting in a pronounced increase in the abundance of Pseudomonadota (from 50% ± 24% to 60% ± 38%; P < 0.001) and a reduction in Shannon diversity (from 2.8 ± 0.4 to 2.4 ± 1.3; P < 0.05). In contrast, metagenomic analysis indicated that cefotaxime exposure did not significantly increase the overall diversity of antimicrobial resistance genes (ARGs) or virulence factor genes (VFGs). However, we observed a marked expansion in the diversity of the CTX-M β-lactamase family (blaCTX-M), which persisted into the recovery phase. We also recovered 10 metagenome-assembled genomes (MAGs) harboring both ARGs and VFGs, identifying them as potential antibiotic-resistant pathogens (ARPs). Their abundance, however, remained unchanged throughout treatment. These findings provide new insights into the effects of short-term antibiotic exposure in giant pandas, highlighting its transient effect on microbial community structure and a limited effect on resistome diversity.},
}

@article {pmid41354859,
year = {2025},
author = {Robas-Mora, M and Fernández-Pastrana, VM and González-Reguero, D and Probanza, A and Jiménez-Gómez, PA},
title = {Effect of PGPB-enriched organic fertilizer ORGAON[®]PK on the rhizospheric microbiota and biomass of Lupinus albus (L.): a sustainable alternative to chemical fertilizer.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00827-x},
pmid = {41354859},
issn = {2524-6372},
support = {TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; TED2021-132285A-I00//European Union NextGenerationEU/PRTR/ ; },
abstract = {The intensive use of agrochemicals is essential to maintain crop yields, but it has led to overexploitation of land and environmental deterioration. To promote more sustainable agriculture, this study evaluates the novel effects of biofertilizers enriched with plant growth promoting bacteria, such as Bacillus pretiosus and Pseudomonas agronomica, on Lupinus albus var. Orden Dorado, to improve the rhizospheric soil health and plant biomass as well as reducing dependence on chemical fertilizers. The organic matrix ORGAON[®]PK and its sterilized version, both derived from horticultural waste, were tested compared with a traditional chemical fertilizer and a water control. After three months of treatment, metagenomic analyses (16 S rRNA gene amplicons) indicated that the strains remained in the rhizosphere, increasing metabolic diversity without altering the microbial structure (Shannon index). In addition, a significant reduction in the minimum inhibitory concentration against clinical antibiotics (p < 0.05) was observed, highlighting the potential of biofertilizers to decrease microbial resistance in the soil. Principal component analysis showed clear differences between treated and control groups, and ANCOM-BC revealed changes in non-culturable bacteria. Biometric analyses revealed increases of 70-88% in shoot weight, ~ 80% in total biomass, and up to 36% in shoot elongation compared with the control. Biofertilizers improved nutritional quality and plant biomass, suggesting their potential as a sustainable and efficient alternative to the use of chemical fertilizers.},
}

@article {pmid41354833,
year = {2025},
author = {M'Bra, PEH and Suárez-Uribe, I and Avino, M and Ng Kwan Lim, E and Mayhue, M and Balthazar, P and Aumont, A and Prévost, K and Massé, E and Fernandes, KJL},
title = {Medium-chain triglycerides and ketogenic diet prevent alterations of the gut microbiome in transgenic Alzheimer's disease mice.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09171-9},
pmid = {41354833},
issn = {2399-3642},
abstract = {The systemic mechanisms underlying the benefits of ketogenic interventions on cognition in Alzheimer's disease (AD) are understudied. Interventions involving a carbohydrate-free high-fat ketogenic diet (KD) or dietary supplementation with medium-chain triglycerides (MCT) both improve cognition in AD mouse models, yet with opposing effects on circulating ketones levels, peripheral insulin sensitivity and inflammation. Since the gut microbiome regulates systemic metabolism and inflammation and is altered by aging and disease, we investigated how it is affected in mice subjected to MCT and KD. At early stages of pathology, AD mice exhibited substantially reduced richness and distinct composition of gut microbiome species. Administration of MCT or KD for 1-month increased microbiome diversity, restoring the levels of more than 50% of the bacteria altered in AD mice and inducing novel alterations. Both diets increased levels of short-chain fatty acid-producing bacteria, such as Lachnospiraceae, which directly correlated with improved hippocampal dendritic spine density. Interestingly, longer term administration of KD increased the obesity-associated Firmicutes/Bacteroidota ratio and bodyweight in AD but not WT mice, suggesting that AD-associated metabolic defects should be considered when designing such intervention. We conclude that MCT and KD may influence AD central and peripheral defects in part via modulation of the gut microbiome.},
}

@article {pmid41354809,
year = {2025},
author = {Ma, X and Qu, L and Wu, Q and Yu, Q and Lin, Z and Yang, Y and Zhou, X},
title = {Advances in ovarian cancer: biological insights, therapeutic innovations, and future perspectives.},
journal = {Journal of ovarian research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13048-025-01921-x},
pmid = {41354809},
issn = {1757-2215},
support = {No.82160552//the National Natural Science Foundation of China/ ; 2024B001//the Health Commission of Jilin Province/ ; 202501-202912//the transverse project/ ; },
abstract = {Ovarian cancer (OC) remains a highly lethal gynecologic malignancy characterized by substantial molecular heterogeneity and diagnostic challenges. Although many reviews examine specific aspects of OC biology or treatment, few attempt to connect recent findings into a broader and coherent picture. This review provides an integrated and forward-looking synthesis of emerging mechanisms and therapeutic trends in OC, understanding OC progression and therapeutic resistance. Unique contributions of this review include providing a unified interpretation of emerging multi-omics evidence that reshapes the biological understanding of individual OC histotypes, delineating key metabolic dependencies such as glutamine addiction, aberrant lipid remodeling, glycolytic plasticity and purine pathway rewiring as potential therapeutic entry points, and elucidating how ascites-driven immune dysfunction remodels antitumor immunity to ultimately influence the effectiveness of cancer vaccines, immune checkpoint blockade and adoptive cell transfer therapies. Additionally, the review articulates underexplored therapeutic intersections, including nanotechnology-enhanced immunotherapy, gene-editing nanocarriers, and microbiome-mediated modulation of drug sensitivity and immune activation. By integrating these diverse yet interconnected domains, this review proposes updated conceptual models and cross-therapeutic strategies aimed at overcoming chemoresistance and advancing precision, personalized treatment paradigms in OC.},
}

@article {pmid41354765,
year = {2025},
author = {Su, H and Han, P and Yan, H and Wu, C and Zeng, S and Zhang, P and Wang, Z and Dong, J and Liang, M and Jing, H and Zhang, D and Yang, C and Xie, N and Liu, X and Weng, S and Dong, G and He, J},
title = {Age-dependent patterns of the gut microbiome, antibiotic resistome, and pathogenicity in captive koalas (Phascolarctos cinereus).},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09302-2},
pmid = {41354765},
issn = {2399-3642},
abstract = {Gut microbiome has a profound influence on koalas' health. Yet, the relationships among the gut bacteriome, virome, antibiotic resistome, and pathogenicity throughout different stages in koala's life remain elusive. Here, we presented a metagenome-resolved survey of gut microbiome utilizing 75 fecal samples from three groups of captive koalas. The diversity of bacteriome and virome were age-dependent, predominating in adult koalas. Lytic viruses increased with age as lysogenic viruses and bacterial hosts declined, and virus-to-microbe ratios rose, revealing concomitant age-related shifts in microbial communities, though causality remains unresolved. Antibiotic resistance genes (ARGs) were more prevalent in young koalas, unlike in humans, where they accumulate with age. Two ARG-carrying pathogens, Klebsiella pneumoniae and Escherichia coli, were identified and cultured, with K. pneumoniae and E. coli predominating in young koalas. One age-dependent lytic virus infecting K. pneumoniae only detected in young koalas, and two lysogenic viruses infecting E. coli identified the in young and adult koalas. Analyses showed a positive correlation between mobile genetic elements (MGEs) and virulence factors (VFs), which facilitated the widespread dissemination of VFs and impacted health. Collectively, this study advances the understanding of gut microbiome in health, providing solutions to the treatment and management of captive koalas.},
}

@article {pmid41354761,
year = {2025},
author = {Al Amaz, S and Poudel, S and Haque, MA and Jha, R and Mishra, B},
title = {Embryonic thermal manipulation improved early cecal microbial diversity, metabolic pathways, and immunity in broiler chickens.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31445-9},
pmid = {41354761},
issn = {2045-2322},
abstract = {Gut microbiota regulates broilers' gastrointestinal functions, digestion, metabolism, and immune responses. Modulating the microbiota in the early stage could present a promising approach for the poultry industry. Embryonic thermal manipulation (TM) constitutes a promising strategy for sustainable broiler production. Our previous research has yielded significant insights into the impact of TM on embryonic thermotolerance, metabolism, post-hatch growth performance, microbial diversity, and immunity. This follow-up study utilized a subset of birds from our previous study to investigate the effects of TM on early cecal microbiota composition, predicted metabolic pathways, and ileum immunity-related genes. A total of 600 fertile Cobb 500 eggs were incubated for 21 d. After candling, 238 eggs underwent TM at 38.5 °C with 55% relative humidity (RH) from embryonic day (ED) 12 to 18, then were transferred to a hatcher at 37.5 °C from ED 19 to 21, while 236 eggs were incubated at 37.5 °C throughout until 21 d. After hatching, 60-day-old unsexed chicks were housed in 12 pens (10 birds/pen, 6 replicates per treatment). The treatments included 1) Control and 2) TM. All birds were raised under standard conditions (22-24 °C) for the first 21 d. This study evaluated the effects of embryonic TM on four parameters: the composition of cecal microbiota (relative abundance at multiple taxonomic levels), microbial diversity indices (both alpha and beta diversity), predicted microbial metabolic pathways, and the expression of ileal immune-related genes on days 7, 14, and 21. TM significantly increased (P < 0.05) microbial beta diversity (Bray-Curtis, Jaccard and, unweighted UniFrac) and metabolic microbial pathways at days 7, 14, and 21. In the ileum, at d 7, the mRNA expression of IL10, IL12, IL18, TLR1, TLR2A, TLR4, TLR21, TBK1, TGFb, TGFb3, IFNg, NFkB, and CD3 was significantly lower (P < 0.05) in the TM group compared to the Control group. There was no significant difference (P < 0.05) between the treatment groups at d 14. However, at d 21, IL4, IL6, AvBD6, and IFNg were significantly lower (P < 0.05), and TLR2A and TGFb3 expression were significantly higher (P < 0.05) in the TM group compared to the Control group. Embryonic TM significantly increased cecal microbial diversity and predicted metabolic pathways, thereby improving ileum immunity in the early stages of life in broiler chickens.},
}

@article {pmid41354674,
year = {2025},
author = {Yang, S and Deng, W and Yang, T and Liu, C and Li, C and Li, G and Wei, R and Li, D and Huang, Y and Zhao, K and Zou, L},
title = {Enriched Streptococcus alactolyticus in non-cub giant panda gut contributes to the regulation of tryptophan and its neuromodulatory derivatives.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00879-4},
pmid = {41354674},
issn = {2055-5008},
support = {031-2222996053//the Scientific Research Foundation from Sichuan Agricultural University/ ; The Giant Panda Microbiome Research and Biobank Establishment//the International Cooperation Funding Project for Giant Pandas/ ; },
abstract = {Despite feeding on a high-lignocellulose bamboo diet, the giant panda (Ailuropoda melanoleuca) retains a typical gut microbiome of Carnivora. We conducted shotgun metagenomic sequencing and functional validation of the giant panda's gut microbiome to elucidate its physiological roles and explore its functional adaptation to the species' specialized diet. Our results revealed that Streptococcus alactolyticus significantly increased in the guts of subadult, adult, and elderly individuals versus that in cubs. The gut microbiome of these non-cub giant pandas was significantly enriched in pathways and modules associated with tryptophan biosynthesis. Whole-genome sequencing and in vitro fermentation of S. alactolyticus demonstrated its ability to biosynthesize tryptophan. Gavage of S. alactolyticus in mice led to the enrichment of aromatic amino acid metabolism pathways in gut microbiome, accompanied by significantly elevated levels of 5-hydroxyindole acetic acid and kynurenine in fecal and/or serum samples (p < 0.05). Transcriptome sequencing of colons from mice revealed that most significant upregulated Gene Ontology (GO) terms mainly were related to spindle checkpoint signaling and chromosome segregation, while most significant downregulated GO terms mainly involved synaptic functional regulation. These findings suggest that S. alactolyticus enriched in the non-cub giant panda gut can regulate tryptophan, influencing host gut physiology via tryptophan metabolites.},
}

@article {pmid41354580,
year = {2025},
author = {Facchin, S and Calgaro, M and Pandolfo, M and Buda, A and Barberio, B and Zingone, F and Vitulo, N and Savarino, EV},
title = {Impact of oral butyrate on clinical and biochemical parameters in IBD: A randomized placebo-controlled study targeting gut microbiota.},
journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.dld.2025.11.014},
pmid = {41354580},
issn = {1878-3562},
abstract = {BACKGROUND AND AIMS: We performed a randomized, double-blind, placebo-controlled, trial to investigate the changes in microbiome composition induced by Butyrate-Lsc-Microincapsulated (BLM) supplementation in IBD patients and its impact on disease activity.

METHODS: 140 IBD patients (n=60 Crohn's disease, CD and n=80 Ulcerative Colitis, UC) were randomized to oral administration of BLM, plus conventional therapy. Stool samples were assessed by 16S sequencing and fecal calprotectin (fCal) analysis. For the microbiota analysis, the Firmicutes/Bacteroidota (F/B) ratio was used. Clinical disease activity was assessed by using the Harvey-Bradshaw-Index (HBI) for CD and partial-Mayo-Score for UC, Quality-of-life (QoL) by using Inflammatory-Bowel-Disease-Questionnaire-32 (IBDQ) and adherence-dietary-recommendation was evaluated before and after supplementation RESULTS: microbiota analysis revealed two principal enterotypes, defined by the F/B ratio, in both CD and UC patients. BLM exerted a more pronounced effect on Enterotype 1 (low F/B ratio), resulting in greater clinical and biochemical improvements and potentially identifying a target population. After supplementation, clinical disease activity (p=0.013) and fCal (p=0.047) improved significantly in CD, while fCal showed a marginal reduction in UC (p=0.09). QoL increased significantly in both CD (p<0.001) and UC (p=0.003).

CONCLUSIONS: Supplementation with BLM, by modulating the gut microbiota, significantly improved disease outcomes and QoL in patients with IBD.

GOV REGISTRATION: NCT04879914.},
}

@article {pmid41354563,
year = {2025},
author = {John, NM and Ashok, B and John, O and V, K and Abraham, D and Samuel, P and Sudhakar, Y and Srai, SKS and Jacob, M},
title = {Daily oral iron supplementation produced greater improvements in hematological parameters than alternate day doses - A pilot double-blind randomized control trial in iron-deficient young women.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnu.2025.11.005},
pmid = {41354563},
issn = {1532-1983},
abstract = {BACKGROUND AND AIMS: There is little universal consensus on the optimal regime for oral iron supplementation to treat iron deficiency (ID) and iron-deficiency anemia (IDA) in women of reproductive age (WRA). A few studies in a high-income country have reported higher fractional absorption from oral iron supplements (OIS) given on alternate days than daily doses; however, there were no significant improvements in hematological indices in the women in these studies who received the alternate-day doses. There are also concerns about adverse gastrointestinal effects resulting from daily OIS. Data on these aspects from low and middle-income countries (LMIC), where the burden of IDA is high, are limited.

METHODS: We conducted a double-blinded, parallel-arm, non-inferiority, randomized controlled trial in non-pregnant WRA aged 18-45 years with ID (serum ferritin <20 μg/L) (CTRI/2020/03/024144). They were randomized to receive either 60 mg elemental iron daily (n = 30) or 120 mg elemental iron on alternate days (n = 30) for 14 days. The primary outcome was to determine the comparative effectiveness of daily versus alternate-day OIS in improving hematological and iron-related parameters in blood, at the end of the intervention. Secondary outcomes included extent of adherence to intervention, adverse events experienced, and changes in fecal calprotectin concentrations (a marker of gut inflammation) and the gut microbiome profile.

RESULTS: Adherence to the regimes was excellent (≥90 %) in both arms. Both regimes significantly improved hematological and iron-related parameters in blood at the end of 14 days. Daily OIS resulted in greater increases in mean corpuscular volume (fL) [1.25 (0.25, 2.32) vs. 0.50 (-0.35, 1.42); p = 0.043], mean corpuscular hemoglobin (pg/cell) [0.52 (0.54) vs. 0.17 (0.56); p = 0.019], and reticulocyte counts (%) [0.32 (0.13, 0.75) vs. 0.27 (0.02, 0.45); p = 0.055] than alternate-day doses. There were no significant differences between the groups in extent of improvements in iron-related parameters, incidence of adverse effects, and effects on gut inflammation and microbiome profile.

CONCLUSION: In iron-deficient WRA in an LMIC setting, daily OIS (60 mg) for 14 days was more effective than equivalent amounts on alternate days in improving hematological parameters.},
}

@article {pmid41354394,
year = {2025},
author = {Ravishankar, S and Ekambaram, B and Boopathi, N and Sakthivel, SR and Christan, M},
title = {Tryptophan-Steroid Interactions in the Brain-Gut-Microbiome Axis: Neuroactive Metabolites as Biomarkers and Therapeutic Targets.},
journal = {The Journal of steroid biochemistry and molecular biology},
volume = {},
number = {},
pages = {106908},
doi = {10.1016/j.jsbmb.2025.106908},
pmid = {41354394},
issn = {1879-1220},
abstract = {Tryptophan metabolism plays a central role in connecting the brain, gut, and microbiome. Microbial and host-derived metabolites influence intestinal integrity, immune activity, and neural signaling, while steroid and neurosteroid hormones shape these pathways through receptor-mediated effects. Disturbance of this metabolic network contributes to neuropsychiatric, metabolic, and inflammatory disorders. This review integrates evidence from preclinical and clinical studies to explain how tryptophan catabolism interacts with microbial activity and steroid regulation. Key neuroactive metabolites involved in these interactions are discussed, along with their potential value as biomarkers and therapeutic targets. Current limitations of animal models and the need for human-focused, multi-omics approaches are also highlighted. Together, these insights outline how coordinated tryptophan-steroid-microbiome signalling influences health and disease and identify opportunities for more precise diagnostic and therapeutic strategies.},
}

@article {pmid41354355,
year = {2025},
author = {Sarkar, D and Roy, P and Saha, S},
title = {Meta-analysis of faecal microbiome studies followed by machine learning to identify intestinal disease-specific taxonomic signatures.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108221},
doi = {10.1016/j.micpath.2025.108221},
pmid = {41354355},
issn = {1096-1208},
abstract = {Alterations in the gut microbiome have been found to be associated with both inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS), suggesting that interaction with the microbiota might drive pathogenesis. Identifying microbial profiles for IBS and IBD will help in the development of treatment strategies tailored to each illness, particularly when coexisting symptoms make clinical management difficult. In this study a meta-analysis approach followed by machine learning was used for elucidating the differences in microbial composition and community dynamics in IBS and IBD respectively. Machine learning models developed using Random Forest classifier was able to achieve an accuracy of 98% on training data and 100% on blind dataset, and the distinctive role of Pseudomonas-associated microbial network, which also includes Streptococcus, Stenotrophomonas, Actinomyces and Intestinibacter, was clearly observed in IBS.},
}

@article {pmid41354242,
year = {2025},
author = {Pang, Y and Kang, R and Shen, Z and Luo, L and Yu, S and Liu, F and Zhang, J and Shen, Q},
title = {Self-lytic Nano-bacterial biohybrid reprograms Intratumoral microbiome-immune interactions for cancer immunotherapy.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {114511},
doi = {10.1016/j.jconrel.2025.114511},
pmid = {41354242},
issn = {1873-4995},
abstract = {Despite significant advances in cancer immunotherapy, therapeutic outcomes remain limited by the dynamic interactions between the microbiome and immune cells in the tumor microenvironment (TME). In particular, Fusobacterium nucleatum (Fn) poses a significant barrier by suppressing the function of immune cells, such as natural killer (NK) cells. Here, we developed a nano-bacterial biohybrid system, LYC@Bac, which integrates IL-15-expressing probiotics (Bac) and pH-sensitive lysozyme nanoparticles (LYC). This system targets the microbiome and immune cells in the TME through simultaneous elimination of Fn and activation of NK cells, thereby potentiating cancer immunotherapy. Briefly, the acidic TME triggers lysozyme release via pH-labile imine bonds, lysing Fn to alleviate immunosuppression and releasing PAMPs that activate dendritic cells. Concurrently, Bac lysed by lysozyme releases IL-15, which subsequently activates the mTOR pathway in NK cells, upregulating NKG2D expression and enhancing granzyme and perforin secretion. This process augments the antitumor immunity of NK cells while concurrently enhancing their antibacterial function, leading to intensified clearance of Fn and further alleviation of immunosuppression, thereby creating a positive feedback loop. The LYC@Bac biohybrid offers a precise strategy to modulate intratumoral microbiome-immune cell interactions, providing a promising approach for enhanced cancer immunotherapy.},
}

@article {pmid41282164,
year = {2025},
author = {Gavini, C and Raux, L and Labouèbe, G and Gornick, E and Hugh, SM and Elshareif, N and Calcutt, N and Summa, PD and Gorostidi, F and Vonaesch, P and Mansuy-Aubert, V},
title = {Dietary Fiber Improves Somatosensory Function in Western Diet-Fed Mice by Remodeling Adipose Immune Cells via FFAR2 Signaling.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {41282164},
issn = {2693-5015},
abstract = {Westernized diets (WDs)-high in fat and sugar and low in fiber-produce somatosensory deficits, chronic pain, and neuropathy, yet the mechanisms linking diet to peripheral nervous system (PNS) pathology remain incompletely defined. Emerging evidence implicates gut-derived metabolites in sensory homeostasis; for example, fecal microbiota transplantation (FMT) from lean donors to WD fed mice reduces hypersensitivity and attenuates PNS inflammation, although FMT outcomes are variable. We therefore tested whether targeted modulation of the gut microbiota with fermentable complex carbohydrates could reproducibly improve somatosensory function in WD-fed mice. Using an integrated pipeline-behavioral and physiological assays, peripheral nerve electrophysiology, and molecular and immune profiling-we show that short-chain fatty acids (SCFAs) generated by fermentation remodel adipose tissue depots and act via the SCFA receptor FFAR2 (GPR43) to ameliorate sensory deficits. These findings identify a microbiota-SCFA-FFAR2 axis that couples dietary fiber to PNS function and provide a tractable alternative to FMT for mitigating WD-associated sensory neuropathy.},
}

@article {pmid41354223,
year = {2025},
author = {Adhikary, P and Maddheshiya, A and Takkar, B and Das, T and Mukherjee, S},
title = {Differential gut microbiome profiles in diabetic retinopathy: A comparative study across continental populations.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {113043},
doi = {10.1016/j.diabres.2025.113043},
pmid = {41354223},
issn = {1872-8227},
abstract = {Gut dysbiosis damages gut barrier, stimulates inflammation, endotoxemia, and breakdown of blood-retina barrier, promoting diabetic retinopathy (DR). Most microbiome studies on DR relied on 16S rRNA gene sequencing, documenting altered microbial richness, diversity, and shifts in dominant phyla and genera, though these findings remain inconsistent across populations. The only shotgun metagenomic study to date identified species Eubacterium hallii, Firmicutes bacterium and Alistipes finegoldii enriched in DR, with altered metabolic pathways. The β-diversity showed distinct inter-individual variations in diseased individuals compared to healthy controls (HC). The objective of this narrative review is to highlight the key microbial biomarkers, metabolic pathways, and putative microbiota-gut-retina axis integrating both 16S rRNA and shotgun data to compare microbial alterations across HC, T2DM, and DR. The review concludes with a comprehensive understanding of dysbiotic gut taxa associated with DM and DR in different populations showing wide variability in results mostly due to small sample size, geography, antidiabetic medications, lack of demographic and clinical data and limited taxonomic classification by 16S sequencing. This emphasizes the need of a large scale, multi-ethnic shotgun metagenomic sequencing study with systematically collected medical data and dietary information to understand the contributions of gut microbiome in the progression of DR.},
}

@article {pmid41353837,
year = {2025},
author = {Liu, Y and Feng, Z and Zhu, D and Zhu, D and He, B and Yu, K and Zhu, DZ and Yao, Z},
title = {Microbial exchange and potential pathogen transmission between diverse habitats within urban park ecosystems.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140676},
doi = {10.1016/j.jhazmat.2025.140676},
pmid = {41353837},
issn = {1873-3336},
abstract = {Urban parks serve as essential ecological networks that support both human and environmental health. However, the interconnection of microbial communities across their multi-habitat interfaces, along with their associated potential biosafety risks, remains insufficiently explored. To address the described knowledge gap, the study conducted a comprehensive microbiome analysis across the air, plant, soil, fauna, and water continuum of a representative urban park using 16S rRNA amplicon sequencing and whole-genome sequencing (WGS). The analysis identified 189 potential zoonotic pathogens shared among all examined habitats. Furthermore, microbial source tracking analysis indicated that the phyllosphere demonstrated strong connectivity with adjacent environments, serving as a central node for microbial exchange within the urban park ecosystem. WGS analyses revealed that the cross-habitat culturable strains (Bacillus altitudinis 41KF2b and Priestia aryabhattai B8W22) possessed a wide spectrum of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), including rank I high-risk ARGs, such as bacA. The phyllosphere of Ophiopogon bodinieri demonstrated extensive microbial exchange with the air, contributing 61.39 % to the airborne microbial community, while its cultural microorganisms harbored elevated cellular copy numbers of ARGs and VFGs. Concurrently, two cross-habitat strains isolated from air displayed the co-localization of ARGs with mobile genetic elements (MGEs), indicating that the phyllosphere-air interface may represent both a potential microbial safety risk and a pathway for ARG dissemination. The current study emphasized the migration-driven dispersal of microbes, pathogens, and ARGs/VFGs in urban parks, offering novel insights into urban ecosystem risk dynamics and providing a scientific basis for incorporating the "One Health" approach into landscape and urban planning.},
}

@article {pmid41353817,
year = {2025},
author = {McDowall, LS and Collado, A and Clarkson, R and Reiss, G and McDermott, K},
title = {Investigating safety aspects of using insect farming to reduce pig and chicken wastes at semi-commercial and lab-scale.},
journal = {Waste management (New York, N.Y.)},
volume = {211},
number = {},
pages = {115278},
doi = {10.1016/j.wasman.2025.115278},
pmid = {41353817},
issn = {1879-2456},
abstract = {Increasing global demand for food is driving the need to reduce wastes produced by agriculture to minimise environmental impacts. Black Soldier Fly, Hermetia illucens, can reduce livestock wastes, but research into the safety and scalability of the system is required. Insect bioconversion concerns include potential bioaccumulation of pathogens, antimicrobial resistance genes and heavy metals in larvae and substrates. Here, a semi-commercial-sized insect rearing facility was used to rear larvae on pig slurry, alongside a lab-based experiment using chicken manure. Larval microbiome composition was impacted by substrate, with increased Clostridia in larvae reared on slurry and manure. Pathogens largely decreased in the larvae from starting levels. Both slurry and manure substrates showed time-related changes regardless of insect presence or absence except for E. coli in chicken manure which was reduced in substrates with larvae added (-2.840 LFC vs -1.168 LFC; p<0.05), suggesting that time-associated alterations in the substrate could be more significant than larval presence. Antimicrobial resistance gene changes were dependent on the substrate and gene, with increases found for tetM in chicken manure after larval bioconversion (9.000 vs 10.370 LFC; p<0.001), and for sul2 in larvae reared on chicken manure (3.509 vs -0.985 LFC; p=0.001). In pig slurry-reared larvae, tetM decreased (-1.578 LFC; p<0.001) but there was no difference in sul2. Heavy metal contents generally met permissible standards for animal feed and organic fertilizers. However, there was some non-significant evidence for bioaccumulation of cadmium in slurry-reared larvae 0.18 to 0.70 mg/kg) compared to starter larvae (0.25mg/kg) requiring further study.},
}

@article {pmid41353545,
year = {2025},
author = {Briggs, P and Trimmell, L and Stiemsma, LT and Monzón, J},
title = {Sexual and regional differences in the microbiome and functional metagenome of the lone star tick, Amblyomma americanum.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-025-00498-6},
pmid = {41353545},
issn = {2524-4671},
}

@article {pmid41353361,
year = {2025},
author = {France, MT and Chaudry, I and Rutt, L and Quain, M and Shirtliff, B and McComb, E and Maros, A and Alizadeh, M and Hussain, FA and Elovitz, MA and Relman, DA and Rahman, A and Brotman, RM and Price, JT and Kassaro, MP and Holm, JB and Ma, B and Ravel, J},
title = {VIRGO2: an enhanced gene catalog of the vaginal microbiome provides insights into its functional and ecology complexity.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67136-2},
pmid = {41353361},
issn = {2041-1723},
support = {UH2AI083264//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; T32AI162579//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; OPP1189217//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; INV048956//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; INV048982//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; },
abstract = {Despite the importance of the cervicovaginal microbiome, the mechanisms that govern its composition and drive its impact on host physiology remain poorly understood. With the aim to expand our understanding of the function and ecology of the vaginal microbiome, we present VIRGO2, an enhanced non-redundant gene catalog comprising over 1.7 million well-annotated genes from body-site specific microbes and viruses. Analyses using VIRGO2 reveal insights such as including the identification of previously uncharacterized vaginal bacteria, features of the vaginal mycobiome and phageome, and differential expression of bacterial carbohydrate catabolic genes. Constructed from over 2500 metagenomes and 4000 bacterial genomes, VIRGO2 broadens geographic representation and microbial diversity compared to its predecessor. This updated catalog enables more precise profiling of taxonomic and functional composition from metagenomic and metatranscriptomic datasets. VIRGO2 is a critical resource for integrative analyses of vaginal microbial communities and their interactions with host tissues, thereby enhancing our mechanistic understanding of vaginal health and disease.},
}

@article {pmid41353355,
year = {2025},
author = {Todorović, I and Abrouk, D and Kyselková, M and Rey, M and López-Mondéjar, R and Raičević, V and Jovičić-Petrović, J and Moënne-Loccoz, Y and Muller, D},
title = {Fluorescent Pseudomonas spp. from suppressive and conducive soils share genomic and functional traits relevant to Fusarium graminearum disease suppression.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-025-12374-3},
pmid = {41353355},
issn = {1471-2164},
support = {grant numbers 670-00-573/1/372/2019-04, 670-00-2590/1/304/2020-04, 670-00-2551/1/298/2021-04 and 670-00-1/1/317/2022-01//Ministry of Youth and Sports, Belgrade, Serbia/ ; grant numbers 964308G, 972203C and 103939T//Campus France/ ; PHC DANUBE 2020: 45296XM//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; Ministry of Education, Youth and Sports of the Czech Republic, project number 8X20052//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; Ministry of Education, Youth and Sports of the Czech Republic, project number 8X20052//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; The Ministry of Education, Science, and Technological Development of the Republic of Serbia, project number: 451-03-01086/2020-09/07//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; PHC DANUBE 2020: 45296XM//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; PHC DANUBE 2020: 45296XM//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; SuppressSOIL ANR-19-EBI3-0007//BiodivERsA3 ERA-Net COFUND programme/ ; SuppressSOIL ANR-19-EBI3-0007//BiodivERsA3 ERA-Net COFUND programme/ ; SuppressSOIL ANR-19-EBI3-0007//BiodivERsA3 ERA-Net COFUND programme/ ; SuppressSOIL ANR-19-EBI3-0007//BiodivERsA3 ERA-Net COFUND programme/ ; project number CZ.02.01.01/00/22_008/0004635//the Ministry of Education, Youth and Sports of the Czech Republic/ ; The Ministry of Education, Science, and Technological Development of the Republic of Serbia, project number: 451-03-01086/2020-09/07//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region, The Ministry of Education/ ; grant number 451-03-137/2025-03/200116//The Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; },
abstract = {BACKGROUND: Soils suppressive to fungal pathogens harbor microbiomes that can inhibit disease development despite the presence of virulent pathogens and susceptible hosts. Fluorescent Pseudomonas are often implicated in such suppressiveness, but their genomic determinants and distribution in suppressive vs. non-suppressive (i.e., conducive) soils remain unclear.

RESULTS: We investigated the taxonomic and functional diversity of Pseudomonas populations from wheat rhizospheres in four agricultural soils with contrasting suppressiveness to Fusarium graminearum-induced seedling disease. rpoD-based metabarcoding and culture-dependent isolation revealed distinct Pseudomonas community structures linked to soil suppressiveness. However, major phylogenetic groups were shared across soils. From 406 isolates, 29 representative strains spanning seven subgroups of the P. fluorescens group were selected for whole-genome sequencing. Comparative genomics revealed 14 putative novel Pseudomonas genomospecies (dDDH < 70% with closest described type strains). Genomic screening revealed wide distribution of genes linked to biocontrol and plant-growth promotion, including siderophore biosynthesis, hormone modulation, phosphate solubilization, and production of antimicrobial compounds. Biosynthetic genes for phenazine and pyrrolnitrin were detected exclusively in P. chlororaphis strains isolated from suppressive soils, and rpoD alleles corresponding to these strains were not found in conducive soils within our metabarcoding dataset. Other traits such as hydrogen cyanide, ACC deaminase, and auxin biosynthesis were broadly distributed across isolates from all soils. Functional assays demonstrated variable expression of predicted traits, indicating regulatory or environmental influence. Several strains inhibited F. graminearum mycelial growth via volatile organic compounds, while two strains also reduced conidia germination, including isolates from both suppressive and conducive soils.

CONCLUSIONS: This study demonstrates that Pseudomonas genomic traits important for biocontrol are not restricted to suppressive soils, and that functional redundancy and context-dependent expression may shape the contribution of Pseudomonas to disease suppression. Our results highlight the need for integrative analyses combining community profiling, genome-based prediction, and phenotyping to better understand microbiome-mediated plant protection. The identification of novel genomospecies and lineage-specific biosynthetic traits advances our knowledge of Pseudomonas diversity in agricultural soils and supports future development of targeted microbial consortia.},
}

@article {pmid41353309,
year = {2025},
author = {Motiwala, ZY and Misra, S and Sharma, I and Bisht, R and Choudhari, S and Yadav, HM},
title = {The uterine and vaginal microbiome in assisted reproductive technologies: implications for maternal and offspring outcomes.},
journal = {Journal of assisted reproduction and genetics},
volume = {},
number = {},
pages = {},
pmid = {41353309},
issn = {1573-7330},
abstract = {PURPOSE: Assisted reproductive technologies (ART) have provided significant advancements in infertility treatment. Despite this, ART-conceived pregnancies are also associated with higher risks for adverse maternal and offspring outcomes. Recent evidence highlights the role of the reproductive tract microbiome (mainly the vaginal and endometrial microbiome) in implantation success and gestational physiology. The purpose of this review is to summarize the state of knowledge pertaining to the content, function, and disruption of the uterine and vaginal microbiome in ART contexts and to consider the adverse effects of changing the microbiome on maternal health, pregnancy outcomes, and development of progeny.

METHODS: A narrative synthesis of the literature covering the period 2005-2025 was undertaken using the PubMed, Scopus, and CINAHL databases. Articles addressing microbiome changes associated with ART and reproductive outcomes were included.

RESULTS: ART procedures such as vaginal antisepsis, oocyte retrieval, embryo transfers, hormone stimulation, and use of prophylactic antibiotics have caused observable disruptions to the reproductive tract microbiome. The loss of Lactobacillus dominance and the development of dysbiosis are linked with lower implantation rates, a higher incidence of gestational disorders, such as preeclampsia and gestational diabetes, a heavy risk of preterm delivery, and an increased risk of adverse neonatal outcomes, such as altered immune development and developmental delay. Furthermore, newer alternatives including probiotics, individual microbiome testing, and multi-omic platforms show promise, but are limited by variability in clinical approaches and a lack of empirical backing.

CONCLUSION: The uterine and vaginal microbiome profoundly impact ART outcomes by modulating implantation, immune tolerance, and fetal development. Integrating microbiome-informed diagnostics and therapies into fertility treatments offers a new frontier in precision reproductive medicine.},
}

@article {pmid41353176,
year = {2025},
author = {Chen, X and Xu, J and Zhang, L and Xie, B and Ren, J and He, J and Liu, T and Liu, Q and Dong, Y and He, X and Yao, J and Wu, S},
title = {Correction: Altered ruminal microbiome tryptophan metabolism and their derived 3-indoleacetic acid inhibit ruminal inflammation in subacute ruminal acidosis goats.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {252},
pmid = {41353176},
issn = {2049-2618},
}

@article {pmid41353161,
year = {2025},
author = {Haque, S and Bima, AI and Babalghith, AO and Jalal, NA and Aldairi, AF and Wahid, M and Ahmad, F and Bantun, F},
title = {Distinct gut microbiota signatures and metabolic dysregulation in individuals with type 1 diabetes: insights into a microbiome-metabolite axis.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-025-00779-0},
pmid = {41353161},
issn = {1757-4749},
abstract = {BACKGROUND: Emerging evidence suggests a pivotal role for gut microbiota in the pathogenesis of Type 1 Diabetes (T1D). However, the compositional and functional characteristics of microbial dysbiosis in T1D remain incompletely understood. This study aimed to comprehensively characterize gut microbial alterations and associated metabolic shifts in individuals with T1D.

METHODS: The present study is based on re-analysis of publicly available 16S rRNA sequencing and fecal untargeted metabolomics data from T1D patients and healthy controls generated by Yuan et al. (2022, Nature Communications). Microbial diversity was assessed using Chao1 and Fisher indices (alpha diversity), and Bray-Curtis-based Principal Coordinates Analysis (PCoA) (beta diversity). Taxonomic differences were examined at phylum, genus, and species levels, and differentially abundant taxa were identified via Linear Discriminant Analysis Effect Size (LEfSe). Correlation analyses were conducted to explore microbe-metabolite interactions.

RESULTS: T1D individuals exhibited reduced alpha diversity and distinct beta diversity clustering compared to controls, indicating substantial shifts in microbial richness and community structure. Taxonomic analysis revealed an increased abundance of Escherichia-Shigella, Veillonella atypica, and Erysipeloclostridium ramosum in T1D, and depletion of beneficial taxa such as Bifidobacterium, Parabacteroides distasonis, Alistipes putredinis, and Bacteroides plebeius. LEfSe analysis confirmed these patterns and highlighted a T1D-specific microbial signature. Integrative correlation analysis uncovered functional dysbiosis, wherein depleted commensals were positively associated with anti-inflammatory and bioenergetic metabolites (e.g., D-gluconic acid, lactic acid, pyruvate), while T1D-enriched taxa were linked to metabolites involved in oxidative stress and immune activation.

CONCLUSION: Our study reveals profound structural and functional alterations in the gut microbiome of individuals with T1D. These findings support the existence of a gut microbial-metabolite axis in autoimmune diabetes and suggest that microbial biomarkers and metabolic pathways may serve as novel targets for early diagnosis and therapeutic intervention. Longitudinal studies are warranted to validate these signatures and explore microbiota-based therapies for T1D prevention and management.},
}

@article {pmid41353127,
year = {2025},
author = {Shternshis, A and Tong, B and Skalkidou, A and Wählby, C and Zachariah, D and Hugerth, LW and Singh, P},
title = {Predicting allergy and postpartum depression from an incomplete compositional microbiome.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-025-12390-3},
pmid = {41353127},
issn = {1471-2164},
abstract = {Time series of compositional data are a common format for many high-throughput studies of biological molecules, e.g., analyzing the response to a treatment or with the aim of predicting an outcome. However, data from some time points may be missing, which reduces the size of the complete dataset. We propose a method for binary classification that includes imputation for missing values, dimensionality reduction, and logarithmic transformation of compositional data. Imputation approaches entail models that incorporate artificial data alongside true measurements, thereby supplementing the dataset. In the application part, we consider two case studies with longitudinal data and associated target labels, aiming to improve prediction accuracy. We predict infants' food allergies from their gut microbiome with a balanced accuracy of 0.72. We forecast postpartum depression based on gut microbiome data collected during pregnancy, with a balanced accuracy of 0.62. Features extracted from the microbiome time series, specifically ratios of bacterial abundance, are statistically significant indicators of depression.},
}

@article {pmid41353126,
year = {2025},
author = {Ustuner, P and Ceylan, AN},
title = {Microbiological analysis of patients with inverse and plaque-type psoriasis.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04594-0},
pmid = {41353126},
issn = {1471-2180},
abstract = {BACKGROUND: The hypothesis that the fungal and/or bacterial microbiome of the flexural folding area may be an etiopathogenetic factor for inverse psoriasis is still under discussion.

AIM: We aimed to compare clinical features, demographic features, and microbiological data of patients with inverse and plaque psoriasis.

MATERIALS AND METHODS: Demographic and clinical data were recorded from patients with inverse psoriasis, psoriasis vulgaris, and control groups. The study took place between October 2023 and March 2024. Microbiological gel swab samples were taken randomly from either axillary or inguinal regions of lesional and non-lesional areas of the three study groups to examine the presence of pathogens, including Staphylococcus aureus and Gram-negative and diphtheroid bacteria.

RESULTS: The rates of positivity in Wood's lamp examination and Psoriasis Area and Severity Index scores were significantly higher in the inverse psoriasis group than the control and psoriasis vulgaris groups. The rates of diphtheroid and Gram-negative bacteria growth were higher in the lesional areas of the inverse psoriasis group than the non-lesional areas of the other groups.

CONCLUSION: The results suggest that the flexural microbiota may play a role in the etiopathogenesis of inverse psoriasis, which warrants further investigation.},
}

@article {pmid41353124,
year = {2025},
author = {Zheng, SH and Chen, XQ and Wang, ZH and Wu, ZC and Xu, SQ and Chen, XX and Wang, ZJ and Chen, LN and Cai, JJ and Huang, JW and Li, XL and Chen, Y},
title = {Microbiome analysis of the cystic fluid in ovarian endometrioma: new avenues for the prevention, diagnosis, and treatment of the disease.},
journal = {Reproductive biology and endocrinology : RB&E},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12958-025-01511-y},
pmid = {41353124},
issn = {1477-7827},
support = {No.2023107//Research Fund Project of Putian University/ ; },
abstract = {OBJECTIVE: This study aimed to investigate the microbiome profile in the cystic fluid of ovarian endometrioma and explore its association with the microbial communities present in the lower and upper reproductive tracts.

DESIGN: A microbial analysis was conducted across multiple compartments of the reproductive tract in patients diagnosed with ovarian endometrioma.

SUBJECTS: Sixteen female patients aged 25-43 years (mean age: 31.56 years) who underwent laparoscopic surgery for ovarian endometrioma at the First Hospital of Putian City between April 2023 and February 2024 were enrolled in this study.

MAIN OUTCOME MEASURES: 16S rDNA sequencing was employed to characterize the microbiome of ovarian endometrioma and assess its correlations with clinical symptoms, inflammatory markers, and serum CA125 levels RESULTS: Microbial communities were detected in the posterior vaginal fornix, endometrial fluid, peritoneal fluid, and cystic fluid, exhibiting distinct compositional profiles. Community diversity significantly increased along the anatomical gradient from the posterior vaginal fornix to endometrial fluid, peritoneal fluid, and cystic fluid, with the highest microbial diversity observed in the cystic fluid. Lactobacillus was the predominant genus in the posterior vaginal fornix, whereas Escherichia-Shigella was most abundant in endometrial fluid samples. Hydrogenophaga and Brevundimonas were the dominant taxa in both peritoneal and cystic fluids. Notably, the microbial composition of peritoneal fluid showed the greatest similarity to that of cystic fluid, and functional prediction analyses indicated largely overlapping biological functions between these two sites. Furthermore, Spearman correlation analysis revealed significant associations between specific microbial taxa and certain clinical manifestations or inflammatory factors.

CONCLUSION: This study demonstrates the presence of a unique and highly diverse microbiome within the cystic fluid of ovarian endometrioma. The site-specific microbial profiles and their correlations with clinical parameters suggest a potential role of microbiota in disease pathogenesis through inflammatory and metabolic mechanisms. These findings contribute novel insights that may inform future strategies for the prevention, diagnosis, and treatment of ovarian endometrioma.},
}

@article {pmid41352799,
year = {2026},
author = {Cheng, W and Jiang, C and Pan, T and Zhu, Q and Liu, G and Li, N and Wu, Z and Li, X},
title = {Effects of quinoa addition on physicochemical properties, microbiome profiles, and volatile organic compounds in medium-temperature Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {223},
number = {Pt 1},
pages = {117868},
doi = {10.1016/j.foodres.2025.117868},
pmid = {41352799},
issn = {1873-7145},
mesh = {*Volatile Organic Compounds/analysis ; *Chenopodium quinoa/chemistry ; *Microbiota ; Fermentation ; Food Microbiology ; Food Handling/methods ; Temperature ; },
abstract = {The selection of raw materials plays a pivotal role in shaping the microbial ecology and metabolic functions of Daqu, a fermentation starter widely used in Baijiu production. Quinoa (Chenopodium quinoa Willd.), a pseudocereal rich in proteins, polyphenols, and bioactive compounds, has recently gained attention as a functional food ingredient. In this study, Quinoa was used to replace a certain proportion of wheat and incorporated into the making process of medium-temperature Daqu (MTD), and its effects on the physicochemical properties, microbial community dynamics, and volatile organic compound (VOC) were investigated. Compared with traditional MTD, quinoa-supplemented Daqu (L-MTD) exhibited significantly higher starch (increased by 8.4 %), reducing sugar (increased by 12.7 %), and acidity (increased by 15.3 %) levels (p < 0.05), along with enhanced esterification and fermentation power of its central part (increased by 10.2 % and 9.5 %, respectively, p < 0.05). High-throughput sequencing revealed that quinoa addition reshaped the microbial community by enriching beneficial lactic acid bacteria (e.g., Lactobacillus and Weissella) and reducing potential spoilage fungi (e.g., Aspergillus and Rhizopus). In addition, Lactobacillus and Saccharomycopsis showed strong correlations with the accumulation of esters and aromatic compounds, including ethyl lactate, phenethyl acetate, DL-(-)-pantoyl lactone, and benzyl alcohol. Redundancy analysis (RDA) indicated strong correlations between Lactobacillus and Saccharomycopsis with the accumulation of esters (such as ethyl acetate and ethyl lactate) and aromatic compounds (such as benzyl alcohol and phenethyl acetate), providing a research basis for identifying functional microbial strains in MTD and conducting subsequent micro-fermentation experiments. These findings highlight the potential of quinoa as a functional additive that modulates the microbial ecology and enhances the aroma complexity of Daqu, thereby offering a novel strategy for improving the quality and potential health value of traditional fermented products.},
}

*Volatile Organic Compounds/analysis
*Chenopodium quinoa/chemistry
*Microbiota
Fermentation
Food Microbiology
Food Handling/methods
Temperature

@article {pmid41352744,
year = {2025},
author = {Wei, D and Sun, Y and Han, J and Liu, J},
title = {Microbiota and Cancer Immunotherapy: Mechanisms, Clinical Implications, and Precision Therapeutics.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2025.12.002},
pmid = {41352744},
issn = {1096-3650},
abstract = {The microbiome has emerged as a pivotal modulator of cancer immunotherapy, offering novel insights into the efficacy and toxicity of immune checkpoint inhibitors (ICIs). Recent evidence highlights that microbial communities and their metabolites dynamically regulate host immunity by priming dendritic cells, enhancing T-cell infiltration, and reprogramming the tumor microenvironment. Microbiome dysbiosis is implicated in immune-related adverse events (irAEs), underscoring its dual role in therapeutic outcomes. Leveraging these findings, precision microbiome interventions, including fecal microbiota transplantation, engineered probiotics, and dietary modulation, which demonstrate potential to enhance ICIs responsiveness and mitigate irAEs in preclinical and early-phase clinical studies. However, translating these strategies into clinical practice requires rigorous validation through multicenter trials to establish safety, efficacy, and standardized protocols. This review synthesizes current knowledge on the microbiome-immune-oncology axis, with a focus on mechanistic underpinnings, translational challenges, and innovative therapeutic strategies. By integrating microbiome profiling with patient-specific factors, proposing a roadmap for personalized immunotherapy, aligning with the emerging paradigm of precision oncology.},
}

@article {pmid41352735,
year = {2025},
author = {Zhang, W and Li, Y and Chen, Y and Du, Z and Ma, Y and Cheng, S and Zhang, Y and Xu, X and Cao, S and Duan, X and Li, X and Makinia, J},
title = {Enhancing butyrate production from food waste fermentation: an overlooked role of fungal yeast.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123503},
doi = {10.1016/j.envres.2025.123503},
pmid = {41352735},
issn = {1096-0953},
abstract = {The recovery of valuable butyrate from organic waste through microbial fermentation represents a significant advancement in sustainable development. An efficient microbiome is a prerequisite for efficient butyrate production. This study conducts a systematic investigation into the efficacy of four representative inocula, e.g., yeast-rich distiller yeast (DY), bacteria-dominated waste activated sludge (WAS) and anaerobic sludge (AS), and cellulose-degrading fungi-rich forest soil (FS), during food waste fermentation. The fermentation results indicated that the use of DY led to a peak in butyrate production on the fourth day, achieving a concentration of 17.54 ± 0.29 g COD/L, which is 2.88, 13.29, and 2.71 times higher than that of inoculating WAS, AS, and FS, respectively. Fermentation pathway analysis indicated that DY enhanced substrate degradation while effectively in situ generating and utilizing electron donors, particularly ethanol. Subsequently, combined sequencing technologies revealed that the relative abundance of butyrate-producing bacteria (Clostridium) in the DY reactor was 15.58%. Furthermore, the relative abundance of ethanol-producing bacteria (Kosakonia) was 17.33%, and ethanol-producing yeast was significantly enriched at 92.27%. Functional gene analysis revealed that butyrate synthesis in the DY reactor primarily relied on the reverse β-oxidation pathway. Further external yeast supplement experiments suggested that the yeast significantly promotes butyrate production through yeast-bacteria synergy. The neglected iso-butyrate biosynthesis and enhancement strategies were proposed and deeply discussed. This study provides new insights into yeast-bacteria interactions, offering a promising strategy for high-value valorization of food waste and advancing the circular bioeconomy.},
}

@article {pmid41352345,
year = {2025},
author = {Rojas-Vargas, J and Wilcox, H and Monari, B and Gajer, P and Zuanazzi, D and Shouldice, A and Parmar, R and Haywood, P and Tai, V and Krakowsky, Y and Potter, E and Ravel, J and Prodger, JL},
title = {The neovaginal microbiota, symptoms, and local immune correlates in transfeminine individuals with penile inversion vaginoplasty.},
journal = {Cell reports},
volume = {},
number = {},
pages = {116546},
doi = {10.1016/j.celrep.2025.116546},
pmid = {41352345},
issn = {2211-1247},
abstract = {Transfeminine people (assigned male at birth) often undergo penile inversion vaginoplasty to create vulva, a clitoris and a vaginal canal (referred to as a neovagina). After vaginoplasty, transfeminine people frequently experience gynecological concerns, but their etiology is unknown due to a lack of knowledge of the neovaginal microenvironment. We characterized neovaginal microbiota and cytokines in 47 transfeminine participants. Participants self-reported sexual behaviors and symptoms, enabling correlation with bacterial (16S rRNA) and immune profiles. Four distinct clusters of co-occurring bacteria with unique immune profiles were identified. One cluster, which included Fastidiosipila, Ezakiella, and Murdochiella, was abundant, stable, and correlated with lower cytokines. Conversely, another cluster containing Howardella, Parvimonas, Fusobacterium, and Lawsonella was linked to higher cytokines. Although Lactobacillus was detected, Lactobacillus dominance was rare. These findings underscore the need for evidence-based clinical guidelines tailored to transfeminine gynecologic care, emphasizing the vital role of the neovaginal microbiome in symptom management and sexual health.},
}

@article {pmid41352344,
year = {2025},
author = {Monari, B and Wilcox, H and Haywood, P and Gajer, P and Rojas-Vargas, J and Zuanazzi, D and Rutt, L and Shouldice, A and Parmar, R and Waetjen, LE and Krakowsky, Y and Potter, E and Prodger, JL and Ravel, J},
title = {The vaginal microbiota, symptoms, and local immune correlates in transmasculine individuals using sustained testosterone therapy.},
journal = {Cell reports},
volume = {},
number = {},
pages = {116632},
doi = {10.1016/j.celrep.2025.116632},
pmid = {41352344},
issn = {2211-1247},
abstract = {Transmasculine individuals (assigned female at birth, masculine gender identity, TM) may use gender-affirming testosterone therapy, and some report adverse genital symptoms during treatment. In cis women, the vaginal microbiota is central to reproductive and sexual health. Lactobacillus-dominant communities are considered optimal, while diverse, Lactobacillus-depleted microbiota are non-optimal. Prior studies suggest Lactobacillus deficiency in TM vaginal microbiota, but associations with symptoms and immune markers remain unclear. We launched the TransBiota study to characterize the TM vaginal microbiota, soluble mediators of local inflammation, and self-reported symptoms over three weeks. Fewer than 10% of TM possess Lactobacillus-dominant microbiota, and most exhibit diverse, Lactobacillus-depleted microbiota. We identify 11 vaginal microbiota community state types (tmCSTs), with Lactobacillus-dominant tmCSTs unexpectedly linked to abnormal odor and elevated interleukin-1α. However, Lactobacillus dominance is not associated with other key symptoms, such as dyspareunia and vaginal dryness, underscoring that microbiome-symptom relationships in TM are more complex and warrant further research.},
}

@article {pmid41352125,
year = {2025},
author = {Taki, AG and Shareef, A and Arora, V and Oweis, R and Jyothi, SR and Singh, U and Sahoo, S and Chauhan, AS and Alimova, F and Sameer, HN and Yaseen, A and Athab, ZH and Adil, M},
title = {Unraveling the microbiome's role in breast cancer progression and treatment response.},
journal = {Current problems in cancer},
volume = {60},
number = {},
pages = {101264},
doi = {10.1016/j.currproblcancer.2025.101264},
pmid = {41352125},
issn = {1535-6345},
abstract = {The human microbiome, encompassing microbial communities in the gut and breast tissue, has emerged as a critical modulator of breast cancer (BC) initiation, progression, and treatment response. This review synthesizes current evidence on the microbiome's role in BC, highlighting its influence on tumorigenesis, tumor microenvironment (TME), and therapeutic outcomes. Breast cancer, the most prevalent malignancy among women globally, exhibits significant heterogeneity across its molecular subtype's hormone receptor-positive, HER2-enriched, and triple-negative-each with distinct clinical challenges. Recent studies reveal that microbial dysbiosis in the gut and breast tissue can drive oncogenesis through mechanisms such as immune modulation, estrogen metabolism, and inflammation. Gut microbes, via the "estrobolome," regulate circulating estrogen levels, impacting hormone-driven BC, while breast tissue microbiota contributes to local inflammation and DNA damage, promoting tumor progression. Specific microbial taxa, including Bacillus, Staphylococcus, and Escherichia coli, are enriched in BC patients, whereas beneficial species like Lactobacillus and Bifidobacterium are diminished. The microbiome also influences treatment efficacy, with gut microbial diversity linked to enhanced chemotherapy and immunotherapy responses, while antibiotic-induced dysbiosis may impair outcomes. Emerging research suggests microbiome signatures as potential biomarkers for predicting therapeutic success, with Akkermansia muciniphila and short-chain fatty acids showing promise in enhancing anti-tumor immunity. Probiotics, prebiotics, and fecal microbiota transplantation offerel therapeutic avenues, though challenges such as standardization, interindividual variability, and safety concerns remain. Integrating multi-omics and machine learning could elucidate microbiome-host interactions, paving the way for precision oncology. This review underscores the transformative potential of microbiome-based diagnostics and interventions in improving BC management, emphasizing the need for large-scale, longitudinal studies to validate these findings and address existing research gaps.},
}

@article {pmid41352001,
year = {2025},
author = {Hofsvang, A and Hanssen, EN and Muinck, EJ and Trosvik, P and Fonneløp, AE},
title = {Forensic geolocation of Norwegian soil samples using random forest analysis of microbiomes.},
journal = {Forensic science international. Genetics},
volume = {82},
number = {},
pages = {103408},
doi = {10.1016/j.fsigen.2025.103408},
pmid = {41352001},
issn = {1878-0326},
abstract = {Soil is a substrate easily picked up during everyday activities due to its ubiquity and adhesiveness. A method to determine the origin of soil precisely would therefore be useful in forensic casework as it can provide insight into a person`s or object`s previous whereabouts. To evaluate the potential of microbiomes for soil provenance determination, we collected soil samples from 15 locations in and around Oslo, Norway. Samples were collected multiple times from the same locations to assess changes in the microbiome over time. Additionally, a mock soil stain on clothing sample was collected at each site to validate this sample type. The microbial composition of samples was determined via amplicon sequencing of the V4 region of the 16S rRNA bacterial gene. Our results showed that the microbiomes were significantly impacted by location, with both soil and soil stain samples from the same site mainly exhibiting greater similarity than those from different sites. Notably, seasonal variations affected microbiome composition, leading to significant changes in some locations. Machine learning was employed to associate samples with their geographic origins, achieving classification accuracies above 85 % for both soil stain samples and soil samples collected within one week of each other. However, accuracies were lower for samples collected across different seasons, between 55 % and 64 %, indicating that temporal variation can limit the reliability of soil microbiome analysis when there is a delay between sample collection times.},
}

@article {pmid41351948,
year = {2025},
author = {Carnell, BH and Jayaraman, J and Dar Juan, JBP and Templeton, MD and Hay, ID},
title = {Understanding the dynamics of Pseudomonas syringae tailocin targeting allows for predictive protective microbial inoculation of Actinidia chinensis.},
journal = {Microbiological research},
volume = {304},
number = {},
pages = {128401},
doi = {10.1016/j.micres.2025.128401},
pmid = {41351948},
issn = {1618-0623},
abstract = {The Pseudomonas syringae complex is an important group within the Gammaproteobacteria and comprises several pathovars of agricultural significance. Genome mining of the P. syringae species complex has uncovered high-molecular-weight phage tail complexes termed tailocins. Tailocins exert specific bactericidal action against both closely and more distantly related bacteria and significantly shape the ecology of the microbiome. Tailocin targeting specificity is currently understood to be dependent on tail-fibers (TFs) binding to specific molecular epitopes, including lipopolysaccharide (LPS) as a bacterial cell surface receptor for tailocin TF-targeting domains. Recent work in P. syringae has strongly correlated variation at the common polysaccharide antigen of LPS with tailocin sensitivity. Here we provide biochemical evidence for LPS as the major receptor for P. syringae tailocins; examine the mechanisms and genetic basis of tailocin TF targeting; and predict strains that can provide protective colonization of plants. We then use the understanding of these mechanisms that determine the tailocin targeting spectrum and genetic knockouts and complementation to modify the bacterial canker pathogen of kiwifruit plants to predict LPS-mediated tailocin targeting by naturally occurring host microbiota, and then demonstrate the efficacy of these applied microbiome-derived tailocin-carrying commensal strains as biocontrol agents.},
}

@article {pmid41351871,
year = {2025},
author = {Yu, L and Hu, Y and Du, W and Hu, X and Shen, Y},
title = {Mapping the Burn Injury Landscape with Omics Techniques.},
journal = {Journal of burn care & research : official publication of the American Burn Association},
volume = {},
number = {},
pages = {},
doi = {10.1093/jbcr/iraf223},
pmid = {41351871},
issn = {1559-0488},
abstract = {In this review, we studied the significance of multi-omics techniques in understanding the complex processes after burns. Severe burns result in both temporary local pathophysiological changes and long-term, profound, and extensive pathophysiological abnormalities. The utilization of multi-omics approaches to identify novel treatment targets or clarify the molecular mechanisms underlying pathophysiological alterations related to burn injury has significant promise. This review encapsulates recent advancements in the utilization of omics approaches to elucidate pathophysiological alterations and biomarkers associated with inflammation, wound healing, and metabolic pathways after burn injuries, encompassing the genome, transcriptome, proteome, metabolome, and microbiome. An enhanced comprehension of the pathophysiological alterations and biomarkers associated with burn injuries can promote the creation of more efficacious and focused therapeutic approaches.},
}

@article {pmid41351823,
year = {2025},
author = {Howard-Stone, R and Măndoiu, II},
title = {MHASS: Microbiome HiFi Amplicon Sequencing Simulator.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf656},
pmid = {41351823},
issn = {1367-4811},
abstract = {SUMMARY: Microbiome HiFi Amplicon Sequence Simulator (MHASS) creates realistic synthetic PacBio HiFi amplicon sequencing datasets for microbiome studies, by integrating genome-aware abundance modeling, realistic dual-barcoding strategies, and empirically derived pass-number distributions from actual sequencing runs. MHASS generates datasets tailored for rigorous benchmarking and validation of long-read microbiome analysis workflows, including ASV clustering and taxonomic assignment.

Implemented in Python with automated dependency management, the source code for MHASS is freely available at https://github.com/rhowardstone/MHASS along with installation instructions. Our code is also published on Zenodo at https://doi.org/10.5281/zenodo.17486364.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid41351803,
year = {2025},
author = {Kuang, R and Levinthal, DJ and Cummings, C and Ramos Rivers, C and Ghaffari, AA and Binion, DG},
title = {Pain and IBD: The Contributing Role of Diet and Nutrition.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {41351803},
issn = {1573-2568},
abstract = {Pain is one of the most debilitating symptoms in patients with inflammatory bowel disease (IBD). We explore the impact of diet, nutrition, and malnutrition in the emergence and worsening of pain in patients with IBD, and potential strategies to prevent this complication. We propose that diet may impact pain in IBD through nociceptive, neuropathic, and nociplastic mechanisms. IBD-related nociceptive pain arises from intestinal inflammation, nerve sensitization, obstruction, and pressure due to chronic remodeling and strictures. Neuropathic pain in IBD may result from vitamin and micronutrient malabsorption. Surgery can leave patients with IBD particularly prone to vitamin B12 deficiency due to anatomical changes that hinder absorption. Nociplastic pain occurs through central pain sensitization and the experience of pain in the absence of inflammation and other known organic causes. The epidemiologic identification of a Western diet high in ultra-processed foods being associated with both IBD as well as neuropsychiatric illness may contribute to increased pain perception in patients through the gut-brain-axis. We highlight actionable clinical factors linking diet and nutrition to pain in IBD, along with emerging hypotheses on the complex interplay between diet, its prebiotic effects on the microbiome and metabolome, and disorders of gut-brain interaction that may exacerbate pain.},
}

@article {pmid41351790,
year = {2025},
author = {Coker, MO and Kreutzberg, R and Sam-Agudu, NA and Macodiyo, E and Jumare, J and Madan, J and Singhal, V and Li, Z and Robbins, R and Shiau, S},
title = {The State of the Science on Chronic Comorbidities and Aging in Children and Adolescents with perinatally-acquired HIV.},
journal = {Current HIV/AIDS reports},
volume = {22},
number = {1},
pages = {56},
pmid = {41351790},
issn = {1548-3576},
support = {R21DE032869//National Institutes for Health/NIDCR/ ; R21DE032869//National Institutes for Health/NIDCR/ ; },
mesh = {Humans ; *HIV Infections/complications/epidemiology/transmission/drug therapy ; Child ; Comorbidity ; *Aging ; Adolescent ; *Infectious Disease Transmission, Vertical ; Chronic Disease ; },
abstract = {The availability and global scale-up of suppressive antiretroviral therapy (ART) has transformed HIV from a fatal infection to a chronic disease. While long-term survival is a positive development for people living with HIV (PLWH), the increased life expectancy comes with age-related comorbidities. These comorbidities affect PLWH at relatively earlier ages than the general population, and examples include cardiometabolic conditions, renal toxicity, lung and respiratory dysfunction, neurocognitive deficits, malignancy, and oral/dental pathology. Anticipatory management of early markers of non-communicable diseases (NCDs) can be especially advantageous for children and adolescents with perinatally-acquired HIV (CAPHIV), the vast majority of whom live in low-and middle-income countries. However, evidence for the mechanisms underlying age-related comorbidities in PLWH and implications for CAPHIV represent a still-emerging area of investigation. In this article, we review the current literature on comorbidities and age-related conditions experienced by CAPHIV, discuss the role of inflammation and chronic immune activation, and highlight accelerated biological aging and/or disruptions to the microbiome as underlying mechanisms. We recommend that HIV clinical care and health policy should reflect evidence on aging and comorbidities to optimize growth, development, and long-term health for CAPHIV globally.},
}

Humans
*HIV Infections/complications/epidemiology/transmission/drug therapy
Child
Comorbidity
*Aging
Adolescent
*Infectious Disease Transmission, Vertical
Chronic Disease

@article {pmid41351781,
year = {2025},
author = {Gim, G and Lee, DG and Park, CH and Kim, OS and Han, K and Heo, YM and Lee, H},
title = {Antarctic soil microbiomes as a reservoir for cosmetic bioactives: continental-scale diversity and predicted functions.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {41351781},
issn = {2092-9293},
support = {PI24020//Korea Polar Research Institute/ ; PI24120//Korea Polar Research Institute/ ; RS-2024-00343166//National Research Foundation of Korea (NRF)/ ; },
abstract = {BACKGROUND: Demand for clean beauty ingredients is driving discovery of safe, effective, and sustainable actives. Microbes inhabiting polar deserts produce biomolecules adapted to stress, relevant to skin protection and regeneration.

OBJECTIVE: To characterize taxonomic diversity and functional potential of Antarctic soil microbiomes from distinct biogeographic regions and identify microbial genes linked to cosmetic efficacy.

METHODS: Public 16S rRNA amplicon datasets from NCBI SRA were compiled and classified into four Antarctic Conservation Biogeographic Regions: North Antarctic Peninsula, East Antarctica, South Victoria Land, and Transantarctic Mountains. Functional profiles were predicted using PICRUSt2 and analyzed for antioxidant, anti-aging, moisturization, skin-barrier, and regeneration pathways via KEGG Orthology terms.

RESULTS: Analysis of 406 sequencing runs identified 54,523 amplicon sequence variants from 48 bacterial and 2 archaeal phyla. Actinobacteria dominated (36.1%), followed by Bacteroidetes (13.0%) and Proteobacteria (10.5%). East Antarctica exhibited highest diversity (Shannon index mean 8.97) and evenness (0.87), with region-distinct communities. Functional prediction revealed enriched antioxidant defense, skin-barrier maintenance, moisturization, and photoprotective genes. Taxonomic and functional ordinations partially decoupled, indicating functional convergence amid taxonomic divergence.

CONCLUSION: Antarctic soils are a rich source of microbial functions for cosmetic innovation, especially in East Antarctica. Multi-omics validation, strain isolation, and sustainable production may accelerate development of next-generation clean beauty actives compliant with access and benefit-sharing regulations.},
}

@article {pmid41351776,
year = {2025},
author = {Hussain, B and Javed, K and Ali, M and Ullah, S and Sun, S and Idris, AM and Singh, S},
title = {Impact of nanoparticles on biogeochemical processes in soil-plant system under heavy metals stress; exploring remediation mechanism and plant health status.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {1},
pages = {31},
pmid = {41351776},
issn = {1573-2983},
mesh = {*Metals, Heavy/toxicity/metabolism ; *Soil Pollutants/toxicity/metabolism/chemistry ; Soil/chemistry ; *Plants/drug effects/metabolism ; *Environmental Restoration and Remediation ; Biodegradation, Environmental ; Stress, Physiological ; *Metal Nanoparticles/chemistry/toxicity ; },
abstract = {Although, NPs have potential to improved plant resistance against abiotic stress, increased nutrient usage efficiency, and sustenance of agricultural production. However, reactions of NPs in soil matrices, particularly their movement, perseverance, and biogeochemical reactions in soil-plant system under heavy metals (HMs) were not well understood. Therefore, this review presents the latest research in order to clarify the molecular interactions, beneficial transformations, and detoxification processes of NPs in plants and evaluates their roles in these processes. It further aims to quantify the benefits and risks, and give future directions for NPs design and applications in environmental remediation and agriculture. NPs significantly enhanced agricultural outcomes through mechanisms such as regulating HMs uptake, boosting antioxidant enzyme activity (up to a 60% increase), altering soil properties, and optimizing physiological metabolism. NPs amendments raised crop output by 20-55% while reducing disease and nutrient leaching to 50% and 30%, respectively, and improving the soil's carbon sink by 15%. Meanwhile, green-synthesized nanomaterials offer eco-friendly alternatives in remediation through processes like adsorption, oxidation, coprecipitation, ion-exchange, photocatalysis, and nanophytoremediation, achieving 100% pollutant removal efficiency for elements like hexavalent chromium using iron NPs. However, challenges such as NPs accumulation in food chains, potential toxicity to non-target species, and physiological disruptions necessitate solutions like microbiome co-delivery and stimuli-responsive systems to balance safety and effectiveness. In order to increase the available resources and address the worldwide food safety issue, the use of NPs in agroecosystems might be a crucial step towards sustainable farming. Therefore, the influence of NPs on soil, and plant antioxidant defense systems and oxidative stress activation under HMs should be studied using molecular, physiological, and biochemical techniques. For this purpose, real-time polymerase chain reaction (RT-PCR) analysis, illumina MiSeq sequencing, pyrosequencing analysis, metagenomics, metabolomics, proteomics, and functional assays etc. could be most useful for NPs risk/benefit evaluation.},
}

*Metals, Heavy/toxicity/metabolism
*Soil Pollutants/toxicity/metabolism/chemistry
Soil/chemistry
*Plants/drug effects/metabolism
*Environmental Restoration and Remediation
Biodegradation, Environmental
Stress, Physiological
*Metal Nanoparticles/chemistry/toxicity

@article {pmid41351765,
year = {2025},
author = {Peters, M and Hegelmaier, T and Wegner, F and Höllerhage, M and Ye, L and Niesmann, C and Schneidereit, IV and Haghikia, A and Klietz, M},
title = {The role of the gut microbiome in the progression of Parkinson's disease: a systematic review of patient cohorts.},
journal = {Journal of neurology},
volume = {273},
number = {1},
pages = {8},
pmid = {41351765},
issn = {1432-1459},
mesh = {Humans ; *Parkinson Disease/microbiology/physiopathology ; *Gastrointestinal Microbiome/physiology ; *Disease Progression ; Dysbiosis ; },
abstract = {INTRODUCTION: Parkinson's disease (PD) is the second most common neurodegenerative disease. The etiology of PD is not yet fully understood. In recent years, the role of the gut microbiome in the progression of the disease came to attention. A deeper understanding of the relationship between the gut microbiome and the development and progression of PD may innovate therapeutic approaches.

AIM: The aim of the present literature analysis is to systematically evaluate alterations in gut microbiome in PD and its correlation with clinical symptoms.

MATERIALS AND METHODS: A search for publications via PubMed using the search terms "Parkinson's disease" AND "gut microbiome" AND "human" was performed. The main inclusion criteria were a subject number ≥ 30 per group, patients with clinically confirmed PD, an analysis of the gut microbiome in a case-control, cross-sectional or longitudinal study design.

RESULTS: The evaluation of the results showed that gut microbiome of PD patients is altered both in early stages of the disease and throughout its progression compared to healthy controls. These alterations correlate with clinical symptoms. In general, the diversity of micro-organisms in the gut is reduced in PD patients, and the composition of the gut microbiome differs significantly from healthy persons. Particularly a reduction in short-chain fatty acid (SCFA) producing genera such as Faecalibacterium and Roseburia and the increase in pro-inflammatory taxa such as Collinsella and Akkermansia is described.

CONCLUSIONS AND DISCUSSION: According to current evidence, the relationship between alterations in the gut microbiome and the pathogenesis of PD is not yet fully understood. Recent findings suggests that intestinal dysbiosis may contribute to the progression of PD.},
}

Humans
*Parkinson Disease/microbiology/physiopathology
*Gastrointestinal Microbiome/physiology
*Disease Progression
Dysbiosis

@article {pmid41351422,
year = {2025},
author = {Jiang, Y and Xu, H and Zhang, W and Jin, S and Piao, H and Yu, J and Yao, H and Shi, J and Liu, Q and Li, N and Shen, Y and Fu, J and Li, M},
title = {Advances in the Study of Intestinal Microbiota and Neuropathic Pain.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {30},
number = {11},
pages = {43051},
doi = {10.31083/FBL43051},
pmid = {41351422},
issn = {2768-6698},
support = {82104838//China National Natural Science Foundation/ ; XH-D001//China Promotion Foundation Spark Program/ ; 2024JH2/102500062//Liaoning Provincial Key Research and Development Programme/ ; 2025-MSLH-490//Liaoning Provincial Natural Science Foundation/ ; },
mesh = {Humans ; *Neuralgia/microbiology ; *Gastrointestinal Microbiome/physiology ; Animals ; },
abstract = {The intestinal microbiota, present in vast numbers within the human body, plays a pivotal role, with its composition and abundance varying significantly across individuals. This gut microbiota not only contributes to normal physiological development but also impacts the initiation, progression, resolution, and prognosis of various diseases. Recent studies have increasingly illuminated the connection between intestinal microbiota and pain, with a particular focus on the relationship between gut microbiota and neuropathic pain (NP). NP, an acute and chronic pain disorder arising from sensory nervous system injury, encompasses both peripheral and central neuropathic pain. Evidence suggests that intestinal microbiota influences NP occurrence and may modulate its severity. This review synthesizes current research findings on the microbiota-NP relationship, aiming to establish a theoretical foundation for future clinical investigations.},
}

Humans
*Neuralgia/microbiology
*Gastrointestinal Microbiome/physiology
Animals

@article {pmid41351421,
year = {2025},
author = {Li, Y and Chen, H and Zhou, S},
title = {Macrophages and Tissue Homeostasis: From Physiological Functions to Disease Onset.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {30},
number = {11},
pages = {42706},
doi = {10.31083/FBL42706},
pmid = {41351421},
issn = {2768-6698},
support = {32200755//National Natural Science Foundation of China/ ; 23JRRA696//Natural Science Foundation of Gansu Province/ ; 23YF1430600//Shanghai Rising-Star Program/ ; },
mesh = {Humans ; *Homeostasis ; Tumor Microenvironment/immunology ; *Macrophages/physiology/immunology/metabolism ; Animals ; *Neoplasms/immunology/pathology/metabolism ; Tumor-Associated Macrophages/immunology ; },
abstract = {The role of macrophages has transcended the traditional binary framework of M1/M2 polarization, emerging as "tissue microenvironment engineers" that dynamically govern organismal homeostasis and disease progression. Under physiological conditions, they maintain balance through phagocytic clearance, metabolic regulation (e.g., lipid and iron metabolism), and tissue-specific functions (such as hepatic detoxification by Kupffer cells and intestinal microbiota sensing), all meticulously orchestrated by epigenetic mechanisms and neuro-immune crosstalk. In pathological states, their functional aberrations precipitate chronic inflammation, fibrosis, metabolic disorders, and neurodegenerative diseases. Notably, this plasticity is most pronounced within the tumor microenvironment (TME): tumor-associated macrophages (TAMs) polarize toward a protumoral phenotype under conditions of low pH and high reactive oxygen species (ROS). They promote angiogenesis via vascular endothelial growth factor (VEGF), suppress immunity through interleukin-10 (IL-10)/programmed death-ligand 1 (PD-L1), and facilitate tumor invasion by degrading the extracellular matrix, ultimately fostering an immune-evasive niche. Novel intervention strategies targeting TAMs in the TME have shown remarkable efficacy: CRISPR-Cas9 spatiotemporal editing corrects aberrant gene expression; pH/ROS-responsive nanoparticles reprogram TAMs to an antitumoral phenotype; chimeric antigen receptor-macrophage (CAR-M) 2.0 enhances antitumor immunity through programmed death-1 (PD-1) blockade and IL-12 secretion; and microbial metabolites like butyrate induce polarization toward an antitumor phenotype. Despite persisting challenges-including the functional compensation mechanisms between tissue-resident and monocyte-derived macrophages, and obstacles to clinical translation-the macrophage-centered strategy of "microenvironmental regulation via cellular engineering" still holds revolutionary promise for the treatment of tumors and other diseases.},
}

Humans
*Homeostasis
Tumor Microenvironment/immunology
*Macrophages/physiology/immunology/metabolism
Animals
*Neoplasms/immunology/pathology/metabolism
Tumor-Associated Macrophages/immunology

@article {pmid41351413,
year = {2025},
author = {Xu, Y and Tao, Y and Pan, H and Wang, Z and Wang, H and Luo, Q},
title = {Microbiome Modulation in Lung Cancer Immunotherapy: Unveiling the Role of Respiratory and Gut Microbiota in the PD-1/PD-L1 Response.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {30},
number = {11},
pages = {41531},
doi = {10.31083/FBL41531},
pmid = {41351413},
issn = {2768-6698},
support = {24ZR1464400//Shanghai Municipal Natural Science Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Lung Neoplasms/therapy/immunology/microbiology ; *Immunotherapy/methods ; Tumor Microenvironment/immunology ; *B7-H1 Antigen/antagonists & inhibitors/immunology ; Programmed Cell Death 1 Receptor/antagonists & inhibitors/immunology ; Immune Checkpoint Inhibitors/therapeutic use ; Dysbiosis/immunology ; Animals ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; },
abstract = {Lung cancer, the leading cause of cancer-related mortality worldwide, poses considerable therapeutic challenges due to the varied responses to programmed death-1/programmed death-ligand 1 (PD-1/PD-L1) inhibitors. Emerging highlight the pivotal role of host-microbiome interactions in modulating antitumor immunity and influencing clinical outcomes. This review examines how the respiratory and gut microbiota contribute to the immunosuppressive tumor microenvironment through dysbiosis-induced T-cell exhaustion and regulatory cell activation, while certain commensals facilitate dendritic cell-mediated recruitment of cytotoxic T lymphocytes. Additionally, this review explores the molecular mechanisms by which microbial metabolites, such as short-chain fatty acids, influence myeloid-derived suppressor cells. Therapeutically, microbiota-modulation strategies-such as tailored probiotic formulations and precision fecal microbiota transplantation-offer potential to enhance immunotherapy efficacy. This review provides a foundation for microbiome-guided immunotherapy, advocating for biomarker-driven patient stratification and the use of engineered microbial consortia to counteract therapeutic resistance. These findings pave the way for the integration of microbiome science into next-generation precision oncology.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Lung Neoplasms/therapy/immunology/microbiology
*Immunotherapy/methods
Tumor Microenvironment/immunology
*B7-H1 Antigen/antagonists & inhibitors/immunology
Programmed Cell Death 1 Receptor/antagonists & inhibitors/immunology
Immune Checkpoint Inhibitors/therapeutic use
Dysbiosis/immunology
Animals
Probiotics/therapeutic use
Fecal Microbiota Transplantation

@article {pmid41351400,
year = {2025},
author = {Zhang, Y and Liu, Y and Liu, Q and Zhang, Q and Zhu, W and Ma, C and Zhu, Z and Fang, Z and Xu, X},
title = {Impact of Dapagliflozin on Gut Microbiota and Plasma Metabolomic Profiles in Patients With Heart Failure.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {30},
number = {11},
pages = {46142},
doi = {10.31083/FBL46142},
pmid = {41351400},
issn = {2768-6698},
support = {2022e07020058//2023 Chizhou City major science and technology special project and Anhui Provincial Key Research and Development Program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Glucosides/therapeutic use/pharmacology ; *Benzhydryl Compounds/therapeutic use/pharmacology ; *Heart Failure/drug therapy/blood/microbiology/metabolism ; Male ; Female ; Aged ; Middle Aged ; Metabolomics/methods ; *Metabolome/drug effects ; *Sodium-Glucose Transporter 2 Inhibitors/therapeutic use/pharmacology ; Bacteria/genetics/classification/drug effects ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Heart failure (HF) remains a leading cause of morbidity and mortality worldwide. Although dapagliflozin, a selective sodium-glucose cotransporter 2 (SGLT2) inhibitor, has demonstrated significant cardiovascular benefits in large clinical trials, the underlying mechanisms beyond glucose lowering remain incompletely understood. Increasing evidence suggests that gut microbiota and its metabolites may contribute to HF progression through gut-heart axis interactions.

METHODS: In this study, a total of 135 individuals with HF were recruited, comprising 84 patients treated with dapagliflozin (Y group) and 51 receiving conventional therapy (N group). Gut microbial communities were characterized through 16S rRNA gene sequencing to evaluate compositional structure, diversity metrics, and taxa differences between groups. Untargeted metabolomic profiling of plasma samples was conducted to identify significantly altered metabolites and enriched metabolic pathways. Furthermore, the interrelationships between gut bacterial taxa and circulating metabolites were systematically explored to delineate potential microbiome-metabolome interactions.

RESULTS: Dapagliflozin treatment significantly altered gut microbial composition (p < 0.05, permutational multivariate analysis of variance [PERMANOVA]), characterized by increased Prevotella, Akkermansia, Collinsella, and Fusobacterium, and reduced Bacteroides, Parabacteroides, Subdoligranulum, and Bifidobacterium in the dapagliflozin group, whereas control-enriched taxa included Lachnoclostridium and the Ruminococcus gauvreauii group. Fourteen plasma metabolites were differentially abundant between groups, including higher levels of O-phospho-L-threonine and epiandrosterone in the dapagliflozin group, while salicyluric acid and L- (+)-rhamnose were enriched in the control group. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated alterations in amino acid and one-carbon metabolism, as well as carbohydrate and steroid-related pathways. Correlation analysis revealed that Collinsella was positively associated with fludarabine phosphate (p < 0.05), whereas Akkermansia and Paraprevotella showed negative correlations with maslinic acid and phospho-L-valine, respectively (p < 0.01 to p < 0.001).

CONCLUSION: Dapagliflozin modulates gut microbiota composition and circulating metabolic signatures in HF patients, supporting a potential gut-heart axis mechanism contributing to its cardioprotective effects.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Glucosides/therapeutic use/pharmacology
*Benzhydryl Compounds/therapeutic use/pharmacology
*Heart Failure/drug therapy/blood/microbiology/metabolism
Male
Female
Aged
Middle Aged
Metabolomics/methods
*Metabolome/drug effects
*Sodium-Glucose Transporter 2 Inhibitors/therapeutic use/pharmacology
Bacteria/genetics/classification/drug effects
RNA, Ribosomal, 16S/genetics

@article {pmid41351294,
year = {2025},
author = {Cai, Y and Zhou, T and Shi, W and Ding, X and Cai, X and Yu, L},
title = {Genetic Evidence Implicating Gut Microbiota and Circulating Cytokines in Sjögren's Syndrome.},
journal = {Journal of clinical laboratory analysis},
volume = {},
number = {},
pages = {e70136},
doi = {10.1002/jcla.70136},
pmid = {41351294},
issn = {1098-2825},
support = {82172234//National Natural Science Foundation of China/ ; 82401309//National Natural Science Foundation of China/ ; 2024409//Shanghai Post-doctoral Excellence Program/ ; 2025M771943//China Postdoctoral Science Foundation/ ; },
abstract = {BACKGROUND: This study investigates the potential interplay between gut microbiota and circulating cytokines in Sjögren's syndrome (SS) through a bidirectional and mediation Mendelian randomization (MR) approach.

METHODS: Summary-level statistics of 473 gut microbiota (n = 5959), 41 circulating cytokines (n = 8293), and SS (ncase = 2735, ncontrol = 399,355) were obtained from genome-wide association studies (GWAS) in European populations. A two-sample MR analysis was employed to investigate the bidirectional causal effects of gut microbiota and circulating cytokines on SS, and mediation analyses were applied to discover potential mediating gut microbiota and circulating cytokines. A series of sensitivity analyses were conducted to address heterogeneity and pleiotropy concerns.

RESULTS: Fifteen taxa were found to be causally associated with SS, and SS had a causal effect on 26 taxa. A bidirectional causal relationship was identified between CAG-269 sp001916065 and SS, and between UBA7703 and SS. Genetically predicted levels of five circulating cytokines-MIG, IL-5, IL-1RA, IL-2RA, and SCGF-β-were found to potentially affect SS, and genetically predicted SS was associated with increased levels of two circulating cytokines, IL-1β and IL-5. A bidirectional causal relationship was identified between circulating IL-5 and SS. Mediation analyses further revealed that circulating cytokines do not mediate the gut microbiome's influence on SS, and conversely, the gut microbiome does not influence circulating cytokines to affect SS.

CONCLUSION: This study provides compelling evidence for causal effects of gut microbiome composition and circulating cytokines on SS risk. Further mediation analysis suggests that these biological factors may operate independently to influence SS development.},
}

@article {pmid41351228,
year = {2025},
author = {Sun, JM and Liu, YX and Zheng, DN and Gao, Y and Zhang, YF and Yu, L},
title = {Ralstonia pickettii - The Potential and Substantial Impact in Capsular Contracture: Insights from 2bRAD-M Analysis and Murine Model.},
journal = {Plastic and reconstructive surgery},
volume = {},
number = {},
pages = {},
doi = {10.1097/PRS.0000000000012570},
pmid = {41351228},
issn = {1529-4242},
abstract = {BACKGROUND: Capsular contracture (CC) is one of the most common complications in augmentation mammaplasty with breast implant, but its etiology remains uncertain. We aimed to apply the 2bRAD-M technique to characterize the microbiome differences between normal and contracture capsules.

METHODS: 10 normal capsules and 10 contractured capsules were used for 2bRAD-M sequencing and corresponding histological evaluation. By constructing a mouse silicone implant infection model, histological staining was used to verify the influence of different microorganisms identified in sequencing results.

RESULTS: Histologic evaluation of patient samples revealed a marked increase in the thickness and stiffness of contracture capsules, along with increased infiltration of macrophages and T cells. Through 2bRAD-M sequencing, we found that the microbial composition of contracture capsules was significantly different from that of normal capsules, with the most significant difference of relative abundance value in Ralstonia pickettii. In vivo, Ralstonia pickettii could significantly increase the thickness, collagen content, and hardness of the capsules, which was more effective than the combined infection with Staphylococcus epidermidis and Cutibacterium acnes. Immunofluorescence results showed both bacterial infections caused increased infiltration of macrophages and T cells, and Ralstonia pickettii infection caused more infiltration of T cells.

CONCLUSION: This is the first study to use 2bRAD-M technique to characterize microbiome differences of relative abundance value between normal and contracture capsules. Ralstonia pickettii can recruit more macrophages and T cells to infiltrate. This study provides new etiological causes of capsular contracture and new clinical insights for the prevention and treatment of capsular contracture.},
}

@article {pmid41351139,
year = {2025},
author = {Park, C and Kim, J and Lee, J},
title = {Inference of causal interaction networks of gut microbiota using transfer entropy.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-025-12384-1},
pmid = {41351139},
issn = {1471-2164},
support = {RS-2023-00220207//Ministry of Education/ ; NRF-2020R1A2C1005956//Ministry of Education/ ; },
}

@article {pmid41351056,
year = {2025},
author = {Stach, TL and Starke, J and Bouderka, F and Bornemann, TLV and Soares, AR and Wilkins, MJ and Goldman, AE and Stegen, JC and Borton, MA and Probst, AJ},
title = {Conserved environmental adaptations of stream microbiomes in the hyporheic zone across North America.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02236-1},
pmid = {41351056},
issn = {2049-2618},
support = {426547801//Deutsche Forschungsgemeinschaft/ ; DE-AC05-76RL01830//U.S. Department of Energy/ ; },
abstract = {BACKGROUND: Stream hyporheic zones represent a unique ecosystem at the interface of stream water and surrounding sediments, characterized by high heterogeneity and accelerated biogeochemical activity. These zones-represented by the top sediment layer in this study-are increasingly impacted by anthropogenic stressors and environmental changes at a global scale, directly altering their microbiomes. Despite their importance, the current body of literature lacks a systematic understanding of active nitrogen and sulfur cycling across stream sediment and surface water microbiomes, particularly across geographic locations and in response to environmental factors.

RESULTS: Based on previously published and unpublished datasets, 363 stream metagenomes were combined to build a comprehensive MAG and gene database from stream sediments and surface water including a full-factorial mesocosm experiment which had been deployed to unravel microbial stress response. Metatranscriptomic data from 23 hyporheic sediment samples collected across North America revealed that microbial activity in sediments was distinct from the activity in surface water, contrasting similarly encoded metabolic potential across the two compartments. The expressed energy metabolism of the hyporheic zone was characterized by increased cycling of sulfur and nitrogen compounds, governed by Nitrospirota and Desulfobacterota lineages. While core metabolic functions like energy conservation were conserved across sediments, temperature and stream order change resulted in differential expression of stress response genes previously observed in mesocosm studies.

CONCLUSIONS: The hyporheic zone is a microbial hotspot in stream ecosystems, surpassing the activity of overlaying riverine surface waters. Metabolic activity in the form of sulfur and nitrogen cycling in hyporheic sediments is governed by multiple taxa interacting through metabolic handoffs. Despite the spatial heterogeneity of streams, the hyporheic sediment microbiome encodes and expresses conserved stress responses to anthropogenic stressors, e.g., temperature, in streams of separate continents. The high number of uncharacterized differentially expressed genes as a response to tested stressors is a call-to-action to deepen the study of stream systems. Video Abstract.},
}

@article {pmid41350930,
year = {2025},
author = {Hashmi, AS and Gupta, ND and Khan, S and Agrawal, N and Ali, SA and Atif, M},
title = {Evaluation of mouthwash-induced antimicrobial resistance in the oral microbiome: a systematic review.},
journal = {British dental journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41415-025-9012-9},
pmid = {41350930},
issn = {1476-5373},
abstract = {Aim Antimicrobial resistance is an emerging global health challenge, driven largely by the overuse of antimicrobial drugs. However, the extent of mouthwash-induced antimicrobial resistance remains poorly understood. This systematic review aimed to assess the influence of commonly used mouthwashes on antimicrobial resistance, focusing on resistance genes, microbial alterations, and cross-resistance to antibiotics.Methods PubMed, Scopus, Web of Science, and grey literature, including Google Scholar, were searched for studies evaluating mouthwash-induced antimicrobial resistance. The search strategy included terms related to 'oral microbiome', 'mouthwash' and 'antimicrobial resistance', with Boolean operators tailored to each database. Risk of bias was assessed using In Vitro Critical Appraisal Tool for in vitro studies and the Modified Joanna Briggs Institute for ex vivo and in vivo studies, respectively.Results Twelve studies were analysed, comprising seven in vitro, four ex vivo and one in vivo study. A total of 91 patients and 213 bacterial isolates were assessed across various mouthwashes, including chlorhexidine digluconate, cetylpyridinium chloride, hydrogen peroxide and others. Due to heterogeneous outcomes, a meta-analysis was not conducted. The findings consistently revealed increased minimum inhibitory concentrations of oral bacteria and the presence of resistance genes, highlighting a potential rise in antimicrobial resistance.Conclusion This systematic review indicates a possible association between mouthwash use and resistance-related changes in the oral microbiome; however, the limited and heterogeneous evidence base warrants cautious interpretation. Further, longitudinal research is needed to elucidate the underlying mechanisms and inform evidence-based guidelines for mouthwash use.},
}

@article {pmid41350800,
year = {2025},
author = {Zheng, W and Yang, C and Bu, W and Wang, H and Ma, T and Bu, F},
title = {Age-dependent variations in leaf-endophytic microbiota and biocontrol potential in Camellia oleifera.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31248-y},
pmid = {41350800},
issn = {2045-2322},
support = {232102110050//the Henan Province Key Research and Development and Promotion Special Project (science and technology research)/ ; 23B22001//the Key Scientific Research Project of Henan Province Colleges and Universities/ ; XNKJTD-004//the Dabie Mountain Forestry Resources Innovation Theory and Technology innovation team of Xinyang Agriculture and Forestry University/ ; 2023XYZD05//Key Project of Xinyang Ecological Research Institute/ ; },
abstract = {Endophytic microorganisms play important roles in plant health, but their diversity and functions can vary with host developmental stage. Camellia oleifera, a major oil-producing crop in China, offers a valuable system for exploring these dynamics. We compared endophytic microbial communities in young (5-year) and old (15-year) C. oleifera leaves using high-throughput 16 S rRNA and ITS sequencing, supported by culture-dependent isolation and inhibition assays. Diversity indices, taxonomic composition, and predicted bacterial functions were analyzed with QIIME2 and PICRUSt2. Ten fungal and nine bacterial strains were isolated and tested for antagonism against key leaf pathogens in confrontation assays (n = 3 replicates). A total of 607 bacterial and 778 fungal ASVs were identified. Young leaves contained greater bacterial richness and diversity (Observed ASVs, Shannon, Simpson indices, P < 0.05), while old leaves hosted higher fungal richness. Beta diversity (Bray-Curtis PCoA) showed clear separation of bacterial communities by leaf age, with weaker separation for fungi. Bacterial functional prediction revealed enrichment of carbohydrate metabolism and amino acid biosynthesis in young leaves, while secondary metabolism and stress response pathways were more prominent in old leaves. Among isolated strains, Coniochaeta velutina inhibited Colletotrichum gloeosporioides, Alternaria alternata, and Botryosphaeria dothidea by 67.4%, 54.8%, and 65.2%, respectively. The bacterium Burkholderia ambifaria achieved the highest inhibition rate of 87.2% against B. dothidea. These findings suggest that leaf age shapes endophytic microbial diversity and bacterial functional potential in C. oleifera. Moreover, C. velutina and B. ambifaria represent promising candidates for biocontrol applications. While limited by small sample size (n = 3 replicates), this exploratory study provides foundational insights into age-associated shifts in endophyte communities and their biocontrol potential.},
}

@article {pmid41350794,
year = {2025},
author = {Huo, F and Liu, Q and Zhang, S and Liu, X and Lv, S and Zhao, M and Liu, Y and Zhu, X and Huang, C and Feng, S and Wang, H and Xu, S and Shen, J and Gao, J and Su, T and Wu, Y and Jiang, R and Zhu, JK and Liu, H},
title = {Circadian Rhythm Disorder-Related Dysfunctions are Exacerbated by Aging and Ameliorated by Time-Restricted Feeding.},
journal = {Neuroscience bulletin},
volume = {},
number = {},
pages = {},
pmid = {41350794},
issn = {1995-8218},
abstract = {Circadian rhythms are present in various species, and circadian rhythm disorder (CRD) affects people of all ages, especially those with age-related neurodegenerative diseases. Gut microbiota, which changes with age, also exhibits circadian rhythms. Disruption of gut microbial balance can trigger neurodegenerative diseases. This study explored the link between aging, CRD, and gut microbes by modeling CRD through light/dark cycle control. We found that aging worsened cognitive and mood disorders, along with gut microbial imbalance, intestinal barrier damage, and systemic inflammation in aged mice with CRD. Abnormal circadian gene expression increased oxidative stress. However, time-restricted feeding (TRF) improved CRD effects in aged mice by boosting Akkermansia muciniphila and inhibiting the NOD-like signaling pathway. This study shows that older mice exhibit increased behavioral and functional issues under CRD-related stress due to complex causes like systemic inflammation from a proinflammatory gut microbiome and oxidative stress from disrupted circadian genes. Maintaining a regular eating schedule significantly alleviates these CRD-induced issues in aged mice.},
}

@article {pmid41350753,
year = {2025},
author = {Kim, K and Park, S and Jinno, C and Ji, P and Liu, Y},
title = {Impact of dietary supplementation of Bacillus subtilis on the metabolic profiles and microbial ecology of weanling pigs experimentally infected with a pathogenic Escherichia coli.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {167},
pmid = {41350753},
issn = {1674-9782},
abstract = {BACKGROUND: Our previous study demonstrated that dietary supplementation of Bacillus subtilis enhanced growth performance and intestinal integrity in weaned pigs challenged with enterotoxigenic Escherichia coli (ETEC). Therefore, this study aimed to explore the impact of Bacillus subtilis on gut health and its role in modulating host-microbe interactions in post-weaning pigs.

RESULTS: ETEC infection disrupted key metabolic pathways in distal colon, including glutathione, beta-alanine, and pyrimidine metabolism, indicating increased oxidative stress, impaired nucleotide balance, and amino acid catabolic stress. Bacillus subtilis supplementation induced distinct metabolomic and microbiome profiles in colon digesta of weaned pigs challenged with ETEC. Bacillus subtilis-treated pigs under ETEC challenge exhibited significant enrichment in amino acid- and energy-related pathways such as arginine biosynthesis, phenylalanine metabolism, pantothenate and CoA biosynthesis. ETEC infection induced microbial dysbiosis in the distal colon, resulting in decrease (P < 0.05) in abundance of Streptococcaceae and Enterobacteriaceae compared to healthy controls. Bacillus subtilis supplementation mitigated the ETEC-induced disruptions by increasing the relative abundance of beneficial bacterial families, including Lachnospiraceae and Bacteroidaceae.

CONCLUSION: Supplementation of Bacillus subtilis improves intestinal health and resilience against ETEC challenge by mitigating infection-induced metabolic disruptions and gut dysbiosis in weaned pigs.},
}

@article {pmid41350681,
year = {2025},
author = {Lin, L and Zhou, X and Peng, B and Ma, J and Zheng, Z and Jiang, C and He, Z and Li, S and Fang, W and Wu, C and Jiang, Z and Chen, Y and Zhong, L and Kwan, HY and Shen, C and Gong, S and Zhao, X},
title = {Extracellular vesicles derived from Kaempferia Galanga L. show promise for targeted oral therapy in the treatment of ulcerative colitis.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-025-03897-8},
pmid = {41350681},
issn = {1477-3155},
support = {20221260//Guangdong Traditional Chinese Medicine Special Fund/ ; 82405279//National Natural Science Foundation of China/ ; 82405279//National Natural Science Foundation of China/ ; 20231800913372//Science and Technology Program of Dongguan/ ; 2023A1515110757//Natural Science Foundation of Guangdong Province/ ; 2023A1515010720//Natural Science Foundation of Guangdong Province/ ; 81830117//the Key Project of the National Natural Science Foundation of China/ ; },
abstract = {Ulcerative colitis (UC) is characterised by chronic intestinal inflammation and its global prevalence is increasing. Although a variety of drugs have been approved for the clinical treatment of UC, their application is often limited by unsatisfactory long-term effects, side effects, and high treatment costs. Therefore, there is an urgent need for the development of effective drugs with fewer side effects. In this study, we found that the extracellular vesicles extracted and purified from rhizomes of Kaempferia galanga L. (KGEVs) exhibit promising therapeutic effects in treating UC disease. With an average diameter of 133.8 nm, KGEVs are rich in functional components, including lipids, proteins, and pharmacologically and immunologically active molecules. In vivo experiments revealed that KGEVs accumulated in the colorectal region 6 h after oral administration, demonstrating targeted enrichment at the site of enteritis. Moreover, we found that KGEVs effectively alleviate DSS-induced colitis in mice, as indicated by reductions in body weight loss, DAI score, spleen index and colon length shortening. Mechanistically, KGEVs may alleviate colitis by repairing the intestinal barrier, inhibiting oxidative stress and colonic inflammation regulating gut microbiota and inhibiting the polarisation of macrophages into pro-inflammatory M1 macrophages during the inflammatory response, indicating significant anti-inflammatory effects. These results suggest the potential of KGEVs as a promising, cost-effective, and efficient oral therapeutic agents for UC treatment.},
}

@article {pmid41350670,
year = {2025},
author = {Huang, Y and Huang, Y and Xu, B and Lin, C and Chen, X and Li, Y and Wang, Y and Liu, X},
title = {The association between a newly proposed gut microbiota dietary index and obesity among U.S. adults: a cross-sectional analysis based on NHANES 1999-2020.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {181},
pmid = {41350670},
issn = {1475-2891},
support = {2022QH1268//Fujian Medical University/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Obesity/epidemiology/microbiology ; Cross-Sectional Studies ; Male ; Female ; Adult ; Nutrition Surveys ; Middle Aged ; *Diet ; United States/epidemiology ; Young Adult ; Body Mass Index ; Aged ; },
abstract = {OBJECTIVE: Obesity is linked to gut microbiota dysbiosis, and diet is a key determinant influencing the gut microbiome. This study examined the association between a newly proposed Dietary Index for Gut Microbiota (DI-GM) and obesity in the National Health and Nutrition Examination Survey (NHANES) from 1999 to 2020.

METHODS: A total of 41,159 adults aged ≥ 20 years were included, with 15,327 individuals classified as obese (BMI ≥ 30 kg/m²) and 25,832 as living without obesity. DI-GM comprises 13 components deemed either beneficial or unfavorable to the gut microbiome, yielding a total score ranging from 0 to 13. Weighted logistic regression assessed the relationship between DI-GM (continuous and categorical) and obesity, adjusting for demographic and lifestyle factors plus comorbidities. Restricted cubic spline, stratified analyses, multiple imputation, and propensity score matching were also performed.

RESULTS: Participants with obesity had a significantly lower mean DI-GM score than those without obesity (4.32 vs. 4.65, P < 0.001). Each 1-point increase in DI-GM was associated with 13% lower obesity odds (OR = 0.87, 95% CI: 0.85-0.88) in the crude model, remaining robust (OR = 0.88, 95% CI: 0.87-0.90, P < 0.001) after full adjustment. Higher DI-GM scores were linearly linked to lower odds of obesity, supported by multiple imputation and propensity score matching (P < 0.001).

CONCLUSION: In this nationally representative U.S. population, a more microbiota-oriented diet, as proxied by higher DI-GM scores, was independently associated with lower odds of obesity. Prospective and randomized trials are warranted to verify causality and investigate underlying mechanisms.},
}

Humans
*Gastrointestinal Microbiome
*Obesity/epidemiology/microbiology
Cross-Sectional Studies
Male
Female
Adult
Nutrition Surveys
Middle Aged
*Diet
United States/epidemiology
Young Adult
Body Mass Index
Aged

@article {pmid41350615,
year = {2025},
author = {Alkan, EN and Hekim, N and Gunes, S and Asci, R and Henkel, R},
title = {Evaluation of the semen microbiome for fertility in men with obesity using next-generation sequencing.},
journal = {Basic and clinical andrology},
volume = {35},
number = {1},
pages = {47},
pmid = {41350615},
issn = {2051-4190},
support = {PYO.TIP.1904.22.022//Ondokuz Mayis Üniversitesi/ ; PYO.TIP.1904.22.022//Ondokuz Mayis Üniversitesi/ ; },
abstract = {BACKGROUND: The study aimed to evaluate the microbial content and diversity in semen samples of men with obesity, determine the differences between infertile and fertile groups, and investigate the effect of seminal microbiota on semen parameters, sperm DNA fragmentation, sperm chromatin condensation, and total antioxidant capacity.

RESULTS: The study included thirteen infertile men with obesity as subjects and five fertile men with obesity as the control group (aged 18-55 years, body mass index > 30 kg/m²). The most abundant bacteria in both groups were seen to be belonging to the phylum of Bacillota, Pseudomonadota, Actinomycetota and Bacteroidota. The most common bacteria at the genus level were Pseudescherichia, Staphylococcus, Paenibacillus, Streptococcus, Klebsiella, and Moraxella, which had similar distributions in both groups. A negative correlation was observed between the percentage of aniline-positive sperm and motility (p < 0.0001), sperm concentration (p = 0.0001) and total sperm count (p = 0.001). It was found that Brevibacterium, Paenibacillus, Alistipes, Lactiplantibacillus, Rhizobacter, Sphingomonas and Venlonella genera were correlated with sperm DNA fragmentation; Pantoea, Devosia, Bacteroides, Acidovorax were correlated with total antioxidant capacity, Fusobacterium was correlated with the histone-rich sperm, and Corynebacterium, Hydrogenophaga, and Paenalcagenes were associated with body mass index.

CONCLUSION: Bacterial species in semen may play a role in male infertility by affecting semen quality, sperm DNA fragmentation or total antioxidant capacity.},
}