@article {pmid41370820,
year = {2025},
author = {Tan, HS and Gilcharan Singh, HK and Mariappan, V and Jamil, NA and Mustapa, SN and Misra, S},
title = {Short-Term Effects of Nonnutritive Sweetener (Sucralose and Saccharin) Consumption on Glycemic Control and Gut Microbiota in Patients With Type 2 Diabetes: Protocol for a Double-Blind, Randomized, Placebo-Controlled, Crossover Trial.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e82695},
doi = {10.2196/82695},
pmid = {41370820},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Diabetes Mellitus, Type 2/microbiology/drug therapy/blood ; Double-Blind Method ; Cross-Over Studies ; *Saccharin/administration & dosage/pharmacology ; *Sucrose/analogs & derivatives/administration & dosage/pharmacology ; Adult ; *Glycemic Control/methods ; *Non-Nutritive Sweeteners/administration & dosage/pharmacology ; Male ; Female ; Middle Aged ; Blood Glucose/drug effects ; *Sweetening Agents/administration & dosage ; Randomized Controlled Trials as Topic ; },
abstract = {BACKGROUND: Nonnutritive sweeteners (NNSs) are widely used as sugar substitutes to help individuals with diabetes manage glycemic control. However, emerging evidence suggests that even low doses of NNSs, such as saccharin and sucralose, may adversely affect metabolic health by impairing glycemic regulation, potentially through alterations in the gut microbiota. In Malaysia, where gut microbiome research is still limited, particularly among individuals with type 2 diabetes mellitus (T2DM), further investigation is warranted to inform safe and evidence-based use of NNSs.

OBJECTIVE: This study aims to evaluate the short-term effects of saccharin and sucralose consumption on glycemic control and gut microbiota composition in adults with T2DM.

METHODS: This is a double-blind, randomized, placebo-controlled, crossover trial. A total of 33 adults with T2DM will consume sucralose (5 mg/kg body weight), saccharin (2 mg/kg body weight), or a placebo (calcium carbonate) in capsule form daily for 7 days per intervention arm, with a 4-week washout period. Data collection will include anthropometric measurements, biochemical assessments for glycemic control, dietary records, physical activity levels, and stool samples. The homeostatic model assessment for insulin resistance will be used to assess insulin sensitivity, while 16S rRNA V3-V4 region sequencing will be conducted to profile gut microbiota composition.

RESULTS: Recruitment is planned to begin in January 2026 and is expected to conclude by September 2026, with study completion anticipated by March 2027. As of December 2025, no participants have been enrolled.

CONCLUSIONS: This trial will contribute novel insights into the effects of short-term NNS consumption on glycemic control and gut microbiota composition in individuals with T2DM. These findings may support evidence-based recommendations for NNS use in diabetes management and enhance understanding of microbiome-diet interactions in an ethnically diverse Asian population.

TRIAL REGISTRATION: ClinicalTrials.gov NCT07124585; https://clinicaltrials.gov/study/NCT07124585.

PRR1-10.2196/82695.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Diabetes Mellitus, Type 2/microbiology/drug therapy/blood
Double-Blind Method
Cross-Over Studies
*Saccharin/administration & dosage/pharmacology
*Sucrose/analogs & derivatives/administration & dosage/pharmacology
Adult
*Glycemic Control/methods
*Non-Nutritive Sweeteners/administration & dosage/pharmacology
Male
Female
Middle Aged
Blood Glucose/drug effects
*Sweetening Agents/administration & dosage
Randomized Controlled Trials as Topic

@article {pmid41370195,
year = {2025},
author = {Miwa, T and Ueda, H and Miyazaki, T and Honda, A and Ikegami, T and Unome, S and Shirakami, Y and Shimizu, M},
title = {Correlations Between Serum Bile Acids and Ammonia Levels in Patients With Cirrhosis.},
journal = {Hepatology research : the official journal of the Japan Society of Hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/hepr.70092},
pmid = {41370195},
issn = {1386-6346},
support = {24K18908//Japan Society for the Promotion of Science/ ; 24KJ2006//Japan Society for the Promotion of Science/ ; },
}

@article {pmid41370181,
year = {2025},
author = {Witkam, WCAM and Mathieu, A and Dal Belo, SE and Moreau, M and Aguilar, L and Verlouw, JAM and Nijsten, TEC and Pardo, LM},
title = {Distinct Bacterial Facial Cutaneous Microbiota Compositions in Adolescents with Acne Vulgaris: A Population-Based Cross-Sectional Observational Study.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljaf508},
pmid = {41370181},
issn = {1365-2133},
abstract = {BACKGROUND: Acne vulgaris (acne) is a prevalent dermatological condition associated with distinct facial cutaneous microbiota compositions. However, existing research has often methodological limitations such as insufficient statistical power and the underrepresentation of diverse adolescents populations, which are highly relevant for understanding acne pathogenesis.

OBJECTIVES: We aimed to compare bacterial facial cutaneous microbiota compositions between acne cases and controls within a large, multiethnic adolescent population, while adjusting for potential confounders.

METHODS: We compared bacterial facial cutaneous microbiota compositions using 16S rRNA sequencing between physician-evaluated acne cases (N=399) and controls (N=527) in adolescents (median age 13) in a population-based study. We additionally evaluated the independent associations of biological sex, puberty stage, perceived skin color, ethnicity, and weight status with facial cutaneous microbiota compositions. Our analytical approaches included assessment of alpha and beta diversity (including Permutational Multivariate Analysis of Variance), relative abundances, univariate coordinate analysis (Analysis of Compositions of Microbiomes with Bias Correction 2), and phylogenetic analyses.

RESULTS: The overall microbiota composition of acne cases was less rich and diverse than controls (Chao1 β -44.98 (SE 4.36) Shannon β -1.01 (SE 0.07), P<0.01). While acne status was a major contributor to variations in overall microbiota compositions (R2 4.32%, P<0.01), skin color, sex, puberty stage, and weight status also independently contributed to variations (R2 0.44-1.05%, P<0.01). Specifically, acne cases showed higher relative abundances of Cutibacterium and Staphylococcus, and lower abundance of Streptococcus. Following confounder adjustment, bias correction, and phylogenetic analysis, Cutibacterium granulosum (C. granulosum), Cutibacterium acnes (C. acnes), and Staphylococcus epidermidis (S. epidermidis) emerged as the most differentially abundant species in acne cases versus controls (log fold changes: 0.75-2.17, P<0.01).

CONCLUSIONS: Our findings reveal distinct facial microbiota compositions in adolescents with acne, identifying C. granulosum, C. acnes, and S. epidermidis as key microbial signature. This study suggests a significant clinical relevance for C. granulosum in acne pathology and a potential protective role for Streptococcus in acne-free skin. These results underscore the importance of representative study populations in microbiome research and provide important methodological and technical insights for future investigations.},
}

@article {pmid41370178,
year = {2025},
author = {Peto, L and Fawcett, N and Kamfose, MM and Scarborough, C and Peniket, A and Danby, R and Peto, TEA and Crook, DW and Llewelyn, MJ and Walker, AS},
title = {The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
doi = {10.7554/eLife.97751},
pmid = {41370178},
issn = {2050-084X},
support = {NIHR200915//National Institute for Health and Care Research/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Adult ; Cross-Sectional Studies ; Middle Aged ; Aged ; *Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Feces/microbiology ; Metagenomics ; United Kingdom ; *Bacteria/drug effects/classification/genetics ; Young Adult ; },
abstract = {Better metrics to compare the impact of different antimicrobials on the gut microbiome would aid efforts to control antimicrobial resistance (AMR). The Antibiotic Resistance in the Microbiome - Oxford (ARMORD) study recruited inpatients, outpatients, and healthy volunteers in Oxfordshire, UK, who provided stool samples for metagenomic sequencing. Data on previous antimicrobial use and potential confounders were recorded. Exposures to each antimicrobial were considered as factors in a multivariable linear regression, also adjusted for demographics, with separate analyses for those contributing samples cross-sectionally or longitudinally. Outcomes were Shannon diversity and relative abundance of specific bacterial taxa (Enterobacteriaceae, Enterococcus, and major anaerobic groups) and antimicrobial resistance genes (targeting beta-lactams, tetracyclines, aminoglycosides, macrolides, and glycopeptides). 225 adults were included in the cross-sectional analysis, and a subset of 79 patients undergoing haematopoietic cell transplant provided serial samples for longitudinal analysis. Results were largely consistent between the two sampling frames. Recent use of piperacillin-tazobactam, meropenem, intravenous co-amoxiclav, and clindamycin was associated with large reductions in microbiome diversity and reduced abundance of anaerobes. Exposure to piperacillin-tazobactam and meropenem was associated with a decreased abundance of Enterobacteriaceae and an increased abundance of Enterococcus and major AMR genes, but there was no evidence that these antibiotics had a greater impact on microbiome diversity than iv co-amoxiclav or oral clindamycin. In contrast, co-trimoxazole, doxycycline, antifungals, and antivirals had less impact on microbiome diversity and selection of AMR genes. Simultaneous estimation of the impact of over 20 antimicrobials on the gut microbiome and AMR gene abundance highlighted important differences between individual drugs. Some drugs in the WHO Access group (co-amoxiclav, clindamycin) had similar magnitude impact on microbiome diversity to those in the Watch group (meropenem, piperacillin-tazobactam) with potential implications for acquisition of resistant organisms. Metagenomic sequencing can be used to compare the impact of different antimicrobial agents and treatment strategies on the commensal flora.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Male
Female
Adult
Cross-Sectional Studies
Middle Aged
Aged
*Anti-Bacterial Agents/pharmacology
*Anti-Infective Agents/pharmacology
Feces/microbiology
Metagenomics
United Kingdom
*Bacteria/drug effects/classification/genetics
Young Adult

@article {pmid41370101,
year = {2025},
author = {Rasheed, S and Uzair, M and Anas, M and Batool Naqvi, SS and Aijaz, U and Raza, AA and Samadi, A},
title = {Exploring the Ketogenic Diet as Adjunctive Therapy in Multiple Sclerosis: A Review.},
journal = {Restorative neurology and neuroscience},
volume = {},
number = {},
pages = {9226028251404071},
doi = {10.1177/09226028251404071},
pmid = {41370101},
issn = {1878-3627},
abstract = {Multiple sclerosis (MS) is a chronic autoimmune disease that affects the central nervous system, leading to inflammation, demyelination, and neurodegeneration. Although disease-modifying therapies (DMTs) have shown efficacy in reducing relapse rates, they offer limited benefit in addressing cognitive symptoms and overall disease burden. The ketogenic diet (KD), a high-fat, low-carbohydrate dietary approach, has emerged as a promising adjunctive strategy. Recent research suggests that KD may modulate key inflammatory pathways, enhance mitochondrial function, and reduce oxidative stress through mechanisms involving ketone bodies such as β-hydroxybutyrate. These effects have been linked to improvements in fatigue, cognition, quality of life, and markers of neuronal injury in individuals with MS. Furthermore, KD may positively influence the gut microbiome, insulin sensitivity, and myelin repair processes. Despite encouraging results, challenges such as dietary adherence, nutrient deficiencies, gastrointestinal side effects, and cardiovascular risks limit widespread adoption. Current evidence is largely based on short-term studies with limited diversity and variable dietary protocols. Future research should focus on long-term safety, standardized guidelines, and personalized strategies to better integrate KD into comprehensive MS care.},
}

@article {pmid41370089,
year = {2025},
author = {Yoshida, E and Arage, G and Rašo, LM and Merino, J and Larsson, SC and Ahmad, S},
title = {Meat Intake in Relation to Metabolomic Signatures, Gut Microbiome, and Cardiovascular Disease Risk: A Narrative Review.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuaf234},
pmid = {41370089},
issn = {1753-4887},
support = {2019-00977//Swedish Research Council/ ; 2022-01460//Swedish Research Council/ ; 20210351//Swedish Heart-Lung Foundation [Hjärt-Lungfonden/ ; //Swedish Cancer Society/ ; 2020-00989//FORMAS/ ; //Marcus Borgström Foundation/ ; //EFSD/Novo Nordisk/ ; //EpiHealth/ ; },
abstract = {Cardiovascular diseases (CVDs) continue to be a leading cause of mortality worldwide, with dietary habits playing a crucial role in CVD prevention. While current guidelines recommend reducing red meat consumption, findings from large-scale observational studies and clinical trials on the impact of red meat intake on CVD risk factors remain inconsistent. The reliance on self-reported dietary intake in observational studies and adherence to intervention in clinical trials might have contributed to inconsistencies. Recent advancements in metabolomics and microbiome research have shed light on the molecular mechanisms through which different types of meat intake may influence cardiovascular health. Meat-derived metabolites, such as trimethylamine N-oxide (TMAO) and branched-chain amino acids (BCAAs), have been implicated in CVD pathogenesis, with the gut microbiota further modulating these effects. In this narrative review we examined the relationship between meat intake, metabolomic profiles, the gut microbiome, and the influence of these variables on CVD risk. Articles published up to June 11, 2025, including reports of both observational and interventional studies, were comprehensively searched in the PubMed and ScienceDirect databases. A total of 74 relevant articles were selected for in-depth analysis. Overall, these studies suggested that red meat intake is linked to higher levels of TMAO, which is associated with increased CVD risk, and that diets rich in red and processed meats were generally associated with reduced gut microbiome diversity more than that found with chicken consumption. Furthermore, the findings of this review highlight the need for future research involving larger sample sizes, multi-omics approaches, and mediation analyses, alongside short-term randomized clinical trials, to elucidate the precise role of meat consumption in CVD risk.},
}

@article {pmid41370066,
year = {2025},
author = {Li, L and Yan, T and Yan, R and Zeng, X and Du, Q and Wu, Z and Pan, D},
title = {Precision probiotic development based on gut microbial biomarkers: from mechanistic insights to clinical translation.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo01850a},
pmid = {41370066},
issn = {2042-650X},
abstract = {The intricate interplay between individualized differences in gut microbiota and host health has garnered significant attention in contemporary biomedical research. This review elucidates the complex mechanisms governing the development of personalized gut microbial ecosystems and examines innovative modulation strategies, underscoring the imperative to transcend conventional "one-size-fits-all" paradigms in probiotic therapeutics. The gastrointestinal tract harbors a complex consortium of trillions of microorganisms. The enterotype paradigm categorizes the gut microbiota into three predominant clusters: Bacteroides-dominant, Prevotella-dominant, and Ruminococcus-dominant configurations. However, an individual's unique microbial signature is influenced by a multifactorial interplay of host genetics, dietary habits, birth modality, and environmental exposures, resulting in a microbial complexity that defies simplistic enterotype classification. Contemporary research has revealed that traditional dietary interventions for the modulation of gut microbiota often lack specificity and fail to account for individual microbial variations. In contrast, emerging probiotic and prebiotic approaches offer promising avenues for targeted microbial manipulation. To establish effective, individualized probiotic and prebiotic interventions, a comprehensive methodological framework is essential. This framework should integrate in vitro gut simulation models to replicate microbial ecosystems, in vivo studies to assess microbial colonization dynamics and metabolic impacts, and advanced computational approaches combining machine learning algorithms with multi-omics data analysis. Such an integrated approach facilitates the identification of gut microbial biomarkers and the development of precision probiotics, while requiring further refinement of algorithm-driven outcome prediction models and establishment of cross-population validation protocols, thereby accelerating the translation of gut microbiome research into personalized therapeutic strategies and advancing the frontier of precision medicine in gastrointestinal health.},
}

@article {pmid41370065,
year = {2025},
author = {Karademir, E and Arı Gedik, B and Bostan, ZZ and Gezmen Karadağ, M},
title = {Understanding the Effect of B Vitamins on Gut Microbiota: A Comprehensive Review.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuaf236},
pmid = {41370065},
issn = {1753-4887},
abstract = {The gut microbiota has important effects on health maintenance, protection against pathogens, modulation of the immune system, and synthesis of vitamins, such as certain B vitamins. Many factors influence the gut microbiome, with diet and micronutrients being of particular interest. B vitamins are water-soluble vitamins that are ingested with food and play a role as cofactors in many metabolic processes in the body. B vitamins are thought to play an active role in the health and functionality of the gut microbiota. B vitamins are both sources for the microbiota and are produced by the gut microbiota. Adequate levels of these vitamins maintain intestinal microbial balance, inhibit the growth of pathogenic bacteria, and support intestinal barrier function. Insufficient or excessive intake of B vitamins leads to changes in the gut microbiota. In addition, changes in the gut microbiota in disease states lead to vitamin deficiency. Adequate B vitamin intake and a healthy microbiota are important for maintaining B-vitamin function in the body. Although the mechanisms underlying the interaction between the gut microbiota and B vitamins are not fully understood, possible mechanisms of action are presented in this article. The aim of this review is to examine the effect of B vitamins on the gut microbiota.},
}

@article {pmid41370004,
year = {2025},
author = {Syed, S and Moayyedi, P and Kao, D and Patel, J and Marshall, JK and Surette, M and Narula, N},
title = {Combination Therapy With Fecal Microbiota Transplantation and Vedolizumab for Induction of Remission in Ulcerative Colitis: An Open-Label Pilot Study.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf284},
pmid = {41370004},
issn = {1536-4844},
support = {//Takeda Canada/ ; },
}

@article {pmid41369916,
year = {2025},
author = {Nguyen, NHA and Marlita, M and Ramis, J and Gomez-Gonzalez, MA and Rysova, M and Duarri, A and Puntes, VF and Sevcu, A},
title = {Response of Ocular Bacteria Exposure to Cerium Oxide Nanoparticles in Eye Drop Formulation.},
journal = {Current microbiology},
volume = {83},
number = {1},
pages = {68},
pmid = {41369916},
issn = {1432-0991},
support = {AC19/00080//Instituto de Salud Carlos III (PI18/00219; LUCIA) and ERA-NET EuroNanoMed III-ISCIII (AC19/00080; CELLUX)/ ; },
mesh = {*Cerium/pharmacology ; Humans ; *Bacteria/drug effects/genetics/isolation & purification/growth & development/classification ; *Nanoparticles/chemistry ; *Ophthalmic Solutions/pharmacology/chemistry ; *Eye/microbiology ; RNA, Ribosomal, 16S/genetics ; Microbiota/drug effects ; Bacterial Proteins/genetics ; },
abstract = {Cerium oxide nanoparticles (CeO2 NPs), a few nanometers in diameter, exhibit strong antioxidant and anti-inflammatory activity and are considered promising candidates for the treatment of ocular diseases. This study investigated the impact of CeO2 NPs, both in their naked form, and formulated as eye drops, on the bacteria inhabiting the ocular surface. The microbiome from healthy eyes was characterized through 16 S rRNA amplicon sequencing. The dominant bacterial genera included Staphylococcus, with lower abundances of Corynebacterium and Streptococcus, varying among the samples. Eye bacteria were isolated and exposed to both forms of CeO2 NPs to investigate cell growth, viability, and gene expression. Neither naked CeO2 NPs nor eye drop formulation affected the growth of Staphylococcus aureus and Staphylococcus epidermidis. In S. aureus, CeO2 caused down-regulation of rho (naked CeO2 NPs) and recA (eye drop form) genes related to the termination of transcription and DNA damage response, respectively. In S. epidermidis, the expression of lexA, recA, ftsZ, rho and icaC remained comparable between treated and control samples, while DNA damage response genes lexA and recA were up-regulated in C. amycolatum following exposure to CeO2 eye drops. These gene expression patterns revealed subtle changes in specific bacteria, indicating a short-term adaptive response to eye drop formulations. Overall, these results suggest that CeO2 NP eye drops have a minimal impact on the isolated bacterial strains. Nonetheless, comprehensive in vivo and clinical studies are necessary to validate these findings, given the inherent limitations of in vitro assays.},
}

*Cerium/pharmacology
Humans
*Bacteria/drug effects/genetics/isolation & purification/growth & development/classification
*Nanoparticles/chemistry
*Ophthalmic Solutions/pharmacology/chemistry
*Eye/microbiology
RNA, Ribosomal, 16S/genetics
Microbiota/drug effects
Bacterial Proteins/genetics

@article {pmid41369910,
year = {2025},
author = {Molnár, A and Lovas, M and Kiss, T and Knapp, DG and Lepres, LA and Váczy, KZ and Geml, J},
title = {From hop (Humulus lupulus L.) to beer: hop pellets as fungal vectors in dry-hopped craft beers.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf138},
pmid = {41369910},
issn = {1574-6968},
abstract = {Dry hopping, a popular technique in modern craft brewing, introduces non-sterile hop material that may act as a source of microorganisms. Although beer is generally considered microbiologically stable, recent findings indicate that hops can harbour viable fungal and bacterial strains with potential effects on beer quality and hop creep enzymes. We investigated the fungal DNA reservoir of commercial hop pellets and its transfer into beer during dry hopping. Using ITS2 metabarcoding, we characterized fungal communities in hop pellets, pre-hopping beer, and dry-hopped beer, complemented by untargeted volatile profiling (HS-SPME-GCMS). Hop pellets contained diverse fungal assemblages dominated by common foliar endophytes. Several yeast genera of fermentative or spoilage relevance were also detected, including Saccharomyces, Wickerhamomyces, Rhodotorula, and Debaryomyces. While most taxa were found only in hops, four genera (Wickerhamomyces, Vishniacozyma, Bipolaris, Curvularia) were additionally found in dry-hopped beer but absent from pre-hopping samples, indicating transfer from hops. Metabolomic screening revealed that, besides enrichment of hop-derived metabolites, dry hopping induced shifts in volatile profiles through increases in ethyl esters, higher alcohols, and short-chain fatty acids. Our results demonstrate that commercial hop pellets carry diverse fungal assemblages and that their DNA is detectable in beer after dry hopping, together with aroma shifts consistent with microbial or enzymatic activity.},
}

@article {pmid41369731,
year = {2025},
author = {Khan, B and Ullah, N and Maqbool, H and Khan, F and Khan, I and Khalid, A and Arshad, M and Paker, NP and Naz, I and Akmal, M and Munis, MFH and Chaudhary, HJ},
title = {Unravelling the Mechanistic Role of Soil Microbial Interactions in the Suppression of Phytopathogens in Vegetable Agroecosystems of Pakistan.},
journal = {Current microbiology},
volume = {83},
number = {1},
pages = {70},
pmid = {41369731},
issn = {1432-0991},
mesh = {*Soil Microbiology ; Pakistan ; *Vegetables/microbiology/growth & development ; *Plant Diseases/microbiology/prevention & control ; Fungi/physiology ; Bacteria/growth & development ; *Microbial Interactions ; Agriculture ; Crops, Agricultural/microbiology/growth & development ; },
abstract = {Soil-borne pathogens pose a significant threat to vegetable production in Pakistan, leading to considerable yield reductions and compromising crop quality. Conventional control methods, such as the use of chemical fungicides, are associated with environmental and health risks, highlighting the urgent need for sustainable and eco-friendly alternatives. Vegetable production in Pakistan is severely affected by loss of yields and degradation in quality due to soil-borne pathogens. The widespread use of chemical fungicides suggests the need for safer substitutes and efficient soil health management. The employment of biological approaches is suggested by concerns about soil health and management. Through competition, antibiosis, and systemically induced resistance, the beneficial soil microflora, growth-promoting bacteria (PGPB), plant growth-promoting fungi (PGPF), including arbuscular mycorrhizal fungi (AMF), Trichoderma spp., and other soil microorganisms work in concert to control soil diseases and restore soil health. When combined with crop rotation, biofumigation, and decreased tillage, organic amendments and agronomic techniques, such as compost, biochar, green manure, and cover crops, have been shown to lower soil pathogen loads, microbial diversity, and resilience while increasing crop yields. Integrated soil health management in vegetable crop profitability (e.g., potatoes, tomatoes, okra, and chilies) and sustainability is improved in the long run with the reduction of chemical inputs through the combination of biological, organic, and agronomic strategies. To improve soil health management in the vegetable sector, integrated microbiome-centered organic strategies are a priority. In-line advanced research, extension services, and a supportive policy framework are all aspects of future vegetable soil health management strategies, soil eco health, and vegetable sector transformation to meet expected soil health management in Pakistan. These strategies are meant to improve the resilience of Pakistan's food systems, promote sustainable agriculture, and safeguard the environment.},
}

*Soil Microbiology
Pakistan
*Vegetables/microbiology/growth & development
*Plant Diseases/microbiology/prevention & control
Fungi/physiology
Bacteria/growth & development
*Microbial Interactions
Agriculture
Crops, Agricultural/microbiology/growth & development

@article {pmid41369576,
year = {2025},
author = {Hakizimana, JC and Alagbonsi, AI},
title = {Genetic and environmental factors associated with lactose digestion in African populations.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00268.2025},
pmid = {41369576},
issn = {1531-2267},
abstract = {Background: Impaired lactose digestion, primarily resulting from lactase non-persistence (LNP), is widely observed across African and non-African populations; however, its prevalence differs according to genetic background and dietary practices. While numerous pastoralist cultures in Africa have independently developed lactase persistence (LP), a sizable portion of the population experiences primary or secondary lactose malabsorption, either as a natural genetic trait or as a secondary impairment resulting from intestinal damage. This review summarizes the genetic variants and environmental contributors associated with lactose digestion in Africa, highlighting ancestry-specific variants and the underrepresentation of African populations in prior studies. Methodology: A PRISMA 2020 guided systematic review searched PubMed, African Journals Online, Wiley Online Library, and Google Scholar (1970-June 2025) for studies on genetic and environmental contributors to lactose digestion in African groups. Inclusion focused on human studies reporting lactase persistence (LP)/LNP or secondary impaired lactose digestion. Data were extracted on variants, diagnostics, and outcomes. Results: Twenty-eight studies were included, predominantly from East African pastoralists (53.3%), where LP alleles, including -13910T and -14010C in MCM6 intron 13, reached frequencies of 40-43%. Southern or West/North African groups showed LNP rates >70%. Secondary impaired lactose digestion affected 65-68% of malnourished/infected children, highlighting enteropathy and infections. Genotype-phenotype discrepancies were noted, with statistical associations due to linkage disequilibrium (LD) but not direct causation. Conclusion: Impaired lactose digestion in Africa reflects genetic adaptations in pastoralists and environmental stressors like malnutrition. Population-specific diagnostics and interventions are needed, integrating microbiome and dietary research for resource-limited settings.},
}

@article {pmid41369321,
year = {2025},
author = {Wieser, NV and van Schajik, Y and Ghiboub, M and Frerichs, NM and Weiss, R and Davids, M and de Meij, TGJ and Niemarkt, HJ and Lefèvre, A and Emond, P and Derikx, JPM and de Jonge, WJ and Sovran, B},
title = {Longitudinal analysis of fecal tryptophan metabolites and microbiome composition in very preterm infants: impact of birth mode and feeding type.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2541031},
doi = {10.1080/19490976.2025.2541031},
pmid = {41369321},
issn = {1949-0984},
mesh = {Humans ; *Tryptophan/metabolism/analysis ; Infant, Newborn ; *Gastrointestinal Microbiome ; Female ; *Feces/chemistry/microbiology ; Longitudinal Studies ; Male ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Breast Feeding ; Infant, Premature/metabolism ; Cesarean Section ; Kynurenine/metabolism ; RNA, Ribosomal, 16S/genetics ; Infant ; },
abstract = {Preterm birth is associated with increased morbidity and mortality due to factors such as prolonged NICU stays, antibiotic treatments, and immature gastrointestinal and immune systems. These factors disrupt early gut microbial colonization, yet the functional metabolic implications remain understudied. Emerging evidence highlights the role of tryptophan metabolism as a mediator of host-microbiome interactions, critical for intestinal homeostasis and immune regulation. However, its dynamics and relationship with microbial composition in preterm infants are poorly understood. In this study, we longitudinally characterized the microbiome and 21 fecal bioactive tryptophan metabolites during the first month of life in 53 very preterm infants <30 weeks of gestation. Targeted tryptophan metabolomics and 16S rDNA sequencing revealed that cesarean delivery and supplemented feeding was associated with elevated host-derived kynurenine metabolites. Breastfeeding promoted beneficial microbiome colonization, including increased Staphylococcus and reduced Proteobacteria. Notably, Bifidobacterium abundance positively correlated with the AhR ligand indole-3-lactic acid, while Staphylococcaceae negatively associated with indole derivatives. Our findings underscore the link between diet, microbial composition, and tryptophan metabolism in very preterm infants. This work provides a foundation for exploring tryptophan's role in development, health, and disease, emphasizing the importance of early nutritional strategies.},
}

Humans
*Tryptophan/metabolism/analysis
Infant, Newborn
*Gastrointestinal Microbiome
Female
*Feces/chemistry/microbiology
Longitudinal Studies
Male
*Bacteria/classification/genetics/isolation & purification/metabolism
Breast Feeding
Infant, Premature/metabolism
Cesarean Section
Kynurenine/metabolism
RNA, Ribosomal, 16S/genetics
Infant

@article {pmid41369293,
year = {2025},
author = {Liu, R and Wei, H and Xu, Z and Liu, Y and He, J and Wang, Z and Wang, L and Luo, M and Fang, J and Baltar, F and Xu, Y and Liang, Q and Huang, L},
title = {Extensive halogenated organic compound reservoirs and active microbial dehalogenation in Mariana Trench sediments.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf273},
pmid = {41369293},
issn = {1751-7370},
abstract = {The hadal trenches, the deepest regions of the ocean, serve as the final sinks for marine particles and "tunnels" for material exchange between the ocean and Earth's interior. Despite their extreme conditions, the trench sediments contain high content of organic carbon and active microbial carbon turnover, are hotspots for deep-sea organic carbon degradation and unique microbial processes. However, little is known about the organic carbon components and microbial metabolisms driving their degradation in trench sediments. This study provides the first comprehensive quantification of total halogenated organic compounds (organohalides) in Mariana Trench sediments. The measured bulk organic halogen concentrations exceeded all previously reported individual compounds by orders of magnitude, with a mean stoichiometric ratio of 1:49 (halogen:carbon) in the sedimentary organic carbon pool. These findings suggest the trench sediments may represent a significant reservoir for organohalides. Metagenomic analysis of global ocean data shows significant enrichment of the genes for organohalides biodegradation (dehalogenation) in trench microbiomes than those in other marine environments. Putative dehalogenating microorganisms in trench sediments encompassed 16 phyla and 52 orders, capable of metabolizing 18 structurally diverse organohalide compounds, revealing an unexpectedly broad phylogenetic distribution of organohalides metabolism and versatile substrate specificity among trench microbial communities. High pressure microcosm experiments demonstrated rapid degradation of typical organohalide compounds and transcription of genes related to organohalides metabolisms, confirming an active organohalides degradation by trench microorganisms. These findings underscore the role of organohalides metabolism in organic carbon remineralization in hadal trenches, advancing our understanding of deep-sea carbon cycling and microbial survival.},
}

@article {pmid41369247,
year = {2025},
author = {Liu, Q and Zou, L and Chen, Y and Feng, J and Wei, Y and Zhang, M and Li, K and Zhao, Y and Zhou, D and Wang, W and Qi, D and Xie, J},
title = {Biocontrol efficiency and mechanism of novel Streptomyces luomodiensis SCA4-21 against banana Fusarium wilt.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0296824},
doi = {10.1128/spectrum.02968-24},
pmid = {41369247},
issn = {2165-0497},
abstract = {UNLABELLED: The soil-borne fungus Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) causes banana Fusarium wilt, a serious threat to global banana production. Biocontrol represents a promising alternative to conventional chemical control for managing this disease. Our previous studies identified Streptomyces luomodiensis SCA4-21 as a novel species with antifungal properties. Here, we show that the extract from strain SCA4-21 significantly inhibits Foc TR4 mycelial growth and spore germination, severely disrupting hyphal and spore ultrastructure. The extract also exhibited broad-spectrum activity against eight other phytopathogenic fungi. We identified 32 volatile organic compounds produced by strain SCA4-21, including five with known antifungal properties. In pot experiments, strain SCA4-21 inoculation not only significantly suppressed Foc TR4 infection in banana seedlings, with a biocontrol efficacy of 59.3%, but also markedly promoted plant growth. The inoculation significantly enriched beneficial bacterial genera (Streptomyces, Bacillus, Sphingomonas, Massilia, and Pseudomonas) and fungal genera (Mortierella, Gibellulopsis, and Xenomyrothecium), while reducing the pathogenic bacterium Pantoea and lowering Fusarium abundance to levels statistically indistinguishable from the control. Microbial function prediction based on 16S rRNA gene sequencing data revealed enhanced metabolic pathways, including carbohydrate metabolism, amino acid metabolism, and metabolism of terpenoids and polyketides. We propose that strain SCA4-21 combats banana Fusarium wilt through a synergistic mechanism involving antifungal compound production and recruitment of beneficial microbiota. These findings highlight strain SCA4-21 as a promising biocontrol agent for sustainable banana production.

IMPORTANCE: Banana (Musa spp.) is one of the most popular fruit crops and the fourth largest food crop in developing countries within tropical and subtropical regions. However, the emergence and rapid spread of strain Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) seriously hinder the development of the banana industry. Currently, there is no effective control measure available. Biological control holds potential due to its safety and effectiveness. Here, we found that the extract of Streptomyces luomodiensis SCA4-21 exhibited significant inhibitory effects on the hyphal growth and spore germination of Foc TR4, as well as severe destructive effects on its cell morphology and ultrastructure, and broad-spectrum antifungal activity. We also discovered that the inoculation of strain SCA4-21 significantly inhibited the infection of Foc TR4 in banana seedling corms, reduced the incidence index of banana Fusarium wilt, promoted the growth of banana seedlings, and enhanced beneficial microbes and metabolic pathways, suggesting that strain SCA4-21 is a promising biocontrol agent.},
}

@article {pmid41369197,
year = {2025},
author = {Moser, T and Moser, MJ and Mahnert, A},
title = {The best from both disciplines: integrating human and microbial signatures from whole genome sequencing to advance cancer diagnostics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0003924},
doi = {10.1128/msystems.00039-24},
pmid = {41369197},
issn = {2379-5077},
abstract = {Liquid biopsies are transforming oncology, enabling earlier diagnosis, dynamic treatment guidance, and personalized precision medicine, yet current approaches focusing mainly on circulating host cell-free DNA (cfDNA) neglect crucial information within co-existing microbial cell-free DNA (mcfDNA). This review argues for the combined potential of simultaneously analyzing host and microbial signals from samples like blood, specifically focusing on circulating tumor DNA (ctDNA) as the key host component. While ctDNA analysis is already used to guide treatment decisions, the detection of mcfDNA-although present in smaller amounts compared to total cfDNA-offers a distinct and complementary opportunity to identify disease-causing microbes and investigate the host-associated microbiome in the context of cancer. Leveraging machine learning strategies is essential to integrate these multi-view data sets and realize their full potential for enhancing liquid biopsy applications, particularly in early cancer detection.},
}

@article {pmid41369187,
year = {2025},
author = {Calderón-Osorno, M and Rojas-Jimenez, K},
title = {Depth-driven decline in viral diversity unveils potential novel viruses in global deep-sea ecosystems.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {12},
pages = {},
doi = {10.1099/mic.0.001632},
pmid = {41369187},
issn = {1465-2080},
mesh = {*Seawater/virology ; *Viruses/genetics/classification/isolation & purification ; *Biodiversity ; Ecosystem ; Metagenomics ; Phylogeny ; Microbiota ; Oceans and Seas ; Metagenome ; },
abstract = {Deep-sea ecosystems remain poorly understood due to exploration challenges. Despite the advancements metagenomics have brought to the understanding of the ocean microbiome, the diversity of marine viruses, particularly in the deep sea, is still not well characterized. In this study, we analysed the impact of depth on the composition and diversity of marine viruses in deep-sea waters at a global scale. Raw reads from deep-sea shotgun DNA sequences were retrieved from the Tara and Malaspina expeditions, encompassing depths from 270 to 4,005 m. A total of 80 samples containing viral reads were identified and analysed through a comprehensive bioinformatics pipeline, including quality assessment, taxonomic classification and metabolic annotation. The analysis reveals that microbial viral diversity significantly decreases with depth, with shallower waters exhibiting higher species richness. We determined that a substantial proportion of deep-sea viral sequences remains unclassified - up to 31.9% at depths of 270-1,000 m and 9.6% at 2,400-4,005 m. Additionally, a higher abundance of auxiliary metabolic genes was observed at shallower depths, indicating potential roles in host metabolism and adaptation. Our findings reveal the deep ocean as a vast, largely unexplored source of microbial viral diversity. This research emphasizes how depth influences viral diversity and community makeup in deep-sea environments, underscoring the need for further exploration to fully grasp their complexity and ecological roles.},
}

*Seawater/virology
*Viruses/genetics/classification/isolation & purification
*Biodiversity
Ecosystem
Metagenomics
Phylogeny
Microbiota
Oceans and Seas
Metagenome

@article {pmid41369016,
year = {2025},
author = {Southwood, LL and Long, A and Perez, J and Daniel, S and Bittinger, K and Aitken, M and Redding, L},
title = {Effect of surgical antimicrobial prophylaxis duration for colic surgery on complications and resistome.},
journal = {Equine veterinary journal},
volume = {},
number = {},
pages = {},
doi = {10.1002/evj.70137},
pmid = {41369016},
issn = {2042-3306},
support = {//Raymond Firestone Research Foundation/ ; },
abstract = {BACKGROUND: Based on human studies, surgical antimicrobial (AMD) prophylaxis (SAP) beyond 24 h is unnecessary and potentially detrimental.

OBJECTIVE: To compare clinical and microbiological outcomes in patients receiving 24- or 72-h of SAP for colic surgery.

STUDY DESIGN: Prospective randomised clinical trial.

METHODS: Horses that recovered from colic surgery were considered. Exclusion criteria were (1) age <2 years; (2) Miniature Horses, pony, and draught breeds; (3) azotaemia; (4) recent hospitalisation, colic surgery, or AMDs; (5) local AMD administration. Eligible horses were randomly assigned to receive SAP with potassium penicillin and gentamicin for 24- or 72-h. Clinical data and complications were compared between SAP groups. Admission and discharge faecal samples from a subset of horses (N = 49) underwent shotgun metagenomic sequencing on an Illumina platform. Host reads were filtered by aligning to reference genomes using the Burrows-Wheeler Aligner, and taxonomic classification was performed with kraken2. Sequencing reads were aligned to the Comprehensive Antimicrobial Resistance Database (CARD)5 and characterised using the AMR++ pipeline. The microbiome/resistome was characterised and compared between SAP groups over time.

RESULTS: One hundred and forty horses completed the study (24-h N = 71 and 72-h N = 69). The only clinical variable that was different between SAP groups was age (24-h median age 16 [IQR 9, 20] and 72-h 12 [6, 18] years, p = 0.03). There was no significant difference between groups for any complications including incisional infection (24-h 17 [95% CI 10-27]% and 72-h 16 [9-26]%, p = 0.9). Time was the main driver of changes in the microbiome/resistome: alpha diversity decreased while AMD resistance genes associated with administered AMD increased between admission and discharge. Discharge beta-lactam resistance genes were significantly higher in the 72-h than the 24-h group.

MAIN LIMITATIONS: Single hospital, small numbers for complications, clinicians not blinded to SAP group.

CONCLUSIONS: SAP for 24-h is recommended for horses undergoing colic surgery.},
}

@article {pmid41368940,
year = {2025},
author = {Choudhury, A and Scano, C and Barton, A and Kearney, CM and Greathouse, KL},
title = {Precision Antimicrobial Therapy Against Fusobacterium nucleatum Using Bioengineered Probiotics Expressing Guided Antimicrobial Peptides (gAMPs).},
journal = {Microbial biotechnology},
volume = {18},
number = {12},
pages = {e70241},
doi = {10.1111/1751-7915.70241},
pmid = {41368940},
issn = {1751-7915},
support = {//Baylor University/ ; //Office of Vice Provost and Research Post-Doctoral Research Fellowship Grant/ ; //Robbins College of Health and Human Sciences Post-Doctoral Fellow Research Support Grant/ ; },
mesh = {*Fusobacterium nucleatum/drug effects/growth & development/physiology ; *Probiotics ; *Antimicrobial Peptides/genetics/pharmacology/metabolism ; Humans ; Biofilms/drug effects/growth & development ; *Anti-Bacterial Agents/pharmacology ; *Fusobacterium Infections/microbiology/therapy ; },
abstract = {Colorectal cancer (CRC) is a leading cause of cancer-related mortality, with Fusobacterium nucleatum (F. nucleatum) identified as a key contributor to its progression. This study explores a novel therapy that targets this pathogen by using a bioengineered probiotic that expresses guided antimicrobial peptides (gAMPs) to selectively inhibit F. nucleatum. Lactococcus lactis MG1363 was engineered to express gAMPs derived from Ovispirin and Cathelin-related peptide SCF, linked to a Statherin-derived guide peptide that binds specifically to the F. nucleatum membrane porin FomA. The bacteria expressed the AMP/gAMP under the induction of the PNisA promoter by nisin and secreted it via the extracellular secretion signal usp45. The resultant synthetic peptides and probiotics were assayed for antimicrobial activity against the targeted F. nucleatum and other non-target bacteria. Biofilm inhibition and growth kinetic assays were performed with synthetic peptides in vitro or the probiotic in co-culture with a polymicrobial community. Statherin-derived guide peptide enhanced the binding affinity to F. nucleatum, significantly increasing attachment compared to control peptides. In vitro assays revealed that both unguided and guided AMPs effectively inhibited biofilm formation in F. nucleatum, with gAMPs showing reduced toxicity against non-target bacteria. The gAMPs were more effective in modulating growth kinetics, exhibiting selective toxicity towards F. nucleatum at lower concentrations. Co-culture experiments in a simulated human gut microbiome showed the gAMP probiotic maintained microbial diversity while effectively reducing F. nucleatum abundance. Quantitative PCR and 16S rRNA sequencing confirmed that gAMP treatment preserved the richness of the microbiota, contrasting with significant dysbiosis observed in control samples. These findings support the potential of engineered probiotics as a therapeutic approach that targets CRC-associated F. nucleatum.},
}

*Fusobacterium nucleatum/drug effects/growth & development/physiology
*Probiotics
*Antimicrobial Peptides/genetics/pharmacology/metabolism
Humans
Biofilms/drug effects/growth & development
*Anti-Bacterial Agents/pharmacology
*Fusobacterium Infections/microbiology/therapy

@article {pmid41368873,
year = {2025},
author = {Honcharyuk, I and Caridi, B and Pinco, P and Ferri, S and De Giani, A and Baeri, A and Amoroso, C and Massironi, S and Facciotti, F},
title = {The intratumor microbiome and cancer immunity: from pathogenesis to therapeutic opportunities through artificial intelligence.},
journal = {Expert review of clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1080/1744666X.2025.2602537},
pmid = {41368873},
issn = {1744-8409},
abstract = {INTRODUCTION: The intratumor microbiome is a key component of the tumor microenvironment, influencing oncogenesis, immune modulation, and therapeutic responses. Bacteria, fungi, and viruses infiltrate tumor tissues, modulating local immunity and potentially conditioning the efficacy of immune checkpoint inhibitors. While mucosal-origin tumors exhibit an expected microbial presence, sterile organ tumors, such as brain and breast, reveal less intuitive microbial infiltration.

AREAS COVERED: This review evaluated the interplay between the intratumoral microbiota and the immune system across different stages of carcinogenesis, including initiation, progression, and metastasis. Sources included PubMed, Embase, and Google Scholar; searches covered December 2024 to October 2025. We examine microbial metabolites, immune hijacking, and routes of dissemination. We also overview technologies for tumor microbiome characterization, including next-generation sequencing, spatial transcriptomics, and artificial intelligence (AI), with machine learning and deep learning, to support diagnostics, prediction of treatment response, and personalized oncology.

EXPERT OPINION: Defining the spatial localization and functions of intratumoral microorganisms is crucial for robust biomarkers and tailored interventions. Integrating AI with spatial and multi-omics data offers major opportunities but faces obstacles - data heterogeneity, model interpretability, and ethical issues. Priorities include standardized protocols, high-resolution spatial profiling, external validation, and expertly annotated datasets to unlock microbiome-informed precision oncology.},
}

@article {pmid41368437,
year = {2025},
author = {Kedlaya Herga, S and Kudva, A and Shenoy M, S and Vasudevan, TG and Prabhu, V and Upadhya, R and Bharath Prasad, AS},
title = {Streptococcus spp. in oral cancer: host-microbe interactions, mechanistic insights, and diagnostic implications.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1688701},
pmid = {41368437},
issn = {2235-2988},
mesh = {Humans ; *Mouth Neoplasms/microbiology/diagnosis/pathology ; *Streptococcus/physiology ; Mouth/microbiology ; *Host Microbial Interactions ; Tumor Microenvironment ; *Streptococcal Infections/microbiology/diagnosis ; Biofilms/growth & development ; *Host-Pathogen Interactions ; *Carcinoma, Squamous Cell/microbiology/diagnosis ; },
abstract = {Cancers of the oral cavity, particularly the widely prevalent oral squamous cell carcinoma, are associated with microbial dynamics within the oral niche. Among them, oral Streptococcus sp. - once neglected as a commensal habitat of the oral cavity - is currently highlighted for its pivotal dual interplay in the progression and suppression of oral cancers. In this comprehensive review, we describe the association of these oral streptococcal species with oral cancer in detail - right from their abundance and depletion during the progression of the disease, mechanistic synergy involving factors such as the surface receptors playing an intricate role in biofilm and co-adhesion strategies, to the inflammatory interplay in cancerous cells, and metabolic reprogramming associated with oral cancer. We also highlight oncogenic and onco-mitigating oral streptococci as biomarkers, observing a complex microbial interaction regulating tumor initiation and development. This review serves as a novel direction to address streptococcal mediators in oral cancer by bridging research gaps in mechanistic evidence and proposing effective prospects that can address deeper exploration of streptococcal dualistic role in the tumor microenvironment to decipher effective theragnostic strategies to manage oral cancer.},
}

Humans
*Mouth Neoplasms/microbiology/diagnosis/pathology
*Streptococcus/physiology
Mouth/microbiology
*Host Microbial Interactions
Tumor Microenvironment
*Streptococcal Infections/microbiology/diagnosis
Biofilms/growth & development
*Host-Pathogen Interactions
*Carcinoma, Squamous Cell/microbiology/diagnosis

@article {pmid41368349,
year = {2025},
author = {Lee, JY and Kim, DH and Choi, JW and Shong, M and Lee, CK},
title = {Utility of Machine Learning to Characterize Gut Microbiota Dysbiosis and Its Clinical Implications in Inflammatory Bowel Disease.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {16857-16870},
pmid = {41368349},
issn = {1178-7031},
abstract = {Inflammatory bowel disease (IBD) arises from complex interactions among host genetics, immune dysregulation, environmental factors, and the gut microbiome. Numerous studies have demonstrated alterations in microbial composition and function, including reduced diversity and changes in metabolic pathways. Traditional biostatistical approaches, such as differential abundance analysis, have advanced our understanding but are remain limited in handling nonlinear and high-dimensional data. Machine learning (ML) complements these methods by integrating heterogeneous datasets and uncovering hidden patterns that improve classification and predictive accuracy. In IBD, delayed diagnosis and the lack of reliable biomarkers highlight the need for computational tools that can translate complex microbiome data into clinically actionable insights. ML and deep learning (DL) have expanded analytical capabilities, enabling disease classification, subtype differentiation, and prediction of therapeutic responses. This review provides an integrative perspective on how ML and DL are reshaping microbiome-based IBD research, summarizing their strengths, limitations, and essential considerations for clinical translation. Future progress will depend on standardized microbiome assays, rigorous benchmarking, and the integration of multi-omics data to elucidate host-microbe interactions. With these advancements, ML- and DL-based approaches may offer precise diagnostics and personalized treatment strategies, transforming microbiome research into practical tools for IBD care.},
}

@article {pmid41368322,
year = {2025},
author = {Pongking, T and Chen, X and Tunbenjasiri, K and Zhang, L and Kraiklang, R and Pinlaor, S and Sangka, A and Lulitanond, A and Blair, D and Pinlaor, P},
title = {Impact of Fermentation on Bacterial and Fungal Microbiome Interactions in Pla-Ra, a Traditional Thai Food.},
journal = {International journal of food science},
volume = {2025},
number = {},
pages = {5530574},
pmid = {41368322},
issn = {2314-5765},
abstract = {Pla-ra, a traditional Thai fermented fish product, undergoes complex microbial and biochemical transformations that contribute to its unique flavor and aroma. This study investigated the effects of fermentation on the microbiome of pla-ra, focusing on bacteria-fungi interactions. Freshwater fish, combined with salt and roasted rice, were sampled after 1 and 6 months of fermentation. Bacterial and fungal communities in these pla-ra samples were characterized using next-generation sequencing of the 16S rRNA (V3-V4 region) and ITS2 regions, respectively. Results demonstrated that initial bacterial contamination levels were within standard limits, while fungal contamination (estimated by culture) exceeded pla-ra guidelines. Both pH and salinity increased slightly during fermentation. A decrease in bacterial alpha diversity and an increase in fungal diversity during fermentation were observed. Bacterial genera such as Candidatus Hydrogenedens, Bellilinea, and various unclassified Acidobacteria groups declined, while Enhydrobacter, Dermacoccus, and Halanaerobium increased, indicating adaptation to increased salinity. Penicillium, the dominant fungal taxon, has a potential role in flavor development. Importantly, microbial network analysis revealed dynamic interactions, including an inhibitory effect of Penicillium on Dermacoccus and Enhydrobacter, but only early in fermentation. KEGG pathway analysis highlighted upregulation of glycerophospholipid metabolism and downregulation of lipid metabolism. In conclusion, our results demonstrate that pla-ra fermentation decreases bacterial and increases fungal diversity, impacting bacteria-fungi interactions and correlations in ways that may influence taste and smell. This information contributes to optimizing traditional fermentation practices and enhancing product quality and safety.},
}

@article {pmid41368282,
year = {2025},
author = {Tian, X and Du, TY and Lu, W and Kumla, J and Tarafder, E and Priyadarshani, TDC and Perera, RH and Hapuarachchi, KK and Suwannarach, N},
title = {The mushroom matrix: an engineered mycelium-derived biochar platform for advanced biotechnological applications.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1707953},
pmid = {41368282},
issn = {2296-4185},
abstract = {Mushroom cultivation generates vast amounts of spent substrate, while the controlled growth of fungal mycelium offers a dedicated feedstock for advanced materials. This review synthesizes the science of mushroom-derived biochars, a distinct class of biomaterials sourced from this underutilized biomass. This review demonstrates that the inherent biological architecture of fungal matter, specifically its chitinous framework and nitrogen-rich composition, is preserved through pyrolysis to create biochars with superior functionality. We demonstrate how these materials transcend their traditional role as soil amendments to serve as programmable platforms for biotechnology. The review explores how pyrolysis parameters and advanced synthesis methods, such as chemical activation and co-pyrolysis, can be precisely tuned to engineer bespoke properties, including ultra-high surface areas (>1200 m[2]/g) and enhanced contaminant affinity. A central focus is placed on the unique capacity of mushroom biochars to act as prebiotic scaffolds that directly modulate microbial communities, drive biogeochemical cycles, and facilitate breakthrough applications. By mapping the journey from mycelium to advanced mycomaterials, this work charts a course for the intentional design of tailored myco-materials to address pressing global challenges in environmental remediation, sustainable agriculture, energy storage, and sensing technologies.},
}

@article {pmid41368212,
year = {2025},
author = {Saint-Cyr, M and Shakya, E and Siebert, JC and Hill, EB and Krebs, NF and deZoeten, E and Borengasser, SJ},
title = {Network-Based Multiomic Nutrient-Associated Predictive Models for Inflammatory Bowel Disease.},
journal = {Current developments in nutrition},
volume = {9},
number = {11},
pages = {107567},
pmid = {41368212},
issn = {2475-2991},
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a multifactorial disease involving a complex interplay between host physiology, the gut microbiome, and environmental factors such as diet and nutrition. Multiomic analyses may help to identify potential nutrient-associated omic predictors of IBD, allowing for the design of targeted dietary approaches for disease prevention and management.

OBJECTIVES: Our objective was to apply the bioinformatics tool, Consolidated Analysis of Network Topology and Regression Elements (CANTARE), to an integrated multiomics dataset to generate nutrient-associated predictive models for IBD.

METHODS: We previously used a published data set of microbiome relative abundance (mb), untargeted metabolomics (met), and microbial-derived enzymes (e) in stool samples from 153 adults (IBD = 111, healthy control = 42) to build a network of cross-omic relationships that differed by IBD status. We now revisit this network to identify diet-associated predictive models of IBD using linear regression via the CANTARE workflow.

RESULTS: The network included 20 literature-supported nutrient-associated predictors across 3 subnetworks. We created 1 predictive model from each subnetwork. These models (M1, M2, and M3) contained 3, 4, and 11 predictors, respectively. Model performance was high, with area under the receiver operating characteristic curve of 0.87, 0.90, and 0.95 and pseudo-R [2] of 0.42, 0.55, and 0.71 (all permutation P values < 0.001) for M1, M2, and M3, respectively. Some metabolites, such as histamine, were associated with greater odds of IBD, whereas others, such as ascorbate (vitamin C), pyridoxamine (vitamin B6), and choline, were associated with lower odds of IBD.

CONCLUSIONS: CANTARE provides an unbiased and comprehensive strategy that can integrate multiple omics to identify potential nutrient-associated predictors of IBD. Our models support the generation of hypotheses for follow-up targeted investigation in future dietary interventions for the management of IBD.},
}

@article {pmid41368208,
year = {2025},
author = {McNamara, KM and Latour, YL and Hawkins, CV and Williams, KJ and Barry, DP and Allaman, MM and Delgado, AG and Chetyrkin, SV and Calcutt, MW and Piazuelo, MB and Washington, MK and Zhao, S and Coburn, LA and Gobert, AP and Wilson, KT},
title = {Aconitate Decarboxylase 1 Downregulates Colitis and Maintains Homeostasis of the Gut Metabolome and Microbiome.},
journal = {Gastro hep advances},
volume = {4},
number = {9},
pages = {100748},
pmid = {41368208},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Aconitate decarboxylase 1 (ACOD1) is implicated in innate immunity and inflammatory responses. We determined the role of ACOD1 in colon inflammation and colitis-associated carcinoma.

METHODS: Human inflammatory bowel disease transcriptomic datasets and banked RNA samples were interrogated. C57BL/6 wild-type (WT) and Acod1 [-/-] mice were infected with Citrobacter rodentium or given 1 or 2 cycles of 4% dextran sulfate sodium (DSS) as models of colitis. For colitis-associated carcinoma, mice were given 12.5 mg/kg azoxymethane followed by 3 cycles of 4% DSS. Clinical and histological parameters were assessed. Tissues and stool were used for metabolomic and 16S microbiome analyses, respectively.

RESULTS: ACOD1 expression is increased in ulcerative colitis and Crohn's disease tissues compared to controls. C. rodentium infection caused body weight loss only in Acod1 [-/-] mice, which had increased histologic injury vs WT. In DSS colitis, we observed decreased colon length and increased histologic injury in Acod1 [-/-] vs WT mice. Azoxymethane-DSS-treated Acod1 [-/-] animals exhibited more inflammation and injury but no difference in tumorigenesis. There was an altered metabolome in Acod1 [-/-] vs WT colon tissues, and during colitis, purine metabolism was most markedly affected. 16S microbiome analysis revealed significant differences in phyla and genera; notably an increase in Bacteroidetes and decrease in Proteobacteria in Acod1 [-/-] mice, indicating a dysbiotic state.

CONCLUSION: While ACOD1 is increased in human inflammatory bowel disease tissues, our data indicate that this enzyme has a protective role in acute and chronic experimental colitis and is associated with prevention of intestinal dysbiosis and stabilization of the metabolome.},
}

@article {pmid41368198,
year = {2025},
author = {Chamarthi, VS and Shirsat, P and Sonavane, K and Parsi, S and Ravi, U and Ponnam, HC and Bindlish, S and Nadler, EP and Kashyap, R and Ro, S},
title = {The impact of ultra-processed foods on pediatric health.},
journal = {Obesity pillars},
volume = {16},
number = {},
pages = {100203},
pmid = {41368198},
issn = {2667-3681},
abstract = {INTRODUCTION: Ultra-processed foods (UPFs) have become increasingly incorporated into pediatric diets, accounting for approximately 67 % of the total energy consumption in United States (US) children. Manufactured through industrial processing and enriched with excess sugars, unhealthy fats, and sodium, while lacking essential nutrients, UPFs present a substantial public health concern. We aimed to conduct a comprehensive review of the impact of UPFs on pediatric health.

METHODS: We reviewed the effects of UPF on pediatric health using data from observational studies, systematic reviews, and policy reports. Our review explored the social, environmental, and economic drivers of UPF consumption, associated health consequences, and proposed mitigation strategies. We also examined National Health and Nutrition Examination Survey (NHANES) data, the 2025 US Dietary Guidelines Advisory Committee's (USDA) report, and the Make America Healthy Again (MAHA) commission findings.

RESULTS: UPF intake has dramatically increased during early childhood, with toddlers and school-aged children obtaining 47 % and 59.4 % of their daily calories, respectively, from UPFs. Higher consumption is linked to pediatric obesity, cardiometabolic risks such as insulin resistance and metabolic dysfunction-associated steatotic liver disease (MASLD), mental health concerns, and gut microbiome disruption. Early-life exposure to UPFs can establish unhealthy dietary patterns that persist into adulthood, raising the risk of chronic disease. Greater UPF consumption is often observed among lower-income families, highlighting a key health disparity.

CONCLUSION: UPF consumption is a modifiable risk factor for non-communicable diseases in children. Addressing it requires urgent, coordinated action at multiple levels. Strategies include UPF and sugar-sweetened beverage screening during well-child visits, policy restrictions on food marketing, clearer nutrition labeling, healthier school meals, and personalized family-centered dietary counseling. Clinicians need standardized tools and training to counsel families effectively. Policy initiatives should prioritize prevention-focused measures to protect children's health.},
}

@article {pmid41368072,
year = {2025},
author = {Bourquin, M and Peter, H and Michoud, G and Geers, A and , and Busi, SB and Battin, TI},
title = {Glacier influence shapes the genomic architecture of the downstream aquatic microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf076},
pmid = {41368072},
issn = {2730-6151},
abstract = {The factors and processes that shape microbial genomes and determine the success of microbes in different environments have long attracted scientific interest. Here, leveraging 2855 metagenome-assembled genomes sampled by the Vanishing Glacier Project from glacier-fed streams (GFSs), we shed light on the genomic architecture of the benthic microbiome in these harsh ecosystems-now vanishing because of climate change. Owing to glacial influence, the GFS benthic habitat is unstable, notoriously cold, and ultra-oligotrophic. Along gradients of glacial influence and concomitant variation in benthic algal biomass across 149 GFSs draining Earth's major mountain ranges, we show how genomes of GFS bacteria vary in terms of size, coding density, gene redundancy, and translational machinery. We develop a novel, phylogeny-rooted analytical framework that allows pinpointing the phylogenetic depth at which patterns in genomic trends occur. These analyses reveal both deep- and shallow-rooting phylogenetic patterns in genomic features associated with key GFS taxa and functional potential relevant to live in these ecosystems. Additionally, we highlight the role of several clades of Gammaproteobacteria in shaping community-level genomic architecture. Our work shows how genome architecture is shaped by selective environmental constraints in an extreme environment. These insights are important as they reveal putatively important adaptations to the GFS environment which is now changing at rapid pace due to climate change.},
}

@article {pmid41368028,
year = {2025},
author = {Huang, T and Tang, X and Ye, Q and Yuan, M and Zhang, X and He, J and Cao, Y and Hu, Q and Xiang, R},
title = {Effect of dietary supplementation with Vitex negundo L. var. cannabifolia extract on the growth performance, blood chemistry, gut morphology, and gut microbiota of broilers.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1713722},
pmid = {41368028},
issn = {2297-1769},
abstract = {The aim of this study is to evaluate the effects of Vitex negundo L. var. cannabifolia extract (VNE) on the growth performance, antioxidant status, blood chemistry, and cecal microbiota of broilers. A total of 240 one-day-old partridge broilers in total were randomly assigned to 5 treatment groups of 48 chicks each, which were divided into 6 replicates of 8 chicks. The first group (Control) was given the basal diet (only); the second group (Positive) was given the basal diet with 300 mg/kg of Macleaya cordata extract, and the low-dose group (Low), the middle-dose group (Mid) and the high-dose group (High) were given the basal diet with VNE at a dose of 1.3, 2.6 and 3.9 g/kg diet, respectively. The results showed significant improvements (p < 0.01) in growth performance, with significant improvements in body weight, weight gain, and feed conversion ratio at 3.9 g/kg diet. Broilers in the high-dose VNE group exhibited a significant reduction in serum total cholesterol (TC), alanine aminotransferase (ALT), and albumin (ALB) compared to the control group. Furthermore, this group showed a concurrent increase in immunoglobulins (IgA, IgG, and IgM). Furthermore, the morphology and microbial content of the jejunum and ileum were improved in broilers fed on a diet supplemented with a high dose of VNE compared to the control group. Cecal microbiome analysis showed that VNE addition obviously improved cecal microbial composition, as indicated by the increased relative abundance of Clostridia vadinBB60, the Rikenellaceae Rc9 gut_group, Christensenellaceae_R-7_group, Clostridia UCG-014, and Anaerofilum. In conclusion, dietary supplementation with VNE increased the productive performance, immunity, and blood chemistry profile, while modulating cecal microbiota in broiler chicks.},
}

@article {pmid41367440,
year = {2025},
author = {Kapinos, A and Rhoads, S and Yossuck, P and Gunasekaran, V},
title = {Distinguishing Intraventricular Hemorrhage From Infectious Etiologies in Febrile Late Preterm Neonates: Case Studies in Antibiotic Stewardship.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e96379},
pmid = {41367440},
issn = {2168-8184},
abstract = {Intraventricular hemorrhage (IVH) is a well-recognized complication in preterm infants, but its presentation as fever can be easily overlooked, leading to extensive sepsis workups and delayed diagnosis. This case report presents two late preterm infants who developed fever as the primary presenting symptom of IVH. Distinguishing IVH-related fever from that due to infectious causes can be challenging in this vulnerable population, where overuse of antimicrobials carries significant risks, including altered microbiome development, necrotizing enterocolitis, and antimicrobial resistance. Incorporating early diagnostic evaluation for IVH through cranial ultrasound in late preterm infants presenting with unexplained fever may avoid unnecessary tests and promote judicious antimicrobial use while improving overall neonatal outcomes.},
}

@article {pmid41367425,
year = {2025},
author = {An, Y and Xu, M and Kang, Y and Fang, J and Zhang, X},
title = {Tripartite exacerbation stratification in AECOPD suggests a gradient of lower airway dysbiosis: a metagenomic transition from commensal taxa to pseudomonadota dominance.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1588029},
pmid = {41367425},
issn = {1664-302X},
abstract = {BACKGROUND: The frequency of acute exacerbations (AECOPD) is a critical predictor of disease progression in chronic obstructive pulmonary disease (COPD). However, the dynamics of the lower respiratory microbiome across a spectrum of exacerbation frequency remain poorly characterized, limiting insights into microbial drivers of susceptibility.

METHODS: We conducted a cross-sectional study of 39 hospitalized AECOPD patients, stratified into non-frequent (NFE, ≤ 1 event/year, n = 11), moderate (ME, 2 events/year, n = 13), and frequent exacerbators (FE, ≥3 events/year, n = 15). Metagenomic next-generation sequencing (mNGS) was performed on bronchoalveolar lavage fluid (BALF) to profile the airway microbiome.

RESULTS: Microbial alpha diversity exhibited a significant, graded decline from NFE to FE groups (e.g., Shannon index: NFE 3.68 ± 0.34, ME 3.02 ± 1.02, FE 0.84 ± 0.54; p < 0.05). Beta diversity analysis revealed distinct community clustering by exacerbation phenotype (PERMANOVA R[2] = 0.19, p = 0.001). The FE group was characterized by a striking dominance of Pseudomonadota (relative abundance: 72.25%), which correlated positively with exacerbation frequency (r = 0.536, p < 0.001). In contrast, commensal taxa including Streptococcus (r = -0.814, p < 0.0001) and others within the Bacillota and Bacteroidota phyla were depleted in FE and were negatively associated with exacerbation frequency. Twelve exacerbation-resilient taxa (83.3% belonging to Bacillota/Bacteroidota) were positively correlated with FEV1% predicted (r = 0.322-0.483, p < 0.05). Alpha diversity indices showed a strong inverse association with exacerbation frequency (r = -0.84 to -0.86, p < 0.001) but not spirometric measures.

CONCLUSION: Our findings delineate a gradient of airway microbial dysbiosis along the exacerbation frequency spectrum in COPD. The exacerbation-prone phenotype is defined by a loss of microbial diversity, expansion of Pseudomonadota, and depletion of potentially protective commensals. These microbiome features represent promising biomarkers for identifying high-risk patients and may inform future microbiome-targeted therapeutic strategies.},
}

@article {pmid41367422,
year = {2025},
author = {Yu, H and Guo, Y and Li, J and Fu, R and Zhang, Y and Guo, W},
title = {Disruption of the gut bile acid-microbiota axis precedes severe bronchopulmonary dysplasia in preterm infants.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1705965},
pmid = {41367422},
issn = {1664-302X},
abstract = {BACKGROUND: Bronchopulmonary dysplasia (BPD) remains a major cause of morbidity in preterm infants, yet current diagnostic criteria are delayed and underlying mechanisms are incompletely defined. Evidence suggests that intestinal dysbiosis may influence pulmonary outcomes via the gut-lung axis, but the metabolic mediators of this interaction remain unclear.

METHODS: We conducted a prospective cohort study of 50 preterm infants (≤ 32 weeks gestation), stratified by BPD severity at 36 weeks. Stool samples collected on postnatal day 7 underwent 16S rRNA sequencing and targeted bile acid metabolomics. Differential features were identified via multivariate statistics and LEfSe. Spearman correlation analysis explored bile acid-microbiota interactions. An interpretable machine learning model (XGBoost) incorporating bile acid and microbial features was developed and validated using five-fold cross-validation and an independent test set.

RESULTS: Infants with severe BPD showed significantly reduced levels of 16 bile acids-including primary, secondary, and sulfated species-compared to non-BPD controls. Gut microbiome β-diversity differed significantly among groups, with enrichment of opportunistic Proteobacteria (e.g., Brevundimonas) in severe BPD. Negative correlations were observed between depleted bile acids and enriched bacterial genera. The XGBoost model predicted BPD severity with 80% accuracy (AUC = 0.91), leveraging key features such as chenodeoxycholic acid (CDCA), hyocholic acid (HCA), and Brevundimonas.

CONCLUSIONS: Preterm infants who develop severe BPD exhibit early disruption of the bile acid-microbiota axis, characterized by reduced bile acid levels and enrichment of opportunistic taxa. Integrating these features within interpretable machine-learning models enables accurate early risk stratification and provides mechanistic insights beyond traditional inflammation-based frameworks. Validation in larger, multicenter cohorts is warranted to refine biomarker panels and explore targeted interventions that modulate bile acid signaling or microbial ecology to prevent or attenuate BPD.},
}

@article {pmid41367416,
year = {2025},
author = {Liu, SH and Yang, XF and Liang, L and Song, BB and Song, XM and Yang, YJ and Alhoot, MA},
title = {Regulatory mechanisms of the gut microbiota-short chain fatty acids signaling axis in slow transit constipation and progress in multi-target interventions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1689597},
pmid = {41367416},
issn = {1664-302X},
abstract = {Slow-transit constipation (STC) is an increasingly prevalent disorder that imposes a substantial health and economic burden. Mounting evidence highlights the "gut microbiota-short-chain fatty acid (SCFA)-motility" axis as a central pathophysiological link between dysbiosis and impaired colonic transit. This review synthesizes current knowledge of how SCFAs, especially acetate, propionate and butyrate, shape motility through serotonergic signaling, enteric nervous system modulation, epithelial barrier integrity and immune regulation. Particular attention is devoted to the biased-signaling properties of the SCFA receptors FFAR2 and FFAR3 (free fatty acid receptors 2 and 3, respectively), including emerging data on their heterodimerization. The article then appraises recent randomized controlled trials and meta-analyses of multi-target interventions (dietary fibers, synbiotics, postbiotics, fecal microbiota transplantation, phytochemicals, and small-molecule FFAR agonists) highlighting their efficacy, safety, and translational hurdles. Finally, the authors propose a precision-medicine framework that integrates multi-omics microbiome profiling, metabolomics, and host genetics to enable phenotype-stratified therapy. Key research gaps include limited long-term safety data, heterogeneous human cohorts and the need for large multicenter trials and machine-learning-guided responder prediction. Collectively, the review provides a roadmap for shifting STC management from symptom control to mechanism-based, personalized care.},
}

@article {pmid41367410,
year = {2025},
author = {Tansirichaiya, S and Songsomboon, K and Wigand, J and Winje, E and Chaianant, N and Leartsiwawinyu, W and Al-Haroni, M},
title = {Geographic signatures in the oral resistome: a comparative metagenomic analysis of healthy individuals from Thailand and Norway.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2589656},
pmid = {41367410},
issn = {2000-2297},
abstract = {BACKGROUND: The oral cavity is an important yet understudied reservoir of antimicrobial resistance genes (ARGs), potentially shaped by geographic variation in antibiotic usage.

OBJECTIVE: To compare the oral resistomes of healthy adults from Thailand and Norway, two countries with contrasting antimicrobial use practices, using shotgun metagenomic sequencing.

DESIGN: Stimulated saliva samples were collected from healthy adults in Thailand (n = 43) and Norway (n = 50). ARGs were identified with AMRPlusPlus against the MEGARes database, and microbial taxonomy was profiled with KrakenUniq. Diversity metrics, ordination, and clustering analyses assessed resistome and microbiome structures.

RESULTS: Thai samples exhibited significantly greater ARG richness, evenness, and diversity (p < 0.001), driven by higher abundances of multi-biocide, nucleoside, and copper resistance genes. Norwegian samples were enriched in aminoglycoside, sulfonamide, and quaternary ammonium compound resistance genes. Both cohorts shared core oral genera, but Thai samples showed greater taxonomic richness without differences in overall microbiome diversity. Non-metric multidimensional scaling and PERMANOVA revealed stronger geographic separation for resistomes (R² = 0.639) than microbiomes (R² = 0.382). Co-occurrence networks highlighted structured associations between ARG groups and bacterial genera, suggesting ecological influences beyond taxonomic composition.

CONCLUSIONS: These results reveal distinct geographic signatures in the oral resistome that are not fully explained by microbiome structure, reflecting the influence of local ecological and societal factors, including antimicrobial exposure. The findings highlight the oral cavity as a dynamic ARG reservoir and support its inclusion in regional antimicrobial resistance surveillance to inform public health strategies.},
}

@article {pmid41367385,
year = {2025},
author = {Cavenaghi, A and Mallah, NEZ and Navarro, L and Martinón-Torres, F and Gómez-Carballa, A and Salas, A},
title = {Decoding the peripheral transcriptomic and meta-genomic response to music in autism spectrum disorder via saliva-based RNA sequencing.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1696704},
pmid = {41367385},
issn = {2296-889X},
abstract = {INTRODUCTION: Behavioral interventions for autism spectrum disorder show variable outcomes, highlighting the need for complementary therapies. Music-based interventions are promising, yet their molecular mechanisms remain unclear. Saliva-based RNA sequencing (RNA-seq) provides a non-invasive framework to monitor neuroimmune and metabolic dynamics, but its application in autism remains underexplored.

METHODS: We explored the buccal transcriptional effects of music exposure in five individuals with autism (8-37 years; 60% female). To overcome saliva-specific limitations, we combined Poly-A selection and Human-Enriched protocols preparation methods to enhance human transcript detection and reproducibility while capturing microbial signals.

RESULTS: Individually, each dataset revealed a few differentially expressed genes, but integrated analysis improved biological resolution. Consistently modulated genes included HERC6, TSPAN5, and REM2, involved in neurodevelopmental and immune functions. Enrichment analyses highlighted pathways associated with immune regulation, oxidative phosphorylation, and epithelial differentiation, hallmarks of autism, such as immune dysregulation and mitochondrial dysfunction. Co-expression network analysis identified modules correlated with music exposure. The AKNA module, previously linked to autism, was downregulated and enriched for Ras-related GTPase and immune pathways, suggesting modulation of intracellular signaling and inflammation. Conversely, upregulation of the UBE2D3 module indicated activation of endoplasmic reticulum stress responses, a contributor to autism. Exploratory metagenomics identified 15 microbial species responsive to music exposure, including Acidipropionibacterium acidipropionici and Propionibacterium freudenreichii, producers of propionic acid, a metabolite associated with autism-like behaviors and neuroinflammation.

CONCLUSION: Saliva-based RNA-seq can stably capture transcriptomic and microbial responses to behavioral stimuli. Music exposure modulates neuroimmune pathways relevant to autism, supporting the biological plausibility of music therapy and demonstrating saliva-based RNA-seq as a viable, non-invasive tool for monitoring intervention outcomes.},
}

@article {pmid41367092,
year = {2025},
author = {Mazumder, M and Tikariha, H and Mayalagu, S and Majedi, SM and Binti Abdul Hamid, NA and Mukhopadhyay, S and Pavagadhi, S and Selvaraj, P and Naqvi, N and Swarup, S},
title = {An Ecology-Driven Microbial Consortium Enhances Plant Growth and Immunity While Sustaining Rhizospheric Microbial Balance.},
journal = {Plant communications},
volume = {},
number = {},
pages = {101665},
doi = {10.1016/j.xplc.2025.101665},
pmid = {41367092},
issn = {2590-3462},
abstract = {Plant growth-promoting (PGP) microbial consortia offer a promising alternative to reduce reliance on chemical fertilizers in crop production. Their regenerative potential makes them ideal candidates for sustainable farm management practices with a lower carbon footprint. However, developing effective, stable, and environmentally friendly PGP consortia remains a major challenge. We developed a novel strategy for designing microbial consortia by integrating natural microbial interactions and metabolic complementarity among selected microbes, using network analysis and genome-scale metabolic modelling, respectively and thereby constructed a three-member microbial consortium (SAB). Both microbiological and genomic analyses demonstrated the significant PGP potential and stability of SAB, which outperformed its individual members. Phenotypic data indicated that SAB treatment enhanced plant growth rate and biomass without disrupting the native soil microbial community. Furthermore, experiments confirmed the consistent and significant performance of SAB treatment on Choy Sum and other plants across different setups and soil conditions, demonstrating its broad-spectrum beneficial activity. Transcriptomic analysis revealed that SAB triggered a parallel activation of growth and defense responses in the shoot, effectively bypassing the typical growth-defense trade-off through microbiome-mediated signaling and beneficial functions. Overall, our study demonstrates the functional potential of an ecologically designed microbial consortium that enhances plant growth by rewiring resource allocation, while exerting minimal impact on the rhizospheric microbial community.},
}

@article {pmid41366892,
year = {2025},
author = {Karm, MH and Kim, CG and Lee, JY and Cho, HJ and Kim, HJ},
title = {The immediate effectiveness of a multi-channeled oral irrigator in reducing dental plaque and oral malodor: A preliminary single-blind clinical trial.},
journal = {Medicine},
volume = {104},
number = {49},
pages = {e46185},
doi = {10.1097/MD.0000000000046185},
pmid = {41366892},
issn = {1536-5964},
support = {rs-2020-kd000241//Korea Medical Device Development/ ; hi19c1085//Korea Health Industry Development/ ; },
mesh = {Humans ; *Halitosis/prevention & control ; Male ; *Dental Plaque/prevention & control/therapy ; Female ; Adult ; Single-Blind Method ; Hydrogen Sulfide/analysis ; Toothbrushing ; Middle Aged ; *Therapeutic Irrigation/instrumentation/methods ; Young Adult ; Sulfhydryl Compounds/analysis ; Sulfur Compounds/analysis ; Oral Hygiene ; Oral Hygiene Index ; },
abstract = {BACKGROUND: This study evaluated the immediate effectiveness of a multi-channeled oral irrigator (MCOI) in removing dental plaque and reducing oral malodor.

METHODS: In 20 healthy volunteers, changes in dental plaque were assessed using the Patient Hygiene Performance index. Volatile sulfur compounds were measured before and immediately after a single use of the MCOI. Participants refrained from tooth brushing for 24 hours prior to the assessment. The device administered 1000 mL of water over a 1.5-minute cycle. Oral malodor was analyzed with gas chromatography focusing on methyl mercaptan (CH₃SH) and hydrogen sulfide. Statistical analysis was performed using the Wilcoxon signed-rank test and chi-square test.

RESULTS: After a cycle of MCOI use, the average and divisions of the tooth Patient Hygiene Performance index scores significantly decreased (P < .001), with an average reduction of 24.76% in initial dental plaque. Additionally, total volatile sulfur compounds and CH₃SH concentrations significantly decreased (P = .011) after oral cleaning. Although the mean hydrogen sulfide concentrations decreased after oral cleaning, this change was not statistically significant (P = .088).

CONCLUSIONS: Tooth brushing typically removes approximately 42% to 60% of the initial dental plaque in healthy adults. A single cycle of MCOI use reduced plaque by approximately 25% and significantly lowered CH₃SH, a compound associated with periodontal disease. These findings suggest that the MCOI may serve as a useful adjunct to tooth brushing, particularly for individuals with limited motor skills, and could help reduce the risk of plaque-related oral diseases.},
}

Humans
*Halitosis/prevention & control
Male
*Dental Plaque/prevention & control/therapy
Female
Adult
Single-Blind Method
Hydrogen Sulfide/analysis
Toothbrushing
Middle Aged
*Therapeutic Irrigation/instrumentation/methods
Young Adult
Sulfhydryl Compounds/analysis
Sulfur Compounds/analysis
Oral Hygiene
Oral Hygiene Index

@article {pmid41366874,
year = {2025},
author = {Kim, J and Choi, S and Kim, H and Roy, M and Ahn, S and Yang, JS and Jung, HW and Jeon, J},
title = {Transgenerational Dynamics of Endophytic Microbiome in Soybean Seeds.},
journal = {The plant pathology journal},
volume = {41},
number = {6},
pages = {856-867},
doi = {10.5423/PPJ.OA.07.2025.0087},
pmid = {41366874},
issn = {1598-2254},
support = {PJ0157682021//Rural Development Administration/ ; RS-2024-00407104//National Research Foundation of Korea/ ; RS-2022-NR072199//National Research Foundation of Korea/ ; },
abstract = {Seeds harbor diverse microbial communities, including endophytes, some of which are vertically transmitted and may contribute to plant health and productivity. However, the temporal dynamics of seed endophytic communities remain poorly understood in many crop species. In this study, we monitored the composition of bacterial and fungal endophytes in soybean (Glycine max) seeds, along with rhizosphere microbiomes, across three plant generations using a culture-independent approach. Our results revealed two key patterns: seed endophytic communities are distinct from those of bulk soil and rhizosphere microbiomes; and the composition of seed endophytes fluctuates over generations, likely influenced by both pre-existing endophytes, environmental factors, and microbial influx from the surrounding soil and rhizosphere, suggesting possible microbial transmission from the rhizosphere into seeds. Interestingly, despite generational variation, the seed fungal endophyte communities consistently maintained higher phylogenetic diversity compared to bacterial endophytes, which showed limited overlap across generations and were composed of fewer, closely related taxa. Analysis of community assembly mechanisms indicated that both seed and rhizosphere microbiomes significantly contributed to the next generation of seed microbiota, primarily through stochastic drift and homogeneous selection processes. Collectively, our findings offer valuable insights into the intergenerational dynamics of seed endophytes in soybean and provide a foundation for future efforts to harness seed-associated microbiomes for improving crop health and productivity.},
}

@article {pmid41366867,
year = {2025},
author = {Khaengraeng, C and Mhuantong, W and Chaiprom, U and Bunkoed, W and Kuncharoen, N and Kasem, S and Chatnaparat, T and Suwannarat, S},
title = {Fungal and Bacterial Communities Associated with Northern Corn Leaf Blight in Resistant and Susceptible Sweet Corn.},
journal = {The plant pathology journal},
volume = {41},
number = {6},
pages = {736-754},
doi = {10.5423/PPJ.OA.05.2025.0060},
pmid = {41366867},
issn = {1598-2254},
support = {FF(KU)2.66//Kasetsart University Research and Development Institute/ ; },
abstract = {Northern corn leaf blight (NCLB), caused by Exserohilum turcicum (Setosphaeria turcica), is a major disease that negatively impacts the yield and quality of sweet corn. Plant-associated microbes hold great potential for enhancing crop productivity and sustainability. This study investigated the fungal and bacterial communities associated with NCLB in resistant and susceptible sweet corn cultivars using amplicon metagenomic sequencing. The structural composition and diversity of the fungal community in symptomatic NCLB-susceptible cultivars differed significantly from those in asymptomatic NCLB-resistant cultivars. In contrast, the bacterial communities showed no significant differences between resistant and susceptible cultivars in both the phyllosphere and rhizosphere. Exserohilum and Alternaria were significantly more abundant in the phyllosphere of symptomatic NCLB-susceptible plants, while fungal genera such as Sporobolomyces and Aureobasidium, along with the order Dothideales and the bacteria Bacillus, were significantly more abundant in the phyllosphere of asymptomatic NCLB-resistant cultivars. Microbial metabolic functions related to sugar metabolism-including sucrose biosynthesis and the degradation of glucose and xylose, compounds abundant in plant cell walls-were enriched in the phyllosphere of symptomatic NCLB-susceptible plants. In contrast, functions associated with detoxification and defense responses to plant phenolic compounds were enriched in microbes from asymptomatic NCLB-resistant cultivars. Additionally, Bacillus, identified ash part of the core microbiome, and the epiphytic yeast Sporobolomyces, identified as a hub in the microbial network, exhibited antimicrobial activity that may suppress E. turcicum. These findings offer valuable insights into the role of microbial communities in plant health and disease resistance, with promising implications for developing microbiome-based strategies to manage NCLB.},
}

@article {pmid41366779,
year = {2025},
author = {Won, SM and Joung, H and Park, IG and Han, SH and Ham, YL and Han, JS and Kwon, Y and Kim, DJ and Suk, KT},
title = {The effects of next generation probiotics on metabolic dysfunction-associated steatotic liver disease: a parallel, double-blind, randomized, placebo-controlled trial.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07478-z},
pmid = {41366779},
issn = {1479-5876},
support = {Hallym University Research Fund//Hallym University Research Fund/ ; NRF-2020R1I1A3073530 and NRF-2020R1A6A1A03043026//Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology/ ; P0020622//KAIST Institute for IT Convergence/ ; },
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is associated with dysbiosis of the gut microbiota. We evaluated the effect of next generation probiotics (Lactobacillus delbrueckii subsp. Lactis [LL001], L. helveticus [LH001], and Pediococcus pentosaceus KID7 [PPKID7]) on liver function parameters and stool microbiome in patients with MASLD.

METHODS: We conducted a double-blind parallel trial of 110 patients diagnosed with MASLD. Participants were randomly assigned to four groups given three probiotics (3 capsules [9 × 10[9] CFU]/day, n = 85) or placebo (n = 25) alongside sylimarin for 8 weeks. Clinical characteristics, serum samples, and stool samples for 16 S rRNA gene sequencing were collected at the start and end point of the study. The primary endpoint was improvement in liver function.

RESULTS: In the probiotic group, LL001 treatment improved alanine transaminase (87.3 ± 8.2 to 71.1 ± 6.0 U/L, P = 0.01) and aspartate transaminase levels (64.9 ± 4.9 to 50.0 ± 3.5 U/L, P < 0.01), LH001 group showed body weight reduction (78.4 ± 3.0 to 77.2 ± 2.8 kg, P = 0.01), and PPKID7 reduced cholesterol levels (186.1 ± 7.0 to 178.0 ± 7.9 mmol/L, P = 0.03). Probiotics treatment decreased the abundance of Proteobacteria and increased the abundance of Ruminococcaceae and Lachnospiraceae in the LL001 group. In the pre- and post-comparison of probiotic treatment at the level of the top 20 genera, a tendency was observed to decrease the genera Haemohlius and Ruminococcus_g2 while increasing the genus Bifidobacterium.

CONCLUSION: Eight weeks of probiotics supplementation was associated with changes in the stool microbiome and improvements in the blood biochemical parameters of MASLD.

NCT04555434.},
}

@article {pmid41366711,
year = {2025},
author = {Rey Redondo, E and Xu, W and Xu, Y and Sun, R and Wan, SH and Leung, SKK and Yung, CCM},
title = {Multi-domain temporal patterns reveal stable community membership but dynamic interactions in the coastal microbiome.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00803-5},
pmid = {41366711},
issn = {2524-6372},
support = {Hong Kong PhD Fellowship Scheme//Research Grants Council of Hong Kong/ ; 16102024//Research Grants Council of Hong Kong/ ; },
abstract = {BACKGROUND: Marine microbial communities drive global biogeochemical cycles and oceanic food webs, yet our understanding of their holistic temporal dynamics remains limited, particularly in the South China Sea. Most studies have focused on specific taxonomic groups or single temporal scales, leaving a gap in comprehensive, multi-domain, and multi-timescale analyses.

RESULTS: Using an integrated multi-omics approach that combined metagenomic, metatranscriptomic, and metaviromic analyses, we conducted time-series sampling over 48-h periods during winter and summer to investigate microbial community dynamics in the coastal South China Sea. Seasonal transitions were identified as the primary drivers of community shifts, with diel variations playing a secondary role across all taxonomic domains. Within seasons, diel changes followed a progressive trajectory rather than recurring cyclic patterns. Eukaryotic communities exhibited the most pronounced temporal fluctuations, while prokaryotic and viral communities displayed remarkable stability. Unlike previous coastal studies, viral communities maintained high similarity between seasons, suggesting the presence of a persistent viral reservoir in this region. Gene expression analysis revealed dynamic population shifts in photosynthetic microorganisms, with Mamiellophyceae green algae and their associated Prasinovirus displaying pronounced seasonal and diel rhythmicity.

CONCLUSIONS: This study provides novel insights into the temporal dynamics of microbial communities and host-virus interactions in the South China Sea. The stability of viral communities, coupled with synchronised host-virus activities, highlights potential mechanisms supporting ecosystem resilience in this coastal region. These findings enhance our understanding of marine ecosystem processes and establish a robust framework for exploring microbial responses to environmental changes on both diel and seasonal scales.},
}

@article {pmid41366699,
year = {2025},
author = {Palmieri, O and Cannarozzi, AL and Latiano, A and Massimino, L and Bossa, F and Riva, M and Ungaro, F and Guerra, M and Di Brina, ALP and Carparelli, S and Fiorino, G and Perri, F and Danese, S},
title = {Machine learning approach and internet of things technologies to unravel the complex interaction between microbiome-metabolome in inflammatory bowel disease: a new frontier in precision medicine.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-025-00758-5},
pmid = {41366699},
issn = {1757-4749},
support = {PNRR-MAD- 2022-12375729//This research was funded by the European Union-Next Generation EU-PNRR M6C2-Investment 2.1 Enhancement and strengthening of biomedical research in the NHS/ ; },
abstract = {Inflammatory bowel diseases (IBD) are chronic, relapsing inflammatory disorders with ulcerative colitis (UC) and Crohns disease (CD) representing the two major phenotypes. While these conditions share common features, they exhibit distinct clinical presentations, disease behaviors, and pathogenetic mechanisms, highlighting the complexity of IBD. The global incidence and prevalence of IBD have risen dramatically in recent decades, probably linked to environmental changes such as dietary habits, urbanization, and reduced microbial exposure during early life, highlighting the interplay between environmental and genetic factors in disease pathogenesis. However, genetic factors alone cannot fully explain disease onset, emphasizing the critical role of environmental and microbial influences. Dysbiosis, characterized by reduced microbial diversity, loss of beneficial commensals, and an overabundance of pathogenic taxa, has emerged as a hallmark of IBD. Recent research has increasingly focused on the functional consequences of dysbiosis, its impact on microbial metabolites and pathways that contribute to chronic inflammation and disease progression. Understanding the functional implications of multi-omics changes, rather than simply cataloguing compositional changes, is now a priority in IBD research. Using artificial intelligence to combine data from noninvasive multi-omics technologies offers a significant opportunity to explore interactions among individual omics. It could represent a shift in IBD research by showing the complex mechanisms behind disease. This approach may revolutionize diagnostics and treatments, improving the quality of life for patients through precision medicine. This review aims to provide a comprehensive assessment of current progress. It highlights critical challenges and suggests possible future directions.},
}

@article {pmid41366581,
year = {2025},
author = {Alimoradi, E and Hashemnejad, MA and Etemad, S and Arabi, M and Bereimipour, A},
title = {Investigation of Transcriptome and Kinome in Non Metastatic and Metastatic Renal Clear Cancer Stem Cells and Their Relationship with Gut Microbiota.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41366581},
issn = {1559-0305},
abstract = {Evidence for the microbiome's role in human health and disease has been piling up ever since the human microbiome project. The composition of one's microbiome can have a major effect on one's risk of developing cancer and the nature of how cancer develops. Several estimates suggest the percentage of cancer cases that can be attributed to microorganisms at around 15%. In addition, researchers are still trying to figure out how the microbiota, and the gut microbiota in particular, affects how a patient responds to chemotherapy, immunotherapy, and radiotherapy. In this light, we conducted an in-depth bioinformatics analysis of the gut microbiota- RCCstem cells axis, utilizing python-based programme and enrichment databases to analyses data from many sources, including clinical data, transcription factors, kinases and gene expression profile of RCCstem cells. Five genes, including SLC16A6, CPNE5, AFAP1L1, SCARF1, and NOTCH4, were shown to be shared by the hub gut microbiota and extracellular proteins. Patients with RCCstem cells had a disproportionately high number of certain types of bacteria. In patients expression profile have high CPNE5, AFAP1L1, SCARF1, and NOTCH4 expression. RCCsurvival rates are reduced by roughly 50% due to all of the genes involved. Also, the Actinobacteria and Gammaproteobacteria possible role in renal cancer development via relation to cancer stem cells. The gut microbiota and its components were considered for their possible relevance in the development of RCC.},
}

@article {pmid41366428,
year = {2025},
author = {Xiong, Z and Dodson, BP and Rogers, MB and Sneiderman, CT and Janesko-Feldman, K and Vagni, V and Manole, M and Li, X and Rajasundaram, D and Clark, RSB and Raphael, I and Morowitz, MJ and Mariño, E and Kochanek, PM and Jha, RM and Kohanbash, G and Simon, DW},
title = {Microbial production of short-chain fatty acids attenuates long-term neurologic impairment after traumatic brain injury.},
journal = {Journal of neuroinflammation},
volume = {22},
number = {1},
pages = {285},
pmid = {41366428},
issn = {1742-2094},
support = {R21 NS131689/NS/NINDS NIH HHS/United States ; R21 NS131689/NS/NINDS NIH HHS/United States ; R01NS 127372/NH/NIH HHS/United States ; },
mesh = {Animals ; *Brain Injuries, Traumatic/metabolism/complications ; Mice ; Mice, Inbred C57BL ; *Fatty Acids, Volatile/metabolism/biosynthesis ; *Gastrointestinal Microbiome/physiology ; Male ; },
abstract = {BACKGROUND: Traumatic brain injury (TBI) triggers persistent gut microbiome dysbiosis characterized by depletion of short-chain fatty acid (SCFA)-producing bacteria. However, the link between SCFA depletion and long-term neurologic impairment (LTNI) after TBI remains unclear. Previously, we and others noted the involvement of metabolite-sensing receptors and SCFA ligands in mouse models of neurodegenerative diseases, including Alzheimer's. Here, we further investigated SCFA-mediated neuroprotection in LTNI at both microbiome and single-cell resolution using the controlled cortical impact (CCI) model of TBI with a high-yielding SCFA diet to examine their mechanistic role in pathogenesis.

METHODS: C57BL6/J mice were randomized to CCI (6 m/s, 2 mm) or sham surgery. Following surgery, mice were randomized to a study diet based on a balanced modification of the AIN93-G diet containing either 15% high amylose maize starch (HAMS) control diet or acetylated and butyrylated HAMS (HAMSAB) for 6 months to model increased SCFA production by bacterial fermentation in the gut. Morris water maze test and nesting assessment were performed at 1, 3, and 6 months after injury. The longitudinal gut microbiome changes were investigated by 16 S rRNA amplicon and metagenomic sequencing of fecal pellets at baseline, 1 month, and 6 months post-injury. At 6 months, pericontusional tissue was collected for single-cell RNA-sequencing following the 10X Genomics protocol or histologic analysis.

RESULTS: Compared to the HAMS control diet, HAMSAB diet remodeled the CCI murine gut microbiome at an early phase, increased various SCFA-producing taxa, and attenuated neurologic deficits up to 6 months after CCI. In mice fed HAMSAB diet, single-cell transcriptomics and pathway analysis identified the promotion of neurogenesis, including increased doublecortin-positive immature neurons. In myeloid cells, HAMSAB induced an anti-inflammatory phenotype, inhibiting pro-inflammatory signaling interaction such as midkine signaling, and promoted differentiation to disease-associated microglia (DAM). Simultaneously, SCFAs reduced neurodegenerative pathway activity in neurons and glial cells and reduced phosphorylated tau deposition in pericontusional cortex.

CONCLUSIONS: Diet-facilitated microbial production of acetate and butyrate attenuates behavioral deficits of LTNI after TBI and produces enduring benefits at the single-cell level on the neuro-inflammatory and neuro-progenitor responses. This therapeutic approach could have a broader potential to prevent neurodegenerative disease.},
}

Animals
*Brain Injuries, Traumatic/metabolism/complications
Mice
Mice, Inbred C57BL
*Fatty Acids, Volatile/metabolism/biosynthesis
*Gastrointestinal Microbiome/physiology
Male

@article {pmid41366231,
year = {2025},
author = {Chen, HW and Yuan, YF and Wang, CL and Wang, DY and Zhou, ZC and Fan, L and Zhang, QX and He, YN and Jiang, WK and Wang, SC},
title = {Dual-Functional Ionic Liquid Varnishes for Dental Caries Management.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345251397916},
doi = {10.1177/00220345251397916},
pmid = {41366231},
issn = {1544-0591},
abstract = {The development of caries management materials has concentrated on the dual objectives of inhibiting cariogenic microorganisms and promoting remineralization. In this study, 2 dual-functional ionic liquid (IL) varnishes, exhibiting both antibacterial and remineralization capabilities, were synthesized as novel anticaries agents. The ionic liquids (ILs) were prepared by modifying 1-hexylimidazolium IL with 3-chloropropyltriethoxysilane, followed by anion exchange with F[-] and a coordination reaction with Sr[2+], respectively. The ILs were characterized using energy-dispersive spectroscopy (EDS), ion chromatography (IC), inductively coupled plasma optical emission spectrometry (ICP-OES), and Fourier transform infrared spectroscopy (FTIR). The antibacterial efficacy of the ILs was evaluated through colony counting, live/dead staining, and scanning electron microscopy (SEM). Subsequently, the ILs were blended with rosin to form IL varnishes. The remineralization potential of the IL varnishes was assessed through microhardness test, acid resistance test, SEM, EDS, and X-ray diffraction. In addition, in vivo anticaries treatment with the IL varnishes was conducted using a dental caries animal model. Histopathological and oral microbiome analyses were performed to evaluate the in vivo biocompatibility of the materials. The comprehensive analysis by EDS, IC, ICP-OES, and FTIR collectively confirmed the successful synthesis of the ILs. Antibacterial assays revealed that ILs at concentrations as low as 25 µM eliminated more than 80% of cariogenic bacteria within 60 min and significantly decreased viable bacteria in biofilms within 24 h. Following a 7-d treatment with the IL varnishes, SEM analysis of acid-etched enamel demonstrated reduced interspace depth, along with substantially increased microhardness and significantly improved acid resistance versus the negative control group. As compared with the fluoride varnish, the IL varnishes are more effective in preventing dental caries in rats, without harming oral buccal mucosa, major organs, or microbiota diversity. In conclusion, the IL varnishes developed in this study are not only straightforward to synthesize but also exhibit significant potential against dental caries.},
}

@article {pmid41366180,
year = {2025},
author = {Fernandez-Ibanez, R and Moreno, S and Fernandez, M},
title = {A Review of Doxycycline Post-Exposure Prophylaxis and Its Implications for Antimicrobial Resistance and the Human Microbiome.},
journal = {Infectious diseases and therapy},
volume = {},
number = {},
pages = {},
pmid = {41366180},
issn = {2193-8229},
abstract = {Sexually transmitted infections (STIs) remain a major global health burden, with rising incidence of Neisseria gonorrhoeae, Chlamydia trachomatis, and Treponema pallidum. Doxycycline post-exposure prophylaxis (DoxyPEP), consisting of a single 200 mg dose within 72 h after condomless sex, has emerged as a promising intervention. Randomized controlled trials demonstrate consistent efficacy in reducing chlamydia and syphilis, while protection against gonorrhea is variable, being strongly influenced by baseline tetracycline resistance and anatomical site. Surveillance data from San Francisco and King County confirm that high-frequency use can drive rapid increases in gonococcal tetracycline resistance. Although no cephalosporin resistance has yet been linked to DoxyPEP, genomic correlations raise concern for co-selection of multidrug-resistant strains, particularly FC428-like clones with mosaic penA alleles. C. trachomatis remains uniformly susceptible, with resistance limited to theoretical horizontal transfer from C. suis. T. pallidum shows no evidence of resistance, supported by genomic constraints and experimental studies. Mycoplasma genitalium demonstrates low intrinsic susceptibility to doxycycline, but no acquired tetracycline resistance has been confirmed. Beyond target pathogens, DoxyPEP alters the functional resistome of the human microbiome, amplifying tetracycline resistance gene expression in gut, skin, and oropharyngeal flora, and selecting for resistant Staphylococcus aureus and commensal Neisseria. These ecological shifts underscore the importance of molecular surveillance to monitor resistance spillover. Overall, DoxyPEP provides substantial benefit in controlling chlamydia and syphilis and conditional utility against gonorrhea in low-resistance settings. Its deployment should be coupled with antimicrobial stewardship, local resistance data, and strengthened genomic surveillance to balance individual protection with population-level risks.},
}

@article {pmid41365939,
year = {2025},
author = {Al Masri, MT and Ali, AS and Vijayan, R and Muzaffar, SB and Al-Deeb, MA},
title = {Influence of farm composition and management on the microbiome of the camel tick (Hyalomma dromedarii).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43448},
pmid = {41365939},
issn = {2045-2322},
support = {UPAR Grant no. G00003718//United Arab Emirates University/ ; },
mesh = {Animals ; *Camelus/parasitology ; *Microbiota ; Farms ; Female ; RNA, Ribosomal, 16S/genetics ; United Arab Emirates ; *Ixodidae/microbiology ; *Ticks/microbiology ; *Tick Infestations/veterinary/parasitology ; },
abstract = {Ticks are obligate ectoparasites and important disease vectors. In the United Arab Emirates (UAE), Hyalomma dromedarii ticks impact the health of camels. This study investigates the effects of farm animal composition and tick management practices on the microbiome of the camel tick (H. dromedarii) in the UAE. We aimed to assess the cumulative microbiome of this tick by analyzing partially-fed adult females. Ticks were collected from monospecific farms (rearing only camels) and polyspecific farms (rearing camels alongside other animal species), as well as from managed farms (where camels are treated with acaricides) and unmanaged farms (no acaricide treatment), across four locations per farm type. DNA was extracted, and 16S rDNA sequencing was performed for microbial profiling. Differences were observed in the microbiome composition between ticks collected from monospecific and polyspecific farms and between those collected from managed and unmanaged farms. The findings of this study are exploratory, providing a baseline for future research. Overall, this work advances current understanding of the H. dromedarii microbiome and underscores its relevance to the One Health approach.},
}

Animals
*Camelus/parasitology
*Microbiota
Farms
Female
RNA, Ribosomal, 16S/genetics
United Arab Emirates
*Ixodidae/microbiology
*Ticks/microbiology
*Tick Infestations/veterinary/parasitology

@article {pmid41365917,
year = {2025},
author = {Duarte, VDS and Franklin, FV and Krysmann, A and Porcellato, D},
title = {Longitudinal study of the udder microbiome using genome-centric metagenomics uncovers pathogen-driven adaptation and succession.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {227},
pmid = {41365917},
issn = {2055-5008},
support = {314733//Norges Forskningsråd/ ; 314733//Norges Forskningsråd/ ; 314733//Norges Forskningsråd/ ; 314733//Norges Forskningsråd/ ; },
mesh = {Animals ; Female ; *Mammary Glands, Animal/microbiology ; Cattle ; *Mastitis, Bovine/microbiology ; Longitudinal Studies ; *Metagenomics/methods ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification/pathogenicity ; Lactation ; RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; },
abstract = {Bovine mastitis remains a major disease affecting dairy herds globally due to its complex and multi-etiological nature. To address gaps in microbial and immunological understanding, this longitudinal study examined the udder microbiome across lactation in 24 Norwegian Red cows. Somatic cell count (SCC) and microbiota composition varied by lactation stage, with low SCC (< 100,000 cells/mL) more frequent in early (80%) and middle (78.9%) than late lactation (53%) and dry-off (53.1%). Microbial diversity was shaped by SCC, lactation stage, and individual variability. Temporal profiling identified persistent infections involving Staphylococcus aureus and Staphylococcus chromogenes, while samples with low SCC were enriched in beneficial genera including Corynebacterium, Bradyrhizobium, and Lactococcus. Shotgun metagenomics revealed pathogen-specific metabolic traits, and genome-centric analysis recovered 142 MAGs characterized via sequence typing, virulence, and resistance profiling. These findings offer valuable insights into microbial adaptation and succession, informing strategies to better manage and prevent mastitis.},
}

Animals
Female
*Mammary Glands, Animal/microbiology
Cattle
*Mastitis, Bovine/microbiology
Longitudinal Studies
*Metagenomics/methods
*Microbiota
*Bacteria/genetics/classification/isolation & purification/pathogenicity
Lactation
RNA, Ribosomal, 16S/genetics
Genome, Bacterial

@article {pmid41365911,
year = {2025},
author = {Zhang, A and Wu, Q and Mayne, J and Ning, Z and Qin, H and Dewar, A and Figeys, D},
title = {Microbiome-dependent functional responses to structurally distinct oligosaccharides revealed by metaproteomics.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00881-w},
pmid = {41365911},
issn = {2055-5008},
support = {CREATE-497995-2017//NSERC-CREATE Technologies for Microbiome Science and Engineering (TECHNOMISE) program/ ; },
abstract = {Dietary oligosaccharides are prebiotics that fuel gut microbes, but individual microbiomes may respond differently depending on oligosaccharide structures as well as microbiome composition and function. The extent to which specific gut microbial communities exhibit personalized functional responses to distinct oligosaccharides remains underexplored. We applied a standardized ex vivo microbiome culture, called RapidAIM, coupled with metaproteomics to examine how six structurally diverse oligosaccharides affect the gut microbiota functional response. Our study shows that while human gut microbiomes share some commonalities in utilizing oligosaccharides (e.g. prioritizing dietary fibers over mucin), the fine-scale metabolic and taxonomic responses are highly individualized. Such findings underscore the importance of considering personal microbiome profiles when predicting the outcome of prebiotic interventions. In a broader context, our metaproteomic approach provides a framework for identifying optimal prebiotic choices tailored to individual microbiomes. Ultimately, understanding these personalized responses could inform precision nutrition strategies.},
}

@article {pmid41365640,
year = {2025},
author = {Till, JM and Brock, OD and Do, EA and Engelhart, MJ and Glowacki, RWP and Hu, S and Hsiao, A and Nemet, I and Ahern, PP},
title = {Variation in Microbiome Composition and Faecal Metabolites Are Associated With Differential Susceptibility to DSS-Induced Colitis.},
journal = {Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imm.70071},
pmid = {41365640},
issn = {1365-2567},
support = {R01DK126772/DK/NIDDK NIH HHS/United States ; LRP0000016021//Division of Loan Repayment/ ; LRP0000045724//Division of Loan Repayment/ ; R01HL160747/HL/NHLBI NIH HHS/United States ; //Cleveland Clinic Foundation/ ; F31AI179030//National Institute of Allergy and Infectious Diseases/ ; R01AI181382//National Institute of Allergy and Infectious Diseases/ ; R01AI157106//National Institute of Allergy and Infectious Diseases/ ; R01AI178908//National Institute of Allergy and Infectious Diseases/ ; R35GM158026/GM/NIGMS NIH HHS/United States ; },
abstract = {Variation in microbiome composition is linked to differences in intestinal immune phenotypes and can be leveraged to identify microbiome-driven contributions to phenotypes of interest. Furthermore, such variation has been associated with differing inter-individual susceptibility to the development of inflammatory bowel disease (IBD), a chronic inflammatory disease of the gastrointestinal tract that is driven by dysfunctional immune-microbiome interactions. Here, we identified that differences in microbiome composition in C57BL/6 mice from two commonly used commercial vendors, Charles River (CR) and Jackson (JAX) Laboratories, were associated with variation in the intestinal immune phenotype, with CR mice having greater Th17 levels and faecal IgA. In turn, CR mice demonstrated enhanced susceptibility to the dextran sulfate sodium (DSS)-induced model of colitis compared to JAX mice. Co-housing studies revealed that CR mice could transmit enhanced susceptibility to colitis to JAX mice, implicating differences in microbiome composition as drivers of disease susceptibility. Faecal metabolomics studies using targeted mass spectrometry revealed several metabolites differentially enriched in colitis-susceptible and colitis-resistant mice. Correlation analysis uncovered metabolites that were both negatively and positively associated with colitis severity. Taken together, our study leveraged natural microbiome variation to identify gut microbial metabolites with the potential to predict the severity of IBD. Importantly, we further establish susceptible and non-susceptible murine microbial communities that represent a tractable system in which to further uncover microbiome contributions to IBD in the DSS-colitis model.},
}

@article {pmid41365533,
year = {2025},
author = {Brown, JR and Sonpavde, G},
title = {Toward a better pan-tumor predictive signature for unleashing precision immuno-oncology.},
journal = {Journal for immunotherapy of cancer},
volume = {13},
number = {12},
pages = {},
doi = {10.1136/jitc-2025-013213},
pmid = {41365533},
issn = {2051-1426},
mesh = {Humans ; *Precision Medicine/methods ; *Neoplasms/immunology/genetics/drug therapy ; *Immunotherapy/methods ; *Biomarkers, Tumor/genetics ; *Medical Oncology/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; },
abstract = {While immune checkpoint inhibition (ICI) has revolutionized therapy across solid tumors, resistance remains an issue. Programmed death ligand-1 immunohistochemistry has limited clinical utility, whereas tumor mutation burden and microsatellite instability are only valuable for a minority of patients and leave room for improvement. Multiomic gene signatures have enhanced prediction of immune response by incorporating interferon-gamma signaling, T-cell dysfunction and exhaustion genes, and myeloid signatures. Single-cell RNA technology has been adopted to further optimize prediction of response to immunotherapy. A novel Immune Profile Score is presented by Zander et al that builds on prior immune signatures, using DNA and RNA profiling to predict outcomes across solid tumors receiving ICIs. While this assay is promising, further prospective validation and refinements will be necessary to realize its full potential in our quest to develop precision immuno-oncology. The incorporation of readily available clinical factors (eg, sites of metastasis), host genetics, orthogonal molecular platforms (microbiome, computational pathology, spatial transcriptomics, epigenetics, proteomics, radiomics) and investigating biomarkers to predict primary refractory disease and severe toxicities may further facilitate precision medicine.},
}

Humans
*Precision Medicine/methods
*Neoplasms/immunology/genetics/drug therapy
*Immunotherapy/methods
*Biomarkers, Tumor/genetics
*Medical Oncology/methods
*Immune Checkpoint Inhibitors/therapeutic use

@article {pmid41365395,
year = {2025},
author = {Nguyen, TTM and Yi, EJ and Jin, X and Zheng, Q and Park, SJ and Yi, GS and Yang, SJ and Yi, TH},
title = {Effects of nutritive and non-nutritive sweeteners on acne vulgaris: A systematic review.},
journal = {Fitoterapia},
volume = {},
number = {},
pages = {107022},
doi = {10.1016/j.fitote.2025.107022},
pmid = {41365395},
issn = {1873-6971},
abstract = {Acne vulgaris is a prevalent inflammatory skin disorder influenced by sebaceous gland activity, hormonal regulation, and microbial proliferation. Dietary factors, including sweetening agents, may modulate acne pathophysiology, affecting sebum production, inflammatory responses, and the skin microbiome. This systematic review summarizes the effects of nutritive and non-nutritive sweeteners on acne-related markers, with a focus on Cutibacterium acnes activity and associated inflammatory pathways. Non-nutritive sweeteners such as mannitol and xylitol show potential in regulating acne pathogenesis and exhibiting antibacterial activity against C. acnes. Strategic combinations of sweeteners with bioactive compounds, such as mannitol with bakuchiol or Ginkgo biloba extract, and xylitol with propanediol and caprylic acid, further enhance anti-inflammatory and antimicrobial effects, offering a multifaceted approach to acne management. For nutritive sweeteners, experimental evidence suggests that glucose may enhance C. acnes biofilm susceptibility when combined with certain antibiotics. These findings emphasize the importance of careful selection and formulation of sweetening agents in dermatological interventions. Incorporating sweeteners, alone or in combination with bioactive compounds, could complement conventional acne therapies, reduce microbial proliferation, modulate inflammatory pathways, and support overall skin health. This review provides a scientific basis for dietary recommendations and the development of adjunctive acne treatments, highlighting sweetening agents as emerging functional modulators of acne pathogenesis.},
}

@article {pmid41365274,
year = {2025},
author = {Wang, Y and Huang, X and Luo, X and He, M and Fang, Y and Yang, D},
title = {Development of ellagic acid-derived bismuth MOF for targeted therapy in colitis.},
journal = {Biomaterials advances},
volume = {181},
number = {},
pages = {214646},
doi = {10.1016/j.bioadv.2025.214646},
pmid = {41365274},
issn = {2772-9508},
abstract = {Oxidative stress plays a key role in inflammatory diseases like colitis, but traditional antioxidants are limited by poor bioavailability and non-specific actions, reducing their effectiveness. This study seeks to overcome these limitations by creating a targeted nanotherapy that combines natural ellagic acid with bismuth-based metal-organic framework (MOF) chemistry. SU-101, a MOF, was synthesized through the coordination of ellagic acid and bismuth acetate. SU-101, with a rod-like shape and a zeta potential of -38.51 mV, effectively targets inflamed colonic tissue. It shows strong radical scavenging and SOD/CAT-mimetic activities, providing dual therapeutic benefits. At 5 mg/kg orally, SU-101 outperforms 5-aminosalicylic acid (5-ASA) by reducing weight loss, lowering pro-inflammatory cytokines (IL-6, TNF-α), restoring intestinal barrier proteins, and altering gut microbiota and arginine metabolism. As the ellagic acid-derived bismuth MOF, SU-101 offers precise, multi-level treatment for oxidative inflammation, with promising oral bioavailability and microbiome remodeling potential for inflammatory bowel disease therapy.},
}

@article {pmid41365182,
year = {2025},
author = {Sampath, V and Kim, NG and Kim, IH},
title = {Integrating bacteriophage with high-and low-protein feeding strategies enhances performance, gut health, and environmental sustainability in ROSS 308 broilers.},
journal = {Poultry science},
volume = {105},
number = {1},
pages = {106135},
doi = {10.1016/j.psj.2025.106135},
pmid = {41365182},
issn = {1525-3171},
abstract = {A 35-day growth trial was conducted to evaluate the effects of dietary protein density and bacteriophage (BP) supplementation on growth performance, nutrient digestibility, gas emissions, organ development, meat quality, and ileal microbiome in ROSS 308 broilers. A total of 1,440 chicks (47.87 ± 1.50 g initial BW) were randomly allocated to four treatments in a 2 × 2 factorial design: high protein (HP) and low protein (LP) diets, with or without 10 mg/kg BP, each with 20 replicates of 18 birds. During the grower phase, birds fed diet supplemented with BP showed tendency (P < 0.1) to improved bodyweight gain (BWG) and feed conversion ratio (FCR). Also, during the finisher phase, birds receiving BP supplementation demonstrated a significantly greater (P < 0.05) BWG and a tendency toward increased feed intake. Furthermore, over the entire experimental period, final BW and cumulative BWG were significantly (P < 0.05) increased in birds fed BP supplementation. At the end of the trial, BP supplementation has tended to improve dry matter and significant increase in nitrogen digestibility. Moreover, ammonia emission was significantly(P < 0.05) reduced in birds fed LP diets. Furthermore, alpha diversity of evenness, Chao1, observed features, Shannon's, Simpson's, and Pielou's indices were highly abundance in birds fed LP diet with BP. Principal coordinate analyses indicated treatment-dependent clustering, with LP+ showing the most distinct separation from HP groups. At phylum level, HP groups exhibited a higher proportion of Bacteriodia compared with LP groups. Whereas phyla firmicutes were more abundant in LP following Desulfobacterotax. At genus level LP- group showed a greater proportion of Bacteroides spp., Faecalibacterium, and Prevotellaceae. Based on the results, we infer that incorporating bacteriophage into broiler diets can serve as a sustainable nutritional strategy to optimize performance, nutrient utilization, and environmental efficiency across varying protein levels.},
}

@article {pmid41365136,
year = {2025},
author = {Chang, G and Zhang, J and Fang, X and Zhang, S and Lu, H and Jiang, Y and Zhu, J},
title = {Environmental microorganisms as heterogeneous sources and shapers of the fermentation microbiome in Zhejiang rosy vinegar.},
journal = {International journal of food microbiology},
volume = {447},
number = {},
pages = {111554},
doi = {10.1016/j.ijfoodmicro.2025.111554},
pmid = {41365136},
issn = {1879-3460},
abstract = {Zhejiang rosy vinegar (ZRV) fermentation is a complex, spontaneous open-system process, where microbial communities are key to its unique characteristics. However, the precise influence of the brewing workshop environment on these dynamic microbial communities remains underexplored, hindering consistent product quality. Here, we characterized the environmental and fermentation microbial communities across three factories using high-throughput sequencing (16S rRNA and ITS), qPCR, and advanced ecological network analyses. Our results establish that the brewing environment acts as a critical, heterogeneous, and factory-specific microbial reservoir, and provides the primary inoculum for fermentation initiation. Our findings revealed significant inter-factory differences in environmental microbial loads and community structures. For instance, the SX environment was characterized by a unique composition, including the notable presence of Monascus on jar lids. Source tracking confirmed this environmental "seeding" significantly shapes initial fermentation communities, with contributions from floor and jar surfaces. During fermentation, bacterial communities consistently shifted (LAB decrease, Acetobacter increase), but fungal successions varied notably by factory. Specifically, the natural fermentation at the SX factory fostered a distinct fungal community trajectory, characterized by a unique decrease in Saccharomyces and the emergence of Monascus as the dominant genus in later stages. This trajectory was directly linked to its distinct environmental fungal populations and their pronounced influence from the initial solid-state phase. While internal selective pressures eventually govern community structure, environmental conditions profoundly dictate overall microbial diversity and succession. A core microbiome (Bacillus, Sphingomonas, Cryptococcus, Monascus), consistently present in both environmental and fermentation niches, served as key microbial bridges. Our results provide a vital basis for optimizing ZRV production by strategically managing the environmental microbiome to enhance quality and consistency.},
}

@article {pmid41365103,
year = {2025},
author = {Salas, A and Navarro, L and Martinón-Torres, F and Gómez-Carballa, A},
title = {Beyond behavioral studies: Exploring the multi-omics impact of music on human health.: Comment on Can arts-based interventions improve health? A conceptual and methodological critique by Martin Skov and Marcos Nadal.},
journal = {Physics of life reviews},
volume = {56},
number = {},
pages = {91-93},
doi = {10.1016/j.plrev.2025.09.002},
pmid = {41365103},
issn = {1873-1457},
}

@article {pmid41365070,
year = {2025},
author = {Zhou, Y and Zhang, XX and Wang, D and Zhao, M and Sun, L and Huang, W and Xie, Z},
title = {Microbial acetyl-CoA synthesis as an emerging metabolic and regulatory hub in plant-microbe interactions.},
journal = {Microbiological research},
volume = {304},
number = {},
pages = {128413},
doi = {10.1016/j.micres.2025.128413},
pmid = {41365070},
issn = {1618-0623},
abstract = {Acetyl-CoA synthetase (ACS) is a well-characterized enzyme that catalyzes the ATP-dependent ligation of acetate and coenzyme A to produce acetyl-CoA, a central metabolite coordinating energy metabolism, carbon flux distribution, and post-translational protein modification. Recently, ACS has emerged as a metabolic nexus with broad implications for plant-microbe interactions in agriculture. Beyond its canonical role in primary metabolism, ACS governs diverse physiological processes in beneficial plant-associated microorganisms, including rhizosphere colonization, stress adaptation, secondary metabolite biosynthesis, and morphological development-all of which enhance plant growth and resilience. In contrast, in phytopathogens, ACS is closely related to the expression of virulence factors. Thus, ACS exerts a dual influence, shaping both mutualistic and antagonistic microbial lifestyles in planta. This review synthesizes recent advances in the structural and catalytic diversity of ACS, delineates its ecological and functional roles in agriculturally relevant microorganisms, and explores the environmental and host-derived signals that regulates its expression and activity. Particular attention is given to the interplay between ACS-mediated carbon metabolism and protein acetylation, which together modulate microbial physiology and plant-associated behaviors. ACS is thereby positioned as a strategic metabolic hub, providing a framework for future research at the interface of microbial metabolism, environmental adaptation, and plant health.},
}

@article {pmid41364914,
year = {2025},
author = {Kujawska, M and Hall, LJ},
title = {Microbe-Diet Interactions and Personalized Nutrition.},
journal = {Annual review of food science and technology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-food-111523-121845},
pmid = {41364914},
issn = {1941-1421},
abstract = {Nutrition plays a fundamental role in shaping human health across the life course, influencing both host physiology and the composition and function of the gut microbiota. In turn, the gut microbiota modulates the effects of dietary intake, creating complex bidirectional interactions with profound implications for metabolic health. Although the concept of personalized nutrition offering tailored dietary advice based on observable traits, environmental factors, and genotype has gained prominence, growing evidence supports the promise of precision nutrition that also considers individual microbiome profiles. This approach is particularly relevant for addressing diet-related conditions such as obesity and type 2 diabetes, where interindividual variability in response to the same diet is well documented. Advances in high-throughput sequencing, metabolomics, and machine learning are driving predictive models that can forecast personalized dietary outcomes. However, methodological heterogeneity, lack of consistency, and limited representation of diverse populations in current studies present significant barriers. Ethical challenges, including data privacy and equitable access to personalized nutrition tools, also warrant urgent attention. To realize the full potential of microbiome-informed nutrition, greater harmonization of research methods, robust validation across large and diverse cohorts, and an interdisciplinary framework are essential.},
}

@article {pmid41364878,
year = {2025},
author = {Yoon, SE and Kang, W and Cho, J and Cho, HJ and Chalita, M and Oh, HS and Hyun, DW and Han, S and Kim, H and Sung, H and Lee, JY and Park, B and Ryu, KJ and Kim, HY and Cho, D and Kim, WS and Kim, SJ},
title = {Microbiome and metabolite biomarkers of CAR T-cell therapy outcomes in relapsed/refractory diffuse large B cell lymphoma.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2025016858},
pmid = {41364878},
issn = {2473-9537},
abstract = {CD19 CAR T-cell therapy has revolutionized treatment for relapsed/refractory diffuse large B-cell lymphoma (RR-DLBCL), but challenges like post-treatment failure and immune-related adverse events (AEs) persist. This study explores the gut microbiome as a predictive biomarker for CAR T-cell therapy outcomes and toxicity. Stool and serum samples from RR-DLBCL patients were analyzed at apheresis (47 samples) and one month post-infusion (32 samples) using whole-genome sequencing metagenomics. When compared with healthy controls and newly diagnosed DLBCL, RR-DLBCL showed significant gut dysbiosis, characterized by increased Proteobacteria and Enterobacteriaceae. Responders to treatment had higher levels of Bacteroides fragilis, while non-responders exhibited higher levels of Faecalibacterium prausnitzii. Functional metagenomic analysis suggested enrichment of inosine biosynthesis pathways in responders, and elevated serum inosine demonstrated an exploratory association with improved progression-free survival. Distinct microbial taxa and serum fatty acid profiles were also linked to CAR T-cell-related AEs, with higher acetate and butyrate levels in patients without AEs, and increased isovalerate in those with AEs. These findings indicate that gut microbiome features-particularly Bacteroides fragilis and inosine metabolism-may serve as candidate biomarkers for CAR T-cell therapy outcomes and toxicity. However, given the exploratory nature of these analyses and the limited cohort size, results should be interpreted cautiously. Larger, prospective studies will be required to validate these observations and to assess the potential of microbiome-based strategies to optimize CAR T-cell therapy in RR-DLBCL.},
}

@article {pmid41364769,
year = {2025},
author = {Ratner, HK and Duong, BD and Miao, P and Bertolli, SK and Shen, BA and Mitchell, U and Gallagher, LA and Radey, MC and Peterson, SB and Mougous, JD},
title = {An electron transport complex required in the gut sensitizes Bacteroides to a pore-forming type VI secretion toxin.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {50},
pages = {e2523503122},
doi = {10.1073/pnas.2523503122},
pmid = {41364769},
issn = {1091-6490},
support = {Investigator Award//HHMI (HHMI)/ ; },
mesh = {*Type VI Secretion Systems/metabolism ; *Gastrointestinal Microbiome ; *Bacteroides/metabolism/genetics ; *Bacterial Proteins/metabolism/genetics ; Humans ; *Bacterial Toxins/metabolism ; Electron Transport ; },
abstract = {Data suggest that antagonism between bacteria is prevalent within the gut microbiome. Such antagonism could have profound consequences on the fitness of species; however, the susceptibility determinants to even the most pervasive antagonistic factors in this ecosystem remain incompletely understood. Here, we screened for genetic factors that impact the susceptibility of Bacteroides to type VI secretion system (T6SS)-delivered toxins. This revealed that the Bte2 family of pore-forming toxins, which are widespread in B. fragilis and other human gut-associated Bacteroidales, strictly requires the H[+]/Na[+]-translocating ferredoxin:NAD[+] reductase (Rnf) electron transport chain within target cells in order to intoxicate. In Bacteroides, the precise metabolic role of the conserved Rnf pathway has not been defined. We establish that the Rnf complex is important for redox balancing within cells utilizing sugars derived from dietary fiber and is critical for fitness in vivo. Surprisingly, we find that while the intact Rnf membrane complex is required for Bte2 intoxication, Rnf-catalyzed electron transport is dispensable. We propose that the Rnf complex facilitates Bte2 membrane insertion, leading to intoxication via membrane depolarization. Our data suggest that T6SS toxins may avoid collateral damage within a complex ecosystem by recognizing discriminatory features of competitor species.},
}

*Type VI Secretion Systems/metabolism
*Gastrointestinal Microbiome
*Bacteroides/metabolism/genetics
*Bacterial Proteins/metabolism/genetics
Humans
*Bacterial Toxins/metabolism
Electron Transport

@article {pmid41364767,
year = {2025},
author = {Wang, N and Westermann, LM and Li, M and Li, CY and Murphy, ARJ and Gu, Z and Silvano, E and Blindauer, CA and Lidbury, IDEA and Zhang, YZ and Scanlan, DJ and Chen, Y},
title = {Structural basis and evolutionary pathways of glycerol-1-phosphate transport in marine bacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {50},
pages = {e2524546122},
doi = {10.1073/pnas.2524546122},
pmid = {41364767},
issn = {1091-6490},
support = {726116//EC | European Research Council (ERC)/ ; 32330001//NSF of china/ ; 883551//EC | European Research Council (ERC)/ ; },
mesh = {Phylogeny ; *Glycerophosphates/metabolism/chemistry ; Evolution, Molecular ; *Bacterial Proteins/metabolism/genetics/chemistry ; Biological Transport ; *Bacteria/metabolism/genetics ; *Aquatic Organisms/metabolism ; Seawater/microbiology ; Membrane Transport Proteins/metabolism/genetics/chemistry ; },
abstract = {All cells use lipid membranes to maintain cellular integrity and function, though Archaea utilize lipids composed of glycerol-1-phosphate (G1P), while Bacteria and Eukaryotes use glycerol-3-phosphate (G3P). Given that Archaea contribute significantly to global marine biomass, accounting for 0.3 gigatonnes (Gt) of carbon in the oceans, we aimed to uncover how archaeal G1P is recycled by marine microorganisms. Through a multidisciplinary approach combining microbiology, biochemistry, and structural biology, we identified a G1P transporter in marine bacteria, which we named GpxB. Phylogenetic analysis revealed that GpxB belongs to the organic phosphonate transporter (PhnT) family and is widely distributed in the marine microbiome, found in approximately 5 to 10% of microbial cells in surface marine waters. Strikingly, we also identified a second G1P transporter, UgpB, that is known to transport G3P and belongs to the carbohydrate uptake transporter-1 (CUT1) family, in the model bacterium Phaeobacter sp. MED193. To explore the evolutionary pathways that led to the formation of G1P binding sites in both the PhnT and CUT1 families, we determined the structures of GpxB and UgpB bound to G1P and G3P. Using structure-guided mutagenesis and a comparative analysis of the binding pockets within the PhnT and CUT1 families, we traced their evolutionary trajectories, highlighting the distinct strategies through which G1P-binding sites developed in these two protein families.},
}

Phylogeny
*Glycerophosphates/metabolism/chemistry
Evolution, Molecular
*Bacterial Proteins/metabolism/genetics/chemistry
Biological Transport
*Bacteria/metabolism/genetics
*Aquatic Organisms/metabolism
Seawater/microbiology
Membrane Transport Proteins/metabolism/genetics/chemistry

@article {pmid41364520,
year = {2025},
author = {Verbitsky, M and Khosla, P and Bivona, D and Khan, A and Gupta, Y and Park, H and Shen, TH and Ghotra, A and Xu, K and Ghavami, IA and Krithivasan, P and Martino, J and Sezin, T and Lim, TY and Kolupaeva, V and Limdi, NA and Luo, Y and Hakonarson, H and Sanna-Cherchi, S and Kiryluk, K and Mendelsohn, CL and Uhlemann, AC and Barasch, J and Gharavi, AG},
title = {Urobiota analysis and genome-wide association study in pediatric recurrent urinary tract infections and vesicoureteral reflux.},
journal = {JCI insight},
volume = {},
number = {},
pages = {},
doi = {10.1172/jci.insight.199689},
pmid = {41364520},
issn = {2379-3708},
abstract = {Urinary tract infections (UTIs) are the most common severe bacterial infections in young children, often associated with vesicoureteral reflux (VUR). To explore host genetic-microbiota interactions and their clinical implications, we analyzed the urinary microbiota (urobiota) and conducted genome-wide association studies (GWAS) for bacterial abundance traits in pediatric UTI and VUR patients from the RIVUR and CUTIE cohorts. We identified four urobiota community types based on relative abundance, characterized by the genera Enterococcus, Prevotella, Pseudomonas, and Escherichia/Shigella, and their associations with VUR, age, and toilet training. Children with VUR exhibited decreased microbial diversity and increased abundance of genera that included opportunistic pathogens, suggesting a disrupted urobiota. We detected genome-wide significant genetic associations with urinary bacterial relative abundances, in or near candidate genes including CXCL12, ABCC1, and ROBO1, which are implicated in urinary tract development and response to infection. We showed that Cxcl12 is induced 12 hours after uropathogenic bacterial infection in mouse bladder. The association with CXCL12 suggests a genetic link between UTI, VUR and cardiovascular phenotypes later in life. These findings provide the first characterization of host genetic influences on the pediatric urobiota in UTI and VUR, offering insights into the interplay between disease, host genetics and the urobiota composition.},
}

@article {pmid41364398,
year = {2025},
author = {Han, N and Peng, X and Zhang, T and Qiang, Y and Li, X and Zhang, W},
title = {Strain-level dynamics of Akkermansia muciniphila in the human gut microbiota.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-025-01982-7},
pmid = {41364398},
issn = {2191-0855},
support = {2018YFC1200100//National Key Research and Development Program of China/ ; },
abstract = {Akkermansia muciniphila (Akk), a mucin-degrading bacterium residing in the human gut, plays a pivotal role in intestinal health. This study investigated its temporal dynamics, strain-level diversity, and cross-regional transmission using longitudinal metagenomic data from the Chinese Microbiome Project (CMP). We observed significant fluctuations in Akk relative abundance across 52 time points in 7 healthy individuals, with detection rates of 56.9% (16S rRNA gene sequencing) and 33.3% (whole-genome sequencing, WGS). Notably, "short-term blooms"--rapid increases followed by declines in relative abundance--were identified in multiple subjects. Genomic analysis of 39 Akkermansia metagenome-assembled genomes (MAGs), combined with 89 publicly available strains with complete genome, revealed phylogenetically distinct clusters (average nucleotide identity, ANI < 98% between clusters). Strikingly, individuals harbored different clusters at varying time points (e.g., AmII replaced by AmIb and later AmIa in subject P4), suggesting strain replacement and recurrent colonization. Furthermore, high-similarity strains (ANI > 99%) were shared between individuals with close contact (e.g., cohabiting subjects P2 and P4) and across geographically distant regions (China, South Korea, and the United States), implicating human-mediated or environmental transmission pathways. These findings underscore the dynamic nature of Akk within the gut microbiota and highlight the need to explore factors driving its colonization, strain competition, and ecological dissemination.},
}

@article {pmid41364342,
year = {2025},
author = {Akhavan, N and Hrynkiewicz, K and Thiem, D and Gardiner, GE and Lawlor, PG and Balakrishnan, S and Guinan, KJ and O'Sullivan, JT and Mangan, M and Stadnicka, K},
title = {In vitro compatibility screening of Bacillus pumilus and Bacillus altitudinis strains with selected candidate prebiotics for in ovo application of synergistic synbiotics.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-025-13624-w},
pmid = {41364342},
issn = {1432-0614},
support = {UMO-2019/35/B/NZ9/03186 OVOBIOM//The National Science Centre in Poland/ ; },
abstract = {Bacillus species have demonstrated beneficial effects on intestinal health, production parameters, and immune function in poultry under both standard and disease-challenged conditions. Previously, we found that several novel ingredients (beta-glucan, vegetable protein hydrolysate, and liquid seaweed extract) demonstrated growth stimulation effects on Bifidobacterium lactis and Lactobacillus plantarum, Here, we extended this approach to examine in vitro synbiotic combinations of five novel marine-derived candidate probiotic Bacillus strains to assess their potential for in ovo applications. Beta-glucan enhanced the growth of all candidate Bacillus probiotic strains compared to a glucose control (p ≤ 0.05), suggesting a broad-spectrum modulatory role over a 24-h period, with variable magnitudes of response observed between strains. Species specificity was also observed, with lentinus stimulating the Bacillus pumilus but not the Bacillus altitudinis strains. A seaweed extract consistently stimulated the growth of one of the B. altitudinis strains (p ≤ 0.05), which, like all of the strains evaluated here, is seaweed-derived. This suggests potential ecological adaptation in substrate utilization. The shared environmental origin may influence substrate specificity and metabolic complementarity between strains and prebiotic candidates. Both B. altitudinis strains also exhibited enhanced growth at almost all time points (p ≤ 0.05) when cultured with vegetable protein hydrolysate. Based on these findings, we evaluated the effect of a potential synbiotic formulation comprising one of the B. altitudinis strains and vegetable protein hydrolysate in chickens, in ovo. The components were administered intra-amniotically at embryonic development day 18.5, utilizing a standard vaccination protocol. The hatchability of the chickens was not affected, thereby demonstrating the established dose as safe and applicable for further investigation. KEY POINTS: • Shared origin of bioactive compounds may enhance probiotic-prebiotic compatibility in vitro • Protein hydrolysate offers a novel alternative to carbohydrate prebiotics • In ovo delivery of Bacillus-based synbiotic formulations offers potential as an early microbiome programming strategy.},
}

@article {pmid41364164,
year = {2025},
author = {Alavi, SE and Ebrahimi Shahmabadi, H and Sharma, LA and Sharma, A},
title = {The Role of the Oral Microbiome in Periodontal Disease: A Systematic Review of Microbial Associations and Therapeutic Implications.},
journal = {Current microbiology},
volume = {83},
number = {1},
pages = {64},
pmid = {41364164},
issn = {1432-0991},
mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; *Bacteria/classification/isolation & purification/genetics ; *Periodontal Diseases/microbiology/therapy ; *Periodontitis/microbiology ; },
abstract = {Periodontitis is a chronic inflammatory disease driven by bacterial pathogens. This meta-analysis aimed to quantitatively assess the association between nine bacterial strains and periodontitis across 11 studies. We extracted odds ratios (ORs) and 95% confidence intervals (CIs) from studies evaluating Streptococcus mutans, Lactobacillus, Fusobacterium nucleatum, Prevotella intermedia, Staphylococcus aureus, Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Tannerella forsythia, and Treponema denticola. Heterogeneity was evaluated using Cochran's Q and I[2] tests. We systematically searched PubMed, Scopus, and Web of Science up to March 2024, following PRISMA guidelines, to identify studies investigating the association between oral bacterial species and periodontitis. Porphyromonas gingivalis was identified as a significant risk factor for periodontitis in all eight studies (ORs: 4.17-97, I[2] = 85.99%). Tannerella forsythia (ORs: 2.75-36.88, I[2] = 85.39%) and Treponema denticola (ORs: 3.12-24.5, I[2] = 85.54%) were also significantly associated with periodontitis. Prevotella intermedia showed a significant association in three out of four studies, despite high heterogeneity (I[2] = 79.82%). Fusobacterium nucleatum and Staphylococcus aureus were not found to be significant risk factors. Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola are key bacterial risk factors for periodontitis. The findings highlight the importance of microbial screening in clinical practice, while the heterogeneity suggests the need for standardized research. Future studies should focus on longitudinal assessments and microbial interactions.},
}

Humans
*Microbiota
*Mouth/microbiology
*Bacteria/classification/isolation & purification/genetics
*Periodontal Diseases/microbiology/therapy
*Periodontitis/microbiology

@article {pmid41364123,
year = {2025},
author = {Chervochkina, AS and Aksenov, AS and Ilmast, NV},
title = {Yolk-Sac Stage Bacteriome: Gaps of Knowledge and Demand for Fish Science.},
journal = {Current microbiology},
volume = {83},
number = {1},
pages = {59},
pmid = {41364123},
issn = {1432-0991},
support = {FSRU-2023-004//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {Animals ; *Fishes/microbiology/growth & development ; *Bacteria/classification/genetics/isolation & purification ; *Yolk Sac/microbiology/growth & development ; *Gastrointestinal Microbiome ; Probiotics ; Larva/microbiology/growth & development ; },
abstract = {The intestinal microbiome of fish at early stages of ontogeny represents a complex and dynamic ecosystem that is critically important for immune system development, physiological resilience, and growth. The yolk-sac stage is of particular significance, as larvae rely exclusively on endogenous nutrient reserves while being colonized by microbes for the first time. During this period, the foundations of microbiota are established, which subsequently influence the development of the digestive system, barrier functions, and pathogen resistance. Recent studies show that microbial communities at this stage are characterized by low alpha diversity and the dominance of Proteobacteria, Firmicutes, and Bacteroidetes. With the transition to exogenous feeding, there is an increase in taxonomic and functional diversity, along with the emergence of probiotic genera (Bacillus, Lactobacillus, Shewanella) that promote enzymatic activity, immune modulation, and increased survival of larvae. This review systematically compiles data from the past 20 years, encompassing both culture-dependent methods and high-throughput sequencing approaches. It has been demonstrated that despite the limitations of culture-based methods, they remain indispensable for isolating probiotic strains. A comparison of methodologies revealed high variability in protocols, complicating the direct comparison of results. The findings underscore the applied significance of studying microbiota for aquaculture during the yolk-sac stage. The management of microbial communities through probiotics, prebiotics, and environmental regulation presents prospects for enhancing the survival, growth, and resilience of fish larvae.},
}

Animals
*Fishes/microbiology/growth & development
*Bacteria/classification/genetics/isolation & purification
*Yolk Sac/microbiology/growth & development
*Gastrointestinal Microbiome
Probiotics
Larva/microbiology/growth & development

@article {pmid41364074,
year = {2025},
author = {Luckey, D and Marietta, E and Taneja, V},
title = {HLA Transgenic Mice as a Model to Uncover Biomarkers and Therapeutic Strategies for Rheumatoid Arthritis.},
journal = {Current protocols},
volume = {5},
number = {12},
pages = {e70263},
doi = {10.1002/cpz1.70263},
pmid = {41364074},
issn = {2691-1299},
mesh = {Animals ; *Arthritis, Rheumatoid/therapy/immunology/genetics ; *Disease Models, Animal ; Mice ; Mice, Transgenic ; Humans ; Biomarkers/metabolism ; *HLA Antigens/genetics/immunology ; *Arthritis, Experimental/immunology ; Collagen Type II/immunology ; },
abstract = {Rheumatoid arthritis (RA) is a chronic disease involving inflammation of the joints. While the etiology of RA remains unknown, evidence exists for a significant contribution of the major histocompatibility complex (MHC). Environmental factors are also indicated as playing an etiological role. Since it is impossible to define the mechanisms contributing to disease onset and progression in humans, mouse models have been used widely. While many animal models have been generated by immunization with self-proteins to induce arthritis, type II collagen (CII)-induced arthritis is one of the most commonly used models utilized to understand the immunopathology of RA. CII constitutes 80% to 90% of total collagen content of hyaline cartilage found in joints and is a genetically conserved sequestered protein. Immunization with heterologous CII with an adjuvant in mice leads to cellular and humoral responses to heterologous and autoreactive CII-specific responses and collagen-induced arthritis (CIA). Mice immunized with CII develop inflammatory arthritis that shares many similarities in clinical, serological, and radiological features with RA in humans. However, selecting an antigen for inducing arthritis and the mouse strain are important, as not all strains are susceptible to CIA. A critical difference between RA and CIA is that in mice that lack the expression of human MHC II, the development of CIA is linked to the H2A locus, which is the homologue of HLA-DQ, while most human studies have linked RA susceptibility with HLA-DR alleles. Mice expressing HLA-DQ and HLA-DR molecules have been used to understand the role of MHC genes in susceptibility to RA. The protocols for inducing CIA in the HLA expressing transgenic mice described in this article can be used to understand how the different HLA molecules confer susceptibility to RA. © 2025 Wiley Periodicals LLC. Basic Protocol 1: Use of mouse strains and humanized mice for modeling rheumatoid arthritis Basic Protocol 2: Use of humanized mice for therapeutic protocols.},
}

Animals
*Arthritis, Rheumatoid/therapy/immunology/genetics
*Disease Models, Animal
Mice
Mice, Transgenic
Humans
Biomarkers/metabolism
*HLA Antigens/genetics/immunology
*Arthritis, Experimental/immunology
Collagen Type II/immunology

@article {pmid41364072,
year = {2025},
author = {Bartman, S and Dawdy, M and Wang, Y and Akens, M and Whyne, C and Nam, D},
title = {A possible treatment for fragility fractures of the pelvis? The impact of probiotic treatment on pelvic bone microstructure and strength in osteoporotic rats.},
journal = {Journal of orthopaedic trauma},
volume = {},
number = {},
pages = {},
doi = {10.1097/BOT.0000000000003138},
pmid = {41364072},
issn = {1531-2291},
abstract = {OBJECTIVES: Healing remains a clinical challenge in non-operatively treated fragility fractures of the pelvis (FFPs). Modifying gut microbiota has been found to impact cytokine pathways involved in bone formation and resorption. This study examined the impact of probiotic treatment pre- and post-unilateral pubic rami fracture on bone microstructure and load-to-failure of healing fractured and intact (unfractured) contralateral hemi-pelvises.

METHODS: Twenty-one 6-month-old female Sprague Dawley rats were bilaterally ovariectomized and housed for 3 months to establish an osteoporotic phenotype. At 9-months old, stable unilateral fractures of the superior and inferior pubic rami of the left hemi-pelvis (Type 1a FFP) were created. Prior to fracture creation, rats were randomly separated into control (phosphate buffered saline (PBS) administered for 12-weeks), pre-fracture treatment (probiotics administered for 12-weeks starting 6-weeks pre-fracture), and post-fracture treatment (probiotics administered for 6-weeks post-fracture) groups. At 6-weeks post-fracture, rats were sacrificed, and their pelvises were harvested, µCT imaged, and evaluated via microstructural analysis and biomechanical testing.

RESULTS: On the intact hemi-pelvises, the pre-fracture treatment group (n=5) had significantly higher bone volume (BV) (p=0.050), bone volume fraction (BV/TV) (p=0.019), bone mineral density (BMD) (p=0.019), and tissue mineral density (TMD) (p=0.014) when compared to those in the post-fracture treatment group (n=7). The intact hemi-pelvises of the pre-fracture treatment group also had significantly increased trabecular thickness (TbTh) (p=0.021) when compared to those in the control group (n=6). On the fractured hemi-pelvises, the pre-fracture group had increased total volume (TV) (p=0.020), BV (p=0.011), and BV/TV (p=0.026) when compared to the control group (n=4). While load-to-failure was correlated with microstructural parameters (BV/TV (r=0.42, p=0.015), trabecular number (TbN) (r=0.42, p=0.014), BMD (r=0.55, p=0.0008), TMD (r=0.40, p=0.019) and trabecular spacing (TbS) (r=-0.58, p=0.0003), no significant differences in bone strength were found between groups.

CONCLUSIONS: Probiotic treatment was shown to improve bone microstructure in osteoporotic rats, however, efficacy was related to treatment timing and duration. Administration of probiotics for 12-weeks beginning 6-weeks pre-fracture significantly enhanced bone quality in both the healing fractured and intact contralateral hemi-pelvises. This suggests a critical timing threshold exists for probiotic therapy to impact the gut microbiome, facilitating an alteration of the immune response post-fracture and producing positive structural changes in osteoporotic pelvic bone.},
}

@article {pmid41363910,
year = {2025},
author = {Armstrong, MT and Antunes, K and Willis, NB and Meyer, MB and Pierre, JF and Ozturk, G},
title = {Whey Protein Phospholipid Concentrate and Its Fractions as a Diet Intervention Enhance Bone Health and Alter the Gut Microbiome in Weanling Mice.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {23},
pages = {e71260},
doi = {10.1096/fj.202502683R},
pmid = {41363910},
issn = {1530-6860},
support = {N/A//University of Wisconsin-Madison Dairy Innovation Hub/ ; DK007665//HHS | National Institutes of Health (NIH)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Whey Proteins/pharmacology ; Mice ; *Phospholipids/pharmacology ; Male ; Bone Density/drug effects ; *Bone Development/drug effects ; Weaning ; Mice, Inbred C57BL ; *Bone and Bones/drug effects/metabolism ; },
abstract = {Early post-weaning growth is a critical window for bone development, and diet plays a central role in establishing peak bone mass in early life. Whey protein phospholipid concentrate (WPPC), a co-product of whey protein isolate manufacturing, is enriched in bioactive lipids and proteins that may support bone development and calcium homeostasis. This study aimed to investigate the effects of WPPC and its protein- and lipid-enriched fractions on bone development, gene expression, and gut microbiota in weanling mice. WPPC was fractionated using temperature-dependent centrifugation, microfiltration, and ultrafiltration, yielding lipid- and protein-rich components that were used to supplement isocaloric diets. Mice were fed either lipid fraction (Fat), protein fraction (Protein), or whole WPPC (WPPC) (10% by kcal; ~8.7% w/w) for 12 weeks. Compared to controls, the Protein and WPPC groups exhibited significantly increased femur length (4.44% and 4.01%, respectively), while the Fat group showed significantly higher bone mineral density (6.15%). Quantitative PCR of jejunal tissues revealed upregulation of calcium transporter genes (Cldn2, Cldn12, and Pmca1) in WPPC-fed mice with no changes in vertebral bone markers of osteocyte differentiation. Circulating iFGF23 levels also remained unchanged, suggesting limited endocrine involvement. Gut microbiota analysis via 16S rRNA sequencing showed diet-specific shifts, including increased Akkermansia and Streptococcus in the WPPC group and elevated Lactobacillaceae in the Protein and Fat groups. These findings demonstrate that WPPC and its enriched macronutrient fractions promote skeletal development and modulate calcium uptake and gut microbial composition, supporting their potential as functional ingredients for bone health applications in early life.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Whey Proteins/pharmacology
Mice
*Phospholipids/pharmacology
Male
Bone Density/drug effects
*Bone Development/drug effects
Weaning
Mice, Inbred C57BL
*Bone and Bones/drug effects/metabolism

@article {pmid41363768,
year = {2025},
author = {Basting, CM and Klatt, NR},
title = {Dissecting the Impact of the Gut Microbiome on HIV Reservoir Dynamics.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf560},
pmid = {41363768},
issn = {1537-6613},
}

@article {pmid41363709,
year = {2025},
author = {Tanwar, H and Gnanasekaran, JM and Ganesh, N and Zhou, C and Plotkin, A and Baima, G and Costalonga, M and Zhou, F and Feng, H and Jani, P and Raufman, JP and Thumbigere-Math, V},
title = {Dextran sodium sulfate confounds causal role of periodontitis in inflammatory bowel disease.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jper.70045},
pmid = {41363709},
issn = {1943-3670},
support = {//University of Maryland School of Dentistry/ ; },
abstract = {BACKGROUND: Emerging evidence supports a bidirectional link between periodontitis and inflammatory bowel disease (IBD). To investigate this relationship, experimental models commonly use dextran sodium sulfate (DSS) to induce colitis. However, DSS is presumed to selectively affect the colon, and its potential off-target effects on the oral cavity remain poorly understood. We examined whether DSS disrupts oral health, potentially confounding oral-gut axis research.

METHODS: C57BL/6 mice received 2% DSS in drinking water for 8 days, followed by 2 days of untreated water. Colitis severity was assessed by weight loss, colon length, histopathology, and quantitative real-time-polymerase chain reaction (qRT-PCR). Oral health was evaluated via micro-computed tomography (micro-CT) analysis of alveolar bone, gingival histology, cytokine expression, and 16S rRNA sequencing of the oral microbiome.

RESULTS: DSS induced hallmark features of colitis, including weight loss, colon shortening, epithelial crypt damage, and mucosal inflammation. Strikingly, DSS also induced significant oral pathology, including alveolar bone loss, gingival epithelial hyperplasia, inflammatory infiltration, and upregulated gingival pro-inflammatory cytokines (interleukin [IL] -6, IL-17, tumor necrosis factor-alpha [TNF-α]). DSS further altered the oral microbiota causing reduced alpha-diversity and a dysbiotic shift, with enrichment of Streptococcus danieliae and depletion of commensals such as Lactobacillus murinus and Clostridium ASF502. These microbial changes were accompanied by upregulated pathways involved in carbohydrate metabolism, oxidative stress response, and environmental sensing.

CONCLUSION: DSS induces periodontal inflammation and oral dysbiosis, independent of colitis. These findings expose a critical confounder in oral-gut axis models and highlight the need to include DSS-only or periodontitis-only controls and alternative models to accurately distinguish systemic effects of DSS from true oral-gut interactions.

PLAIN LANGUAGE SUMMARY: This study shows that dextran sodium sulfate (DSS), a chemical used to model gut inflammation in mice, also causes gum disease-like changes-including bone loss, inflammation, and changes in oral bacteria. These findings reveal that DSS alone can affect the mouth and may confound studies investigating links between gum disease and inflammatory bowel disease, highlighting the need for better-controlled models.},
}

@article {pmid41363662,
year = {2025},
author = {Liu, B and Li, W and Zhao, R and Klauer, RR and Hansen, A and Miller, N and Chen, Y and Blenner, MA and Tang, YJ},
title = {Leveraging Retrieval-Augmented Generation to Accelerate Discoveries on Mealworm Larvae and Plastic Degradation.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c14258},
pmid = {41363662},
issn = {1520-5851},
abstract = {Large language models (LLMs) are transforming broad research areas, yet concerns about their trustworthiness remain. This study explored the use of Retrieval-Augmented Generation (RAG) to improve LLMs' knowledge extraction in the field of mealworm-mediated plastic degradation. We integrated publications up to June 2024 (75 papers) to evaluate the model performance using a curated data set of 100 queries. GraphRAG, LightRAG, and a traditional RAG were examined with five LLM models (GPT-4o, GPT-5, Deepseek-V3.1, Qwen-plus, and Llama-3.3). Our results reveal that LightRAG improved LLMs the most in information extraction. Specifically, for quantitative information extraction, the best performing RAG + LLM pipeline achieves over 92% accuracy. Meanwhile, for open-ended queries, LightRAG + Llama answers the questions with the best balance of precision and information coverage. Moreover, empirical results validated the answers about the mealworm gut microbiome composition and plastic deconstruction patterns through the LightRAG + Llama pipeline. In designing plastic biodegradation experiments, the original LLMs outperformed RAG-trained LLMs. The expandable nature of RAG enables timely updates to the knowledge base. This study demonstrates a reliable application of advanced LLMs in the emerging environmental science field. Our findings identify challenges, such as conflict handling, and guide future research in scientific artificial intelligence.},
}

@article {pmid41363528,
year = {2025},
author = {Huang, PC and Ngo, CQ and Dewalt, A and Kolomiets, MV and Edwards, JA},
title = {A Broadly Distributed Rhizobacterium, Roseateles chitinivorans P500, Promotes Growth and Systemic Resistance via Jasmonic Acid-Dependent Oxylipin Signaling in Grasses.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {},
doi = {10.1094/MPMI-10-25-0142-FI},
pmid = {41363528},
issn = {0894-0282},
abstract = {Harnessing root-associated microbiomes to promote beneficial microbial compositions could offer a sustainable strategy to increase crop resilience. Major challenges impeding this strategy are the lack of understanding of which native members of the microbiome benefit the host and molecular signaling events underlying these benefits. In this study, we isolated a strain of Roseateles chitinivorans, RcP500, corresponding to the most abundant bacterial taxon in the switchgrass root microbiome. Inoculation of roots with RcP500 promoted growth and induced systemic resistance (ISR) to Bipolaris leaf spot of switchgrass and closely related Panicum hallii. R. chitinivorans is also highly abundant in rhizosphere and root microbiomes of maize and rice and enhanced growth of these two plant species. Furthermore, RcP500 elicited ISR in maize against anthracnose leaf blight and southern corn leaf blight. Bioassays and root metabolite profiling in maize wild-type (WT) and jasmonic acid (JA)-deficient opr7opr8 mutant plants revealed the requirement of JA-dependent processes in RcP500-elicited synthesis of the JA precursor, 12-OPDA (cis-(+)-12-oxo-phytodienoic acid) and an α-ketol, 9,10-KODA (9-hydroxy-10-oxo-12(Z)-octadecadienoic acid), two oxylipins previously implicated in ISR signaling. Xylem sap transfusion of RcP500 colonized plants to naïve receiver plants corroborated the role of JA in promoting these signaling intermediates. While root JA synthesis was downregulated upon RcP500 colonization, gibberellic acid was induced, suggesting a potential mechanism behind simultaneous growth promotion and ISR triggered by this bacterium. Overall, this study identified a novel rhizobacterium with a broad host range that promotes growth and systemic resistance across multiple plant species in a JA-dependent, ketol-driven manner.},
}

@article {pmid41363457,
year = {2025},
author = {Koetsier, RA and Reitz, ZL and Belzer, C and Chevrette, MG and Handelsman, J and Zhu, Y and van der Hooft, JJJ and Medema, MH},
title = {Using cross-species co-expression to predict metabolic interactions in microbiomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0132125},
doi = {10.1128/msystems.01321-25},
pmid = {41363457},
issn = {2379-5077},
abstract = {In microbial ecosystems, metabolic interactions are key determinants of species' relative abundance and activity. Given the immense number of possible interactions in microbial communities, their experimental characterization is best guided by testable hypotheses generated through computational predictions. However, widely adopted software tools-such as those utilizing microbial co-occurrence-typically fail to highlight the pathways underlying these interactions. Bridging this gap will require methods that utilize microbial activity data to infer putative target pathways for experimental validation. In this study, we explored a novel approach by applying cross-species co-expression to predict interactions from microbial co-culture RNA-sequencing data. Specifically, we investigated the extent to which co-expression between genes and pathways of different bacterial species can predict competition, cross-feeding, and specialized metabolic interactions. Our analysis of the Mucin and Diet-based Minimal Microbiome (MDb-MM) data yielded results consistent with previous findings and demonstrated the method's potential to identify pathways that are subject to resource competition. Our analysis of the Hitchhikers of the Rhizosphere (THOR) data showed links between related specialized functions, for instance, between antibiotic and multidrug efflux system expression. Additionally, siderophore co-expression and further evidence suggested that increased siderophore production of the Pseudomonas koreensis koreenceine BGC deletion-mutant drives siderophore production in the other community members. In summary, our findings confirm the feasibility of using cross-species co-expression to predict pathways potentially involved in microbe-microbe interactions. We anticipate that the approach will also facilitate the discovery of novel gene functions through their association with other species' metabolic pathways, for example, those involved in antibiotic response.IMPORTANCEAn improved mechanistic understanding of microbial interactions can guide targeted interventions or inform the rational design of microbial communities to optimize them for applications such as pathogen control, food fermentation, and various biochemical processes. Existing methodologies for inferring the mechanisms behind microbial interactions often rely on complex model-building and are, therefore, sensitive to the introduction of biases from the incorporated existing knowledge and model-building assumptions. We highlight the microbial interaction prediction potential of cross-species co-expression analysis, which contrasts with these methods by its data-driven nature. We describe the utility of cross-species co-expression for various types of interactions and thereby inform future studies on use-cases of the approach and the opportunities and pitfalls that can be expected in its application.},
}

@article {pmid41363449,
year = {2025},
author = {Meyer, KM and Lindow, SE},
title = {Microbial dispersal from surrounding vegetation influences phyllosphere microbiome assembly of corn and soybean.},
journal = {mBio},
volume = {},
number = {},
pages = {e0333525},
doi = {10.1128/mbio.03335-25},
pmid = {41363449},
issn = {2150-7511},
abstract = {Non-crop plants surrounding agricultural fields provide numerous ecological services to crops but have rarely been considered a source of microorganisms during the early stages of crop growth. In this study, we test whether crops in close proximity to surrounding woodland habitat fragments develop a denser microbiome that more closely resembles the microbiome composition of the surrounding vegetation than plants farther away. We sampled epiphytic bacteria from corn and soybean plants weekly for 4 (corn) and 3 (soybean) weeks during early development using a spatially explicit design, and on the final time point, we sampled additional cohorts of younger leaves. To contextualize the source strength of the surrounding vegetation, we also sampled soil at each sampling location. Both crop species exhibited a microbiome density gradient and a decay of microbiome similarity to the surrounding vegetation over a distance of 100 m from the vegetation at many time points. Phyllosphere microbiome similarity to the soil tended to increase into the field interior. The strength of host microbiome filtering also depended on the proximity to the surrounding vegetation, with intermediate to most distant locations exhibiting the highest values of host filtering. Last, the microbiomes of younger leaves tended to more closely resemble those of the older surrounding conspecific leaves than the soil or surrounding woodland vegetation. Overall, our study demonstrates that dispersal of bacteria from nearby leaves can shape the abundance and composition of developing crop phyllosphere microbiomes and highlights the diminishing role that soil plays when plant sources are closer or more abundant.IMPORTANCEA central concern in microbial ecology is understanding the sources of microbial colonists and how proximity to such sources impacts community assembly. This area of research is especially important for plants during early stages of development, where the arrival of leaf-specialized bacteria plays an influential role in priming plant immunity and consequently promoting disease resistance. In this study, we test the effect of dispersal from surrounding vegetation on the phyllosphere assembly of corn and soybean using a time series over the early stages of growth. Our work demonstrates that at these early developmental stages, non-crop vegetation surrounding croplands acts as a meaningful source of phyllosphere microorganisms. We further show that the influence of soil on the phyllosphere depends on host proximity to surrounding vegetation and that microbiomes of young leaves emerging on more mature plants tend to be more influenced by older surrounding crop leaves than soil or non-crop leaves.},
}

@article {pmid41363330,
year = {2025},
author = {Licata, AG and Zoppi, M and Dossena, C and Rossignoli, F and Rizzo, D and Bergamaschi, L and Nigro, O and Chiaravalli, S and Massimino, M and De Cecco, L},
title = {A QIIME2-based workflow for multi-amplicon 16S rRNA profiling.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0083625},
doi = {10.1128/mra.00836-25},
pmid = {41363330},
issn = {2576-098X},
abstract = {We present an open-source QIIME2 pipeline for 16S multi-amplicon sequencing. Benchmarked against proprietary software with a mock community, our workflow demonstrates comparable sequencing depth and taxonomic accuracy (F1-Score=0.875). The multi-region approach outperforms single amplicons, validating our pipeline as a robust alternative for semiconductor-based sequencing data.},
}

@article {pmid41363094,
year = {2025},
author = {Fu, W and Li, P and Sun, C and Sun, B and Kong, Z and Zhu, Y and Tian, H and Guo, Q and Lai, H},
title = {Lysobacter Orchestrates Plant-Microbiome Crosstalk to Enhance Tomato Fruit Quality.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c09587},
pmid = {41363094},
issn = {1520-5118},
abstract = {Lysobacter can promote plant growth and induce disease resistance, but its potential contribution to fruit quality remains understudied. This study investigated the role of Lysobacter fragariae P25 in regulating tomato fruit quality through integrated metabolomics, transcriptomics, and metatranscriptomics. We found that P25 inoculation modified fruit flavor and nutrition by increasing the accumulation of soluble sugars, unsaturated fatty acids, and essential amino acids and decreasing the tomatidine content. Fruit color and functional quality were enhanced upon inoculation with higher levels of flavonoids, lycopene, vitamins, and phenolic acids. The inoculated soil showed greater fertility and biological activity coupled to heightened microbial diversity and recruitment of potentially beneficial taxa in the rhizosphere, shifting community functions and networks toward healthier patterns. Cross-kingdom interactions between microbial genes and fruit metabolites were identified, linking rhizosphere microbiomes to fruit quality. Our results demonstrate P25-mediated plant-microbiome crosstalk in tomatoes, which drives metabolic reprogramming and consequently enhances the overall fruit quality.},
}

@article {pmid41362927,
year = {2025},
author = {Sun, D and Hua, Z and Xiao, Y and He, D and Wu, H and Lin, X and Chen, Q and Li, Z and Hou, Y},
title = {Bidirectional microbial regulation by tyrosine metabolism enhances palmatine-mediated colitis protection.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2596405},
doi = {10.1080/19490976.2025.2596405},
pmid = {41362927},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Berberine Alkaloids/pharmacology ; *Tyrosine/metabolism ; *Colitis/microbiology/prevention & control/chemically induced/drug therapy ; Mice, Inbred C57BL ; Cresols/metabolism ; Dysbiosis ; Disease Models, Animal ; Th17 Cells/immunology/drug effects ; Male ; Dextran Sulfate ; },
abstract = {Gut microbiota dysbiosis and intestinal immune dysfunction contribute to the disease pathogenesis of ulcerative colitis (UC), therapeutic strategies aim to reshape microbial balance and reduce inflammation. It is unclear that how this bidirectional regulation between microbe-immune system is achieved and what is a possible nexus point for this regulation. Here, we demonstrated that palmatine (PAL) alleviates colitis by modulating interference competition between two microbes through the mediation of microbial tyrosine metabolites. Specifically, PAL directly inhibits B. acidifaciens while indirectly promoting the growth of B. stercorirosoris in mice with DSS-induced colitis. Notably, p-cresol (PC), a crucial microbial metabolite produced by B. acidifaciens, exacerbates colitis by promoting Th17 cells activation and inhibiting the growth of B. stercorirosoris. Furthermore, the immediate reduction in p-hydroxyphenylacetic acid, which is metabolized by B. stercorirosoris, contributes to the aggravation of colitis. Mechanistically, PC significantly inhibited the glycolysis of B. stercorirosoris, with downregulation of gene expression associated with glycolysis. In addition, we found that the inhibitory function of PC was offset by the addition of large amounts of polysaccharide and glucose in the medium of B. stercorirosoris. In summary, this study uncovers the mechanism by which palmatine‒microbiome‒host crosstalk cooperatively alleviate colitis through PC-mediated the bidirectional regulation. These findings propose that microbial metabolites function as regulators of microbiota‒host interactions, offering potential interventions for the treatment or prevention of dysbiosis-driven diseases.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Berberine Alkaloids/pharmacology
*Tyrosine/metabolism
*Colitis/microbiology/prevention & control/chemically induced/drug therapy
Mice, Inbred C57BL
Cresols/metabolism
Dysbiosis
Disease Models, Animal
Th17 Cells/immunology/drug effects
Male
Dextran Sulfate

@article {pmid41362921,
year = {2025},
author = {Müller, P and Schmidtchen, V and de la Cuesta-Zuluaga, J and Pérez Jiménez, L and Gekeler, C and Mateus, A and Maier, L},
title = {Antagonistic drug interactions protect commensal Bacteroidaceae from macrolides via an RND-type efflux pump.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2596806},
doi = {10.1080/19490976.2025.2596806},
pmid = {41362921},
issn = {1949-0984},
mesh = {*Macrolides/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Gastrointestinal Microbiome/drug effects ; *Bacteroidetes/drug effects/genetics/metabolism ; *Bacterial Proteins/metabolism/genetics ; Drug Resistance, Bacterial ; *Membrane Transport Proteins/metabolism/genetics ; Drug Interactions ; },
abstract = {Antibiotics are essential to modern medicine, but their broad-spectrum activity can unintentionally disrupt the gut microbiota. This collateral damage may be alleviated by antagonistic drug interactions, in which specific compounds used in combination therapies selectively protect beneficial gut microbes from antibiotic activity. Using efflux pump inhibitors, transcriptomic and proteomic analyses, and targeted gene deletions, we show that a variety of non-antibiotic pharmaceuticals-from diverse therapeutic classes and at sub-inhibitory concentrations-can protect multiple Bacteroidales species from macrolide antibiotics. In Bacteroidaceae, this protection is mediated by a resistance-nodulation-division (RND)-type efflux pump, which is induced by the non-antibiotic drug but not by macrolides alone. Notably, protection persists even after the non-antibiotic drug is removed, and prolonged exposure results in stable macrolide resistance that is dependent on the RND-type efflux pump. Our findings illustrate how non-antibiotic drugs can inadvertently activate otherwise silent detoxification systems in gut microbes, uncovering resistance mechanisms that arise without antibiotic selection or gene transfer. While this can be harnessed to protect the microbiome during antibiotic therapy, it also reveals hidden resistance phenotypes that may escape detection in standard antimicrobial resistance assays.},
}

*Macrolides/pharmacology
*Anti-Bacterial Agents/pharmacology
Gastrointestinal Microbiome/drug effects
*Bacteroidetes/drug effects/genetics/metabolism
*Bacterial Proteins/metabolism/genetics
Drug Resistance, Bacterial
*Membrane Transport Proteins/metabolism/genetics
Drug Interactions

@article {pmid41362820,
year = {2026},
author = {Lanton, T and Eidelshtein, D and Rachmilewitz, J and Abramovitch, R and Pappo, O and Udi, S and Baraghithy, S and Tam, J and Perles, S and Williams, E and Elgavish, S and Ruppo, S and Benyamini, H and Mor, U and Elinav, E and Schmidt-Arras, D and Rehman, A and Rosenstiel, P and Giannou, A and Huber, S and Rose-John, S and Galun, E and Axelrod, JH},
title = {Blockade of Interleukin-6 Trans-signaling in the Presence of Certain Gut Microbiota Induces Mature-onset Obesity in Mice.},
journal = {Gastro hep advances},
volume = {5},
number = {2},
pages = {100819},
pmid = {41362820},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Interleukin-6 (IL-6) performs multiple roles in regulating metabolic pathways in both mice and man. Here, we examined the age-dependent metabolic phenotype of SGP mice-mice overexpressing sgp130, a factor that specifically blocks IL-6 trans-signaling-that were housed in distant vivaria.

METHODS: Transgenic SGP mice engineered to block IL-6 trans-signaling and wild-type littermates were raised in a Jerusalem animal facility to up to 14 months of age and assessed for weight gain, body composition, and metabolic determinants of energy expenditure in young versus aged mice. Proteomic and RNA-seq analyses were performed on liver samples as a function of age and genotype.

RESULTS: At ∼6 months of age, weight gain, body fat accumulation, hepatosteatosis, hyperglycemia, and macrophage recruitment to adipose tissue emerged and progressed with age in SGP mice maintained in the Jerusalem animal facility, but not in 3 other vivaria. IL-6/sIL-6R blockade strongly reduced signal transducer and activator of transcription 3 phosphorylation in the liver, and hepatocyte-targeted ablation of signal transducer and activator of transcription 3 recapitulated the IL-6 trans-signaling blockade phenotype. Multiomics analyses of mouse livers revealed age- and genotype-related changes in gene expression profiles attributable to bacterial byproducts. Depletion of the gut microbiota by antibiotic treatment from the age of 6 months reversed the obese phenotype in transgenic mice, confirming the crucial role of the microbiome in the phenotype. Accordingly, the microbiome of mice from the Jerusalem animal facility differed significantly from that of mice from animal facilities in Kiel and Hamburg, Germany, where the same mice did not develop a metabolic phenotype.

CONCLUSION: These findings reveal the crucial functions of IL-6 trans-signaling in preventing mature-onset body fat accumulation induced by certain intestinal microbiota.},
}

@article {pmid41362765,
year = {2025},
author = {Luo, J and Yang, J and Li, S and Liu, J and Qin, X and Li, L and Liu, W and Xing, H},
title = {Tumor-resident microbiota in gynecologic malignancies: Molecular mechanisms, clinical correlations, and translational potential.},
journal = {iScience},
volume = {28},
number = {11},
pages = {113729},
pmid = {41362765},
issn = {2589-0042},
abstract = {Intratumoral microbiota refers to the microbial communities, including bacteria, fungi, and viruses, residing within tumor tissues and forming part of the tumor microenvironment. Evidence shows that it significantly influences solid tumors like colorectal and breast cancer. Advances in sequencing have revealed the specific distribution of these microbes in gynecologic malignancies. Their dynamic composition is closely linked to tumor initiation, progression, and response to therapy, providing new insights for precision medicine. This review examines their molecular mechanisms and clinical relevance, focusing on impacts on diagnosis (e.g., microbial biomarkers), personalized treatment (e.g., modulation of chemotherapy/immunotherapy efficacy), and prognosis (e.g., recurrence risk prediction). It also discusses the translational potential and clinical application challenges of targeting microbiota, aiming to provide new strategies for precision medicine in gynecologic oncology.},
}

@article {pmid41362728,
year = {2026},
author = {Li, Q and Xia, S and Zhang, X and Liu, Y and Xiao, X and Yang, J},
title = {Gut Microbiota-Driven Pathways Linking Chronic Stress to Tumor Progression.},
journal = {International journal of biological sciences},
volume = {22},
number = {1},
pages = {258-279},
pmid = {41362728},
issn = {1449-2288},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Neoplasms/microbiology/metabolism/pathology ; Dysbiosis/microbiology ; Disease Progression ; Animals ; },
abstract = {Chronic stress is increasingly recognized as a critical factor influencing tumor progression, but its underlying mechanisms remain incompletely understood. This review examines the role of gut microbiota as a critical mediator linking chronic stress to tumor progression. Recent evidence suggests that chronic stress triggers gut dysbiosis, characterized by reduced microbial diversity, depletion of beneficial bacteria, and enrichment of potentially harmful species. We summarize the mechanisms by which chronic stress regulates gut microbial dysbiosis, including stress-related hormone signaling, intestinal inflammation, mucosal barrier disruption, and altered gut motility. Additionally, we examine how stress-induced dysbiosis contributes to tumor progression through immune suppression, metabolic reprogramming, enhanced tumor stemness, and potentially through barrier dysfunction, and chronic inflammation. We further discuss potential therapeutic interventions, including specific probiotics, prebiotics and other strategies that may help suppress tumor development by modulating the stress-microbiota-cancer axis. In conclusion, these emerging insights provide a foundation for novel therapeutic strategies that target the stress-microbiome-cancer axis, which may help suppress tumor progression and complement conventional cancer treatments to improve clinical outcomes in cancer patients.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Neoplasms/microbiology/metabolism/pathology
Dysbiosis/microbiology
Disease Progression
Animals

@article {pmid41362644,
year = {2025},
author = {Wu, H and Sun, D and Fang, S and Pan, Q and Yue, C},
title = {Genetically Predicted Causal Risk Factors for Preeclampsia: A Comprehensive Mendelian Randomization Study.},
journal = {International journal of women's health},
volume = {17},
number = {},
pages = {5105-5116},
pmid = {41362644},
issn = {1179-1411},
abstract = {BACKGROUND: Preeclampsia is a complex hypertensive disorder of pregnancy, significantly impacting maternal and fetal health worldwide. Despite extensive research, its pathogenesis, involving inflammatory, immune, microbiological, and metabolic factors, requires comprehensive elucidation.

METHODS: This study applied Mendelian randomization (MR) to investigate causal relationships between multi-omics traits and the risk of preeclampsia. The genome-wide association studies (GWAS) datasets used consisted of immune cells (N = 3757), inflammatory factors (N = 14,824), gut microbiota (N = 7738), circulating metabolites (N1 = 7824, N2 = 8299), plasma proteins (N = 3301), and preeclampsia (7212 cases, 194,266 controls). The inverse variance-weighted method was used in the main analysis, and the weighted median, weighted mode, and MR Egger regression were used in sensitivity analyses.

RESULTS: Our analysis identified 81 potential causal factors for preeclampsia. Among the most novel and clinically significant findings were several druggable plasma proteins, including Astacin-like metalloendopeptidase (ASTL) and Baculoviral IAP repeat-containing protein 3 (BIRC3), which exhibited strong causal evidence. Furthermore, we identified specific gut microbiota genera, notably Bifidobacterium, as potential protective factors. We also validated the causal roles of key metabolic disturbances, like cysteine and guanidinoacetate, and dysfunctions in specific immune cell populations, particularly regulatory T and B cells.

CONCLUSION: These findings highlight the intricate interplay of immune, inflammatory, microbiological, metabolic, and protein factors in preeclampsia, suggesting novel diagnostic and therapeutic targets. Further research is warranted to explore these associations in detail.},
}

@article {pmid41362618,
year = {2025},
author = {Ma, Y and Chen, X and Li, J and Ma, J},
title = {Atopobium vaginae advances endometrial cancer growth via macrophage function in mouse models.},
journal = {iScience},
volume = {28},
number = {12},
pages = {113820},
pmid = {41362618},
issn = {2589-0042},
abstract = {The female genital tract microbiome is essential for health. This study investigated the endometrial microbiota in endometrial cancer (EC) patients and explored their role in disease progression. We collected samples from patients with benign uterine conditions, endometrial hyperplasia, and EC. Microbial diversity was analyzed using 16S sequencing. The effects of Atopobium vaginae on macrophage phagocytosis, polarization, and EC progression were examined in vitro and in vivo. Atopobium vaginae was significantly upregulated in EC and hyperplasia patients, correlating with increased levels of inflammatory cytokines IL-6 and IL-10. Experiments demonstrated that Atopobium vaginae inhibited macrophage phagocytosis, promoted M2 polarization, and increased tumor size, thereby advancing EC progression. Our findings highlight Atopobium vaginae as a key factor in EC progression by regulating macrophage function and inflammatory cytokines. The study provides new insights into EC pathogenesis and reveals potential therapeutic avenues.},
}

@article {pmid41362405,
year = {2025},
author = {Jena, S and Lawore, D and Green, LN and Brubaker, DK},
title = {Characterizing species-specific metabolic signatures in vaginal microbiota across planktonic and biofilm states.},
journal = {Biofilm},
volume = {10},
number = {},
pages = {100330},
pmid = {41362405},
issn = {2590-2075},
abstract = {Bacterial vaginosis (BV) affects about 29 % of U.S. women, with higher rates in some groups and up to 50-69 % recurrence within a year. It increases the risk of STIs, pregnancy complications, and can cause significant discomfort and reduced quality of life. Prior studies mapped vaginal metabolomes, but individual microbial metabolite signatures remain poorly understood. Given that biofilms exhibit distinct metabolic requirements compared to planktonic cultures, analyzing biofilm vs. planktonic culture metabolites with their unique metabolic needs may uncover novel treatment targets. This study provides a comprehensive metabolomic comparison of key vaginal microbes-Lactobacillus crispatus, Gardnerella vaginalis, and Lactobacillus iners under both planktonic and biofilm conditions. Our analysis showed that metabolite production and consumption vary by microbe and growth mode. G. vaginalis formed biofilms in multiple media, with limited shared metabolic pathways between its biofilm types, indicating unique metabolic processes. Despite L. crispatus suspension and biofilm cultures sharing 142 consumed and 104 produced metabolites, the biofilm culture demonstrated a remarkable metabolic shift. Comparing all three species, we observed convergence in nutrient utilization, but divergence in metabolic outputs reflecting growth-specific adaptations, highlighting the importance of considering microbial state in vaginal microbiome studies.},
}

@article {pmid41362323,
year = {2025},
author = {Zhang, X and Zhu, L and Han, Y and Wang, K and Ji, N and Fan, J and Zhou, Y and Yao, X and Li, B and Lu, S and Guan, L},
title = {Comparative analysis of metabolite and microbial community dynamics during spontaneous fermentation of Lonicera caerulea berries.},
journal = {Food chemistry: X},
volume = {32},
number = {},
pages = {103301},
pmid = {41362323},
issn = {2590-1575},
abstract = {Spontaneous fermentation of Lonicera caerulea berries was monitored using integrated widely targeted metabolomics and high-throughput microbiome sequencing to elucidate the dynamic changes in metabolites and microbial communities. Throughout fermentation, 90 non-volatile metabolites and 52 volatile compounds were identified with variable importance in projection (VIP) ≥ 1 and p ≤ 0.05. The evolution of distinct flavor profiles of the fermented L. caerulea berries was attributed to significant changes in the transformation and accumulation of organic acids, lipids, saccharides, phenolic compounds, and amino acids. Metabolic pathway analysis indicated that linoleic acid and phenylalanine metabolism were dominant in the early fermentation stage, whereas aminoacyl-tRNA biosynthesis, cyanoamino acid metabolism, and arginine biosynthesis prevailed in the later phase. Fungal communities were prevalent throughout fermentation. Early fermentation was dominated by Valsa, Actinobacillus, Mortierella, and Ascomycota, and late fermentation was Gluconobacter and Wickerhamomyces enrichment. Notably, strong and significant correlations (|r| > 0.8, p < 0.05) were observed between specific microorganisms, such as Wickerhamomyces and Gluconobacter, and key metabolites, including glucose-6-phosphate, methionine, leucine, isoleucine, and glutamic acid. These findings offer fundamental insights into the biochemical mechanisms of spontaneous fermentation of L. caerulea and provide a scientific basis for developing controlled fermentation strategies to improve the quality of fruit-based foods.},
}

@article {pmid41362317,
year = {2025},
author = {Pajuelo, E and Romano-Rodríguez, E and Mateos-Naranjo, E and Flores-Duarte, NJ and Rodríguez-Llorente, ID and Redondo-Gómez, S},
title = {Halophytes as holobionts: disentangling the contribution of plant genotype and environmental factors to the associated microbiome of hydro- and xerohalophytes.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100511},
pmid = {41362317},
issn = {2666-5174},
abstract = {Halophytes are of great interest for their ecosystemic benefits and valuable secondary metabolites. However, they are threatened by factors such as heat waves, drought, increased salinity and pollution, associated with climate change and human activity. In this context, their associated microbial communities are crucial for their survival. Despite that, there are no comparative studies on microbial communities associated with two types of halophytes: hydrohalophytes (plants from humid saline environments) and xerohalophytes (plants from saline arid environments). This study aimed to investigate the factors that determine the structure of microbial communities of three hydrohalophytes of the Southwest Spain (Atlantic coastal), in particular Atriplex portulacoides, Salicornia perennis and Suaeda vera; and three xerohalophytes of Southeast Spain (Mediterranean coast and inland saltmarshes), namely, Atriplex glauca, Anabasis articulata and Halocnemum strobilaceum. Samples were collected in three locations and two seasons (autumn and spring) to analyze how plant genetics and environmental factors influence their microbiota. The analysis was done by sequencing the 16S V3-V4 region in samples of different plant compartments: endophytes, rhizosphere soils and bare soils. The results showed strong attraction of bacteria and archaea to the rhizosphere, although further tight selection limits the number of endophytes. A "core" of endophytes common to both functional halophytes was identified, including the genera Kushneria, Halomonas, Pseudoalteromonas and Zunongwangia, which were considered generalists. In addition, specific genera considered as specialists were found: hydrohalophytes showed affinity for Vibrio, Pseudomonas and Marinomonas, while xerohalophytes harbored Marinilactobacillus, Alkalicoccus, Alkalibacterium and Arthrobacter. Although most endophytes persist across seasons, their relative abundances can change for better adaptation. Clear differences were also encountered among the rhizosphere inhabitants in both functional halophytes: whereas halophilic ammonia oxidizing archaea were prevalent in the rhizosphere of hydrohalophytes, versatile adaptive bacteria were predominant in that of xerohalophytes. These microorganisms play vital roles, including promoting plant growth, participating in the carbon and nitrogen metabolisms, and recycling organic matter. In conclusion, the study determined that the main factors shaping the microbial populations associated to halophytes were: halophyte type > halophyte species > soil characteristics > seasonality.},
}

@article {pmid41362316,
year = {2025},
author = {Ling, X and Yim, CC and Sun, Q and Peng, Y and Zhang, Y and Kam, KW and Young, AL and Ip, P and Tsui, SK and Tham, CC and Pang, CP and Chen, LJ and Yam, JC},
title = {The pediatric ocular surface microbiome in pet-owning households.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100518},
pmid = {41362316},
issn = {2666-5174},
abstract = {INTRODUCTION: Pet exposure is associated with the allergy development in children. The influence of pet exposure on the pediatric ocular surface microbiome (OSM), a potential mediator of ocular immunity, remains uncharacterized. This study investigates OSM alterations in children with household pet contact.

METHODS: In this cross-sectional study, conjunctival swabs from 347 children (aged 5-15 years) in the CUHK Hong Kong Children Eye Study were analyzed. 16S rRNA sequencing (V3-V4 region) was performed, followed by bioinformatic analysis (QIIME2, DADA2, SILVA 138) and functional prediction (PICRUSt2). Alpha/beta diversity, taxonomic composition, and KEGG pathways were compared.

RESULTS: Pet-exposed children had higher alpha diversity (Shannon/Simpson/Observed indexes; P < 0.05) with positive dose-response to contact time. Compositionally, these children showed distinct beta diversity (Bray-Curtis Distance, P = 0.015) and enriched genera (Streptococcus, Actinomyces, Neisseria; LDA Score > 2.0). NF-κB signaling and VEGF signaling were predicted to enrich in pet-exposed children while non-exposed children showed increased macrolide biosynthesis pathways.

CONCLUSION: Pet exposure associates with increased diversity, enrichment of taxa associated with animals and the environment, and NF-κB/VEGF pathway activation in the pediatric OSM. This suggests OSM as a novel mechanism for pet-related immune modulation, potentially influencing ocular surface health and allergy susceptibility.},
}

@article {pmid41361940,
year = {2025},
author = {Zheng, J and Wang, K and He, J and Guan, Y and Wu, Y and Wu, J},
title = {Surface Microbiome Profiling of Dental Elevators Using Third-Generation Sequencing: Implications for Infection Control in Dental Practice.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70178},
doi = {10.1002/mbo3.70178},
pmid = {41361940},
issn = {2045-8827},
support = {//This work was supported by Beijing Natural Science Foundation (7214274) and National Natural Science Foundation of China (52473286)./ ; },
mesh = {Humans ; Biofilms/growth & development ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; *Dental Instruments/microbiology ; Cross Infection/prevention & control/microbiology ; DNA, Bacterial/genetics ; Equipment Contamination ; Infection Control ; Sequence Analysis, DNA ; },
abstract = {This study aimed to characterize the biofilm-forming microbial communities on clinically used dental elevators to assess their potential risks of cross-contamination and nosocomial infections resulting from percutaneous injuries in dental healthcare settings. Over a period of 3 consecutive weeks starting on August 1, 2024, biofilm samples were collected from the tips of 15 dental elevators used on the first five wisdom teeth extraction patients daily. Total DNA was extracted, and specific barcoded primers were synthesized to construct SMRTbell sequencing libraries, which were subsequently sequenced using the PacBio Sequel II platform. The sequencing generated 923,990 circular consensus sequences (CCS), with an average of 61,599 CCS per sample. Taxonomic annotation revealed a diverse microbial community dominated by genera such as Prevotella, Fusobacterium, Streptococcus, and Lactobacillus, alongside unclassified taxa from the Candidatus Saccharibacteria (TM7) group. Alpha and beta diversity analyses demonstrated significant variations in microbial composition across samples, highlighting the heterogeneity of biofilm formation, while strong positive correlations observed between specific bacterial genera, such as Bacillus and Paenibacillus, suggested potential co-colonization patterns. These findings underscore the complexity of microbial contamination on dental instruments and emphasize the need for improved sterilization protocols to mitigate infection risks. Consequently, this study provides valuable insights into the microbiological safety of dental practices and highlights the utility of third-generation sequencing in advancing infection control strategies.},
}

Humans
Biofilms/growth & development
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing
*Dental Instruments/microbiology
Cross Infection/prevention & control/microbiology
DNA, Bacterial/genetics
Equipment Contamination
Infection Control
Sequence Analysis, DNA

@article {pmid41361886,
year = {2025},
author = {Liu, Y and Yu, S and Wang, X and Ye, D and Aili, M and Fu, X and Zou, J and Ma, Q},
title = {Integrated salivary microbiome and metabolome profiling reveals ecological and functional alterations in severe early childhood caries.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07541-9},
pmid = {41361886},
issn = {1479-5876},
support = {82170947//National Natural Science Foundation of China/ ; 32400094//National Natural Science Foundation of China/ ; 2025ZNSFSC0771//Natural Science Foundation of Sichuan Province/ ; RD-02-202402//Fundamental Research Funds for the Central Universities, Research and Develop Program, West China Hospital of Stomatology Sichuan University/ ; RCDWJS2023-10//Research Funding from West China School/Hospital of Stomatology Sichuan University/ ; },
abstract = {BACKGROUND: Early childhood caries (ECC), particularly severe early childhood caries (S-ECC), remains a prevalent chronic disease, significantly affecting children's health and quality of life. Despite extensive research, the detailed ecological and metabolic shifts underlying S-ECC pathogenesis are still poorly characterized. Integrating microbial and metabolic profiling of saliva may provide crucial insights and identify novel biomarkers and therapeutic targets.

METHODS: We performed high-throughput 16S rRNA gene sequencing and untargeted metabolomics to comprehensively profile the salivary microbiome and metabolome in children with S-ECC (n = 30) compared to caries-free (CF) controls (n = 30). Differential microbial taxa and metabolites were identified, and their functional implications were explored through KEGG pathway enrichment analysis. Furthermore, integrated correlation analysis was conducted to uncover interactions between key microbial taxa and metabolites.

RESULTS: Microbial community analysis revealed significant ecological alterations in the saliva of children with S-ECC, characterized by enrichment of potentially cariogenic taxa, including Rothia, Lautropia, Lactobacillus, Achromobacter, as well as Streptococcus mutans, Prevotella histicola, and Lachnoanaerobaculum saburreum. Conversely, health-associated genera such as Bergeyella and Acinetobacter were more abundant in CF children. Metabolomics identified a total of 4,325 salivary metabolites, among which 1,226 differed significantly between groups. Notably, metabolites involved in amino acid metabolism pathways-phenylalanine, tyrosine, D-amino acids, aminobenzoate, arginine, and proline-were upregulated in S-ECC saliva. Integrated analysis further revealed strong positive correlations between key cariogenic bacteria (S. mutans, P. histicola, L. saburreum) and multiple metabolites, including succinic acid, 2-piperidone, D-3-phenyllactic acid, 5-aminovaleric acid, L-malic acid, 2-hydroxypalmitic acid, LPE (16:0), vitamin K1 2,3-epoxide, leucylproline, and L-valine.

CONCLUSIONS: Our findings demonstrate distinct ecological and functional signatures in the salivary microbiome and metabolome associated with S-ECC. The identified microbial and metabolic alterations, particularly in amino acid metabolism, provide novel insights into the pathogenesis of S-ECC and highlight potential biomarkers for early detection and targeted intervention. However, the cross-sectional design and single time-point saliva collection limit the ability to assess longitudinal dynamics. Future longitudinal studies are warranted to track microbial and metabolomic changes during disease progression and intervention.},
}

@article {pmid41361854,
year = {2025},
author = {Dawkins, JJ and Gerber, GK},
title = {MMETHANE: interpretable AI for predicting host status from microbial composition and metabolomics data.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02270-z},
pmid = {41361854},
issn = {2049-2618},
support = {MTM2 2025512//National Science Foundation/ ; R35GM149270/GM/NIGMS NIH HHS/United States ; President's Scholar Award//Brigham and Women's Hospital/ ; },
abstract = {BACKGROUND: Metabolite production, consumption, and exchange are intimately involved with host health and disease, as well as being key drivers of host-microbiome interactions. Despite the increasing prevalence of datasets that jointly measure microbiome composition and metabolites, computational tools for linking these data to the status of the host remain limited.

RESULTS: To address these limitations, we developed MMETHANE, a purpose-built deep learning model for predicting host status from paired microbial sequencing and metabolomic data. MMETHANE incorporates prior biological knowledge, including phylogenetic and chemical relationships, and is intrinsically interpretable, outputting an English-language set of rules that explains its decisions. Using a compendium of six datasets with paired microbial composition and metabolomics measurements, we showed that MMETHANE always performed at least on par with existing methods, including blackbox machine learning techniques, and outperformed other methods on 80% of the datasets evaluated. We additionally demonstrated through two cases studies analyzing inflammatory bowel disease gut microbiome datasets that MMETHANE uncovers biologically meaningful links between microbes, metabolites, and disease status.

CONCLUSIONS: MMETHANE is an open-source software package that brings state-of-the-art interpretable AI technologies to the microbiome field, emphasizing usability with simple written explanations of its decisions and biologically relevant visualizations. This robust and accurate tool enables investigation of the interplay between microbes, metabolites, and the host, which is critical for understanding the mechanisms of host-microbial interactions and ultimately improving the diagnosis and treatment of human diseases impacted by the microbiome. Video Abstract.},
}

@article {pmid41361834,
year = {2025},
author = {Compare, D and Fosso, B and Nunziato, M and Sgamato, C and Di Maggio, F and D'Argenio, V and Granata, I and Zamparelli, MS and Lovero, D and Casaburi, G and Rocco, A and Coccoli, P and Pesole, G and Salvatore, F and Nardone, G},
title = {Gut mucosa-associated microbiota signatures in healthy individuals and patients at different stages of liver disease: a pilot study.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {99},
pmid = {41361834},
issn = {1757-4749},
support = {CIRO//Regione Campania/ ; PON03PE_00060_2//Ministero dell'Università e della Ricerca/ ; },
abstract = {BACKGROUND: The gut microbiota plays a key role in the progression of chronic liver disease and the development of hepatocellular carcinoma (HCC). However, findings on microbiota composition in such patients remain inconsistent, likely due to differences in disease aetiology and sample type. The mucosa-associated microbiota (MAM), residing in the intestinal mucin layer, more accurately reflects mucosal health than faecal microbiota, being more stable and less influenced by diet. This study aimed to characterise the ileal and sigmoid MAM in patients with chronic hepatitis C (CHC), liver cirrhosis (LC), and HCC.

METHODS: We performed DNA metabarcoding sequencing of mucosa samples collected from the ileum and sigmoid colon of patients at different stages of liver disease and healthy controls (HC). The predicted functions were analysed via phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) to infer metabolic pathways that can be expressed in the microbiome.

RESULTS: Among 33 participants (20 HCV-related liver disease and 13 healthy controls), MAM α-diversity decreased significantly in advanced disease stages, particularly in LC and HCC, regardless of the metric applied (p ≤ 0.05). β-diversity analyses showed distinct microbial community structures across groups. Both ileal and sigmoid MAM were dominated by Bacteroidetes, Firmicutes, and Proteobacteria, with enrichment of Firmicutes_D, Proteobacteria, and Fusobacteria in LC and HCC. Several genera, including Bulleidia, Pantoea, Clostridium_Q, Rothia, and Streptococcus, were significantly increased in HCC, whereas beneficial taxa such as Akkermansia and Butyricimonas were depleted. Functional predictions indicated enrichment of degradative pathways (e.g., taurine, chitin derivatives, and carbohydrate metabolism) in LC and HCC.

CONCLUSION: Our pilot study suggests that MAM alterations do not directly mirror liver disease progression but show distinct patterns associated with different stages. These associations, more evident in advanced disease, involve bacterial taxa linked to gut integrity, inflammation, and carcinogenesis. This exploratory work lays the groundwork for future studies to validate these findings and investigate their relevance to microbiome-based diagnostics and therapies in HCC.},
}

@article {pmid41361827,
year = {2025},
author = {Tao, M and Wu, T and Li, S and Tan, Y and Zhou, X and Chen, Y and Huang, L and Wang, W and Li, S and Wang, L and Luo, Z and Wang, Y and Ling, K and Liang, Z},
title = {Intratumoral Collinsella aerofaciens exhibits antitumor activity in endometrial carcinoma through activation of the p53 signaling pathway.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07543-7},
pmid = {41361827},
issn = {1479-5876},
support = {2019YFC1005202//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: The intratumoral microbiota plays dual roles in cancer progression and suppression, but its composition and functional mechanisms in endometrial carcinoma (EC) remain incompletely defined. This study aimed to characterize the EC intratumoral microbiome, elucidate microbial spatial localization, and identify bacteria with tumor-suppressive properties.

METHODS: Tumor and adjacent normal tissues from patients with EC were analyzed using 5R 16S rRNA sequencing to profile microbial communities, with fluorescence in situ hybridization (FISH) validating bacterial localization. Spatial transcriptomics (ST), single-cell RNA sequencing (scRNA-seq), and FISH were integrated to map microbiota-niche cell interactions. RNA sequencing was performed on EC cells treated with bacterial supernatant. Fecal microbiota transplantation (FMT) from EC patients to mice was used to assess gut-tumor microbial crosstalk.

RESULTS: Collinsella aerofaciens (C. aerofaciens), Haloamaerobium gallinarum, and Massilia oculi were enriched in adjacent normal tissues, while Bacteroides vulgatus (B. vulgatus) and Delfia tsuruhatensis dominated tumor tissues. Tumors exhibited reduced microbial richness versus normal tissues. C. aerofaciens localized predominantly to smooth muscle cells and modulated the tumor microenvironment, as revealed by FISH and ST-scRNA-seq integration. RNA sequencing suggested that C. aerofaciens suppressed EC progression by activating the p53 signaling pathway. FMT experiments demonstrated gut microbiota-driven remodeling of the tumor microbiome.

CONCLUSIONS: This study identifies C. aerofaciens as a novel tumor-suppressive bacterium in EC, with mechanistic evidence linking its activity to p53 pathway activation. Gut microbiota modulates intratumoral microbial composition, suggesting potential dual-target therapeutic strategies for EC.},
}

@article {pmid41361740,
year = {2025},
author = {Thompson, W and Al-Ahmad, A and Cieplik, F and Hbibi, A and Jakubovics, NS and Scholz, KJ and Teoh, L and Charles-Ayinde, M and Fox, CH},
title = {The IADR Policy Statement on Antimicrobial Resistance.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345251388914},
doi = {10.1177/00220345251388914},
pmid = {41361740},
issn = {1544-0591},
abstract = {Antimicrobial resistance (AMR) poses an urgent global health threat, with significant implications for dentistry, which accounts for an estimated 10% of global antibiotic prescriptions. In response, the International Association for Dental, Oral, and Craniofacial Research (IADR) developed a new policy statement recognizing the critical role of oral health professionals and research in addressing AMR. This statement, adopted at the 103rd IADR General Session, highlights the misuse and overuse of antibiotics and antiseptics in dental settings and underscores the role of the oral microbiome as a potential AMR gene reservoir. Drawing on World Health Organization priorities, it outlines key research areas across prevention, diagnosis, treatment, health systems, environmental surveillance, and gender equity. The IADR calls for integrated, evidence-based approaches to antimicrobial stewardship, emphasizing the need for improved diagnostics, context-specific interventions, and cross-sectoral collaboration. This policy reinforces IADR's commitment to advancing science-based solutions to preserve antimicrobial efficacy and promote global oral and public health.},
}

@article {pmid41361574,
year = {2025},
author = {Lee, Y and Yoo, DM and Choi, SH},
title = {Long-term risk of dry eye disease following gastrectomy and colectomy in a nationwide cohort study.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31570-5},
pmid = {41361574},
issn = {2045-2322},
support = {No. RS-2023-00211930//the National Research Foundation of Korea(NRF) grant funded by the Korean government(MSIT)/ ; },
abstract = {Dry eye disease (DED) is a complex symptomatic disorder characterized by a multifactorial etiology. Among those factors, the gut microbiome is one of the emerging factors related to dry eye disease (DED). But the relationship between gastrointestinal (GI) surgery, one of the obvious factors that alters gut microbiome, and DED has not been studied. This study evaluated the incidence of DED after gastrectomy and colectomy. The Korean National Health Insurance Service-National Sample Cohort (2002-2019) was used. A total of 2346 patients who underwent gastrectomy and 3086 who underwent colectomy, and 1:4 matched controls were included. Cox proportional hazards models with overlap weighting were used to estimate adjusted hazard ratios (HRs). Gastrectomy was significantly associated with increased DED risk (adjusted HR: 1.09; 95% CI 1.02-1.16; p = 0.007), while colectomy was not significantly associated with DED (HR: 1.00; 95% CI 0.94-1.07). In subgroup analysis, total gastrectomy showed a stronger association than subtotal gastrectomy (HR: 1.40; 95% CI 1.29-1.52). Gastrectomy, particularly total gastrectomy, is associated with ea higher incidence of dry eye disease. Colectomy showed no such association. These findings suggest the importance of ocular monitoring after gastric surgery.},
}

@article {pmid41361503,
year = {2025},
author = {Lebeuf-Taylor, E and Meltzer, A and Lubrano, S and Cottenie, K and Griesser, M},
title = {Passive environmental and group-level processes drive gut microbiome composition in a wild corvid.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-025-00496-8},
pmid = {41361503},
issn = {2524-4671},
support = {Vanier Canada Graduate Scholarship//Natural Sciences and Engineering Research Council of Canada/ ; Discovery Grant//Natural Sciences and Engineering Research Council of Canada/ ; EXC 2117 L21-04//Deutsche Forschungsgemeinschaft/ ; },
}

@article {pmid41361489,
year = {2025},
author = {Zhao, SY and Hausbeck, J and Coon, KL},
title = {Historical mosquito colonization dynamics are associated with patterns of microbial community assembly in aboveground aquatic habitats.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00831-1},
pmid = {41361489},
issn = {2524-6372},
support = {DGE-1747503//Directorate for STEM Education/ ; 5T32AI007414-27//National Institute of Allergy and Infectious Diseases/ ; 2019368//Directorate for Biological Sciences/ ; 2018-67012-2991//National Institute of Food and Agriculture/ ; },
abstract = {Mosquito larvae develop in aquatic habitats that harbor highly variable communities of bacteria and other microorganisms, which have been well demonstrated to shape individual fitness outcomes in laboratory settings. However, relatively little is known about how this microbial variation contributes to or is influenced by mosquito population dynamics in the field. To investigate potential associations between mosquito population dynamics and microbial community assembly, we characterized bacterial communities in naturally occurring larval habitats with variable historical mosquito productivity using amplicon sequencing. We then applied a null model approach to quantify the relative importance of selection, dispersal, and drift processes in bacterial community assembly. Habitat microbiota clustered into two distinct biotypes: Biotype 1 communities were dominated by Proteobacteria, while Biotype 2 communities were dominated by Cyanobacteria. Both biotypes were shaped by a combination of selection and neutral (i.e., dispersal and drift) processes. However, selection played a more prominent role in habitats with Biotype 1 communities, whereas drift was more influential in Biotype 2 habitats. Variation partitioning further identified historical mosquito productivity and the spatial aggregation of sites with similar productivity histories as key drivers of selection. These findings suggest that mosquito population dynamics are associated with differences in microbial community structure, potentially through feedbacks between mosquito activity and habitat conditions. This study lays the foundation for future work to disentangle causal relationships and to integrate patterns of microbiota diversity and mosquito occurrence into vectorial capacity models for improved prediction of mosquito-borne disease transmission dynamics in the field.},
}

@article {pmid41361482,
year = {2025},
author = {Shang, T and Zhang, R and Liu, Y and Shi, S},
title = {Intestinal oxygen and microbiota crosstalk: implications for pathogenesis of gastrointestinal diseases and emerging therapeutic strategies.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {100},
pmid = {41361482},
issn = {1757-4749},
support = {82474008, 82173902 and 82104274//National Natural Science Foundation of China/ ; },
abstract = {The gut microbiota and its hypoxic host environment play a critical role in human health. Despite its importance, the mechanisms maintaining homeostasis and the characteristics defining dysbiosis remain largely undefined. In particular, the regulation of intestinal oxygen (IO) levels emerges as a critical factor in maintaining microbial balance. Host-driven factors, including epithelial oxygen consumption, mucosal perfusion, and luminal gas diffusion, establish a hypoxic gradient essential for the stable colonization by obligate anaerobes. Disruptions to this gradient, leading to pathological hyperoxia, are associated with overgrowth of facultative anaerobic bacteria and contribute to gastrointestinal diseases like ulcerative colitis, colorectal cancer, and irritable bowel syndrome. Emerging therapeutic approaches focus on modulating IO homeostasis to address dysbiosis. Compounds like sodium tungstate inhibit microbial respiratory pathways, while PPAR-γ agonists enhance mitochondrial efficiency in colonic epithelial cells, thereby restoring proper hypoxia. Dietary interventions and probiotic therapies also hold promise by promoting local anaerobic conditions and enhancing barrier functions, thus supporting the restoration of a healthy microbial community. This review highlights the role of IO in shaping host-microbe interactions, focusing on how host IO levels influence microbial homeostasis. We evaluate the potential for IO modulation to improve gut microbiota structure and explore its impact on microbial metabolism and disease pathogenesis. Additionally, we discuss the promise of dietary, probiotic, and pharmacological interventions in restoring the host's control over the IO microenvironment and microbiota, aiming to prevent and treat related diseases.},
}

@article {pmid41361374,
year = {2025},
author = {Kim, I and Jung, DR and Jung, Y and Ha, JH and Lee, EK and Kim, JM and Kim, JY and Cho, YS and Shin, JH},
title = {Complete genome sequence of Heyndrickxia oleronia EISK28 isolated from human facial skin.},
journal = {BMC genomic data},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12863-025-01388-1},
pmid = {41361374},
issn = {2730-6844},
support = {RS-2023-KH140949//Korea Health Industry Development Institute/Republic of Korea ; },
abstract = {OBJECTIVES: Heyndrickxia oleronia is a Gram-positive, rod-shaped bacterium originally isolated from termites but has gained clinical importance due to its association with Demodex mites and rosacea, a chronic inflammatory skin disease. Despite its clinical relevance, genomic resources from human-associated environments remain limited, with existing reference genomes derived from ecologically distant sources. This study aimed to provide the first complete genome sequence of H. oleronia EISK28 isolated from human facial skin to support future research on its role in skin health and disease.

DATA DESCRIPTION: H. oleronia EISK28 was isolated from human facial skin and sequenced using Oxford Nanopore long-read technology. De novo assembly resulted in a single complete circular chromosome of 5,118,808 bp with 164× coverage depth. Structural annotation identified 5,143 genes comprising 4,958 CDSs, 36 rRNAs, 144 tRNAs, 5 non-coding RNAs, and 65 pseudo genes. Functional annotation assigned the predicted CDSs to 22 of 25 COG categories and identified 93 carbohydrate-active enzymes. Secondary metabolite analysis revealed three biosynthetic gene clusters, and genome-based antibiotic resistance profiling predicted 11 resistance genes, while phenotypic testing confirmed resistance to ampicillin and penicillin. Mobile genetic element screening detected 34 insertion sequences, 2 prophages, and 16 genomic islands but no association with antibiotic resistance genes.},
}