@article {pmid41330219,
year = {2025},
author = {Guo, J and Xu, Y and Chen, Q and Zhang, H},
title = {Integrative analysis of transcriptomics and gut microbiome in grass carp under alkalinity stress.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {57},
number = {},
pages = {101698},
doi = {10.1016/j.cbd.2025.101698},
pmid = {41330219},
issn = {1878-0407},
abstract = {Alkalinity, a key environmental stressor in saline-alkali ecosystems, adversely affects the growth and survival of aquatic organisms. Genetic improvement of alkali-tolerant fish strains offers a promising strategy for utilizing saline-alkaline water resources; however, the molecular mechanisms underlying the response to alkalinity stress remain inadequately understood. This study aimed to identify novel molecular signatures of alkaline exposure in grass carp by integrating gut microbiome profiling with host transcriptome data. Histological analysis revealed significant alterations in the height of intestinal folds, muscle layer thickness, and fold width in response to NaHCO3 exposure, along with an increased number of goblet cells under alkalinity stress. Differential gene expression (DEGs) analysis identified 1620, 6564, and 3190 genes with significant expression changes at 24, 48, and 72 h of NaHCO3 treatment, respectively, compared to controls. Several known alkalinity-responsive genes, such as aquaporin 1a (aqp1a), carbonic anhydrase 6 (ca6), heat shock protein 30 (hsp30), prostaglandin-endoperoxide synthase 2b (ptgs2b), caspase 23 (casp23), solute carrier family 7a (slc7a), toll-like receptor 5 (tlr5), and toll-like receptor 13 (tlr13), were identified and validated through real-time quantitative PCR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that immune- and disease-related signaling pathways played critical roles in mitigating acute alkaline stress. Furthermore, a total of 1,521,323 quality-filtered sequences with an average of 416 bp in length were generated through 16S rRNA sequencing. Bioinformatics analysis indicated that NaHCO3 exposure reduced microbial diversity and altered the gut microbiota composition in grass carp. Notably, Fusobacteriota abundance significantly increased, while Firmicutes and Proteobacteria decreased substantially at 48 h post-alkalinity stress. Integrative analysis further highlighted strong correlations between specific bacterial taxa and alkalinity-responsive differentially expressed genes (DEGs). These findings provided valuable insights into the molecular mechanisms underlying alkalinity stress and identified potential targets for molecular breeding to enhance alkaline tolerance in grass carp.},
}

@article {pmid41330099,
year = {2025},
author = {Barman, P and Paul, A and Sinha, S and Saha, T and Mondal, N and Dutta, S and Chatterjee, S and Ghosh, W and Chakraborty, R},
title = {Microbial-viral synergy in Eisenia fetida gut supports earthworm survival, detoxification, and functional resilience.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181101},
doi = {10.1016/j.scitotenv.2025.181101},
pmid = {41330099},
issn = {1879-1026},
abstract = {The ecological success of Eisenia fetida within decomposer food webs is closely linked to the functional diversity of its gut microbiome. This study integrates 16S rRNA gene profiling, whole-metagenome sequencing, and virome analysis to elucidate how microbial and viral communities within the earthworm gut contribute to nutrient biosynthesis, xenobiotic degradation, and environmental adaptation. Earthworms reared on compost feed enriched with Quisqualis indica plant matter showed selective enrichment of bacterial genera such as Ohtaekwangia, Nocardioides, and Steroidobacter, which are associated with hydrocarbon degradation and aromatic compound detoxification. Functional annotation of the gut metagenome revealed complete biosynthetic pathways for riboflavin, lysine, and methionine, and degradation routes for 3-nitropropionic acid (3-NPA) and aromatic pollutants. The gut virome, dominated by Siphoviridae and Myoviridae, carried auxiliary metabolic genes (AMGs) related to redox and xenobiotic metabolism, highlighting viral contributions to microbial adaptability. Reconstruction of metagenome-assembled genomes (MAGs), including a high-quality Flavobacterium MAG encoding both riboflavin biosynthesis and denitrification genes, underscored metabolic specialization within the gut. Collectively, these findings demonstrate that bacterial-viral metabolic synergy underpins E. fetida survival and ecological resilience, suggesting new microbiome-informed strategies for biowaste valorization and soil health restoration through vermicomposting.},
}

@article {pmid41329990,
year = {2025},
author = {Choi, HI and Cha, JM},
title = {Non-invasive colorectal cancer screening: emerging tools and clinical evidence.},
journal = {Clinical endoscopy},
volume = {},
number = {},
pages = {},
doi = {10.5946/ce.2025.246},
pmid = {41329990},
issn = {2234-2400},
abstract = {The fecal immunochemical test (FIT) is a widely used non-invasive screening method for colorectal cancer (CRC) in many countries, valued for its simplicity, affordability, and reasonable sensitivity. Typically recommended on an annual or biennial basis, the FIT is effective in reducing CRC incidence and mortality by facilitating early detection. Stool DNA tests, including multitarget DNA tests and DNA methylation assays, demonstrate higher sensitivity than FIT for CRC and advanced adenomas, although they have slightly lower specificity and higher cost. These tests are generally performed at longer intervals, such as every 3 years, and are useful alternatives for individuals who are unwilling or unable to undergo a colonoscopy. Emerging non-invasive CRC screening tools, such as liquid biopsy, microRNA, microbiome tests, and urine-based tests, are being developed to improve patient compliance and test convenience. In particular, liquid biopsy offers a minimally invasive option that may be more acceptable to populations hesitant to undergo stool-based tests. Furthermore, the integration of machine learning with metagenomic sequencing data has shown promise in distinguishing patients with CRC from healthy individuals. As CRC screening evolves, these novel approaches may enable the development of more personalized, accessible, and effective screening strategies, ultimately improving adherence and reducing CRC-related mortality.},
}

@article {pmid41329940,
year = {2025},
author = {Aguilar-Fuentes, AN and Montes García, JF and Salcedo-Álvarez, MO and Sanchez Alonso, P and Vazquez-Cruz, C and Rojas, L and Meneses-Romero, EP and Erasmo, NA},
title = {Epinephrine and norepinephrine affect the cellular morphology, composition, and structure of Gallibacterium anatis biofilm.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0135},
pmid = {41329940},
issn = {1480-3275},
abstract = {Gallibacterium anatis is a Gram-negative bacterium that is a pathogen and part of the microbiome of both domestic and wild birds. It is also the cause of reproductive infections, primarily when birds are stressed. Its pathogenicity has been associated with the expression of virulence factors. The effect of Epinephrine (Epi) and Norepinephrine (NEpi) hormones on the composition and structure of G. anatis biofilms is evaluated here. Catecholamines induced compaction and fragmentation of biofilms at 24h. Biofilm amount diminishes (50%) by NEpi. At 48h, biofilm fragments are immersed in exopolymer material, and the control biofilm shows a high quantity of filamentous cells, not observed with hormones. Enzymatic digestion of biofilm polymers showed increased protein levels in the presence of Epi at 24 or 48h and NEpi at 24 or 72h. Epi increased carbohydrate quantity, but NEpi diminished, and DNA quantities diminished at 48h by Epi. Epi diminishes the expression of proteins in the 70 to 200 kDa range but increases the expression of secreted proteins. NEpi induces proteolytic activity in the range of 20 to 110 kDa. A 55 kDa protease was induced at 72h by both hormones. G. anatis biofilm changes could be significant in its dispersion and pathogenesis.},
}

@article {pmid41329729,
year = {2025},
author = {Zhou, C and Hibberd, MC and Lee, EM and Pilgaard, B and Vuillemin, M and Kiehn, E and Henrissat, S and Crane, MA and Cheng, J and Pfaff, L and Meyer, AS and Holck, J and Terrapon, N and Castillo, JJ and Couture, G and Lebrilla, CB and Rodionov, DA and Barratt, MJ and Henrissat, B and Gordon, JI},
title = {Glycoside hydrolase-mediated glucomannan catabolism in Segatella copri, a target of microbiota-directed foods for malnourished children.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {49},
pages = {e2521522122},
doi = {10.1073/pnas.2521522122},
pmid = {41329729},
issn = {1091-6490},
support = {DK30292//HHS | NIH (NIH)/ ; INV016367//Bill and Melinda Gates Foundation (GF)/ ; F30DK131866//HHS | NIH (NIH)/ ; NNF20SA0067193 NNF22OC0077058//KU | Novo Nordisk Foundation Center for Protein Research, University of Copenhagen (CPR)/ ; T32HG000045//HHS | NIH (NIH)/ ; },
mesh = {*Mannans/metabolism ; Animals ; Mice ; *Gastrointestinal Microbiome ; *Glycoside Hydrolases/metabolism/genetics ; Humans ; Prebiotics ; *Malnutrition/diet therapy/microbiology ; Polysaccharides/metabolism ; Child ; },
abstract = {Evidence is emerging that perturbed postnatal gut microbiota development is causally related to childhood undernutrition. Clinical trials in undernourished Bangladeshi children found that a polysaccharide-rich, microbiota-directed complementary food (MDCF-2) designed to repair this perturbation produced superior ponderal and linear growth compared to a standard ready-to-use supplementary food. Subsequent analyses disclosed several candidate bioactive polysaccharides in the MDCF and their bacterial targets, notably strains of Segatella copri that possess carbohydrate-active enzymes (CAZymes) organized into polysaccharide utilization loci (PULs) targeting these glycans. A Bangladeshi S. copri isolate (BgF5_2) containing these PULs metabolized MDCF-2 glycans and promoted MDCF-dependent weight gain in a gnotobiotic mouse model emulating the clinical trials. Identifying prebiotic mixtures that mimic the effects of MDCF-2 would offer new options for treatment and prevention. Here, we describe a CAZyme-based approach to characterize the effects of glucomannan, a component of MDCF obtainable from sustainable sources, on growth and gene expression in S. copri BgF5_2 in vitro and in gnotobiotic mice. Biochemical characterization of purified CAZymes expressed by two of its MDCF-2 and glucomannan-targeted PULs disclosed a multifunctional GH26|GH5_4 CAZyme, inducible by glucomannan, that degrades several bioactive MDCF-2 glycans; glucomannan, arabinoxylan, xyloglucan, and mixed-linkage β-glucan. Our data suggest that this CAZyme functions as a multisubstrate "sentinel" that can produce diverse oligosaccharides from a variety of β-linked glycans, with each oligosaccharide able to induce corresponding PULs and non-PUL enzymes. This observation, plus the restricted distribution of the multifunctional CAZyme among S. copri strains, may partially explain strain responsiveness to MDCF-2.},
}

*Mannans/metabolism
Animals
Mice
*Gastrointestinal Microbiome
*Glycoside Hydrolases/metabolism/genetics
Humans
Prebiotics
*Malnutrition/diet therapy/microbiology
Polysaccharides/metabolism
Child

@article {pmid41329536,
year = {2025},
author = {Hojná, S and Mráziková, L and Shánělová, A and Pelantová, H and Montezano, A and Touyz, RM and Maletínská, L and Kuneš, J},
title = {Oxidative Stress, Metabolic Impairment and Neuroinflammation are Associated With Target Organ Damage in SHRSP.},
journal = {Physiological research},
volume = {74},
number = {5},
pages = {779-795},
pmid = {41329536},
issn = {1802-9973},
mesh = {Animals ; *Oxidative Stress/physiology ; Rats, Inbred SHR ; Rats, Inbred WKY ; Rats ; Male ; *Hypertension/metabolism/pathology ; *Neuroinflammatory Diseases/metabolism/pathology ; *Stroke/metabolism/pathology ; Gastrointestinal Microbiome ; },
abstract = {Stroke-prone spontaneously hypertensive rats (SHRSP) are widely used as a model to study cerebral small vessel disease (CSVD) and its association with chronic hypertension. This study investigated the relationship between metabolic, cardiovascular, and neuronal comorbidities in 32-week-old SHRSP rats versus Wistar-Kyoto (WKY) controls, with a focus on oxidative stress, inflammation, and metabolic alterations. Despite hypertension and cardiac and renal hypertrophy, no significant cerebral vascular changes or microbleeds and no cerebral edema were detected in SHRSP. NMR-based urinary metabolomics revealed reduced gut microbiome-derived metabolites, such as p-cresylglucuronide, hippurate, and phenylacetylglycine, alongside increases in methylamine and dimethylamine. These findings reflect gut dysbiosis and altered microbial composition in hypertensive conditions. Elevated markers of oxidative stress, including thiobarbituric acid-reactive substances, and increased expression of NADPH oxidase (NOX) 2 and NOX4 in peripheral tissues suggested oxidative damage in SHRSP rats. Astrocytic hyperreactivity, indicated by increased expression of glial fibrillary acidic protein in brain cortex and hippocampus, was suggestive of neuroinflammatory responses. Our findings highlight complex interplay between hypertension, metabolism, and neuroinflammation while underscoring the variability in SHRSP models. Key words SHRSP " Neuroinflammation " Oxidative stress " Metabolomics.},
}

Animals
*Oxidative Stress/physiology
Rats, Inbred SHR
Rats, Inbred WKY
Rats
Male
*Hypertension/metabolism/pathology
*Neuroinflammatory Diseases/metabolism/pathology
*Stroke/metabolism/pathology
Gastrointestinal Microbiome

@article {pmid41329386,
year = {2025},
author = {Pandupuspitasari, NS and Sugiharto, S and Khan, FA and Raza, MA and Lestari, DA and Setiaji, A and Agusetyaningsih, I},
title = {Gut microbiota profile, potential engineering techniques and its genetic and epigenetic implications in poultry health.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {12},
pages = {488},
pmid = {41329386},
issn = {1573-0972},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Poultry/microbiology/genetics ; *Epigenesis, Genetic ; Meat ; Fatty Acids, Volatile/metabolism ; Bacteria/genetics/metabolism/classification ; Genetic Engineering ; },
abstract = {Poultry-derived meat and eggs represent economically viable and nutritionally rich resources for the burgeoning global population. The engineering of the gut microbiota has demonstrated potential in enhancing poultry health by establishing a homeostatic milieu and refining immune responses, optimizing metabolic pathways, and augmenting the physiological responses and structural integrity of the involved organs. The processes of fermentation, nutrient uptake, and absorption, alongside their optimized utilization by the host, are governed by complex interactions within the functional population of the gut microbiota. Microbiota influences these responses through the synthesis of distinct microbial metabolites, especially in the form of short-chain fatty acids (SCFAs) which affect host gene expression through both genetic and epigenetic mechanisms. The widespread use of antibiotic growth promoters disrupts the composition and function of the gut microbiota, resulting in adverse effects on host health and long-term sustainability. These concerns underscore the urgent need to develop alternative, safer, and more organic methodologies for sustainable poultry production. In addition, we examine the bidirectional influence of the host on the modulation of the gut microbiota in hope of future personalized treatments. The engineering of gut microbiota by various means is a viable alternative to antibiotic growth promoters, having been shown to significantly enhance both the quality and quantity of eggs and meat within the poultry industry.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Poultry/microbiology/genetics
*Epigenesis, Genetic
Meat
Fatty Acids, Volatile/metabolism
Bacteria/genetics/metabolism/classification
Genetic Engineering

@article {pmid41329359,
year = {2025},
author = {Feng, L and Yi, H and Xie, Z and Zhou, P and Zhang, Y and Cheng, L and Chen, S and Chen, L and Jiang, C and Diao, H and Yan, H},
title = {Dietary Houttuynia cordata Thunb attenuates redox imbalance and inflammation possibly induced by heat stress in dairy cows associated with altered fecal microbiota and metabolomics profile.},
journal = {Tropical animal health and production},
volume = {57},
number = {9},
pages = {523},
pmid = {41329359},
issn = {1573-7438},
support = {2022ZYDF081//the Local Science and Technology Development/ ; 2022YFH0063//Sichuan Science and Technology Program/ ; },
}

@article {pmid41329233,
year = {2025},
author = {Guarino, M and Di Ciaula, A and Portincasa, P and De Giorgio, R},
title = {Narrative review on microbiota and sepsis: the host's betrayal?.},
journal = {Internal and emergency medicine},
volume = {},
number = {},
pages = {},
pmid = {41329233},
issn = {1970-9366},
abstract = {Sepsis remains a leading cause of morbidity and mortality worldwide. Increasing evidence suggests that the gut microbiota, long considered a "less relevant" to human body health, it plays a crucial role in the pathophysiology of sepsis. Disruption of the host-microbe balance contributes to impaired barrier integrity, microbial translocation, and dysregulated immune responses. This perspective raises the possibility that dysbiosis is not merely a consequence of critical illness, rather an active driver of septic progression. This narrative review explores the relationship between sepsis and gut microbiome. PubMed, Scopus, and EMBASE were searched from inception to September 2025. Recent studies have highlighted the triangular interplay between the intestinal barrier, gut microbiota, and immune system. Altered microbial composition and increased permeability foster systemic inflammation and immune dysfunction. Biomarkers such as diamine oxidase and intestinal fatty acid-binding protein are emerging as promising indicators of gut injury. Experimental therapies (i.e., faecal microbiota transplantation, targeted probiotics, prebiotics, postbiotics, and personalized antibiotic regimens guided by microbial profiling) provide potential to modulate host-microbe interactions. Integration of microbiome analysis with multi-omics and advanced bioinformatics may enable stratification of septic patients by microbial signatures, paving the way for precision medicine approaches. Modulation of gut microbiota represents a novel therapeutic frontier in sepsis. Conceptualizing sepsis as a disease of disrupted host-microbe symbiosis may unravel new diagnostic and therapeutic strategies. Future research should aim at prioritizing high-quality trials, innovative designs, and equitable implementation to target microbiota to improve survival and recovery in patients with sepsis.},
}

@article {pmid41329062,
year = {2025},
author = {Yun, Y and Xu, GQ and Jiang, XJ and Ren, XY and Lu, MF and Chen, JW and Zhang, SX},
title = {Gut Microbiota in Rheumatoid Arthritis: Unraveling Pathogenic Mechanisms and Therapeutic Opportunities.},
journal = {Comprehensive Physiology},
volume = {15},
number = {6},
pages = {e70078},
doi = {10.1002/cph4.70078},
pmid = {41329062},
issn = {2040-4603},
support = {202203021221269//Natural Science Foundation of Shanxi Province/ ; 82001740//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Arthritis, Rheumatoid/microbiology/immunology/therapy ; *Gastrointestinal Microbiome/physiology/immunology ; Animals ; Dysbiosis/immunology ; Antirheumatic Agents/therapeutic use ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; },
abstract = {Rheumatoid arthritis (RA), a chronic autoimmune disorder driven by genetic-environmental interplay, manifests as progressive synovitis and irreversible joint damage. Despite mechanistic advances in disease-modifying antirheumatic drugs (DMARDs) and biologics, upstream mucosal triggers of autoimmunity remain elusive. Mounting evidence implicates gut microbiota dysbiosis as a pivotal environmental factor in RA pathogenesis through multifaceted mechanisms: (1) compromising intestinal barrier integrity, (2) facilitating molecular mimicry via cross-reactive microbial antigens, (3) skewing mucosal immunity toward pro-inflammatory T helper 17 (Th17)/T follicular helper (Tfh) cell responses, and (4) generating bioactive metabolites with dual roles in regulating osteoclastogenesis and synovial inflammation. This review synthesizes recent advances in gut microbiome profiling, mechanistic studies, and preclinical models, elucidating microbial-host crosstalk in autoimmune cascades. Furthermore, we critically evaluate microbiota-directed strategies, including dietary and probiotic modulation, microbiome-informed optimization of conventional DMARDs and biologics, and investigational approaches like fecal microbiota transplantation and Chinese herbal medicine, that may offer promising adjunctive approaches to complement conventional RA management.},
}

Humans
*Arthritis, Rheumatoid/microbiology/immunology/therapy
*Gastrointestinal Microbiome/physiology/immunology
Animals
Dysbiosis/immunology
Antirheumatic Agents/therapeutic use
Probiotics/therapeutic use
Fecal Microbiota Transplantation

@article {pmid41328989,
year = {2025},
author = {Charbel, N and Masri, A and Rammal, F and Aramouni, K and Jabbour, K and Hodroj, MH and Rizkallah, J and Kabbara, F and Kreidieh, F},
title = {Unveiling the interplay between gut and skin microbiomes and their influence on skin cancer.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0027024},
doi = {10.1128/cmr.00270-24},
pmid = {41328989},
issn = {1098-6618},
abstract = {SUMMARYThe interplay between the gut and skin microbiomes and their influence on skin cancer development has garnered significant attention. The gut and skin microbiomes, composed of bacteria, fungi, and viruses, play vital roles in immune modulation, inflammation regulation, and maintaining skin health. Dysbiosis in either microbiome may contribute to inflammatory skin conditions and cancer development through the gut-skin axis. The gut microbiota influences immune responses, skin barrier function, and carcinogenesis via microbial metabolites, such as short-chain fatty acids. These compounds impact systemic inflammation, immune cell activity, and response to immunotherapy, particularly in melanoma and non-melanoma skin cancers. Emerging evidence links distinct microbial profiles to skin cancer progression, with specific taxa associated with advanced stages. Conversely, certain skin commensals exhibit potential anti-tumor effects. In addition, microbial imbalances correlate with tumorigenesis via inflammatory and metabolic pathways. Advancements in microbiome profiling have further elucidated these associations, offering diagnostic and therapeutic opportunities. Potential interventions include probiotic therapies to restore microbial balance and enhance immunotherapy efficacy. However, the intricate dynamics of the gut-skin axis necessitate further investigation into causal mechanisms, microbial metabolite impacts, and personalized therapeutic strategies. This review highlights the dualistic role of the gut and skin microbiomes in skin cancer, emphasizing their diagnostic and therapeutic potential while proposing future research directions to unravel their complexities and clinical implications.},
}

@article {pmid41328924,
year = {2025},
author = {Arnadottir, AT and Skirnisdottir, S and Knobloch, S and Corral-Jara, KF and Klonowski, AM and Gunnarsdottir, I and Marteinsson, VT},
title = {Results from the IceGut study: tracking the gut microbiome development from mothers and infants up to five years of age.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0074525},
doi = {10.1128/msphere.00745-25},
pmid = {41328924},
issn = {2379-5042},
abstract = {UNLABELLED: The infant gut microbiome plays a critical role in the early development of the immune system, brain function, metabolism, and defense against pathogens. However, data from underrepresented populations, like Iceland, with its distinct dietary and lifestyle habits, remain limited. This paper presents the initial findings from the Icelandic Diet and the Infant Gut Microbiome Development (IceGut) study. Fecal samples were collected at multiple time points, representing 328 unique study identifiers, with one to five samples per child, from before the introduction of solid foods up to 5 years of age, and postpartum samples from 214 mothers. Microbial composition and predicted functional potential were assessed using 16S rRNA gene sequencing. Children in the cohort followed typical gut microbiome maturation, but at 1 year of age, they showed a notably higher relative abundance of Blautia than reported in comparable cohorts. This time point marked a transition in both taxonomic composition and predicted functional gene counts. By 5 years, the children had higher observed richness than their mothers but lower Shannon and Simpson diversities. At 2 and 5 years, and in the mothers, samples positive for archaea had significantly higher alpha diversity than samples that tested negative for archaea. Mothers with gestational diabetes mellitus (GDM) exhibited a higher relative abundance of Blautia but a lower alpha diversity. The variance in offspring gut microbiome explained by maternal GDM became progressively stronger over time, being significant at the age of 5 and explaining 2.5% of the variance.

IMPORTANCE: This study provides the first comprehensive analysis of gut microbiome development in Icelandic children, covering the time from before the introduction of solid foods to 5 years of age. Although the overall developmental patterns of the gut microbiome in Icelandic children were similar to what has been seen in other studies, interesting differences were observed, such as a higher abundance of Blautia at an earlier age compared to other study populations. Higher alpha diversity in archaeal-positive samples, both in mothers and in children at the ages of 2 and 5, compared with archaeal-negative samples seen in the present study, is worth further investigation. Additionally, the study suggests a potential role of maternal and perinatal factors, particularly GDM, which was not evident until the age of 5 years, emphasizing the necessity of long-term studies.},
}

@article {pmid41328917,
year = {2025},
author = {Ghorbani, M and Kvedaraite, A and Al-Manei, K and Too, CB and Cederberg, S and Johannessen, A and Reikvam, DH and Valentini, D and Maucourant, C and Björkström, NK and Aleman, S and Sällberg Chen, M},
title = {Oral Microbiome Diversity Matters on Nucleos(t)ide Analogue Cessation in Chronic Hepatitis B.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf591},
pmid = {41328917},
issn = {1537-6613},
abstract = {BACKGROUND: Withdrawal of nucleos(t)ide analog (NUC) therapy in HBeAg-negative chronic hepatitis B (CHB) may lead to functional cure in a subset of patients. Although gut microbiota is known to influence both CHB-progression and treatment outcomes, the oral microbiome in NUC-cessation remains unexplored.

METHODS: This long-term longitudinal study aimed to explore the oral microbiome in CHB patients who have been on NUC therapy >2 years having a planned NUC cessation. Oral microbiome composition was analyzed in 110 saliva samples across seven timepoints from 18 HBeAg-negative patients with 36 months of follow-up. Favorable outcome was defined as either HBsAg loss or decline of >1 log10 or sustained off-therapy HBV DNA level <2000 IU/ml during year 3. Hepatic flare was defined as ALT >80 U/L or 2x baseline level.

RESULTS: The overall microbial composition remained stable during the study period. Patients with favorable outcome (n=8) showed consistently higher alpha diversities (Shannon and Simpson indices, p<0.001) from baseline, with lower inter-sample variations across all timepoints (Bray-Curtis and Jaccard distances, p<0.05), compared to unfavorable (n=10). HBsAg, ALT and AST correlated inversely with several Prevotella taxa with specific pathways (Spearman´s rho>-0.5, p<0.01). Unfavorable outcome and high HBsAg level correlated with opportunistic taxa Haemophilus parainfluenzae and Porphyromonas catoniae at multiple timepoints. Random forest model incorporating ANCOM-validated microbial markers predicting favorable vs unfavorable outcome achieved higher predictive performance than clinical markers alone (AUC 0.78 vs. 0.66).

CONCLUSION: Our exploratory study suggests that oral microbiome profiling at NUC cessation in HBeAg-negative CHB could support prognostication of virological outcome.},
}

@article {pmid41328870,
year = {2025},
author = {Cihan, E and Penney, JL and Humphreys, GJ and Ledder, RG and Sreenivasan, PK and Willmott, T and Wu, Y and McBain, AJ},
title = {Exploring Intra-individual Oral Microbiome diversity and Streptococcal Colonisation Patterns.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf296},
pmid = {41328870},
issn = {1365-2672},
abstract = {AIMS: We have investigated bacterial colonisation and site-specific distribution across hard and soft oral tissues focusing on both intra- and inter-individual patterns of Streptococcus clonality and overall microbial composition.

METHODS AND RESULTS: Thirty samples were collected from five healthy adults, covering six oral sites (buccal mucosa, tongue dorsum, maxillary central incisors, mandibular molar fissure, and saliva). Repetitive sequence-based PCR (rep-PCR) assessed Streptococcus clonality, while 16S rRNA gene sequencing characterised broader microbial communities. Among 98 Streptococcus isolates, 67.3% were clonal and frequently recovered from multiple sites within individuals. Identical S. vestibularis clones were detected across all sampled sites in one participant and across several sites in others, indicating shared intra-oral reservoirs. Amplicon sequencing revealed distinct microbial compositions across oral sites, with saliva displaying the highest alpha diversity (Shannon index) and significant beta-diversity differences between most sites, except saliva and tongue. Firmicutes predominated overall, and Streptococcus was the most abundant genus. Differential-abundance testing (ANCOM-BC2) identified 26 genera varying significantly across sites, with lower abundance generally observed on soft tissues.

CONCLUSIONS: These findings suggest that while microbial communities vary by oral site, certain streptococcal clones, including S. vestibularis, occur across multiple habitats. This suggests potential intra-oral reservoirs that may contribute to microbiome stability.},
}

@article {pmid41328492,
year = {2025},
author = {Knoll, RL and Podlesny, D and Fortmann, I and Göpel, W and Zemlin, M and Lynch, S and Bork, P and Gehring, S and Härtel, C},
title = {Staphylococcus aureus colonization and bloodstream infection in very preterm infants.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2592423},
doi = {10.1080/19490976.2025.2592423},
pmid = {41328492},
issn = {1949-0984},
mesh = {Humans ; *Staphylococcal Infections/epidemiology/microbiology ; Infant, Newborn ; Feces/microbiology ; *Staphylococcus aureus/isolation & purification/genetics/growth & development/classification ; Female ; Male ; Infant, Premature ; *Bacteremia/microbiology/epidemiology ; Gastrointestinal Microbiome ; Germany/epidemiology ; Infant ; Cohort Studies ; Infant, Very Low Birth Weight ; Metagenomics ; Incidence ; Gestational Age ; },
abstract = {BACKGROUND: Staphylococcus (S.) aureus remains a frequent pathogen for neonatal late-onset bloodstream infections (BSIs). The impact of colonization screening on BSI incidence is less understood.

METHODS: We assessed the epidemiology of late-onset S. aureus BSI in two independent multicenter cohorts of preterm infants born at < 33 weeks' gestation, the German Neonatal Network (GNN, very low birth weight infants) and PRIMAL (infants with a gestational age 28-32 weeks). In the PRIMAL cohort, we determined S. aureus colonization in fecal samples by culture and shotgun metagenomic sequencing (metaG) during the first year of life. In addition, we integrated publicly available metaG data from preterm infant cohorts born at 23-34 weeks' gestation.

RESULTS: Late-onset S. aureus BSI was noted in 1.5% (336/21491) in preterm infants in the GNN cohort and 0.5% (3/638) in the PRIMAL cohort, respectively. At day 30 of life, 7.6% (42/553) of fecal samples were positive for S. aureus, while available metaG data of corresponding samples revealed S. aureus positivity in 36.6% (159/434). Every 10-fold increase in S. aureus relative abundance (metaG) was associated with a 2.9-fold higher odds of S. aureus detection in blood culture. We also confirmed S. aureus detection in 22% (393/1782) of samples across several published cohorts of preterm infants by metaG, while 95 samples carried at least one Staphylococcus-specific virulence gene (SVG).

CONCLUSION: Our study demonstrates that metagenomic quantification of pathobionts such as S. aureus in intestinal samples provides a stronger predictor of colonization than culture. Future prevention strategies should focus on promoting S. aureus colonization resistance through microbiome-informed approaches.},
}

Humans
*Staphylococcal Infections/epidemiology/microbiology
Infant, Newborn
Feces/microbiology
*Staphylococcus aureus/isolation & purification/genetics/growth & development/classification
Female
Male
Infant, Premature
*Bacteremia/microbiology/epidemiology
Gastrointestinal Microbiome
Germany/epidemiology
Infant
Cohort Studies
Infant, Very Low Birth Weight
Metagenomics
Incidence
Gestational Age

@article {pmid41328416,
year = {2025},
author = {Ueira-Vieira, C and Santos, ACC and Araújo, TN and Augusto, SC and de Avila, NB and Bonetti, AM and Dos Santos, AR},
title = {A Deep Metagenomic Snapshot as a Proof-of-Concept for Resource Generation: Simultaneous Assembly of Host, Food, and Microbiome Genomes From Stingless Bee Larval Food.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72546},
pmid = {41328416},
issn = {2045-7758},
abstract = {Characterizing the complex web of ecological interactions is a central challenge in molecular ecology. Shotgun metagenomics of environmental samples offers a powerful, high-resolution approach, yet its potential for simultaneously generating multiple genomic resources from different trophic levels remains underexplored. This study serves as a proof-of-concept, using deep sequencing of a single, complex sample-the larval food of the stingless bee Tetragonisca angustula-to demonstrate the method's capacity to recover genomic information across varying template abundances. We successfully assembled three genomes of different completeness levels: a near-complete bacterial genome (Acetilactobacillus jinshanensis, 2,097,977 bp with 0.002% ambiguous bases), a draft mitochondrial genome (T. angustula, 15,498-15,549 bp), and a fragmented chloroplast genome (Lactuca sativa, 130,532 bp with 23.47% ambiguous bases). The assembly quality gradient, observed from complete to fragmented, directly reflects the relative abundance of each DNA template in the environmental sample, demonstrating the method's sensitivity and ecological informativeness. Beyond these genomic resources, the data provided a comprehensive biodiversity profile, revealing DNA from seven major taxonomic groups, including 209 bacterial genera, 123 plant families, and 55 insect taxa. Additionally, genomic comparisons using Average Nucleotide Identity (ANI) and digital DNA-DNA Hybridization (dDDH) analyses suggest that the dominant bacterial strain represents a putative novel species within the genus Acetilactobacillus. This approach simultaneously provided insights into host genetics, food sources, and microbial communities, illustrating the potential of single metagenomic datasets to generate multiple valuable genomic resources for molecular ecology research.},
}

@article {pmid41328415,
year = {2025},
author = {Long, D and Zhao, W and Li, X and Sun, Q and Li, J and Lin, X},
title = {Rhizosphere Effect Enhances Belowground Competition of Coastal Invasive Spartina alterniflora With Mangroves.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72565},
pmid = {41328415},
issn = {2045-7758},
abstract = {Spartina alterniflora has severely invaded mangroves in China. In order to explore the possible belowground interspecific interaction along with its invasion, the rhizosphere effect enhancing the competition of S. alterniflora neighboring mangroves was hypothesized. Here, both rhizosphere soil of S. alterniflora and bulk soil were collected from the center of S. alterniflora marsh and border sites where S. alterniflora was adjacent to Kandelia obovata and Aegiceras corniculatum, respectively, in both vigorous growth and senescent periods. Soil nutrient properties, rhizospheric low-molecular-weight organic acids (LMWOAs), soil microbiomes, and microbial functional genes were analyzed. Soil total carbon and total nitrogen contents of S. alterniflora neighboring mangroves were increased, and its LMWOAs were altered when adjacent to mangroves in both vigorous growth and senescent periods. These changes were significantly correlated with variation in the composition of S. alterniflora rhizosphere microbiome. Microbial interkingdom co-occurrence networks were simplified when S. alterniflora neighbored mangroves, while network modularity significantly increased. Metagenomics indicated that genes involved in methanogenesis (ackA, mvhD, etc.) and nitrogen fixation (nifH, nifK, etc.) were significantly enriched in those S. alterniflora neighboring K. obovata, and genes related to phosphate transporter (pstA, pstB, etc.) were significantly enriched in those S. alterniflora neighboring A. corniculatum. These results demonstrated that the rhizosphere effect intensified the belowground interspecific competition of S. alterniflora adjacent to mangroves by altering root exudates, changing the soil microbial composition, and modulating strategies for core nutrient metabolism.},
}

@article {pmid41328252,
year = {2025},
author = {Ge, X and Pan, J and Mo, K and Chen, H and Sun, J and Huang, H and Zhang, Y and Mai, K and Gu, H and Hu, Y},
title = {The versatility of Bacillus tequilensis Bt-CO as an additive: Antagonizing pathogens, enhancing immunity, promoting intestinal health, and optimizing gut microbiota of tilapia.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {23},
number = {},
pages = {502-515},
pmid = {41328252},
issn = {2405-6383},
abstract = {Probiotics are gaining increasing attention as potential alternatives to antibiotics for enhancing the health and welfare of aquatic organisms. However, identifying and developing highly effective probiotic strains with superior intestinal colonization and antagonistic properties remains a significant challenge. This study identified a strain of Bacillus tequilensis, designated as Bt-CO, from coral in a tropical marine environment. Following an in vitro assessment of its antimicrobial activity and colonization properties, the potential of Bt-CO as an antibiotic alternative was evaluated through in vivo trials. A total of 720 fish (initial body weight 2.06 ± 0.01 g) were randomly distributed across four dietary treatments in triplicates, consisting of a basal diet (CON group), and the diet supplemented with 1 × 10[7] (T1 group), 1 × 10[8] (T2 group), or 1 × 10[9] colony-forming unit (CFU)/g (T3 group) of Bt-CO. After a feeding period of 4 weeks, fish were sampled or challenged with Aeromonas hydrophila. For the challenge, 30 fish in each tank were intramuscularly injected with 50 μL of A. hydrophila at a concentration of 5 × 10[6] CFU/mL. Tilapia survival was monitored for 20 d post-infection. The results demonstrated that Bt-CO possessed pronounced antagonistic effects against several important pathogenic bacteria affecting tilapia, particularly A. hydrophila. Bt-CO also demonstrated excellent physiological characteristics, including auto-aggregation, adhesion, biofilm formation, and exhibited remarkable tolerance to bile and gastrointestinal conditions. Notably, Bt-CO possessed colonization potential in the intestines of tilapia without negatively impacting the growth performance. Following a 4-week supplementation with Bt-CO at an optimal concentration of 1 × 10[8] CFU/g, tilapia displayed an increased resistance to A. hydrophila infection (P = 0.011), suggesting its potential to enhance disease resistance. Additionally, Bt-CO significantly augmented the hemocyte respiratory burst (P < 0.001), serum bactericidal activity (P = 0.002), complement C3 (P = 0.027), lysozyme (P < 0.001), alkaline phosphatase (P = 0.031), and superoxide dismutase (P = 0.003) levels in tilapia. In addition, Bt-CO supplementation modulated inflammatory responses by inhibiting pro-inflammatory cytokines such as interleukin-1β (P = 0.045) and tumor necrosis factor-α (P = 0.020) and promoting anti-inflammatory cytokines such as transforming growth factor-β (P = 0.013) and interleukin-10 (P = 0.021), concurrently enhancing the expressions of intestinal barrier related factors such as claudin-1 (P = 0.051) and claudin-3 (P = 0.014) thereby improving intestinal health. Microbiome analysis indicated that Bt-CO supplementation increased the diversity of gut microbiota, promoted beneficial microorganisms but suppressed pathogenic microorganisms within the intestines of tilapia. In conclusion, incorporating Bt-CO into the diet at 1 × 10[8] CFU/g shows significant probiotic potential and effectively enhances tilapia's disease resistance, which is likely attributed to its role in strengthening non-specific immunity and improving fish intestinal health and microecology.},
}

@article {pmid41328072,
year = {2025},
author = {Zheng, L and Wang, H and Zhang, Z and Gu, J and Yin, Y},
title = {Structure and diversity of microbial communities in the rhizosphere soil of Trichosanthes kirilowii from different cultivation patterns.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20459},
pmid = {41328072},
issn = {2167-8359},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Trichosanthes/growth & development/microbiology ; Bacteria/classification/genetics ; Soil/chemistry ; Fungi/classification/genetics/isolation & purification ; Biodiversity ; Nitrogen/analysis ; },
abstract = {BACKGROUND: To analyze the effects of different cultivation patterns on the structure and diversity of the microbial community in the rhizosphere soil of Trichosanthes kirilowii (T. kirilowii) arms to establish reasonable and effective strategies to mitigate the continuous cropping barriers and promote the high-quality cultivation of T. kirilowii.

METHODS: Three distinct cultivation patterns were investigated: open-field cultivation (TM1), film-mulched cultivation (TM2), and soybean intercropping cultivation (TM3). High-throughput sequencing and bioinformatic analyses were employed to evaluate the rhizosphere microbiome, and redundancy analysis was utilized to investigate the relationship between the microbial communities and soil nutrient indicators.

RESULTS: TM2 and TM3 increased soil bacterial community diversity, reduced fungal community diversity, elevated the relative abundance of beneficial bacterial genera, and reduced the abundance of detrimental fungal genera in the rhizosphere soil. The relative abundance of Pseudarthrobacter, unclassified_Steroidobacteraceae, and Nocardioides in TM2 and TM3 was markedly higher than in TM1. Conversely, the relative abundance of Fusarium, Rhizoctonia, Ceratobasidium, and Plectosphaerella in TM2 and TM3 was significantly reduced compared to TM1. The contents of available potassium (AK), total nitrogen (TN), total phosphorus (TP), and pH in the rhizosphere soil of TM2 and TM3 were significantly higher than those in TM1. The distribution of soil bacterial genera was significantly influenced by the contents of TN and AK, while the distribution of soil fungal genera was significantly or extremely significantly impacted by the contents of TP, total potassium (TK), soil organic matter (SOM), and pH. The content of AK was extremely significantly positively correlated with the relative abundance of Nocardioides, whereas the content of TK showed an extremely negative correlation with the relative abundance of Ceratobasidium. Similarly, pH demonstrated an extremely negative correlation with the relative abundance of Rhizoctonia and Ceratobasidium.

CONCLUSIONS: Film-mulched cultivation and soybean intercropping cultivation altered the soil nutrients, as well as the structure and diversity of soil microbial communities. Thus, in agricultural production, film-mulched cultivation and soybean intercropping cultivation can serve to regulate soil nutrients and microbial communities, thereby mitigating the barriers of continuous cropping of T. kirilowii.},
}

*Rhizosphere
*Soil Microbiology
*Microbiota
*Trichosanthes/growth & development/microbiology
Bacteria/classification/genetics
Soil/chemistry
Fungi/classification/genetics/isolation & purification
Biodiversity
Nitrogen/analysis

@article {pmid41328046,
year = {2025},
author = {Imbroane, M and Bussies, P and Schachter, C and Frankel, L and Bosch, A and Santarosa, J and Falcone, T and Richards, EG},
title = {The role of pharmacotherapy in the treatment of endometriosis: an update.},
journal = {Expert opinion on pharmacotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14656566.2025.2597272},
pmid = {41328046},
issn = {1744-7666},
abstract = {INTRODUCTION: Endometriosis is a chronic inflammatory condition affecting ~10% of reproductive-age individuals and contributing significantly to infertility, pain, and reduced quality of life. Since our 2020 review, new pharmacologic strategies, updated guidelines, and advances in clinical trial evidence have reshaped the therapeutic landscape. Effective, patient-centered management is essential to lessen the burden of disease.

AREAS COVERED: This review synthesizes current evidence-based pharmacotherapy for endometriosis, integrating 2022 European Society of Human Reproduction and Embryology recommendations and including a literature review of PubMed, with an emphasis on articles published after 2020. First-line therapies, including NSAIDs, combined oral contraceptives, and progestins such as dienogest, remain central, while GnRH agonists/antagonists and aromatase inhibitors are considered in refractory cases. Recent data highlight add-back therapy to reduce hypoestrogenic side effects. We also review postoperative regimens, fertility-preserving strategies, management in post-hysterectomy and postmenopausal populations, and therapies under investigation - including anti-inflammatory, antifibrotic, angiogenesis-modulating, and microbiome-targeting approaches.

EXPERT OPINION: Hormonal suppression remains the cornerstone of treatment, but novel nonhormonal strategies and advances in precision medicine hold promise for more durable and individualized care. Ongoing clinical trials, artificial intelligence - assisted diagnostics, and fertility-focused pharmacotherapies represent exciting frontiers. Multimodal, patient-tailored approaches will be key to optimizing long-term outcomes in endometriosis management.},
}

@article {pmid41328036,
year = {2025},
author = {Woo, J and Cheng, D and Long, EA and Whitney, KL and Shen, G and Reddivari, L and Jiang, Q and Simsek, S and Ju, T and Wang, W},
title = {Hemp seed mitigates colonic inflammation through macrophage polarization and microbiota-barrier axis restoration.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04119h},
pmid = {41328036},
issn = {2042-650X},
abstract = {Hemp seed, historically considered a byproduct of the hemp fiber industry, has gained increasing attention for its nutritional and functional properties. Recent advances in hemp seed research have elucidated its benefits for gut health; however, its impact on colitis remains unclear. In this study, we demonstrate that hemp seed consumption reduced colonic inflammation and mitigated tissue injury in an experimental colitis mouse model. Notably, hemp seed reduced macrophage infiltration and promoted a phenotypic shift from pro-inflammatory M1 to anti-inflammatory M2 macrophages. It also enhanced intestinal barrier function by restoring goblet cells, upregulating tight junction proteins, and reducing systemic lipopolysaccharide translocation. Furthermore, hemp seed optimized gut microbiota composition by enriching beneficial taxa, particularly Bifidobacterium, while suppressing colitis-associated genera. Collectively, these findings indicate that hemp seed, as a whole-food dietary approach, confers protection against colitis by modulating immune responses, preserving barrier integrity, and reshaping gut microbiome. These results underscore the potential of hemp seed as a sustainable nutritional strategy for promoting gut health.},
}

@article {pmid41328031,
year = {2025},
author = {Delaroque, C and Desai, MS},
title = {Context-dependent roles of the gut microbiome in food allergy tolerance versus sensitization.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2590830},
doi = {10.1080/19490976.2025.2590830},
pmid = {41328031},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/immunology ; *Food Hypersensitivity/immunology/microbiology ; Humans ; Animals ; *Immune Tolerance ; Intestinal Mucosa/immunology/microbiology ; T-Lymphocytes, Regulatory/immunology ; Immunoglobulin E/immunology ; Host Microbial Interactions ; },
abstract = {Exposure to food antigens that can trigger aberrant type-2 immunity is ubiquitous. However, only a subset of individuals develops allergy, implicating environmental drivers of sensitization, among which diet- and antibiotic-induced changes in intestinal microbiome activity stand out for their ability to alter host-microbe interactions at the gut mucosa. While efforts seek microbial signatures and microbiome-based therapies, the same microbes or pathways may foster either tolerance or sensitization depending on host and environmental context, which must be considered when designing interventions. We synthesize recent molecular insights into mucosal host-microbiome crosstalk, focusing on regulatory T cells, the colonic mucus barrier, and host immunoglobulins (IgA and IgE). Using examples of microbiome functional duality in which diet-driven altered microbial activities and secreted molecules such as lipopolysaccharides and flagellins yield opposing effects, we discuss the context-dependent mechanisms by which microbes either protect against or promote food allergy.},
}

*Gastrointestinal Microbiome/immunology
*Food Hypersensitivity/immunology/microbiology
Humans
Animals
*Immune Tolerance
Intestinal Mucosa/immunology/microbiology
T-Lymphocytes, Regulatory/immunology
Immunoglobulin E/immunology
Host Microbial Interactions

@article {pmid41328024,
year = {2025},
author = {Abbas, R and Javaid, N},
title = {Role of Oral microbiome in modulating immune response in Oral cancer development. A systematic review.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2025.2599227},
pmid = {41328024},
issn = {1744-8352},
abstract = {BACKGROUND: Oral squamous cell carcinoma, the most common head and neck cancer, is characterized by aggressive invasion, frequent lymph node metastasis, and high recurrence.

OBJECTIVE: This review explores the role of microbial dysbiosis in shaping the immune landscape of oral squamous cell carcinoma. It aims to identify key microbial taxa altered in Oral squamous cell carcinoma, examine the immunological pathways they influence, and assess their impact on tumor progression and immune evasion.

METHODS: A comprehensive literature search was conducted across three major databases: PubMed, Scopus, and Embase. A total of 300 records were initially identified (PubMed: n = 68; Scopus: n = 63; Embase: n = 169). After screening and eligibility assessment, 17 studies meeting inclusion criteria were selected for final analysis.

RESULTS: Fusobacterium was the most frequently enriched genus in Oral squamous cell carcinoma, followed by Peptostreptococcus, Prevotella, Porphyromonas, Campylobacter, Treponema, Capnocytophaga, and Dialister. Streptococcus was the most consistently depleted, along with Rothia, Veillonella, Leptotrichia, Capnocytophaga, and Neisseria.

CONCLUSION: Cancer remains a leading cause of death. Oral microbial dysbiosis, with loss of beneficial species and enrichment of pathogens, has been linked to oral cancer, but its mechanistic role remains hypothetical and requires validation.},
}

@article {pmid41327907,
year = {2025},
author = {Ranson, A and Vazquez Gomez, M and Alili, R and Durrafourd, J and Vitalis, O and Taillandier, P and Rebière, C and Merabtene, F and Belda, E and Crespo-Piazuelo, D and Gonzalez-Bulnes, A and Marcelin, G and Mardinoglu, A and Chikh, K and Le Roy, T and Clément, K},
title = {Moderate increase in dietary fat induces alterations of microbiota and metabolome along the digestive tract prior to systemic metabolic changes: insights from a pig model.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2587964},
doi = {10.1080/19490976.2025.2587964},
pmid = {41327907},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Swine ; *Metabolome ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Male ; Female ; *Dietary Fats/metabolism/administration & dosage ; *Gastrointestinal Tract/microbiology/metabolism ; Intestine, Small/microbiology/metabolism ; },
abstract = {The small intestine is a key site for nutrient sensing and host-microbiota interactions, yet how it functionally adapts to dietary changes remains poorly understood. Using a translational porcine model, we investigated the impact of moderate dietary fat increase on the gut microbiota and metabolome across five locations in the digestive tract. Pigs were fed either a low-fat (3%) or a medium-fat (12%) diet for 12 weeks without developing obesity. Multiomics profiling revealed significant dietary effects on bile and duodenojejunal metabolomic profiles, particularly lipid and stachydrine, with notable sex-specific responses. These metabolite shifts were accompanied by segment- and sex-specific changes in microbial communities, including the depletion of metabolically beneficial taxa (e.g., Limosilactobacillus reuteri and Lactobacillus johnsonii) and the enrichment of bacteria linked to metabolic dysfunction (e.g., Streptococcus alactolyticus). In the small intestine lumen, multiple bacterial-metabolite associations correlated with host metabolic markers, suggesting early diet-induced alterations with potential relevance for metabolic disease onset. Our findings position the small intestine as a critical site for early diet-induced microbial and metabolic remodeling, potentially influencing metabolic disease risk and shaping the downstream intestinal environment. This study also underscores the importance of considering both region- and sex-specific responses in diet-microbiota-metabolome research.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Swine
*Metabolome
*Bacteria/classification/genetics/metabolism/isolation & purification
Male
Female
*Dietary Fats/metabolism/administration & dosage
*Gastrointestinal Tract/microbiology/metabolism
Intestine, Small/microbiology/metabolism

@article {pmid41327880,
year = {2025},
author = {Jadhav, NK and Magdum, AB and Shinde, KV and Nimbalkar, MS},
title = {Next-Generation Probiotics: From Traditional Strains to Personalized Therapeutics.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70339},
doi = {10.1002/mnfr.70339},
pmid = {41327880},
issn = {1613-4133},
support = {//Council of Scientific and Industrial Research (CSIR), Government of India/ ; },
abstract = {Traditional probiotics such as Lactobacillus and Bifidobacterium have long supported gut health, but recent advances in microbiome research have introduced next-generation probiotics (NGPs) such as Akkermansia muciniphila and Faecalibacterium prausnitzii. These strains are associated with more specific functions, including mucin degradation, butyrate production, enhanced gut barrier integrity, immune regulation, and modulation of host metabolism and inflammation. Unlike conventional probiotics, which mainly promote general digestive balance, NGPs demonstrate targeted mechanisms that link them to metabolic, inflammatory, and even neurological conditions. This review provides a critical comparison of traditional and NGPs, highlighting mechanistic distinctions and functional advancements. It also explores recent innovations in synthetic biology, including programmable gene circuits, and examines how artificial intelligence and microbiome profiling are paving the way toward personalized probiotic therapies, though widespread clinical application remains in its early stages. Key safety, regulatory, and translational challenges are also addressed, outlining barriers to clinical adoption. By integrating omics technologies and precision medicine, NGPs represent a promising frontier with the potential to advance personalized nutrition and therapeutic strategies.},
}

@article {pmid41327627,
year = {2025},
author = {Ma, X and Ling, L and Wang, B and Nian, H and Ma, Q and Zhao, S and Lian, T},
title = {Chemical Communication Between Plant and Microbe in the Phyllosphere.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70314},
pmid = {41327627},
issn = {1365-3040},
support = {//This study was supported by the National Natural Science Foundation of China (grant no. 32470090), the Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops (grant no. FCBRCE-202506), the Natural Science Foundation of Xinjiang Province (grant no. 2025D01D47), the Guangdong Provincial Construction Project for Modern Agriculture Industry Technology System Innovation Teams (Oil Crop Industry Technology System) (grant no. 2024CXTD06), the Science and Technology Plan Project of Guangzhou (grant no. 2024A04J5487), the Double First-Class Discipline Promotion Project (grant no. 2021B10564001) and the Science and Technology Plan Project of Shanwei (grant no. 2024E005). Guangdong Basic and Applied Basic Research Foundation (grant no. 2023A1515030275)./ ; },
abstract = {The phyllosphere encompasses all above-ground plant parts, covering ~10[9] km[2] and hosting as many as 10[26] microbial cells, yet its chemical ecology remains understudied compared to the rhizosphere. This review synthesizes recent advances in metabolite-mediated communication orchestrating phyllosphere microbiome assembly, function and host feedback. Leaf structural traits, host immune genes, developmental stage, and fluctuating environmental drivers create spatiotemporal chemical niches that filter incoming microbes. We then examine four major classes of plant-derived signals, including primary metabolites, secondary metabolites and phytohormones, with an emphasis on their dual functionality. Microbial feedback occurs through phytohormone synthesis/catabolism, volatile and soluble effectors and antimicrobial metabolites that collectively modulate plant immunity, growth and stress tolerance while structuring inter-microbial competition. These bidirectional exchanges form a dynamic network where plants and microbes continuously negotiate cooperation and conflict under diurnal and seasonal oscillations. We outline translational prospects, including probiotic foliar applications, metabolite priming and breeding for beneficial consortia, while identifying key challenges in signal attribution, microbiota stabilization and deciphering community-level crosstalk dynamics for sustainable crop protection.},
}

@article {pmid41327409,
year = {2025},
author = {Jin, J and Wang, X and Zhang, X and Mei, J and Zheng, W and Guo, L and Sun, H and Zhang, L and Liu, C and Ye, W and Guo, L},
title = {Grapevine phyllosphere pan-metagenomics reveals pan-microbiome structure, diversity, and functional roles in downy mildew resistance.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02287-4},
pmid = {41327409},
issn = {2049-2618},
support = {ZR2024QC241//Shandong Provincial Natural Science Foundation Youth Project/ ; 2024CXPT031//Key R&D Program of Shandong Province/ ; ZR2023JQ010//Natural Science Foundation for Distinguished Young Scholars of Shandong Province/ ; },
abstract = {BACKGROUND: Grapevines are among the most economically important fruit crops, and the microbiome profoundly influences their health, yield, and quality. However, mechanistic insights into microbiome-orchestrated grapevine biology remain limited.

RESULTS: Here, we conduct large-scale pan-metagenomic and pan-metatranscriptomic analyses of the phyllosphere microbiome from 107 grapevine accessions spanning 34 Vitis species. We show that the grapevine core microbiome is dominated by phyla Bacillota and Pseudomonadota. Leveraging PacBio sequencing, we assembled 19 high-quality metagenome-assembled genomes (MAGs) from the grapevine pan-microbiome, representing the first MAG reconstruction in plant-associated microbial communities using PacBio reads. These MAGs encode genes associated with antibiotic resistance, secondary metabolism, and carbohydrate-active enzymes (CAZymes), which could potentially influence grapevine biology. During downy mildew (DM) infection, DM-resistant grapevines exhibit significantly higher microbial network complexity than susceptible counterparts. Among the key taxa contributing to this complexity, Bacillota emerged as the dominant phylum, displaying strong abundance correlations with phylum Euglenozoa and Cyanobacteriota, and an isolated Bacillota species from the grapevine leaves, Bacillus cereus, demonstrated potent biocontrol activity against DM infection. Pan-metatranscriptomic analysis further revealed significant upregulation of eukaryotic microbial genes involved in primary and secondary metabolism.

CONCLUSIONS: This pan-metagenomic study offers unprecedented insights into the complex structure, diversity, and functional roles of the grapevine phyllosphere microbiome and presents valuable genomic and microbial resources for microbiome research and engineering to enhance viticulture productivity and quality. Video Abstract.},
}

@article {pmid41327304,
year = {2025},
author = {Zhang, X and Li, Y and Xiong, Z and Zheng, N and Wang, J and Zhao, S},
title = {Biochanin A improves nitrogen utilization efficiency by regulating ruminal microbial community in dairy goats.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02275-8},
pmid = {41327304},
issn = {2049-2618},
support = {32402768//National Natural Science Foundation of China/ ; 2004DA125184G2108//State Key Laboratory of Animal Nutrition and Feeding/ ; CARS-36//Earmarked Fund for CARS/ ; 2022YFD1301000//National Key R&D Program of China/ ; CAAS-ZDRW202304//Agricultural Science and Technology Innovation Program/ ; },
abstract = {BACKGROUND: Rumen microbial nitrogen metabolism is crucial for animal health, productivity, and environmental sustainability in ruminants. Natural products like biochanin A are garnering interest as potential feed additives due to their beneficial effects and safety profiles. Here, we collected total mixed diet, plasma, milk, urine, and feces samples of dairy goats to evaluate the impact of biochanin A on nitrogen metabolism and elucidated regulatory mechanisms of nitrogen metabolism using multi-omics approaches by analyzing plasma metabolites and ruminal microbial communities.

RESULTS: Supplementation with biochanin A significantly enhanced nitrogen utilization efficiency of dairy goats. Plasma metabolomics revealed that biochanin A altered pathways related to amino acid biosynthesis/metabolism and glycolysis/gluconeogenesis. In the rumen, biochanin A enriched microbial strains from the families Selenomonadaceae and Aminobacteriaceae. Up-regulated proteins predominantly associated with glycolysis were identified by metaproteomics. Integrated metagenomic and metaproteomic analyses demonstrated that biochanin A positively influenced carbohydrate metabolism, amino acid metabolism, and energy metabolism pathways.

CONCLUSION: Biochanin A enhances nitrogen metabolism by regulating rumen microbial community function, supporting its potential as a natural feed additive to improve nitrogen utilization of ruminants. Video Abstract.},
}

@article {pmid41327300,
year = {2025},
author = {Ni, J and Hernández-Cacho, A and Nishi, SK and Babio, N and Belzer, C and Konstati, P and Vioque, J and Corella, D and Castañer, O and Vidal, J and Moreno-Indias, I and Torres-Collado, L and Coltell, O and Fitó, M and Ruiz-Canela, M and Wang, DD and Tinahones, FJ and Salas-Salvadó, J},
title = {Mediterranean diet, gut microbiota, and cognitive decline in older adults with obesity/overweight and metabolic syndrome: a prospective cohort study.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {669},
pmid = {41327300},
issn = {1741-7015},
support = {FPU 20/00385//Ministerio de Ciencia, Innovación y Universidades/ ; 2022PMF-INV-01//predoctoral grant from Martí Franquès - INVESTIGO research fellowship funded and supported by NextGenerationEU, Servicio Público de Empleo Estatal and Universitat Rovira i Virgili/ ; CIHR, MFE-171207/CAPMC/CIHR/Canada ; PI13/00233, PI13/00728, PI13/00462, PI14/01206, PI14/ 00696, PI16/00533, PI16/00366, PI16/00501, PI17/01441, PI17/00855, PI19/00017, PI19/00781, PI19/00576, PI20/ 00557, PI21/0046//Spanish Institutions for funding scientific biomedical research, CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN) and Instituto de Salud Carlos III (ISCIII), through the Fondo de Investigación para la Salud (FIS), which is co-funded by the European Regional Development Fund/ ; PI0458/2013, PS0358/2016, PI0137/2018//Consejería de Salud de la Junta de Andalucía/ ; PROMETEO/ 2017/017 and PROMETEO/2021/21//Conselleria de Innovación, Universidades, Ciencia y Sociedad Digital from the Generalitat Valenciana/ ; CPII21/00013//"Miguel Servet Type II" program of the ISCIII-Madrid (Spain) and cofounded by the European Union/ ; R01DK127601//NIH grant/ ; 2013ACUP00194//Recercaixa/ ; grant agreement #847879//Eat2beNICE/H2020-SFS-2016-2 EU- H2020 European grant, and the Horizon 2020 PRIME study/ ; },
mesh = {Humans ; *Diet, Mediterranean ; *Gastrointestinal Microbiome/physiology ; Aged ; Female ; Male ; Prospective Studies ; *Cognitive Dysfunction/microbiology ; *Obesity/complications/psychology/microbiology ; *Metabolic Syndrome/complications/microbiology/psychology ; *Overweight/complications/microbiology/psychology ; Middle Aged ; },
abstract = {BACKGROUND: Emerging evidence highlights that diet dynamically shapes the gut microbiome, which in turn influences cognitive function through bidirectional gut-brain communication, offering a promising target for mitigating cognitive decline and neurodegenerative disorders. While the Mediterranean diet (MedDiet) is a well-established dietary pattern with demonstrated neuroprotective benefits, the interplay between MedDiet adherence, gut microbiota, and longitudinal cognitive trajectories remains poorly understood. We aimed to identify a gut microbial signature of the MedDiet adherence and prospectively examine the associations of MedDiet adherence and MedDiet gut microbial signature (MedDiet-GMS) with cognitive changes over time in older adults at high risk of cognitive decline.

METHODS: This study included 746 participants (mean age 65 ± 5 years, 48% women) with overweight/obesity and metabolic syndrome. Adherence to the MedDiet was assessed using a validated 14-item Mediterranean Diet Adherence Screener (MEDAS). Baseline gut microbiota composition was profiled via 16S rRNA sequencing. Cognitive function was evaluated at baseline, 2, 4, and 6 years using a comprehensive neuropsychological battery. Elastic net regressions were applied to derive a MedDiet-GMS, and linear mixed models were used to assess associations of both MEDAS and MedDiet-GMS with trajectories of cognitive function, adjusting for potential confounders.

RESULTS: Higher adherence to the MedDiet was associated with greater gut microbial diversity (p < 0.05) and distinct microbial composition (PERMANOVA, p = 0.001). The MedDiet-GMS comprised 20 taxa, including short-chain fatty acid-producers (e.g., Barnesiella, Butyricicoccus) positively weighted and pro-inflammatory taxa (e.g., Eggerthella) negatively weighted. Both higher MEDAS scores (p = 0.007) and MedDiet-GMS (p = 0.036) were independently associated with slower global cognitive decline. The MedDiet-GMS was additionally linked to preserved executive function (p = 0.049), while MEDAS was associated with attenuated general cognitive decline (p = 0.028). Eggerthella, inversely associated with MedDiet adherence, was linked to greater executive function decline (FDR < 0.05).

CONCLUSIONS: Greater adherence to the MedDiet was associated with a favorable gut microbiota profile and slower cognitive decline over 6-year of follow-up. A microbiome-derived signature of MedDiet adherence was prospectively associated with favorable cognitive trajectories in older adults at risk of cognitive decline. External validation and experimental research are warranted to translate these findings into targeted microbiome-based dietary interventions for healthy cognitive aging.},
}

Humans
*Diet, Mediterranean
*Gastrointestinal Microbiome/physiology
Aged
Female
Male
Prospective Studies
*Cognitive Dysfunction/microbiology
*Obesity/complications/psychology/microbiology
*Metabolic Syndrome/complications/microbiology/psychology
*Overweight/complications/microbiology/psychology
Middle Aged

@article {pmid41327182,
year = {2025},
author = {Zhang, Y and Zheng, W and Yan, X and Zhang, Y and Peng, B and Wu, D and Zhang, L and Pang, H and Yang, R and Wang, Y and Li, G and Ma, X},
title = {Influence from the intestinal microbiota of neonate on early child development.},
journal = {BMC pediatrics},
volume = {25},
number = {1},
pages = {976},
pmid = {41327182},
issn = {1471-2431},
support = {2022GJM04//Central Public-interest Scientific Institution Basal Research Fund of China/ ; 2016YFC1000307//National Key Research and Development Program of China/ ; 2016YFC1000301//National Key Research and Development Program of China/ ; 2016YFC1000307//National Key Research and Development Program of China/ ; 2016YFC1000307//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant, Newborn ; Case-Control Studies ; Male ; *Child Development ; Female ; *Developmental Disabilities/microbiology ; Meconium/microbiology ; Infant ; Child, Preschool ; },
abstract = {OBJECTIVE: The early-life microbiome is gaining appreciation as a major influencer in human development and long-term health. The present study explored the influence from the intestinal microbiota of neonate on early child development.

METHODS: The first internal discharge was collected from the Beijing Birth Cohort Study (BBCS) located in Beijing, China. Then these children were followed up using the Ages & Stages Questionnaires (ASQ). 77 children were found with at least one domain of developmental delay, and 259 children with no delays were randomly selected as control group, as a nested case-control study. Their meconium microbiome were profiled using multi-barcode 16 S rRNA sequencing at V1-V9 hypervariable region.

RESULTS: There were significant difference in alpha-diversity and beta-diversity measures of intestinal microbiota between groups of children with or without developmental delays(P<0.05), as group of children with developmental delays had less diversity in intestinal microbiota. And there were significant differences on the species composition as well. On genus level, linear discriminant analysis effect size (LefSe) showed higher abundances of Serratia, Burkholderia-Caballeronia-Paraburkholderia, and Enterococcus in the group with developmental delays. It indicated that the lower diversity of intestinal microbiota, and higher abundances of certain intestinal microbiota might be related to developmental delays.

CONCLUSION: There were significant differences in the intestinal microbiota of neonate between children with or without developmental delays. Lower diversity of intestinal microbiota, and higher abundances of certain intestinal microbiota might be related to developmental delays.},
}

Humans
*Gastrointestinal Microbiome
Infant, Newborn
Case-Control Studies
Male
*Child Development
Female
*Developmental Disabilities/microbiology
Meconium/microbiology
Infant
Child, Preschool

@article {pmid41327157,
year = {2025},
author = {Zhang, XY and Li, YT and Guo, J and Feng, Y and Han, Q and Zhang, SH and Gao, Y and Yin, HT and Ding, XX and Li, XJ and Liang, BB},
title = {Saliva from oral squamous cell carcinoma patients promotes tumor progression via Inflammation, stromal remodeling, and metabolic reprogramming in a mouse model.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-025-07413-0},
pmid = {41327157},
issn = {1472-6831},
support = {ZF2025241//Hebei Provincial Government-Funded Clinical Medicine Talent Cultivation Program/ ; ZF2024151//Hebei Provincial Government-Funded Clinical Medicine Talent Cultivation Program/ ; 2025350//Research projects under the Hebei Provincial Administration of Traditional Chinese Medicine/ ; 2025350//Research projects under the Hebei Provincial Administration of Traditional Chinese Medicine/ ; 2025350//Research projects under the Hebei Provincial Administration of Traditional Chinese Medicine/ ; 2025350//Research projects under the Hebei Provincial Administration of Traditional Chinese Medicine/ ; 2025350//Research projects under the Hebei Provincial Administration of Traditional Chinese Medicine/ ; 20240101//Hebei Province Medical Science Research Project/ ; 25297704D//S&T Program of Hebei/ ; },
abstract = {BACKGROUND: Oral squamous cell carcinoma (OSCC) is a prevalent and aggressive malignancy with increasing evidence implicating the oral microbiome and tumor microenvironment in its progression. However, the mechanistic impact of OSCC patient-derived saliva on tumor development remains poorly understood.

METHODS: We established an orthotopic OSCC mouse model and topically applied saliva collected from OSCC patients to assess its effects on tumor progression. Multi-omics analyses, including 16 S rRNA sequencing, tumor transcriptomics (RNA-seq), and metabolomics (LC-MS), were performed to explore changes in the oral microbiota, gene expression profiles, and metabolic pathways.

RESULTS: Treatment with OSCC patient saliva significantly accelerated tumor growth compared to controls. Saliva application altered the oral microbiota, most notably causing a significant enrichment of the genus Staphylococcus. Tumor transcriptomics revealed upregulation of genes associated with chronic neutrophilic inflammation (Mpo), cancer-associated fibroblast (CAF) activation, and extracellular matrix (ECM) remodeling (Angptl4, Col2a1). Metabolomic analysis demonstrated profound metabolic reprogramming within the tumors, including enhanced amino acid metabolism (tryptophan, glutamate), fatty acid oxidation, and accumulation of the oncometabolite succinate. Integrated analysis showed that Staphylococcus abundance was strongly correlated with these inflammatory and metabolic signatures.

CONCLUSIONS: This study demonstrates that saliva from OSCC patients promotes tumor progression in vivo through a multifactorial mechanism involving inflammation, stromal remodeling, and metabolic rewiring. These findings highlight the tumor-promoting potential of salivary and microbial components, suggesting new avenues for diagnostic and therapeutic strategies targeting the oral microenvironment in OSCC.},
}

@article {pmid41326814,
year = {2025},
author = {Kelliher, JM and Mirzayi, C and Bordenstein, SR and Oliver, A and Kellogg, CA and Hatcher, EL and Berg, M and Baldrian, P and Aljumaah, M and Miller, CML and Mungall, C and Novak, V and Palucki, A and Smith, E and Tabassum, N and Bonito, G and Brister, JR and Chain, PSG and Chen, M and Degregori, S and Dundore-Arias, JP and Emerson, JB and Moreira C Fernandes, V and Flores, R and Gonzalez, A and Hansen, ZA and Jackson, SA and Moustafa, AM and Northen, TR and Pariente, N and Pett-Ridge, J and Record, S and Reji, L and Reysenbach, AL and Rich, VI and Richardson, L and Roux, S and Schriml, LM and Shabman, RS and Sierra, MA and Sullivan, MB and Sundaramurthy, P and Thibault, KM and Thompson, LR and Tighe, S and Vereen, E and , and Eloe-Fadrosh, EA},
title = {STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies.},
journal = {Nature microbiology},
volume = {10},
number = {12},
pages = {3059-3068},
pmid = {41326814},
issn = {2058-5276},
mesh = {Humans ; *Microbiota ; *Guidelines as Topic ; *Research Design/standards ; *Rivers/microbiology ; },
abstract = {The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research. Here, in this Consensus Statement, we present the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. The guidelines expand on STORMS and include 67 items to support the reporting and review of environmental (for example, terrestrial, aquatic, atmospheric and engineered), synthetic and non-human host-associated microbiome studies in a standardized and machine-actionable manner. Based on input from 248 researchers spanning 28 countries, we provide detailed guidance, including comparisons with STORMS, and case studies that demonstrate the usage of the STREAMS guidelines. STREAMS, like STORMS, will be a living community resource updated by the Consortium with consensus-building input of the broader community.},
}

Humans
*Microbiota
*Guidelines as Topic
*Research Design/standards
*Rivers/microbiology

@article {pmid41326813,
year = {2025},
author = {},
title = {STREAM-lining guidelines for microbiome research.},
journal = {Nature microbiology},
volume = {10},
number = {12},
pages = {3041-3042},
pmid = {41326813},
issn = {2058-5276},
}

@article {pmid41326768,
year = {2025},
author = {Polizel, GHG and Cánovas, Á and Diniz, WJS and Ramírez-Zamudio, GD and Cesar, ASM and Fukumasu, H and Fernandes, AC and Furlan, É and de Almeida Santana, MH},
title = {Unveiling long-term prenatal nutrition biomarkers in beef cattle via multi-tissue and multi-OMICs analysis.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {22},
number = {1},
pages = {8},
pmid = {41326768},
issn = {1573-3890},
support = {23/09113-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 17/12105-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 307593/2021-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Animals ; Cattle ; Female ; Pregnancy ; *Biomarkers/metabolism/analysis ; *Metabolomics/methods ; Male ; Liver/metabolism ; Transcriptome ; *Maternal Nutritional Physiological Phenomena ; *Prenatal Nutritional Physiological Phenomena ; Multiomics ; },
abstract = {INTRODUCTION: Maternal nutrition during gestation plays a crucial role in shaping offspring development, metabolism, and long-term health, yet the underlying molecular mechanisms remain poorly understood.

OBJECTIVES: This study investigated potential biomarkers through multi-OMICs and multi-tissue analyses in offspring of beef cows subjected to different gestational nutrition regimes.

METHODS: A total of 126 cows were allocated to three groups: NP (control, mineral supplementation only), PP (protein-energy supplementation in the last trimester), and FP (protein-energy supplementation throughout gestation). Post-finishing phase, samples (blood, feces, ruminal fluid, fat, liver, and longissimus muscle/meat) were collected from 63 male offspring. RNA sequencing was performed on muscle and liver, metabolomics on plasma, fat, liver, and meat, and 16S rRNA sequencing on feces and ruminal fluid. Data were analyzed via DIABLO (mixOmics, R).

RESULTS: The muscle transcriptome showed strong cross-block correlations (|r| > 0.7), highlighting its sensitivity to maternal nutrition. Plasma glycerophospholipids (PC ae C30:0, PC ae C38:1, lysoPC a C28:0) were key biomarkers, particularly for FP. The PP group exhibited liver-associated markers (IL4I1 gene, butyrylcarnitine), reflecting late-gestation effects, while NP had reduced ruminal Clostridia (ASV151, ASV241), suggesting impaired microbial energy metabolism.

CONCLUSIONS: This integrative multi-OMICs approach provided deeper insights than single-layer analyses, distinguishing nutritional groups and revealing tissue- and OMIC-specific patterns. These findings demonstrate the value of combining transcriptomic, metabolomic, and microbiome data to identify biomarkers linked to maternal nutrition in beef cattle.},
}

Animals
Cattle
Female
Pregnancy
*Biomarkers/metabolism/analysis
*Metabolomics/methods
Male
Liver/metabolism
Transcriptome
*Maternal Nutritional Physiological Phenomena
*Prenatal Nutritional Physiological Phenomena
Multiomics

@article {pmid41326607,
year = {2025},
author = {Tovar-Herrera, OE and Grinshpan, I and Sorek, G and Lybovits, I and Levin, L and Moraïs, S and Mizrahi, I},
title = {Core rumen microbes are functional generalists that sustain host metabolism and gut ecosystem function.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {41326607},
issn = {2397-334X},
support = {866530//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 101000213//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101000309//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {Some microbes persist across diverse gut microbiomes, raising the question of what features define these core taxa and allow them to persist across hosts. Using the rumen microbiome as a model system, we show that core microbes exhibit distinct attributes of ecological generalists, including greater strain variability and broader functional capacity, linked to larger genome sizes. By analysing ~3,000 genomes of core and non-core microbes and metabolically measuring their functional attributes with both biochemical assays and untargeted/targeted metabolomics, we find that these traits enable core microbes to be metabolically independent while also supporting non-core microbes and the host. Core taxa produce essential metabolites, such as amino acids and vitamins, and encode fibre-degrading enzymes crucial for host nutrition. Additionally, they engage in cross-feeding, providing non-core microbes with vital nutrients. This independence positions core microbes as foundational pillars of gut ecosystem stability, and influencing these microbes could modulate microbiome functionality and ruminant host metabolism, with possible downstream consequences for food security and environmental sustainability.},
}

@article {pmid41326565,
year = {2025},
author = {Wiśniewska, K and Przemieniecki, SW and Krawczyk, K and Piwowarczyk, R},
title = {Diversity and functional traits of the flower stigma microbiome in heterotrophic and autotrophic plants: Phelipanche ramosa vs. its host Nicotiana tabacum.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30322-9},
pmid = {41326565},
issn = {2045-2322},
support = {2021/05/X/NZ8/01154//National Science Centre, Poland/ ; SUPB.RN.24.207, SUPB.RN.25.234 (2024, 2025)//Jan Kochanowski University/ ; },
abstract = {Phelipanche ramosa is a widespread parasitic weed of significant economic importance, particularly affecting tomatoes and tobacco. Despite its well-documented impact on agriculture, its microbial associations remain poorly understood. For the first time, we used Next-Generation Sequencing (NGS) to determine the composition of microorganisms (bacteria and fungi) on the flower stigma of P. ramosa and its host, Nicotiana tabacum, as well as to explore their potential functions. The stigma is a nutrient-rich environment that fosters a varied microbial community, encompassing both beneficial and pathogenic organisms affecting plant health and reproductive success. Unique bacterial populations were identified in P. ramosa stigmas, which were absent or less abundant in N. tabacum stigmas. We identified 49 bacterial OTUs in P. ramosa stigmas, primarily Proteobacteria (87.5%) with dominant genera like Pantoea and Pseudomonas. In contrast, N. tabacum stigmas (18 OTUs) were also rich in Proteobacteria (69.6%) but showed higher levels of Leuconostoc and Enterobacteriaceae. Phelipanche ramosa stigmas exhibited a higher abundance of Actinobacteria, while N. tabacum stigmas had a greater proportion of Firmicutes. Fungal communities differed significantly: P. ramosa stigmas (109 OTUs) were dominated by Basidiomycota, while N. tabacum (69 OTUs) was primarily colonised by Ascomycota, with the genus Candida common in the host but absent in the parasite. Specific genera such as Chalastospora, Ustilaginaceae, and Bensingtonia were more abundant or exclusive to P. ramosa stigmas. Nicotiana tabacum stigmas hosted a potentially functionally rich bacterial microbiome, while P. ramosa harbored a more limited one. In contrast, both the structural diversity and functional (metabolic) potential of the fungal communities were higher in P. ramosa compared to N. tabacum. Microbiome network analysis highlighted distinct physiological functions associated with autotrophic and heterotrophic lifestyles. Some identified microorganisms may play key roles in nutrient availability and pathogenicity, including potentially beneficial ones that could provide new opportunities for biological control. This study highlights the significant relationships between microbial diversity and functional traits, underscoring the importance of these dynamics in the structure and functioning of the stigma microbiome.},
}

@article {pmid41326564,
year = {2025},
author = {Daniels, S and Martin, S and Harris, P and Moore-Colyer, M},
title = {Using culture 'omics to explore the microbial structure and function in an equid in vitro digestion model.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29936-w},
pmid = {41326564},
issn = {2045-2322},
abstract = {The in vitro gas production system (GPS), developed to estimate degradation of ruminant feedstuffs, has been adapted for equine use. This study aimed to characterise the bacterial community profile and metabolome of donor faeces and faecal inoculum within the GPS when fermenting the same diet as faecal donors. Six Welsh ponies on identical diets were faecal donors with samples collected for microbiome profiling and system inoculation. Gas production (manual pressure transducer technique) was performed for 156 h with 2 replicate bottles from each donor harvested at 8,20,28 and 36 h. Faecal and inoculum samples were subject to PMAxx for viability PCR, 16S rRNA sequencing and 1[H] NMR metabonomics. Time in the GPS effected bacterial community profile, metabolic phenotype and predicted metabolic pathways. Collectively a system dysbiosis was observed at 8 h. End point metabolic profile was similar to the donor faeces but GP fibre degrading microbiota better reflected previously reported literature on rumen microbiota, rather than those found in horses. The GPS estimates dry matter digestibility similar to in vivo digestibility, resulting in a similar metabolic profile to donor faeces. However, the GPS either favours rumen dwelling microbiota or demonstrates functional microbial redundancy compared to the donor faeces of equids.},
}

@article {pmid41326479,
year = {2025},
author = {Marawan, AE and Elmetwally, OA and Marwan, MM and El-Sokkary, MMA and Abass, SA and Eissa, LA},
title = {Diagnostic significance of gut Microbiome dysbiosis and biomarker expression in Egyptians with hepatocellular carcinoma.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {42932},
pmid = {41326479},
issn = {2045-2322},
mesh = {Humans ; *Carcinoma, Hepatocellular/diagnosis/microbiology ; *Gastrointestinal Microbiome ; *Liver Neoplasms/diagnosis/microbiology ; *Dysbiosis/microbiology/diagnosis/complications ; Male ; Female ; Middle Aged ; Egypt/epidemiology ; Liver Cirrhosis/microbiology/diagnosis ; Adult ; *Biomarkers, Tumor ; Matrix Metalloproteinase 9/blood/metabolism ; Vascular Endothelial Growth Factor A/blood ; Biomarkers ; Feces/microbiology ; Case-Control Studies ; Hepatitis C/complications ; North African People ; },
abstract = {Egypt has the greatest incidence of hepatitis C virus (HCV) infection globally, which is a considerable trigger of fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). The gut microbiome has been recognized for contributing to various hepatic conditions. Nevertheless, its correlation with HCV and HCC is not well understood. Our study is conducted to investigate the potential relevance of some biomarkers: matrix metalloproteinase 9 (MMP9), Signal transducer and activator of transcription 3 (STAT3), superoxide dismutase (SOD), vascular endothelial growth factor (VEGF), and nuclear factor-κB (NF-κB), along with gut microbial variations, for the differentiation between HCV-related cirrhosis and HCC. The 90 fecal and blood samples were collected from 30 healthy controls, 30 HCV-related cirrhosis, and 30 HCC for detecting gut microbial abundance and biochemical markers examination. Our findings displayed the existence of intestinal microbiome dysbiosis with marked enrichment of specific species, including Bifidobacterium, Fusobacterium, Providencia, E. faecium, and Pseudomonas aeruginosa in HCC patients. Furthermore, the most enriched genera in HCV-related cirrhosis patients were Bifidobacterium, Porphyromonas, and Bacteroides. MMP9 exhibited the highest diagnostic performance of the five measured biomarkers, discriminating against HCC vs. HCV-related cirrhosis with specificity and sensitivity of 100% and 90%, respectively, at a cut-off value > 166.8. Additionally, SOD and NF-κB were statistically significant discriminators of HCC from cirrhosis at cutoff values of ≤ 0.197 and > 166.8. A significant correlation between microbiome abundance and VEGF and MMP9 was observed. This study illustrated that gut microbiomes contribute to HCC and HCV-related cirrhosis pathogenesis, opening approaches for cancer management and prevention.},
}

Humans
*Carcinoma, Hepatocellular/diagnosis/microbiology
*Gastrointestinal Microbiome
*Liver Neoplasms/diagnosis/microbiology
*Dysbiosis/microbiology/diagnosis/complications
Male
Female
Middle Aged
Egypt/epidemiology
Liver Cirrhosis/microbiology/diagnosis
Adult
*Biomarkers, Tumor
Matrix Metalloproteinase 9/blood/metabolism
Vascular Endothelial Growth Factor A/blood
Biomarkers
Feces/microbiology
Case-Control Studies
Hepatitis C/complications
North African People

@article {pmid41326384,
year = {2025},
author = {Lu, K and Zhang, Z and Zhu, X and Ibánhez, JSP and Yang, B and Jiang, S},
title = {Coastal rest during the COVID-19 pandemic enhances microbial community stability and metabolic potential in a subterranean estuary.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00873-w},
pmid = {41326384},
issn = {2055-5008},
support = {41706081//the National Natural Science Foundation of China/ ; },
abstract = {This study examines a subterranean estuary seepage face in China's Sanggou Bay by comparing environmental parameters and microbiome data before and after the COVID-19 lockdown, in order to reveal the regulatory mechanisms of coastal resting on microbial community stability and biogeochemical functions. The results revealed that reduced human activities significantly decreased sediment nutrient loading and shifted organic matter sources from terrestrial- to marine-dominated. This environmental restructuring drove profound microbial community reorganization: while α-diversity indices declined, the relative abundance of core species increased, with marked enhancements in community stability and metabolic efficiency, particularly in pathways related to amino acid metabolism, carbohydrate metabolism, and biogeochemical cycling. The study confirms that a coastal rest period can enhance ecosystem resilience by reducing anthropogenic disturbance, optimizing resource allocation, and activating microbial functional plasticity. These findings suggest that rest periods may represent a potential strategy for supporting ecosystem resilience and sustainability.},
}

@article {pmid41326075,
year = {2026},
author = {Wang, R and Liu, B and Wu, Y and Wang, Y and Xia, X and Yan, X and Huang, L},
title = {Regulation of phenazine-1-carboxylic acid synthesis by hmgL in Pseudomonas chlororaphis and its role in restructuring plant microbiomes for disease resistance.},
journal = {Pesticide biochemistry and physiology},
volume = {216},
number = {Pt 1},
pages = {106762},
doi = {10.1016/j.pestbp.2025.106762},
pmid = {41326075},
issn = {1095-9939},
mesh = {*Pseudomonas chlororaphis/metabolism/genetics ; *Phenazines/metabolism ; *Malus/microbiology ; *Microbiota ; *Disease Resistance ; Plant Diseases/microbiology ; },
abstract = {The hmgL, encoding 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) lyase, is known for its metabolic role in cleaving HMG-CoA into acetyl-CoA and acetoacetate, but its involvement in antimicrobial activity remains unclear. In this study, we isolated Pseudomonas chlororaphis H2Q4, from vigorous and healthy apple branches, demonstrating strong biocontrol potential. Genetic analysis revealed that deletion of hmgL, significantly impaired the antimicrobial activity and colonization capacity of the H2Q4 strain in plant tissues. Notably, the deletion of hmgL led to a marked reduction in the production of phenazine-1-carboxylic acid (PCA). While phzD is recognized as essential for PCA synthesis in P. chlororaphis, our findings highlight a previously unrecognized role of hmgL in modulating PCA production. Furthermore, treatment with strain H2Q4 and PCA altered the bacterial community composition across various plant compartments in apple seedlings, with the leaf microbiome exhibiting enhanced resistance to plant pathogenic fungi. Interestingly, PCA treatment significantly increased the relative abundance of Bacillus species in the phyllosphere microbiome. These results underscore the dual role of hmgL in both secondary metabolism and microbial community dynamics, providing new insights into the biocontrol mechanisms of P. chlororaphis and its potential applications in sustainable agriculture.},
}

*Pseudomonas chlororaphis/metabolism/genetics
*Phenazines/metabolism
*Malus/microbiology
*Microbiota
*Disease Resistance
Plant Diseases/microbiology

@article {pmid41326067,
year = {2026},
author = {Liu, H and Huang, H and Wang, Y and An, M and Bai, J and Zhou, J and Lan, H and Qi, A and Song, B and Wu, Y},
title = {Multifactorial synergistic strategies mediate the biocontrol of Fusarium oxysporum-induced root rot by Bacillus velezensis SYL-3.},
journal = {Pesticide biochemistry and physiology},
volume = {216},
number = {Pt 1},
pages = {106745},
doi = {10.1016/j.pestbp.2025.106745},
pmid = {41326067},
issn = {1095-9939},
mesh = {*Fusarium/physiology ; *Bacillus/physiology ; *Plant Roots/microbiology ; *Plant Diseases/microbiology/prevention & control ; Nicotiana/microbiology/genetics ; Soil Microbiology ; Rhizosphere ; *Pest Control, Biological/methods ; Biological Control Agents ; },
abstract = {Soil health and the management of soil-borne diseases are recognized as crucial challenges, and microbial control technologies have emerged as a vital component of sustainable agriculture. This study aimed to assess the mechanisms involved in the control of Fusarium oxysporum, the causative agent of the root rot disease, by Bacillus velezensis SYL-3 (thereafter SYL-3), focusing on the interconnection among this biocontrol agent, native soil microbial communities, soil physicochemical properties, and plant gene expression. In vitro, SYL-3 inhibited the growth of F. oxysporum, affected fungal sporulation, and caused hyphae deformation. Colonization of tobacco by this bacterium occurred in roots and also in stems and leaves, and enhanced root development was observed in SYL-3-treated plants. Field trials demonstrated a 74.7 ± 8.1 % reduction in the incidence of root rot by day 30 following tobacco transplantation in SYL-3 irrigated plants. Microbiome analyses revealed changes in the rhizosphere microbial community under SYL-3 treatment, with recruitment of beneficial bacteria and reduction of plant pathogens. Improvements in soil physicochemical properties under SYL-3 treatment were also corroborated, with organic matter, pH, and alkali-hydrolyzable nitrogen identified as key factors driving changes in microbial community composition. The expression of several plant genes associated with carbon and nitrogen cycling was up-regulated in the roots of SYL-3-treated plants. Overall, the findings indicate that B. velezensis SYL-3 employs direct and indirect strategies resulting in improved tobacco root development and lower incidence of root rot disease. New insights into the potential of biocontrol bacteria for sustainable agriculture are presented.},
}

*Fusarium/physiology
*Bacillus/physiology
*Plant Roots/microbiology
*Plant Diseases/microbiology/prevention & control
Nicotiana/microbiology/genetics
Soil Microbiology
Rhizosphere
*Pest Control, Biological/methods
Biological Control Agents

@article {pmid41282940,
year = {2025},
author = {Özkan, A and Merry, G and Piatok, J and Naziripour, A and LoGrande, N and Matthiessen, T and Posey, RR and Sperry, M and Gould, R and Ho, K and Neukelmance, A and Contreas-Panta, E and Riccardi, R and Bordeianou, L and Chou, D and Breault, D and Goyal, G and Ingber, DE},
title = {Discovery of a radiation countermeasure therapeutic for intestinal injury enabled by human organ chips combined with AI.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {41282940},
abstract = {There is a need for better therapies for acute radiation injury (ARI) of the human intestine as current treatments offer limited efficacy. As the ileum is most sensitive to radiation in patients receiving cancer radiation therapy, we created human Organ Chip microfluidic culture models lined by primary patient-derived ileal epithelial cells interfaced with intestinal microvascular endothelium and exposed them to clinically relevant doses of γ-radiation. These Ileum Chips recapitulated key features of ARI, including cell loss, barrier dysfunction, and inflammation, as well as a therapeutic response to a probiotic formulation (VSL#3) that protects against radiation injury in patients. Use of an AI-enabled drug repurposing algorithm (NemoCAD) with transcriptomic data led to the identification of the antifungal agent miconazole as a potential radiation countermeasure drug, and its protective activity was confirmed on-chip. Combination of AI and human Organ Chip studies may offer a powerful way to repurpose drugs for novel disease applications.},
}

@article {pmid41325973,
year = {2025},
author = {Meng, D and He, S and Wei, M and Lv, Z and Yang, G and Wang, Z},
title = {Gut microbiota's causal effect on physical activity: Insights from two-sample Mendelian randomization analysis.},
journal = {Physiology & behavior},
volume = {},
number = {},
pages = {115190},
doi = {10.1016/j.physbeh.2025.115190},
pmid = {41325973},
issn = {1873-507X},
abstract = {INTRODUCTION: Gut microbiota has been implicated in influencing various health-related behaviors, including physical activity. This study aimed to investigate the causal relationship between gut microbiota and physical activity in individuals of European ancestry.

MATERIALS AND METHODS: We conducted a two-sample Mendelian randomization analysis using genome-wide association data from the MiBioGen consortium and the UK Biobank. Numerous gut microbiome taxa were assessed for their causal effect on physical activity measures, including moderate-to-vigorous physical activity, vigorous physical activity, accelerometer-based average acceleration, and higher acceleration levels. Sensitivity analyses evaluated heterogeneity, pleiotropy, and potential reverse causation.

RESULTS: The analysis identified significant causal links between specific gut microbiome genera and physical activity levels. Key taxa were associated with physiological conditions conducive to exercise and behavior related to physical exertion. Sensitivity analyses confirmed the robustness of these findings, with minimal evidence of heterogeneity or pleiotropy, and reverse causality was largely excluded.

CONCLUSION: Gut microbiota may play a causal role in influencing physical activity levels, offering potential for microbiome-targeted interventions to promote physical health.},
}

@article {pmid41325637,
year = {2025},
author = {Pieterse, CMJ},
title = {The Extended Plant Immune System.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {},
doi = {10.1094/MPMI-10-25-0144-HH},
pmid = {41325637},
issn = {0894-0282},
abstract = {When disease resistance was still viewed as a vague physiological response rather than a genetically defined process, Flor laid the foundation for our modern understanding of plant immunity with his gene-for-gene concept. Initially developed for simple host-pathogen interactions, this idea evolved into a more complex framework in which plants engage in continuous dialogue with a diverse microbiome. Within this community, beneficial, commensal, and pathogenic microbes interact both directly and indirectly through the plant host, extending the boundaries of plant immunity beyond the individual organism. This broader perspective envisions an "extended plant immune system" that integrates the plant's microbial partners into a coordinated, community-level defense. Like early views of disease resistance, this concept was first described in broad physiological or ecological terms. As the field has matured with the advent of next-generation sequencing, it has become clear that the microbiome-mediated extension of the plant immune system is also grounded in genetically determined molecular processes. These range from host-driven recruitment of protective microbiota, to microbial traits that suppress pathogens, and to plant mechanisms that enable beneficial microbes to trigger induced systemic resistance. This review is a symphony composed of historical progression of research from molecular recognition to community-level defense, distilling the principles that connect classical plant immunity with emerging plant-microbiome concepts and framing microbiome-mediated disease protection as an extension of the plant's innate immune system. This integrated perspective not only reframes our understanding of plant immunity but also offers a conceptual foundation for harnessing the extended immune system in sustainable crop protection.},
}

@article {pmid41325498,
year = {2025},
author = {Laric, PP and Mortazavi, A and Węgrzyn, E and Simon, K and Rittel, PS and Trefz, FM and Sabass, B},
title = {A reliable in vitro rumen culture system and workflow for screening anti-methanogenic compounds.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0335844},
doi = {10.1371/journal.pone.0335844},
pmid = {41325498},
issn = {1932-6203},
mesh = {*Rumen/microbiology/metabolism/drug effects ; Animals ; *Methane/metabolism/biosynthesis ; Cattle ; Workflow ; },
abstract = {Arguably the biggest man-made challenge of the century is halting climate change. Livestock's methane (CH4) emissions, a greenhouse gas with a higher global warming potential than carbon dioxide (CO2), represent a prime target for reducing anthropogenic impact. While the reduction of enteric methane emissions through feed additives has been demonstrated, potent and affordable compounds inhibiting methanogenesis in ruminants are not yet well established. Reliable methods for reproducible cultivation of the rumen microbiome in the laboratory are an essential tool for the study of methanogenesis. We have developed a versatile setup that allows for the cultivation of the ruminal microbiome in a benchtop configuration and combines, miniaturizes, and improves existing systems. The design is based on standard laboratory equipment, including bottles, serological pipettes, tubing, and Luer-Lock valves. The apparatus enables long-term cultivation of primary cultures extracted from the rumen of slaughtered cattle. We describe rumen content acquisition, preparation, the cultivation procedure, and demonstrate the system's performance. The efficacy of the system is demonstrated through the administration of various concentrations of state-of-the-art methanogenesis inhibitors. These inhibitors include lyophilized Asparagopsis taxiformis (AT), bromoform (BF), iodoform (IF), 3-nitrooxypropanol (3-NOP), rapeseed oil, and BF dissolved in rapeseed oil, with maximum CH4 reductions of 96.29% (p = 5.00E-05, Cohen's d = 30.29), 98.22% (p = 2.88E-05, d = 23.07), 96.26% (p = 1.03E-05, d = 30.29), 74.63% (p = 8.88E-05, d = 13.32), 28.96% (p = 0.001, d = 3.99), and 98.51% (p = 4.18E-06, d = 39.94), respectively, in comparison to the negative control. The gas production dynamics in our setup align with previously published results, which supports the validity of the system. Compared to conventional methodologies, the described setup offers enhanced versatility and ease of use. Furthermore, Fourier-transform-infrared-spectroscopy is implemented in a novel and low-cost approach for quantifying CH4 and CO2 in the headspace gas. Together, these methodological advances provide an accessible and reproducible platform for long-term in vitro rumen cultivation for the screening of anti-methanogenic additives.},
}

*Rumen/microbiology/metabolism/drug effects
Animals
*Methane/metabolism/biosynthesis
Cattle
Workflow

@article {pmid41325459,
year = {2025},
author = {Paredes-Vázquez, A and Balsa-Canto, E and Banga, JR},
title = {Identification of dynamic models of microbial communities: A workflow addressing identifiability and modeling pitfalls.},
journal = {PLoS computational biology},
volume = {21},
number = {12},
pages = {e1013204},
doi = {10.1371/journal.pcbi.1013204},
pmid = {41325459},
issn = {1553-7358},
abstract = {Microbial communities, complex ecological networks crucial for human and planetary health, remain poorly understood in terms of the quantitative principles governing their composition, assembly, and function. Dynamic modeling using ordinary differential equations (ODEs) is a powerful framework for understanding and predicting microbiome behaviors. However, developing reliable ODE models is severely hampered by their nonlinear nature and the presence of significant challenges, particularly critical issues related to identifiability. Here, we address the identification problem in dynamic microbial community models by proposing an integrated methodology to tackle key challenges. Focusing on nonlinear ODE-based models, we examine four critical pitfalls: identifiability issues (structural and practical), unstable dynamics (potentially leading to numerical blow-up), underfitting (convergence to suboptimal solutions), and overfitting (fitting noise rather than signal). These pitfalls yield unreliable parameter estimates, unrealistic model behavior, and poor generalization. Our study presents a comprehensive workflow incorporating structural and practical identifiability analysis, robust global optimization for calibration, stability checks, and rigorous predictive power assessment. The methodology's effectiveness and versatility in mitigating these pitfalls are demonstrated through case studies of increasing complexity, paving the way for more reliable and mechanistically insightful models of microbial communities.},
}

@article {pmid41325413,
year = {2025},
author = {Piekielko-Witkowska, A and Elisei, R and Léger, J and Bendlova, B and Bulanová Pekova, B and Caron, P and Durante, C and Fassnacht, M and Feldt-Rasmussen, U and Filipsson Nyström, H and Jansen, H and Köhrle, J and Kus, A and Ludgate, M and Mertens, J and Oczko-Wojciechowska, M and Peters, C and Schoenmakers, N and Stoupa, A and van Santen, H and Trimboli, P and van Trotsenburg, P and Visser, WE},
title = {EndoCompass Project: Research Roadmap for Thyroid Endocrinology.},
journal = {Hormone research in paediatrics},
volume = {},
number = {},
pages = {1-14},
doi = {10.1159/000549075},
pmid = {41325413},
issn = {1663-2826},
abstract = {BACKGROUND: Endocrine science remains underrepresented in European Union research programs despite the fundamental role of hormone health in human well-being. Analysis of the CORDIS database reveals a persistent gap between the societal impact of endocrine disorders and their research prioritization. At national funding level, endocrine societies report limited or little attention of national research funding toward endocrinology. The EndoCompass project - a joint initiative between the European Society of Endocrinology and the European Society of Paediatric Endocrinology, aimed to identify and promote strategic research priorities in endocrine science to address critical hormone-related health challenges.

METHODS: Research priorities were established through comprehensive analysis of the EU CORDIS database covering the Horizon 2020 framework period (2014-2020). Expert consultation in thyroid endocrinology was conducted to identify key research priorities, followed by broader stakeholder engagement including society members and patient advocacy groups.

RESULTS: For thyroid disorders, research priorities encompass neoplastic and nonneoplastic conditions, focusing on disease mechanisms, improved diagnostics and treatments, and the impact of environmental and metabolic factors. Key areas include personalized medicine approaches, artificial intelligence applications, and the establishment of pan-European registries to advance understanding of rare thyroid conditions.

CONCLUSIONS: The thyroid component of the EndoCompass project provides an evidence-based roadmap for strategic research investment. This framework identifies crucial investigation areas into thyroid disease pathophysiology, prevention, and treatment strategies, ultimately aimed at reducing the burden of thyroid disorders on individuals and society. The findings support the broader EndoCompass objective of aligning research funding with areas of highest potential impact in endocrine health.},
}

@article {pmid41325179,
year = {2025},
author = {Hertl, V and Lackner, S and Ramirez-Obermayer, A and Baranyi, A and Wagner-Skacel, J and Mörkl, S},
title = {The Use of Nutritional Psychiatry in the Treatment of a Patient With Treatment-resistant Depression: A Biopsychosocial Case Report.},
journal = {Journal of psychiatric practice},
volume = {31},
number = {6},
pages = {337-345},
pmid = {41325179},
issn = {1538-1145},
mesh = {Humans ; Adult ; *Depressive Disorder, Treatment-Resistant/therapy/diet therapy ; Electroconvulsive Therapy ; Male ; *Malnutrition/diet therapy ; *Nutrition Therapy/methods ; },
abstract = {This case study describes a 30-year-old patient with recurrent depressive disorder and pharmacological treatment resistance. After 2 courses of electroconvulsive therapy without significant improvement, the illness was classified as treatment-refractory. A comprehensive nutrient analysis and dietary history identified malnutrition, nutrient deficiencies, and gastrointestinal issues. By supplementing the treatment-as-usual approach with personalized nutritional and nutrient therapy, a significant reduction in depressive symptoms was achieved, and the pharmacological medication could be reduced. This case suggests that targeted nutritional and nutrient interventions may help enhance the effectiveness of pharmacological treatment and support mental health by promoting metabolic processes.},
}

Humans
Adult
*Depressive Disorder, Treatment-Resistant/therapy/diet therapy
Electroconvulsive Therapy
Male
*Malnutrition/diet therapy
*Nutrition Therapy/methods

@article {pmid41324840,
year = {2025},
author = {Wu, Y and Wang, C and Yu, J and Zhou, X and Wang, Y and Chen, ZJ and Du, Y},
title = {Akkermansia muciniphila PROBIO therapy promotes arginine biosynthesis and reverses reproductive impairments in polycystic ovary syndrome rats.},
journal = {Frontiers of medicine},
volume = {},
number = {},
pages = {},
pmid = {41324840},
issn = {2095-0225},
abstract = {Polycystic ovary syndrome (PCOS) is a prevalent chronic disorder characterized by reproductive, endocrine, and metabolic abnormalities in women worldwide. Increasing evidence has implicated the gut microbiota in the pathogenesis of PCOS, raising the possibility that probiotic interventions could offer therapeutic benefits. Akkermansia muciniphila (AKK), known for its metabolic and immunomodulatory properties, remains underexplored in the context of PCOS. In this study, we utilized a dehydroepiandrosterone (DHEA)-induced PCOS model in Sprague-Dawley (SD) rats to investigate the therapeutic potential of a novel AKK strain, PROBIO (referred to as AP). Treatment with AP significantly alleviated multiple PCOS-related phenotypes, including hyperandrogenism, elevated luteinizing hormone to follicle-stimulating hormone (LH/FSH) ratio, disrupted estrous cycle, abnormal ovarian morphology, and impaired glucose metabolism. Mechanistically, 16S rRNA gene sequencing and untargeted metabolomics revealed that AP partially exerted its beneficial effects by modulating DHEA-induced gut microbiota dysbiosis. Notably, metabolomic profiling indicated enhanced arginine biosynthesis and increased serum L-arginine levels in AP-treated rats. Consistently, in vivo supplementation with L-arginine reproduced the therapeutic effects of AP, ameliorating hyperandrogenism, LH/FSH imbalance, ovarian abnormalities, and estrous cycle irregularities in DHEA-induced PCOS rats. Taken together, these findings suggest that AP ameliorates PCOS phenotypes by restoring gut microbial composition, modulating host metabolism, and promoting L-arginine biosynthesis. This study highlights the potential of AP as a novel probiotic-based intervention for PCOS and underscores the therapeutic relevance of L-arginine in managing this disorder.},
}

@article {pmid41324703,
year = {2025},
author = {Uwimbabazi, A and Ramasamy, S and Mwamba, TM and Syampungani, S},
title = {Microbial communities in mine waste- contaminated soil of Sub-Saharan Africa: potential application for ecoremediation.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {1},
pages = {22},
pmid = {41324703},
issn = {1573-2983},
mesh = {Biodegradation, Environmental ; *Mining ; *Soil Pollutants/metabolism/analysis ; *Soil Microbiology ; Africa South of the Sahara ; *Microbiota ; Bacteria/metabolism/classification ; *Industrial Waste/analysis ; },
abstract = {In recent years, mining activities have increased significantly across SSA (Sub-Saharan Africa), leading to adverse environmental and health impacts. Our review examined diverse microbiota inhabiting various types of mine waste in SSA, emphasizing their natural adaptive mechanisms to withstand extreme conditions. We highlighted key gaps and directions for future studies to support the use of mine waste-resistant microorganisms in ecoremediation efforts. A comprehensive literature search was conducted using reputable online databases to cover studies published between January 2010 and 2024 for information synthesis. Our analysis has revealed microbial communities mainly comprising Proteobacteria (33%), Firmicutes (22%), Actinobacteria (12%), and Acidobacteria (4.1%) of all reported microbial phyla, along with other microbial phyla such as Nitrospirae, Bacteroidetes and Ascomycota distributed across different mine-impacted ecosystems in SSA. The mine wastes reported in this study primarily consist of metals and metalloids (66.7%), followed by oil and hydrocarbons (16%), coal (6.3%), salt (6.2%), and smaller portions of rare metals, and phosphate, each accounting for 1.6%. Microbial species within these phyla exhibit the ability to thrive in polluted environments due to their inherent capacity to metabolize, degrade, and transform toxic compounds, thereby facilitating natural attenuation. However, technical, scientific, operational, implementation, regulatory, and economic challenges hinder bioremediation practices in SSA. Despite these challenges, the region offers significant opportunities that can serve as the foundation for overcoming such constraints. To support scalable and sustainable bioremediation, it is essential to conduct pilot studies focusing on indigenous microbes, alongside systemic monitoring to assess progress and optimize outcomes over time in bioremediation efforts.},
}

Biodegradation, Environmental
*Mining
*Soil Pollutants/metabolism/analysis
*Soil Microbiology
Africa South of the Sahara
*Microbiota
Bacteria/metabolism/classification
*Industrial Waste/analysis

@article {pmid41324625,
year = {2025},
author = {Majhi, S and Sikdar, M},
title = {Isolation and characterization of root nodule-associated bacteria from chickpea (Cicer arietinum) for evaluating plant growth-promoting activities and heavy metal tolerance.},
journal = {Archives of microbiology},
volume = {208},
number = {1},
pages = {44},
pmid = {41324625},
issn = {1432-072X},
support = {F.16-6(DEC. 2016)/2017(NET)//University Grants Commission/ ; SR/FST/LSI-560/2013(c)//DST-FIST Programme of Department of Life Sciences, Presidency University, Kolkata/ ; BT/ INF/22/SP45088/2022//DBT-BUILDER Grant of Department of Life Sciences, Presidency University, Kolkata/ ; },
mesh = {*Cicer/microbiology/growth & development ; *Metals, Heavy/metabolism/toxicity ; Phylogeny ; Indoleacetic Acids/metabolism ; *Enterobacter/isolation & purification/genetics/metabolism/classification/drug effects ; *Root Nodules, Plant/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/isolation & purification/classification/genetics/metabolism ; Ammonia/metabolism ; Soil Microbiology ; Plant Growth Regulators/metabolism ; },
abstract = {Two bacterial strains were isolated from root nodules of the chickpea plant (Cicer arietinum) in West Bengal and characterized to assess their potential for heavy metal (HM) tolerance and plant growth-promoting (PGP) attributes. Phylogenetic analysis based on the 16 S rRNA gene identified these strains, SMAJ_63 and SMAJ_180, belonging to the genera Enterobacter sp. and Labrys sp, respectively. The two strains were screened for tolerance to multiple HMs, including arsenic (As), cadmium (Cd), cobalt (Co), chromium (Cr), and copper (Cu), with particular emphasis on chromium (Cr) due to its high environmental relevance and comparatively limited exploration in the literature. Two strains, SMAJ_63 and SMAJ_180, were evaluated for their tolerance to HMs, and their IC50 values were determined. PGP attributes, including phosphate solubilization, indole acetic acid (IAA), and ammonia production were determined. Strain SMAJ_63 exhibited IAA production of 23.29 µg/mL, whereas strain SMAJ_180 did not produce any detectable IAA. However, both strains were capable of producing ammonia, with strain SMAJ_63 and strain SMAJ_180 yielding 27.24 mM and 0.75 mM, respectively. Both strains demonstrated the ability to solubilize inorganic phosphate into soluble forms, indicating their potential contribution to enhanced phosphorus availability. Furthermore, strain SMAJ_63 exhibited exopolysaccharide (EPS) production, yielding 0.67 g/L, whereas strain SMAJ_180 did not produce any detectable EPS. In conclusion, these findings highlight the potential of the selected strains as effective PGP bacteria under heavy metal stress, indicating their applicability in enhancing crop productivity and contributing to sustainable agricultural practices.},
}

*Cicer/microbiology/growth & development
*Metals, Heavy/metabolism/toxicity
Phylogeny
Indoleacetic Acids/metabolism
*Enterobacter/isolation & purification/genetics/metabolism/classification/drug effects
*Root Nodules, Plant/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/isolation & purification/classification/genetics/metabolism
Ammonia/metabolism
Soil Microbiology
Plant Growth Regulators/metabolism

@article {pmid41324463,
year = {2025},
author = {Furman, O and Sorek, G and Moraïs, S and Levin, L and Tovar-Herrera, OE and Winkler, S and Mizrahi, I},
title = {Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf252},
pmid = {41324463},
issn = {1751-7370},
abstract = {The early life assembly of the rumen microbiome is a critical process with lasting implications for host development and function. Using high-resolution longitudinal metagenomics in calves tracked from birth to three years (∼800 days) of age, we reconstructed 2873 high-quality metagenome-assembled genomes (MAGs), including 517 novel genomes primarily detected in early life. These novel genomes, spanning 274 genera and largely classified as non-core taxa, reveal a diverse and functionally distinct auxiliary microbiome. Unlike in other ecosystems, this early microbial community persists into adulthood, retaining ecological and functional relevance despite a decline in abundance. Temporal clustering revealed strong associations between auxiliary taxa and dietary transitions, with functional enrichments in environmental sensing, nutrient biosynthesis, and volatile fatty acid metabolism. Metabolic network analyses showed that auxiliary genomes complement non-auxiliary community members in key functions, with potential effects on the host. Our findings suggest that early colonizers act as ecosystem engineers, with the potential to shape the developmental trajectory of the rumen microbiome. This study thus positions the early microbiome not as a transient feature of colonization, but as a structured, functionally coherent auxiliary community that interacts with the mature rumen ecosystem.},
}

@article {pmid41324448,
year = {2025},
author = {Donald, K and Serapio-Palacios, A and Bozorgmehr, T and Tabusi, M and Finlay, BB},
title = {Milk IgA promotes symbionts and limits pathobionts in the early life gut.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf266},
pmid = {41324448},
issn = {1751-7370},
abstract = {Secretory Immunoglobulin A (SIgA) is the dominant mucosal antibody and a key regulator of the gut microbiota. In early life, infants rely on breastmilk as their primary source of SIgA, but the role of milk-derived SIgA in early life microbiota colonization dynamics remains incompletely understood. Here, we show that species-specific SIgA in milk is antigen-inducible and discriminates between closely related but immunologically diverging microbes in the neonatal gut. More specifically, milk species-specific SIgA promotes colonization by an anti-inflammatory Escherichia coli strain while restricting the expansion of pro-inflammatory Proteus mirabilis. These findings uncover a dual role of maternal milk SIgA in actively sculpting the early life gut microbiota with species-level precision.},
}

@article {pmid41324297,
year = {2025},
author = {Lirakis, M and Dolezal, M and Nolte, V and Schlötterer, C},
title = {Diet-induced transgenerational effects on Drosophila dormancy are not mediated by the microbiome.},
journal = {The Journal of experimental biology},
volume = {},
number = {},
pages = {},
doi = {10.1242/jeb.250069},
pmid = {41324297},
issn = {1477-9145},
support = {641456//H2020 Marie Skodowska-Curie Actions/ ; FWF, P27630, W1225//Austrian Science Fund/ ; },
abstract = {Environmental signals exert influences not only on the current generation, but also extend to subsequent generations, even when these signals no longer persist. These transgenerational effects can be mediated through several mechanisms, including epigenetic inheritance and composition of the gut microbiome. In this study we investigated the contribution of the microbiome to diet-induced transgenerational effects on reproductive dormancy. Multiple strains of Drosophila simulans were subjected to a shift from sugar-rich to sugar-poor diet and the impact of this diet switch on dormancy was determined over multiple generations. Consistent with significant transgenerational effects, we observed a gradual reduction in dormancy incidence with an increasing number of generations exposed to the new, sugar-poor diet. Despite the variation in dormancy induced by the dietary shift, the microbiome composition remained largely stable. Consequently, we conclude that these transgenerational effects are not determined by changes in the bacterial microbiome composition.},
}

@article {pmid41324262,
year = {2025},
author = {Kuar, KD and Sarker, AK and Nelson, I and Plett, JM and Stack, CM and Morton, CO and Moffitt, MC},
title = {Screening leaf-associated fungi from the critically endangered plant Rhodamnia rubescens suggests biocontrol potential against myrtle rust.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf293},
pmid = {41324262},
issn = {1365-2672},
abstract = {AIMS: Myrtle rust, caused by the obligate pathogen Austropuccinia psidii, is a significant disease of myrtaceous plants. Species in Australia, such as Rhodamnia rubescens, are now critically endangered as a result of this disease. This research aimed to evaluate the culturable fungal communities present on, and within, leaves of symptomatic and asymptomatic R. rubescens plants as inhibitors of myrtle rust disease. We hypothesised that microbes present in asymptomatic leaves may possess biocontrol activity, thereby providing a mechanism of resistance observed in the field.

METHODS AND RESULTS: Fungal communities were isolated on three types of media and were identified using ITS sequencing. Of the 143 isolates obtained from both leaf types, germinating spores from nine isolates from the genera Nemania, Corynespora, Cladosporium, Pestalotiopsis, Quambalaria, Kalmanozyma, and Coniothyrium were found to inhibit the germination of A. psidii spores in vitro. However, no link was found between biocontrol activity of the isolates recovered and the degree of disease found on R. rubescens leaves. Isolates were also screened for antifungal activity during active hyphal growth using an unrelated pathogenic fungus Stagonosporopsis cucurbitacearum to test for broader bioprotective activity.

CONCLUSIONS: Isolates with antagonistic activities could be further explored in conservation efforts to protect plants against A. psidii symptoms, either in isolation, as part of a synthetic microbial community, or in more agricultural contexts to improve food security.},
}

@article {pmid41324164,
year = {2025},
author = {Zhang, H and Huang, X and Wang, S and Lei, Z and Wang, Y and Pan, K and Sheng, J and He, Z and Wang, Z and Zhu, H and Zhao, X},
title = {Root-Exuded Metabolites Recruit Selenium-Transforming Microbiota to Enhance Plant Selenium Acquisition.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70307},
pmid = {41324164},
issn = {1365-3040},
support = {//This study was supported by the National Key Research and Development Program of China (2023YFD1900904), 2025 Science and Technology Project of Hubei Geological Bureau (Grant KJ2025-5), the joint support from the Hubei Provincial Natural Science Foundation and Hubei Geological Bureau of China (Grant 2023AFD215), Wuhan Academy of Agricultural Sciences Innovation Project (XKCX202526), special fund of Xinjiang Key Laboratory of Soil and Plant Ecological Processes (24XJTRZW13), the Funding for Scientific Research Projects from Wuhan Municipal Health Commission (WY22B04), the Science and Technology Research Project of Hubei Province (D20234501), the Foundation of Talent Introduction Project of Hubei Polytechnic University (23xjz05R)./ ; },
abstract = {Microbial fortification represents a promising approach for selenium biofortification in crops. Building on the previous discovery that Bacillus cereus SESY enhances selenium uptake in Brassica napus, this study employed an integrated multi-omics approach to investigate the mechanism by which B. cereus SESY enhances Se bioavailability in the Brassica napus rhizosphere. Inoculation with B. cereus SESY significantly increased selenium content in Brassica napus roots and shoots in calcareous soil by 42.9% and 21.5%, respectively, and increased the selenium content of shoots in yellow brown soil by 30.7%. B. cereus SESY promoted the transformation of residual Se into bioavailable forms and enriched bacterial taxa with high motility and Se-transforming capacity (e.g., Lysobacter, Rhodanobacter, Sphingomonas and Burkholderiaceae) in rhizosphere soil. Key genes of these bacteria involved in Se metabolism (e.g., trxA, narH, cysE, cysK, metB) and cell motility genes (e.g., FlgG, CheW, FliH) were up-regulated. Core rhizosphere metabolites such as N-formylmethionine and xanthine correlated strongly with enriched bacteria abundance and available Se. Joint application of these metabolites with enriched bacteria increased plant Se content by 144% and rhizosphere soil available Se by 13.4%. These results reveal a metabolite-mediated microbial network that enhances Se mobility and plant uptake, providing a novel strategy for microbiome-driven biofortification.},
}

@article {pmid41324109,
year = {2025},
author = {Butt, SA},
title = {Letter to Editor: Gut-Microbiome and Nutritional Analysis Reveals Food Intake as a Key Factor in the Incidence and Prevention of Colon Polyps: A Cross-Sectional Study.},
journal = {Health science reports},
volume = {8},
number = {12},
pages = {e71582},
pmid = {41324109},
issn = {2398-8835},
}

@article {pmid41323826,
year = {2025},
author = {Wang, J and Lu, X and Zhao, Y and Jiang, Z and Wang, J and Wang, Z and Zhang, X},
title = {Dietary Index for Gut Microbiota and Leisure Time Physical Activity: The Potential Combined Protective Impact on Hypertension Risk.},
journal = {Food science & nutrition},
volume = {13},
number = {12},
pages = {e71245},
pmid = {41323826},
issn = {2048-7177},
abstract = {Emerging evidence highlights the gut microbiome's role in hypertension via microbial metabolites and endothelial dysfunction, while the Dietary Index for Gut Microbiota (DI-GM) quantifies diet quality for microbiota health. In addition, leisure-time physical activity (LTPA) also reduces blood pressure, but their combined impact on population-level hypertension remains unclear. Therefore, this study explores the individual and joint effects of DI-GM and LTPA on hypertension risk. To address this objective, we conducted a cross-sectional study analysis of data from 27,643 adults in the National Health and Nutrition Examination Survey (NHANES 2007-2020). Excluding individuals with incomplete data, key variables included the DI-GM and LTPA pattern (categorized by intensity, frequency, and regularity; regularly active defined as > 2 days/week). Weighted logistic regression models and restricted cubic splines (RCS) evaluated independent, joint, and non-linear associations of DI-GM and LTPA with hypertension, adjusting for covariates. The results showed that higher DI-GM scores and greater weekly LTPA were inversely correlated with hypertension risk, exhibiting dose-dependent patterns (16% lower odds for DI-GM ≥ 6 vs. lowest groups; 16%-24% lower odds for LTPA (≥ 150 min/week) vs. lowest groups). RCS analysis showed a linear inverse dose-response relationship between DI-GM and hypertension. The regularly active LTPA pattern (> 2 days/week) was linked to a 24% lower risk of hypertension (OR = 0.76, 95% CI = 0.69-0.84), and there was also a significant association observed for the weekend warrior LTPA pattern (1-2 days/week) (OR = 0.80, 95% CI = 0.64-0.99). Notably, joint analysis demonstrated that individuals with DI-GM > 4 scores and LTPA ≥ 150 min/week or regularly LTPA pattern exhibited the lowest hypertension odds. In conclusion, both a high DI-GM score (≥ 6 points) and sufficient LTPA (≥ 150 min/week) were independently associated with reduced odds of hypertension, with their combined effect amplifying protective benefits. Prospective studies are warranted to confirm temporality and causal pathways.},
}

@article {pmid41323692,
year = {2025},
author = {Thompson, L and Goh, YE and Jamwal, M and Singh, BL and Brar, GK and Arnold, CD and Westcott, J and Long, JM and Krebs, NF and Zivkovic, A and Das, R and Duggal, M and McDonald, CM},
title = {The Effect of Quintuply-Fortified Salt on the Gut Microbiome of Young Children 1-5 y of Age in Punjab, India; A Substudy of a Randomized, Community-Based Trial.},
journal = {Current developments in nutrition},
volume = {9},
number = {11},
pages = {107580},
pmid = {41323692},
issn = {2475-2991},
abstract = {BACKGROUND: Young children in India often face multiple micronutrient deficiencies, yet interventions such as micronutrient powders have raised concerns about potential adverse effects on the gut microbiome. Large-scale food fortification is an effective strategy to improve micronutrient intake; however, its impact on the gut microbiome of children remains unclear.

OBJECTIVES: To determine whether intake of quintuply-fortified salt (QFS) for 12 mo adversely affects gut microbiome composition in children aged 1-5 y.

METHODS: In a double-blind, randomized, controlled trial in Punjab, India, children received: 1) QFS with iron as encapsulated ferrous fumarate [eFF], zinc, vitamin B12, folic acid, and iodine (eFF-QFS); 2) QFS with the same micronutrients, but iron as encapsulated ferric pyrophosphate [eFePP] plus ethylenediaminetetraacetic acid (eFePP-QFS); or 3) standard iodized salt for 12 mo. Stool samples were collected from 125 children (eFF-QFS, n = 43; eFePP-QFS, n = 45; iodized salt, n= 37) at baseline and 12 mo and analyzed via 16S rRNA gene sequencing. Changes in alpha diversity (Shannon, abundance-based estimator index) between groups were assessed with linear mixed models, beta diversity (Bray-Curtis dissimilarity) with linear regression and permutational multivariate analysis of variance, and relative abundance of Enterobacteriaceae, Lactobacillus, Bifidobacterium, Bacteroides, Prevotella, or Escherichia-Shigella with zero-inflated negative binomial mixed models.

RESULTS: Average discretionary salt utilization was estimated to be 3.5 g/child equivalent/d across groups. Abundance-based estimator index was higher in the iodized salt arm compared with eFePP-QFS, but similar to eFF-QFS. Permutational multivariate analysis of variance revealed no overall group differences; however, pairwise Bray-Curtis distances from baseline were modestly greater in eFF-QFS compared with the other groups. No significant changes in relative abundance were identified.

CONCLUSIONS: After 12 mo, QFS resulted no major changes in abundance of key taxa and minimal, inconsistent shifts in certain diversity metrics and relative to the iodized salt control, suggesting no adverse effects on microbiome composition among young children in this setting. Additional studies in settings with improved iron status are needed.This trial was registered at clinicaltrials.gov as NCT05166980 and at Clinical Trials Registry-India as CTRI/2022/02/040333.},
}

@article {pmid41323559,
year = {2025},
author = {Tian, S and Liu, Y and Yang, H and Chen, K and Li, J and Chen, L and Wu, T and Zhang, L},
title = {Multi-Omics Reveal That Gut Microbial Dysbiosis Drives Lipid Metabolic Disturbances and Inflammation in Gestational Hypertension.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {16411-16425},
pmid = {41323559},
issn = {1178-7031},
abstract = {BACKGROUND: Gestational hypertension (GH) is a common complication during pregnancy that poses serious health risks to both mother and fetus. Recent studies have underscored the potential roles of gut microbiota, lipid metabolism, and inflammatory response in GH's development and progression. However, the exact mechanisms behind these interactions are still unclear. Understanding how gut microbial composition impacts lipid metabolism and inflammation could offer valuable insights into GH's pathogenesis and may lead to new prevention and treatment methods.

METHODS: In this study, we conducted ELISA experiments to detect inflammatory cytokines in the serum of GH patients. Additionally, we performed 16S-rDNA sequencing analysis on the feces of GH patients to investigate the characteristics of their intestinal microbial communities; GH mouse model was constructed to assess the impact of intestinal flora on offspring. Furthermore, we utilized non-targeted lipid metabolomics to analyze lipid metabolic characteristics in the feces and blood of GH patients and established connections between the microbiome and lipidome through correlation analysis.

RESULTS: ELISA tests suggested the levels of inflammatory factors in the serum of GH patients increased significantly, including IL-6, IL-8, IL-17, IL-18, and IFN-γ. In comparison to the normal group, the GH group exhibited a marked reduction in microbial richness. LEfSe analysis found 16 distinct bacterial communities between the two groups. Animal models suggested that fecal microbiota transplantation from the GH group's intestinal flora resulted in a significant decrease in the birth weight of the offspring. Furthermore, comparative analysis of fecal and blood metabolic profiles suggested that TG (54:5/FA22:5) may serve as a key metabolite. Correlation analysis demonstrated that f-Oxalobacteraceae exhibited a significant negative correlation with the inflammatory factor IL-17 and TG (54:5/FA22:5) in the blood, while showing a significant positive correlation with g-Oxalobacter and s-formigenes.

CONCLUSION: Our results establish a connection between gut microbiota, lipid metabolism, and the inflammatory response in patients with GH. This understanding may enhance our comprehension of the underlying mechanisms associated with GH.},
}

@article {pmid41323349,
year = {2025},
author = {Garcia, I and Kilic, F and Bryan, CA and Castro-Vildosola, J and Jonnalagadda, SA and Kasturi, A and Tilly, J and Smith, J and Valentin, S and Moncayo, S and Hala, T and Klein, E and Corbett, BF},
title = {Social stress changes gut microbiome composition in male, female, and aggressor mice.},
journal = {Brain, behavior, & immunity - health},
volume = {50},
number = {},
pages = {101138},
pmid = {41323349},
issn = {2666-3546},
abstract = {Psychological stress causes gut dysbiosis, which is associated with adverse effects on physical and mental health in humans and mice. Identifying taxa of gut bacteria changed by stress, and whether stress differentially alters their relative abundance in males and females, has important implications for stress-related disorders. We modeled individual differences in resilience or susceptibility using the chronic social defeat stress (CSDS) paradigm. Here, C57BL/6 mice are exposed to a novel retired breeder CD-1 aggressor for 10 min per day for 10 days. In this paradigm, resilient and susceptible subpopulations can be identified using the social interaction paradigm following CSDS. Fecal samples were collected immediately following Day 1 and Day 10 of CSDS. 16S ribosomal RNA sequencing was used to identify the relative abundance of 200 bacteria species. We analyzed group differences in phyla, genera, and species in resilient, susceptible, and non-stressed control male and female C57/BL/6 intruders along with CD-1 aggressors. Stress reduced microbiome diversity and caused gut dysbiosis in all groups, including aggressors. These changes were not observed in non-stressed mice. CSDS altered the relative abundance of every gut bacteria phylum. CSDS reduced genera in the Firmicutes phylum whereas sex altered fewer genera. The relative abundance of an uncultured Ruminococcus species on Day 1 predicted social avoidance following CSDS, with a stronger correlation in stressed females compared to males. Together, our findings demonstrate that CSDS changes gut microbiome composition in male and female mice.},
}

@article {pmid41323231,
year = {2025},
author = {Wang, Z and Zhou, L and He, Y and Xv, X and Lv, M and Zhang, Z and Wang, F and Wang, S and Wang, Y},
title = {Preliminary analysis of gut microbiome characteristics in children with obstructive sleep apnea hypopnea syndrome.},
journal = {Frontiers in neurology},
volume = {16},
number = {},
pages = {1615891},
pmid = {41323231},
issn = {1664-2295},
abstract = {OBJECTIVE: To analyze the characteristic changes in the gut microbiome in children with obstructive sleep apnea-hypopnea syndrome (OSAHS) and to investigate the relationship between the gut microbiome and polysomnography (PSG) results.

METHODS: Children diagnosed with primary snoring and OSAHS by PSG were enrolled in the study group. Nonsnoring children undergoing elective surgery were selected as the control group. Stool, sleep monitoring data, and medical history data were collected. The clinical history data were analyzed by SPSS 25.0 software. 16S rRNA high-throughput sequencing technology was used to analyze the gut microbiome, and relevant biostatistical methods were used to analyze and describe the characteristics of the gut microbiome.

RESULTS: A total of 62 OSAHS patients (42 mild OSAHS and 20 moderate to severe OSAHS), 16 primary snoring patients and 46 controls were enrolled in this study. There were significant differences in the partial alpha diversity index (observed otus index, Chao1 index) and beta diversity under the Jaccard and unweighted UniFrac distance methods between the mild OSAHS group and the moderate to severe OSAHS group. There were differences in some gut microbiome at different levels of phylum, class, order, family, genus and species between the control group and OSAHS group. There was a significant difference in the abundance ratio between Firmicutes and Bacteroidetes (F/B), and the ratio gradually increased among the three groups. The predictive model for OSAHS diagnosis established by the receiver operating characteristic (ROC) curve showed that the area under the curve (AUC) of Firmicutes and the F/B were more than 50%. At the genus level, Akkermansia was positively correlated with sleep efficiency (SE), Dialister was positively correlated with mean oxygen saturation (SaO2mean) and lowest oxygen saturation (LSaO2), Escherichia-Shigella was negatively correlated with total sleep time (TST), and Faecalibacterium was negatively correlated with the obstructive apnea index (OAI).

CONCLUSION: The gut microbiome of children with OSAHS is slightly different at the phylum, class, order, family, genus and species levels. The F/B and Firmicutes abundance detection have limited predictive capability for the diagnosis of OSAHS. At the genus level, some gut microbiota were correlated with PSG indicators.},
}

@article {pmid41322988,
year = {2025},
author = {Chávez-Domínguez, RL and Torres, M and Acevedo-Domínguez, AA and Ibarra-Inocente, JA and Carranza, C},
title = {Reprogramming the host: Mycobacterium tuberculosis as a silent architect of the immuno-tumoral.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1697874},
pmid = {41322988},
issn = {2235-2988},
mesh = {Humans ; *Mycobacterium tuberculosis/pathogenicity/immunology ; *Host-Pathogen Interactions/immunology ; *Lung Neoplasms/immunology/microbiology/etiology ; *Tuberculosis, Pulmonary/complications/immunology/microbiology ; Tuberculosis/complications ; Tumor Microenvironment ; Virulence Factors/metabolism ; Animals ; },
abstract = {Pulmonary tuberculosis, caused by Mycobacterium tuberculosis (Mtb), remains one of the leading causes of infectious disease-related mortality worldwide. In parallel, lung cancer represents the most lethal neoplasm, with high mortality rates globally. Emerging studies suggest that chronic Mtb infection may contribute to the development of lung cancer, particularly adenocarcinoma. Several biological mechanisms support this hypothesis. Chronic inflammation from tuberculosis creates a microenvironment enriched in proinflammatory cytokines, reactive oxygen species (ROS), and growth factors that favor cell proliferation, genomic instability, angiogenesis, and immune evasion, which are considered classic hallmarks of cancer. Additionally, both protein and non-protein virulence factors of Mtb have been shown to interfere with critical cellular signaling pathways related to tumor cell survival and invasion. Clinically, multiple observational studies and meta-analyses report an increased incidence of lung cancer among individuals with a history of tuberculosis, especially when both conditions coexist in the same pulmonary regions. Specific mutations, including EGFR, have been identified in patients with prior tuberculosis, influencing both prognosis and therapeutic response. Nevertheless, key questions remain regarding the causal nature of this association, the role of Mtb strains, and the molecular factors such as epigenetic modifications or the lung microbiome. This review proposes that infection with Mtb could function as a carcinogenic agent. Further in vitro experiments, cellular models, and clinical investigations are urgently needed to support potential reclassification of this pathogen by international agencies such as the IARC.},
}

Humans
*Mycobacterium tuberculosis/pathogenicity/immunology
*Host-Pathogen Interactions/immunology
*Lung Neoplasms/immunology/microbiology/etiology
*Tuberculosis, Pulmonary/complications/immunology/microbiology
Tuberculosis/complications
Tumor Microenvironment
Virulence Factors/metabolism
Animals

@article {pmid41322953,
year = {2025},
author = {Krueger, Q and Shore, M and Reitzel, AM},
title = {Influence of Temperature and Saline Conditions on Bacteria Naturally Associated With the Cnidarian Host Nematostella vectensis.},
journal = {International journal of microbiology},
volume = {2025},
number = {},
pages = {4107949},
pmid = {41322953},
issn = {1687-918X},
abstract = {The associated microorganisms ("microbiome") of multicellular individuals ("host") are important for the physiology and survival of the host. Individual bacterial species vary in environmental tolerances that may limit their associations with hosts, especially when their range of survivable conditions is narrower. To elucidate the roles for different environmental niche spaces of bacteria that may compose the microbiome, we evaluated the survival and growth of individual and combinations of bacteria with and without an animal host, the sea anemone Nematostella vectensis (Cnidaria, Anthozoa). We assessed 62 environmental bacteria from seven genera (Alteromonas, Bacillus, Grimontia, Photobacterium, Pseudoalteromonas, Shewanella, and Vibrio) isolated from six estuaries and the host to determine their tolerance across a gradient of temperatures (30°-40°C) and salinities (5-30 ppt). Growth rates and plate counts revealed members of the Vibrio genus had the highest growth rate at higher salinities (15 and 30 ppt), while Bacillus and Alteromonas spp. exhibited consistent growth over a broader range of salinities and temperatures. Only 15% of isolates were capable of growth at the combination of highest temperature and lowest salinity (40°C, 5 ppt), suggesting that these environmentally relevant conditions may limit microbiome diversity. We further assessed three isolates (Bacillus velezensis, Pseudoalteromonas spiralis, and Vibrio diabolicus) for how bacterial growth changed when associated with N. vectensis. When anemones were exposed to environmentally relevant heat stress over 3 days, bacterial concentrations varied significantly. P. spiralis grew more under lower salinities and maintained stable concentrations. Conversely, V. diabolicus grew more with higher salinity and maintained these high concentrations in nearly all conditions. At sustained extreme temperatures for the anemones, the microbial composition exerted a small impact on survival. Together, these results support that environmental conditions are important drivers for the relative abundance of particular bacteria in the context of the host's microbiome.},
}

@article {pmid41322804,
year = {2025},
author = {Singh, P and Saini, P and Kalyankar, PP and Kailey, KR and Chauhan, R and Pannu, AK and Singh, N and Garg, K},
title = {Drug Management of Inflammatory Bowel Disease (IBD): A Narrative Review.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e95635},
pmid = {41322804},
issn = {2168-8184},
abstract = {The exact underlying etiopathogenesis of inflammatory bowel disease (IBD) remains unclear. Conventionally, autoimmune mechanisms have been linked with IBD, and thus various immunomodulatory or anti-inflammatory drugs have proven useful. The understanding of the complex gut mucosal immune system and the trafficking of leukocytes toward the intestine from lymphoid organs has allowed us to use molecular drugs that may target specific pathways, like the Janus kinase (JAK) pathway, phosphodiesterase, interleukins (IL)-12, 23, and adhesion molecules such as selectins. These agents have brought about a drastic change in the management strategy of IBD. Since many patients may not improve on conventional therapy, newer treatments are tried, which show better efficacy with fewer side effects. The present review highlights the concepts of newer therapeutic drugs, their interaction with host microbiome and gut-brain axis, and the new targets in the autoimmune phenomena, thereby providing a promising treatment for a better management of IBD in the present and future times.},
}

@article {pmid41322719,
year = {2025},
author = {Conway, J and January, GG and Muddiman, KJ and Dorrington, R and Howell, KL and Upton, M},
title = {Impact of growth conditions on the abundance and diversity of cultivable bacteria recovered from Pheronema carpenteri and investigation of their antimicrobial potential.},
journal = {FEMS microbes},
volume = {6},
number = {},
pages = {xtaf016},
pmid = {41322719},
issn = {2633-6685},
abstract = {The deep sea is a largely unexplored extreme environment supporting a diverse biological community adapted to low temperatures and high pressures. Such environments support microbial life that may be a source of novel antibiotics and other drugs. Whilst this is often the case, many species with bioactive capabilities may be missed with traditional culturing methods. In this study, a total of 16 different concentrations and types of media were employed, to culture 389 bacterial isolates using Dilution to Extinction methods and Actinobacteria Directed Cultivation techniques. This generated 72 (18.6%) isolates with narrow and broad-spectrum activity against ESKAPE pathogens including Escherichia coli (E. coli), methicillin-resistant Staphylococcus aureus, and vancomycin-resistant Enterococci. We also report that an early-stage 'One Strain Many Compounds' approach can reveal a greater number of bioactive isolates that otherwise would have been missed; 12 isolates initially deemed 'inactive' were seen to exhibit activity towards S. aureus and/or E. coli. We emphasize the importance of a thorough initial screening method to capture bioactive isolates and show how selecting only morphologically distinct isolates for screening may result in species with promising bioactivity being overlooked. Our findings justify on-going investigation of Pheronema sponges for bioactive microbiota.},
}

@article {pmid41322709,
year = {2025},
author = {Gaballah, K and Sekar, P and Abuzayed, D and Alowais, A and Shakir, A and Razouk, A and Mohammed, MM},
title = {Oral Microbial and Systemic Lipid Profiles in Patients With Asymptomatic Retained Partially Erupted Third Molars: A Preliminary Cross-Sectional Study.},
journal = {International journal of dentistry},
volume = {2025},
number = {},
pages = {4770383},
pmid = {41322709},
issn = {1687-8728},
abstract = {BACKGROUND: Partially erupted (PE) third molars are frequently retained in the oral cavity and may contribute to localized inflammation. Chronic subclinical inflammation at these sites has been suggested to influence systemic markers such as lipid profiles, potentially increasing cardiovascular risk. Additionally, microbial colonization, particularly by bacteria and Candida species, may exacerbate inflammatory responses.

OBJECTIVE: To investigate the lipid panel parameters and oral microbial burden in individuals with PE third molars compared to those with fully erupted (FE) third molars and to assess potential associations with systemic inflammation.

METHODS: A cross-sectional study was conducted on 64 participants aged 20-35 years, divided into two groups: group 1 with PE third molars and group 2 with FE third molars. Fasting lipid profiles were measured using the CardioChek PA Analyzer. Gingival crevicular fluid (GCF) samples were collected from under the operculum in group 1 and from the gingival sulcus in group 2. Quantitative PCR (qPCR) was used to assess Candida and bacterial load. Statistical analysis included unpaired t-tests and multivariate logistic regression, adjusting for confounders.

RESULTS: A higher prevalence of elevated total cholesterol (TC) was observed in group 1 (15.63%) compared to group 2, with an odds ratio (OR) of 7.215 (95% CI: 0.992-52.5; p=0.051). Candida presence was significantly greater in PE sites (p=0.0036), though load differences were not statistically significant except in triglyceride (TG)-associated samples. All samples were positive for bacteria; however, bacterial load was unexpectedly higher in FE sites (p=0.0066). Associations between lipid abnormalities and microbial presence were noted but not statistically conclusive.

CONCLUSION: PE third molars may be linked to elevated cholesterol levels and increased microbial colonization, particularly by Candida species. While no statistically significant associations were found, the trends suggest a potential inflammatory and metabolic role of third molar retention. Further longitudinal studies with larger sample sizes and detailed microbial profiling are needed to clarify these relationships.},
}

@article {pmid41322357,
year = {2026},
author = {Modeel, S and Siwach, S and Dolkar, P and Chaurasia, M and Yadav, P and Atri, A and Yadav, A and Negi, T and Negi, RK},
title = {Emerging risk factors and the role of gut microbiota in immunomodulation and therapeutic implications in colorectal cancer.},
journal = {Cancer pathogenesis and therapy},
volume = {4},
number = {1},
pages = {14-30},
pmid = {41322357},
issn = {2949-7132},
abstract = {The pathophysiology of many ailments, including neurological, gastrointestinal, and metabolic problems, is well known to be influenced by intestinal dysbiosis. Clinical research has provided evidence suggesting a strong correlation between dysbiosis of the gut microbiome and colorectal cancer (CRC) development. The active reprogramming of metabolic pathways to boost glycolysis, fatty acid production, lipogenesis, and glutaminolysis constitutes a major metabolic shift in cancer development, including CRC. The complex combination of different factors leads to CRC, making it an environmental disease. These factors include food and lifestyle choices, genetics and family history, age, underlying intestinal diseases, and dysbiosis of the gut microbiota. One of the primary risk factors for carcinoma development is diet, which impacts an individual's gut microbiome. In addition to impacting CRC formation, the gut microbiome also has immunomodulatory effects, including various immunological interactions and the underlying mechanisms governing them. Microbial interactions in CRC have been extensively studied, yet numerous unresolved queries exist on how gut bacteria can influence treatment. It is possible to perform microbiome-driven immunotherapies focusing on probiotics, prebiotics, and synbiotics. However, large-scale treatment utilization in CRC patients is limited by several issues, including variations in the microbial makeup of each patient's gut and a lack of established methods. The study highlights the impact of several risk factors, including dysbiosis of the gut microbiome and different approaches to halting and treating CRC progression with a focus on diet changes and modulation of the gut flora. Given the foregoing, we propose that if research gaps are addressed and immunotherapy is paired with microbial interventions, microbiota-based therapeutics could potentially impede the growth of tumors and treat CRC.},
}

@article {pmid41322272,
year = {2025},
author = {Kim, JM and Choi, BJ and Bayburt, H and Lee, JK and Jeon, CO},
title = {Identifying potential keystone bacterial species within the phycosphere of marine algae and unveiling their metabolic characteristics.},
journal = {Marine life science & technology},
volume = {7},
number = {4},
pages = {989-1007},
pmid = {41322272},
issn = {2662-1746},
abstract = {UNLABELLED: Metabolic interactions between microbiomes and algal hosts within the phycosphere of marine macroalgae are drawing increasing attention due to their roles in food webs, global nutrient cycles, industries, and their potential as food resources. However, these relations remain poorly understood. In this study, 43 marine macroalgae, including red, brown, and green algae, were collected from the coastal areas of Korea. We identified the bacterial communities within the loosely and tightly attached environments (LAEs and TAEs, respectively) of the phycosphere, along with those in the surrounding seawater, using 16S rRNA gene sequencing. β-Diversity analysis revealed significant differences between the bacterial communities among the three, with minimal variation related to sampling location or algal color. Indicator value analysis identified Pseudoalteromonas (in the LAE and TAE), Psychromonas (in the LAE), Marinomonas (in the LAE), and Litorimonas (in the TAE) as the dominant taxa in the phycosphere, in contrast to seawater. Network analysis suggested positive correlations among taxa within the same environments and negative correlations between those in the LAE and TAE, highlighting their distinct ecological conditions. Analysis using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States and Kyoto Encyclopedia of Genes and Genomes pathways revealed functional variations between the phycosphere- and seawater-residing microbes. The microbial taxa-function relationships were assessed through Spearman's rank-order correlation. Additionally, bacterial species belonging to the core taxa were isolated and their genomes sequenced. Their metabolic traits were analyzed via bioinformatics, recognizing key metabolic features essential for symbiotic interactions with algal hosts and survival within the phycosphere. The findings of this study advance our understanding of the marine algal phycosphere microbiome by detailing the metabolic characteristics of potential keystone species.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00325-6.},
}

@article {pmid41322104,
year = {2025},
author = {Khawaja, TW and Zhao, L and Siddiq, R and Ahmad, MU and Burns, CP and Parker, JM and Wakefield, MR and Fang, Y},
title = {Unmasking the microbiome: the hidden role of gut bacteria in the pathogenesis of colorectal cancer and its prevention strategies.},
journal = {Exploration of targeted anti-tumor therapy},
volume = {6},
number = {},
pages = {1002351},
pmid = {41322104},
issn = {2692-3114},
abstract = {Colorectal cancer (CRC) is a significant global health problem, ranking as the third most common cancer and the second leading cause of cancer deaths in the world. The highest incidence of CRC is found in developed regions, thus underlining its characterization as a Western disease. Major risk factors for CRC include an unhealthy diet, lack of physical exercise, and cigarette smoking. The gut microbiota refers to the complex community of microorganisms inhabiting the digestive tract and plays a crucial role in the maintenance of host health and modulation of immune responses. Gut dysbiosis can be caused by poor diet and alcohol consumption, increasing CRC risk. Specific bacteria, such as Fusobacterium nucleatum and Escherichia coli, may have a close relationship with CRC development, while the beneficial bacteria are frequently depleted in CRC patients. This paper will discuss the mechanisms of colorectal carcinogenesis, focusing on the effects of bacterial genotoxins, immune evasion, inflammation, and diet. Additionally, it reviews preventative strategies including short-chain fatty acids (SCFAs), prebiotics, probiotics, synbiotic supplements, and the method of fecal microbiota transplantation (FMT), showing their potential to improve overall gut health and reduce the risk for CRC. Understanding these mechanisms and implementing specific preventative strategies could significantly enhance clinical interventions and reduce the global burden of CRC.},
}

@article {pmid41322070,
year = {2025},
author = {Amirinia, F and Motamedi, M and Ardi, P and Jabrodini, A},
title = {Evaluating the Role of Candida albicans as a Potential Oral Carcinogen.},
journal = {Interdisciplinary perspectives on infectious diseases},
volume = {2025},
number = {},
pages = {4057977},
pmid = {41322070},
issn = {1687-708X},
abstract = {Oral cavity cancers, especially oral squamous cell carcinoma (OSCC), are a major subset of head and neck malignancies. Increasing evidence indicates that oral microbiota, particularly Candida albicans (C. albicans), plays a significant role in OSCC development and progression. While C. albicans is normally a commensal organism in the human microbiome, it can become pathogenic under certain conditions. The carcinogenic potential of C. albicans contributes to oral cancer by acting both as a co-factor and a direct pathogen. This involves complex interactions with the host immune system and the expression of multiple virulence factors. The dynamic relationship between C. albicans and its host influences disease outcomes and cancer progression. This review focuses on key virulence mechanisms of C. albicans, including adhesion to host cells, secretion of hydrolytic enzymes, production of carcinogenic metabolites, induction of chronic inflammation, and release of candidalysin, a cytolytic peptide toxin. Understanding these factors is essential to clarify how C. albicans promotes OSCC initiation and progression. Improved knowledge of C. albicans virulence may lead to targeted therapies, preventive strategies, and novel biomarkers for early detection, ultimately enhancing treatment outcomes and prognosis for patients with oral cavity cancers.},
}

@article {pmid41321998,
year = {2025},
author = {Aksornkitti, V and Visuthranukul, C and Leelahavanichkul, A and Joyjinda, Y and Sriswasdi, S},
title = {Gut microbiome enterotypes and temporal variations during a six-month inulin-supplemented weight loss randomized controlled trial in Thai children with obesity.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {5007-5019},
pmid = {41321998},
issn = {2001-0370},
abstract = {Gut microbiome profiles can reflect the host's health status and have the potential to predict the effectiveness of medical interventions. In this study, gut microbiome enterotypes of 143 Thai children with obesity who participated in a randomized controlled trial of inulin supplementation were analyzed to identify microbial markers for weight loss responses and healthier lifestyles. Two gut microbiome enterotypes, which encompass 25 % of the children with obesity, were exclusive to children with obesity, including a rarely described Megasphaera enterotype. Megasphaera enterotype was also positively associated with dietary fiber intake specifically in the inulin group. Prevotella and Bacteroides enterotypes are significantly associated with poor health status, including longer times spent on electronic devices and lower concentrations of butyrate, a beneficial short-chain fatty acid. Children with these enterotypes also exhibited some of the best weight loss outcomes after receiving only behavioral and dietary advice. Observed associations between enterotypes and clinical parameters are consistent with earlier research of different populations. Intervention-specific associations suggest potential criteria for a personalized selection of weight loss interventions.},
}

@article {pmid41321962,
year = {2025},
author = {Heneberg, P},
title = {Commensal, pathogen, or passenger? Rethinking the role of Blastocystis in human health.},
journal = {One health (Amsterdam, Netherlands)},
volume = {21},
number = {},
pages = {101272},
pmid = {41321962},
issn = {2352-7714},
abstract = {Blastocystis is one of the most prevalent intestinal protists, colonizing more than one billion people worldwide. Nevertheless, its role in health and disease remains blurred. Blastocystis was historically dismissed as a commensal. However, it can have pathogenic or protective effects. This review synthesizes molecular epidemiology, clinical research, microbiome studies, and experimental models through a One Health approach to reassess Blastocystis. Subtypes ST1-ST4 are dominant in humans, but their health outcomes vary. ST4 is associated with irritable bowel syndrome and inflammatory responses. However, it has also been shown to exert protective effects on murine colitis models. In contrast, ST3 is frequently detected in healthy individuals with a diverse gut microbiota. Blastocystis is also widespread in animals, untreated water, wastewater, and food, reflecting complex transmission dynamics and raising concerns in low- and middle-income countries where poverty-related exposures increase risks. Diagnostic advances have improved detection, although mixed infections and inconsistent clinical interpretations persist, and treatment guidelines remain absent. Rather than being a uniform pathogen or benign passenger, Blastocystis emerges as a context-dependent component of the gut ecosystem and environmental microbiota. Its ubiquity across humans, animals, and the environment requires integrated surveillance, subtype-informed research, and interdisciplinary health strategies. Recognizing the ecological complexity of Blastocystis is essential for equitable diagnostics, treatment, and public health responses within the One Health framework.},
}

@article {pmid41321951,
year = {2025},
author = {Gao, W and Wang, H and Jia, H and Zhang, J and Yan, Z and He, D and Zheng, C},
title = {Microbiome shifts during Fusarium oxysporum and F. solani (syn. Neocosmospora solani)-induced Ligusticum chuanxiong root rot: endophtic bacterial protective responses and fungal pathogenic tendencies.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20369},
pmid = {41321951},
issn = {2167-8359},
mesh = {*Plant Diseases/microbiology ; *Plant Roots/microbiology ; *Fusarium/pathogenicity ; *Microbiota ; *Ligusticum/microbiology ; Rhizosphere ; Soil Microbiology ; Rhizome/microbiology ; Endophytes ; Bacteria ; },
abstract = {Root rot disease is a globally significant threat to the health of diverse economically important crops. Understanding shifts in the plant microbiome during disease progression can aid in identifying beneficial microbes with disease-resistant potential and developing ecofriendly biocontrol strategies. However, microbiome changes during root rot progression in the medicinal plant Ligusticum chuanxiong remain poorly understood. This study aimed to investigate the response of host-associated microbiomes to pathogen stress (Fusarium oxysporum and F. solani syn. Neocosmospora solani) during L. chuanxiong root rot. The diversity, composition, function, and network interactions of bacterial and fungal communities were examined using high-throughput sequencing and network analysis in healthy rhizomes, healthy layers of diseased rhizomes, rotten layers of diseased rhizomes, and rhizosphere and non-rhizosphere soils. The bacterial diversity decreased as root rot progressed in end ophytic (from 0.72 to 0.38) and rhizosphere soils (from 0.80 to 0.68), whereas the fungal diversity showed no significant changes. The diseased samples were enriched with root rot pathogens and other potential pathogens, such as the soil bacterium Pectobacterium and the soil fungus Gibberella, whereas beneficial taxa, including endophytic Bacillus and Trichoderma, and soil-dwelling Candidatus_Solibacter and Beauveria, were significantly reduced. Notably, in the healthy layers of diseased rhizomes, which represent a "transitional phase", fungal communities resembled those in rotten tissues with increased pathogenic taxa (e.g., Ceratocystis and Plectosphaerella), whereas bacterial communities were more similar to healthy rhizomes and enriched in beneficial genera (e.g., Microbacterium and Variovorax). Functional prediction indicated suppressed bacterial activity and enhanced fungal saprotrophy in rotten rhizomes. The cross-kingdom network complexity decreased in both endophytic and soil microbial communities during root rot, while positive correlations within endophytic networks increased. Overall, as root rot progresses, the stability and competitive interactions within endophytic and soil microbiomes of L. chuanxiong weaken. Early in infection, endophytic bacterial and fungal communities exhibit divergent responses: bacteria likely contribute to disease resistance, whereas fungi may promote pathogenesis. This findings suggest that a more beneficial role for endophytic bacteria in controlling L. chuanxiong root rot. Restoring microbial community complexity may offer a viable biocontrol strategy. Our findings provide a theoretical foundation for future identification of specific beneficial microbes and the development of safe biocontrol approaches.},
}

*Plant Diseases/microbiology
*Plant Roots/microbiology
*Fusarium/pathogenicity
*Microbiota
*Ligusticum/microbiology
Rhizosphere
Soil Microbiology
Rhizome/microbiology
Endophytes
Bacteria

@article {pmid41321837,
year = {2025},
author = {Sundaray, JK and Mohapatra, M and Rasal, A and Udit, UK and Mohanty, S and Mohanty, D and Das, II and Sahoo, L and Sahoo, PK},
title = {Sex-specific gut microbiome dynamics in Labeo catla: links to reproductive hormones, metabolic dimorphism, and environmental factors.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1651975},
pmid = {41321837},
issn = {1664-302X},
abstract = {INTRODUCTION: Gut microbiota play a critical role in aquaculture by enhancing nutrient metabolism, digestion, immune response, and reproductive performance in fish. Labeo catla, one of the most commercially important Indian major carps, demands better reproductive management; however, insights into its gut microbiome composition and functional dynamics, particularly during the crucial pre-spawning phase, remain limited.

METHODS: In this study, we investigated the structural and functional attributes of gut microbial communities in male and female L. catla reared in ICAR-CIFA ponds using high-throughput Illumina MiSeq 16S rRNA gene sequencing and examined their associations with reproductive traits.

RESULTS AND DISCUSSION: Histological analysis confirmed active gametogenesis in both sexes, while hormonal assays showed higher estradiol levels in females compared to males. Microbiome profiling revealed Proteobacteria as the dominant phylum, followed by Fusobacteria, Bacteroidetes, and Firmicutes. Cetobacterium and Shewanella were the most prevalent genera, with sex-specific differences in microbial diversity and composition. Functional prediction analysis identified genes associated with reproduction, lipid metabolism, digestion, and immunity. Correlation studies revealed a negative association between Bacteroidetes and 11-KT, while Shewanella and Serratia showed positive correlations with estradiol, indicating a potential role of gut microbes in modulating reproductive readiness. Canonical Correspondence and variance partitioning analyses revealed that gut microbiome variation in male and female L. catla was predominantly influenced by biological factors (63.97%) compared to environmental factors (20.99%). Notably, despite their low abundance, Clostridium perfringens and Pseudomonas stutzeri were identified as keystone taxa significantly shaping microbial network structure and stability.

CONCLUSION: This study provides the first comprehensive insight into the sex-specific gut microbiome's dynamics in L. catla during the pre-spawning season and highlight their application in broodstock management and sustainable aquaculture practices.},
}

@article {pmid41321829,
year = {2025},
author = {de Bruyn, C and Scott, K and Panter, H and Bezombes, F and Ralebitso-Senior, K},
title = {Advancing time-since-interval estimation for clandestine graves: a forensic ecogenomics perspective into burial and translocation timelines using massively parallel sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1684366},
pmid = {41321829},
issn = {1664-302X},
abstract = {Forensic taphonomy and entomology has focused on estimating the post-mortem interval (PMI), particularly for surface depositions, using human cadavers and other mammalian models by considering morphological changes of the body and insect activity during decomposition. The PMI is crucial in forensic investigations as it provides key information regarding the victim's identity, the circumstances of their death and can confirm or refute a suspect's alibi. Gravesoil microbial communities are a potential tool that can complement traditional approaches to detect and confirm the presence of human remains in clandestine burials, aiding forensic investigations. The estimation of the time-since-burial (post-burial interval; PBI), and the time-since-translocation (post-translocation interval; PTI), a new concept, have potential to aid clandestine grave location but have received relatively little attention in forensic ecology research. Advances in massively parallel sequencing (MPS) provide a high-throughput means to estimate PBI and PTI by characterising soil microbial communities in graves with remains, from early to skeletal stages of decomposition, or where remains have been intentionally removed from crime scenes and relocated. This review presents a perspective on the use of the soil microbiome as an indicator for post-mortem time-since-interval estimations, with specific focus on the PBI and PTI. In addition, it provides a framework, supported within forensic ecogenomics, on how the PBI and PTI can be used as a forensic tool complemented by MPS. The review highlights the need for further research to validate microbial community analysis across diverse biogeographical regions to enhance its precision and reliability as a forensic investigative tool. Such validation could potentially enhance the accuracy of post-burial and post-translocation interval estimations, ultimately improving methods for clandestine grave identification.},
}

@article {pmid41321827,
year = {2025},
author = {Ji, H and Yang, Z and Hao, Y and Wang, Y and Cao, Z and Yang, H and Wang, W and Li, S},
title = {Alpha-linolenic acid reshapes the gastrointestinal ecology to enhance immune function in dairy cows: insights from microbiome and metabolome profiling.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1687786},
pmid = {41321827},
issn = {1664-302X},
abstract = {INTRODUCTION: Alpha-linolenic acid (ALA), an essential polyunsaturated fatty acid, modulates gastrointestinal microbiota and host immunity, yet its regulatory mechanisms in dairy cows remain unclear.

METHODS: This study investigated how dietary ALA influenced gut microbiota, metabolome, and immune function in lactating Holstein cows. Ten cows were randomly assigned to two groups (n = 5) receiving either a low-ALA (LALA, 5.02 ± 0.09% ALA of total fatty acids) or high-ALA diet (HALA, 32.04 ± 1.55% ALA of total fatty acids). Rumen fluid, feces, and blood samples were analyzed post-intervention.

RESULTS: The HALA group exhibited increased ruminal abundance of Eubacterium coprostanoligenes group and Ruminococcus (p < 0.05), alongside reduced proinflammatory metabolites including dodecanoic acid, myristic acid, and prostaglandin I2 in the rumen. Plasma leukotriene C4 levels were also decreased (p < 0.05). Metabolomic enrichment analysis revealed significant downregulation of arachidonic acid metabolism. Correlation analyses demonstrated that Eubacterium coprostanoligenes group negatively associated with suppressed prostaglandin I2 (rumen metabolite) and leukotriene C4 (plasma metabolite), but positively correlated with enriched fecal Clostridia UCG-014 and Ruminococcus.

DISCUSSION: These findings indicate that high dietary ALA reshapes gastrointestinal microbiota and attenuates inflammatory responses by inhibiting microbial-metabolite-driven arachidonic acid metabolism, thereby enhancing immune regulation in dairy cows.},
}

@article {pmid41321823,
year = {2025},
author = {Zheng, Z and Xie, D and Han, Y and Li, G and Wang, S and Zhang, X and Huang, T and Xu, W and Wu, G},
title = {Deciphering the urinary microbiome and urological cancers: from correlation to mechanisms and treatment.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1699308},
pmid = {41321823},
issn = {1664-302X},
abstract = {Given that the sterility of urine and the urinary tract has been questioned by research, urinary microbiome dysbiosis has been recognized as one of the potential cancer-promoting factors. The composition of the urinary microbial community in healthy individuals has a relatively high similarity at the phylum level, with factors like age and gender influencing the expression and distribution. In contrast, the urinary microbiome of patients with urologic cancers shows significant variability and diversity depending on the type of cancer. Most of the early studies focused on the distribution, aggregation, and expression of microbiota in urologic cancers, warranting advanced studies on the causal relationship between microbes and urologic cancers. Bladder and prostate cancer tumorigenesis and progression can be influenced by microbes through chronic inflammatory or immunomodulatory pathways making them cancer models strongly associated with the urinary microbiome. Here, we summarize the expression characteristics of the microbiomes associated with these cancers and analyze the pathophysiological mechanisms and signaling pathways of the microbiome in the tumor promotion or suppression. By examining the role played by the urinary microbiome in the pathogenesis of urologic cancers, we assess the potential of specific microbial groups as biomarkers for diagnosis and surveillance. Additionally, involving the microbiome or using adjunctive participation in tumor therapy is becoming an emerging cancer treatment option. Improving urinary microbial homeostasis in urinary cancers by direct treatment with microbial products, microbial co-immunotherapy, probiotic-assisted therapy, and fecal microbial transplantation may broaden the scope of therapy and enhance the efficacy of conventional medicines.},
}

@article {pmid41321819,
year = {2025},
author = {Jiang, J and Zhou, S and Song, J and Xia, C and Yang, X and Yang, K and Li, F},
title = {Diet-microbiome coevolution: the core mechanism for semi-aquatic adaptation and cross-habitat niche coexistence of the web-footed shrew (Nectogale elegans).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1711143},
pmid = {41321819},
issn = {1664-302X},
abstract = {The adaptation of mammals to semi-aquatic niches represents a pivotal ecological transition, in which the coevolution of dietary specialization and gut microbiome is regarded as playing a fundamental role. However, the general mechanisms that link these traits to survival across habitats remain insufficiently investigated, particularly in small mammals with high metabolic constraints. Using the web-footed shrew (Nectogale elegans), a rare small mammal with extreme semi-aquatic specialization, this study supplements the understanding of host-microbe symbiosis in the process of small mammals adapting to new ecosystem. To address how diet facilitates semi-aquatic adaptation, we integrated benthic community surveys and dietary DNA metabarcoding. Our results showed that the web-footed shrew primarily utilizes benthic macroinvertebrates (Diptera, Ephemeroptera, and Trichoptera), consistent with the composition of local benthic biomass, and supplemented by Cypriniformes fish. Comparative analysis of DNA metabarcoding with sympatric terrestrial rodents further revealed that semi-aquatic shrews achieve niche differentiation through two complementary mechanisms: habitat partitioning (aquatic vs. terrestrial) and trophic level differentiation (secondary consumers of invertebrates vs. consumers of plants). This discovery extends niche theory, demonstrating how habitat-specific resource utilization shapes trophic stratification. Compared to the terrestrial group, the gut microbiome of the semi-aquatic shrew exhibited significant differences in both microbiome composition and functional potential: dominance of Proteobacteria and Firmicutes, reduced abundances of carbohydrate-active enzymes (CAZymes), as well as selective enrichment of genes involved in fatty acid metabolism. These results reflect the high-fat, high-protein niche of semi-aquatic shrews. Additionally, the seasonal stability of the microbiome of the semi-aquatic shrew mirrors the consistency of benthic resources, and maintaining metabolic homeostasis is key to long-term adaptation to fluctuating environments. Overall, this study demonstrates a framework for semi-aquatic adaptation in small mammals: dietary specialization drives niche differentiation, which in turn selects for gut microbiome adaptation, optimizing habitat-specific resource utilization. This research underscores the role of diet-microbiome coevolution in enabling semi-aquatic adaptation, offering novel insights into ecological niche differentiation and specialization mechanisms in small mammals.},
}

@article {pmid41321665,
year = {2025},
author = {Lahtinen, E and Hugerth, LW and Edfeldt, G and Säfholm, A and Kornfält, S and Engstrand, L and Strevens, H and Schuppe-Koistinen, I},
title = {pHyph, a novel antibiotic-free treatment for bacterial vaginosis, promotes Lactobacillus growth and reduces the abundance of pathogens in the vagina.},
journal = {AJOG global reports},
volume = {5},
number = {4},
pages = {100566},
pmid = {41321665},
issn = {2666-5778},
abstract = {BACKGROUND: Bacterial vaginosis (BV) is the most common vaginal infection among women of reproductive age worldwide, caused by dysbiosis of the vaginal microbiome. Despite its prevalence, the underlying molecular mechanisms remain poorly understood, making diagnosis and treatment challenging. Although antibiotics are the standard therapy, recurrence rates are high, up to 50% within 1 year, and repeated treatments contribute to the rise of antimicrobial resistance. There is an urgent need for alternative, sustainable, and microbiome-friendly treatment options.

OBJECTIVE: To evaluate whether pHyph, a novel antibiotic-free treatment, promotes a shift in the vaginal microbiome toward a health-associated composition in women with clinically diagnosed BV.

STUDY DESIGN: In a randomized, double-blind, placebo-controlled trial, vaginal swabs were collected from 152 women diagnosed with BV. Microbiome composition was assessed before and after a 6-day treatment with pHyph or a placebo-like comparator, using qPCR targeting 25 bacterial, 2 viral, and 8 eukaryotic species.

RESULTS: pHyph significantly increased the abundance of Lactobacillus iners, Lactobacillus gasseri and Lactobacillus jensenii after treatment, while decreasing the abundance of BV-associated species, such as Gardnerella vaginalis, BVAB2, and Fannyhessea vaginae (Wilcoxon signed rank test, P<.05). The growth-promoting effect on Lactobacillus was more pronounced in women who had detectable levels at baseline. Notably, a substantial number of participants in the pHyph group (n=33) transitioned to a Lactobacillus-dominated community state type (CST), compared to none in the comparator group.

CONCLUSIONS: pHyph supports BV resolution by promoting a Lactobacillus-dominated vaginal microbiome and reducing BV-associated species, offering a promising antibiotic-free alternative.},
}

@article {pmid41321569,
year = {2025},
author = {Xie, J and Wang, C and Zhao, Y and Li, X and Ma, G and Yang, K},
title = {Metabolomic and microbial diversity perspectives on Aspergillus oryzae culture-induced modifications in ovine feed utilization and rumen ecosystem.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1658361},
pmid = {41321569},
issn = {2297-1769},
abstract = {INTRODUCTION: Aspergillus oryzae culture (AOC) is widely used as a feed additive to enhance ruminant productivity and rumen function. However, the underlying mechanisms at the microbiome-metabolome interface remain poorly understood. This study aimed to elucidate how dietary AOC supplementation influences sheep production performance, rumen fermentation, microbial communities, and metabolomic profiles.

METHODS: Twelve rumen-fistulated sheep were randomly assigned to a control group (basal diet) and a trial group (basal diet + 1% AOC). The experiment lasted 30 days, during which production performance, nutrient digestibility, ruminal pH, volatile fatty acids (VFA), ammonia nitrogen, microbial diversity (16S rDNA sequencing), and metabolomic profiles (LC-MS) were systematically assessed.

RESULTS: AOC supplementation significantly increased average daily gain (ADG) and neutral detergent fiber (NDF) digestibility by 7.00% (p < 0.05), and improved nitrogen retention. Total VFA and acetate concentrations were elevated, with a stable ruminal pH. Microbiome analysis revealed an increased relative abundance of Succiniclasticum and beneficial fiber-degrading taxa. Metabolomic profiling identified upregulation of antioxidant metabolites (e.g., ginsenoside Rg3, lipoamide) and activation of key pathways such as phenylalanine metabolism and the TCA cycle, alongside downregulation of inflammatory markers.

DISCUSSION: AOC enhances sheep productivity and rumen health by modulating fibrolytic microbiota, promoting VFA synthesis, and activating antioxidant and energy metabolism pathways. These findings provide a theoretical basis for the use of AOC as a sustainable feed additive to improve ruminant production efficiency and welfare.},
}

@article {pmid41321522,
year = {2025},
author = {Cai, W and Xu, Y and Cheng, W and Xu, J and Chen, X and Fei, H and Chen, X and Wang, C and Mao, H},
title = {Multi-omics reveal beneficial effects of chrysanthemum stalks on growth performance and immune function in Hu sheep.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {23},
number = {},
pages = {44-61},
pmid = {41321522},
issn = {2405-6383},
abstract = {Chrysanthemum stalks (CS), a plant by-product, often face underutilization and resource wastage. This study aimed to explore the effects of partially replacing peanut vines (PV) in the diet with CS on the growth performance, rumen fermentation performance and microbiota, as well as the plasma physiology, biochemistry, and metabolism of Hu sheep. Twenty-seven 6-month-old male Hu sheep (weighing 39.4 ± 0.5 kg; mean ± SD) were randomly assigned to three groups: 1) basal diet (CON); 2) CS replaced 7.88% of PV (low substitution [LS]); and 3) CS replaced 15.57% of PV (high substitution [HS]). The feeding trial lasted for 91 d. Replacement of peanut vines with chrysanthemum stalks significantly increased dry matter intake in both LS and HS groups as compared to the CON group (P = 0.021; linear effect, P = 0.050), while average daily weight gain only increased significantly in the LS group (P = 0.020; quadratic P = 0.042). The concentrations of volatile fatty acids (VFAs) and ammonia nitrogen (NH3-N) were the highest in rumen of LS group (P < 0.05; quadratic effect, P < 0.05). The LS group also had the highest relative abundance of Prevotella (P = 0.011; quadratic P = 0.001). The rumen metabolomic analysis showed elevated levels of flavonoids, terpenoids, and amino acids in the LS group (P < 0.05). Additionally, the LS group exhibited significantly higher levels of total antioxidant capacity, immunoglobulin A, and immunoglobulin M (P < 0.05; quadratic P < 0.05), while tumor necrosis factor-α and interferon-γ levels were lower (P < 0.05; quadratic P < 0.05). The plasma metabolomic analysis revealed increases in phospholipids, amino acids, and indole derivatives in the LS group (P < 0.05). In general, CS improved the growth performance of Hu sheep by increasing VFA concentrations and promoting beneficial bacteria like Prevotella in the rumen. Additionally, flavonoids and terpenoids in CS were positively associated with immune response and antioxidant capacity. These beneficial effects were more pronounced in the LS group compared to the HS group, highlighting the potential of CS as a roughage substitute for improving sheep growth performance and immune function.},
}

@article {pmid41321514,
year = {2025},
author = {Liu, Z and Jiang, A and Kong, Z and Lv, X and Zhang, J and Wu, J and Zhou, C and Tan, Z},
title = {Multi-omics analysis reveals the mechanism of rosemary extract supplementation in increasing milk production in Sanhe dairy cows via the "rumen-serum-milk" metabolic pathway.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {23},
number = {},
pages = {396-414},
pmid = {41321514},
issn = {2405-6383},
abstract = {Rosemary extract (RE) has shown potential as a plant-derived feed additive, but its effects on Sanhe dairy cows are still unknown. In this study, 30 multiparous Sanhe dairy cows (days in milk 171 ± 17 days) with similar body condition were randomly divided into two groups: the RE group (n = 15) was fed the basal diet plus 20 g RE/d, and the CON group (n = 15) was fed only the basal diet. The experiment lasted for 57 days, including a one-week adaptation period. Compared with the CON group, milk yield (P = 0.022) increased significantly with RE supplementation, while milk fat (P = 0.071) also tended to increase. Milk urea nitrogen (P = 0.003) and serum urea nitrogen (P = 0.013) contents were significantly reduced in the RE group compared with the CON group. In rumen fermentation, the content of butyric acid (P = 0.035) in RE group was significantly increased, while valeric acid (P = 0.080) content had an increasing trend. In addition, RE supplementation improved the antioxidant capacity of Sanhe dairy cows by significantly increasing the serum total antioxidant capacity (P < 0.001), superoxide dismutase activity (P = 0.001), immunoglobulin A content (P < 0.001), and immunoglobulin G content (P = 0.005), while decreasing serum malondialdehyde content (P < 0.001), to improve immunity and also affect the composition of serum free amino acids. Metabolomic results showed that a total of 13 co-differential metabolites were identified in rumen and serum, including ursolic acid, a major component of RE, which was higher in both rumen and serum. The milk metabolome analysis identified glycerides, glycerophospholipids, and sphingolipids as the three lipid types that exhibited higher identification intensity in RE. Rumen metagenomic results showed that RE supplementation affected the composition of rumen microorganisms, and differential microbial Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses revealed that the RE group was significantly enriched in the fatty acid biosynthesis pathway and the glycerophospholipid metabolism pathway; two pathways related to lipid synthesis. By associating the genus-level differential microorganisms in the rumen with the "rumen-serum-milk" metabolome and mapping the correlation network, it was found that g_Sharpea, g_Tistlia, and g_Acetobacter, which were more abundant in RE, correlated with more differential metabolites and clustered in the same module. Among the 10 microbial biomarkers screened in the rumen, g_Acetobacter and g_Prevotella were more abundant in the RE, and Mantel's analysis showed that they correlated with rumen fermentation parameters and oxidative and immunological indicators in serum. These results reveal the regulatory mechanism of RE supplementation feeding to enhance milk production and improve milk quality by improving oxidative stress capacity and immunity and reducing nitrogen loss in Sanhe dairy cows, suggesting that RE has the potential as a feed additive for dairy cows.},
}

@article {pmid41321512,
year = {2025},
author = {Li, Y and Ko, K and Liu, X and Kačániová, M and Lee, Y and Zhang, G},
title = {Effects of inulin on growth performance and intestinal health of broilers by modulating intestinal microbiota and metabolome.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {23},
number = {},
pages = {257-270},
pmid = {41321512},
issn = {2405-6383},
abstract = {Inulin, a natural dietary fiber, confers multiple physiological benefits. However, the effects of inulin on the liver and intestinal health of broilers remain unclear. The study investigated the effects and mechanisms of inulin supplementation on hepatic and intestinal health of broilers. A total of 192 male broilers (821.15 ± 14.99 g) at 21 d of age were randomly allocated to four treatment groups, comprising eight replicates per group with six broilers each. The dietary treatments included: a control group (CON) receiving a basal diet and three treatment groups fed the basal diet supplemented with 0.5, 1.0, or 2.0 g/kg inulin (designated as INU-0.5, INU-1.0, and INU-2.0, respectively). Results indicated that dietary inulin supplementation elicited a quadratic response in final body weight (FBW, P = 0.032). Inulin supplementation produced linear improvements in average daily gain (ADG, P = 0.044) alongside quadratic reductions in both average daily feed intake (ADFI) and feed-to-gain ratio (F/G ratio) (P < 0.001). Notably, inulin supplementation linearly decreased malondialdehyde (MDA) levels (P < 0.001) while significantly enhancing superoxide dismutase (SOD) activity (P < 0.001). Furthermore, inulin supplementation demonstrated dose-dependent effects on lipid metabolism, including a linear reduction in abdominal fat deposition (P < 0.001), decreased hepatic and serum concentrations of total cholesterol (TCHO, both P < 0.001) and triglycerides (TG, P < 0.001 and P = 0.001, respectively), and reduced serum levels of both high-density lipoprotein (HDL, P = 0.010) and low-density lipoprotein (LDL, P < 0.001) (P < 0.01). Parallel improvements in intestinal barrier function were observed, with linear increases in jejunal expression of tight junction proteins (claudin-5, occludin, and zonula occludens-1 [ZO-1]), mucin 2 (MUC2), and diamine oxidase (DAO) (P < 0.001). Additionally, inulin supplementation selectively increased the abundances of key microbes, including Bacteroides, Lactobacillus, and Akkermansia, while decreased the abundances of Alistipes, Odoribacte, Parabacteroides, Rikenella, and Erysipelatoclostridium (P < 0.001). These microbial shifts were associated with modulation of key metabolic pathways, including taurine and hypotaurine metabolism, purine metabolism, arginine and proline, and phenylalanine metabolism. Collectively, these findings demonstrate that inulin supplementation enhances broiler productivity while improving both intestinal and hepatic health (P < 0.05) through microbiota-mediated metabolic regulation. Therefore, dietary inulin supplementation would be a recommendable nutritional strategy to optimize production efficiency in commercial broiler industry.},
}

@article {pmid41321511,
year = {2025},
author = {Pi, Y and Mu, C and Gao, K and Liu, Z and Peng, Y and Yu, K and Su, Y and Zhu, W},
title = {Increasing carbohydrates or nitrogenous compounds by cecal infusion leads to an opposite influence on colonic microbiota and host metabolism in a pig model.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {23},
number = {},
pages = {62-77},
pmid = {41321511},
issn = {2405-6383},
abstract = {Gut microbes, particularly those in the hindgut, play an important role in fermenting undigested nutrients (carbohydrates and proteins) and in regulating host metabolism via the gut-liver metabolic axis. However, the effects of variations in the ratio of carbohydrates to proteins on host metabolism remain largely unknown. In this study, we investigated the response of large intestinal microbiota and host metabolism to changes in nutrient substrate availability by infusing corn starch or casein hydrolysate via cecal cannulas. Twenty-four growing pigs with cecal cannulas were randomly divided into three groups (n = 8): a control group infused with saline; a starch group infused with corn starch; and a casein group infused with casein hydrolysate (50 g/d) dissolved in saline. The infusion was performed daily for 19 d. Compared with the control, starch infusion significantly increased the relative abundances of Bifidobacterium, Bacteroidales S24-7 group and Megasphaera (P < 0.05), while decreasing Anaerovibrio, Campylobacter and Veillonella (P < 0.05). Conversely, casein hydrolysate infusion significantly increased Streptococcus, Desulfovibrio and Mogibacterium (P < 0.05), while decreasing Coprococcus and Ruminococcus at the genus level (P < 0.05). Starch infusion increased short-chain fatty acid (SCFA) concentrations (P = 0.001), whereas casein hydrolysate infusion reduced them (P = 0.001); these effects were observed in both colonic digesta and liver. Additionally, serum metabolomics and liver gene expression analysis revealed that host metabolic states were significantly altered in different ways following starch and casein hydrolysate infusion (P < 0.05). Starch infusion enhanced host energy metabolism, gluconeogenesis and lipid metabolism by increasing concentrations of tricarboxylic acid (TCA) cycle-related metabolites (e.g., succinic acid, oxaloacetic acid, and L-malic acid) and fatty acid (FA) synthesis (e.g., D-glyceric acid, stearic acid, and palmitic acid) (P < 0.05), alongside upregulation of FA synthase (FAS), stearoyl-CoA desaturase (SCD), acetyl-CoA carboxylase (ACC), phosphoenolpyruvate carboxykinase 1 (PCK1) and pyruvate kinase (PK) gene expression (P < 0.05). In contrast, casein hydrolysate infusion enhanced glycolysis and reduced FA synthesis by increasing glucose-6-phosphate, L-lactic acid, glycerol, glycolic acid, etc. (P < 0.05), in parallel with upregulation of acyl-CoA oxidase 1 (ACOX-1), peroxisome proliferator-activated receptors α (PPAR-α), carnitine palmitoyltransferase-1α (CPT-1α) and PK gene expressions in the liver (P < 0.05). Correlation result demonstrated a strong association between altered gut microbiota and several serum metabolites (P < 0.05). In summary, these results indicate that increasing carbohydrate or nitrogenous compound levels in the large intestine can distinctly alter microbiota composition, thereby influencing host metabolism. These findings provide novel insights into the crosstalk between the large intestinal microbiome and host metabolism.},
}

@article {pmid41321425,
year = {2026},
author = {Hartsgrove, CE and Walker, GS and Silva, KD and Nunez, K and Alejos, K and Joseph, M and Wright, JR and McMullen, B and Lamendella, R and Maeng, LY},
title = {Acute 17β-Estradiol Administration Enhances Fear Extinction Memory and Alters Gut Microbiota in Female Rats.},
journal = {Biological psychiatry global open science},
volume = {6},
number = {1},
pages = {100620},
pmid = {41321425},
issn = {2667-1743},
abstract = {BACKGROUND: Previous studies have shown that fear extinction memory and the gut microbiome are impacted by ovarian hormones. Elevated 17β-estradiol (E2) levels during fear extinction learning have been shown to enhance fear extinction recall 24 hours later. In this study, we concurrently examined the long-term maintenance of this facilitation and the role of the gut microbiome as a potential mediator.

METHODS: Naturally cycling adult female Sprague Dawley rats underwent an auditory-cued fear conditioning/extinction paradigm, during which the estrous cycle was tracked and fecal samples were collected. Habituation and conditioning took place when the rats were in estrus on day 1. On day 2, rats were administered either a sesame oil vehicle (n = 24) or E2 (15 μg/kg) (n = 25) before extinction training. Recent recall took place 24 hours after extinction training, and remote recall took place 1 to 2 weeks after extinction training (vehicle n = 13, E2 n = 12).

RESULTS: E2-treated rats showed significantly lower freezing behavior compared with vehicle-treated rats during recent recall, but not remote recall. Gut bacterial analysis using 16S ribosomal RNA sequencing revealed unique enrichment of estrogen-regulating and anxiety-related bacterial families during remote recall.

CONCLUSIONS: The current data suggest that E2-enhanced fear extinction consolidation may be linked to alterations in gut microbiome composition. These findings may reveal a novel potential target for anxiety and other fear-based psychiatric disorders.},
}

@article {pmid41321404,
year = {2025},
author = {Shalbaf, N and Sadeghi, S and Homaee, S and Saberian, F},
title = {Probiotics, prebiotics, synbiotics, and FMT for glycemic control: A systematic review of clinical efficacy and mechanistic readouts in type 2 diabetes and related dysglycemia.},
journal = {Metabolism open},
volume = {28},
number = {},
pages = {100419},
pmid = {41321404},
issn = {2589-9368},
abstract = {OBJECTIVE: To systematically evaluate the clinical efficacy of probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT) on glycemic control in adults with type 2 diabetes (T2D) and related dysglycemia, and to synthesize associated mechanistic changes in microbial metabolites and composition.

METHODS: A systematic review was conducted following PRISMA 2020 guidelines. PubMed/MEDLINE, Scopus, and Web of Science were searched from inception through August 2025 for randomized controlled trials (RCTs) in adults with T2D, prediabetes, or metabolic syndrome. Interventions included probiotics, prebiotics, synbiotics, or FMT compared to control. Outcomes were glycemic indices (e.g., HbA1c, HOMA-IR) and mechanistic biomarkers (e.g., SCFAs, bile acids). Risk of bias was assessed using the Cochrane RoB 2 tool. A narrative synthesis was performed.

RESULTS: Thirty studies were included. Multi-strain probiotics, prebiotics, and synbiotics yielded modest but significant improvements in HbA1c (≈-0.2 to -0.4 %), fasting glucose, and HOMA-IR, particularly with durations ≥12 weeks. These benefits were linked to mechanistic shifts, including increased circulating butyrate and ursodeoxycholate, enrichment of SCFA-producing taxa, and reduced endotoxemia. Efficacy was moderated by concomitant medications: metformin use was synergistic, while sulfonylureas attenuated effects. FMT consistently improved clamp-measured insulin sensitivity in insulin-resistant phenotypes, but its effects on HbA1c were less consistent and donor-dependent.

CONCLUSION: Microbiome-targeted interventions, especially multi-strain probiotics and substrate-matched synbiotics, are effective adjuncts for improving glycemic control, with effects mediated through microbial metabolite production. FMT primarily modulates insulin sensitivity. Clinical outcomes are context-dependent, influenced by intervention design, duration, and pharmacomicrobiomic interactions.},
}

@article {pmid41321285,
year = {2025},
author = {Blanton, MB and Napier, EG and Keen, KE and Stuart, EV and Cinco, IR and Hemati, H and Bruntz, RC and Khadka, R and Grant, KA and Messaoudi, I},
title = {Short-Term Alcohol Consumption Is Sufficient to Disrupt Microbial Communities and the Intestinal and Circulating Metabolites in a Non-Human Primate Model.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {23},
pages = {e71280},
doi = {10.1096/fj.202503336R},
pmid = {41321285},
issn = {1530-6860},
support = {1R01AA028735-01//HHS | NIH | National Institute on Alcohol Abuse and Alcoholism (NIAAA)/ ; U01AA013510//HHS | NIH | National Institute on Alcohol Abuse and Alcoholism (NIAAA)/ ; R24 AA019431/AA/NIAAA NIH HHS/United States ; F31AA031600-01A1//HHS | NIH | National Institute on Alcohol Abuse and Alcoholism (NIAAA)/ ; T32 AA027488/AA/NIAAA NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Macaca mulatta ; *Alcohol Drinking/adverse effects/metabolism ; Male ; *Dysbiosis/microbiology/metabolism ; *Intestines/microbiology ; *Ethanol ; Disease Models, Animal ; },
abstract = {The gut microbiome is a complex and dynamic community of microorganisms that play a crucial role in maintaining host health and facilitating inter-organ communication. The microbiome is altered by the exposome, a phenomenon known as dysbiosis. Alcohol misuse can disrupt the gut microbial community in a dose- and duration-dependent manner. Previous studies showed that chronic alcohol misuse can induce intestinal hyperpermeability and significantly shift microbial communities. However, these data were obtained primarily from cross-sectional clinical and rodent-based studies following long-term chronic alcohol consumption. Clinical studies often utilize samples from patients with alcoholic liver disease and are confounded by variability in factors that can modulate the microbiome and reliance on self-reported data. The intestinal cellular and microbial composition of rodent models differs significantly from that of humans, limiting the clinical translation of those findings. Therefore, the impact of alcohol misuse on the gut microbial communities and their metabolic implications remains poorly understood. Since rhesus macaques share significant genetic/physiological traits, as well as gut microbial communities, with humans, we assessed the impact of 6 months of voluntary daily alcohol consumption on the gut microbiome and its implications for the circulating and intestinal metabolomes. We report that short-term drinking induces dynamic changes in the abundance of short-chain fatty acid producers and increases microbes associated with the negative regulation of inflammation. Finally, altered fatty- and amino-acid metabolite signatures were observed. Taken together, these data enhance our understanding of the longitudinal implications of alcohol use.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Macaca mulatta
*Alcohol Drinking/adverse effects/metabolism
Male
*Dysbiosis/microbiology/metabolism
*Intestines/microbiology
*Ethanol
Disease Models, Animal

@article {pmid41321251,
year = {2025},
author = {Sharma, N and Roy, S},
title = {Dysbiosis and Dyslipidemia: Unraveling the Microbiome's Role in Lipid Metabolism and Therapeutic Potential.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {12},
pages = {e70100},
doi = {10.1111/apm.70100},
pmid = {41321251},
issn = {1600-0463},
mesh = {Humans ; *Dyslipidemias/microbiology/therapy/metabolism ; *Dysbiosis/microbiology/metabolism/therapy/complications ; *Gastrointestinal Microbiome ; *Lipid Metabolism ; Probiotics/therapeutic use ; Animals ; Prebiotics ; Cardiovascular Diseases ; },
abstract = {Dysbiosis, an imbalance in the gut microbiota, has emerged as a critical factor in the development of various metabolic diseases, including dyslipidemia. Dyslipidemia, a multifactorial disorder influenced by both genetic and environmental factors, is a significant risk factor for cardiovascular diseases (CVD), such as coronary artery disease (CAD) and stroke. The gut microbiota plays a pivotal role in maintaining lipid homeostasis, interacting with the host's immune, metabolic, and endocrine systems. Recent studies have highlighted the involvement of microbiota-derived metabolites, such as bile acids, lipopolysaccharides, and short-chain fatty acids (SCFAs), in modulating lipid levels and regulating hyperlipidemia. Understanding these complex microbiome-host interactions opens new avenues for therapeutic interventions aimed at correcting lipid imbalances and restoring microbial balance. Approaches such as probiotics, prebiotics, synbiotics, and dietary modifications hold promise in managing dyslipidemia and preventing associated cardiovascular diseases. As research continues to unravel these connections, the microbiome is increasingly recognized as a promising target for therapeutic strategies in dyslipidemia.},
}

Humans
*Dyslipidemias/microbiology/therapy/metabolism
*Dysbiosis/microbiology/metabolism/therapy/complications
*Gastrointestinal Microbiome
*Lipid Metabolism
Probiotics/therapeutic use
Animals
Prebiotics
Cardiovascular Diseases

@article {pmid41320950,
year = {2025},
author = {Reljic, D and Hermann, HJ and Dieterich, W and Neurath, MF and Zopf, Y},
title = {Exercise improves gut microbial metabolites in an intensity-dependent manner: a pooled analysis of randomized controlled trials.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2579354},
doi = {10.1080/19490976.2025.2579354},
pmid = {41320950},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Middle Aged ; Fatty Acids, Volatile/metabolism ; Female ; Feces/chemistry/microbiology ; *Metabolic Syndrome/microbiology/therapy/metabolism ; *Obesity/microbiology/therapy/metabolism ; Randomized Controlled Trials as Topic ; *Exercise/physiology ; Adult ; Bacteria/metabolism/classification/isolation & purification/genetics ; Resistance Training ; Cardiorespiratory Fitness ; },
abstract = {BACKGROUND: Obesity and the metabolic syndrome (MetS) are global health challenges. The gut microbiome, particularly its fermentation products, short-chain fatty acids (SCFAs), is increasingly recognized as a key modulator of cardiometabolic health. Growing evidence suggests that exercise may play a critical role in SCFA production. This study presents a pooled analysis of data from three randomized controlled trials to examine the effects of low-volume high-intensity (HIGH-EX) versus moderate-intensity (MOD-EX) interval training, each combined with single-set resistance training, on SCFAs and cardiometabolic health in obese MetS patients.

METHODS: Data from 113 patients allocated to 12 weeks of HIGH-EX, MOD-EX, or a control group (CON) were analyzed. Fecal SCFA concentrations, cardiorespiratory fitness (VO2max), muscle strength, inflammation (hsCRP), and MetS severity (MetS z-score) were assessed pre- and post-intervention. Exercise intensity was monitored via regular blood lactate measurements during interval training.

RESULTS: HIGH-EX and MOD-EX improved VO2max (+4.2 and +2.7 mL/kg/min), strength across major muscle groups (+19 to 29%), hsCRP (-2.2 and -1.3 mg/L), and MetS z-score (-1.1 and -0.5 units). Only HIGH-EX significantly increased total fecal SCFAs (+30%), including acetate (+27%), propionate (+28%), and butyrate (+43%). Mean blood lactate concentrations during training were strongly correlated with SCFA increases (r = 0.68, p < 0.001). No changes were observed in CON.

CONCLUSIONS: Low-volume combined interval and resistance training improved fitness and metabolic health at both moderate and higher intensities. However, only HIGH-EX enhanced SCFA production, potentially associated with lactate-mediated microbial adaptations. Exercise intensity may thus be a key determinant of gut-metabolic benefits.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
Middle Aged
Fatty Acids, Volatile/metabolism
Female
Feces/chemistry/microbiology
*Metabolic Syndrome/microbiology/therapy/metabolism
*Obesity/microbiology/therapy/metabolism
Randomized Controlled Trials as Topic
*Exercise/physiology
Adult
Bacteria/metabolism/classification/isolation & purification/genetics
Resistance Training
Cardiorespiratory Fitness

@article {pmid41320781,
year = {2025},
author = {Shapira, E and Voinsky, I and Klin, H and Gurwitz, D},
title = {Butyrate-Mediated Upregulation of Insulin Pathway Gene Expression Suggests Potential Antidiabetic Effects.},
journal = {Drug development research},
volume = {86},
number = {8},
pages = {e70203},
doi = {10.1002/ddr.70203},
pmid = {41320781},
issn = {1098-2299},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Humans ; Up-Regulation/drug effects ; *Insulin/metabolism/genetics ; *Hypoglycemic Agents/pharmacology ; *Diabetes Mellitus, Type 2/drug therapy/genetics/metabolism ; Cell Line ; Insulin Resistance/genetics ; Signal Transduction/drug effects/genetics ; *Butyric Acid/pharmacology ; *Butyrates/pharmacology ; Adult ; },
abstract = {Type 2 diabetes (T2D) is a major cause of morbidity in developed countries and involves insulin resistance, a failure to correctly respond to insulin. Numerous studies in rodent T2D models suggested that the short-chain fatty acid butyrate, produced by gut microbiota species through fermentation of dietary fibers, improves T2D symptoms. Here, we explored the potential antidiabetic effects of butyrate by measuring the transcription of selected T2D-implicated genes in human B lymphocyte-derived lymphoblastoid cell lines (LCLs) from 17 unrelated adult healthy donors. Human LCLs were cultured with and without sodium butyrate (1 mM for 48 h), followed by RNA extraction and real-time PCR analysis of the selected T2D-related genes. Butyrate significantly upregulated the expression of MT2A, RRAGD, IGF1R, OXTR, and INSR, while no changes were observed in the expression of other selected genes implicated in insulin signaling. Our findings, which should be considered preliminary until demonstrated by in vivo T2D animal models, suggest that butyrate is a potential modulator of metabolic pathways relevant to insulin resistance. Future studies should explore the tentative therapeutic potential of butyrate and its upregulated genes using proteomics and metabolomics in relevant tissues of T2D animal models, possibly followed by controlled clinical trials.},
}

Humans
Up-Regulation/drug effects
*Insulin/metabolism/genetics
*Hypoglycemic Agents/pharmacology
*Diabetes Mellitus, Type 2/drug therapy/genetics/metabolism
Cell Line
Insulin Resistance/genetics
Signal Transduction/drug effects/genetics
*Butyric Acid/pharmacology
*Butyrates/pharmacology
Adult

@article {pmid41320718,
year = {2025},
author = {Liu, Y and Zhou, N and Liu, J and Li, G and Chen, R and Li, G and Li, Y},
title = {The Impact of Fluoride Varnish Application on the Supragingival Plaque Microbiome in Preschoolers: A Dynamic Study.},
journal = {Current microbiology},
volume = {83},
number = {1},
pages = {50},
pmid = {41320718},
issn = {1432-0991},
support = {202401AU070088//Science and Technology Support Program of Jiangsu Province/ ; XDYC-YLWS-2023-0047//Xingdian Talent Support Plan of Yunnan Province-Medical and Health Talents Special Project/ ; D2019-007//Academic Leader Project of Yunnan Province/ ; 2019-35//Famous Doc tor Special Project of Yunnan Province/ ; 202201AY070001-174//the Joint Fund of Yunnan Provincial Science and Technology Office and Kunming Medical University/ ; 202301AY070001-046//the Joint Fund of Yunnan Provincial Science and Technology Office and Kunming Medical University/ ; 202501AY070001-052//the Joint Fund of Yunnan Provincial Science and Technology Office and Kunming Medical University/ ; },
mesh = {Humans ; *Dental Plaque/microbiology ; Child, Preschool ; *Fluorides, Topical/administration & dosage/pharmacology ; *Microbiota/drug effects ; *Bacteria/classification/genetics/drug effects/isolation & purification ; Male ; Female ; Dental Caries/prevention & control/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Fluoride varnish application is used in many studies as a minimally invasive technique to prevent caries. Notably, oral microorganisms play a crucial role in the incidence and progression of tooth caries. However, the effect of fluoride varnish application on the dynamic microbial alterations that occur in dental plaques remains unclear. In this study, we investigated the impact of fluoride varnish application on the supragingival microbial composition and structure in preschoolers. We enrolled 27 preschoolers and collected supragingival plaque samples from the same sites at multiple time points: baseline (0 h, F0 group), 24 h (F1 group), 1 month (F2 group), 3 months (F3 group), and 6 months (F4 group). To unravel the changes in microbial composition and structure after fluoride varnish application, all specimens underwent high-throughput sequencing of the 16 S rRNA gene. The Shannon and Simpson indices showed no significant differences across groups (P > 0.05). Principal co-ordinates analysis (PCoA) revealed significant differences in microbial community structures across all time points (P < 0.001, R[2] = 0.44), with F0 and F1 groups showing similarity. Significant variations in bacterial composition were observed among eight strains, including Neisseria mucosa and Corynebacterium matruchotii (P < 0.05). This study found that Duraphat fluoride varnish application effectively modifies the composition and structural characteristics of supragingival plaque in preschoolers, enhancing anti-caries properties.},
}

Humans
*Dental Plaque/microbiology
Child, Preschool
*Fluorides, Topical/administration & dosage/pharmacology
*Microbiota/drug effects
*Bacteria/classification/genetics/drug effects/isolation & purification
Male
Female
Dental Caries/prevention & control/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid41320670,
year = {2025},
author = {Chen, H and Zhang, X and Li, S and Fang, Y and Han, Y and Jing, X},
title = {Multi-Omics Analysis Reveals OBSCN as a Key Modulator of Tumor Microenvironment, Microbial Signatures and Clinical Outcomes in Gastric Cancer.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70186},
doi = {10.1002/mbo3.70186},
pmid = {41320670},
issn = {2045-8827},
support = {//This work was supported by Scientific Research Project of Weifang Health Commission (No. WFWSJK-2023-268)./ ; },
mesh = {Humans ; *Stomach Neoplasms/genetics/microbiology/therapy/pathology ; *Tumor Microenvironment/genetics ; Mutation ; *Cytoskeletal Proteins/genetics/metabolism ; Immunotherapy ; MicroRNAs/genetics ; Biomarkers, Tumor/genetics ; Multiomics ; },
abstract = {Emerging evidence suggests that OBSCN, a giant cytoskeletal protein gene, plays multifaceted roles in cancer progression, yet its impact on gastric cancer (GC) remains poorly understood. Through integrative analysis of multi-omics datasets, we observe a close relationship between OBSCN expression and outcome of immunotherapy. Besides, elevated expression of OBSCN strongly associated with adverse disease free survival (DFS). Tumor-resident microbes, such as Fusobacterium, can impact the expression of microRNAs (miRNAs) targeting OBSCN. In terms of genomic alterations, mutational status of OBSCN is substantially associated with the alpha- and beta-diversity of intratumoral microbiome and patients with mutated OBSCN exhibit elevated higher tumor mutational burden (TMB) and better response to immunotherapy. Furthermore, machine learning models based on the OBSCN mutation-related gene signatures (OMRGS) achieve outstanding performance in prediction of response to immune checkpoint inhibitors. In summary, our findings position OBSCN as a novel molecular nexus linking genomic alterations, intratumoral microbiome dysbiosis, and immune infiltration in GC, providing a rationale for future biomarker-driven therapeutic strategies.},
}

Humans
*Stomach Neoplasms/genetics/microbiology/therapy/pathology
*Tumor Microenvironment/genetics
Mutation
*Cytoskeletal Proteins/genetics/metabolism
Immunotherapy
MicroRNAs/genetics
Biomarkers, Tumor/genetics
Multiomics

@article {pmid41320596,
year = {2025},
author = {Klironomos, J and Zhang, J and Wang, G},
title = {From feedbacks to functional teams in the rhizosphere.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.11.013},
pmid = {41320596},
issn = {1878-4380},
abstract = {Johnson and Marín's paper presents functional team selection (FTS) as a major conceptual advance in plant-microbiome ecology. FTS explains how limiting resources and/or stress selects cooperative microbial teams that promote plant adaptation, integrating ecological feedback and evolutionary selection to predict when and where resilient plant-microbiome partnerships will arise.},
}

@article {pmid41320400,
year = {2026},
author = {Karagöz, MF and Ünaldı, BÖ and Buhurcu, CA and Şen, N and Aydoğdu, GS and Demirci, KŞ and Gündüz, ZG and Güler, MS and Ağagündüz, D and Coreta-Gomes, F},
title = {Seaweed polysaccharides and their potential health effects via gut microbiota modulation.},
journal = {Carbohydrate polymers},
volume = {373},
number = {},
pages = {124621},
doi = {10.1016/j.carbpol.2025.124621},
pmid = {41320400},
issn = {1879-1344},
mesh = {*Seaweed/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Polysaccharides/pharmacology/chemistry ; Humans ; Fermentation ; Bacteroidetes/drug effects ; Carrageenan/chemistry/pharmacology ; Fatty Acids, Volatile/metabolism ; Molecular Weight ; Firmicutes/drug effects ; Alginates/chemistry/pharmacology ; },
abstract = {Macroalgae, commonly known as seaweeds, are a valuable source of polysaccharides known to modulate gut microbiota. In this work, the impact of polysaccharide structural features on gut microbiota was explored. The low molecular weight algae polysaccharides showed better degradation by gut bacteria. Moreover, the content of sulfate and carboxylic groups seem to promote high fermentation, triggering an increase in gut microbiota health. The effect of ramification degree of algae polysaccharides on fermentability is still unclear. Agar polysaccharides with low molecular weight and a higher degree of sulfation have been shown to produce higher amounts of SCFA, and decrease in Firmicutes/Bacteroidetes ratio. An increase of sulfation degree of porphyran showed to increase the total SCFA production and a decrease on the ratio of butyric to propionic acid. Carrageenan's molecular weight does not seem to affect SCFA production, and the effect of sulfation degree is not clear. The consumption of these polysaccharides was shown to decrease the Firmicutes/Bacteroidetes ratio. Fucoidans of low molecular weight seem to promote a lower Firmicutes/Bacteroidetes ratio. Alginate consumption both of high and low molecular weight has been shown to increase Bacteroidetes. Low molecular weight laminarans are highly fermented and significantly increase the production of SCFA. Ulvan and sulfated rhamnan polysaccharides have been shown to increase the production of SCFA, although microbiota modulation data are still undisclosed. Overall, seaweed polysaccharides have shown several health benefits, which have been related with gut microbiota modulation.},
}

*Seaweed/chemistry
*Gastrointestinal Microbiome/drug effects
*Polysaccharides/pharmacology/chemistry
Humans
Fermentation
Bacteroidetes/drug effects
Carrageenan/chemistry/pharmacology
Fatty Acids, Volatile/metabolism
Molecular Weight
Firmicutes/drug effects
Alginates/chemistry/pharmacology

@article {pmid41320393,
year = {2026},
author = {Wang, S and De Paepe, K and Onyango, SO and Zhang, B and Huang, Q and Wang, S and Van de Wiele, T},
title = {Starch-entrapped microspheres selectively promote propionate or butyrate production through individual-specific modulation of the human fecal microbiome.},
journal = {Carbohydrate polymers},
volume = {373},
number = {},
pages = {124614},
doi = {10.1016/j.carbpol.2025.124614},
pmid = {41320393},
issn = {1879-1344},
mesh = {Humans ; *Starch/chemistry/pharmacology ; *Feces/microbiology ; *Microspheres ; Prebiotics ; *Butyrates/metabolism ; *Propionates/metabolism ; *Gastrointestinal Microbiome/drug effects ; Adult ; Male ; Zea mays/chemistry ; Female ; Inulin/chemistry ; Fermentation ; Young Adult ; },
abstract = {Starch microspheres encapsulated with chitosan synergistically and beneficially modulate the microbiota composition and metabolic activity of a pooled fecal slurry compared to starch, suggesting a superior prebiotic potential. Interindividual differences in prebiotic potential are, however, unexplored. Therefore, we incubated starch-entrapped microspheres (MS), high amylose maize starch (HAMS) and the reference prebiotic inulin with the separate fecal microbiota derived from six healthy individuals. The variation in microbial community composition was largely driven by inter-individual variability (effect size of 71.7 %). Despite the inter-individual variability, the different prebiotic substrates significantly affected the microbiota composition (effect size of 9.5 %) and metabolic activity over the course of fermentation. MS delayed the fermentation and reduced the gas production and acidification in all donors compared to HAMS and inulin. Furthermore, compared to HAMS, MS more effectively promoted propionate or butyrate production in a donor-dependent manner. MS increased butyrate levels with 0.1 ± 0.72 mM per unit of starch across all donors. Additional, MS increased the propionate production with 0.52 ± 0.71 mM per unit of starch in donors 1, 2, 4, 6. The donor-specific propiogenic and butyrogenic effects of MS were linked to the enrichment of Bacteroides and Agathobacter species. Our findings confirm the superior prebiotic effect of MS and provide directions for the design and manufacture of starch-based functional foods to enhance gut health.},
}

Humans
*Starch/chemistry/pharmacology
*Feces/microbiology
*Microspheres
Prebiotics
*Butyrates/metabolism
*Propionates/metabolism
*Gastrointestinal Microbiome/drug effects
Adult
Male
Zea mays/chemistry
Female
Inulin/chemistry
Fermentation
Young Adult

@article {pmid41320368,
year = {2026},
author = {Li, S and Deng, R and Sang, J and Zhu, Y and Ma, C and Nan, W and Wang, T and Si, H and Li, Z},
title = {Integrated microbial and metabolic coordination orchestrates antler growth induced by guar gum and xylo-oligosaccharides.},
journal = {Carbohydrate polymers},
volume = {373},
number = {},
pages = {124586},
doi = {10.1016/j.carbpol.2025.124586},
pmid = {41320368},
issn = {1879-1344},
mesh = {Animals ; *Mannans/pharmacology/chemistry ; *Galactans/pharmacology/chemistry ; *Plant Gums/pharmacology/chemistry ; *Antlers/growth & development/drug effects/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Oligosaccharides/pharmacology/chemistry ; Osteogenesis/drug effects ; Bile Acids and Salts/metabolism ; Glucuronates ; },
abstract = {Antlers are a unique mammalian bone organ characterized by rapid growth, a process critically dependent on nutrient availability and the gastrointestinal tract microbiome. Polysaccharides and oligosaccharides shape microbiome output, but their roles in antler development remain unclear. Here, the strongest short-chain fatty acid effect was found with guar gum (GG) and xylo-oligosaccharides, which altered the rumen microbiome in vitro incubations with six polysaccharides and oligosaccharides. GG enriched Lachnospiraceae and Oscillospiraceae, and glycoside hydrolase families, enhancing butyrate biosynthesis and amino acid catabolism, while xylo-oligosaccharides selectively enriched Selenomonadaceae, supporting vitamin and fatty acid biosynthesis in vivo in the rumen. GG increased the fecal microbiome involved in bile acid deconjugation and dihydroxylation. Targeted metabolomics demonstrated that GG elevated the circulating levels of bile acids (chenodeoxycholic acid, deoxycholic acid, taurohyodeoxycholic acid) and osteogenic factors (IGF-1, BMP2, FGF2), and resulted in free fatty acid changes in the serum. Transcriptomics and RT-PCR revealed activation of angiogenic pathways in reserve mesenchyme and osteogenic signaling in mineralized cartilage of antlers. In vitro assays demonstrated that taurohyodeoxycholic acid significantly promoted osteogenic differentiation of mesenchymal cells. Our results revealed the distinct microbial adaptations of specific carbohydrates and elucidated a "GIT-antler" axis intervention for enhancing bone growth in mammals.},
}

Animals
*Mannans/pharmacology/chemistry
*Galactans/pharmacology/chemistry
*Plant Gums/pharmacology/chemistry
*Antlers/growth & development/drug effects/metabolism
*Gastrointestinal Microbiome/drug effects
*Oligosaccharides/pharmacology/chemistry
Osteogenesis/drug effects
Bile Acids and Salts/metabolism
Glucuronates

@article {pmid41320317,
year = {2025},
author = {Kushima, H and Ishii, H and Umeyama, T and Kinoshita, Y and Fujita, M and Tsunoda, T and Makimura, K and Miyazaki, Y},
title = {The Lung Mycobiome in Idiopathic Interstitial Pneumonia, Collagen Tissue Disease-related Interstitial Lung Disease, and Sarcoidosis.},
journal = {Medical mycology journal},
volume = {66},
number = {4},
pages = {177-184},
doi = {10.3314/mmj.25-00016},
pmid = {41320317},
issn = {2186-165X},
mesh = {Humans ; Male ; Female ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Mycobiome ; *Lung Diseases, Interstitial/microbiology ; *Lung/microbiology ; DNA, Fungal/genetics ; *Idiopathic Interstitial Pneumonias/microbiology ; Adult ; *Sarcoidosis/microbiology ; *Fungi/classification/genetics/isolation & purification ; DNA, Ribosomal Spacer/genetics/chemistry ; Sequence Analysis, DNA ; },
abstract = {Dysbiosis of the lung microbiome may be associated with the development and progression of respiratory diseases. As fungal spores invade the lungs more easily than bacteria, it seems likely that fungi colonizing the lungs are also involved in respiratory diseases. In this study, we investigated the relationship between fungal flora (mycobiome) and diffuse lung disease. Of the 185 patients who underwent bronchoalveolar lavage (BAL) during the diagnostic process, 42 with diffuse lung disease were selected for a mycobacterial analysis of BAL fluid. Twenty patients with idiopathic interstitial pneumonia (IIP), 8 with collagen tissue disease-related interstitial lung disease (CTD-ILD), 8 with sarcoidosis, and 6 with other diseases were included. Fungal DNA was extracted, and internal transcribed spacer 2 (ITS2) regions were sequenced. Of the 42 patients, 29 had polymerase chain reaction amplification products in the ITS2 region. Significant differences in alpha diversity (observed species, Shannon, and Simpson indices) were found between the CTD-ILD and sarcoidosis groups, and between the IIP and sarcoidosis groups. A comparison of the mycobiomes of individual patients (beta diversity) showed that the clustering patterns differed among the groups. In particular, BAL fluid samples from patients with sarcoidosis showed a clear clustering pattern of mycobacterial composition. Our results may lead to significant advances in our understanding of the etiology of these diseases.},
}

Humans
Male
Female
Middle Aged
Bronchoalveolar Lavage Fluid/microbiology
Aged
*Mycobiome
*Lung Diseases, Interstitial/microbiology
*Lung/microbiology
DNA, Fungal/genetics
*Idiopathic Interstitial Pneumonias/microbiology
Adult
*Sarcoidosis/microbiology
*Fungi/classification/genetics/isolation & purification
DNA, Ribosomal Spacer/genetics/chemistry
Sequence Analysis, DNA

@article {pmid41320171,
year = {2026},
author = {Ying, F and Shao, W and Li, L and Cao, X and Xu, X and Tao, Y},
title = {Banxia Xiexin Decoction Ameliorates Ulcerative Colitis via a Flora-Metabolite-Inflammation Axis Through Integrated Metabolomic and Microbiome Analysis.},
journal = {Biomedical chromatography : BMC},
volume = {40},
number = {1},
pages = {e70275},
doi = {10.1002/bmc.70275},
pmid = {41320171},
issn = {1099-0801},
support = {2023-4-282//Jinhua Science and Technology Project/ ; },
mesh = {Animals ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Colitis, Ulcerative/metabolism/drug therapy/microbiology ; *Gastrointestinal Microbiome/drug effects ; Mice ; Metabolomics/methods ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; *Metabolome/drug effects ; Cytokines/metabolism ; Inflammation/metabolism/drug therapy ; Colon/drug effects ; },
abstract = {Banxia Xiexin Decoction (BXD), a classic traditional Chinese medicine formula traditionally used for gastrointestinal disorders, has demonstrated considerable therapeutic potential in ulcerative colitis (UC). Yet, its mechanism of action remains incompletely elucidated. In this study, we applied an integrated strategy incorporating UPLC-Q-TOF/MS-based plasma metabolomics and gut microbiome analysis to explore the anti-UC effects of BXD. In a DSS-induced murine model of UC, BXD treatment mitigated colonic inflammation, as evidenced by reduced levels of pro-inflammatory cytokines (IL-1β, IL-6, and TNF-α), repaired intestinal barrier integrity, and restored metabolic homeostasis via regulation of tryptophan and nitrogen metabolism. Notably, BXD promoted the production of microbially derived tryptophan metabolites, including indole-3-propionic acid (IPA) and indole-3-carboxaldehyde (IAld). IAld acts as a ligand for the aryl hydrocarbon receptor (AhR), facilitating the differentiation and function of regulatory T cells (Tregs) and thereby helping to suppress excessive inflammation. Gut microbiota analysis further indicated that BXD enriched beneficial genera such as Akkermansia and Bifidobacterium, while reducing the abundance of pro-inflammatory bacteria belonging to the Lachnospiraceae family. These results demonstrate the role of BXD in modulating the flora-metabolite-inflammation axis, providing a scientific rationale for its use in UC and highlighting its multi-target actions involving anti-inflammatory effects, metabolic reprogramming, and microbiota restoration.},
}

Animals
*Drugs, Chinese Herbal/pharmacology/therapeutic use
*Colitis, Ulcerative/metabolism/drug therapy/microbiology
*Gastrointestinal Microbiome/drug effects
Mice
Metabolomics/methods
Male
Mice, Inbred C57BL
Disease Models, Animal
*Metabolome/drug effects
Cytokines/metabolism
Inflammation/metabolism/drug therapy
Colon/drug effects

@article {pmid41319485,
year = {2025},
author = {Liu, H and Ou, Y and Wang, X and Yang, L and Yan, L and Shang, M},
title = {Rhizosphere microbiome-driven acetochlor biodegradation in biofilters: Unveiling the mechanisms of process enhancement by wetland plants.},
journal = {Journal of hazardous materials},
volume = {502},
number = {},
pages = {140635},
doi = {10.1016/j.jhazmat.2025.140635},
pmid = {41319485},
issn = {1873-3336},
abstract = {Acetochlor (ACT), a selective herbicide from the chloroacetanilide class, is widely used in the black soil region of Northeast China. Due to its high solubility and persistence, it is frequently detected in both water and soil, posing potential threats to ecosystems and human health. This study established biofilters planted with Canna indica (CAN-BF) and Iris pseudacorus (CAL-BF), using a plant-free filter (CK) as a control. We systematically compared acetochlor removal efficiency, changes in physicochemical parameters, microbial community structure, and functional gene distribution, and explored the degradation pathways. The results showed that after 48 h of operation, the acetochlor removal rates in CAN-BF and CAL-BF increased by 19.31 ± 0.88 % and 15.80 ± 1.99 %, respectively, compared to CK. The greater performance of CAN-BF was attributed to its higher biomass, well-developed root system, and stronger radial oxygen loss. High-throughput sequencing identified Tolumonas, Dechloromonas, and Pseudomonas as key potential degraders of acetochlor, with these genera being significantly enriched in the planted biofilters. GC-MS and functional gene predictions indicated that ACT degradation involves multiple enzymatic steps, including de-ethoxymethylation, dechlorination, decarbonylation, hydroxylation, and nitration, resulting in the formation of products like 2-ethyl-6-methylphenol. Key functional genes (such as dhaA, fdhA, mxaJ, K01455, norB, and nemA) were significantly enriched in the planted filters. This study highlights how plants enhance ACT degradation by regulating microbial communities and metabolic enzymes in the rhizosphere, providing theoretical and technical support for ecological engineering strategies to address chloroacetanilide pesticide pollution.},
}