@article {pmid41575215,
year = {2026},
author = {Zang, W and Zhou, Z and Shen, Y and Zhang, B and Chen, X and Yue, W and Li, X and Cai, Y and Chen, J and Bian, J and Huang, L and Li, H and Dai, Y and Yang, H},
title = {Desaminotyrosine promotes tuft cell expansion and integrates intestinal type 2 immunity.},
journal = {mBio},
volume = {},
number = {},
pages = {e0328925},
doi = {10.1128/mbio.03289-25},
pmid = {41575215},
issn = {2150-7511},
abstract = {Intestinal microbiota are essential for maintaining the host's immune homeostasis, but the mechanism is not fully understood. While microbial metabolite desaminotyrosine (DAT) is recognized for its protective role in viral immunity, its potential involvement in anti-parasitic defense remains unexplored. Here, we demonstrate that DAT orchestrates tuft cell hyperplasia and subsequent type 2 immunity, establishing critical defense against helminth infection. Mechanistically, DAT-mediated intestinal epithelial remodeling requires histone deacetylase 3 (HDAC3), as pharmacological inhibition of this epigenetic regulator abrogates both tuft cell expansion and impairs type 2 immune responses. Collectively, our findings not only explore DAT novel effects in anti-parasitic defense but also reveal a pathway whereby the small molecule metabolites calibrate intestinal type 2 immunity.IMPORTANCEA small molecule metabolite DAT drives tuft cell hyperplasia and type 2 immunity in the small intestine. DAT-mediated tuft cell hyperplasia depends on HDAC3 and an intact microbiota; our findings reveal how small molecule metabolites fine-tune intestinal type 2 defenses against parasites.},
}

@article {pmid41575201,
year = {2026},
author = {Kleinhans, M and Lissen, A and Hewitson, L and Rijkers, GT},
title = {From fecal microbiota transplants to targeted intervention for improvement of immune checkpoint inhibition therapy: how far down the road are we?.},
journal = {Expert review of anticancer therapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737140.2026.2621240},
pmid = {41575201},
issn = {1744-8328},
abstract = {INTRODUCTION: The outcome of immune checkpoint inhibition (ICI) therapy of cancer appears to be influenced by the gut microbiota composition of the patient. Microbiome-based therapy by fecal microbiota transplantation (FMT) appears to improve the outcome of ICI therapy. The ideal composition of the microbiota as well as treatment schedule are not yet established.

AREAS COVERED: The most recent published studies are reviewed, as well as the study designs of registered clinical trials which are ongoing. The effect of pretreatment of patients with antibiotics, aimed to improve engraftment of the transplant, is evaluated.

EXPERT OPINION: The optimal treatment schedule would be to start with FMT, followed by ICI, implying FMT should be given to ICI naive patients. Rather than donor derived FMT, defined consortia of microbiota could be preferred.},
}

@article {pmid41575196,
year = {2026},
author = {Asaduzzaman, M and Oláh, P and Yaseen, NJ and Taifi, A and Járay, T and Gulyás, G and Boldogkői, Z and Tombácz, D},
title = {Longitudinal long-read microbiome profiling in a canine model reveals how age, diet, and birth mode shape gut community dynamics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0127925},
doi = {10.1128/msystems.01279-25},
pmid = {41575196},
issn = {2379-5077},
abstract = {The gut microbiome undergoes dynamic age-related changes shaped by diet and maternal factors. Here, we present a species-level, long-read 16S rRNA survey of the developing gut microbiome in a translational canine model, profiling 89 purebred Hungarian Pumis across early-life and reproductive stages. We collected 456 fecal samples longitudinally: 60 puppies followed from birth to 81 weeks, their mothers sampled during pregnancy and lactation, and adult controls from six kennels. We recorded detailed dietary metadata and reproductive status throughout the study. Age was the strongest determinant of alpha diversity, with a rapid increase during weaning and stabilization by 6 months of age. Beta diversity analyses revealed structured compositional transitions from early developmental phases to adulthood, including a shift toward more uniform, adult-like communities. Within-kennel variation was modest, consistent with shared environmental exposures. Mixed-effects models showed robust associations between specific taxa and age, diet, and kennel, while SparCC-inferred co-occurrence networks indicated increasing ecological complexity with age. We also demonstrated that the delivery mode-vaginal versus cesarean-impacted early-life microbiome composition: Lactobacillus spp. were significantly more abundant in cesarean-born puppies than in vaginally delivered littermates during the 8-10-week window. We also observed reproducible maternal microbiome shifts during pregnancy and lactation, with potential implications for vertical microbial transfer. Taken together, our results show that domestic dogs follow a reproducible, age-structured trajectory of microbial maturation that parallels human development, including delivery-mode effects and diet-responsive taxa.IMPORTANCEMicrobiome research is among the fastest-moving areas in biomedicine driven by major global efforts to understand how microbial communities shape human health and disease. Dogs provide an ideal translational model because their gut microbiota more closely resembles that of humans than that of other studied animals; moreover, breeds show high within-breed genetic homogeneity; diets can be tightly regulated; and longitudinal sampling across the lifespan is feasible. Mapping shifts driven by diet and maternal factors-from early-life events through later life, including senior stages-is essential to leverage microbial plasticity for prevention, with implications for inflammation, metabolic disease, and neurodegeneration. Here, we advance this goal by providing a longitudinal, high-resolution data set and demonstrating that full-length 16S rRNA sequencing is a powerful tool for resolving fine-scale patterns of gut colonization and maturation.},
}

@article {pmid41575036,
year = {2026},
author = {Boudaud, M and Arnone, D and Touly, N and Chassaing, B},
title = {[Intestinal microbiota biodiversity and the modern diet: consequences for human health].},
journal = {Medecine sciences : M/S},
volume = {42},
number = {1},
pages = {65-70},
doi = {10.1051/medsci/2025253},
pmid = {41575036},
issn = {1958-5381},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diet/adverse effects/trends ; *Biodiversity ; Dysbiosis/microbiology ; *Health ; },
abstract = {The advent of the modern diet - characterized by increased consumption of ultra-processed foods rich in saturated fats and simple sugars, but deficient in fiber and micronutrients - has profoundly altered the biodiversity of the intestinal microbiota. This dysbiosis disrupts the intricate metabolic, immune, and nutritional interactions between the host and its microbiota, leading to significant downstream impacts on human health. Dietary imbalances result in reduced production of beneficial microbial metabolites, increased intestinal permeability, chronic inflammation, and heightened risks of obesity, diabetes, and inflammatory diseases. Conversely, diversified diets rich in fiber, unsaturated fatty acids, and plant-based proteins support a resilient and diverse microbial ecosystem that enhances gut barrier function, immunity, and the synthesis of protective compounds. A deeper understanding of these complex host-microbiota-nutrition interactions can pave the way for preventive and therapeutic strategies targeting the microbiome to promote human health.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Diet/adverse effects/trends
*Biodiversity
Dysbiosis/microbiology
*Health

@article {pmid41575016,
year = {2026},
author = {Hamza, MA and Un Nisa, N},
title = {Combining Robotics and Microbiome Science to Treat Unusual Post-Herpetic Neuralgias Resembling Complex Regional Pain Syndrome.},
journal = {Pain practice : the official journal of World Institute of Pain},
volume = {26},
number = {2},
pages = {e70119},
doi = {10.1111/papr.70119},
pmid = {41575016},
issn = {1533-2500},
}

@article {pmid41574983,
year = {2026},
author = {Qian, S and Hou, J and Xiong, X and Duan, Q and Jiang, T and Zheng, Y and Quan, W and Xu, J and Chen, K and Qian, J and Gao, H and Xie, C},
title = {Exploring the Fecal Microbiome Dysbiosis and Its Plasma Metabolome Determinants in Advanced Parkinson's Disease With Motor Complications.},
journal = {CNS neuroscience & therapeutics},
volume = {32},
number = {1},
pages = {e70750},
pmid = {41574983},
issn = {1755-5949},
support = {82001363//Projects of the National Science Foundation of China/ ; 81600977//Projects of the National Science Foundation of China/ ; 82271469//Projects of the National Science Foundation of China/ ; LQ23H090007//the Projects of the Natural Science Foundation of Zhejiang Province/ ; Y19H090059//the Projects of the Natural Science Foundation of Zhejiang Province/ ; LZ23H090001//the Projects of the Natural Science Foundation of Zhejiang Province/ ; 2023R01002//Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang/ ; 2025C02111//the "Pioneer" and "Leading Goose" R&D Program of Zhejiang Province/ ; Y20220164//The Projects of the Wenzhou City Committee of Science and Technology/ ; 2024Y0194//The Projects of the Wenzhou City Committee of Science and Technology/ ; },
mesh = {Humans ; Male ; *Dysbiosis/microbiology/blood/metabolism ; Female ; *Parkinson Disease/complications/blood/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Aged ; Middle Aged ; *Metabolome/physiology ; *Feces/microbiology ; Metabolomics ; },
abstract = {BACKGROUND: Parkinson's disease with motor complications (PD-MC) lacks effective diagnostic and therapeutic strategies. The perturbations of the gut microbiota and plasma metabolites are closely associated with the etiopathogenesis of PD. However, whether fecal microbiome dysbiosis and changed plasma metabolites are involved in PD progression, particularly in the development of PD-MC, is still unclear.

METHODS: In this study, we performed an extensive multiomics analysis involving 108 PD patients for 16S rRNA gut microbiome profiling and 246 PD patients for plasma nontargeted metabolomics. Our findings revealed distinct gut microbiota and plasma metabolites associated with PD-MC. Utilizing these discriminative features, we developed a multivariate diagnostic model for PD-MC. The relationships between differential metabolites and microorganisms were evaluated using Spearman correlation analysis. Functional interpretation of the key metabolites was conducted through enrichment and pathway analysis, employing the KEGG and SMPDB databases.

RESULTS: PD-MC patients had distinct gut microbial signatures as compared with PD without motor complications (PD-NMC) individuals and were increased in fecal Lactobacillus, Limosilactobacillus, Bifidobacterium, and Ligilactobacillus genera along with depleted Agathobacter. Moreover, metabolomic analysis revealed the differences in plasma 3-deoxysappanchalcone (3-DSC), 1,3-Dimethyluracil (1,3-DTl), Leucine, and N-Acetylisoleucine (N-AIL), Dodec-6-enoic acid (D-6-E), N-butyl Oleate (N-BO), and 4-hydroxyundecanoic acid (4-HUA) in PD-MC compared to PD-NMC. Spearman correlation analysis showed that the fecal microbiota aberrations in PD-MC patients were linked to plasma metabolic changes, indicating the association between key microbial populations and metabolomic profiles in PD-MC.

CONCLUSIONS: This study underscores the value of employing integrated multiomics profiling of the fecal microbiome and plasma metabolome to enhance the mechanistic understanding of PD-MC and to identify potential diagnostic biomarkers.},
}

Humans
Male
*Dysbiosis/microbiology/blood/metabolism
Female
*Parkinson Disease/complications/blood/microbiology/metabolism
*Gastrointestinal Microbiome/physiology
Aged
Middle Aged
*Metabolome/physiology
*Feces/microbiology
Metabolomics

@article {pmid41574946,
year = {2026},
author = {Cho, M and Chu, J and No, CW and Kim, YW and Lee, J and Joung, H and Kwon, YJ and Shin, CH and Lee, J and Ha, JH},
title = {Lactiplantibacillus plantarum Q180 Supplementation Restores High-Fat Diet-Induced Gut Dysbiosis and Intestinal Barrier Dysfunction in Mice.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag021},
pmid = {41574946},
issn = {1365-2672},
abstract = {AIMS: Gut microbiota dysbiosis and intestinal barrier disruption are key features of metabolic disorders associated with high-fat diet (HFD) consumption. While probiotics show promise in modulating these pathways, the role of Lactiplantibacillus plantarum Q180 (LPQ), formerly Lactobacillus plantarum Q180, in restoring gut microbial balance and intestinal barrier integrity remains unclear. In this study, we aimed to investigate whether LPQ supplementation alleviated high-fat diet (HFD)-induced gut dysbiosis, intestinal barrier dysfunction, and systemic endotoxemia in a mouse model.

METHODS AND RESULTS: Male C57BL/6 J mice received either a normal control diet or an HFD, with the latter administered with or without LPQ or resmetirom (positive control). Gut microbiota composition was assessed via 16S rRNA gene sequencing, and intestinal barrier function was assessed by fecal and serum endotoxin quantification and colonic expression of tight junction and mucin proteins. LPQ supplementation restored microbial balance, increasing short-chain fatty acid-producing genera (Lactobacillus, Bifidobacterium, Blautia, and Faecalibaculum) and reducing potentially pathogenic taxa. These microbial alterations were accompanied by decreased endotoxin levels, upregulation of epithelial tight junction genes (Zo-1, Ocln, and Claudin-1), and downregulation of mucin genes (Muc2 and Muc4). Positive correlations were noted between specific commensal bacteria and barrier-related gene expression, suggesting a microbiota-linked mechanism supporting epithelial integrity.

CONCLUSION: LPQ attenuated HFD-induced gut microbial imbalance and intestinal barrier dysfunction, accompanied by reduced systemic endotoxemia. These findings suggest that LPQ may serve as a microbiota-targeted intervention for gut dysbiosis-related metabolic disturbances. Further studies are warranted to validate its long-term and translational potential in humans.},
}

@article {pmid41574913,
year = {2026},
author = {Sawan, HM and Ledder, RG and McBain, AJ},
title = {Screening of Human and Environmental Microbiota-Derived Extracts Reveals Pathogen-Specific Anti-Virulence Activity.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf299},
pmid = {41574913},
issn = {1365-2672},
abstract = {AIMS: Targeting bacterial virulence is a promising alternative to traditional antibiotics. In this study, we aimed to identify microbiome-derived factors capable of suppressing virulence traits in pathogenic bacteria.

METHODS AND RESULTS: Eighty-two cell-free extracts (CFEs) applied at 10% (v/v), from human (n = 56) and soil (n = 26) bacterial isolates were screened for effects on planktonic growth, biofilm formation, and virulence using a Galleria mellonella infection model. Growth inhibition was rare, observed only for S. aureus exposed to a Bacillus flexus extract. Anti-biofilm activity was frequent against P. aeruginosa (65/82 CFEs, 79%), less so for S. aureus (20/82, 24%), and absent or reversed for E. coli. Eight CFEs improved larval survival in P. aeruginosa infections; one partly protected against S. aureus, while (47/82, 57%) increased mortality in E. coli-infected larvae. Thirty-eight of 65 anti-biofilm CFEs (58%) for P. aeruginosa tested positive (i.e. observed) in a violacein-based quorum-sensing inhibition assay. One extract (Streptococcus australis) also protected keratinocytes from P. aeruginosa-induced cell loss. Proteomic analysis of P. aeruginosa exposed to S. australis CFE indicated modulation of proteins associated with biofilm regulation and quorum-sensing pathways (e.g. the RsmA/CsrA family), consistent with anti-virulence activity.

CONCLUSIONS: Of 82 microbiome-derived CFEs, (65/82, 79%) partially inhibited P. aeruginosa biofilm formation, (20/82, 24%) affected S. aureus, and none inhibited E. coli biofilms. Ten % improved in vivo survival in P. aeruginosa infections, while (47/82, 57%) increased mortality in E. coli-infected larvae. Anti-virulence effects were pathogen-specific and occurred without measurable impacts on planktonic growth under the conditions tested.},
}

@article {pmid41574888,
year = {2026},
author = {Wang, L and Ni, Y and Gaynanova, I},
title = {Truncated Gaussian copula principal component analysis with application to pediatric acute lymphoblastic leukemia patients' gut microbiome.},
journal = {Statistical methods in medical research},
volume = {},
number = {},
pages = {9622802251412844},
doi = {10.1177/09622802251412844},
pmid = {41574888},
issn = {1477-0334},
abstract = {Increasing epidemiologic evidence suggests that the diversity and composition of the gut microbiome can predict infection risk in cancer patients. Infections remain a major cause of morbidity and mortality during chemotherapy. Analyzing microbiome data to identify associations with infection pathogenesis for proactive treatment has become a critical research focus. However, the high-dimensional nature of the data necessitates the use of dimension-reduction methods to facilitate inference and interpretation. Traditional dimension reduction methods, which assume Gaussianity, perform poorly with skewed and zero-inflated microbiome data. To address these challenges, we propose a semiparametric principal component analysis method based on a truncated latent Gaussian copula model that accommodates both skewness and zero inflation. Simulation studies demonstrate that the proposed method outperforms existing approaches by providing more accurate estimates of scores and loadings across various copula transformation settings. We apply our method, along with competing approaches, to gut microbiome data from pediatric patients with acute lymphoblastic leukemia. The principal scores derived from the proposed method reveal the strongest associations between pre-chemotherapy microbiome composition and adverse events during subsequent chemotherapy, offering valuable insights for improving patient outcomes.},
}

@article {pmid41574450,
year = {2026},
author = {Chen, S and Hoang, MH and Hu, D and He, Q and Gao, Y},
title = {Gut microbiota in early and established stages of rheumatoid arthritis: from pathogenesis to promising prevention and treatment.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2613484},
doi = {10.1080/07853890.2026.2613484},
pmid = {41574450},
issn = {1365-2060},
mesh = {Humans ; *Arthritis, Rheumatoid/microbiology/immunology/prevention & control/therapy ; *Gastrointestinal Microbiome/immunology/physiology ; Probiotics/therapeutic use ; Disease Progression ; Animals ; Antirheumatic Agents/therapeutic use ; },
abstract = {Background: Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease whose etiology is not fully understood. Before overt disease, genetically prone individuals may undergo a lengthy pre-clinical phase during which loss of tolerance triggers autoantibody emergence. The gut-joint axis was proposed decades ago, and mounting evidence now suggests that alterations in the gut microbiome may matter most in early, rather than established, RA.Results: By modulating intestinal permeability, mucosal and systemic immunity, genetic-risk pathways, molecular mimicry, and microbial metabolites, the gut microbiota plays a pivotal role in the onset and progression of RA. The window of opportunity for RA therapy may lie before joint inflammation becomes evident, and microbiota-targeted interventions are emerging. Probiotics, dietary interventions, and natural compounds hold promise as potential strategies for both RA prevention and adjunctive therapy after onset.Conclusions: This review highlights the gut microbiota not merely as a modulator of established RA, but - more critically - as a driver of early disease pathogenesis and a promising therapeutic target, thereby providing new insights for managing pre-clinical RA and refining treatment of established RA.},
}

Humans
*Arthritis, Rheumatoid/microbiology/immunology/prevention & control/therapy
*Gastrointestinal Microbiome/immunology/physiology
Probiotics/therapeutic use
Disease Progression
Animals
Antirheumatic Agents/therapeutic use

@article {pmid41574347,
year = {2025},
author = {Du, H and Lin, Y and Qi, M and Qu, P and Xu, Z and Lin, R and Xie, C and Xiao, T and Dong, S and Wang, B and Ge, Y},
title = {Intercropping Amomum villosum enhances soil stratification, nutrient complementarity, and microbial communities in rubber plantations.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1720828},
pmid = {41574347},
issn = {1664-302X},
abstract = {Intercropping is widely promoted to sustain soil function, yet evidence for its application in rubber-based agroforestry, particularly with the shade-tolerant herb Amomum villosum, is limited. We evaluated whether A. villosum intercropping improves soil properties and reorganizes microbiomes across the vertical profile of mature rubber plantations. Soil samples were taken at 0-10, 10-20, and 20-30 cm depths in both intercropped and monoculture stands. Physical and chemical properties were quantified, and bacterial (16S rRNA V3-V4) and fungal (ITS2) communities were analyzed using high-throughput amplicon sequencing with depth-resolved data on diversity, composition, and functional inference (FAPROTAX, FUNGuild). Intercropping consistently improved soil structure and fertility, with the strongest effects at 0-10 cm. Total porosity (12%), organic matter (38.9%), alkali-hydrolyzable nitrogen (75.4%), and available phosphorus (131%) were markedly higher than in monoculture. Benefits extended to mid-depth with a 65.2% increase in alkali-hydrolyzable nitrogen. Microbial richness (bacteria and fungi) increased, and communities separated clearly by treatment and depth. Intercropped soils showed higher relative abundances of copiotrophic and particle-attached phyla (e.g., Proteobacteria, Planctomycetota), while Acidobacteriota and several Chloroflexi declined. Nitrospirota increased with depth. Fungal trophic structure shifted away from pathotrophs at 20-30 cm and toward symbiotrophs, particularly arbuscular mycorrhizal lineages, at subsurface layers. Functional predictions indicated greater potential for nitrogen transformations (e.g., nitrogen fixation, nitrification), greater C1/hydrocarbon utilization, and a reduced bacterial plant-pathogen signal under intercropping. Collectively, A. villosum intercropping reorganizes the soil environment and microbiome in mutually reinforcing ways-improving physical structure, enlarging near-term nitrogen supply, and favoring beneficial fungal guilds. These depth-resolved effects help explain the agronomic appeal of rubber-A. villosum systems and support their wider deployment in rubber plantations.},
}

@article {pmid41574346,
year = {2025},
author = {Kuizenga, M and Shankregowda, AM and Siriyappagouder, P and Delahaut, V and Calboli, FCF and Bervoets, L and Yadav, BS and Volckaert, FAM and De Boeck, G and Raeymaekers, JAM},
title = {Differential gut microbiome composition in three-spined stickleback populations with contrasting levels of mercury accumulation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1673354},
pmid = {41574346},
issn = {1664-302X},
abstract = {INTRODUCTION: Environmental micropollutants and other anthropogenic xenobiotics are potential drivers behind compositional shifts and functional dysregulation of gut microbial communities. Mercury and many of its compounds are highly toxic and ubiquitous environmental pollutants that pose a risk for aquatic biota and humans. Here we compared the gut microbial communities of natural three-spined stickleback (Gasterosteus aculeatus Linnaeus, 1758) populations in Flanders, Belgium, with contrasting muscle mercury concentrations. We hypothesized that exposure to a high mercury load selects for gut flora species with the capacity to tolerate or adapt to this stressor and, thus, leads to a change in the composition of the gut microbiota.

METHODS: The gut microbiota of 128 host individuals from four populations with low levels of accumulated mercury and four populations with high mercury levels were characterized using 16S rRNA amplicon sequencing. Gut microbial communities were compared across host muscle mercury content levels, host populations and sexes to consider the contribution of these factors in the observed differences in gut microbial diversity and composition.

RESULTS: Microbial community composition varied significantly between males and females, as well as between host populations with high and low muscle mercury content. While the abundance of 22 amplicon sequence variants (ASVs) was associated with the host's muscle mercury content, we detected no specific indicator species for high mercury.

CONCLUSION: Overall, our results suggest that local factors specific to a host population, potentially including mercury accumulation and sex-specific factors, differentiate the microbial communities inhabiting the gastrointestinal tracts of the three-spined stickleback.},
}

@article {pmid41574344,
year = {2025},
author = {Liu, J and Wang, H and Tang, Y and Bao, J and Tan, P and Peng, F},
title = {Soil nifH-harboring community assemblage varies across pecan cultivars.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1716240},
pmid = {41574344},
issn = {1664-302X},
abstract = {INTRODUCTION: This study focused on three pecan (Carya illinoinensis) cultivars ('Pawnee', 'Mahan', and 'Jinhua'), systematically assessing variations in soil nitrogenase activity, characteristics traits of nifH-harboring microbial communities across these cultivars.

METHODS: Using high-throughput sequencing technology, differences in the diversity, community composition, and network structure of nifH-harboring communities in the rhizosphere and bulk soils of pecan were examined across cultivars.

RESULTS: Both cultivar type and soil compartment had significant effects on nitrogenase activity (p < 0.01). Among the three cultivars, 'Mahan' exhibited the highest soil nitrogenase activity in both its rhizosphere and bulk soils relative to the other two cultivars. Notably, rhizosphere soils across all cultivars displayed significantly stronger soil nitrogenase activity than their bulk soil counterparts. 'Mahan' harbored significantly higher microbial α-diversity (Sobs, Shannon, and Chao indices) than other cultivars (p < 0.05). β-diversity analysis revealed marked community divergence among cultivars, with the most pronounced differences observed in bulk soils. Specifically, the bulk soil of 'Jinhua' harbored a distinct microbial signature, marked by significant enrichment of Cyanobacteria and depletion of Alphaproteobacteria. Linear discriminant analysis effect size (LEfSe) further identified Rhizobiales and Burkholderiales as distinct biomarkers for the rhizosphere and bulk soils of 'Jinhua', respectively (LDA score > 4.0, p < 0.05). Microbial co-occurrence network analysis showed that the bulk soil of 'Jinhua' harbored the most complex microbial interaction network, characterized by the highest number of edges, and average connectivity. In co-occurrence networks, Azohydromonas, Bradyrhizobium, Azoarcus, Rhodomicrobium were found as the keystone taxa in maintaining network stability.

DISCUSSION: This research elucidates the regulatory roles of pecan cultivars in shaping soil nitrogen fixation functions and microbial community assembly, providing valuable practical implications for precision microbiome management in pecan production.},
}

@article {pmid41574341,
year = {2025},
author = {Destras, G and Sabatier, M and Bal, A and Simon, B and Semanas, Q and Regue, H and Boyer, T and Ploin, D and Gillet, Y and Lina, B and Anani, H and Josset, L},
title = {Comparison between metatranscriptomics and viral metagenomics, 16S, and host transcriptomics for comprehensive profiling of the respiratory microbiome and host response.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1685035},
pmid = {41574341},
issn = {1664-302X},
abstract = {INTRODUCTION: Omics-based studies focusing on a single kingdom, such as bacterial 16S gene sequencing, viral metagenomics, and human mRNA sequencing, are commonly used to explore the microbiome and its association with host responses. But combining these approaches is often expensive and time-consuming. Metatranscriptomics provides a snapshot of the entire active microbiome through bulk RNA sequencing in a single test, yet its performance relative to kingdom-specific methods has not been systematically assessed.

METHODS: We compared metatranscriptomics with three kingdom-specific sequencing approaches in 20 nasopharyngeal aspirates from infants 7 months of age hospitalized for bronchiolitis at the Hospices Civils de Lyon.

RESULTS: Applying specific sequencing depth thresholds (≥1,000 bacterial reads, ≥100,000 human reads, and detection of an internal RNA control), metatranscriptomics showed high detection concordance and correlated abundance for RNA viruses and human coding genes. Metatranscriptomics also detected RNA from both eukaryotic and prokaryotic DNA viruses, suggesting potential for identifying transcriptional activity. For the bacteriome, 82% of genera exceeding 0.5% relative abundance were captured, revealing distinct transcriptional profiles at the species level. Metatranscriptomics reproduced multi-omics-derived host-microbiome endotypes and revealed stronger key microbial associations, particularly for transcriptionally active microorganisms.

DISCUSSION: These findings indicate that a single metatranscriptomics run can complement or replace kingdom-specific approaches for profiling RNA viruses and the host transcriptome, while also identifying transcriptionally active bacteria and DNA viruses. Low-abundance or latent microorganisms may still require targeted assays. Metatranscriptomics thus provides a cost- and time-efficient strategy for integrated microbiome research and holds promise for clinical applications in acute infections and cases of diagnostic uncertainty.},
}

@article {pmid41574336,
year = {2025},
author = {Shen, W and Yang, W and Qin, S and Liu, Y and Li, G and Zhang, X and Bao, M and Lu, Y and Sun, K and Ma, W and Li, H and Ismayil, A and Cao, A},
title = {Soil fertility and rhizosphere microbiome affecting hydroxysafflor yellow A accumulation in safflower.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1738669},
pmid = {41574336},
issn = {1664-302X},
abstract = {INTRODUCTION: Safflower (Carthamus tinctorius L.) is a prized medicinal species whose therapeutic value hinges on the abundance of bioactive metabolites. Accumulation of these metabolites are influenced by a range of environmental and edaphic factors, including soil physicochemical parameters, extracellular enzyme activities, composition and function of rhizosphere microbiome. However, how these factors individually and synergistically orchestrate the biosynthesis, transport, and ultimate storage of pharmaceutically active compounds within Safflower tissues remains unknown.

METHODS: Here, high-throughput amplicon sequencing coupled with comprehensive physiological profiling was employed to investigate soil characteristics, enzyme activities, and rhizosphere microbial communities of safflower across 36 soil samples collected at two distinct altitudes and two growth stages.

RESULTS: The effective component content was detected in 18 samples, and our results revealed that the safflower stigmas from the high- altitude site (YM) contained significantly elevated levels of hydroxysafflor yellow A (HSYA) compared to those from the lowland site (YF). Soils at the YM site exhibited markedly higher fertility, with available phosphorus, total nitrogen, and organic matter identified as key drivers of HSYA accumulation. Both sites showed high diversity and abundance in rhizosphere microbial communities, with Actinobacteria and Proteobacteria dominating the bacterial communities, and Ascomycota being the predominant fungal phylum.

DISCUSSION: Taken together, our findings show that soil properties, microbial communities, and climatic conditions work interactively to influence the buildup of bioactive compounds in safflower. These insights suggest that precise management of soil nutrients and the rhizosphere microbiome can improve medicinal safflower quality.},
}

@article {pmid41574321,
year = {2025},
author = {Torres, FN and Donda, ALV and Melo, DF},
title = {Scalp Apocrine Glands: The Neglected Component of the Hair Follicle Complex.},
journal = {Skin appendage disorders},
volume = {},
number = {},
pages = {},
pmid = {41574321},
issn = {2296-9195},
abstract = {BACKGROUND: In humans, apocrine glands are generally associated with chemical signaling and body odor. Their presence in the scalp is poorly documented, commonly being associated with benign and malignant tumors. If apocrine glands are consistently present in the normal scalp or become apparent only under pathological circumstances remains unclear. Moreover, their potential physiological role in relation to the hair follicle and microbiome modulation has yet to be fully elucidated.

SUMMARY: The role of scalp apocrine glands is often considered rudimentary and may be underestimated. However, the higher excretions of urea and potassium compared to eccrine glands suggest a potential role in the removal of metabolic waste products and electrolyte balance. Additionally, the openings of apocrine ducts drain into the hair follicle, mixing with follicular contents and sebum before reaching the skin's surface. This highlights a possible close interaction between the apocrine glands and microbiome. Furthermore, given the anatomical and functional association between follicular units and apocrine glands, it is likely that they participate in the pathogenesis of follicular occlusion diseases.

KEY MESSAGES: This article aimed to review existing research on scalp apocrine glands, clarifying this underexplored topic and highlighting them as a potentially relevant component of scalp physiology and pathology.},
}

@article {pmid41574302,
year = {2025},
author = {Mehrnia, N and Van Dyke, TE},
title = {Microbial dysbiosis and immune dysregulation in periodontitis and peri-implantitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1678163},
pmid = {41574302},
issn = {2235-2988},
mesh = {*Dysbiosis/immunology/microbiology ; *Peri-Implantitis/immunology/microbiology/pathology ; Humans ; *Periodontitis/immunology/microbiology/pathology ; Microbiota/immunology ; Inflammation/immunology ; Animals ; Cytokines/metabolism ; Adaptive Immunity ; Immunity, Innate ; Biofilms/growth & development ; },
abstract = {Periodontitis and peri-implantitis are chronic inflammatory diseases which are primarily driven by excessive and dysregulated immune responses. This would result in irreversible tissue destruction around teeth and implants. Although the microbiome serves as an initiator of inflammation and leads to microbial dysbiosis, persistent and unresolved inflammation is the primary driver of tissue and bone loss. These conditions result from a dynamic interplay between the host immune response and pathogenic biofilms. Microbial dysbiosis results from a shift from a eubiotic (symbiotic) oral microbiome to a dysbiotic microbial community. This is initiated by excessive inflammation and manipulates host immunity to promote chronic inflammation. Concurrently, immune dysregulation, including imbalances in innate and adaptive immune responses that result from a failure of resolution of inflammation pathways, exacerbates tissue destruction through the overproduction of pro-inflammatory cytokines and the activation of destructive pathways, such as neutrophil-mediated degradation and osteoclast activation. This review explores the mechanisms underlying microbial dysbiosis and immune dysregulation in periodontitis and peri-implantitis, emphasizing their contribution to inflammation, bone resorption, and disease progression.},
}

*Dysbiosis/immunology/microbiology
*Peri-Implantitis/immunology/microbiology/pathology
Humans
*Periodontitis/immunology/microbiology/pathology
Microbiota/immunology
Inflammation/immunology
Animals
Cytokines/metabolism
Adaptive Immunity
Immunity, Innate
Biofilms/growth & development

@article {pmid41574121,
year = {2026},
author = {Kramp, RD and Janecka, MJ and Tardent, N and Jokela, J and Kohl, KD and Stephenson, JF},
title = {Host Genetics and the Skin Microbiome Independently Predict Parasite Resistance.},
journal = {Ecology and evolution},
volume = {16},
number = {1},
pages = {e72923},
pmid = {41574121},
issn = {2045-7758},
abstract = {Host responses to parasite infection involve several interacting systems. Host genetics determine much of the response, but it is increasingly clear that the host-associated microbiome also plays a role. Host genetically determined systems and the microbiome can also interact; for example, the microbiome can modulate the immune response, and vice versa. However, it remains unclear how such interactions between the host immune system and the microbiome may influence the host's overall response to parasites. To investigate how host genetics and the microbiome interact to shape responses to parasites, we imposed truncation selection on Trinidadian guppies (Poecilia reticulata) for low and high resistance to the specialist ectoparasite Gyrodactylus turnbulli. After 3-6 generations of breeding without parasites, we sampled the skin-associated microbiome and infected fish from each line. We applied Dirichlet Multinomial Modeling (DMM) machine-learning to identify bacterial community types across lines and evaluated how selection line and community type explained variations in infection severity. Our findings showed that among females, the resistant line had significantly lower infection severity, while the susceptible line had higher infection severity. Among males, only the susceptible line experienced higher infection severity compared to the other lines. Line did not explain skin microbial diversity, structure or composition. Our DMM analysis revealed three distinct bacterial community types, independent of artificial selection lines, which explained just as much variation in infection load as selection line. Overall, we found that the microbiome and host genetics independently predict infection severity, highlighting the microbiome's active role in host-parasite interactions.},
}

@article {pmid41574027,
year = {2026},
author = {Lin, A and Xiong, M and Jiang, A and Chen, L and Huang, L and Li, K and Wong, HZH and Zhang, J and Liu, Z and Cheng, Q and Tang, B and Zhang, P and Luo, P},
title = {Tumor Immunotherapy and Microbiome: From Bench-to-Bedside Applications.},
journal = {MedComm},
volume = {7},
number = {2},
pages = {e70454},
pmid = {41574027},
issn = {2688-2663},
abstract = {Cancer immunotherapy has emerged as a transformative therapeutic strategy that harnesses the immune system to combat malignant tumors, overcoming critical limitations such as the nonspecific cytotoxicity of conventional chemotherapy and radiotherapy and drug resistance arising from target mutations in targeted therapies. Growing evidence demonstrates that the human microbiome plays a pivotal role in modulating immune responses and influencing the efficacy of immunotherapeutic interventions. Although the impact is increasingly recognized, the molecular mechanisms and translational potential of microbiome-based strategies remain incompletely explored. This review systematically elucidates how microorganisms from distinct anatomical sites (including bacteria, fungi, and viruses residing in the gut, oral cavity, skin, respiratory tract, and urogenital tract) and intratumoral microbes modulate the tumor immune microenvironment through metabolites, immune cell priming, and antigen mimicry. Furthermore, we discuss how specific microbial signatures predict responses to immune checkpoint inhibitors (ICIs) and CAR-T cell therapy, and highlight emerging interventional strategies, including fecal microbiome transplantation (FMT), probiotics, and engineered bacteria, that demonstrate synergistic effects with immunotherapy in preclinical and clinical settings. By integrating mechanistic insights with translational advances, this review provides a comprehensive scientific foundation for microbiome-based precision immunotherapy, aimed at improving patient survival outcomes and reducing treatment-related adverse events.},
}

@article {pmid41574026,
year = {2026},
author = {Hernández-Cacho, A and Ni, J and García-Gavilán, JF and Konstanti, P and Belzer, C and Vioque, J and Corella, D and Fitó, M and Vidal, J and Torres-Collado, L and Coltell, O and Babio, N and Hernando-Redondo, J and Moreno-Indias, I and Ruiz-Canela, M and Tinahones, FJ and Salas-Salvadó, J},
title = {The Gut Microbiota as a Mediator in the Relationship Between Dietary Patterns and Depression.},
journal = {MedComm},
volume = {7},
number = {2},
pages = {e70562},
pmid = {41574026},
issn = {2688-2663},
abstract = {The interplay between diet, gut microbiota, and depressive symptoms is increasingly recognized, but underlying mechanisms remain unclear. We investigated whether adherence to several dietary patterns relates to gut microbial signatures and whether these profiles are associated with depressive symptoms in an elderly Mediterranean cohort. In 644 participants, 16S ribosomal RNA gene sequencing and dietary intake from a food-frequency questionnaire were obtained at baseline and 1-year follow-up. Adherence scores were computed for the Mediterranean diet adherence score (MEDAS), energy-reduced MEDAS (erMEDAS), Dietary Approaches to Stop Hypertension (DASH), Healthy Plant-Based Diet Index (HPDI), Unhealthy Plant-Based Diet Index (UPDI), and Western Diet Score (WESTDIET). Healthy patterns (erMEDAS, MEDAS, DASH, HPDI) were associated with 22, 28, 24, and 16 genera, of which 82%, 75%, 79%, and 88% showed a protective profile (more abundant with lower, or less abundant with higher, depressive symptoms). UPDI and WESTDIET were associated with 20 and 27 genera, but only 25% and 26% were protective. Mediation analyses indicated that gut microbiota mediated the associations of MEDAS (ACME = -0.066, p = 0.006) and erMEDAS (ACME = -0.029, p = 0.011) with depressive symptoms. This study is among the first to test whether diet shapes a microbiota signature that mediates the diet-depression relationship, adding mechanistic insight into diet-mental health research.},
}

@article {pmid41573938,
year = {2025},
author = {Holmes, ZA and Shyti, I and Hoffman, AL and Duncker, KE and Ma, HR and Zhou, Z and Lee, D and Maddamsetti, R and Kim, K and Şimşek, E and Hamrick, GS and Son, H and Villalobos, CA and Lu, J and Ha, Y and Shende, AR and Yao, Z and Liu, S and Shapiro, DM and Kholina, K and Davis, H and Baig, Y and Wu, F and Wang, S and Wang, X and Chatterjee, P and Lynch, M and Lopatkin, AJ and David, L and Chory, E and You, L},
title = {A foundation model for microbial growth dynamics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.01.691707},
pmid = {41573938},
issn = {2692-8205},
abstract = {Microbial growth dynamics contain rich information about microbial populations, which support applications from antibiotic testing to microbiome engineering. However, the high dimensionality of growth data and the scarcity of large, task-specific datasets have limited generalizable modeling analysis across systems. Here, we develop a foundation model for microbial growth dynamics. It is a large-scale, self-supervised representation model trained on ∼370,000 experimental and simulated growth curves spanning diverse microbial species, environmental conditions, and community contexts. The model learns lower-dimensional latent embeddings that capture essential dynamical features of raw growth data and enable accurate reconstruction of these data. The concise representations enhance predictive performance in diverse downstream applications. Using these embedding, we achieve few-shot learning for antibiotic classification and concentration prediction, accurate forecasting of simulated and experimental communities, and inference of total abundance from relative-abundance data. By extracting transferable representations from heterogeneous datasets, our model provides a general framework for analyzing and predicting microbial community dynamics from limited measurements.},
}

@article {pmid41573876,
year = {2025},
author = {de Oliveira Andrade, F and Bouker, KB and Ozgul-Onal, M and Jin, L and Cruz, I and Helferich, W and Gao, A and Andrade, K and Verma, V and Staley, C and Foley, PL and Hilakivi-Clarke, L},
title = {Isoflavones impair response to anti-PD1 therapy in murine breast cancer models, irrespective of dietary fiber and fecal short chain fatty acid levels.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.05.692375},
pmid = {41573876},
issn = {2692-8205},
abstract = {BACKGROUND: Fermentable dietary fibers, also called microbiota-accessible carbohydrates (MAC), and the consequent increase in fecal short-chain fatty acids (SCFAs) are linked to improved responsiveness to immune checkpoint blockade (ICB) therapy in human and mouse studies. However, experimental diets high in MAC also often contain estrogenic isoflavones, which may counter fiber's beneficial effects by causing immunosuppression.

METHODS: We studied the effects of feeding female C57BL/6Tac mice low-MAC (AIN93G), low-MAC supplemented with isoflavone genistein, high-MAC (5V5M) or high-MAC isoflavone (high-MACi; 5058D) diet on their gut microbiome and response to anti-PD1 therapy against E0771 allografted triple negative breast cancer (TNBC) and 7,12-dimethylbenz[a]anthracene (DMBA)-initiated estrogen receptor α positive (ERα+) mammary tumors. We also determined whether blocking ERα with tamoxifen (TAM) impacted responsiveness to anti-PD1 therapy in mice fed different diets. The effect of diet and treatments on immune cell signaling pathways was investigated using NanoString PanCancer Immune Profiling Panel.

RESULTS: High-MAC and high-MACi diets increased fecal microbial alpha-diversity and the abundances of SCFA producing families Lachnospiraceae, and Oscillospiraceae as well as fecal SCFA levels, compared with low-MAC diet. E0771 tumors responded to anti-PD1 in mice fed high-MAC, while mice fed high-MACi did not respond. Low-MAC fed mice with single E0771 allograft also responded to anti-PD1, but genistein supplementation eliminated responsiveness. E0771 tumors in high-MAC fed mice contained elevated levels of exhausted CD8+ T cells, which were decreased after anti-PD1 therapy. Opposite effects were seen in mice fed high-MACi diet. Mice with DMBA-initiated ERα+ mammary tumors did not respond to anti-PD1. TAM converted TNBC and ERα+ tumors to become sensitive to anti-PD1 therapy in mice fed high-MACi or low-MAC diets, respectively. Genes in TH17 differentiation pathways were linked to TAM-induced improved anti-PD1 response both in TNBC and ERα+ mammary tumors.

CONCLUSIONS: Our results highlight the role of diet in impacting the effectiveness of ICB therapies. We found that increased SCFA levels alone are not predictive of response to anti-PD1, but if tumor expresses ERα or if diet contains ERα activating compounds, such as isoflavones, blocking ERα+ might convert unresponsive tumors responsive to anti-PD1. Word count : 339.

Dietary fiber is proposed to improve response to checkpoint inhibitor therapy against melanoma, but this has been challenged by a recent preclinical study in which different mouse tumor models were used. None of the studies have been done in breast cancer or preclinical breast cancer models.

WHAT THIS STUDY ADDS: Our study showed, using triple negative breast cancer (TNBC) and estrogen receptor positive (ER+) breast cancer models, that indeed high levels of microbiota accessible carbohydrates (MACs) in diet did not alone determine responsiveness to anti-PD1 therapy, but diet high in plant isoflavones/ hormones impaired anti-PD1 effectiveness, regardless of whether diet contained high fiber levels or not. We also found that the adverse effects of isoflavones were counteracted by tamoxifen, partial estrogen receptor antagonist.

Our findings could indicate that breast cancer patients, both those with TNBC and ER+ disease, should not consume diets high in isoflavones when treated with anti-PD1.},
}

@article {pmid41573853,
year = {2025},
author = {Bresette, N and Ericsson, AC and Woods, C and Lin, AL},
title = {MeLSI: Metric Learning for Statistical Inference in Microbiome Community Composition Analysis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.04.692328},
pmid = {41573853},
issn = {2692-8205},
abstract = {UNLABELLED: Microbiome beta diversity analysis relies on distance-based methods including PERMANOVA combined with fixed ecological distance metrics (Bray-Curtis, Euclidean, Jaccard, and UniFrac), which treat all microbial taxa uniformly regardless of their biological relevance to community differences. This "one-size-fits-all" approach may miss subtle but biologically meaningful patterns in complex microbiome data. We present MeLSI (Metric Learning for Statistical Inference), a novel machine learning framework that learns data-adaptive distance metrics optimized for detecting community composition differences in multivariate microbiome analyses. MeLSI employs an ensemble of weak learners using bootstrap sampling, feature subsampling, and gradient-based optimization to learn optimal feature weights, combined with rigorous permutation testing for statistical inference. The learned metrics can be used with PERMANOVA for hypothesis testing and with Principal Coordinates Analysis (PCoA) for ordination visualization. Comprehensive validation on synthetic benchmarks and real datasets shows that MeLSI maintains proper Type I error control while delivering competitive or superior F-statistics when signal structure aligns with CLR-based weighting and, crucially, supplies interpretable feature-weight profiles that clarify which taxa drive group separation. On the Atlas1006 dataset, MeLSI achieved stronger effect sizes than the best traditional methods, and even when performance was comparable, the learned feature weights provided biological insight that fixed metrics cannot supply. MeLSI therefore offers a statistically rigorous tool that augments beta diversity analysis with transparent, data-driven interpretability.

IMPORTANCE: Understanding which microbes differ between groups of interest could reveal therapeutic targets and diagnostic biomarkers. However, current analysis methods treat all microbes equally (similar to using the same ruler to measure everything, regardless of what matters most). This means subtle but clinically important differences may go undetected, especially when only a few key species drive disease while hundreds of "bystander" species add noise. MeLSI solves this by learning which microbes matter most for each specific comparison. In comparing male and female gut microbiomes, MeLSI identified specific bacterial families driving the differences, providing actionable biological insights that standard methods miss. This capability is particularly crucial for detecting early disease biomarkers, where differences are subtle and masked by biological variability. By telling researchers not just whether groups differ, but which specific microbes drive those differences, MeLSI accelerates the path from microbiome data to testable biological hypotheses and clinical applications.},
}

@article {pmid41573687,
year = {2026},
author = {Cui, Q and Wang, J and Huang, Y and Zhou, F and Wu, J and Song, F and Zhao, Q and Feng, R and Zhang, X},
title = {Isolation, identification, and plant growth-promoting mechanisms of strain BN5, with a focus on exogenously Trp-independent IAA biosynthesis, and its impact on cucumber cultivation.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100549},
pmid = {41573687},
issn = {2666-5174},
abstract = {The genus Niallia was recently separated as a taxonomic group from Bacillus based on conserved signature insertions and deletions in the genome. Unlike its role in bioremediation, its function in plant growth promotion has not attracted widespread attention. This study identifies Niallia taxi BN5, focusing on the role of tryptophan in IAA synthesis and regulation, as well as the effects of cucumber. The study employed pot and greenhouse experiments to evaluate the impacts of BN5 on cucumber growth, yield, and quality. Genome analysis explored the tryptophan-regulated IAA biosynthesis pathway, with transcriptome and qPCR examining expression of IAA-related, tryptophan synthesis, and motility genes. It also evaluated impacts on rhizosphere microbial communities and soil enzyme activities. BN5 significantly enhanced cucumber growth (height: +24.29 %, stem diameter: +11.23 %), yield (+17.55 %), and quality (vitamin C: +17.2 % soluble sugar: +37.41 %, all p < 0.05). It increased soil enzyme activities (urease by +52.12 %, dehydrogenase by +44.70 %, p < 0.05) and reshaped the microbial structure. Owing to its possession of a complete tryptophan synthase operon (trpE-D-G-C-F-B-A), strain BN5 is able to produce IAA at a concentration of 17.64 μg/mL via a tryptophan-dependent biosynthetic pathway, with no reliance on exogenous tryptophan. Exogenous tryptophan downregulated the trp cluster but upregulated motility genes (mcp and fliC, p < 0.05), indicating adaptive regulation of IAA precursors. This study clarifies the plant growth-promoting mechanisms of Niallia spp., focusing on tryptophan-mediated regulation of IAA biosynthesis that is independent of exogenous tryptophan. It lays a foundation for efficient microbial fertilizers, highlighting BN5's potential in sustainable agriculture.},
}

@article {pmid41573337,
year = {2026},
author = {Liu, J and Chen, Y and Wang, Y and Li, D and Xu, Z and Zhang, J and Qin, L and Han, B and Jing, Y and Cui, D and Zhu, Y and Xia, S and Jiang, C},
title = {Diversity of Gut Microbiota and Metabolites in Benign Prostatic Hyperplasia with Different Prostate Volumes.},
journal = {European urology open science},
volume = {84},
number = {},
pages = {40-49},
pmid = {41573337},
issn = {2666-1683},
abstract = {BACKGROUND AND OBJECTIVE: The gut microbiota, influenced by age and sex hormones, may correlate with the development and progression of benign prostatic hyperplasia (BPH). This study aims to characterize gut microbiota and metabolite profiles in BPH patients with varying prostate volumes.

METHODS: Fecal samples from BPH patients were analyzed using 16S rDNA sequencing and untargeted metabolomics. Microbial and metabolic differences were assessed via the Linear discriminant analysis Effect Size, KEGG pathway enrichment, and a mediation analysis.

KEY FINDINGS AND LIMITATIONS: We identified 26 differential amplicon sequence variants (ASVs) and 70 metabolites, with 18 microbes correlating significantly with clinical BPH indicators. The key pathways included unsaturated fatty acid and steroid hormone biosynthesis. Akkermansia (ASV549) may affect prostate volume through the regulation of intestinal amino acid metabolism and may negatively affect prostate-specific antigen levels by inhibiting heat shock protein (HSP) 90 (luminespib). Limitations include sample size and unmeasured confounders.

Gut microbiota and metabolite diversity are associated with prostate volume; further studies are warranted to elucidate the potential interventions via microbiome modulation or metabolic targeting for BPH management.

PATIENT SUMMARY: In this study, we identified the potential associations between gut and both prostate volume and benign prostatic hyperplasia symptoms. These findings suggest that dietary interventions or fecal microbiota transplantation may represent potential strategies for modulating prostate health in the future.},
}

@article {pmid41573287,
year = {2026},
author = {Kassaian, N and Ahangarzadeh, S and Vakili, B and Shoaei, P and Alibakhshi, A and Rostami, S and Gavanji, S and Arbabnia, S and Mohammadi, E},
title = {Assessment of Breastmilk Microbiome Focusing on Probiotics.},
journal = {Iranian journal of nursing and midwifery research},
volume = {31},
number = {1},
pages = {133-138},
pmid = {41573287},
issn = {1735-9066},
abstract = {BACKGROUND: Breastmilk is an important factor affecting the infant's gut microbiota and health. Both milk microbiome and the content of oligosaccharides play a role in this effect. The mother's lifestyle can affect the breast milk microbiome. In this study, we assessed the breast milk microbiome in healthy mothers in Iran and its relationship to the mother's lifestyle during lactation.

MATERIALS AND METHODS: In a cross-sectional study, from May 2022 to January 2023, 20 mother-neonates participated by donating their breastmilk samples and completing two questionnaires (food recall for nutritional status and DASS-21 for psychological status). Milk samples in aerobic and anaerobic conditions were cultured to isolate bacterial strains, and the probiotic strains were determined. Data entrees and analysis were done using SPSS-15, and the independent T-student or Mann-Whitney U test was used for statistical analysis.

RESULTS: Seven bacterial species were isolated, including Pedicoccus acidilactici, Lactobacillus fermentum (potential probiotics), Corynebacterium kroppenstedtii, Staphylococcus epidermidis, Rothia kristinae, Streptococcus rubneri, and Streptococcus parasanguinis. It was shown that the consumption of dairy products in the diet was related to probiotic strains in breast milk (p value = 0.03).

CONCLUSIONS: Among the microbiome isolated from breast milk, two probiotics, Pedicoccus acidilactici and Lactobacillus fermentum, were detected. In the mother's diet, dairy product intake during lactation can increase the probiotics in breast milk and give the infant more valuable content.},
}

@article {pmid41573256,
year = {2025},
author = {Manzano-Marín, A and Böhne, A and Monteiro, R and Marcussen, T and Struck, TH and Oomen, RA and , and , and , and Howard, C and Howe, K and Blaxter, M and McCarthy, S and Wood, JMD and Martin, F and Lazar, A and Haggerty, L and Bortoluzzi, C},
title = {ERGA-BGE reference genome of Hirudo verbana, a once neglected freshwater haematophagous European medicinal leech.},
journal = {Open research Europe},
volume = {5},
number = {},
pages = {395},
pmid = {41573256},
issn = {2732-5121},
abstract = {Hirudo verbana Carena, 1820, commonly known as the southern medicinal leech, is one of several European medicinal leeches, whose full diversity has just recently started to be uncovered. Historically, it has been widely used as a medicinal leech and for centuries it was treated erroneously under the specific name of Hirudo medicinalis L. 1758. Recent molecular and taxonomic analyses have revealed subspecific diversity within the morphospecies H. verbana. Hirudo verbana is a blood-feeding species sucking blood from amphibians, fish, and mammals. It occupies freshwater habitats, typically shallow ponds and lakes. Studies show that this leech species has a "naturally limited microbiome", suggesting it may serve as a powerful model system for the study of gut microbiota. We expect this chromosome-level assembly of H. verbana to serve as a high-quality genomic resource for this most famous leech genus and to serve as a foundation to the study of the diversification and biodiversity of European medicinal leeches, as well as their gut-associated symbionts. The genome of H. verbana was assembled into two haplotypes through a phased assembly approach; however, only the primary haplotype was designated as the reference genome for annotation and downstream analyses. The entirety of the primary haplotype was assembled into 14 contiguous chromosomal pseudomolecules, including the mitogenome. This chromosome-level assembly encompasses 0.18 Gb, composed of 277 contigs and 27 scaffolds, with contig and scaffold N50 values of 1.3 Mb and 13.4 Mb, respectively.},
}

@article {pmid41573225,
year = {2025},
author = {Calderon, RB and Gouli, S and Barphagha, I and Ham, JH},
title = {Growth promotion and stress tolerance of soybean plants driven by seed treatment with synthetic bacterial community of soybean-associated beneficial bacteria.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1729743},
pmid = {41573225},
issn = {1664-462X},
abstract = {INTRODUCTION: Beneficial microbes provide a sustainable approach to improving crop production and reducing risks from intensive farming. Microbial consortia, complementary traits, often outperform single strains in promoting plant health. This study aimed to develop an effective biological strategy to enhance soybean growth and health using beneficial bacterial consortia.

METHODS: Bacteria were isolated from the root endosphere and rhizosphere of field-grown soybean plants and screened for traits such as nutrient solubilization, hormone production, and pathogen suppression. Seven synthetic bacterial communities (SBCs), each comprising 5 to 20 SABB strains, were constructed to evaluate their potential in promoting soybean growth and health. Impact of SBC seed treatments on the structure of soybean microbiota was also investigated.

RESULTS: Two SBC sets, Set2 and Setm4, demonstrated superior performances in enhancing plant growth and resistance to the fungal pathogen Rhizoctonia solani when applied via seed treatment. Notably, seed treatment with Set2 or Setm4 also improved soybean resilience to abiotic stresses, including drought and waterlogging. Profiling of the root endosphere and rhizosphere microbiota revealed that SBC application through seed treatment significantly altered the composition of soybean-associated microbial community, including the enrichment of key symbiotic taxa, such as Bradyrhizobium elkanii, and increased microbial network complexity.

DISCUSSION: The beneficial effects of SBC through seed treatment are closely related to microbiome restructuring in soybean roots. This study provides valuable insights into the development of innovative and sustainable crop management strategies, highlighting the potential of SBC-based seed treatments to enhance growth and stress resilience in soybeans and other major crops.},
}

@article {pmid41573214,
year = {2025},
author = {Ren, Y and Yan, H and Ma, A},
title = {Plant genomic and microbial interplay in the rhizosphere under salt stress: a review.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1667328},
pmid = {41573214},
issn = {1664-462X},
abstract = {Soil salinization has been considered as a global problem in agriculture, which decreases crop productivity and threatens food security. Salt stress causes complex physiological damages in plants such as ionic imbalance, osmotic stress, and oxidative damage. However, plants have developed several genomic mechanisms to reduce these negative influences that are further supported by dynamic interactions with rhizosphere microbial communities. This review integrates current advances in understanding the interplay between plant genomes and the rhizosphere microbiome under salt stress. It highlights the role of plant-growth-promoting rhizobacteria (PGPR), arbuscular mycorrhizal fungi (AMF), and microbial volatiles in modulating gene expression and root architecture. Notably, PGPR such as Enterobacter sp. SA187 and Bacillus velezensis have been shown to upregulate key stress-related genes and increase antioxidant enzyme activities, which boost plant resilience under salinity. These microbes also influence stress signaling pathways such as SOS and ABA. Furthermore, this review also discusses the effect of root exudates on microbial communities, the application of synthetic microbial consortia, and genome-scale strategies such as transcriptomics, GWAS, and CRISPR. Our findings show that root exudation patterns shift significantly under salt stress, which enriches beneficial microbial taxa such as Sphingomonas and Streptomyces, while volatile compounds like benzenoids and ketones contribute to systemic stress responses. Understanding the synergistic plant-microbe interactions provides a foundation to engineer salt-resilient crops and for the advancement of sustainable agricultural practices in saline soils.},
}

@article {pmid41573169,
year = {2026},
author = {Nap, B and Weston, B and Brandt, A and Wodak, MF and Bergheim, I and Thiele, I},
title = {The nutrition toolbox permits in silico generation, analysis, and optimization of personalized diets through metabolic modelling.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbaf325},
pmid = {41573169},
issn = {2635-0041},
abstract = {MOTIVATION: Nutrition is an important factor in human health, used to alleviate or prevent symptoms of various diseases. However, the effects of nutrition on the gut microbiome and human metabolism are not well understood. Whole-body metabolic models (WBMs) have been applied to study relationships between regional diets and human/microbiome metabolism. This method requires diets to be defined at the metabolite level, rather than the food item level, which has gated the application of personalized diets to WBMs.

RESULTS: We developed the Nutrition Toolbox, which leverages open-source databases containing metabolite composition for over ten thousand food items to convert food items into their metabolic composition to create in silico diets. Additionally, when used with a previously published nutrition algorithm, minimal changes to a diet can be identified to achieve desirable shifts in human and microbiome metabolism. Taken together, we believe that the Nutrition Toolbox can help to understand the effects of nutrition on human metabolism and has the potential to contribute to personalized nutrition.

The Nutrition Toolbox is written in MATLAB. The code can be found at https://github.com/opencobra/cobratoolbox. A tutorial explaining the code is available in the COBRA toolbox and as view-only supplementary tutorial. Details on installing the COBRA toolbox are available at https://opencobra.github.io/cobratoolbox/stable/installation.html.},
}

@article {pmid41572842,
year = {2026},
author = {Ahmadi, P and Honardoost, M and Janzadeh, A and Taherkhani, S},
title = {Flavonoids and Their Influence on the Gut Microbiome: Implications for Cardiovascular Health.},
journal = {Nutrition bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1111/nbu.70039},
pmid = {41572842},
issn = {1467-3010},
abstract = {Cardiovascular disease (CVD) remains a leading cause of mortality worldwide, necessitating effective preventive and therapeutic strategies. Flavonoids and polyphenols, which are abundant in colourful fruits and vegetables, have emerged as promising bioactive compounds for mitigating CVD. This study elucidates the mechanisms by which flavonoids exert cardioprotective effects through their antioxidant, prebiotic, and mitochondrial restorative properties. Flavonoids function as hydrogen donors, scavenging free radicals such as nitric oxide (NO[•]), superoxide anions (O[•]), and hydroxyl radicals (OH[•]), thereby reducing oxidative stress by decreasing inducible nitric oxide synthase (iNOS) and reactive oxygen species (ROS) activity while enhancing endothelial nitric oxide synthase (eNOS) functionality to promote vasodilation and prevent hypertension. Additionally, flavonoids act as prebiotics, fostering the symbiotic gut microbiota (GM), including Bifidobacteria and Lactobacillus, which produce short-chain fatty acids (SCFAs) and suppress pathogenic trimethylamine-N-oxide (TMAO)-producing bacteria. This enhances gut epithelial barrier integrity, reduces inflammation mediated by lipopolysaccharide (LPS), and protects against heart failure, ischaemia, and atherosclerosis. Under ischemic and heart failure conditions, flavonoids inhibit apoptosis, necrosis, ferroptosis, and fibrosis by restoring hypoxia-damaged mitochondrial function and cardiac energy metabolism. Furthermore, flavonoids prevent arteriosclerosis by inhibiting low-density lipoprotein (LDL) oxidation, reducing cholesterol absorption, promoting bile salt-hydrolysing bacteria, and decreasing vascular cell adhesion molecule (VCAM)-1 expression on coronary vessels. Here, we aim to advance the understanding of flavonoid-mediated cardioprotection by considering their antioxidant, anti-inflammatory, and gut microbiome-modulating effects, offering novel insights into dietary interventions for CVD prevention and management. The findings underscore the potential of flavonoids as accessible, natural agents to address global health disparities in CVD burden.},
}

@article {pmid41572827,
year = {2026},
author = {Xu, B and Liu, P and Yan, N and Wang, T and Liu, L and Cheng, Y},
title = {Multi-omics insights into gut microbial dysbiosis and metabolic alterations in immune checkpoint inhibitor-induced thrombocytopenia.},
journal = {Immunotherapy},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/1750743X.2026.2618937},
pmid = {41572827},
issn = {1750-7448},
abstract = {BACKGROUND: Immune checkpoint inhibitors-induced thrombocytopenia (ICIs-TCP) is a rare immune-related adverse events (irAEs). The physiological changes underlying ICIs-TCP remain incompletely elucidated.

METHODS: We performed multi-omics analysis (gut microbiome, plasma metabolomics/proteomics) comparing microbial/metabolic alterations in cancer patients with (n = 8) and without ICIs-TCP (n = 8). Fecal metagenomic shotgun sequencing was performed to assess microbial composition and function, while plasma metabolomics and proteomics analyses identified systemic metabolic and protein expression changes associated with ICIs-TCP.

RESULTS: Patients with ICIs-TCP exhibited distinct gut microbiota profiles, with an increased abundance of Segatella, Prevotella, and Clostridium, alongside a depletion of Bacteroides and Roseburia. Functional analysis revealed significant downregulation of metabolic pathways, including arginine biosynthesis, alanine, aspartate, and glutamate metabolism. Plasma metabolomics identified reduced arginine levels and disruptions in key amino acid and energy metabolism pathways, suggesting systemic arginine depletion. Proteomic analysis further demonstrated down-regulation of folate hydrolase 1 (FOLH1), a key enzyme in glutamate metabolism, implicating metabolic dysregulation in TCP pathogenesis.

CONCLUSION: The depletion of arginine and associated metabolic disruptions are associated with ICIs-TCP and may represent a potential therapeutic target for mitigating TCP risk in patients receiving ICIs.},
}

@article {pmid41572814,
year = {2026},
author = {Fathima, N and Mascarenhas, R and Umar, D and Rekha, PD and Shetty, S and Amin, V},
title = {Impact of removing fixed orthodontic appliances on oral microbial dysbiosis: A longitudinal study and metagenomic sequencing analysis.},
journal = {Journal of orthodontics},
volume = {},
number = {},
pages = {14653125251408048},
doi = {10.1177/14653125251408048},
pmid = {41572814},
issn = {1465-3133},
abstract = {OBJECTIVE: To investigate the impact of appliance removal on oral microbial diversity, composition, and abundance using metagenomic sequencing. It aims to identify the core microbiome and assess changes between mid-treatment and 2 weeks after debonding to better understand the relationship between orthodontic therapy and oral health.

METHODS: This longitudinal cohort study recruited 26 patients undergoing fixed orthodontic treatment between January 2022 and June 2023. Saliva samples were collected at two predefined time points: mid-treatment (T0, defined as before appliance removal) and 2 weeks after debonding (T1). Microbial DNA was extracted and the V1-V3 hypervariable regions of the 16S rRNA gene were sequenced using Illumina NovaSeq. Bioinformatics analysis was performed using QIIME and the SILVA database to evaluate microbial diversity and composition at T0 and T1. Beta diversity metrics and statistical tests, including PERMANOVA and Wilcoxon signed-rank tests, were applied to identify significant differences (P < 0.05). Effect sizes with 95% confidence intervals (CIs) were reported.

RESULTS: The analysis revealed significant shifts in microbial diversity and composition between T0 and T1. A total of 189 species across 63 genera were identified, with Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria as dominant phyla. Genera such as Fusobacterium periodonticum (↑ 12.4%, 95% CI = 10.1-14.7) and Veillonella parvula (↑ 9.8%, 95% CI = 7.6-11.3) increased after debonding, while Prevotella melaninogenica (↓ 10.2%, 95% CI = 8.1-12.0) and Rothia dentocariosa (↓ 7.9%, 95% CI = 6.3-9.2) decreased. Beta diversity analysis confirmed a statistically significant microbial community shift (P < 0.05).

CONCLUSION: This study demonstrated significant microbial shifts between mid-treatment and 2 weeks after debonding, including increases in potentially pathogenic genera and alterations in the core microbiome. These findings indicate microbial changes persist for at least 2 weeks after appliance removal. Further research with pre-treatment baselines and extended follow-up is required to better define the long-term trajectory of these changes.},
}

@article {pmid41572811,
year = {2026},
author = {Jana, A and Mukhopadhyay, D and Sinha, S and Basak, A and Paramanik, B and Mondol, SA},
title = {Exploring the nano revolution: trends and risks in soil nanotechnology.},
journal = {Nanotoxicology},
volume = {},
number = {},
pages = {1-25},
doi = {10.1080/17435390.2026.2617638},
pmid = {41572811},
issn = {1743-5404},
abstract = {Technical advances have improved scientists' ability to think critically and turn theoretical ideas into actual research. Nanotechnology's potential allows it to spread in modern agriculture. Agricultural nanotechnology may improve food supply, security, sustainability and climate change. Nanoparticles' effects on the soil-plant system reveal their soil ecological hazards. Nano-enzymes promote the balance of ROS by acting as strong antioxidants, thereby enhancing the stress tolerance of plants. They activate antioxidant enzymes like SOD, CAT, and POD, stabilize cellular membranes, and protect photosynthetic machinery. Nanomaterials influence soil pollutants' fate, mobility and toxicity in remediation methods. Nanomaterials' performance and fate rely on soil interactions. Despite many potential benefits, its field applications are restricted. Current research lacks practical ways to assess risk and nanoparticle toxicity to plants, soil and soil microbiomes after release. Environmental safety and risk evaluation need understanding of the manufactured nanoparticle-soil interactions. Nanotechnologies in ecosystems raise health risks. Given the circumstances, nanoparticles in soil must be evaluated and security measures be taken.},
}

@article {pmid41572742,
year = {2026},
author = {Patil, S and Doshi, G},
title = {Gut Microbiota in the Hepato-Cardiorenal Axis: Microbial Metabolites, Inflammation, and Emerging Therapeutic Targets.},
journal = {Current pharmaceutical design},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113816128413464251209115653},
pmid = {41572742},
issn = {1873-4286},
abstract = {INTRODUCTION: To sustain systemic homeostasis, the gut microbiota manages immunological, metabolic, and inflammatory processes. Multiorgan diseases, especially those impacting the liver, kidney, and cardiovascular system through the hepato-cardiorenal axis, have been strongly associated with dysbiosis.

METHODS: A comprehensive literature search was conducted using PubMed, Scopus, Web of Science, Science Direct, and Google Scholar, with the focus on articles till 2025. Eligible sources included clinical trials, systematic reviews, and peer-reviewed academic publications that discussed metabolites, gut microbiota, and treatment approaches for diseases of the liver, kidney, and heart. A qualitative synthesis of the data indicated important mechanisms and potential treatments.

RESULTS: SCFAs have anti-inflammatory and intestinal barrier integrity-enhancing qualities, whereas uremic toxins and TMAO promote oxidative stress, fibrosis, and vascular dysfunction. Hepatic steatosis, insulin resistance, and systemic inflammation are all affected by the dysbiosis-induced bile acid imbalance. Microbiotatargeted therapies include fecal microbiota transplantation, fiber- or polyphenol-rich diets, probiotics, prebiotics, synbiotics, and pharmacological modification of bile acid or TMAO pathways, which have potential but need more comprehensive validation.

DISCUSSION: The findings show that, among other factors, gut metabolites-such as uremic toxins, bile acids, TMAO, and SCFAs - are key players in mediating inflammation and metabolic dysregulation across the hepato-cardiorenal axis. However, the lack of consistent treatment protocols and differences in microbiome composition limit the practical application of preclinical research that has clearly demonstrated the existence of mechanistic links. Future research should focus on long-term clinical outcomes, biomarker identification, and precise microbiome modifications to establish causation and improve therapy effectiveness.

CONCLUSION: The gut microbiota significantly influences the hepato-cardiorenal axis through metabolitemediated signalling. While therapeutic modulation shows promise, precision medicine approaches and highquality randomized trials are essential to tackle multi-organ metabolic and inflammatory diseases.},
}

@article {pmid41572689,
year = {2026},
author = {Ibrahim, HA and Mohamad, WMW and Mohamad, N and Kassim, NK and Ismail, TNNT and Ab Rahman, WSW and Yudin, ZM and Das, S and Zin, SRM},
title = {Insight into Molecular Mechanisms and Pathways Related to the Association of Periodontal Disease and Type 2 Diabetes Mellitus.},
journal = {Endocrine, metabolic & immune disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715303415067251124044844},
pmid = {41572689},
issn = {2212-3873},
abstract = {INTRODUCTION: Periodontal disease is a condition that damages the supporting tissues, potentially resulting in tooth extraction, while type 2 diabetes is a condition that involves insulin resistance, leading to hyperglycaemia and systemic inflammation.

METHODS: A broad literature search was conducted in PubMed, Scopus, Web of Science, Google Scholar, and ProQuest. Search terms included combinations of keywords related to periodontal disease, type 2 diabetes, bone metabolism, genetics/epigenetics, inflammation, and oxidative stress, refined using Boolean operators. Titles and abstracts were screened, and eligible full-text articles were reviewed for relevant data.

RESULTS: This review found that periodontal disease, a major cause of tooth loss in adults, is strongly influenced by the bidirectional relationship with type 2 diabetes. Hyperglycaemia in poorly controlled diabetes exacerbates periodontal inflammation by enhancing the formation of advanced glycation end-products, triggering pro-inflammatory pathways such as the activation of Nuclear Factor kappa-light-chain-enhancer of activated B cells and cytokine release (e.g., Tumour Necrosis Factor-α, Interleukin [IL]-6, IL-18). Concurrent dysbiosis of the oral microbiome disrupts immunoregulation, while an imbalance in the receptor activator of nuclear factor kappa-B ligand (RANKL) and osteoprotegerin (OPG) system promotes osteoclastogenesis, collectively leading to accelerated tissue destruction, impaired healing, and an increased risk of complications.

CONCLUSION: This review clarifies the molecular mechanisms of the triad axis of oral microbiota- inflammatory factors-bone metabolism markers in the bidirectional association between periodontal disease and type 2 diabetes. Understanding the underlying mechanisms of this bidirectional relationship can provide valuable information for researchers to identify potential targets for effective management strategies for periodontal disease in patients with type 2 diabetes.},
}

@article {pmid41572685,
year = {2026},
author = {Chen, H and Liu, H and Zeng, Y and Yang, Y},
title = {Preliminary Study on Laboratory Indicators and Gut Microbiota Differences between Genders with Gastrointestinal Inflammation.},
journal = {Endocrine, metabolic & immune disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715303394944251031095347},
pmid = {41572685},
issn = {2212-3873},
abstract = {INTRODUCTION: The human gastrointestinal tract is home to a vast array of microorganisms, and the imbalance of these microorganisms is closely linked to various diseases. The composition of gut microbiota in individuals is influenced by many factors, among which gender differences are often overlooked and lack targeted treatment plans in clinical practice. Based on this, we conducted this study aimed at exploring the pathogenesis of gastrointestinal inflammation and the importance of gender specificity, providing new ideas and targets for the diagnosis and treatment of gastrointestinal inflammation stratified by gender.

METHODS: We collected fecal samples from 89 patients with gastrointestinal inflammation (40 males and 49 females) for DNA extraction, DNA library construction, sequencing, and clinical data analysis.

RESULTS: In laboratory indicators, male patients had significantly lower mean LDH levels than females (P < 0.05), whereas median GGT, HB, M, and E values were significantly higher (P < 0.05). Additionally, significant differences in microbial α diversity at the species level were observed between the two groups (all P < 0.05). In the prediction analysis of microbial population function, the mean values of heterologous biodegradation and metabolism, signal transduction, cell activity, metabolism of other amino acids, and bacterial infectious disease pathways in the female patient group were higher than those in the male patient group (all P<0.05), and the mean values of nucleotide metabolism, replication and repair, and transcription and translation were lower than those in the male patient group (all P<0.05).

DISCUSSION: Gender differences affect gastrointestinal inflammation progression, with male and female patients showing distinct gut microbiota and laboratory indicators. Males have lower LDH but higher GGT, HB, M, and E, linked to hormonal effects. The gut microbiome composition differs by gender, with males having a higher prevalence of Prevotella and altered metabolic pathways. Females show higher activity in xenobiotic degradation and infection-related functions. Diet, exercise, and clinical interventions, such as FMT, can modulate the microbiota, but gender-specific responses exist.

CONCLUSION: Analysis revealed significant sex-based differences in gastrointestinal disease patients, including variations in laboratory indicators (LDH, GGT, HB, M, E), gut microbiome composition and diversity, and predicted microbial functional profiles. This provides insights for precise medical treatment of gastrointestinal inflammation stratified by gender.},
}

@article {pmid41572438,
year = {2026},
author = {Maes, M and Almulla, AF and Vasupanrajit, A and Jirakran, K and Tunvirachaisakul, C and Maes, A and Chancham, P and Klomkliew, P and Payungporn, S and Zhang, Y},
title = {Functional Shotgun Metagenomic Insights into Gut Microbial Pathway and Enzyme Disruptions Linking Metabolism, Affect, Cognition, and Suicidal Ideation in Major Depressive Disorder.},
journal = {Acta neuropsychiatrica},
volume = {},
number = {},
pages = {1-47},
doi = {10.1017/neu.2026.10056},
pmid = {41572438},
issn = {1601-5215},
abstract = {BACKGROUND: Major depression (MDD) is linked to neuro-immune, metabolic, and oxidative stress (NIMETOX) pathways. The gut microbiome may contribute to these pathways via leaky gut and immune-metabolic processes.

AIMS: To identify gut microbial alterations in MDD and to quantify functional pathways and enzyme gene families and integrate these with the clinical phenome and immune-metabolic biomarkers of MDD.

METHODS: Shotgun metagenomics with taxonomic profiling was performed in MDD versus controls using MetaPhlAn v4.0.6, and functional profiling was conducted using HUMAnN v3.9, aligning microbial reads to species-specific pangenomes (Bowtie2 v2.5.4) followed by alignment to the UniRef90 v201901 protein database (DIAMOND v2.1.9).

RESULTS: Gut microbiome diversity, both species richness and evenness, is quite similar between MDD and controls. The top enriched taxa in the multivariate discriminant profile of MDD reflect gut dysbiosis associated with leaky gut and NIMETOX mechanisms, i.e., Ruminococcus gnavus, Veillonella rogosaem and Anaerobutyricum hallii. The top four protective taxa enriched in controls indicate an anti-inflammatory ecosystem and microbiome resilience, i.e., Vescimonas coprocola, Coprococcus, Faecalibacterium prausnitzii, and Faecalibacterium parasitized. Pathway analysis indicates loss of barrier protection, antioxidants and short-chain fatty acids, and activation of NIMETOX pathways. The differential abundance of gene families suggests that there are metabolic distinctions between both groups, indicating aberrations in purine, sugar, and protein metabolism. The gene and pathway scores explain a larger part of the variance in suicidal ideation, recurrence of illness, neurocognitive impairments, immune functions, and atherogenicity.

CONCLUSION: The gut microbiome changes might contribute to activated peripheral NIMETOX pathways in MDD.},
}

@article {pmid41572422,
year = {2026},
author = {Ahmad, HH and Peck, B and Terry, D},
title = {Probiotics and developmental progression in healthy preschool-aged children: a double-blind, placebo-controlled trial.},
journal = {Nutritional neuroscience},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/1028415X.2026.2617360},
pmid = {41572422},
issn = {1476-8305},
abstract = {BACKGROUND: The gut-brain axis is well known to have a bilateral relationship. Recent research has shown the positive influence of probiotic supplementation on mental flexibility and stress scores among healthy elderly population. However, no similar research has been conducted for young children.

AIM: To investigate the influence of probiotic supplementation on the developmental progress of healthy children.

METHODS: A prospective, randomised, double-blind, placebo-controlled trial was conducted among 105 healthy children, who received either probiotic or placebo supplementation over a six-month period. Of those, 51 were allocated to the probiotic group and 54 to the placebo group. Pre - and post-developmental assessments were conducted using the ASQ-3 and ASQ:SE-2 questionnaires.

RESULTS: Per-protocol analysis showed that children in both the probiotic and placebo groups demonstrated significant improvements in 3 of the 6 ASQ-3 developmental domains. However, baseline analysis by age group revealed significant differences in 3 of the 6 ASQ-3 domains, with children older than 44 months showing better developmental scores. Moreover, increasing age and higher consumption of fruits and vegetables were identified as significant confounders associated with developmental progress.

CONCLUSION: This first-of-its-kind study conducted among healthy preschoolers concludes that probiotic supplementation did not significantly influence developmental progress. However, the study was underpowered for its primary outcome. Future large-scale studies involving diverse populations are recommended.Trial registration: Australian New Zealand Clinical Trials Registry identifier: ACTRN12622000153718..},
}

@article {pmid41572381,
year = {2026},
author = {Choi, Y and Kang, A and Seo, E and Lee, DJ and Park, J and Kim, Y and Yu, K and Yun, CH and Jang, KB and Kim, WK and Shim, K and Kang, D and Kim, Y},
title = {Combination of bacteriophage-probiotics alleviates intestinal barrier dysfunction by regulating gut microbiome in a chick model of multidrug-resistant Salmonella infection.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {14},
pmid = {41572381},
issn = {1674-9782},
support = {NRF-2021R1A2C3011051//National Research Foundation of Korea/ ; RS-2023-00218476//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: The rapid emergence of multidrug-resistant Salmonella in poultry demands alternative control strategies beyond conventional antibiotics. In this study, we evaluated a combination of lytic Salmonella-infecting bacteriophages (SLAM_phiST45 and SLAM_phiST56) and a probiotic bacterium Limosilactobacillus reuteri (SLAM_LAR11) in a chick model challenged with Salmonella enterica serovar Typhimurium infection.

RESULTS: Co-administration with two-phage cocktail and a probiotic showed markedly reduced Salmonella colonization in the gut and systemic organs of chicks, comparable to the effect of phage-only treatment. In contrast with phage-only treatment, the combined therapy significantly improved the rate of body-weight change from the day of infection to necropsy (P < 0.0001) and alleviated infection-associated splenomegaly (P = 0.028) and hepatomegaly (P = 0.011). In the ileum, the villus height-to-crypt depth ratio (VH/CD) increased significantly (P = 0.044). In the colon, expression of tight-junction genes OCLN (P = 0.014), TJP1 (P < 0.0001), and MUC2 (P = 0.011) was elevated, whereas the pro-inflammatory cytokine IL6 was reduced (P = 0.018). These improvements were accompanied, in the cecum, by trends toward decreases in Escherichia-Shigella (P = 0.09) and Clostridium (P = 0.16) and a trend toward an increase in Blautia (P = 0.11); additionally, in the ileum, Lactobacillus (P = 0.037) and Blautia (P = 0.016) increased significantly, yielding a more balanced microbiota than with phage-only treatment. Consistently, levels of functional metabolites, including acetic acid (LDA = 3.32) and lactic acid (LDA = 5.29), were increased.

CONCLUSION: Taken together, these findings demonstrate that phage-probiotic co-administration not only enhances the clearance of multidrug-resistant Salmonella more effectively than phage treatment alone but also promotes intestinal health, highlighting its potential as an antibiotic-alternatives strategy to improve intestinal health and ensure food safety in poultry production systems.},
}

@article {pmid41572341,
year = {2026},
author = {Ornelas, MAS and Ortiz Sanjuán, JM and Leonard, FC and Correia-Gomes, C and Estellé, J and O'Neill, L and Manzanilla, EG},
title = {Cross-sectional study characterizing the porcine faecal microbiome in commercial farms.},
journal = {Porcine health management},
volume = {12},
number = {1},
pages = {1},
pmid = {41572341},
issn = {2055-5660},
support = {2020EN510//International Coordination of Research on Infectious Animal Diseases (ICRAD)/ ; },
}

@article {pmid41572302,
year = {2026},
author = {Einarsson, GG and Das, S and Silversides, JA and Fundano, N and Lonsdale, E and McMullan, R and McAuley, DF and Irwin, NJ and McCoy, CP and Wylie, MP and Sherrard, LJ},
title = {Biofilm communities above and below the cuff of endotracheal tubes are spatially homogenous.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-025-03485-2},
pmid = {41572302},
issn = {1465-993X},
support = {NICHS 2020_C05//Northern Ireland Chest Heart and Stroke/ ; NICHS 2020_C05//Northern Ireland Chest Heart and Stroke/ ; NICHS 2020_C05//Northern Ireland Chest Heart and Stroke/ ; NICHS 2020_C05//Northern Ireland Chest Heart and Stroke/ ; NICHS 2020_C05//Northern Ireland Chest Heart and Stroke/ ; NICHS 2020_C05//Northern Ireland Chest Heart and Stroke/ ; NICHS 2020_C05//Northern Ireland Chest Heart and Stroke/ ; },
}

@article {pmid41572173,
year = {2026},
author = {Kim, H and Siddiqui, NY and Karstens, L and Ma, L},
title = {A negative binomial latent factor model for paired microbiome sequencing data.},
journal = {BMC bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12859-025-06362-3},
pmid = {41572173},
issn = {1471-2105},
support = {R03-AG060082/AG/NIA NIH HHS/United States ; R01-GM135440/GM/NIGMS NIH HHS/United States ; EEC-2133504//National Science Foundation/ ; },
abstract = {BACKGROUND: Microbiome sequencing data are often collected from several body sites and exhibit dependencies. Our objective is to develop a model that enables joint analysis of data from different sites by capturing the underlying cross-site dependencies. The proposed model incorporates (i) latent factors shared across sites to explain common subject effects and to serve as the source of correlation between the sites and (ii) mixtures of latent factors to allow heterogeneity among the subjects in cross-site associations.

RESULTS: Our simulation studies demonstrate that stronger associations between two sites lead to greater efficiency loss in regression analysis when such dependence is ignored in modeling. In a case study involving samples collected from a study on the female urogenital microbiome with aging, our model leads to the detection of covariate associations of the vaginal and urine microbiomes that are otherwise not statistically significant under a similar regression model applied to the two sites separately.

CONCLUSIONS: We propose a latent factor model for microbiome sequencing data collected from multiple sites. It captures the presumptive underlying cross-site associations without compromising estimation accuracy or inference efficiency in the absence of such associations. In addition, our proposed model improves predictive performance by enabling the prediction of microbial abundance at one site based on observations from another. We also provide an extended framework that allows for clustering of subjects (samples) and cluster-specific levels of paired association. Under this extended framework, clusters can be classified according to their association strengths.},
}

@article {pmid41572156,
year = {2026},
author = {Zhang, S and Shi, H and Liu, B and Ge, Z and Zhang, N and Liu, Q and Duan, Z and Chang, Q},
title = {Influences of transcutaneous neuromodulation on fecal microbiota and short chain fatty acids in patients with functional constipation.},
journal = {BMC gastroenterology},
volume = {26},
number = {1},
pages = {51},
pmid = {41572156},
issn = {1471-230X},
support = {2015F11GH098//Dalian municipal science and technology plan project/ ; },
mesh = {Humans ; *Constipation/therapy/microbiology/metabolism/blood ; *Fatty Acids, Volatile/metabolism ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Feces/microbiology/chemistry ; Adult ; *Transcutaneous Electric Nerve Stimulation ; Serotonin/blood ; },
abstract = {OBJECTIVES: Transcutaneous neuromodulation (TN) has been reported effective for functional constipation (FC). The underlying mechanism remains unclear. In this study, we aimed to investigate the gut microbiota (GM) and short chain fatty acids (SCFAs) metabolism changed in FC patients due to TN treatment. The correlation between GM and 5-HT was evaluated.

METHODS: Fourteen FC patients were recruited, and the FC related symptoms were evaluated by questionnaires before and after 4-week TN treatment. Blood and fecal samples were collected to assess the fecal microbiome and SCFAs.

RESULTS: The richness and diversity of fecal microbiota were both found to be increased in FC patients before TN treatment. Fecal metabolomic differences between FC patients and healthy controls were observed at baseline, including elevated branched-chain SCFAs (isobutyric, isovaleric, and valeric acids) in FC. TN treatment did not significantly alter SCFA levels but improved constipation symptoms and increased plasma 5-HT. The correlation of Blautia-serotonin and 5-HT was observed in FC patients (r = 0.574, P = 0.035) and disappeared after TN treatment (r = 0.160, P = 0.584).

CONCLUSION: TN treatment significantly improved the symptoms of FC patients and increased their plasma 5-HT expression levels. The correlation between 5-HT and Blautia-serotonin (which changed after TN treatment) indicated that the 5-HT changes caused by TN treatment might have a potential interaction with the dynamic changes of the intestinal microbiota.},
}

Humans
*Constipation/therapy/microbiology/metabolism/blood
*Fatty Acids, Volatile/metabolism
Male
Female
*Gastrointestinal Microbiome/physiology
Middle Aged
*Feces/microbiology/chemistry
Adult
*Transcutaneous Electric Nerve Stimulation
Serotonin/blood

@article {pmid41571971,
year = {2026},
author = {Wang, H and Dean, LE and Li, X and Fitzjerrells, RL and Wang, K and Mangalam, AK and Marek, RF and Kennedy, CL and Ridlon, MM and Spiegelhoff, A and Stietz, KPK and Lehmler, HJ},
title = {The influence of an environmentally relevant polychlorinated biphenyl mixture on the intestinal microbiota in post-weaning mouse dams.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41571971},
issn = {1614-7499},
abstract = {Polychlorinated biphenyls (PCBs) are environmental pollutants linked to neurological impairments by mechanisms involving the gut microbiome. This study examines the effects of maternal exposure to a PCB mixture on the gut microbiome of post-weaning mouse dams. Female C57BL/6 J mice were exposed daily to PCBs at different doses (0, 0.1, 1, or 6 mg/kg body weight/day) before mating, and throughout gestation and lactation. Post-weaning intestinal contents from dams were analyzed to assess microbiome abundance and quantify PCBs and their metabolites. PCB exposure affected the composition of microbial taxa, though not significantly. However, topic modeling analysis identified a distinct microbial community that was significantly more prevalent in the control group compared to post-weaning mouse dams exposed to the MARBLES mixture at medium and high doses. Complex PCBs and metabolite mixtures were detected in the intestinal contents. Certain PCBs and their metabolites were associated with changes in bacterial abundance, as determined by network analysis. These findings show that individual PCBs and their metabolites can affect gut microbial communities, potentially contributing to neurological impairments in mice exposed to PCBs during gestation and lactation.},
}

@article {pmid41571898,
year = {2026},
author = {Guedes, MS and Yildiz, D},
title = {Sex matters: mechanistic insights into sex-driven patterns of autoimmunity and implications for pharmacotherapy.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {41571898},
issn = {1432-1912},
abstract = {Autoimmune diseases (AiDs) affect up to 10% of the global population and exhibit striking differences between sexes. These disparities encompass prevalence, incidence, age at onset, disease severity and how patients respond to treatment. This review provides a comprehensive overview of the key biological mechanisms underlying sex-biased autoimmunity across multiple levels, including the immunomodulatory roles of sex hormones, sex-specific innate and adaptive immune responses, X-chromosome gene dosage and escape from inactivation as well as epigenetic regulation of immune pathways. In addition, we address how environmental and lifestyle factors, such as smoking, infections and the gut microbiome interact with sex-specific biology to shape autoimmune risk. Finally, we consider the pharmacological implications of sex differences, including variability in drug efficacy, safety and immune-related adverse events, further highlighting current gaps in sex-stratified clinical research. Recognizing sex as a fundamental biological variable is essential for advancing the understanding of AiDs and for the development of more effective, tailored therapeutic strategies.},
}

@article {pmid41571815,
year = {2026},
author = {Chen, E},
title = {What your breath says about the bacteria in your gut.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41571815},
issn = {1476-4687},
}

@article {pmid41571673,
year = {2026},
author = {Bautista, J and Lamas-Maceiras, M and Hidalgo-Tinoco, C and Guerra-Guerrero, A and Betancourt-Velarde, A and López-Cortés, A},
title = {Gut microbiome-driven colorectal cancer via immune, metabolic, neural, and endocrine axes reprogramming.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00883-8},
pmid = {41571673},
issn = {2055-5008},
abstract = {Colorectal cancer (CRC) is a leading cause of cancer mortality worldwide and is increasingly recognized as the outcome of complex host-microbe interactions. Beyond established genetic and environmental drivers, the gut microbiome has emerged as a causal and mechanistic contributor to CRC initiation, progression, and therapy response. This review synthesizes current molecular, ecological, and translational evidence to explain how gut microbial communities reprogram immune, metabolic, neural, and endocrine networks within the tumor microenvironment. CRC-associated dysbiosis is characterized by enrichment of pathobionts such as Fusobacterium nucleatum, pks[+] Escherichia coli, and enterotoxigenic Bacteroides fragilis, and by loss of protective, short-chain-fatty-acid-producing commensals. These microbes promote carcinogenesis through genotoxin-induced DNA damage, epithelial barrier disruption, metabolic rewiring, and chronic inflammation that collectively sustain immune suppression and tumor growth. Defined mutational signatures from bacterial metabolites, including colibactin, cytolethal distending toxin, and indolimines, now directly link microbial exposures to human cancer genomes. By integrating these findings, this review conceptualizes CRC as a biofilm-structured, microbiome-driven ecosystem disease, where polymicrobial consortia coordinate barrier breakdown, immune evasion, and metabolic cooperation. Finally, we highlight emerging microbiota-targeted strategies, including dietary modulation, pre- and probiotics, postbiotics, bacteriophage therapy, engineered live biotherapeutics, and fecal microbiota transplantation, that translate these insights into precision prevention and therapy. Through this integrative framework, the review aims to reposition the microbiome from a correlative feature to a tractable determinant of CRC pathogenesis and treatment response.},
}

@article {pmid41571653,
year = {2026},
author = {Yuan, Y and DeMott, MS and Byrne, SR and Flores, K and Poyet, M and Groussin, M and Berdy, B and Bahunde, JR and Girard, C and Lehtimäki, J and Mabulla, AZP and Mwikarago, IE and Nartey, YA and Nguyen, LTT and Onyekwere, CA and Roberts, LR and Shapiro, BJ and Vatanen, T and Comstock, LE and Alm, EJ and Dedon, PC},
title = {Phosphorothioate DNA modification by BREX type 4 systems in the human gut microbiome.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68412-5},
pmid = {41571653},
issn = {2041-1723},
support = {R01AI093771//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; T32-ES007020//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Among dozens of microbial DNA modifications regulating gene expression and host defense, phosphorothioation (PT) is the only known backbone modification, with sulfur inserted at a non-bridging oxygen by dnd and ssp gene families. Here we explored the distribution of PT genes in 13,663 human gut microbiome genomes, finding that 6.3% possessed dnd or ssp genes predominantly in Bacillota, Bacteroidota, and Pseudomonadota. This analysis revealed several previously undescribed PT synthesis systems, including type 4 Bacteriophage Exclusion (BREX) type 4 brx genes, which we genetically validated in Bacteroides salyersiae. Mass spectrometric analysis of DNA from 226 gut microbiome isolates possessing dnd, ssp, and brx genes revealed 8 PT dinucleotide settings confirmed in 10 consensus sequences by PT-specific DNA sequencing. Genomic analysis showed PT enrichment in rRNA genes and depletion at gene boundaries. These results illustrate the power of the microbiome for discovering prokaryotic epigenetics and the widespread distribution of oxidation-sensitive PTs in gut microbes.},
}

@article {pmid41571627,
year = {2026},
author = {Ta, LP and Corrigan, S and Abeysekera, H and Horniblow, RD},
title = {Extremely oxygen-sensitive next-generation probiotics: can current microcomposite formulations ensure effective colonic delivery?.},
journal = {Microsystems & nanoengineering},
volume = {12},
number = {1},
pages = {37},
pmid = {41571627},
issn = {2055-7434},
abstract = {This narrative review evaluates the suitability of conventional biopolymer-based microencapsulation strategies, originally developed for facultative and aerotolerant probiotics, for the protection and delivery of extremely oxygen-sensitive (EOS) next-generation probiotics (NGPs). With increasing interest in NGPs, there is a pressing need to establish whether conventional formulation approaches can be effectively translated for these highly oxygen-sensitive bioactives. We reviewed commonly used microencapsulation materials and techniques, assessing their suitability and potential to preserve EOS bacterial viability. Hydrated pectin- and gellan-based microcomposite systems, particularly when combined with xanthan gum or other polymers, exhibited the strongest oxygen-protection performance. In contrast, alginate alone demonstrated inconsistent barrier properties, though its performance improved when blended or coated with chitosan. Dehydrated microcomposite systems did not yield additional viability benefits compared to their hydrated counterparts. Importantly, none of the studies explicitly quantified oxygen exposure parameters or established threshold levels required for effective protection of EOS strains. Despite some microcomposite systems demonstrating potential for EOS colonic delivery, our findings highlight a critical gap in formulation science for these sensitive bioactives and underscore the need for the development of bespoke, tailored delivery systems that advance beyond conventional approaches designed for facultative or aerotolerant strains. Addressing these gaps will support the advancement of microencapsulation technologies, improve biotherapeutic NGP formulation, and ultimately facilitate the translation of exploratory clinical findings into rationally designed, accessible, and effective microbiome-based interventions.},
}

@article {pmid41571367,
year = {2026},
author = {Lin, Y and Jiang, Z and Yu, Z and Huang, T and Gui, W and Wang, Z and Li, F and Xiao, P and Li, C and Liu, E},
title = {Honokiol attenuates diabetes by enriching Akkermansia muciniphila andregulating tryptophan metabolism in mice.},
journal = {Chinese journal of natural medicines},
volume = {24},
number = {1},
pages = {59-72},
doi = {10.1016/S1875-5364(26)61077-1},
pmid = {41571367},
issn = {1875-5364},
mesh = {Animals ; *Lignans/administration & dosage/pharmacology ; *Tryptophan/metabolism ; Gastrointestinal Microbiome/drug effects ; Mice ; *Biphenyl Compounds/administration & dosage/pharmacology ; Male ; Mice, Inbred C57BL ; *Hypoglycemic Agents/administration & dosage ; Glucagon-Like Peptide 1/metabolism ; *Akkermansia/drug effects ; Receptors, Aryl Hydrocarbon/metabolism ; *Diabetes Mellitus, Experimental/drug therapy/metabolism/microbiology ; Humans ; *Diabetes Mellitus/drug therapy/metabolism/microbiology ; Fecal Microbiota Transplantation ; Allyl Compounds ; Phenols ; },
abstract = {Diabetes mellitus (DM) is a chronic disease influenced by gut microbiome disturbances. Honokiol (HON), a low oral bioavailability compound from Magnolia officinalis bark, has demonstrated potential as a treatment for DM. This research investigates the effects of HON on gut microbiota and host metabolism to elucidate its mechanism of action in DM. After 8 weeks of intervention through fecal microbiota transplantation (FMT) or antibiotic treatment, HON improved glucose tolerance and lipid metabolism in a gut microbiota-dependent manner. Specifically, HON administration significantly increased Akkermansia muciniphila (AKK) abundance and modulated tryptophan (TRP) metabolism, as evidenced by 16S ribosomal ribonucleic acid (rRNA) gene sequencing and untargeted/targeted metabolomics analysis. Notably, research revealed that AKK metabolized TRP into tryptamine (TA) and other metabolites in vitro. Both AKK and TA activated the aryl hydrocarbon receptor (AHR) pathway, increasing circulating glucagon-like peptide-1 (GLP-1) levels and ameliorating diabetes-related symptoms in DM mice. These findings indicate that HON's hypoglycemic effect primarily stems from AHR-GLP-1 pathway activation through targeted modulation of AKK and microbial TRP metabolite TA, potentially enhancing HON's clinical applications.},
}

Animals
*Lignans/administration & dosage/pharmacology
*Tryptophan/metabolism
Gastrointestinal Microbiome/drug effects
Mice
*Biphenyl Compounds/administration & dosage/pharmacology
Male
Mice, Inbred C57BL
*Hypoglycemic Agents/administration & dosage
Glucagon-Like Peptide 1/metabolism
*Akkermansia/drug effects
Receptors, Aryl Hydrocarbon/metabolism
*Diabetes Mellitus, Experimental/drug therapy/metabolism/microbiology
Humans
*Diabetes Mellitus/drug therapy/metabolism/microbiology
Fecal Microbiota Transplantation
Allyl Compounds
Phenols

@article {pmid41571088,
year = {2026},
author = {Dantas, LO and Candeiro, GTM and Pereira, ACB and Pereira, ACC and Mita, D and Zajac, N and Attin, T and Schwendener, S and Karygianni, L and Pinheiro, ET},
title = {Metatranscriptomic Insights into Bacterial Activity, Virulence, and Antimicrobial Resistance in the Root Canal Microbiome of Acute Apical Abscesses.},
journal = {Journal of endodontics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joen.2026.01.002},
pmid = {41571088},
issn = {1878-3554},
abstract = {INTRODUCTION: This study employed metatranscriptomics to investigate the endodontic microbiome and resistome in acute apical abscesses (AAA) and asymptomatic apical periodontitis (AAP).

METHODS: Root canal samples were collected from 20 patients, including 10 cases of AAA and 10 cases of AAP. RNA sequencing was conducted using the NovaSeq 6000 system (Illumina). Taxonomic analysis utilized the expanded Human Oral Microbiome Database (eHOMD) database, while functional annotation was executed using the DIAMOND and EGGNOG databases. Resistome analysis was conducted with the Comprehensive Antibiotic Resistance Database (CARD) and BacMet - Antibacterial Biocide and Metal Resistance Database. Differential expression analysis was carried out using DESeq2 from the DESeq2 R package (P<0.05).

RESULTS: Taxonomic analysis showed more Gram-negative species in AAA samples (P<0.05), particularly from the Bacteroidota phylum. In functional analysis, Tannerella forsythia and Streptococcus anginosus group (SAG) showed the highest transcriptional activity in AAA. T. forsythia displayed high expression of Rag/SusD proteins, suggesting a potential virulence mechanism. The main protein family found in both conditions was the adenosine triphosphate-binding cassette (ABC) transporter. Transcripts possibly involved in resistance against various antibiotics (cephalosporins, fluoroquinolones, lincosamides, macrolides, tetracyclines), metals (silver, chromium, zinc), and disinfectants (phenolic compounds, acids, and bases) were identified.

CONCLUSIONS: T. forsythia and SAG demonstrated high activity within the root canal microbiome in cases of AAA, suggesting their involvement in the pathogenicity of the community associated with acute infections. The ABC transporter may play a significant role in antimicrobial resistance through an antibiotic efflux mechanism and contribute to tolerance against disinfectants and antiseptics.},
}

@article {pmid41571080,
year = {2026},
author = {Yan, L and Wang, H and Shi, J and Tan, H and Liu, Q},
title = {Bibliometric analysis of neuroinflammation in Alzheimer's Disease: Insights from APP/PS1 mouse model research in the past two decades.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2026.01.020},
pmid = {41571080},
issn = {1873-7544},
abstract = {BACKGROUND: The APP/PS1 transgenic mouse is a foundational model in Alzheimer's disease (AD) research, particularly for investigating the pivotal role of neuroinflammation in disease pathogenesis. Although substantial experimental work has explored inflammatory mechanisms in AD, the field still lacks a comprehensive overview of how research hotspots have evolved, which key scientific questions remain unresolved, and how global research efforts align with existing mechanistic gaps. Therefore, this investigation systematically evaluated scholarly trends, geographic contributions, institutional productivity, and thematic evolution to synthesize actionable insights that will guide subsequent experimental designs.

METHODS: Bibliometric analysis was conducted on peer-reviewed articles indexed in the Web of Science Core Collection (2005-2024). Analytical tools, including VOSviewer, CiteSpace, and Bibliometrix, were employed to quantify research output, collaborative networks, citation metrics, and keyword co-occurrence patterns.

RESULTS: Annual publication numbers exhibited exponential growth post-2015, reflecting an intensified focus on neuroinflammatory mechanisms in AD. China and the United States contributed 83.4 % of total publications, with the University of Barcelona as the most productive institution. High-impact journals such as Nature, Nature Neuroscience, and Brain Behavior Immunity. The analysis identified key scientific issues and evolving research fronts, with current hot topics focusing on oxidative stress, activated microglia releasing inflammatory cytokines, and abnormal autophagy-lysosome pathways.

CONCLUSION: The APP/PS1 mice have a significantly enhanced mechanistic understanding of neuroimmune interactions in AD pathogenesis. Future research should explore microglia-mediated neuroinflammation and brain-gut microbiome interactions to uncover novel diagnostic and therapeutic strategies for AD. This study offers an evidence-based framework to guide researchers using APP/PS1 mice model.},
}

@article {pmid41570877,
year = {2026},
author = {Wang, Y and Wang, X and Gan, B and Jia, T and Xu, T and Xu, H},
title = {Ferroptosis and Hepatic Fibrosis induced by Cooperative Exposure to Polylactic Acid Nanoplastics and Copper: Emphasis on Gut Microbiota Dysbiosis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127698},
doi = {10.1016/j.envpol.2026.127698},
pmid = {41570877},
issn = {1873-6424},
abstract = {Co-exposure to polylactic acid nanoplastics (PLA-NPs) and copper (Cu) in the environment poses a health risk, yet their combined toxic effects remain poorly understood. This study investigated the synergistic hepatotoxicity and underlying mechanisms, focusing on the gut-liver axis, in a mouse model of subacute exposure. Results demonstrated that co-exposure caused significant synergistic effects, including exacerbated changes in body weight (BW), increased hepatic index ratio, and severe liver injury marked by elevated Aspartate Aminotransferase/Alanine Aminotransferase/Alkaline Phosphatase (AST/ALT/AKP) activities and histopathological damage. Crucially, co-exposure synergistically induced hepatic ferroptosis (evidenced by dysregulated Glutathione (GSH), Malondialdehyde (MDA), and iron homeostasis), disrupted lipid metabolism, and promoted oxidative stress. These hepatic injuries were indeced by intestinal barrier damage and gut microbiota dysbiosis, characterized by reduced beneficial Lactobacillus murinus. The fecal microbiota transplantation (FMT) experiment definitively confirmed the causal role of gut microbiota, as transferring microbiota from donor mice to healthy recipients recapitulated the key hepatointestinal injuries. This study demonstrates that co-exposure to PLA-NPs and Cu induces synergistic hepatotoxicity primarily mediated through gut microbiota disruption and gut-liver axis dysfunction, leading to hepatic ferroptosis and fibrosis. These findings highlight the critical role of the gut microbiome in modulating the synergistic toxicity of environmental contaminants and provide new insights into the health risks of mixed pollutant exposure.},
}

@article {pmid41570819,
year = {2026},
author = {Xie, QY and Hamilton, JK and Danska, JS},
title = {Gut microbiota and metabolic disease risk in youth.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102571},
doi = {10.1016/j.xcrm.2025.102571},
pmid = {41570819},
issn = {2666-3791},
abstract = {The rapidly increasing global incidence of youth-onset diabetes is a critical public health concern. Earlier type 2 diabetes (T2D) onset in children and young people is characterized by faster progression and higher risk for complications. An area of expanding research is understanding how obesogenic environments modify the composition and function of the gut microbiota and, in turn, modulate host immune response as well as metabolism. The association between obesity and altered gut microbiota is complicated by hormonal changes during puberty and chronic inflammation that potentiates insulin resistance in multiple responsive tissues. This review examines the risk factors and mechanisms underlying T2D pathogenesis in children and young people and current evidence connecting gut microbiota to stages of disease progression and treatment opportunities. The potential for early intervention through modifications of the gut microbiota opens avenues to alleviate metabolic complications in critical developmental period and blunt the risk for early T2D onset.},
}

@article {pmid41570686,
year = {2026},
author = {Jiao, P and Xu, Y and Zhao, X and Zhang, Q and Zheng, R and Zhang, L and Huang, Y and Bai, B and Liu, S and Xue, Y and Hao, L},
title = {Comparative yak and Simmental rumen microbiome-metabolome across lactation stages: Implications for milk nutritional superiority.},
journal = {Food chemistry},
volume = {505},
number = {},
pages = {148068},
doi = {10.1016/j.foodchem.2026.148068},
pmid = {41570686},
issn = {1873-7072},
abstract = {Both yaks and Simmental are dual-purpose highland varieties, but the mechanisms behind the differences in their milk production are not yet fully understood. This study compared milk composition, rumen microbial communities, and metabolomes across a range of lactation stages for both breeds. Yak milk yields were lower and it had higher levels of fat, protein, long-chain and polyunsaturated fatty acids, key amino acids, and essential minerals than Simmental milk. The microbial community of yak rumen exhibited unique characteristics, with the Family_XIII_AD3011_group persistently enriched and positively correlated with rumen fermentation parameters and milk quality, and the content of glutamate and glutamine in yak rumen was higher than in Simmental and positively correlated with milk quality. Therefore, key microorganisms and metabolites in yak rumen are crucial factors for high-yield dairy production, providing new insights to enhance milk production in ruminant dairy cattle.},
}

@article {pmid41570523,
year = {2026},
author = {Alizadeh, M and Oladokun, S and Fazel, F and Fletcher, C and Blake, K and Sharif, S and Rodriguez-Lecompte, JC},
title = {Modulation of gut immunity and microbiota by Bacteroides thetaiotaomicron confers dose-dependent protection against necrotic enteritis in broiler chickens.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106480},
doi = {10.1016/j.psj.2026.106480},
pmid = {41570523},
issn = {1525-3171},
abstract = {Necrotic enteritis (NE), caused by Clostridium perfringens, remains a major challenge in broiler chicken production. Probiotics represent a promising alternative strategy to mitigate NE by modulating intestinal immunity and microbiota composition. This study evaluated the effects of oral administration of the commensal bacterium Bacteroides thetaiotaomicron on immune responses, microbial profiles, and lesion development in broiler chickens challenged with C. perfringens. One-day-old male broilers (n = 120) were assigned to four groups and received either a low (1 × 10[7] CFU) or high (5 × 10[7] CFU) dose of B. thetaiotaomicron on days 1, 7, 14, and 21 post-hatch. Birds were subsequently challenged to induce NE. Ileal and cecal tonsil tissues were collected for gene expression analysis, and cecal contents were analyzed by 16S rRNA gene sequencing. High-dose B. thetaiotaomicron significantly reduced intestinal lesion scores compared with the positive control, whereas the low dose was ineffective. High-dose supplementation enhanced intestinal immune signaling, with increased expression of TLR2 and TLR4, primarily in the ileum. This was associated with increased expression of pro-inflammatory cytokines (IFN-γ and IL-1β) during the early post-challenge phase and sustained upregulation of regulatory cytokines (IL-10 and IL-2). The epithelial defense-associated cytokine IL-22 was upregulated in both the ileum and cecal tonsils, while TGF-β showed transient induction in the ileum. Markers of epithelial barrier integrity were improved, as evidenced by increased occludin expression, whereas ZO-1 expression remained unchanged. Microbiome profiling revealed that high-dose supplementation enriched beneficial taxa such as Lactobacillus while reducing the abundance of the pathogenic species Enterococcus cecorum. These findings highlight the potential of B. thetaiotaomicron as a probiotic strategy to enhance intestinal immunity and resilience against necrotic enteritis in broiler chickens.},
}

@article {pmid41570295,
year = {2026},
author = {Ma, J and Jiang, G and Hong, L and Luo, L},
title = {Global clinical trial landscape of microbiome modulator therapy in sepsis: gut microbiota interventions and challenges.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000004472},
pmid = {41570295},
issn = {1743-9159},
}

@article {pmid41570114,
year = {2026},
author = {Zhao, Y and Lee, TF and Zhou, B and Wang, C and Schmidt, AM and Liu, M and Li, H and Hu, J},
title = {Joint Modeling of Longitudinal Biomarker and Survival Outcomes with the Presence of Competing Risk in the Nested Case-Control Studies with Application to the TEDDY Microbiome Dataset.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag038},
pmid = {41570114},
issn = {1367-4811},
abstract = {MOTIVATION: Large-scale prospective cohort studies collect longitudinal biospecimens alongside time-to-event outcomes to investigate biomarker dynamics in relation to disease risk. The nested case-control (NCC) design provides a cost-effective alternative to full cohort biomarker studies while preserving statistical efficiency. Despite advances in joint modeling for longitudinal and time-to-event outcomes, few approaches address the unique challenges posed by NCC sampling, non-normally distributed biomarkers, and competing survival outcomes.

RESULTS: Motivated by the TEDDY study, we propose "JM-NCC", a joint modeling framework designed for NCC studies with competing events. It integrates a generalized linear mixed-effects model for potentially non-normally distributed biomarkers with a cause-specific hazard model for competing risks. Two estimation methods are developed. fJM-NCC leverages NCC sub-cohort longitudinal biomarker data and full cohort survival and clinical metadata, while wJM-NCC uses only NCC sub-cohort data. Both simulation studies and an application to TEDDY microbiome dataset demonstrate the robustness and efficiency of the proposed methods.

AVAILABILITY: Software is available at https://github.com/Zhaoyn-oss/JMNCC and archived on Zenodo at https://zenodo.org/records/18199759 (DOI: 10.5281/zenodo.18199759).

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

@article {pmid41570019,
year = {2026},
author = {Murdoch, B and Kleinschmit, AJ and Santibáñez-López, CE and Graham, MR},
title = {Microbiota discovered in scorpion venom.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0328427},
pmid = {41570019},
issn = {1932-6203},
mesh = {*Scorpion Venoms ; Animals ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Scorpions/microbiology ; Phylogeny ; *Bacteria/genetics/classification/isolation & purification ; },
abstract = {With low nutrient availability and presence of numerous antimicrobial peptides, animal venoms have been traditionally considered to be harsh sterile environments that lack bacteria. Contrary to this assumption, recent studies of animal venom and venom-producing tissues have revealed the presence of diverse microbial communities, warranting further studies of potential microbiota in other venomous animals. In this study we used 16S rRNA amplicon sequencing to elucidate whether scorpion venom contained bacteria, to characterize the bacterial communities, and determine if venom microbiomes differed across geologically complex geographic locations. Our study compares the venom microbiome of two scorpion species, sampled from sites in the Mojave and Great Basin deserts, Paruoctonus becki (family of Vaejovidae) and Anuroctonus phaiodactylus (family of Anuroctonidae), and represents the first assessment of microbial diversity ever conducted using the venom secretion itself, rather than the venom-producing organ and its surrounding tissues.},
}

*Scorpion Venoms
Animals
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Scorpions/microbiology
Phylogeny
*Bacteria/genetics/classification/isolation & purification

@article {pmid41569851,
year = {2026},
author = {Kabil, AK and Cait, A and Reynolds, LA and Chopra, S and Bilenky, M and Moksa, M and Li, Y and Cait, J and Hernaez, DC and Scott, RW and Fogarty, E and Finlay, BB and Mohn, WW and Hirst, M and Hughes, MR and McNagny, KM},
title = {Early-life microbiota skews long-term gene expression and chromatin states of bone marrow hematopoietic precursors.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116871},
doi = {10.1016/j.celrep.2025.116871},
pmid = {41569851},
issn = {2211-1247},
abstract = {Early life is a critical window during which the gut microbiota sculpts immunity and long-term susceptibility to allergic disease. Using neonatal antibiotic administration and bone marrow transplantation assays, we show that depletion of short-chain fatty acid (SCFA)-producing bacteria alters gene expression in hematopoietic stem and progenitor cells (HSPCs) and imprints a persistent, transplantable atopic immune phenotype. Bone marrow transplants from exposed mice generate recipients with elevated serum immunoglobulin E (IgE), downstream increased IgE bound to basophils, and exacerbated allergic lung inflammation following papain challenge. Depletion of SCFA-producing bacteria also impairs recovery from chemotherapy-induced myelosuppression and increases DNA damage in long-term HSPCs in an antibiotic-specific manner. Histone 3 lysine 27 (H3K27) chromatin immunoprecipitation sequencing (ChIP-seq) analyses further reveal differential histone acetylation in HSPCs, consistent with an SCFA-mediated epigenetic regulatory mechanism. Collectively, these findings establish a link between gut microbiota composition, hematopoiesis, and long-term immune function, offering a mechanistic explanation for microbiota-driven susceptibility to atopic disease and hematopoietic dysfunction.},
}

@article {pmid41569365,
year = {2026},
author = {Duarte, M and Mansilha, C and Melo, A and Sobral, D and Ferreira, R and Gomes, JP and Rebelo, H and Veber, A and Puskar, L and Schade, U and Jordao, L},
title = {Detection of polycyclic aromatic hydrocarbons, microplastic presence and characterization of microbial communities in the soil of touristic zones at Alqueva's edges (Alentejo, Portugal).},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41569365},
issn = {1614-7499},
abstract = {Environmental pollution is a growing concern. Here, we assessed the occurrence of two groups of persistent organic pollutants (POPs-polycyclic aromatic hydrocarbons (PAHs) and microplastics (MPs)) and bacterial populations in the topsoil of three tourist spots located at the Alqueva's edges during 1 year, once per season. Soil chemical analysis revealed low content of total organic carbon, pH close to neutrality, and nitrogen and phosphorus levels consistent with acquisition of these nutrients only by atmospheric deposition. PAH's concentrations were in the range of ng/kg, being significantly below the "reference values" for contaminated soils. Nevertheless, potentially carcinogenic PAHs, detected at all locations, raise ecotoxicological concerns. Polyamide, polyester, polystyrene, and styrene acrylonitrile resin MPs were found. Six bacterial phyla constitute the core microbiome in the three locations and include genera of bacteria reported as plastic degraders, such as Bacillus, Exiguobacterium, Paenibacillus, and Pseudomonas. The presence of POPs, even at low levels, in the soil at the edges of a water reservoir should be monitored. The identification of bacteria reported as plastic degraders in the soil, and previously in the water, is promising, and their ability to spontaneously ensure the detoxification of the ecosystem should be further investigated.},
}

@article {pmid41569044,
year = {2026},
author = {Chitre, S and Gharaibeh, RZ and Newsome, RC and Jiang, J and Brock, A and Schmittgen, TD and Jobin, C},
title = {Campylobacter jejuni infection impacts host-derived miRNAs targeting bacterial and host genes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0318425},
doi = {10.1128/spectrum.03184-25},
pmid = {41569044},
issn = {2165-0497},
abstract = {UNLABELLED: The intestinal microbiota has been shown to influence host-derived microRNAs (miRNAs), small regulatory RNAs involved in host-pathogen interactions. However, the specific role of individual bacterial species in modulating host extracellular vesicles (EV)-derived miRNA profiles remains unclear. We compared stool miRNA profiles from three groups: (i) Germ-free (GF) mice, (ii) mice colonized with a consortium of 13 bacteria (C13), and (iii) mice colonized with C13 and Campylobacter jejuni 81-176 (C13 + C. jejuni). miRNA profiling revealed unique differential expression of 8 miRNAs in C13 vs GF, 38 in C13 + C. jejuni vs C13, and 159 in C13 + C. jejuni vs GF (Padj < 0.05), indicating a substantial shift in host miRNA landscape following C. jejuni exposure. Notably, C13 + C. jejuni mice showed increased expression of miRNAs predicted to target bacterial virulence genes, suggesting a potential host response mechanism aimed at regulating microbial activity. Integration with spatial transcriptomics of the mouse colon revealed that specific EV-derived miRNAs, including mmu-miR-155-5p, mmu-miR-122-5p, mmu-miR-21a-5p, mmu-let-7i-5p, and mmu-miR-142a-3p target epithelial genes involved in immune regulation, inflammation, and barrier function. C. jejuni exposure selectively enriched these host miRNAs, suggesting a mechanism by which EVs modulate epithelial transcriptional responses and potentially influence microbial gene expression. In conclusion, C. jejuni infection modified host EV-derived miRNA expression profile that may have a potential to bind to the bacterial gene targets.

IMPORTANCE: Host-derived microRNAs (miRNAs) are known to regulate bacterial gene expression and maintain gut homeostasis. However, how these miRNAs survive harsh gut conditions to remain functional is not fully understood. This study tested whether extracellular vesicles (EV) carry microRNAs in the gut and whether infection with the enteric pathogen Campylobacter jejuni alters the microRNA profile packaged in these vesicles. We utilized fecal samples from mice, either maintained germ-free (absence of microbiota) or, C13 (defined 13 bacterial consortium), and C13 + C. jejuni to analyze the EV-derived miRNA pattern across the groups. Our results revealed distinct sets of miRNAs in each group and suggested possible interactions between these miRNAs and gene transcripts from both the host and bacteria. These findings provide new insights into how C. jejuni infection may change communication between the host and its microbiome, potentially affecting gut health and disease.},
}

@article {pmid41569026,
year = {2026},
author = {Hazra, L and Biswas, S and Saha, KK and Chatterjee, S and Dutta, S and Mandal, S},
title = {Endophytic Drought-Tolerant Bacterial Community Dynamics Across Contrasting Agroclimatic Zones.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovag013},
pmid = {41569026},
issn = {1472-765X},
abstract = {Rice (Oryza sativa) sustains more than half of the global population but is particularly vulnerable to water limitation in rainfed upland and lowland ecosystems. Endophytic microbiomes represent a sustainable strategy for improving drought resilience, yet their diversity and functional potential in traditional rice landraces remain underexplored. This study investigated endophytic bacterial communities associated with indigenous upland and lowland cultivars of West Bengal, India, using 16S rRNA amplicon sequencing, predictive functional profiling, culture-based screening, and biochemical validation. Distinct microbial assemblages revealed for diverse agro-ecosystems, with upland cultivars enriched in stress-adapted taxa such as Proteobacteria, Actinobacteria, and Firmicutes. PICRUSt2 predictions indicated higher representation of KEGG pathways associated with osmolyte biosynthesis, antioxidant defence and compatible solute metabolism in upland microbiomes. Culture isolates, notably Enterobacter sp. KNR1 and Klebsiella sp. GBR1, exhibited strong tolerance to PEG-induced osmotic stress, producing elevated proline, glycine betaine, EPS, and IAA, alongside efficient root colonization in susceptible rice. Collectively, these findings establish indigenous upland rice as a reservoir of functionally resilient endophytes and provide a foundation for developing microbial consortia to enhance rice performance under water-limited conditions.},
}

@article {pmid41568957,
year = {2026},
author = {George, SD and Amerson-Brown, MH and Sousa, LGV and Rinehart, AH and Tamhane, A and Riegler, AN and Leal, SM and Lammons, JW and Elnaggar, JH and Graves, KJ and Łaniewski, P and Herbst-Kralovetz, MM and Taylor, CM and Cerca, N and Muzny, CA},
title = {Spatial organization of Gardnerella species, Prevotella bivia, and Fannyhessea vaginae in the bacterial vaginosis biofilm.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0063025},
doi = {10.1128/iai.00630-25},
pmid = {41568957},
issn = {1098-5522},
abstract = {Key bacterial vaginosis (BV)-associated bacteria implicated in biofilm formation include Gardnerella species, Prevotella bivia, and Fannyhessea vaginae. We investigated their spatial organization in the BV biofilm over time from longitudinal vaginal specimens obtained from women with incident BV (iBV) using peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH). Heterosexual women with optimal vaginal microbiota self-collected vaginal specimens twice daily for 60 days or until iBV development (Nugent score 7-10 on ≥4 consecutive specimens). Women who developed iBV were matched to healthy controls by age, race, and contraceptive method. Gardnerella spp., P. bivia, and F. vaginae were quantified using PNA-FISH 2 days pre-iBV, the day of iBV, and 2 days post-iBV across five optical layers (z, z + 2, z + 4, z + 6, and z + 8 μm). Total counts of all three bacterial species were significantly higher on the day of iBV compared to 2 days pre-iBV (P = 0.011) and remained elevated 2 days post-iBV. Across most layers and time points, pooled mean Gardnerella spp. counts were significantly higher than F. vaginae counts (P ≤ 0.022-0.0003). On the day of iBV and 2 days post-iBV, pooled mean counts of Gardnerella spp. and F. vaginae progressively increased across most biofilm layers (P ≤ 0.043-0.0012). Controls had significantly lower counts of Gardnerella spp. and F. vaginae. P. bivia had low counts in all specimens. During the critical time period surrounding iBV, Gardnerella spp. are abundant throughout the developing biofilm and facilitate F. vaginae incorporation at later time points and higher biofilm layers. Additional research, including other Prevotella spp., is needed.IMPORTANCEBacterial vaginosis (BV) is the most common vaginal infection in reproductive-age women worldwide with a global prevalence of 30%. Recurrence rates can be up to 60% within 1 year of treatment. While BV is characterized as a polymicrobial biofilm infection, the exact etiology remains unknown. The BV biofilm may persist after antibiotic treatment, possibly due to incomplete eradication by current antimicrobial therapies, contributing to recurrent infection. Data are limited in evaluating the spatial formation of the BV biofilm around the time of incident BV. Providing a better understanding of this critical time period in incident BV pathogenesis is necessary to inform the development of prevention methods aimed at inhibiting biofilm formation and improving long-term treatment outcomes.},
}

@article {pmid41568748,
year = {2026},
author = {Wang, Y and Qiu, J and Wang, C and Yang, R and Guo, F and Li, T and Li, S and Yang, L and Ding, W},
title = {Sustainable Strategy of Natural trans-Anethole in Controlling Bacterial Wilt: Virulence Suppression and Beneficial Microbiome Enrichment.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c13627},
pmid = {41568748},
issn = {1520-5118},
abstract = {Plant-derived terpenoids are essential secondary metabolites exhibiting broad-spectrum antibacterial properties. However, the bioactivities of terpenoids against Ralstonia solanacearum remain unexplored. Herein, the bioactivities of 30 terpenoids against R. solanacearum were assessed, and trans-anethole (TAN) was identified as a potent antibacterial agent with a minimum inhibitory concentration and minimum bactericidal concentration of 50 and 75 mg/L, respectively. TAN was low-toxic to silkworms, earthworms, seeds, and E. coli. Furthermore, TAN (>25 mg/L) significantly impeded the R. solanacearum growth, blocked ATP and exopolysaccharide (EPS) synthesis, caused DNA damage and cell rupture, and affected swimming motility and biofilm formation, and suppressed expressions of related genes. Compared with thiodiazole copper, and ethylicin, 100 mg/L TAN had a significantly greater control efficiency in both greenhouse and field tests. Importantly, TAN enhanced the abundance of the beneficial bacteria Bacillus and Sphingomonas. These findings highlight TAN as a potential bacterial wilt control agent.},
}

@article {pmid41568738,
year = {2026},
author = {Warren, A and Wynia, Z and Corr, PG and Devin, MF and Celikkol, Z and Gordon, L and Farah, M and Karam, M and Villarreal, D and Jackson, SA and Frame, LA},
title = {The microbiota-gut-brain axis in mild cognitive impairment and Alzheimer's disease: a scoping review of human studies.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {22},
number = {1},
pages = {e71023},
pmid = {41568738},
issn = {1552-5279},
support = {//TMCity/ ; },
mesh = {Humans ; *Cognitive Dysfunction/microbiology ; *Alzheimer Disease/microbiology ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; Probiotics/therapeutic use ; *Brain ; },
abstract = {Alzheimer's disease (AD) is projected to become the highest-burden neurological disorder globally. Mounting evidence implicates the gut microbiome in AD pathogenesis. This scoping review of gut microbiomes in mild cognitive impairment (MCI) and AD included dietary and probiotic interventions. We included original research and systematic reviews/meta-analyses. Animal and non-English studies were excluded. We searched PubMed, Scopus, and Cochrane Library through February 2023. Using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA)-Extension for Scoping Reviews (ScR) checklist, we screened 4751 articles, with 58 meeting predefined inclusion criteria. Our results demonstrated that gut dysbiosis was frequently reported in MCI and AD, including increased Pseudomonadota and Actinomycetota in AD and reduced diversity in some cases. Probiotic and dietary interventions showed promise in modulating cognition and microbiota, inconsistently. Emerging evidence links dysbiosis to cognitive decline; however, methodological heterogeneity and limited follow-up impede causal inference. Research should prioritize standardized protocols, functional microbiome analysis, and longitudinal human studies to clarify therapeutic potential. HIGHLIGHTS: Gut dysbiosis is a common feature of MCI and AD, with phylum-level microbial shifts frequently observed. Pseudomonadota and Actinomycetota are enriched in AD across multiple human studies. Beneficial genera like Faecalibacterium and Roseburia are consistently reduced in MCI and AD in a small number of studies. Probiotic and dietary interventions are promising to modulate the microbiota-cognition axis. More longitudinal human studies are needed to assess causal microbiome relationships.},
}

Humans
*Cognitive Dysfunction/microbiology
*Alzheimer Disease/microbiology
*Gastrointestinal Microbiome/physiology
*Dysbiosis/microbiology
Probiotics/therapeutic use
*Brain

@article {pmid41568432,
year = {2026},
author = {Harford, TJ and Singh, KD and Pardhi, TR and Desnoyer, R and Ravi, T and Jara, ZP and Zalavadia, A and Stenson, K and Naga Prasad, SV and Karnik, SS},
title = {Microbial Metabolite 4EPS Inhibits AT1R to Reduce Blood Pressure and Aortic Aneurysm Outcome.},
journal = {Hypertension (Dallas, Tex. : 1979)},
volume = {},
number = {},
pages = {},
doi = {10.1161/HYPERTENSIONAHA.125.25364},
pmid = {41568432},
issn = {1524-4563},
abstract = {BACKGROUND: Plasma accumulation of the gut microbial metabolite 4-ethylphenylsulfate (4EPS), derived from dietary amino acid, tyrosine, has been associated with cardiovascular, renal, metabolic, and neurological disorders. AngII (angiotensin II) infusion increases circulating 4EPS in mice, suggesting a potential mechanistic role. We hypothesized that 4EPS modulates AngII-regulated pathophysiology and disease progression by directly inhibiting AT1R (angiotensin II type 1 receptor).

METHODS: This hypothesis was tested by combining AT1R pharmacology, cell signaling assays, ex vivo vascular studies, an AngII-induced aortic aneurysm growth model, and plasma proteomics analysis.

RESULTS: in vitro, 4EPS reduced the binding of both AngII and the antagonist candesartan to AT1R and suppressed AngII-induced calcium signaling. Ex vivo, 4EPS attenuated AngII-mediated vasoconstriction. In vivo, high-fat diet-fed ApoE-null mice coinfused with AngII and 4EPS showed significant blunting of blood pressure elevation and a marked reduction in aortic aneurysm-related mortality compared with mice infused with AngII alone. Analysis of aortic remodeling revealed increased elastin preservation and decreased thickening of the intimal and medial layers in 4EPS-treated animals. Plasma proteomics indicated alterations in actin-cytoskeletal signaling pathways consistent with reduced activation of ERK (extracellular-regulated kinase) 1/2, filamin-A, and proteins involved in vascular smooth muscle cell motility.

CONCLUSIONS: These findings identify 4EPS as a benign, endogenous AT1R antagonist that diminishes AngII-mediated hemodynamic and vascular pathology. By suppressing cytoskeletal signaling associated with vascular remodeling, 4EPS provides significant protection against hypertension and aortic aneurysm progression in mice, revealing a previously unrecognized protective role for a gut microbial metabolite in modulating renin-angiotensin system activity.},
}

@article {pmid41568344,
year = {2025},
author = {Doshier, J and Anderson, B and Yang, F and Stewart, SD and Calapa, KA and Cooper, R and Wilson-Robles, H and Embree, M and Khanna, C},
title = {Pilot study evaluating tolerability and changes in fecal microbiota associated with novel probiotic administration to dogs with diarrhea.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1720932},
pmid = {41568344},
issn = {2297-1769},
abstract = {BACKGROUND: Diarrhea is one of the most common reasons for visiting canine veterinary clinics or emergency centers. Common treatment approaches include dietary modification, antibiotics, and/or probiotics, which are frequently initiated empirically. Antibiotics can have detrimental long-term effects on the gut microbiome and contribute to antimicrobial resistance, prompting a need for alternative therapies. Probiotics are a promising option; however, their strain-specific effects on the canine gut microbiome have been insufficiently characterized in vivo, particularly in dogs with diarrhea.

HYPOTHESIS/OBJECTIVES: This study aimed to evaluate tolerability and changes in fecal microbiota in dogs with diarrhea during the administration of a novel, advanced microbiome-derived probiotic (AMP) consisting of live Peptacetobacter hiranonis, Megamonas funiformis, and Enterococcus faecium, strains of which were all originally isolated from the feces of a healthy dog.

ANIMALS: This single-arm, prospective observational pilot study consisted of 11 client-owned adult dogs of various breeds presenting for chronic diarrhea (>5 days) with a Purina Fecal Score (PFS) between 4 and 7.

METHODS: Tolerability of the AMP was assessed through serial clinical examinations and comparison of PFS to baseline. Dogs were classified as responders if their PFS improved to <4 by day 7, and as non-responders otherwise. Fecal samples collected at baseline, day 7, and day 56 of AMP administration underwent Illumina amplicon next-generation sequencing (NGS) of 16S rRNA gene fragments (V4 region) to assess the fecal microbiome composition and diversity in each patient.

RESULTS: No adverse events were noted in any dogs receiving the AMP. Clinical improvement in diarrhea was noted in eight of 11 dogs after administration of the AMP. Increases in fecal microbiome alpha-diversity were observed after 1 week of AMP administration for six out of seven long-term participants.

This pilot study indicates that the AMP was well tolerated in dogs with diarrhea, with dogs maintaining or improving clinical appearance during administration. These preliminary findings justify larger controlled studies to evaluate AMP efficacy and to explore associations between treatment, fecal microbiome changes, and clinical response.

CLINICAL TRIAL REGISTRATION: Identifier: VCT23005615.},
}

@article {pmid41568321,
year = {2026},
author = {Yahyapour, A and Najafi, A and Ahmadi, A and Salarizadeh, N},
title = {Immunoprotective and neuroprotective properties of gut microbiome in psoriasis.},
journal = {Journal of translational autoimmunity},
volume = {12},
number = {},
pages = {100348},
pmid = {41568321},
issn = {2589-9090},
abstract = {Psoriasis impacts nearly 100 million people globally and is associated with neuropsychiatric comorbidities such as depression and anxiety. With gut microbiome dysbiosis serving as a primary pathophysiological factor, the gut-brain-skin axis provides a crucial framework for understanding this relationship. This review evaluates the mechanisms of the gut-brain-skin axis in psoriasis pathophysiology and assesses the therapeutic potential of microbiome-based treatments, combining preclinical, clinical, and multi-omics data. Patients with psoriasis show specific gut dysbiosis patterns, including reduced microbial diversity, lower SCFA-producing bacteria (especially Faecalibacterium and Akkermansia), and increased pro-inflammatory bacteria. This microbial imbalance damages intestinal barrier integrity, triggers systemic inflammation, activates cutaneous Th17 pathways, and induces neuroinflammation through blood-brain barrier disruption. Axis communication occurs through immune-inflammatory mechanisms mediated by SCFAs and neuroendocrine pathways involving microbially-derived neurotransmitters (GABA, serotonin, dopamine). Metagenomic research indicates functional deficiencies in neurotransmitter and SCFA synthesis pathways are more significant than taxonomic alterations. Machine learning models can utilize these functional features to identify patients at risk for neuropsychiatric comorbidities and predict treatment response. Recent randomized controlled trials demonstrate that targeted interventions (probiotics, prebiotics, postbiotics, fecal microbiota transplantation) significantly improve Psoriasis Area and Severity Index scores, inflammatory markers, and microbiota composition. The evidence supports a shift toward integrated microbiome strategies, emphasizing functional approaches including mitochondrial therapies, psychobiotics, precision nutrition, and multi-omics-guided therapies.},
}

@article {pmid41568320,
year = {2025},
author = {Perry, S and Pillarisetti, L and Gelfman, T and Agrawal, DK},
title = {Gut-Brain Axis in Inflammatory Bowel Disease: Pathogenesis and Therapeutics.},
journal = {Archives of internal medicine research},
volume = {8},
number = {4},
pages = {339-345},
pmid = {41568320},
issn = {2688-5654},
support = {R25 AI179582/AI/NIAID NIH HHS/United States ; },
abstract = {Inflammatory Bowel Disease (IBD), encompassing Crohn's disease and ulcerative colitis, is a chronic inflammatory disorder of the gastrointestinal tract driven by complex interactions between genetic susceptibility, environmental triggers, microbial dysbiosis, and immune dysregulation. The gut microbiome, composed primarily of Firmicutes and Bacteroidetes, plays a crucial role in maintaining intestinal barrier integrity, immune balance, and neuroimmune signaling. Disruption of this microbial ecosystem is characterized by loss of beneficial short chain fatty acid producing bacteria and expansion of pathogenic species which promotes mucosal inflammation, cytokine release, and neuroimmune signaling that can disrupt mental health through the gut-brain axis. Emerging evidence links microbial metabolites, vagal tone, and the hypothalamic-pituitary-adrenal axis in a feedback loop that perpetuates inflammation and alters mood regulation. Current therapeutic approaches include diet modification, osteopathic manipulative treatments, fecal microbiota transplantation and phage therapy. This article focuses on understanding mechanisms linking dysbiosis, immune activation, and neuroinflammation to guide future interventions. A holistic model addressing the gut-brain axis holds the greatest promise for improving outcomes and personalizing care for IBD.},
}

@article {pmid41568235,
year = {2026},
author = {Sun, M and Zang, D and Chen, J},
title = {Redefining microbial clearance and ecological recovery in periodontal microbiome studies.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2616968},
pmid = {41568235},
issn = {2000-2297},
}

@article {pmid41568050,
year = {2025},
author = {Yang, J and Yuan, N and Guo, T and Feng, Y and Guo, S and Zhou, D and Lin, P and Wang, A and Jin, Y},
title = {Comparative study of milk microbiota and metabolome in long-lived dairy cows with different persistent production capacities.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1725031},
pmid = {41568050},
issn = {1664-302X},
abstract = {Improving dairy cow lifespan is essential for sustainable livestock production. The milk microbiome and metabolome are closely associated with mammary gland health and influence the persistent productivity of dairy cows. However, the characteristics of the milk microbiome and metabolome underlying persistent productivity remain unknown. In this study, 16S rRNA sequencing and untargeted metabolomics were applied to evaluate the milk microbiome and milk metabolome composition of long-lived, high-yielding cows (LH) and long-lived, low-yielding cows (LL). The results showed that no significant differences were observed in the α- and β-diversity of milk microbiota between the two groups (p > 0.05). However, the community assembly processes differed significantly. The LH group exhibited significantly higher levels of homogeneous selection, drift (and others) (p < 0.05). In contrast, dispersal limitation, homogeneous dispersal, and heterogeneous selection were significantly lower (p < 0.05). In addition, in the milk of LH cows, UCG-005, Prevotellaceae UCG-003, Ruminococcus, unclassified f Oscillospiraceae, norank f Fodinicurvataceae, and unclassified f Ruminococcaceae were significantly enriched (LDA > 2, p < 0.05). The bacterial functions of protein digestion and absorption and N-glycan biosynthesis were significantly enriched in the LH group, while thyroid hormone synthesis and pathogenic Escherichia coli infection were significantly enriched in the LL group (LDA > 2, p < 0.05). Additionally, the milk of LH cows exhibited elevated levels of omega-3 polyunsaturated fatty acids (PUFAs), including PE (20:5/0:0), LPC (20:5 (5Z, 8Z, 11Z, 14Z, 17Z)/0:0), LPE (0:0/20:5 (5Z, 8Z, 11Z, 14Z, 17Z)), and PE (22:5/0:0) (LDA > 2, p < 0.05). Milk PE (18:3/0:0) showed a significant positive correlation with milk Prevotellaceae UCG-003 and UCG-005 (|r| > 0.50, p < 0.05). These bacterial genera were significantly negatively correlated with the predicted microbial function pathogenic E. coli infection (|r| > 0.50, p < 0.05). The accumulation of omega-3 PUFAs in milk may help maintain the homeostasis of mammary microbial environment and promote mammary health. These results provide novel insights into the microbial and metabolic signatures underlying persistent productivity, offering potential targets for nutritional and microbial interventions to enhance dairy cow longevity.},
}

@article {pmid41568046,
year = {2025},
author = {Pîrvu, AS and Biţă, A and Scorei, IR and Gheonea, DI and Mogoşanu, GD},
title = {Boron symbiotaxis: a new concept in host-microbiome communication.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1719918},
pmid = {41568046},
issn = {1664-302X},
abstract = {Boron (B) participates in biological systems through reversible complexation with diols and phosphate esters, enabling it to stabilize labile furanosyl intermediates and to modulate the chemical landscape in which QS signals operate. Dietary B appears to enter two functional pools: plasma-accessible boron (PAB), composed of freely diffusible B(OH)3/B(OH)4 [-], and microbiota-accessible boron complexes (MABCs), formed in situ with polyols, chlorogenic acids, and fructans/inulins. MABCs persist at the mucus-epithelium interface, creating local reservoirs that can influence the persistence, diffusion, and recognition of AI-2-related molecules. Here we propose a structured, testable framework-"boron symbiotaxis"-to describe how B may stabilize 4,5-dihydroxypentane-2,3-dione (DPD)-derived intermediates (and, in defined lineages, form the furanosyl borate diester AI-2B), localize chemical potential via MABCs at the mucosal surface, and orient microbial behavior toward particular community states. This framework does not assume that enhanced AI-2 signaling is inherently beneficial; QS coherence can also support opportunistic growth or virulence, depending on ecological context. We therefore outline experimental approaches-including speciation-resolved [11]B-NMR, targeted LC-MS for AI-2/AI-2B, and bacterial reporter strains with defined AI-2 receptors-to discriminate beneficial from adverse outcomes. Altogether, we highlight B as a chemically plausible modulator of QS architectures in the gut, propose falsifiable predictions linking diet → B speciation → AI-2 dynamics → host phenotypes, and identify scenarios in which B-driven stabilization or localization could be either advantageous or detrimental.},
}

@article {pmid41568044,
year = {2025},
author = {Kan, Y and Ma, XY and Wang, YL and Sun, B and Wang, S},
title = {A comprehensive comparison of web-based tools for amplicon-metagenomic analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1711000},
pmid = {41568044},
issn = {1664-302X},
abstract = {Amplicon sequencing provides a suitable approach for microbiome profiling, supported by a variety of R-based and web-based tools. In this review, we systematically evaluated eight freely accessible web-based tools suitable for users without scripting experience, comparing their performance across modules including alpha and beta diversity, taxonomic composition, differential comparison, network and correlation analysis, functional profiling, machine learning, tree-plot and user experience. While all tools exhibit limited data filtering and normalization options, performance varied considerably across modules. Mian and MicrobiomeAnalyst 2.0 excelled in alpha diversity analysis and taxonomic composition analysis, METAGENassist outperformed others in beta diversity, and MicrobiomeAnalyst 2.0 achieved the highest score in differential comparison and functional analysis. Namco and Mian outperform in network analysis and correlation analysis, respectively. Machine-learning functions were comparable across animalcules, MicrobiomeAnalyst 2.0 and METAGENassist, with the best treeplot visualization in animalcules and MicrobiomeAnalyst 2.0. And, user experience was highest for animalcules and Mian. Overall, MicrobiomeAnalyst 2.0 achieving the highest overall performance, followed by Mian and Namco. Several limitations among evaluated tools include inconsistent accessibility, diverse input data formats, restricted feature sets, and incomplete retention of key information in exported figures. Future development should integrate preprocessing, interactive visualization and figure export, alongside advanced statistical methods, multi-omics integration and meta-analytical capabilities, to enhance flexibility, reproducibility and interpretability. This comprehensive assessment provides a practical reference for researchers in selecting the most suitable web-based tools for specific microbiome analysis tasks, highlighting the importance of both module-specific performance and overall tool capabilities.},
}

@article {pmid41568043,
year = {2025},
author = {Li, P and Peng, H and Huang, Z and Sun, Z and Li, Y and Wu, S and Lin, L and Zhang, S and Li, H and Cao, Y},
title = {Integrated metabolomics and gut microbiota to reveal the anti-tumor mechanism of Jinfu'an decoction in tumor-bearing mice.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1643268},
pmid = {41568043},
issn = {1664-302X},
abstract = {INTRODUCTION: Jinfu'an Decoction (JFAD), a traditional Chinese medicine, is used to treat lung cancer and has shown significant anti-tumor effects in clinical and experimental studies. This study integrates metabolomics and gut microbiota analysis to elucidate JFAD's anti-tumor mechanisms.

METHODS: A suspension of A549-luc cells, approximately 1 × 10[6] in number, was injected subcutaneously into the right axilla of mice to establish a tumor-bearing nude mouse model. Mice were randomly assigned to four groups: model group (MG), low-dose JFAD (JFAD-L), medium-dose JFAD (JFAD-M), and high-dose JFAD (JFAD-H), receiving treatments via gavage for 21 days. Additionally, three nude mice formed the normal group (NG), receiving no treatment. Changes in gut microbiota and serum metabolites were assessed using 16S rRNA gene sequencing and UHPLC-QE-MS non-targeted metabolomics.

RESULTS: JFAD may help restore the balance of intestinal flora in mice with lung cancer to a more normalized state. Our findings indicate that JFAD increases the abundance of Bacteroidia and decreases the presence of Firmicutes and Clostridia, thereby altering intestinal bacterial composition. Primary metabolic pathways associated with significant differences include nicotinate and nicotinamide metabolism, glycine, serine and threonine metabolism, and pyrimidine metabolism. A key differential metabolite identified was succinic acid, part of the central carbon metabolism pathway in cancer. Succinic acid showed a negative correlation with gut microbiota families Tannerellaceae and Campylobacterota. In the MG group, essential amino acid levels were markedly diminished but were significantly elevated after JFAD-M intervention. KEGG pathway analysis identified these amino acids as being linked to the PI3K/AKT and mTOR signaling pathways.

DISCUSSION: JFAD regulates the homeostasis of intestinal flora and influences amino acid and succinic acid metabolism through various pathways. These mechanisms could serve as potential targets for JFAD in inhibiting lung cancer invasion and metastasis.},
}

@article {pmid41568034,
year = {2025},
author = {Yu, F and Song, J and Qi, L and Liu, J and Yang, Y and Li, W and Li, L and Ma, ZS},
title = {Gene and function diversity-area relationships in the inflammatory bowel disease fecal and mucosal microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1660973},
pmid = {41568034},
issn = {1664-302X},
abstract = {The diversity-area relationship (DAR), an extension of the classic species-area relationship (SAR), provides a powerful framework for understanding how biodiversity scales across space. In this study, we applied DAR and its metagenomic counterpart (m-DAR) to investigate the spatial scaling of metagenomic genes (MGs) and metagenomic functional gene clusters (MFGCs) of seven functional databases in the gut microbiomes of individuals with inflammatory bowel disease (IBD) and healthy cohorts. Using shotgun sequencing data from 42 mucosal and 22 fecal samples from both healthy and IBD cohorts, we modeled how this MGs and MFGCs accrues with area (samples), estimating diversity scaling parameters (z), pair-wise diversity overlap (PDO), and maximal accrual diversity (MAD), which reflects the total potential diversity. We found that mucosal communities exhibited greater dissimilarity (less pair-wise diversity overlap) between individuals than fecal cowmmunities at the levels of gene richness and evenness (q = 1, 2), whereas fecal communities showed a stronger influence from dominant, abundant genes (q = 2, 3). Furthermore, healthy gut microbiomes showed greater similarity than those of IBD at the level of gene richness (q = 0), but showed greater dissimilarity at the level of abundant genes and dominant genes. Healthy gut microbiomes generally demonstrated a higher potential total diversity compared to those from IBD patients. Notably, fecal samples captured a broader range of microbial diversity than mucosal samples. Additionally, mucosal communities showed greater dissimilarity than fecal communities in almost all the MFGCs of the seven databases except ARDB, which showed the same trend as MGs. We also identified that specific functional clusters related to antibiotic resistance, such as genes for chloramphenicol and vancomycin resistance, displayed distinct scaling behaviors, suggesting their potential role in IBD pathogenesis. These findings demonstrate that the gut microbiome in IBD is not merely less diverse but is fundamentally restructured in its spatial architecture. The application of DAR provides a novel, quantitative insight to diagnose and understand this dysbiosis, moving beyond simple diversity metrics to capture the spatial diversity scaling of microbial genes and functions.},
}

@article {pmid41568032,
year = {2025},
author = {Wang, M and Sun, Y and Gong, W},
title = {Machine learning models diagnose oral squamous cell carcinoma based on cross-cohort oral microbial signatures.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1692186},
pmid = {41568032},
issn = {1664-302X},
abstract = {INTRODUCTION: The saliva microbiome of oral squamous cell carcinoma (OSCC) patients has been gradually unveiled, but there is a lack of cross-cohort studies, and there is no non-invasive diagnostic model across cohorts for OSCC.

METHODS: This study aimed to investigate the differences in saliva microbial composition between OSCC patients and healthy individuals using cross-cohort saliva microbiome data, comprising 354 healthy individuals and 311 OSCC patients (total n=665).

RESULTS: We found significant differences in saliva microbial composition between OSCC patients and healthy people. Seven microorganisms were significantly reduced and seven were significantly increased in OSCC patients, serving as potential biomarkers. Machine learning models, including Random Forest, Extra Trees, Gradient Boosting, and XGBoost, were constructed to diagnose OSCC using saliva microorganisms. These models achieved area under the curve (AUC) values ranging from 63.1% to 96.9% at both genus and species levels in a rigorous leave-one-cohort-out cross-validation.

DISCUSSION: Our study provides a robust non-invasive diagnostic model for OSCC and demonstrates that high diagnostic accuracy is achievable at both genus and species levels, suggesting that taxonomic resolution is not the primary limiting factor. Instead, the choice of model construction methods is crucial. Therefore, greater attention should be paid to the selection of model methods in clinical applications.},
}

@article {pmid41568030,
year = {2025},
author = {Van den Abbeele, P and Vu, LD and Poppe, J and van Hengel, IAJ and Baudot, A and Zhang, Y and Chen, Z and Yan, J},
title = {Yeast protein modulates metabolites derived from the human gut microbiota of older male adults ex vivo to strengthen gut barrier function and reduce inflammation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1697734},
pmid = {41568030},
issn = {1664-302X},
abstract = {INTRODUCTION: The rising global demand for protein is accelerating interest in sustainable alternatives with health benefits. While glycans are well-known for supporting gut health, the role of dietary proteins in promoting healthy aging via microbiome modulation is less understood. Yeast protein (YP) represents a sustainable, non-animal, hypoallergenic option.

METHODS: Using the clinically predictive ex vivo SIFR[®] technology (Systemic Intestinal Fermentation Research), we examined how YP influences the microbiome of older human adults (50-65 years, n = 6), comparing its effects to whey protein isolate (WPI) and soy protein isolate (SPI).

RESULTS: At a dose equivalent to 40 g/day, all protein sources supported gut barrier integrity and reduced inflammation, reflected by decreased pro-inflammatory markers and increased IL-10. These benefits were linked to higher short-chain fatty acid (SCFA) production, mainly from Bacillota and Bacteroidota, including microbial markers associated with healthy aging. YP and SPI specifically restored butyrate-producing microbes and increased microbial diversity, which is linked to longevity. Untargeted metabolomics revealed numerous beneficial amino acid-derived metabolites, including indoles and polyamines, known to act through gut-organ axes to extend health span. Despite similar overall profiles, product-specific differences emerged: YP most strongly reinforced barrier integrity, produced the lowest gas levels (suggesting superior tolerability), and yielded the lowest trimethylamine N-oxide, a compound linked to increased mortality in older adults.

DISCUSSION: Collectively, these findings highlight the potential of YP as a sustainable protein source that modulates the microbiome and metabolome, reduces inflammation, and reinforces gut barrier function, which are key mechanisms for preserving health span and mitigating age-related decline.},
}

@article {pmid41567836,
year = {2026},
author = {Yang, J and Park, JS and Oh, SO and Oh, SY and Hur, JS},
title = {Fungal Microbiome Within Lichen as a Potential Bioindicator of Climate Change: Insights from Transplant Field Study.},
journal = {Mycobiology},
volume = {54},
number = {1},
pages = {146-160},
pmid = {41567836},
issn = {1229-8093},
abstract = {Global warming is a major driver of ecological change, yet its impacts on bioindicators such as lichens remain unclear. Lichens, formed by symbiotic associations between fungi and photosynthetic partners, are widely used to assess environmental conditions. However, studies relying on traditional physiological measures, including chlorophyll content and photosynthetic activity, have reported inconsistent responses to climate change. We hypothesized that short-term exposure of lichens to elevated temperatures would not alter these conventional physiological traits but might instead lead to changes in their associated microbiomes. Using a field transplant experiment, we exposed lichens to higher temperature environments and assessed both physiological and microbiome responses. Chlorophyll content and tissue damage showed no significant differences between control and warmed conditions. In contrast, high-throughput sequencing of 16S and ITS regions revealed pronounced shifts in microbial communities. Fungal assemblages exhibited marked declines in alpha diversity, co-occurrence network complexity, and stability of the core microbiome. By comparison, bacterial communities demonstrated greater resilience. Notably, the black yeast Cutaneotrichosporon debeurmannianum became dominant in high-temperature environments. Our findings show that while traditional physiological traits of lichens remain stable under short-term warming, their fungal microbiomes are highly sensitive to thermal stress. We identify fungal community structure-particularly the presence of C. debeurmannianum-as a promising indicator of climate change. These results highlight the importance of considering microbial symbionts when evaluating the ecological responses of lichens to global warming.},
}

@article {pmid41567684,
year = {2025},
author = {Lanas, A and Alvarez-Mercado, AI},
title = {Editorial: Improving the gut microbiome: applications of fecal transplantation in disease, volume II.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1758943},
doi = {10.3389/fmed.2025.1758943},
pmid = {41567684},
issn = {2296-858X},
}

@article {pmid41567608,
year = {2025},
author = {Kayashima, A and Fukuhara, S and Miyamoto, K and Iwasaki, E and Kato, M and Sujino, T},
title = {Correction: Biliary stents reshape the bile microbiome in the absence of cholangitis.},
journal = {Endoscopy international open},
volume = {13},
number = {},
pages = {a27723924},
doi = {10.1055/a-2772-3924},
pmid = {41567608},
issn = {2364-3722},
abstract = {[This corrects the article DOI: 10.1055/a-2733-3468.].},
}

@article {pmid41567559,
year = {2026},
author = {Mu, Y and Li, D and Deng, X and Lei, Y and Wang, Y and Wu, K and Jiang, L and Zhang, H and Zhao, C and Huang, Y and Yu, S and Liu, X and Zhang, C},
title = {Effects of region and ripening on the physicochemical properties, microbiome, metabolome, and volatilome of Chinese dry-cured ham.},
journal = {Food chemistry: X},
volume = {33},
number = {},
pages = {103502},
pmid = {41567559},
issn = {2590-1575},
abstract = {Long-term ripened dry-cured ham is popular across China, but the mechanisms by which production region and ripening time regulate its quality remain incompletely understood. Therefore, the temporal dynamics of multi-dimensional characteristics of Zhejiang Jinhua, Yunnan Xuanwei, and Guizhou Panxian hams were explored. Results showed decreased moisture and fat but increased pH, NaCl, protein, and amino acid nitrogen with prolonged ripening. Bacterial α-diversity and fungal β-diversity were closely related to ripening and region, respectively, while the relative abundance of dominant genera (Staphylococcus, Kocuria, Aspergillus, and Debaryomyces) varied by both factors. GC-TOF-MS and GC-IMS detected 76 non-volatile metabolites (predominantly amino acids and their derivatives) and 84 volatile compounds (mainly alcohols and aldehydes), highlighting the crucial role of region in shaping the metabolic profile. Moreover, correlation analysis and functional prediction confirmed the indispensable contribution of bacteria to quality formation. These results provide scientific support for the high-quality development of the dry-cured ham industry.},
}

@article {pmid41567401,
year = {2025},
author = {Gahlot, KD},
title = {Microbial strategies for drought stress mitigation- a sustainable frontier in plant resilience.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1740879},
pmid = {41567401},
issn = {1664-462X},
abstract = {Drought stress is a major constraint on global agriculture, exacerbated by climate change and increasing water scarcity. Conventional strategies such as breeding and genetic engineering have improved drought tolerance in crops, yet their scalability and adaptability remain limited. Microbial interventions, particularly those involving beneficial plant-associated microorganisms, offer a sustainable and complementary approach to enhance plant resilience under water-deficit conditions. This opinion article explores microbial strategies for drought mitigation, emphasizing the role of Rhizobium strains, digested distillery spent wash, and multi-omics technologies. Recent studies demonstrate that developed Rhizobium strains significantly improve soil fertility, nodulation, and nitrogen fixation in legumes, contributing to higher yields and better soil health in drought-prone regions. Similarly, the application of digested distillery spent wash in chickpea (Cicer arietinum) enhances nutrient uptake, photosynthetic activity, and drought tolerance. Advances in genomics, transcriptomics, proteomics, and metabolomics have revealed complex plant-microbe interactions, identifying microbial metabolites and signaling pathways that activate drought-responsive genes and osmo-protective mechanisms. Despite these promising findings, challenges persist in translating laboratory results to field conditions due to soil heterogeneity and microbial competition. Precision microbiome engineering, informed by multi-omics data, and the development of tailored microbial consortia represent a transformative frontier for sustainable agriculture. By integrating ecological complexity with technological innovation, microbial strategies can reduce chemical inputs, promote regenerative practices, and build resilient agroecosystems. This article advocates elevating microbes from supporting roles to central players in addressing drought stress and ensuring global food security.},
}

@article {pmid41567168,
year = {2026},
author = {Arshad, MT and Ali, MKM and Awlqadr, FH and Maqsood, S and Ikram, A and Hossain, MS and Abdullahi, MA and Rashed, MM},
title = {Mitigation of Metabolic Diseases Through Personalized Nutrition: A Critical In-Depth Review.},
journal = {Food science & nutrition},
volume = {14},
number = {1},
pages = {e71387},
pmid = {41567168},
issn = {2048-7177},
abstract = {Obesity, cardiovascular disease, and type 2 diabetes mellitus (T2DM) represent major global health and economic concerns. Traditional dietary recommendations frequently overlook individual heterogeneity in metabolic health. Personalized nutrition will provide a more focused approach to preventing chronic diseases by tailoring dietary recommendations according to lifestyle, metabolic, and genetic factors. This review examines the role of personalized nutrition in preventing metabolic diseases, with a focus on key components of nutrient-gene interactions, including nutrigenomics, nutrigenetics, the gut microbiome, and biomarker-based therapies. The main aim of this article is to investigate how variation within the microbiome and among genes impacts nutrient metabolism and make a case for successful evidence of individualized dietary intervention for obesity, diabetes, and cardiovascular disease. Future advancements in artificial intelligence, and genetic testing may make personalized nutrition more accessible, but there are questions about the price, feasibility, and ethics of its widespread use. The scope for personalized nutrition is wide and has strong potential to impact preventative health. An independent assessment calls for sustained scientific research, equitable accessibility, and ethical considerations that can make public health policies clinically relevant.},
}

@article {pmid41567085,
year = {2026},
author = {Jackson, CM and Collado, MC and Dallas, DC and Insel, RA and Macpherson, AJ and Palmer, DJ and Seppo, AE and Verhasselt, V and Järvinen, KM},
title = {An Old Story Back: Human Milk Antibodies' Protective Roles Against Allergy Development.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70218},
pmid = {41567085},
issn = {1398-9995},
support = {639226//H2020-ERC/ ; //Horizon Europe Program/ ; //European Joint Programming Initiative "A Healthy Diet for a Healthy Life" (JPI-HDHL)/ ; PCI2021-122059-2A//Programación Conjunta Internacional/ ; PID2022-139475OB-I00//Spanish Ministry of Science and Innovation/ ; R01HD109193/GF/NIH HHS/United States ; R01HD097367/GF/NIH HHS/United States ; R01HD106140/GF/NIH HHS/United States ; //Family Larsson Rosenquist Foundation/ ; //Stan Perron Charitable Foundation Fellowship/ ; U19AI175113//National Institute of Allergy and Infectious Diseases of the National Institutes of Health/ ; U01AI173032//National Institute of Allergy and Infectious Diseases of the National Institutes of Health/ ; },
abstract = {Human milk is a rich source of immunomodulatory factors that influence the development of the infant immune system, including susceptibility to allergic diseases. Among these components, milk antibodies have been extensively studied for their role in protecting against infections; however, their potential contribution to allergy prevention may be equally important. The mechanisms of protection include allergen exclusion, enhanced and targeted antigen presentation, immune modulation via shaping of the infant gut microbiome, and direct regulation of gut immune responses. This review summarizes current evidence on the secretion of human milk antibodies, highlights what is known and what remains unclear about their role in allergy prevention and outlines the need for further research to develop antibody-based strategies for early allergy prevention.},
}

@article {pmid41566746,
year = {2026},
author = {Navarro, A and Rodea, GE and de la Cruz-Montoya, AH and Díaz-Velásquez, CE and Vaca-Paniagua, F and Navarro-Cid Del Prado, A and Tirado-Gómez, LL and Vilchis-Reyes, A and García de la Torre, G and Cruz-Licea, V and Eslava-Campos, C and Castelán-Sánchez, HG},
title = {Gut Microbiota Composition in Adolescents From Mexico City, Associations With Nutritional and Socioeconomic Factors: Results From a Pilot Study.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {2},
pages = {e70386},
pmid = {41566746},
issn = {1613-4133},
support = {//Programa de Innovación Tecnológica (PAPIIT)/ ; },
mesh = {Humans ; Adolescent ; *Gastrointestinal Microbiome/physiology ; Mexico ; Male ; Female ; Child ; Pilot Projects ; Diet ; Socioeconomic Factors ; Feces/microbiology ; Body Mass Index ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics ; Nutritional Status ; },
abstract = {The gut microbiota is a key determinant of metabolic health in adolescence, a critical period for the onset of obesity. Understanding its associations with body mass index (BMI), diet, and socioeconomic status (SES) helps identify early determinants of metabolic risk. We analyzed stool samples from 95 Mexican adolescents (11-15 years) using 16S rRNA V3-V4 sequencing. The main phyla were Bacteroidetes, Firmicutes, and Proteobacteria, with. At the genus level Azobacteroides Candidatus, Parabacteroides, Bacteroides, and Prevotella being the most abundant. Overweight and obese adolescents showed lower diversity and more Bacteroidetes, while normal-weight peers had more Firmicutes and beneficial taxa. Lactobacillus was enriched in normal-weight individuals, while Parabacteroides and Prevotella were more abundant in adolescents with low SES. A diet high in sugar-sweetened beverages and low in whole grains was associated with a predominance of Bacteroides and lower diversity. Low SES was also associated with potential pathogens, including Escherichia and Salmonella, and gastrointestinal symptoms. In particular, Vibrio and Salmonella were inversely associated with cholesterol and triglycerides, while Clostridiodes was positively correlated with triglycerides. Diet and SES influenced the adolescent gut microbiome, by shaping diversity, potentially pathogenic taxa, and their associations with metabolic health indicators.},
}

Humans
Adolescent
*Gastrointestinal Microbiome/physiology
Mexico
Male
Female
Child
Pilot Projects
Diet
Socioeconomic Factors
Feces/microbiology
Body Mass Index
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics
Nutritional Status

@article {pmid41566434,
year = {2026},
author = {Xu, L and Lv, X and Lu, X and Zhang, X and Liu, J and Meng, Y and Wu, D},
title = {Microbial and metabolic responses of maize silage to leaf blight: implications for fermentation and protein stability.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08142-4},
pmid = {41566434},
issn = {1471-2229},
support = {202301AU070035//Yunnan Fundamental Research Projects/ ; 2023//Xingzhao Talent Support Program/ ; 2025//Yunnan "Colorful Clouds Postdoctoral Program" Innovation Project/ ; 202301BA070001-120//Special Basic Cooperative Research Programs of Yunnan Provincial Undergraduate Universities' Association/ ; },
abstract = {Foliar fungal diseases lead to a significant reduction in dry matter of plants, thereby negatively affecting silage fermentation kinetics. This study investigated the effects of leaf blight on ensiling kinetics, microbial succession, and nitrogen metabolism in whole-crop maize, and further examined whether inoculation with Lactiplantibacillus plantarum HT1 could mitigate disease-induced proteolysis through remodeling of the metabolic pathways. Three treatments were established: (i) healthy maize silage (CON), (ii) maize silage affected by leaf blight (DCON), and (iii) maize silage affected by leaf blight and inoculated with L. plantarum HT1 (HT1, 1 × 10[5] cfu/g FM based on the fresh weight basis). Samples of 300 g fresh material were packed into polyethylene vacuum bags (300 × 400 × 0.2 mm) and vacuum-sealed to establish anaerobic conditions for 60 days of ensiling. Before ensiling, DCON had significantly lower crude protein content (7.06% vs. 8.91% DM, P = 0.001) compared with CON. In addition, the WSC content markedly decreased by leaf blight (88.7 vs. 119 g/kg DM, P = 0.016). LAB abundance was significantly lower (3.22 vs. 4.22 log CFU/g FM, P = 0.022), whereas mold counts sharply increased (4.25 vs. 3.22 log CFU/g FM, P = 0.001) in DCON than in CON. The DCON showed elevated pH, significantly reduced lactic acid content, and markedly increased butyric acid content compared with those of the CON (P < 0.05). DCON had the highest NH3-N content (17.2 g/kg TN), exceeding those of CON (12.3 g/kg TN) and HT1 (10.3 g/kg TN, P = 0.005). Aminopeptidase and carboxypeptidase activities increased to 46.4 and 167 U·h[- 1]·g FM[- 1], respectively, which were much higher than those of the CON (27.4 and 140 U·h[- 1]·g FM[- 1]). Microbiome β-diversity separated DCON from CON and HT1, with enrichment of putative proteolytic taxa. Metabolomics indicated upregulated amino acid degradation (branched chain and glutamate pathways) and disrupted nitrogen homeostasis in the DCON treatment. Leaf blight created an early high-pH window that amplified proteolysis and nitrogen loss through coordinated shifts in substrates, microbiota, and amino acid catabolism. Inoculation with L. plantarum HT1 caused rapid acidification, curtailed proteolysis, and rewired metabolic and community networks toward a healthy state, achieving coordinated restoration of fermentation quality and protein preservation in disease-challenged maize.},
}

@article {pmid41566339,
year = {2026},
author = {Fernández-Trapote, E and Cobo-Díaz, JF and Oliveira, M and Puente, A and Berdejo, D and Puente, H and Cordero-García, R and López, M and Prieto, M and Argüello, H and Alvarez-Ordóñez, A},
title = {Microbiome and resistome successions in pig carcasses and fresh pork meat throughout slaughtering, processing and shelf-life.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02288-3},
pmid = {41566339},
issn = {2049-2618},
support = {FPU21/03421//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; PRE2021-098910//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; CNS2022-136066//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; No 818368//European Commission under the European Union´s Horizon 2020/ ; PID2020-118813GB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; },
abstract = {BACKGROUND: Slaughterhouses and meat cutting plants represent potential hotspots for the spread and transfer of spoilage and pathogenic, including antimicrobial resistant, bacteria to meat and meat products. Here, we characterise the progression of the microbiome and resistome of two pork cuts (loin and sirloin) at different stages of processing, from the slaughter line to the end of shelf-life. To this end, we analysed samples from facility surfaces, carcasses, and meat cuts using whole metagenome sequencing.

RESULTS: The taxonomic and antimicrobial resistance gene (ARG) profiles of carcasses and meat cuts were significantly influenced by the point of sampling and the processing room. The facility surfaces were found to be the main source of some abundant genera, such as Anoxybacillus, Acinetobacter, Pseudomonas, and Brochothrix, in carcasses and meat cuts. A total of 1,291 metagenome-assembled genomes were reconstructed, corresponding to the most prevalent species identified in the taxonomic analysis at the read level. A reduction in bacterial and ARGs richness and diversity was observed for carcasses and meat cuts along the production chain, which suggests that processing procedures are effective in reducing bacterial and ARGs loads. Nonetheless, an increase in the ARGs load was observed at two sampling points: the carcass after evisceration and the sirloin at the end of its shelf-life (in this case linked to the increase of a single gene, tet(L)). The ARGs most frequently detected were those associated with resistance to tetracyclines, aminoglycosides, and lincosamides. Acinetobacter (in processing environments and carcass/meat samples) and Staphylococcus (in carcasses and meat) were identified as the main genera associated with the ARGs found.

CONCLUSIONS: Overall, our results provide the most detailed metagenomics-based perspective on the microbial successions of pig carcasses and fresh meat cuts during slaughtering, processing, and commercialisation. The observations made suggest that selection pressures imposed by processing steps and contact with facility surfaces contribute to shaping the microbiome and resistome of the two pork products throughout their production line and shelf-life. Video Abstract.},
}

@article {pmid41566333,
year = {2026},
author = {Liu, W and Sha, X and Zhao, N and Liu, B and Yang, G and Jia, L and Sui, G},
title = {Multi-omics reveals an association of the gut butyrate-IDO1-tryptophan axis with Yinchenhaotang plus Zexietang-ameliorated NASH in a microbiota-dependent manner.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {44},
pmid = {41566333},
issn = {1749-8546},
support = {82374423//National Natural Science Foundation of China/ ; 82474221//National Natural Science Foundation of China/ ; 2024-MSLH-290//Liaoning Province Science and Technology Plan Joint Program (Natural Science Foundation - Surface Project/ ; LJ222410162041//the Education fund item of Liaoning province/ ; },
abstract = {BACKGROUND: Nonalcoholic steatohepatitis (NASH) is a complex metabolic disorder with limited effective treatments, and its pathogenesis involves intricate crosstalk between gut microbiota, metabolism, and host signaling. Yinchenhaotang plus Zexietang (YCHZX), a traditional Chinese medicine (TCM) formulation, exhibits therapeutic potential in NASH, but its underlying mechanism-especially its interactions with the gut microbiota and metabolic networks-remains unclear.

METHODS: A NASH mouse model was established via a high-fat/high-fructose/high-cholesterol diet. Mice were treated with YCHZX or its individual components (YCH, ZX). Serum biochemistry and liver histopathology were used to evaluate systemic therapeutic effects. Integrated multi-omics analyses (16S rRNA microbiome, serum metabolomics, colon transcriptomics) combined with immunofluorescence, immunohistochemistry, RT‒qPCR and ELISA were employed to explore regulatory networks. Complementarily, the effects of sodium butyrate and indolelactic acid (ILA) were investigated using an LPS-stimulated Caco-2 cell model. Antibiotic-mediated gut microbiota ablation was performed to verify microbiota dependency.

RESULTS: YCHZX outperformed YCH and ZX in improving TC, LDL-C and hepatic pathology. Integrated multi-omics analysis demonstrated that the efficacy of YCHZX was associated with a distinct restructuring of the gut microbiota, specifically enriching butyrate-producing genera such as Lachnospiraceae_NK4A136_group. Concomitantly, YCHZX intervention suppressed colonic indoleamine 2,3-dioxygenase 1 (IDO1) and significantly elevated serum levels of ILA, a shift validated in vitro by the direct inhibitory effect of sodium butyrate on IDO1. The elevated ILA was shown to strengthen the gut barrier by upregulating occludin expression in LPS-stimulated Caco-2 cells via an aryl hydrocarbon receptor (AhR)-dependent mechanism. Further, YCHZX activated the AhR, upregulating tight-junction proteins (occludin) to reduce lipopolysaccharide (LPS) translocation, and inhibiting hepatic LPS/TLR4 signaling, TG accumulation, and IL-1β inflammation. All these effects of YCHZX were diminished by antibiotic-induced gut microbiota depletion.

CONCLUSION: Our findings demonstrate that YCHZX alleviates NASH in a gut microbiota-dependent manner. We propose a mechanism whereby YCHZX enriches butyrate-producing bacteria, which is associated with the suppression of colonic IDO1 and a shift in tryptophan metabolism toward ILA production. The increased ILA, in turn, contributes to the activation of the AhR, thereby restoring gut barrier integrity and mitigating liver inflammation.},
}

@article {pmid41566206,
year = {2026},
author = {Aliyat, FZ and Ibijbijen, J and El Mderssa, M and Hijri, M and Ahmed, B},
title = {Argan fruit microbiomes: influence of biogeographic and soil driven environmental factors.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08168-8},
pmid = {41566206},
issn = {1471-2229},
support = {AS-77//OCP Group/ ; Seed Grant - 151STPR07-4//Université Mohammed VI Polytechnique/ ; },
}

@article {pmid41565962,
year = {2026},
author = {Simms, C},
title = {Sending babies to nursery completely reshapes their microbiomes.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41565962},
issn = {1476-4687},
}

@article {pmid41565819,
year = {2026},
author = {Ricci, L and Heidrich, V and Punčochář, M and Armanini, F and Ciciani, M and Nabinejad, A and Fazaeli, F and Piperni, E and Servais, C and Pinto, F and Valles-Colomer, M and Asnicar, F and Segata, N},
title = {Baby-to-baby strain transmission shapes the developing gut microbiome.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41565819},
issn = {1476-4687},
abstract = {The early infant microbiome is largely primed by microbial transmission from the mother between birth and the first few weeks of life[1-3], but how interpersonal transmission further shapes the developing microbiome in the first year remains unexplored. Here we report a metagenomic survey to model microbiome transmission in the nursery setting among babies attending the first year, their educators and their families (n = 134 individuals). We performed dense longitudinal microbiome sampling (n = 1,013 faecal samples) during the first year of nursery and tracked microbial strain transmission within and between nursery groups across 3 different facilities. We detected extensive baby-to-baby microbiome transmission within nursery groups even after only 1 month of nursery attendance, with nursery-acquired strains accounting for a proportion of the infant gut microbiome comparable to that from family by the end of the first term. Baby-to-baby transmission continued to grow over the nursery year, in an increasingly intricate transmission network with single strains spreading in some classes, and with multiple baby-acquisition and species-transmissibility patterns. Having siblings was associated with higher microbiome diversity and reduced strain acquisition from nursery peers, while antibiotic treatment was the condition that most accounted for the increased influx of strains. This study shows that microbiome transmission between babies is extensive during the first year of nursery, and points to social interactions in infancy as crucial drivers of infant microbiome development.},
}

@article {pmid41565754,
year = {2026},
author = {Solís-Marín, FA and Vergara-Ovando, C and Rojas-Oropeza, M and Calderón-Gutiérrez, F and Medina-Tanco, G and Cabirol, N},
title = {Asterinides sp. an endemic stygobitic seastar from an anchialine cave and its interactions among prokaryotic communities.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-36065-5},
pmid = {41565754},
issn = {2045-2322},
support = {PAPIIT-IN207021//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; PAPIIT-IN207021//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; Posgraduate grant//Universidad Nacional Autónoma de México/ ; },
abstract = {Anchialine caves house a vast variety of organisms that support complex ecological relationships among themselves and their environment. The following study was made in the anchialine karst cave El Aerolito, found on Cozumel Island, Quintana Roo, Mexico. It explores the relationship between wall microbial mats and the diet of Asterinides sp., an endemic stygobitic seastar. Wall microbial mats inside the cave were sampled and the stomach microbiome of Asterinides sp. was obtained through regurgitation. Asterinides sp. sampling was made through the Catcher Collection Chamber (CCC), an innovative technology for the exploration of these ecosystems. The obtained results suggest that microbial mats are part of the diet of Asterinides sp. The following results highlight the potential relevance of the microbial communities inside the trophic chain present in El Aerolito. Additionally, the methodology presented here provides a useful framework for future ecological research in El Aerolito cave.},
}

@article {pmid41565726,
year = {2026},
author = {Moreno-León, A and Majó, N and Lavín, JL},
title = {Exploring the chicken respiratory microbiome: a comprehensive meta-analysis of factors shaping chicken respiratory microbiota.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-33989-2},
pmid = {41565726},
issn = {2045-2322},
support = {PID2020-114060RR-C33//Agencia Estatal de Investigación/ ; },
}

@article {pmid41565669,
year = {2026},
author = {Schneeberger, PHH and Dommann, J and Rahman, N and Hürlimann, E and Sayasone, S and Ali, S and Coulibaly, JT and Keiser, J},
title = {Profound taxonomic and functional gut microbiota alterations associated with trichuriasis: cross-country and country-specific patterns.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00911-1},
pmid = {41565669},
issn = {2055-5008},
support = {101019223/ERC_/European Research Council/International ; },
abstract = {The human gut microbiota is vital for immune function, metabolism, and resistance to pathogens. Soil-transmitted helminths like Trichuris trichiura can disrupt this microbial community, but the extent and functional significance of these disruptions across diverse regions remain unclear. We investigated the impact of T. trichiura infection on gut microbiota composition and function in three endemic regions-Côte d'Ivoire, Laos, and Tanzania-using standardized, high-resolution metagenomic profiling. Our findings reveal consistent depletion of key short-chain fatty acid (SCFA) producers, including Blautia sp. MSJ 9 and Holdemanella biformis, and enrichment of mucin-degrading genera such as Ruminococcus and Bacteroides. These changes coincided with increased microbial utilization of host-derived carbohydrates and destabilization of microbial networks, notably with the emergence of Segatella copri in infected individuals. Although taxa-level responses varied by region, similar trends in SCFA depletion and mucin degradation were observed across sites, pointing to a potentially shared metabolic response to infection. These alterations suggest compromised gut barrier function and immune modulation, potentially promoting parasite persistence. Our results underscore the potential of microbiome-based strategies, such as targeted probiotics or dietary interventions, to support helminth control by restoring microbial balance and improving host resilience.},
}

@article {pmid41565496,
year = {2026},
author = {Hassert, M and Harty, JT},
title = {The endemic dilemma: why whole sporozoite malaria vaccine efficacy falls in the field.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2025.12.003},
pmid = {41565496},
issn = {1471-5007},
abstract = {Whole sporozoite vaccines (WSVs) are the most effective malaria vaccines developed to date. However, their durable efficacy declines sharply when moving from homologous CHMI studies to field trials in endemic regions. We argue this reduced efficacy reflects the complex context of vaccine deployment rather than a single cause. The antigen mismatch hypothesis postulates that limited genetic diversity in current vaccines fails to capture the diversity of field parasites, reducing immune recognition. The host-context hypothesis describes how genetics, infection history, microbiome, and nutrition influence vaccine outcomes. We propose that the future of malaria vaccines will depend on integrating parasite genomics, systems immunology, and the development of animal models which more accurately depict the context of individuals living in malaria endemic regions.},
}

@article {pmid41564849,
year = {2026},
author = {Terry, CE and Halle-Smith, JM and Merali, N and Marudanayagam, R and Chatzizacharias, N and Dasari, BVM and Bartlett, DC and Raza, SS and Frampton, AE and Sutcliffe, RP and Roberts, KJ},
title = {Colonization of bile with gammaproteobacteria is associated with reduced survival after surgery for pancreatic cancer in patients receiving gemcitabine-based adjuvant chemotherapy.},
journal = {European journal of surgical oncology : the journal of the European Society of Surgical Oncology and the British Association of Surgical Oncology},
volume = {52},
number = {3},
pages = {111396},
doi = {10.1016/j.ejso.2026.111396},
pmid = {41564849},
issn = {1532-2157},
abstract = {BACKGROUND: Evidence suggests that the biliary microbiome influences the progression of pancreatic ductal adenocarcinoma (PDAC) in patients undergoing adjuvant chemotherapy. Specifically, Gammaproteobacteria (GPB) has been shown to have the potential to develop mutations which can metabolise gemcitabine into an inactive form. This study hypothesised that GPB influences survival in patients with PDAC undergoing adjuvant gemcitabine-based chemotherapy following surgery.

METHODS: This was a retrospective study of patients undergoing pancreatoduodenectomy from 2010 to 2020. Associations between patient and tumour characteristics, survival data, and results of intraoperative bile cultures (GPB + or GPB-) were investigated. Analysis of patients matched by chemotherapy regimen and numbers of cycles of adjuvant therapy was also performed. Survival was analysed using Kaplan-Meier curves and Cox regression analysis.

RESULTS: Analysis of 313 patients revealed that adjuvant gemcitabine-based therapy improved overall survival (OS). Patients who receive gemcitabine-based chemotherapy with a GPB + biliary culture had a shorter OS compared to those who were GPB-, and a median survival of 17.9 vs 26.2 months, P = 0.002. After matching for key chemotherapy variables, survival was greater in the GPB- group 26.8 vs 19.8 months, P = 0.016. This association was not seen among patients who received no adjuvant therapy or non-gemcitabine based therapy.

CONCLUSION: Patients receiving gemcitabine-based chemotherapy after surgery are likely to have reduction in OS if they have a biliary culture positive for GPB.},
}

@article {pmid41564716,
year = {2026},
author = {Limo, L and Donovan, J and Frisbee, S and Gomaa, N},
title = {The exposome and the human oral microbiome through the one health lens.},
journal = {Archives of oral biology},
volume = {183},
number = {},
pages = {106504},
doi = {10.1016/j.archoralbio.2026.106504},
pmid = {41564716},
issn = {1879-1506},
abstract = {OBJECTIVES: To map and synthesise current evidence on how lifelong biological, environmental, and social exposures, collectively conceptualised as the exposome, interact with the human oral microbiome to influence oral disease development and progression within a One Health framework.

DESIGN: A scoping review was conducted to identify peer-reviewed studies published in English that examined the relationships between the exposome and the human oral microbiome. The review followed the Arksey and O'Malley framework, applying its five-stage methodological approach. Comprehensive searches were performed in MEDLINE, Embase, PsycInfo, Scopus, Web of Science, and CINAHL. Study quality was assessed using the Joanna Briggs Institute (JBI) tools, and results were reported in accordance with PRISMA-ScR guidelines.

RESULTS: A total of twenty-nine studies were included in this review. These showed that health status, non-communicable diseases, medication use, and psychosocial factors influence the biodiversity, abundance, and function of the human oral microbiome. Other studies suggested that animal interactions and physical and chemical exposures can alter host-microbiome interactions, as well as microbial community dynamics within the oral cavity. While the studies reviewed used reliable methods and standardized protocols, they were of moderate quality due to small sample sizes, potential reverse causality, and limited control for confounding and multiple testing.

CONCLUSION: This review highlights the complexity of the human oral microbiome and its interactions with the various components of the exposome, emphasizing the focus on disease impact and health behaviours, while noting a gap in research on non-bacterial communities, interaction mechanisms, and long-term effects on dysbiosis.},
}

@article {pmid41564597,
year = {2026},
author = {Rogozarski, J and Steiner-Gager, GM and Preindl, K and Wicik, Z and Eyileten, C and Skos, C and Gerner, C and Dizdarevic, A and Postula, M and Meier-Menches, SM and Siller-Matula, JM},
title = {Plasma metabolomic profiling of patients with acute coronary syndrome treated with potent platelet inhibitors.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {195},
number = {},
pages = {119013},
doi = {10.1016/j.biopha.2026.119013},
pmid = {41564597},
issn = {1950-6007},
abstract = {Ticagrelor and prasugrel are key antiplatelet agents used in patients with acute coronary syndrome (ACS) undergoing percutaneous coronary intervention (PCI). Beyond their antiplatelet effects, both drugs exhibit pleiotropic actions that may contribute to side effects. Notably, ticagrelor has been associated with dyspnea in clinical trials. This study aimed to identify metabolomic markers linked to the effects of ticagrelor and prasugrel using targeted metabolomics. Plasma samples from 207 ACS patients treated with either prasugrel (n = 106) or ticagrelor (n = 101) were analyzed for up to 631 metabolites. Several metabolites differed significantly between the groups (p < 0.05). The most notable changes were found in DHEAS (p = 0.0004, FC = -1.66) and 3-Met-His (p = 0.0024, FC = 1.75). After adjusting for risk factors, lysoPC a C17:0, 3-Met-His, and DHEAS remained significantly altered. Subgroup analysis revealed that diabetic patients had distinct metabolic profiles, including elevated TMAO and choline and reduced GUDCA levels, compared to non-diabetics. Additional changes were observed in hexoses, Met-SO, and TCDCA. The findings support a novel hypothesis that ticagrelor-induced dyspnea may be linked to low DHEAS levels. Reduced methionine and Met-SO levels could suggest lower oxidative stress. Moreover, diabetic patients showed a gut microbiome-related metabolic shift associated with a more ischemic profile.},
}