@article {pmid41963410,
year = {2026},
author = {Tahara, T and Shijimaya, T and Yamazaki, J and Shimogama, T and Kobayashi, S and Nakamura, N and Takahashi, Y and Tomiyama, T and Fukui, T and Shibata, T and Naganuma, M},
title = {Enrichment of T: A→A: T substitutions in the TP53 gene in esophageal carcinoma with high Fusobacterium burden.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41963410},
issn = {2045-2322},
support = {22K08089//Japan Society for the Promotion of Science/ ; },
abstract = {UNLABELLED: Exogenous lifestyle and environmental risk factors impact mutation burden in both benign and cancerous tissues. Moreover, interactions between the mucosa-associated microbiome and such genotoxic changes have been implicated in several cancer types. This study aimed to characterize the TP53 mutation spectrum in esophageal carcinoma (EC) with high amounts of Fusobacterium species. Quantitative PCR analysis of Pan-Fusobacterium species and Fusobacterium nucleatum was performed in 112 EC cases (89 squamous cell carcinomas [SCCs] and 23 adenocarcinomas). Results were correlated with TP53 mutation spectra and clinicopathological features. Both Pan-Fusobacterium species and F. nucleatum were significantly enriched in EC tissues compared with adjacent normal esophagus (both P < 0.001). The TP53 mutation spectrum in Pan-fusobacterium-high EC was characterized by a decrease in C: G→A: T and an increase in T: A→A: T substitutions (P < 0.001). Pan-fusobacterium-high EC was associated with male sex, tumors located in the upper or middle esophagus, and squamous cell histopathology. Cases of EC with detectable levels of Pan-Fusobacterium and F. nucleatum were also associated with more invasive tumors and more advanced cancer stages at diagnosis. These results suggest that EC with high numbers of Fusobacterium species was associated with a distinct mutation spectrum. Future studies should be conducted to investigate the mechanisms of how Fusobacterium species induce specific somatic mutations.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-45806-5.},
}

@article {pmid41975253,
year = {2026},
author = {Aquino, CI and La Vecchia, M and Pasolli, E and Sala, G and Ligori, A and Boldorini, R and Ferrante, D and Dianzani, I and Aspesi, A and Surico, D and Remorgida, V},
title = {Decoding the microbial landscape of endometrial cancer: a case-control study.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41975253},
issn = {1471-2180},
support = {IG 2021-ID. 25886//Associazione Italiana per la Ricerca sul Cancro/ ; },
abstract = {BACKGROUND: The human microbiome plays an emerging role in cancer biology, yet its contribution to endometrial cancer (EC) remains poorly defined. This study investigates the microbial composition of the vaginal, rectal, and endometrial sites in women with and without EC, aiming to uncover microbial signatures associated with the disease.

RESULTS: We performed shotgun metagenomic sequencing on vaginal, rectal, and endometrial samples from 25 patients with EC and 27 control women undergoing hysterectomy for benign conditions. Vaginal and rectal swabs were collected before surgery, while endometrial swabs were obtained post-hysterectomy using a sterile brushing technique to prevent cross-contamination. Vaginal microbiota in patients with EC showed significantly higher microbial diversity and distinct community composition compared to controls. These differences remained significant after adjusting for age and body mass index. Several bacterial species, including Peptococcus niger, Anaerococcus murdochii, Mobiluncus, Porphyromonas, and Prevotella, were more abundant in the vaginal microbiota of patients with cancer. In contrast, Lactobacillus spp. were more abundant in vaginal and rectal samples of control subjects.

CONCLUSIONS: This work represents one of the few studies to comprehensively examine the relationship between the vaginal, rectal, and endometrial microbiomes in the context of EC, suggesting a potential role for microbial imbalance in disease development. The findings underscore the importance of site-specific microbial analyses in gynecologic oncology and support further investigation into the microbiome as a possible biomarker for early detection and a target for preventive strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-05017-4.},
}

@article {pmid41975427,
year = {2026},
author = {Zhang, Z and Bai, J and Liu, Y and Wang, J and Lv, Z and Tang, L and Wang, R and Gao, L and Liu, C and Lu, S and Fu, X and Ni, J and Wan, P},
title = {Effects of synthetic breast milk on the gut metagenome and whole blood transcriptome in lambs.},
journal = {BMC veterinary research},
volume = {22},
number = {1},
pages = {},
pmid = {41975427},
issn = {1746-6148},
support = {NYHXGG.2023AA206-3//Agricultural GG Project of Xinjiang Production and Construction Corps/ ; 2025AB5012//Tacheng Talents Project/ ; 2025AA01504//Project of Major Science and Technology Project of the Corps/ ; 2022TSYCCX0124//Young Science and Technology Top Talent Program of Tianshan Talent Training Program in Xinjiang Province/ ; XJARS-09-26//Xinjiang Agriculture Research System/ ; CARS-39-07//China Agriculture Research System/ ; },
abstract = {UNLABELLED: Early postnatal nutrition is crucial for the growth and development of lambs, and artificial milk formulas are widely used as alternatives to breast milk in intensive sheep production. However, the molecular and microbial mechanisms underlying the differences between breast milk and formula feeding remain unclear. This study aimed to compare the fecal metagenomic and whole blood transcriptomic profiles of lambs fed breast milk (BF group) and commercial formula (FF group) from 4 to 45 days of age, to provide a theoretical basis for optimizing formula compositions. A total of 6 lambs were randomly divided into two groups (n = 3 per group), with body weight and body dimensions measured at 45 days of age, followed by fecal metagenomic sequencing and whole blood transcriptomic sequencing. The results showed that BF lambs had significantly higher body weight, body length, heart girth, and chest width than FF lambs. Metagenomic analysis revealed that at the phylum level, Bacteroidetes was enriched in FF lambs, whereas Firmicutes predominated in BF lambs. Differential abundance was also observed at the genus level (higher Desulfovibrio in FF lambs) and the pathway level, with BF lambs enriched in quorum sensing and FF lambs showing higher abundances of pathways related to ubiquinone and other terpenoid-quinone biosynthesis. Moreover, transcriptomic analysis identified 3290 differentially expressed genes (DEGs) between the two groups, with DEGs mainly enriched in metabolic pathways, mTOR signaling pathway, osteoclast differentiation, B cell receptor signaling pathway and MAPK signaling pathway. Collectively, compared with FF, BF enhanced lamb growth, optimized gut microbiome structure and modulated blood transcriptomic profiles related to metabolism, signaling and immunity. These findings highlight the key microbial taxa and functional pathways modulated by breastfeeding, providing valuable insights for the development of more effective milk formula alternatives.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12917-026-05460-5.},
}

@article {pmid42179543,
year = {2026},
author = {de Figueiredo, VSA and Canto Bueno, P and Ponce Fuentes, EA and Dini, C and Alves de Brito Júnior, A and Busato de Feiria, SN and Mattos-Graner, RO and Ricomini Filho, AP and Klein, MI},
title = {Putative Prebiotics Can Disrupt 3D Architecture and Modulate the Microbial Population to Prevent Cariogenic Biofilm Build-Up In Vitro.},
journal = {ACS omega},
volume = {11},
number = {19},
pages = {27942-27957},
pmid = {42179543},
issn = {2470-1343},
abstract = {Background/Objective(s)/Introduction: Prebiotics are substances that metabolically favor certain microorganisms of a microbiome, promoting homeostasis. Dental biofilm microorganisms are enmeshed in a matrix of extracellular polymeric substances that they produce. A diet rich in sucrose can lead to a dysbiotic biofilm associated with microbial acid production and a change in the matrix's composition (mostly water-insoluble glucans), which allows acids to accumulate within biofilms and contribute to teeth demineralization. Thus, the effects of putative prebiotics were evaluated to verify their impact on exopolysaccharides, the microbial population, and biofilm formation. Materials and methods: Five potential prebiotics (N-acetyl-d-glucosamine, arginine, proline, sodium nitrate, and urea) were evaluated compared with a substance-free control. A Streptococcus mutans biofilm model on polystyrene plates was used to determine the concentrations of substances that would inhibit sucrose-derived biofilm formation. Selected concentrations were then used to verify the production of insoluble glucans by glucosyltransferase B. Afterward, S. mutans and mixed-species (S. mutans, Actinomyces naeslundii, and Streptococcus gordonii) biofilms were grown on saliva-coated hydroxyapatite discs with sucrose to evaluate the microbial population and 3D biofilm structure (exopolysaccharides and bacterial biovolume). Lastly, a microcosm biofilm formed on polystyrene plates was used to assess the effects of the substances on biomass and the proportion of distinct viable microbial populations. Results: Only arginine inhibited insoluble glucan production and S. mutans biofilm accretion (≅ 90%). Arginine and proline inhibited a biofilm build-up in mixed-species and microcosm models and modulated microbial counts of species associated with cariogenic biofilms. In the microcosm biofilm, urea hindered biomass accretion in initial biofilms and the counts of aciduric microbiota and fungi, but N-acetyl-d-glucosamine stimulated microbial growth. Sodium nitrate affected the size and shape of microcolonies in S. mutans and mixed-species biofilms. Conclusion(s): Among the substances tested, arginine and proline modulated the microbial population and hindered biofilm accretion, especially arginine, which hampered glucan production. However, urea is the only substance able to impede fungal growth.},
}

@article {pmid42179783,
year = {2026},
author = {Chae, S and You, HS and Kim, JG and Cho, JY},
title = {Exploratory Serum Metabolomics Identifies Metabolic Subgroups Across the Gastric Dysplasia-Early Cancer Spectrum.},
journal = {Journal of Cancer},
volume = {17},
number = {5},
pages = {968-978},
pmid = {42179783},
issn = {1837-9664},
abstract = {BACKGROUND: Gastric carcinogenesis involves progressive molecular and metabolic alterations, yet non-invasive biomarkers for early detection and risk stratification remain limited. This study aimed to characterize systemic metabolomic changes across the gastric carcinogenesis spectrum and to investigate potential associations between serum metabolites and gastric microbiome-related pathways.

METHODS: In this exploratory study, untargeted serum metabolomics was performed on samples from patients with gastric dysplasia or early gastric cancer (n = 40) and healthy controls (n = 14). Differential metabolite analysis, principal component analysis, and k-means clustering were used to identify metabolic alterations and potential metabolic subgroups. Microbial pathway associations were examined using metabolite origin inference based on gastric-resident taxa reported in prior studies.

RESULTS: Eighteen metabolites were significantly altered in gastric carcinogenesis compared with healthy controls. Six metabolites displayed distinct profiles that suggest two metabolic subgroups, including one subgroup showing a metabolic pattern closer to that of healthy controls, independent of histologic severity. Microbial pathway inference suggested contributions from Pseudomonadota, Actinomycetota, and Bacillota, with ornithine-related metabolites emerging as a key metabolic link previously implicated in dysplasia-to-carcinoma progression. These findings highlight inter-patient heterogeneity and potential metabolic-microbial interactions underlying gastric carcinogenesis.

CONCLUSION: These findings suggest that serum metabolomic profiling may capture metabolic heterogeneity across the gastric dysplasia-early gastric cancer spectrum and generate hypotheses regarding microbiome-related metabolic alterations. While exploratory in nature, this study provides preliminary evidence supporting the potential of serum metabolites as non-invasive indicators of early gastric carcinogenesis, warranting validation in larger and longitudinal cohorts.},
}

@article {pmid42179876,
year = {2026},
author = {Theodorea, CF and Azzahra, NA and Idrus, E and Nurkolis, F and Djais, AA and Mashima, I},
title = {The role of Veillonella species in oral carcinogenesis: is prevalence linked to oral squamous cell carcinoma?.},
journal = {Frontiers in oral health},
volume = {7},
number = {},
pages = {1740043},
pmid = {42179876},
issn = {2673-4842},
abstract = {Oral squamous cell carcinoma (OSCC) remains a significant health challenge because of its aggressive nature and poor survival outcomes. While established risk factors such as tobacco use, alcohol consumption, and human papillomavirus play critical roles, increasing evidence suggests that oral microbial dysbiosis may contribute to carcinogenesis. Among oral commensals, Veillonella species have gained attention because of their ecological role in oral biofilms and metabolic interactions with other microbes, and have also been increasingly identified in altered abundances within OSCC patient samples. This narrative review synthesizes available clinical, epidemiological, and molecular studies investigating the prevalence and biological roles of Veillonella species in OSCC. Relevant English-language publications between 2000 and 2025 were identified through database searches in Pubmed Scopus and Web of Science using keywords related to Veillonella, oral microbiome, dysbiosis, and OSCC. The reviewed evidence reveals a dynamic and stage-dependent shift in Veillonella abundance during oral carcinogenesis. Several studies report enrichment of Veillonella in oral potentially malignant disorders and early tumorigenesis, whereas reduced levels are frequently observed in advanced OSCC. These findings suggest that Veillonella may function as an ecological modulator of tumor-associated microbiota rather than as a single pathogenic driver. Proposed mechanisms include metabolic cross-feeding with lactic-acid-producing bacteria, modulation of inflammatory pathways, biofilm restructuring, and host-microbe metabolic signaling. Overall, current evidence supports a microbial ecological shift model, in which Veillonella participates in early dysbiotic transitions preceding OSCC development but may decline as tumor microenvironments evolve. Further standardized and multiomics studies are needed to clarify its potential as a microbiome-based biomarker and therapeutic target.},
}

@article {pmid42179978,
year = {2026},
author = {Chen, S and Xu, B and Lu, M},
title = {Metformin-Associated Gastrointestinal Intolerance: A Narrative Review of Mechanisms and Clinical Management.},
journal = {Clinical medicine insights. Endocrinology and diabetes},
volume = {19},
number = {},
pages = {11795514261453485},
pmid = {42179978},
issn = {1179-5514},
abstract = {Metformin-associated gastrointestinal (GI) intolerance is a frequent clinical problem that can limit treatment initiation, delay dose escalation, and reduce long-term adherence in patients with type 2 diabetes mellitus. Common symptoms include nausea, diarrhea, abdominal discomfort, and bloating, although symptom pattern and severity vary substantially between individuals. This narrative review summarizes current evidence on the determinants, mechanisms, and clinical evaluation of metformin-associated GI intolerance. In routine practice, assessment should begin with potentially modifiable exposure-related factors, including dose, single-dose burden, titration pace, formulation, administration with meals, kidney function, and concomitant medications. If symptoms persist or appear disproportionate to treatment exposure, clinicians should then consider broader host susceptibility, including baseline GI vulnerability, microbiome-related influences, altered bile acid handling, mucosal and neuroregulatory responses, comorbidity burden, and polypharmacy. This exposure-susceptibility framework provides a practical way to interpret metformin-related GI symptoms in routine care. It supports a stepwise clinical approach in which modifiable contributors are addressed first, broader context is reviewed when needed, and premature discontinuation is avoided whenever possible. Despite limitations in the current evidence base, available data support a structured and clinically useful approach to metformin intolerance.},
}

@article {pmid42180143,
year = {2026},
author = {Beaulieu, ML and Patel, NB and Wojtys, EM},
title = {The gut microbiome's role in the development and progression of post-traumatic osteoarthritis: A systematic review.},
journal = {Osteoarthritis and cartilage open},
volume = {8},
number = {2},
pages = {100807},
pmid = {42180143},
issn = {2665-9131},
abstract = {OBJECTIVE: Gut microbiome dysbiosis is linked to osteoarthritis (OA), but its specific association with post-traumatic osteoarthritis (PTOA) is less understood. This systematic review synthesizes evidence linking PTOA and the gut microbiome to clarify its role in PTOA pathogenesis.

METHOD: Literature searches were conducted in PubMed, Embase, SPORTDiscus, and Web of Science through October 2025. Quantitative, original human and animal studies examining associations between the presence/severity of PTOA and gut microbiota composition and diversity were included. These measures were extracted and synthesized. Risk of bias was assessed using ROBINS-I for non-randomized and RoB 2 for randomized studies (PROSPERO registration: CRD42024496152).

RESULTS: Thirteen studies met inclusion criteria, all utilizing small animal PTOA models. Generally, they found significant gut microbiome differences between PTOA and control groups. Collectively, these preclinical studies provided evidence that the gut microbiome can influence biological processes underlying PTOA, particularly via inflammatory and metabolic pathways, and vice versa. Two studies examined exercise, showing it can reduce PTOA severity by slowing articular cartilage degeneration and subchondral bone loss, increase microbiome diversity, and mitigate negative effects of poor diet.

CONCLUSIONS: Current literature from animal models suggests the gut microbiome may play a role in PTOA development and progression, emphasizing a bidirectional "gut-joint axis." Traumatic joint injuries may lead to systemic inflammation affecting the gut microbiome, which may exacerbate joint inflammation and PTOA progression. Significant gaps remain, particularly the lack of human studies. Future research should prioritize clinically relevant animal models and human studies to elucidate the gut microbiome's role in PTOA pathogenesis.},
}

@article {pmid42180198,
year = {2026},
author = {Nnorom, MA and Du, B and Wang, Z and Tian, Z and Hough, R and Avery, L and Saroj, D and Guo, B},
title = {Dynamics of the Microbiome and Antibiotic Resistome in Hyper-Mesophilic Anaerobic Digestion of Cattle Manure Assisted with Granular Activated Carbon.},
journal = {ACS environmental Au},
volume = {6},
number = {3},
pages = {435-448},
pmid = {42180198},
issn = {2694-2518},
abstract = {The use of conductive materials, such as granular activated carbon (GAC), for optimization of the anaerobic digestion (AD) process has garnered attention in recent years; however, its impact on the dynamics of the microbiome and resistome in continuous AD systems remains unclear, especially under temperature variation. This study combined culture-based bacterial enumeration and shotgun metagenomics to investigate the impact of two GAC application strategies, suspended and packed, on the fate of pathogens (viable Escherichia coli) and ARGs during the AD of cattle manure at 40 and 45 °C. The results show that GAC mitigated the process imbalance and shock induced by temperature transition. The microbial community in the AD sludge was highly impacted by temperature but not GAC, while GAC biofilms showed notably higher archaeal abundance. All AD reactors reduced viable E. coli, with the highest reduction occurring in the packed GAC reactors (95.70-96.24%), followed by the suspended GAC (94.53-95.69%), and then the non-GAC (92.77-94.24%). Culturable tetracycline-resistant bacteria were reduced below the quantification limit in all reactors. Reduction of ampicillin-resistant bacteria showed stochastic trends at 40 °C but improved at 45 °C, indicating limited impact by GAC. ARGs and mobile genetic elements (MGEs) were reduced in all reactors at comparable levels, regardless of GAC addition. Temperature transition exerted a mixed effect, with higher reduction of some resistance classes (MLS, tetracycline, and multidrug) and lower reduction of others (bacitracin, aminoglycoside, beta-lactam, and streptothricin). Mantel test and Procrustes analysis revealed a significant correlation between the resistome and the bacterial community, inferring that shifts in the ARG host population were a major determinant of the fate of ARGs. Overall, GAC was beneficial to reactor stability but had a minimal influence on the reduction of E. coli, ARGs, and MGEs. It is highly recommended to monitor antimicrobial resistance using both culture-based and culture-independent methods.},
}

@article {pmid42180244,
year = {2026},
author = {Jiang, Z and Li, G},
title = {Microbiome mediation analysis: methods, assumptions, and practical considerations.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1832981},
pmid = {42180244},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; Bayes Theorem ; *Mediation Analysis ; },
abstract = {Microbiome mediation analysis provides a principled framework for understanding how environmental, behavioral, or clinical exposures influence human health through microbiomemediated biological pathways. However, its application is complicated by the compositional, sparse, and high-dimensional nature of microbiome data. A growing body of methods has been developed to address these challenges, drawing on structural equation modeling, counterfactual causal inference, distance-based testing, Bayesian variable selection, and nonparametric approaches. This paper reviews methodological developments designed to address these challenges and enable valid and interpretable mediation analysis in microbiome studies with particular emphasis on their underlying assumptions, limitations, and appropriate contexts of use, while also highlighting existing gaps and outlining future research directions.},
}

Humans
*Microbiota
Bayes Theorem
*Mediation Analysis

@article {pmid42180251,
year = {2026},
author = {Naorem, RS and Dutta, K and Bora, SS and Teli, AB},
title = {Proton pump inhibitor exposure modulates functional and transcriptional responses in Lactobacillus acidophilus: a comprehensive computational and experimental insights.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1781831},
pmid = {42180251},
issn = {2235-2988},
mesh = {*Proton Pump Inhibitors/pharmacology ; *Lactobacillus acidophilus/drug effects/genetics/metabolism ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Gene Expression Regulation, Bacterial/drug effects ; Gene Expression Profiling ; Pantoprazole/pharmacology ; Probiotics ; Computational Biology ; Bacterial Proteins/metabolism/genetics ; Humans ; },
abstract = {Proton pump inhibitors (PPIs) are among the most widely prescribed medications for gastric acid-related disorders. However, their effect on the gut microbiota remains incompletely understood, despite emerging evidence suggesting potential long-term alterations in microbial composition and reductions in beneficial taxa. In this study, Lactobacillus acidophilus, a well-known probiotic species, was used as a representative model organism to investigate the microbiological effects of PPIs. This specific bacterium is linked to immune modulation, vitamin metabolism, and the preservation of the epithelial barrier. The effects of PPIs on L. acidophilus at the structural and functional levels were elucidated by an integrated framework including subtractive genomics, molecular docking, molecular dynamics (MD) simulations, antimicrobial assays, and transcriptional analysis. Using a multi-criteria scoring system, essential, non-redundant, non-human homologous cytoplasmic proteins were ranked and mapped to important pathways such as ATP synthesis, peptidoglycan biosynthesis, amino-sugar metabolism, nucleotide metabolism, and protein maturation. Molecular docking suggested potential binding of pantoprazole and rabeprazole to targets such as MurA, MurB, MurE, GlmS, NadE, AtpD, Def, and PyrH proteins. MD simulation showed stable protein-PPI complexes with localized flexibility changes near catalytic domains while preserving the global fold. Consistent with in-silico expectations, both pantoprazole and rabeprazole exhibited dose-dependent growth inhibition of L. acidophilus, whereas qRT-PCR revealed transcriptional downregulation of genes involved in cell-wall production, NADH metabolism, and energy generation. Pantoprazole elicited the most uniform transcriptional suppression, whereas rabeprazole had stronger but more varied effects. The present findings provide preliminary insights into potential interactions between PPIs and probiotic bacteria at the molecular and cellular levels. However, the results reflect species-specific responses under in vitro conditions and should be interpreted cautiously, as transcriptional changes do not directly confirm functional inhibition and the concentrations tested may represent upper-range exposure scenarios. Further in vivo and multi-species studies are required to validate this observation and better understand their clinical implications for microbiome stability during PPI therapy.},
}

*Proton Pump Inhibitors/pharmacology
*Lactobacillus acidophilus/drug effects/genetics/metabolism
Molecular Docking Simulation
Molecular Dynamics Simulation
Gene Expression Regulation, Bacterial/drug effects
Gene Expression Profiling
Pantoprazole/pharmacology
Probiotics
Computational Biology
Bacterial Proteins/metabolism/genetics
Humans

@article {pmid42180283,
year = {2026},
author = {Pazla, R and Antonius, A and Mohd-Aris, A and Ikhlas, Z and Fitri, Y and Bansi, H and Dewi, YL and Hadiatry, MC and Qomariyah, N and Wahyuwardani, S and Yusriani, Y and Rohaeni, ES and Bakrie, B},
title = {The role of tannin-based products in mitigating enteric methane emissions in ruminant livestock: A review.},
journal = {Journal of advanced veterinary and animal research},
volume = {13},
number = {1},
pages = {192-206},
pmid = {42180283},
issn = {2311-7710},
abstract = {Global greenhouse gas accumulation receives significant contributions from methane emitted by ruminant livestock, thereby exacerbating climate change. Tannin-based feed additives are being investigated by researchers as a potential means to alter rumen fermentation and reduce methanogenesis. The researchers build on previous studies on the impact of tannins on methane reduction in the digestive tract and investigate the biological mechanisms of tannins, which are coupled with the potential of animal feed sources. Tannins kill methanogenic archaea by reducing protozoa and altering volatile fatty acid composition. This simultaneously results in reduced methane emissions and improved feed and nitrogen utilization efficiency. As a result, animal production is made more efficient by the reduction of nitrogen excretion and the enhancement of protein metabolism. The use of tannins, essential oils, biochar, and probiotics together is being researched as a way to treat the diet. Yet there are still issues, such as the adverse effects of tannins on nutrition, inconsistent tannin supply across sources, and microbial adaptation over time. The effectiveness of tannins also varies and is connected to the plant source, concentration, and processing methods. Besides, scientists are developing encapsulation methods and selecting optimal feeding protocols to increase tannin effectiveness while minimizing unwanted effects. Future researchers must improve the administration techniques for tannins, develop more efficient delivery systems, and conduct a comprehensive assessment of how tannins affect rumen microbiome health and animal performance. Tannin application emerges as an ecological approach that serves sustainability in livestock management systems and helps environmental adaptation practices.},
}

@article {pmid42180286,
year = {2026},
author = {Nguyen, TT and Nguyen, CK and Tran, PD and Duong, KN and Nguyen, HT},
title = {Insights into milk microbiota differences among healthy, mastitis-suspected, and subclinical mastitis cows at dairy farms in Southern Vietnam.},
journal = {Journal of advanced veterinary and animal research},
volume = {13},
number = {1},
pages = {207-220},
pmid = {42180286},
issn = {2311-7710},
abstract = {Objectives: This study aimed to characterize and compare the milk microbiota composition among Holstein Friesian cows with healthy (HU), mastitis-suspected (MSU), and subclinical mastitis (SM) udders in Southern Vietnam. Materials and Methods: Sixty milk samples were collected from two dairy farms and classified based on somatic cell counts (SCC) into three groups: HU (<200,000 cells/ml), MSU (200,000-400,000 cells/ml), and SM (>400,000 cells/ml). Bacterial communities were profiled using Illumina MiSeq sequencing of the 16S rRNA gene. Results: The prevalence of subclinical mastitis was 46.67% (p < 0.05). The core microbiome was dominated by phyla of Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes (>90%); and taxa of Moraxellaceae, Sphingomonadaceae, Enterobacteriaceae, Erysipelotrichaceae, and Streptococcaceae. Analysis revealed significant dysbiosis in the SM group, characterized by elevated relative abundances of mastitis-associated taxa (Mycobacteriaceae, Streptococcaceae, Moraxellaceae, Pasteurellaceae, and Mycoplasmataceae) compared to healthy udders (p < 0.05). Conversely, commensal taxa typical of healthy milk (Rikenellaceae, Lactobacillaceae, Sphingomonadaceae, and Opitutaceae) were significantly depleted in SM samples but remained abundant in both HU and MSU groups (p < 0.05). Notably, the microbial profile of the MSU group was statistically similar to that of the HU group (p > 0.05), with no distinct variation in key bacterial families. Principal coordinate analysis further confirmed that SM samples formed a distinct cluster separate from the HU and MSU groups. Conclusions: Subclinical mastitis drives significant shifts in the milk microbiome. However, mastitis-suspected cows retain a microbiome similar to that of healthy udders, suggesting that SCC thresholds alone may require careful interpretation in borderline cases.},
}

@article {pmid42180552,
year = {2026},
author = {Chen, Y and Wei, X and Yi, X and Jiang, DS},
title = {Interactions between the gut microbiome and ferroptosis in degenerative diseases: Novel mechanisms and potential therapeutic strategies.},
journal = {Acta pharmaceutica Sinica. B},
volume = {16},
number = {5},
pages = {2711-2729},
pmid = {42180552},
issn = {2211-3835},
abstract = {Degenerative diseases are a group of medical conditions characterized by the progressive and irreversible deterioration of cells, tissues, and organs over time. Emerging evidence highlights the alteration and functions of the gut microbiome in the development of degenerative diseases. Ferroptosis, a regulated form of cell death characterized by iron-dependent lipid peroxidation, has been implicated as a pivotal factor in the regulatory effect of the gut microbiome on degenerative diseases. Moreover, gut metabolites, particularly short-chain fatty acids and trimethylamine N-oxide, are closely related to iron overload, redox imbalance, and lipid peroxidation. Recently, microbiome-based therapies, such as fecal microbiota transplantation, have been considered novel therapeutic strategies. In this review, we focus on degenerative diseases and explore the interactions between the gut microbiome and ferroptosis, aiming to provide new insights into the underlying mechanisms and clinical implications.},
}

@article {pmid42180556,
year = {2026},
author = {Ruhle, M and Espinosa-Maldonado, C and de Anda-Jáuregui, G and Vadillo-Ortega, F and Hernández-Lemus, E},
title = {Leakage-aware machine learning reveals structured clinical and vaginal microbiome patterns associated with preterm birth in a Mexican cohort.},
journal = {Frontiers in global women's health},
volume = {7},
number = {},
pages = {1799518},
pmid = {42180556},
issn = {2673-5059},
abstract = {BACKGROUND: Preterm birth (PTB, <37 weeks of gestation) remains a major cause of neonatal morbidity and mortality worldwide, with Hispanic/Latino populations markedly underrepresented in microbiome-based studies, particularly in intensive data analytics scenarios.

METHODS: We applied leakage-aware machine learning as a descriptive analytical framework to characterize clinical and vaginal microbiome patterns associated with preterm birth in 43 pregnant Mexican women (110 longitudinal samples, 14 preterm births) recruited from public hospitals in Mexico City. Vaginal microbiome profiles (genus-level 16S rRNA V3-V4 sequencing) were analyzed using centered log-ratio transformation. We evaluated 12 model configurations representing combinations of two algorithms (Random Forest, Elastic Net), three clinical feature selection strategies (minimal DREAM-style adjustment, literature-based comprehensive features, data-driven empirical selection), and two microbiome representations (ANCOM-BC2 differentially abundant taxa, full filtered profiles). Random Forest and Elastic Net models were implemented within a rigorous subject-level nested cross-validation design to prevent data leakage. Model discrimination metrics were interpreted as indicators of internal cohort structure rather than as estimates of clinical predictive performance. Differential abundance analyses were conducted using ANCOM-BC2 both globally and within cross-validation folds to assess feature robustness.

RESULTS: The best-performing descriptive model (Random Forest with data-driven feature selection and full microbiome) exhibited AUROC 0.813 ± 0.110 , consistent with structured clinical-microbiome patterning within the cohort. Global differential abundance analysis (ANCOM-BC2, adjusted for maternal age and pre-pregnancy BMI) identified Mycoplasma as the only genus achieving FDR-corrected significance (LFC = + 1.004 , q = 0.049), with ten additional genera reaching nominal significance (p < 0.05). Within-fold feature importance and stability analyses consistently prioritized anthropometric variables (BMI, pre-pregnancy weight) alongside Peptostreptococcus and Mycoplasma, both detected in 100% of cross-validation iterations, indicating relative signal stability despite limited sample size.

CONCLUSIONS: This study illustrates how descriptive, leakage-aware machine learning can organize, prioritize, and interpret clinical and microbiome signals in small, underrepresented cohorts. At this stage, it does not yet present a clinically deployable predictor for preterm birth, but we are working towards this definite goal in the future, with prenatal screening strategies in mind. The observed internal discrimination reflects, in this sense, cohort-specific structure rather than validated predictive performance and establishes a methodological basis for future externally validated classifiers in Latin American populations.},
}

@article {pmid42180801,
year = {2026},
author = {He, Y and Liu, B and Li, W and Zhou, X and Tao, H},
title = {COPD-Lung Cancer Comorbidity: Mechanistic Insights and Precision Oncology Implications.},
journal = {International journal of chronic obstructive pulmonary disease},
volume = {21},
number = {},
pages = {606647},
pmid = {42180801},
issn = {1178-2005},
mesh = {*Pulmonary Disease, Chronic Obstructive/complications/epidemiology ; *Lung Neoplasms/diagnosis/epidemiology/etiology ; Comorbidity ; Humans ; Early Diagnosis ; Biomarkers ; Precision Medicine ; },
abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) and lung cancer frequently coexist, constituting a clinically consequential comorbidity with major implications for precision medicine.

MECHANISTIC INSIGHTS: Beyond shared environmental exposures such as tobacco smoke and air pollution, COPD has emerged as an independent driver of pulmonary carcinogenesis, mediated through persistent inflammation, genomic instability, epigenetic remodeling, and microbiome-immune dysregulation. Patients with COPD-associated lung cancer exhibit distinct molecular hallmarks, including reduced EGFR mutation frequency, enrichment of LRP1B truncations, and elevated tumor mutational burden, which collectively reprogram tumor immunogenicity and therapeutic responsiveness, favoring immune checkpoint blockade over targeted EGFR-directed therapy.

Recent advances integrating low-dose CT (LDCT) with spirometry, liquid biomarkers (eg, S100A12, TLR4), and AI-enhanced radiomic algorithms have substantially improved early detection capabilities. In parallel, microbiome-derived signatures provide novel tools for risk stratification and treatment personalization.

THERAPEUTIC IMPLICATIONS: Preventive and therapeutic strategies, including statin therapy, inhaled corticosteroids, preoperative pulmonary optimization, and microbiome modulation, are emerging as promising approaches to intercept the COPD-lung cancer continuum and improve clinical outcomes.

CONCLUSION: This review synthesizes current evidence spanning epidemiology, molecular pathogenesis, diagnostic innovations, and comorbidity-tailored interventions, culminating in a "comorbidity-centered precision management" framework. By bridging mechanistic discoveries with clinical implementation, this paradigm may contribute to reducing COPD-lung cancer mortality and could support the advancement of the global precision oncology agenda.},
}

*Pulmonary Disease, Chronic Obstructive/complications/epidemiology
*Lung Neoplasms/diagnosis/epidemiology/etiology
Comorbidity
Humans
Early Diagnosis
Biomarkers
Precision Medicine

@article {pmid42181048,
year = {2026},
author = {Quigley, EMM},
title = {The Gut-Brain Axis-From Science to Clinical Practice.},
journal = {Gastro hep advances},
volume = {5},
number = {7},
pages = {100975},
pmid = {42181048},
issn = {2772-5723},
abstract = {While the idea that the gut and brain communicate has been appreciated for centuries and commented on in many literary works, the formal introduction of the term "gut-brain axis" was much more recent. To the lay person, the operations of this axis are best represented by the effects of stress on gastrointestinal function. Indeed, exactly how stress impacts on such functions as motility and secretion has been extensively studied and its modus operandi revealed. Brain-to-gut communications can be effected via the autonomic nervous system or the hypothalamic pituitary adrenal axis. The recognition that the vagus nerve is predominantly comprised of sensory neurons led to the realization that gut-to-brain traffic is ubiquitous and largely subconscious only achieving conscious recognition at times of alarm or when the gut is injured or diseased. As the field of neurogastroenterology has developed, our understanding of the parallel involvement of "big" and "little" brains by neurodegenerative diseases has increased with Parkinson disease being the exemplar. Of late, the microbiome has entered the fray, and the concept of the microbiome-gut-brain axis emerged. Animal studies have provided considerable evidence to indicate that the gut microbiome can influence brain morphology and function and, thereby, modify behavior. Studies in animal models have also revealed that signals from on high can alter microbiome composition and function. For understandable reasons, it has proven more challenging to explore the microbiota-gut-brain axis and its implications to health and disease in humans. Nevertheless, the possibility that microbiome modulation could exert positive impacts on neurologic and psychological disorders has attracted considerable interest and some hints of efficacy have begun to emerge. For now, pending further studies in humans caution needs to be exerted in assigning pathogenic significance to interactions between the gut microbiome and the brain.},
}

@article {pmid42181089,
year = {2026},
author = {Souf, IB and Saidani, M and Mhamdi, L and Darej, C and Ben Larbi, M and M'Hamdi, N},
title = {Nutrigenomics in precision livestock and poultry farming: Enhancing productivity, welfare, and sustainability through gene-tailored diets.},
journal = {Veterinary and animal science},
volume = {33},
number = {},
pages = {100680},
pmid = {42181089},
issn = {2451-943X},
abstract = {Nutrigenomics has emerged as a valuable framework for improving precision livestock and poultry production by elucidating how diet interacts with genetic and molecular pathways to shape animal performance, health, product quality, and sustainability. This review provides a structured synthesis of current research on nutrigenomic applications across major livestock and poultry species, focusing on precision feeding, productivity, disease resilience, reproductive performance, environmental efficiency, and product quality. The review followed a structured narrative approach informed by PRISMA 2020 principles and included peer-reviewed studies published between 2015 and 2026 that examined diet-related genomic, transcriptomic, proteomic, metabolomic, or epigenetic responses in production animals. The reviewed evidence indicates that nutrigenomics can support improvements in feed efficiency, metabolic adaptation, immune function, and environmental outcomes, particularly when integrated with precision nutrition strategies. The manuscript also highlights emerging technologies that are accelerating progress in the field, including multi-omics platforms, microbiome-informed interventions, epigenetic tools, artificial intelligence-based predictive systems, and genome editing for target validation. Despite these advances, translation into commercial practice remains constrained by limited large-scale validation, inconsistent reporting, cost barriers, and regulatory and societal concerns. Nutrigenomics nonetheless represents a promising pathway toward more efficient, resilient, and sustainable animal production systems.},
}

@article {pmid42181191,
year = {2026},
author = {Kaminska, H and Wieczorek, W and Pruc, M and Janeczko, M and Siudak, Z and Szarpak, L},
title = {Gut microbiota and the early prevention window in type 1 diabetes and latent autoimmune diabetes in adults: a state-of-the-art narrative review on diet and metabolites.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1837746},
pmid = {42181191},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetes Mellitus, Type 1/prevention & control/microbiology/metabolism ; *Latent Autoimmune Diabetes in Adults/prevention & control/microbiology/metabolism ; *Diet ; Adult ; Autoimmunity ; },
abstract = {Autoimmune type 1 diabetes (T1D) is typically the end point of a prolonged process involving genetic susceptibility, the emergence of islet autoimmunity, and progressive loss of pancreatic beta-cell reserve rather than the day hyperglycaemia is first diagnosed. In parallel, research on the gut microbiome has shifted from searching for single causal taxa to examining ecosystem-level functions, microbial metabolites, and host-pathway interactions. In this narrative review, we synthesise prospective, mechanistic, and translational evidence on the role of the gut microbiome in T1D and latent autoimmune diabetes in adults (LADA) using a stage-aware, function-first framework. Across the current literature, the most consistent signals concern impaired intestinal barrier homeostasis, reduced fermentation-related capacity, altered short-chain fatty acid signalling, perturbations in tryptophan-derived and bile acid-related pathways, and their downstream effects on immune regulation and inflammatory tone. In T1D, evidence from prospective early-life cohorts suggests that microbiome maturation, together with diet, infections, and antibiotic exposure, may influence the risk of islet autoimmunity and the tempo of progression toward clinical disease. In LADA, the available evidence is more limited and largely cross-sectional, but supports an immunometabolic interpretation that includes altered microbiome and metabolomic profiles. We propose that the main translational priority is not taxon-specific manipulation, but identification of stage- and age-specific windows of susceptibility across the life course and alignment of these windows with low-risk, mechanistically plausible dietary and microbiome-modulating strategies. This framework may help guide microbiome-informed counselling, study design, and research prioritisation in autoimmune diabetes.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Diabetes Mellitus, Type 1/prevention & control/microbiology/metabolism
*Latent Autoimmune Diabetes in Adults/prevention & control/microbiology/metabolism
*Diet
Adult
Autoimmunity

@article {pmid42181229,
year = {2026},
author = {Nakhal, MM and Nafees, F and Mydeen, AB and Baydoun, I and Hamad, MIK},
title = {Gestational dysbiosis is associated with altered early-life microbial seeding and favors pathobiont expansion in offspring.},
journal = {iScience},
volume = {29},
number = {6},
pages = {115925},
pmid = {42181229},
issn = {2589-0042},
abstract = {Maternal gut microbiota shape early-life microbial community assembly, yet how maternal dysbiosis alters microbial inheritance remains poorly defined. Here, we investigated whether antibiotic-induced maternal dysbiosis affects microbial patterns in offspring using a gestational vancomycin mouse model. 16S rRNA profiling revealed that dysbiotic dams exhibited reduced microbial richness and evenness, with the enrichment of pathobionts including Enterococcus faecium and Cronobacter muytjensii. Offspring of dysbiotic dams displayed distinct microbial community structures, lower diversity, and reduced similarity to their mothers (21.5%) compared with controls (61%). Notably, maternal dysbiosis was associated with the enrichment of Gammaproteobacteria pathobionts in offspring, whereas control dyads were characterized by commensal Bacteroidia and Clostridia. These findings indicate that maternal dysbiosis during pregnancy is associated with altered maternal-offspring microbial similarity and shifts in early-life microbial community composition.},
}

@article {pmid42181274,
year = {2026},
author = {Akbar, M and Yadav, S and Naseer, A and Hameed, R and Sarkar, A and Nazir, A},
title = {Gut microbiota-derived succinate links proteostasis collapse to α-synuclein pathology and aging.},
journal = {iScience},
volume = {29},
number = {6},
pages = {115941},
pmid = {42181274},
issn = {2589-0042},
abstract = {The gut microbiome profoundly influences brain health, yet the specific microbial metabolites and mechanisms contributing to Parkinson's disease pathology remain poorly defined. Using the Caenorhabditis elegans model expressing human α-synuclein, we systematically tested key microbial fermentation products and identified succinate as a potent driver of pathology. Succinate exposure markedly increased α-synuclein aggregation, disrupted proteostasis, and compromised mitochondrial function - manifesting as oxidative stress, reduced mitochondrial content, and attenuated UPR[mt]. These cellular defects led to dopaminergic neurodegeneration, locomotory impairments, and reduced lifespan, establishing succinate as a pro-neurodegenerative and pro-aging metabolite. Transcriptomic and genetic analyses revealed the involvement of nutrient-sensing pathways, prominently mTORC1, in promoting proteotoxic stress. Together, these findings highlight a direct link between microbial metabolism, proteostasis collapse, and neurodegeneration, establishing succinate as an active modulator of aging. Targeting succinate signaling mechanisms may therefore represent a tractable strategy for microbiome-based interventions in Parkinson's disease and age-associated neurodegeneration.},
}

@article {pmid42181833,
year = {2026},
author = {Ren, M and Jia, J and Li, Y and Shen, N and Shi, Y and Wang, Z and Huang, X and Li, G and Xiong, G and Peng, R},
title = {The emerging role of non-Helicobacter pylori microbiome in gastric carcinogenesis: a comprehensive review of pathogenic mechanisms and clinical implications.},
journal = {Gastroenterology report},
volume = {14},
number = {},
pages = {goag033},
pmid = {42181833},
issn = {2052-0034},
abstract = {Gastric cancer remains a leading global health concern, with its etiology shaped by complex interactions between the host and its microbiome. The primary etiological role of Helicobacter pylori (H.pylori) has been well-established, but recent research has pointed to the significant contributions of non-H.pylori pathogens in the onset and progression of gastric cancer. These pathogens contribute to gastric tumorigenesis by directly compromising the gastric epithelial barrier and invading gastric epithelial cells, affecting long-range processes, disrupting microbial balance, and influencing the host's immune microenvironment. In the following, we comprehensively elucidated the potential mechanisms by which Streptococcus anginosus, Methylobacterium, Prevotella, Candida albicans, and Epstein-Barr virus actively participate in gastric tumorigenesis. Beyond this, ongoing investigations seek to identify additional microorganisms that may contribute to gastric cancer development, offering new insights into the multifactorial nature of the disease. Collectively, these findings highlight the critical involvement of diverse non-H.pylori microorganisms at various stages of gastric cancer progression, advancing our understanding of microbe-driven carcinogenesis.},
}

@article {pmid42181960,
year = {2026},
author = {Rahimah, S and Tallei, TE and Savitri, M and Yamada, C and Kim, HJ and Choi, M and Park, MN and Ophinni, Y and Kim, B},
title = {Molecular basis of precision nutrition: Food components, microbiome-derived metabolites, and multi-omics modeling.},
journal = {Food chemistry. Molecular sciences},
volume = {12},
number = {},
pages = {100411},
pmid = {42181960},
issn = {2666-5662},
abstract = {Metabolic disorders, including obesity, type 2 diabetes, metabolic syndrome, and fatty liver disease, reflect multifactorial interactions among diet, host genetics, the environment, and the gut microbiome. However, conventional population-level dietary guidance often fails to capture the marked interindividual variability in metabolic responses to identical foods and nutrients. Precision nutrition has therefore emerged as an integrative paradigm that combines genomics, epigenomics regulation, microRNA-mediated control, and microbiome profiling to refine dietary recommendations, with a growing emphasis on targeted functional food-based strategies for metabolic health. This narrative review synthesizes the mechanistic foundations of precision nutrition, emphasizing how functional foods and their bioactive constituents engage nutrient-sensing and regulatory pathways that connect dietary exposures to gene regulation and downstream metabolic phenotypes. We summarize evidence for diet-gene interactions at key metabolic loci, epigenetic programming shaped by early-life nutrition, and diet-responsive microRNAs as candidate biomarkers of nutritional response. We further examine microbiome-derived signaling, specifically short-chain fatty acids and bile-acid metabolism within the gut-liver axis, as a major route by which functional dietary components can influence host pathways and condition metabolic outcomes. We highlight insights from large cohorts and controlled metabolic profiling studies and discuss enabling methodological advances, including multi-omics integration, causal inference, and machine learning models for response prediction. Key limitations remain, notably incomplete reproducibility, heterogeneity in exposure and outcome measurements, data governance challenges, and barriers to clinical implementation. In summary, precision nutrition provides a biologically grounded framework for personalized functional-food and dietary strategies, but robust validation and responsible translation are required before routine adoption.},
}

@article {pmid42182002,
year = {2026},
author = {Chen, S and Hu, X and Pan, W and Chen, T and Xie, X and Zhang, Y},
title = {Integrated metagenomic and culture-dependent profiling reveals electric shavers as selective reservoirs for multidrug-resistant opportunistic pathogens.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1839764},
pmid = {42182002},
issn = {1664-302X},
abstract = {INTRODUCTION: Personal care items are commonly viewed as passive vehicles for microbial transfer; however, the physicochemical stresses they impose may actively shape microbial persistence, community composition, and the distribution of resistance-associated determinants. Electric shavers may therefore constitute an underrecognized anthropogenic niche for the enrichment of clinically relevant antimicrobial resistance traits.

METHODS: We sampled electric shavers from 10 individuals at early (day 2) and mature (day 21) usage stages, generating 8 high-quality metagenomes and recovering 97 viable isolates spanning 16 bacterial species. Deep metagenomic sequencing, combined with whole-genome sequencing of 45 representative isolates, was used to resolve the ecological, functional, and evolutionary features of shaver-associated microbiomes.

RESULTS: Shaver-associated community assembly was dominated by stringent environmental filtering, which promoted the repeated enrichment of stress-adapted lineages across hosts, notably Acinetobacter ursingii MLST3244 and Klebsiella pneumoniae MLST995 and MLST23. We further identified recurrent mobile genetic element-associated resistance islands and plasmid backbones in different host cohorts, suggesting repeated selection under shared anthropogenic pressures rather than direct evidence of de novo convergent evolution. Importantly, viable Klebsiella pneumoniae isolates co-carried extended-spectrum β-lactamase genes such as bla SHV and major virulence determinants, while metagenomic profiling detected reads assigned to mcr- and tet(X)-like gene variants at the community level, targeted PCR further confirmed the presence of these resistance determinants.

DISCUSSION: Because routine shaving can generate barrier-disrupting micro-abrasions, electric shavers may function as selective reservoirs for multidrug-resistant bacteria. Our findings reveal a previously overlooked exposure interface through which everyday personal care practices may promote the enrichment and persistence of clinically important resistance and virulence determinants.},
}

@article {pmid42182007,
year = {2026},
author = {Brown, AL and McGovern, MJ and Schickle, A and Sharp, KH and Apprill, A},
title = {Controlled temperature-induced dormancy leads to predictable microbial recovery in the temperate coral microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1799468},
pmid = {42182007},
issn = {1664-302X},
abstract = {INTRODUCTION: Dormancy is a common response to harsh conditions across the tree of life. Increasingly, the animal microbiome is suggested to mediate dormancy, including onset, maintenance and exit or recovery periods. However, it is unclear what triggers dormancy and the consistency of microbial patterns across populations. Because it regularly undergoes dormancy during winter in the northernmost part of its range, the temperate coral Astrangia poculata can serve as a model for studying coral-microbiome dynamics during environmental stress and recovery.

METHODS: Here, we experimentally manipulated temperature to induce dormancy and measured the microbial community shifts associated with dormancy and during the days that the corals were exiting dormancy in two populations.

RESULTS: Our treatments successfully induced dormancy, which was maintained through low temperatures. We found consistent and predictable shifts in the microbiome during dormancy and during the recovery period while corals exited dormancy.

DISCUSSION: We suggest Sulfitobacter, a key genus in tropical corals, may be involved in early recovery in the assembly of the microbiome. Broadly, our results highlight that the inducible, consistent, and persistent microbial restructuring associated with Astrangia dormancy can be applied more generally to tropical coral recovery from stress.},
}

@article {pmid42182016,
year = {2026},
author = {Su, S and Li, H and Li, W and Yang, Z and Zhang, Q},
title = {Differences in microbial community structure induced by tillage practices under straw return associated with metabolic functions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1794771},
pmid = {42182016},
issn = {1664-302X},
abstract = {This study aimed to elucidate the biological mechanisms through which different tillage practices affect wheat yield and nutrient use efficiency under straw return conditions, focusing on rhizosphere microbial communities, metabolite profiles, and their interactions to inform improved agricultural management. The field experiment tested three treatments: no-tillage with all straw mulching (SN), rotary tillage straw return (SR), and plow tillage straw return (SP). Using high-throughput sequencing and liquid chromatography-tandem mass spectrometry, we investigated how different treatments affected the microbial community in wheat rhizosphere soil and metabolic functions through microbiome and non-targeted metabolomics analyses. SN helped to increase the wheat yield, soil nutrient content in the plow layer, and enzyme activity. Compared with SN, the yields were 8.3% and 12.4% lower under SR and SP, respectively, the soil organic carbon contents were 13.2% and 5.6% lower, and the pH values were 2.7% and 1.2% higher. Tillage practices significantly altered the composition and diversity of the bacterial and fungal communities. The species richness of bacterial and fungal communities followed the order of: SP > SR > SN and SN > SP > SR, respectively. The stabilities of the bacterial and fungal communities exhibited the same distribution pattern. Principal coordinate analysis and PERMANOVA indicated that under straw return, different tillage practices led to significant separation of soil bacterial and fungal communities. Furthermore, Actinobacteria and Proteobacteria contributed most significantly to differences in the bacterial community structures, and Ascomycota and Basidiomycota contributed most significantly to differences in the fungal community structures. Under straw return, different tillage practices significantly altered soil metabolite composition. Bacterial communities correlated more strongly with soil metabolites than fungal communities. Compared with SN, metabolic pathways for different metabolites were enriched under SR and SP, and all were related to amino acid metabolism, putatively mainly in the valine, leucine, and isoleucine biosynthesis pathways. Collectively, our findings demonstrate that tillage practice is a key regulator of straw-amended soil ecosystems, and that no-till with straw mulching optimizes yield and nutrient efficiency primarily by enhancing the functional synergy between the rhizosphere microbiome and metabolome.},
}

@article {pmid42182017,
year = {2026},
author = {Li, J and Qiu, X},
title = {Neurodevelopmental disorders and the gut microbiome: insights into ADHD and tic disorders.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1779746},
pmid = {42182017},
issn = {1664-302X},
abstract = {This review examines the relationship between tic disorders (TD), attention deficit hyperactivity disorder (ADHD), and the gut microbiota within the framework of the gut-brain axis. We summarize current evidence on the clinical characteristics and neurobiological features of TD and ADHD, and discuss how genetic susceptibility, environmental exposures, and dietary factors may interact with gut microbial composition. We further review studies comparing the gut microbiota of affected individuals and healthy controls, with attention to recurrent taxa-level findings, functional hypotheses, and emerging microbiome-targeted interventions such as probiotics and fecal microbiota transplantation. Importantly, most available human studies remain associative rather than mechanistic, and cross-study comparability is limited by heterogeneity in sequencing approaches, cohort characteristics, medication exposure, and dietary control. Overall, current findings support the gut microbiota as a relevant component of neurodevelopmental disorders such as ADHD and TD, while highlighting the need for larger longitudinal and mechanistic studies to clarify causality and therapeutic potential.},
}

@article {pmid42182018,
year = {2026},
author = {Abilda, Z and Isgandarov, I and Kanat, R and Daurov, D and Sapakhova, Z and Zhambakin, K and Daurova, A and Begaliyeva, D and Choi, K and Shamekova, M},
title = {Genome-resolved metagenomics reveals co-selection of antibiotic and metal resistance in chronically polluted industrial soils.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1829529},
pmid = {42182018},
issn = {1664-302X},
abstract = {INTRODUCTION: Chronic heavy metal contamination can restructure soil microbiomes and may co-select for antibiotic resistance, yet genome-resolved evidence from industrial soils remains limited.

METHODS: In this study, we applied Oxford Nanopore long-read metagenomic sequencing to soil samples collected across industrially influenced sites in East Kazakhstan to characterize strain-level community composition, profile antibiotic resistance genes and metal resistance genes, and relate these patterns to soil physicochemical properties.

RESULTS: Across all samples, we identified 3,053 strains, with Actinobacteria and Proteobacteria together accounting for 94.1% of the total community. Heavy metal concentrations varied markedly among sites. The resistome comprised antibiotic resistance genes from several drug classes and 238 distinct metal resistant genes, with aminoglycoside, glycopeptide, and multidrug resistance dominating the antibiotic resistance gene profile, while czcA, ruvB, arsM, and arsT were among the most abundant Metal resistant genes. Multivariate analyses showed that heavy metals, particularly Zn, significantly shaped microbial community structure as well as antibiotic resistance gene and metal resistance gene composition, and redundancy analysis identified Zn and soil pH as the principal environmental drivers. Network analyses further revealed that Bradyrhizobium icense and Conexibacter woesei acted as key super-hosts linking ARGs and MRGs, supporting heavy metal-driven co-selection within the soil microbiome.

DISCUSSION: Together, these findings show that long-read genome-resolved metagenomics can uncover how chronic industrial pollution maintains metal-adapted microbial communities while promoting the persistence and potential dissemination of antibiotic resistance in soil ecosystems.},
}

@article {pmid42182019,
year = {2026},
author = {Wu, L and Li, S and Han, F and Guo, J and Zhang, X and Xu, L},
title = {Restoring circadian disrupted gut microbial metabolite rhythms with phytochemicals: a new avenue against metabolic disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1801367},
pmid = {42182019},
issn = {1664-302X},
abstract = {The global epidemic of metabolic diseases-encompassing obesity, type 2 diabetes mellitus (T2DM), non-alcoholic fatty liver disease (NAFLD), and cardiovascular disease-represents a defining public health challenge of our era. The traditional model of simple caloric excess vs. expenditure has proven insufficient, giving way to a paradigm that acknowledges complex interactions between genetics, environment, and lifestyle, mediated by intricate physiological systems. Among these, the host circadian timing system and the gut microbiome have ascended as pivotal, deeply intertwined regulators of metabolic homeostasis. The gut microbiome, far from a static collection of microbes, constitutes a dynamic and metabolically active community whose composition and, critically, its functional output exhibit profound and predictable diurnal oscillations. The host's circadian clocks regulate microbial rhythms primarily by controlling the daily cycle of feeding and fasting. Modern life induces circadian disruption (CD) through ubiquitous exposure to artificial light at night, shift work, social jet lag, and erratic eating patterns. It perturbs the rhythmic dynamics of the gut ecosystem, leading to a fundamental dysregulation in the temporal production of key microbial metabolites. These metabolites, including short-chain fatty acids, secondary bile acids (BAs), indoles and other tryptophan derivatives, function as indispensable chemical messengers that coordinate peripheral metabolism, immune responses, and energy homeostasis in a precise, time-of-day-dependent manner. Their desynchronization-manifesting as mistimed, deficient, or incessant signaling-directly instigates the core pathologies of metabolic disease: insulin resistance, adipocyte dysfunction, hepatic lipid accumulation, and chronic low-grade inflammation. This review synthesizes current evidence to delineate the multilevel mechanisms through which CD drives the dysregulation of gut microbiome metabolite rhythms and establishes the causal pathways linking this dysrhythmia to metabolic pathogenesis. Furthermore, we undertake a critical evaluation of the promising therapeutic potential of dietary phytochemicals-a diverse class encompassing polyphenols, glucosinolates, and prebiotic fibers-to act as chrono-therapeutic agents. Through their multifaceted capacity to remodel microbial ecology, calibrate microbial enzymatic output, and reinforce host circadian-metabolic coupling, phytochemicals present a novel, physiologically aligned, and sustainable dietary strategy for the prevention and management of metabolic disorders. We conclude by outlining key translational challenges and propose future research directions essential for harnessing the potential of the "clock-microbiome-metabolite" axis within the framework of precision nutrition and medicine.},
}

@article {pmid42182023,
year = {2026},
author = {Duan, J and Chen, Y and Zhang, X and Li, C and Gao, T and Li, K},
title = {Metagenomic analysis suggests that tomato root-knot nematode infestation disrupts rhizosphere microbial networks, consistent with reduced disease suppression.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1798902},
pmid = {42182023},
issn = {1664-302X},
abstract = {INTRODUCTION: The rhizosphere microbiome serves as a critical line of defense for plant health and soil-borne disease suppression. However, the underlying mechanisms by which root-knot nematodes (RKN), a devastating soil-borne pathogen, undermine putative disease-suppressive function through destabilizing microbial interaction networks remain poorly understood.

METHODS: This study employed metagenomic sequencing coupled with microbial co-occurrence network analysis to systematically compare the community structure, interaction network topology, and functional gene profiles of the rhizosphere microbiome between healthy and RKN-infected tomato plants.

RESULTS: Our findings revealed that RKN infection significantly altered the community structure of bacteria, fungi, and viruses. This disturbance was associated with a systematic simplification and loss of modularity within microbial interaction networks. Specifically, intra-domain bacterial networks exhibited reduced scale and connectivity, whereas fungal networks showed strengthened internal cohesion. Cross-kingdom interactions (e.g., bacteria-fungi) were severely weakened, resulting in a topological imbalance characterized by "tight within domains, loose between domains." Functional profiling further indicated a distinct metabolic reprogramming in the infected rhizosphere, with a shift in resource allocation from growth and biosynthesis toward core energy acquisition and stress response.

DISCUSSION: Collectively, our results suggest that the putative decline in disease-suppressive function following RKN infection may be mechanistically rooted in the destabilization of microbial cooperative networks and the consequent loss of functional redundancy. This study provides a novel network-level ecological framework for understanding plant-microbe-pathogen interactions and lays a theoretical foundation for microbiome-based ecological management strategies against soil-borne diseases.},
}

@article {pmid42182024,
year = {2026},
author = {Kostelnikova, K and Frejlichova, L and Spetik, M and Sochor, J and Eichmeier, A and Baron, M},
title = {Impact of winemaking technologies on polyphenolic composition and wine microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1846196},
pmid = {42182024},
issn = {1664-302X},
abstract = {INTRODUCTION: This study investigates how different oenological practices, including spontaneous and inoculated alcoholic fermentation (AF), variations in malolactic fermentation (MLF) and ageing, are associated with changes in microbial diversity and polyphenolic profile of Sauvignon blanc wines.

METHODS: Microbial composition was investigated through high-throughput DNA sequencing, while polyphenolic compounds were analysed using LC-MS together with total phenolic content through Folin-Ciocalteu assay and antiradical activity by DPPH assay.

RESULTS AND DISCUSSION: AF was associated with a pronounced homogenization of the microbiota, particularly through the dominance of Saccharomyces and stable epiphytic bacteria. At later stages, microbial communities showed notable compositional divergence, with their development closely linked to technological interventions and the extent of phenolic extraction. The pomace-fermented treatment exhibited the highest polyphenol content along with the greatest compositional heterogeneity, whereas treatments with lower phenolic loads exhibited simpler microbial profiles and the stable dominance of Leuconostoc after malolactic fermentation. Polyphenols appear to act as modulatory factor in microbial succession, with extraction intensity showing a more distinct association with community shifts than the fermentation regime itself. Overall, the study highlights that technological practices affecting phenolic extraction appear to play a notable role in the observed microbial trends and the resulting wine characteristics.},
}

@article {pmid42182071,
year = {2026},
author = {Qin, R and Yu, P and Wang, H and Zhou, J and Gong, R and Duan, Y and Jia, H and Xie, M and Zhou, Y and Hu, J},
title = {Gut-bone axis crosstalk: Microbiota-driven immune-metabolic-neural networks in bone disorders and precision interventions.},
journal = {Journal of orthopaedic translation},
volume = {58},
number = {},
pages = {101126},
pmid = {42182071},
issn = {2214-031X},
abstract = {UNLABELLED: The gut microbiota regulates bone metabolism via a complex gut-bone axis involving short-chain fatty acids (SCFAs), immune modulation, and neuroendocrine signals. However, the precise mechanisms remain unclear, and microbiota-targeted interventions (probiotics, prebiotics, fecal microbiota transplantation) are not yet optimized for clinical use. This review systematically synthesizes the immune-metabolic-neural interaction network within the gut-bone axis, highlighting non-linear crosstalk among SCFAs, bile acids, tryptophan derivatives, immune cells (macrophages, Treg/Th17), and vagus nerve signaling. We critically assess translational hurdles, including heterogeneous study designs, confounding factors, and lack of causal evidence. Based on this network perspective, we propose a framework for future research that prioritizes multi-omics approaches, stratified interventions, and rigorous trials. This synthesis advances understanding of how gut dysbiosis drives bone disorders and paves the way for precision skeletal medicine.

This review identifies microbial markers for risk stratification of bone metabolic disorders and discusses SCFA-based strategies and fecal microbiota transplantation (FMT) in conditions including osteoporosis, impaired fracture healing, rheumatoid arthritis, and glucocorticoid-associated osteonecrosis. It provides testable hypotheses for large-scale randomized controlled trials (RCTs), directly supporting translation of microbiome research into clinical practice for bone disorders.},
}

@article {pmid42182110,
year = {2026},
author = {Zhang, Z and Holton, M and Ferrer, DM and Tripp, AD and Richter, A and Dixit, PD and Urtecho, G},
title = {Metagenome-scale Modeling to Assess Microbiome Metabolic Complementarity for Precision Microbiota Transplantation Therapies.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.15.725570},
pmid = {42182110},
issn = {2692-8205},
abstract = {Fecal microbiota transplantation (FMT) holds therapeutic promise beyond recurrent Clostridioides difficile infection, but clinical outcomes remain unpredictable, in part because existing computational models do not fully capture the metabolic compatibility between donor and recipient communities. Here, we present a metagenome-scale metabolic modeling framework that quantifies metabolic niche complementarity between donor and recipient microbiomes to predict transplantation outcomes. Using MICOM-derived community metabolic models, we show that donor taxa whose metabolic flux profiles are more dissimilar from the recipient community engraft at significantly higher rates in both murine and human FMT cohorts. In a human IBS trial, metabolic models accurately predicted post-FMT community composition via leave-one-out cross-validation and recapitulated disease-associated alterations in short-chain fatty acid, sulfur, and gas metabolism. We then performed 2,548 in silico FMT simulations between IBS-D/M patients and donors from the OpenBiome biobank to demonstrate a platform for personalized donor screening. This screen identified super-donors characterized by high taxonomic diversity, broad metabolic niche coverage, and community interaction networks dominated by cross-feeding rather than competition, as quantified by a flux-derived ecological network balance index that strongly predicted engraftment potential. This framework provides a mechanistic, scalable tool for rational donor-recipient matching that could guide personalized microbiome-based therapies.},
}

@article {pmid42182112,
year = {2026},
author = {Buchanan, LB and Khan, Y and Vargas, JR and Shao, Z and Biribawa, VM and Ssemunywa, HR and Namuniina, A and Okech, B and Tobian, AA and Park, DE and Liu, CM and Kaul, R and Galiwango, RM and Prodger, JL},
title = {CD11c+ myeloid cells are the predominant CD4+CCR5+ immune population in the foreskin and are increased in men with HIV-associated penile anaerobes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.11.724468},
pmid = {42182112},
issn = {2692-8205},
abstract = {Specific anaerobic species within the penile microbiome - Bacteria Associated with Seroconversion, Inflammation and Immune Cells (BASIC) - have been linked to increased HIV-1 susceptibility. These bacteria can directly disrupt epithelial integrity and are believed to increase local inflammation, resulting in an increased density of HIV-susceptible T cells in the inner foreskin. It is currently unknown whether other immune cells bearing the HIV entry receptors, CD4 and CCR5, are also elevated in individuals with a high abundance of BASIC species. Using inner foreskin tissues and penile swabs from males undergoing voluntary medical male circumcision, we performed a retrospective cross-sectional study to assess the relationship between BASIC species and the tissue density of such immune cells, including CD68+ macrophages, CD11c+ dendritic cells, and CD207+ Langerhans cells. The most abundant cells in the inner foreskin expressing the HIV co-receptors were CD11c+ dendritic cells (48.6% of CD4+/CCR5+ cells), followed by CD68+ macrophages (28.6%), CD3+ T cells (18.8%), and CD207+ Langerhans-like (8.8%) cells. The absolute abundance of BASIC species was associated with elevated tissue densities of both CD4+/CCR5+ T cells (as previously reported) and a heterogeneous population of CD3-/CD4+/CCR5+ cells of myeloid origin. In the dermis, BASIC species abundance was linked to elevated densities of cells expressing CD11c, CD68, and CD207, as well as those co-expressing CD11c and CD207; furthermore, CD11c+ and CD207+ cells were farther from the basement membrane in participants with a high abundance of BASIC species. Myeloid cells were not elevated in participants with a high abundance of control taxa. In an integrated analysis including previously published data from this same cohort, myeloid-cell densities clustered tightly together, positively correlated with BASIC species and pro-inflammatory cytokines, and had trends to negative correlations with control taxa (significant for CD207+ cell density). Overall, our findings suggest that BASIC species are associated with a broader foreskin immune phenotype marked by increased densities of HIV-susceptible myeloid and T cells, alongside epithelial disruption.},
}

@article {pmid42182121,
year = {2026},
author = {Hendricks, SF and Tan, AL and Williams, AG and Buckley, KM and Strader, ME},
title = {Environmental microbial communities and host selection shape larval microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.14.725214},
pmid = {42182121},
issn = {2692-8205},
abstract = {UNLABELLED: Ocean warming is altering abiotic environments and biotic interactions experienced by marine organisms, where sensitive early developmental windows occur in biologically complex seawater communities. The impact of these interactions on developmental processes and fitness in hosts is not well understood, but likely contingent on the establishment of a host-associated microbiome. Here, we hypothesize that temperature and microbial exposure during embryogenesis influence larval microbiome assembly and host morphology. Strongylocentrotus purpuratus embryos were raised in low microbial richness (LMR) or high microbial richness (HMR) seawater at ambient (14 °C) or elevated (18 °C) temperature, then collected at 2, 4, and 6 days post-fertilization (dpf) following multiple feedings. Higher microbial diversity was observed in larvae that developed in HMR seawater when compared to LMR. Differences in relative abundances of dominant microbial families between seawater and larvae suggest some degree of host selectivity in microbiome assembly. Temperature did not strongly alter microbiome composition, but both temperature and microbial condition led to differences in larval morphology by 6 dpf, potentially due to enrichment of microbes with chemoheterotrophic functions. By linking how temperature and microbial communities interact with host development, we contribute novel insights into how early-life environmental conditions impact holobiont formation and morphology.

ONE SENTENCE SUMMARY: Early developmental temperature and microbial conditions shape larval microbiome establishment and morphology.},
}

@article {pmid42182128,
year = {2026},
author = {Nguyen, TH and Su, M and Lu, NT and Trotter, V and McKeithen-Mead, SA and Lopez, JA and Sun, J and Hallberg, Z and Shi, H and Ho, PY and DeFelice, BC and Taga, ME and Deutschbauer, AM and Hryckowian, AJ and Huang, KC},
title = {Phage-based microbiome manipulation reveals ecological interactions within gut communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.13.724931},
pmid = {42182128},
issn = {2692-8205},
abstract = {Mechanistic understanding of gut ecology is limited by the availability of tools for precise manipulation of microbiome composition. Here, we isolate lytic phages to enable targeted removal of gut commensal Escherichia fergusonii (Ef) from complex, undefined stool-derived in vitro communities. A single phage drove resistance without fitness cost in monoculture, but resistant Ef exhibited reduced fitness in communities, enabling expansion of closely related Proteobacteria. Resistance arose via reversible promoter inversion linked to outer-membrane function. A phage cocktail overcame resistance to achieve Ef knockout across communities with minimal collateral effects. Using knockout communities, we show that Ef is necessary and sufficient for preventing Salmonella invasion. Replacement with an Ef transposon-mutant library revealed that community-specific fitness defects are enriched in genes involved in outer-membrane assembly. Disruption of these genes sensitized Ef to antagonistic community members, highlighting interspecies warfare as a key driver of microbiome ecology. These results establish phage-mediated perturbation as a framework for linking species to community-level function and for enabling precision microbiome engineering.},
}

@article {pmid42182130,
year = {2026},
author = {Tossas, KY and Zhu, B and Tyc, KM and Rhodes, C and Strauss, JF and Serrano, MG and Buck, GA},
title = {HPV co-infection burden, vaginal microbiota restructuring, and host context are associated with Cervical precancer risk in a racially restricted observational cohort.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.13.724979},
pmid = {42182130},
issn = {2692-8205},
abstract = {BACKGROUND: High-risk human papillomavirus (HPV) infection is necessary for cervical carcinogenesis, but HPV detection alone does not distinguish transient infection from lesions at greatest risk of progression. We evaluated whether HPV burden, vaginal microbiota structure, and host-context variables jointly characterize cervical intraepithelial neoplasia grade 3 (CIN3) in a Black/African American and White analytic cohort from the Vaginal Microbiome Health Project (VaMHP), integrating L1-based HPV typing, 16S rRNA vaginal microbiota profiling, and linked clinical metadata.

RESULTS: Among 1181 participants, 75 had CIN3. CIN3 was associated with HPV positivity (55/75, 73.3% vs 431/1106, 39.0%; odds ratio [OR] 4.31, 95% CI 2.55-7.29; Fisher exact p = 7.9 x 10^-9) and with multiple HPV infection among HPV-positive participants (35/55, 63.6% vs 176/431, 40.8%; OR 2.54, 95% CI 1.42-4.54; p = 0.0022). HPV communities in CIN3-positive samples showed higher Shannon diversity, greater observed strain richness, higher evenness, and significant beta-diversity separation. In vaginal microbiota analyses, alpha diversity did not differ by CIN3 status, but community composition did, and Lactobacillus crispatus was the only taxon depleted in CIN3 after multiple-testing correction. Race, age, and metronidazole exposure were central nodes in the host-factor network. In predictive modeling, a full integrated model combining metadata, HPV, and vaginal microbiota features (auROC = 0.745) outperformed both HPV + vaginal microbiota (auROC = 0.670) and HPV-only (auROC = 0.440) models.

CONCLUSIONS: CIN3 in this cohort was associated with coordinated shifts in virologic burden, vaginal community structure, and host social-clinical context. The results support a structure-function interpretation in which loss of Lactobacillus crispatus-dominant states and enrichment of dysbiosis-associated communities define a host-microbiome context that is more permissive to HPV persistence and precancer. These findings move beyond descriptive omics by showing that microbiome and host-context features add nonredundant discriminatory signal beyond HPV-only models.},
}

@article {pmid42182226,
year = {2026},
author = {Sokolik, CC and Sahadeo, K and Vyce, J and Thomas, M and Celeste, C and Gachunga, W and Calixte, T and Ledford, I and Williams, J and Estess, E and Wilder, C and Parker, IK},
title = {Microbiome Composition Regulates Cathepsin Expression in Vaginal Fluid Across BV Diagnoses and Community State Types.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.07.723359},
pmid = {42182226},
issn = {2692-8205},
abstract = {PURPOSE: Bacterial vaginosis (BV) is associated with disruption of the vaginal microbiome and extracellular matrix (ECM) remodeling, yet the contribution of host proteases to this process remains unclear. This study investigated whether expression and activity of cathepsins K, L, S, and V differ by BV diagnosis and community state type (CST). We hypothesized that BV and BV associated CSTs would exhibit increased expression and activity of collagen and elastin-degrading cathepsins.

METHODS: Vaginal fluid samples were collected and classified by BV diagnosis and CST. Cathepsin expression was evaluated by Western blotting to distinguish inactive and active enzyme forms. Proteolytic activity was assessed using multiplex cathepsin zymography. Statistical analyses compared cathepsin expression and activity across diagnoses and CSTs. Principal component analysis and linear regression were performed to assess associations between cathepsin activity, microbial diversity, and CST.

RESULTS: Procathepsin K expression was significantly increased in BV-positive and CST IV samples, while total cathepsin L expression was significantly elevated in samples with Nugent-intermediate scores. Cathepsins S and V showed variation in inactive and active forms in Nugent-intermediate and CST III samples. In contrast, total cathepsin activity, including cathepsins K and V, did not significantly differ across BV diagnoses or CSTs. Overall, cathepsin activity varied between individuals rather than by clinical classification.

CONCLUSIONS: Cathepsin expression and maturation state differ by microbiome composition, suggesting that the vaginal microbiome may regulate post-translational processing of cathepsins. As a result, cathepsin activity appears to be regulated at the individual level rather than strictly by BV diagnosis or CST. These findings link vaginal microbiome composition to ECM remodeling and potential adverse reproductive outcomes.},
}

@article {pmid42182364,
year = {2026},
author = {Diaz Olea, X and Beede, K and Pereira, G and Scott, D and Petucci, C and Martens, E and Rodionov, D and Shah, A and Martinez, MP and Kim, H and Sharma, AK and Martin, A and Zhang, T and Faries, MB and Hamid, O and Devkota, S and Osterman, A and Knott, S and Voest, EE and Ajami, NJ and Wargo, J and Ramer-Tait, AE and Ronai, ZA},
title = {Tryptophan degradation by intestinal Bacteroides induces anti-tumor immunity and limits melanoma growth.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.06.723300},
pmid = {42182364},
issn = {2692-8205},
abstract = {Defining mechanisms used by gut microbiota to control anti-tumor immunity may offer novel therapeutic modalities. Here, we demonstrate that Bacteroides rodentium and closely related Bacteroides uniformis species induce anti-tumor immunity and limit melanoma development when colonized in either germ-free (GF) mice, mice with a complex microbiome, or WT mice. Enhanced CD8 [+] T cell infiltration seen in tumors of mice harboring B. rodentium coincided with increased expression of immune-stimulating pathways and activation of bone marrow-derived dendritic cells that were co-cultured with the B. rodentium secretome. Metabolomic analyses of cecal samples from GF mice colonized with Altered Shedlar Flora (ASF) plus B. rodentium revealed lower tryptophan levels than in ASF-colonized controls, and WT mice fed a tryptophan-deficient diet exhibited inhibition of melanoma development. In silico genomic reconstruction of metabolic pathways revealed that both B. rodentium and B. uniformis harbor tryptophanase A (TnaA) and aromatic amino transferase (ArAT) genes, both of which function in tryptophan degradation. Administration of a B. uniformis harboring TnaA mutant failed to inhibit melanoma growth in gnotobiotic mice. Notably, administration of indoles, but not kynurenines, also effectively inhibited melanoma development, increasing immune cell infiltration into the tumors. Correspondingly, levels of bacterially encoded tryptophan-degrading enzymes were higher in cohorts of melanoma patients responding to immune checkpoint blockade. These findings highlight a novel mechanism of anti-tumor immunity and tumor growth inhibition dependent on the tryptophan degradation products, indoles, produced by intestinal Bacteroides species.},
}

@article {pmid42182438,
year = {2026},
author = {Fuerte-Stone, J and Ghali, J and Valaitis, S and Mimee, M},
title = {Engineered gut symbionts mediate cross-phylum antagonism to suppress uropathogenic Escherichia coli colonization.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.11.724322},
pmid = {42182438},
issn = {2692-8205},
abstract = {UNLABELLED: Urinary tract infections (UTIs) are among the most common bacterial infections globally and create a large burden on the healthcare system. Uropathogenic Escherichia coli (UPEC) account for the majority of UTIs and increase the risk of recurrence. The standard treatment is antibiotics and, with the rise of multi-drug resistant UPEC lineages, there is a need for alternative treatments and prevention. Colicins, bacteriocins targeting and produced by E. coli , have previously been shown to inhibit the growth of pathogenic E. coli and are a promising alternative. Here, we engineer commensal Bacteroidaceae to secrete colicins via outer membrane vesicle (OMV) targeting signal peptides to suppress E. coli in the mouse gut. Secreted colicins were assessed for their ability to kill primary clinical isolate UPEC strains, including epidemic multi-drug resistant ST131 strains, along with other pathogenic and type strains. Specifically, secreted colicin E7, from Phocaeicola vulgatus fully eliminated of several UPEC strains in culture. In mice, P. vulgatus secreting colicin E7 prevented the extended colonization of two clinical UPEC strains and restored microbiome diversity. Together, this work shows the viability of secreted, heterologous antimicrobials from P. vulgatus as prophylactic treatment against the colonization of pathogenic E. coli utilizing cross-phylum antagonism in the gut.

SIGNIFICANCE STATEMENT: Recurrent urinary tract infections can be driven by intestinal reservoirs of uropathogenic Escherichia coli that are difficult to eliminate and increasingly recalcitrant to conventional antibiotic therapy. Here, we show that engineered gut symbionts from the Bacteroidaceae family can secrete targeted protein antibiotics to selectively kill these uropathogenic E. coli . Leveraging outer membrane vesicle-based secretion, we demonstrate that bacteriocin secretion can prevent gut colonization by clinically relevant pathogens, while preserving overall microbiome diversity. This work establishes a strategy for programmable, cross-phylum antimicrobial delivery within the gut microbiome, providing a potential alternative to conventional antibiotics for preventing recurrent infections and other enteric diseases.},
}

@article {pmid42182451,
year = {2026},
author = {Wei, W and Graf, R and Wang, Y and Oalmann, CJ and Lau, JT and Wang, X and Chien, M and Conrad, MC and Simon, J and Ganguly, S and Yamazaki, T and Harberts, A and Chen, S and Fondevila, MF and Dhar, D and Campbell, SA and Senter, RK and Schnabl, B},
title = {Targeting Microbial Bile Salt Hydrolase Reprograms Bile Acid Metabolism and Ameliorates Metabolic Dysfunction-Associated Steatohepatitis in Mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.12.724693},
pmid = {42182451},
issn = {2692-8205},
abstract = {UNLABELLED: Microbial bile salt hydrolase (BSH) plays a central role in shaping bile acid composition and gut-liver metabolic signaling, yet its therapeutic potential in metabolic dysfunction-associated steatohepatitis (MASH) remains incompletely defined. Here, we evaluated the efficacy of the non-absorbable BSH inhibitor GR-7 in a diet induced mouse model of steatohepatitis using early and late intervention strategies with different dosing regimens. GR-7 reduced food intake and exerted stage- and dose-dependent therapeutic effects, with early intervention robustly suppressing hepatic fibrosis even at low dose, whereas late-stage administration of high-dose GR-7 markedly reduced hepatic steatosis and inflammation, as evidenced by decreased liver weight, hepatic triglyceride and cholesterol levels, and plasma ALT. Although late intervention did not result in statistically significant histological reversal of fibrosis, a trend toward improvement was observed, together with suppression of fibrogenic gene expression, suggesting that prolonged treatment may further enhance antifibrotic efficacy. Mechanistically, GR-7 effectively inhibited microbial BSH activity in vivo, leading to reduced cecal unconjugated primary and secondary bile acids-including deoxycholic acid and lithocholic acid, which was associated with improved gut barrier integrity and reduced hepatic inflammation. In parallel, BSH inhibition reprogrammed hepatic bile acid metabolism toward activation of the alternative CYP27A1-mediated synthesis pathway, accompanied by reduced food intake, thereby contributing to improved hepatic lipid accumulation. Furthermore, late-stage high-dose treatment selectively remodeled the hepatic immune landscape rather than fully restoring homeostasis, highlighting immune recalibration as a key component of therapeutic response. Together, these findings identify microbial BSH inhibition as a promising microbiome-targeted therapeutic strategy for MASH.

HIGHLIGHTS: The non-absorbable BSH inhibitor GR-7 improves steatosis, inflammation, and fibrosis in of Western diet-induced steatohepatitis model in mice in a dose-dependent manner.GR-7 reduces food intake and body weight gain.GR-7 reduces cytotoxic secondary bile acids, including DCA and LCA.GR-7 reprograms hepatic bile acid metabolism and immune responses.},
}

@article {pmid42182456,
year = {2026},
author = {Ryu, EP and Keller, CA and Nichols, RG and Tran, HN and Brocious, PR and Harris, LR and Koltun, WA and Yochum, GS and Davenport, ER},
title = {Integrative host transcriptomic and mucosal microbiome profiling reveals region-specific host-microbiome associations across the human intestine.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.13.725025},
pmid = {42182456},
issn = {2692-8205},
abstract = {UNLABELLED: Host genetics shapes gut microbiome composition, yet the physiological mechanisms underlying this relationship remain poorly understood. Characterizing associations between host gene expression and the mucosal microbiome offers a promising route to identifying the host pathways and microbial taxa most likely to interact physiologically. However, existing investigations have been conducted primarily in acute disease contexts and within the colon, leaving host-microbiome associations outside of acute inflammatory contexts and those in undersampled regions such as the terminal ileum poorly characterized. To address these gaps, we profiled paired host gene expression from full-thickness resections and mucosal microbiome data, both from macroscopically non-inflamed tissue from Crohn's disease patients undergoing surgery across three intestinal sites: terminal ileum (n = 32), cecum (n = 35), and right colon (n = 30). Using a multi-level analytical framework including Procrustes analysis, sparse canonical correlation analysis, and elastic net regression, we identified significant associations between the mucosal transcriptome and microbiome. Intestine-wide, genes enriched in immune and intestinal barrier integrity pathways were associated with heritable taxa including Fusicatenibacter , consistent with patterns observed in microbiome genome-wide association studies. Region-specific analysis identified the terminal ileum as a distinct site of host-microbiome interaction, with associations involving metabolic and barrier-related pathways not observed in the large intestine. Notable terminal ileum-specific associations included PCDH20 with Faecalitalea and ACAT1 with Lactococcus , implicating epithelial barrier maintenance and host-microbiome metabolic interactions, respectively. These findings advance our understanding of the physiological basis of host-microbiome interactions across the intestine.

IMPORTANCE: The human gut is home to trillions of microorganisms that interact with the intestinal lining, yet we have a limited understanding of the specific biological processes involved in these interactions. Most studies characterizing the relationships between host gene expression and the gut microbiome have focused on the colon and on active disease contexts, leaving it unclear whether the associations observed reflect fundamental host-microbiome biology or disease-specific responses. By examining mucosal tissue, where host cells and microbes are in direct contact, across three sites in non-acutely inflamed tissue, we show that expression of immune defense and barrier maintenance genes is broadly associated with the microbiome across the intestine. We also identify distinct classes of associations in the terminal ileum, including host genes involved in metabolic processes. These findings provide a foundation for understanding how host biology and the gut microbiome are linked outside of acute disease.},
}

@article {pmid42182508,
year = {2026},
author = {Wang, XW and Huang, D and Yu, P and Weiss, ST and Liu, YY},
title = {Machine learning-based Personalized Dietary Recommendations to Achieve Desired Gut Microbial Compositions.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.12.724618},
pmid = {42182508},
issn = {2692-8205},
abstract = {Dietary intervention is an effective way to alter the gut microbiome to promote human health. Yet, due to our limited knowledge of diet-microbe interactions and the highly personalized gut microbial compositions, an efficient method to prescribe personalized dietary recommendations to achieve desired gut microbial compositions is still lacking. Here, we propose a machine learning framework to resolve this challenge. Our key idea is to implicitly learn the diet-microbe interactions by training a machine learning model using paired gut microbiome and dietary intake data from a population-level cohort. The well-trained machine learning model enables us to predict the microbial composition of any given species collection and dietary intake. Next, we prescribe personalized dietary recommendations by solving an optimization problem to achieve the desired microbial compositions. We systematically validated this Machine learning-based Personalized Dietary Recommendation (MPDR) framework using synthetic data generated from an established microbial consumer-resource model. We then validated MPDR using real data collected from a diet-microbiome association study. The presented MPDR framework demonstrates the potential of machine learning for personalized nutrition.},
}

@article {pmid42182514,
year = {2026},
author = {Gallo, H and Bucci, V},
title = {Dynamical Systems-Constrained Metabolic Modeling Enables Forecasting of Host-Microbiome Dynamics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.08.723020},
pmid = {42182514},
issn = {2692-8205},
abstract = {Forecasting how microbiome-host ecosystems evolve through time simultaneously at the compositional and functional level remains a central challenge in biology. While dynamical systems models (DSMs) can infer and predict community composition from longitudinal abundance data, and constraint-based metabolic models (CBMMs) can estimate metabolic fluxes from genome-scale reconstructions, no existing framework unifies these approaches to generate mechanistically grounded, time-resolved forecasts of both microbial abundances and metabolite dynamics from ecological data alone. Here, we introduce the Dynamical Systems Constrained Metabolic Modeling (DySCoMeMo) framework, a new hybrid computational pipeline that integrates ecological DSMs with CBMMs to predict temporal dynamics of biomass and metabolites across microbial communities and hosts. DySCoMeMo leverages parameters inferred from application of DSMs to microbiome time series data to constrain metabolic modeling over time, thereby bridging ecological interaction networks with genome-scale metabolic modeling. DySCoMeMo is able to predict future community and metabolite dynamics in vitro with accuracy that is superior or on-par compared to that achieved with established methods that require actual microbial abundances and/or metabolites data for metabolite network inference or for estimating the per-microbe contribution to the extracellular metabolic pool. DySCoMeMo also generalizes to in vivo data as it is capable of accurately forecasting microbial and metabolite dynamics in response to dietary perturbations even when host metabolism is included. Finally, DySCoMeMo uniquely enables the identification of keystone species by quantifying their contributions to sustaining metabolic environments. Together, our work establishes a generalizable, mechanistically grounded framework for time-resolved forecasting of microbiome-host microbial and metabolic dynamics, bridging ecological interaction inference with genome-scale metabolism of communities.},
}

@article {pmid42182529,
year = {2026},
author = {Lai, H and Gao, K and Qiu, L and Huang, M and Yu, W and Li, H and Peng, Z and Wei, S and Wei, F and Zhou, W},
title = {Exploring phylosymbiosis in the skin microbiome of coral reef fish: synergistic effects of environmental and host-specific factors.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag121},
pmid = {42182529},
issn = {2730-6151},
abstract = {The skin is the largest organ in vertebrates, and its microbiome plays a crucial role in immune function and host health. Coral reef fish, characterized by rapid adaptive radiation and complex functional diversity, provide an ideal model for studying the assembly of vertebrate skin microbiomes and the mechanisms that drive this process. In this study, we used 16S rRNA gene amplicon sequencing to investigate the factors influencing the skin microbiomes of coral reef fish across a broad spatial scale. We analyzed 447 skin microbiome samples from 138 fish species, collected from different regions along the latitudinal gradient in coral reef ecosystems of the South China Sea. Our results revealed significant differences in the skin microbiomes of coral reef fish between coastal and offshore habitats in terms of taxonomic composition, diversity, and predicted functional potential. The microbiome structure was influenced by a combination of environmental factors, host traits, and phylogenetic relationships. Notably, we observed a phylosymbiotic pattern in the skin microbiomes of coral reef fish, with more closely related fish exhibiting more similar microbial communities. Temperature and silicate concentration were identified as the primary environmental drivers of microbial community structure, while host-specific factors such as mobility and diet indirectly influenced microbiome assembly by shaping host-associated microenvironment and feeding habitats. Our study highlights the complex interplay between environmental and host-specific factors in shaping coral reef fish skin microbiomes and provides new insights into host-microbe interactions in coral reef ecosystems.},
}

@article {pmid42182532,
year = {2026},
author = {Villegas, V and Rajarajan, A and Martínez-Ruiz, EB and Sánchez, KF and Wolinska, J},
title = {Nanoplastic-induced microbiome shifts reduce Daphnia fitness and increase parasite reproduction.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag109},
pmid = {42182532},
issn = {2730-6151},
abstract = {Environmental pollutants can profoundly influence host-associated microbiomes, with cascading effects on host health and susceptibility to disease. Here, we investigated whether nanoplastic particles (NPs), a pervasive contaminant, influence host-parasite interaction by altering the microbiome of the water flea Daphnia magna. Microbiomes from NP-exposed and control Daphnia donors were transplanted to axenic Daphnia recipients, which were subsequently challenged with the fungal parasite Australozyma monospora sp. nov. Host and parasite fitness were then compared across treatments. NP exposure induced marked shifts in bacterial community structure and increased microbial diversity in donor microbiomes. These shifts persisted after transplantation, with recipient microbiomes remaining distinct from controls throughout the host lifespan, despite the absence of direct NP exposure. Microbiome shifts associated with NP exposure corresponded to elevated parasite reproduction and reduced host fecundity, while host survival was unaffected. Our findings demonstrate that NP pollution can indirectly compromise host health by reshaping microbial communities, highlighting microbiome-mediated pathways as important mechanisms through which emerging pollutants may shape ecological and evolutionary dynamics.},
}

@article {pmid42182637,
year = {2026},
author = {Cai, X and Pang, S and Tang, C and Li, S},
title = {Relationship between airway stents and airway microorganisms: a literature review.},
journal = {Journal of thoracic disease},
volume = {18},
number = {4},
pages = {418},
pmid = {42182637},
issn = {2072-1439},
abstract = {BACKGROUND AND OBJECTIVE: Airway stent placement is widely used for the management of airway stenosis; however, it can be associated with complications such as granulation, stent migration, and infection, all of which affect patient outcomes. Among these complications, infection is a major concern, yet the relationship between airway stents and microbial colonization remains insufficiently studied. This review aims to summarize the current evidence on the effects of airway stents on the airway microbiome and to discuss their potential clinical implications.

METHODS: A literature search was conducted in PubMed for relevant studies published from database inception to December 31, 2025. Search terms included "airway stent", "tracheal stent", "bronchial stent", "airway microbiome", "biofilm", and "respiratory infection". Relevant studies were screened according to predefined criteria, and the available evidence was narratively synthesized.

KEY CONTENT AND FINDINGS: Available evidence suggests that airway stents can alter the airway microenvironment and facilitate microbial colonization, most commonly involving Pseudomonas aeruginosa (P. aeruginosa), Staphylococcus aureus (S. aureus), and Klebsiella pneumoniae (K. pneumoniae). Both metallic and silicone stents lead to similar microbial profiles, dominated by P. aeruginosa and S. aureus. Although microbial colonization frequently occurs after stent implantation, colonization does not necessarily reflect clinically significant infection, and microbiological findings should be interpreted in the clinical context. Most clinical studies report an increased risk of respiratory infection following airway stent placement. In certain specific clinical situations, such as patients with tracheoesophageal fistula, infection rates may decrease after stenting due to restoration of airway integrity. Conventional culture-based methods remain adequate for detecting common respiratory pathogens, while emerging techniques such as metagenomic next-generation sequencing (mNGS) enable broader characterization of airway microbial communities.

CONCLUSIONS: Airway stents appear to alter the airway's microbial environment by promoting the growth of potentially pathogenic microorganisms. Different stent materials, including silicone stents and self-expanding metallic stents (SEMS), seem to affect the biofilm formation on the stents' surface, which may influence microbial colonization. More studies with larger sample sizes, standardized methodologies, and advanced techniques like metagenomic sequencing are needed to further clarify the microbial changes and improve clinical management.},
}

@article {pmid42182816,
year = {2026},
author = {Webber, M and Humphrey, E and van Asselt, A and Chang, A and Morien, E and Simon, ADF},
title = {Diatoms (Bacillariophyta) of the Salish Sea, Northeast Pacific: annotated checklist and new species reports.},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e189060},
pmid = {42182816},
issn = {1314-2828},
abstract = {BACKGROUND: Diatoms are major primary producers known to respond rapidly to environmental change, making them useful indicators for ecological assessment and monitoring. In the Salish Sea bioregion, diatom records date back to early inventories by Lord (1866) and Bailey and MacKay (1916), followed by scattered surveys throughout the 20[th] and 21[st] centuries. Due to this fragmented record, a consolidated regional baseline has been lacking.

NEW INFORMATION: We report 924 diatom taxa for the Salish Sea from historical records, voucher specimens and molecular data, forming a curated dataset of 11,469 records. Forty-two species, including six previously unreported genera, are newly recorded for the region, based on combined morphological and molecular evidence. For these taxa, including the recently described Andrzeja fenestrata, we provide taxonomic accounts with diagnostic light and electron micrographs. These data establish a baseline record of diatom diversity in the Salish Sea, setting an example for how collaboration amongst community and academic researchers can help establish data foundations for phytoplankton monitoring.},
}

@article {pmid42182925,
year = {2026},
author = {Yin, S and Fu, S and Cheng, J and Wang, M and Zhou, Y and Wei, H and Peng, J},
title = {Functional fiber supplementation improves reproductive performance in sows by reshaping gut microbial functions related to immunity and metabolic health.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1834008},
pmid = {42182925},
issn = {2297-1769},
abstract = {INTRODUCTION: Dietary fiber has been reported to regulate reproductive performance, yet its role in microbial functions during late gestation remains unclear. This study aimed to explore the effect of functional fiber supplementation on the gut microbiome and reproductive performance of sows in late gestation, as well as the potential underlying mechanisms.

METHODS: A subset of sows from a large-scale feeding trial was selected and assigned to either a control diet (CON, n = 501) or a functional fiber-supplemented diet (DF, n = 409). Relevant indicators including reproductive performance, plasma physiological parameters, and gut microbiome were detected and analyzed.

RESULTS: Compared with the CON group, DF treatment significantly increased the numbers of total born, born alive and healthy piglets (P < 0.05). Sows in the DF group exhibited higher plasma IL-10 levels, lower plasma reactive oxygen species, reduced insulin resistance and improved insulin sensitivity (higher HOMA-IS) (P < 0.05). Microbiome analyses revealed enrichment of NK4A214_group associated taxa and suppression of Treponema-dominated communities. Further functional profiling showed increased antigen processing and presentation, estrogen signaling pathway, IL-17 signaling pathway, progesterone-mediated oocyte maturation and Th17 cell differentiation pathways, alongside decreased biofilm formation - Pseudomonas aeruginosa pathways. These microbial changes were associated with improved reproductive performance.

DISCUSSION: Taken together, these results indicate that functional fiber improves reproductive outcomes by functionally remodeling the gut microbiome toward enhanced immune regulation and metabolic homeostasis during late gestation, providing a theoretical basis for the application of functional fiber in late gestation sow feeding.},
}

@article {pmid42183058,
year = {2026},
author = {Zhao, X and Zhang, Y and Chu, X and Ma, W and Zhan, R and Wang, Y and Fang, H and Guo, P and Wang, Z and Chen, X and Yang, J and Sun, X},
title = {Gut-engineered Bacillus subtilis-mediated BAMBI delivery for the treatment of thioacetamide-induced liver fibrosis through mechanotransduction inhibition.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {14},
number = {},
pages = {1817519},
pmid = {42183058},
issn = {2296-4185},
abstract = {Liver fibrosis, driven by chronic injury and excessive extracellular matrix (ECM) deposition, lacks effective clinical therapies. This study pioneers a strategy employing genetically engineered Bacillus subtilis (strain Bs-BAMBI-8) to constitutively secrete bone morphogenetic protein and activin membrane-bound inhibitor (BAMBI), which is subsequently delivered to the liver via the gut-liver axis to therapeutically antagonize liver fibrosis. Methodologically, liver fibrosis was induced in mice via 6-week intraperitoneal injections of thioacetamide (TAA), followed by a 19-week daily oral gavage of live Bs-BAMBI-8 (10[9] CFU). This longitudinal intervention achieved sustained intestinal colonization (>10[5] CFU) and BAMBI translocation via the gut-liver axis. This intervention significantly reduced hepatic fibrosis, evidenced by decreased NAFLD Activity Score from six to four and regression of fibrosis stage from S3 to S2. Mechanistically, BAMBI acted as a decoy receptor for transforming growth factor-beta (TGF-β), inhibiting TGF-β signaling and downregulating fibrotic markers (α-smooth muscle actin, collagen I, phosphorylated focal adhesion kinase). This suppression disrupted ECM-mediated mechanotransduction pathways, attenuating hepatic stellate cell activation. Concomitantly, serum markers (alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, total bilirubin) recovered, while albumin synthesis and platelet count recovered. Crucially, this engineered microbiome-based approach integrates synthetic biology with mechanobiology to simultaneously target biochemical signaling and mechanical transduction. It establishes a potentially translatable paradigm for chronic liver disease therapy.},
}

@article {pmid42183083,
year = {2023},
author = {Ke, S and Wang, XW and Ratanatharathorn, A and Huang, T and Roberts, AL and Grodstein, F and Kubzansky, LD and Koenen, KC and Liu, YY},
title = {Association of Probable Post-Traumatic Stress Disorder with Dietary Pattern and Gut Microbiome in a Cohort of Women.},
journal = {Nature. Mental health},
volume = {1},
number = {11},
pages = {900-913},
pmid = {42183083},
issn = {2731-6076},
support = {R01 AI141529/AI/NIAID NIH HHS/United States ; },
abstract = {Post-Traumatic Stress Disorder (PTSD) is a psychiatric condition that may occur in people who have experienced or witnessed traumatic events. The microbiota-gut-brain axis has been suggested to play an important role in mental health. Here we analyzed information on trauma exposure and PTSD symptoms with the gut microbiome data and dietary information in 191 individuals enrolled in a substudy of an ongoing longitudinal cohort of women. We demonstrated that higher PTSD symptom levels were associated with less adherence to the Mediterranean diet pattern, and this association was also linked to specific PTSD putative protective species such as Eubacterium eligens. Moreover, the microbial pathways involved in the biosynthesis of pantothenate and coenzyme A were identified as PTSD putative protective, and these pathways were mainly contributed by PTSD putative protective species such as Akkermansia muciniphila. These findings have the potential to inform dietary- or microbiome-based interventions for PTSD prevention or amelioration.},
}

@article {pmid42183252,
year = {2026},
author = {Jin, R and Wang, M and Ke, J and Gao, X and Zhang, L},
title = {Correlation between Staphylococcus aureus colonization and disease severity in atopic dermatitis: a systematic review and meta-analysis of randomized controlled trials.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1820411},
pmid = {42183252},
issn = {1664-3224},
mesh = {*Dermatitis, Atopic/microbiology/diagnosis ; Humans ; *Staphylococcus aureus ; Randomized Controlled Trials as Topic ; Severity of Illness Index ; *Staphylococcal Infections/microbiology ; *Staphylococcal Skin Infections/microbiology ; },
abstract = {BACKGROUND: A positive association between Staphylococcus aureus (S. aureus) colonization and atopic dermatitis (AD) severity has been reported. However, the strength and consistency of this relationship remain unclear.

METHODS: We systematically searched PubMed, Embase, Cochrane Library, and Web of Science up to July 19, 2025. The reported correlation coefficients of studies have been extracted and converted into Fisher's z-scores. The calculated values have been generated using a random-effects model in RevMan software and the final pooled result was converted to a correlation coefficient (r) with 95% confidence intervals. We tested the heterogeneity between the included studies using I². We also provide sensitivity analyzes and subgroup.

RESULTS: Seven RCTs with 929 participants were included. The pooled analysis showed a moderate positive correlation between S. aureus colonization and AD severity (r = 0.42, 95%CI: 0.31-0.52). The observed heterogeneity was moderate but not significant (I² = 38%, P = 0.14). Sensitivity and subgroup analyzes supported the robustness of the main findings.

CONCLUSIONS: S. aureus colonization is moderately associated with AD severity. However, it should not be interpreted as evidence of a direct causal relationship.

https://www.crd.york.ac.uk/prospero/, identifier CRD420251104116.},
}

*Dermatitis, Atopic/microbiology/diagnosis
Humans
*Staphylococcus aureus
Randomized Controlled Trials as Topic
Severity of Illness Index
*Staphylococcal Infections/microbiology
*Staphylococcal Skin Infections/microbiology

@article {pmid42183274,
year = {2026},
author = {Hu, N and Wang, Z and Liu, M and Guo, D and Jiang, C and Chen, Y and Zhang, Z and Bai, M and Cheng, B and Hsu, JC and Wu, L and Sui, X},
title = {Multi-omics biomarkers for predicting resistance, hyperprogression, and immune-related toxicity during PD-1/PD-L1 therapy in lung cancer: a literature review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1780459},
pmid = {42183274},
issn = {1664-3224},
mesh = {Humans ; *Lung Neoplasms/drug therapy/immunology/metabolism/genetics ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; *Biomarkers, Tumor/genetics ; *Drug Resistance, Neoplasm/genetics ; *B7-H1 Antigen/antagonists & inhibitors/immunology ; *Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Genomics/methods ; Disease Progression ; Proteomics ; Immunotherapy/adverse effects ; Multiomics ; },
abstract = {Immune checkpoint inhibitors targeting programmed cell death protein 1 (PD-1) and its ligand programmed death-ligand 1 (PD-L1) have transformed the management of advanced lung cancer, yet most patients experience primary resistance, hyperprogressive disease (HPD), or clinically significant immune-related adverse events (irAEs). Multi-omics technologies now enable integrated interrogation of tumor, microenvironmental, host, and clinical determinants of these divergent outcomes. In this review, we first discuss the biological and clinical foundations of PD-1/PD-L1 blockade in non-small cell and small cell lung cancer, and summarize the spectrum of resistance, HPD, and irAEs observed in trials and real-world practice. We then describe multi-omics study frameworks that connect genomics, transcriptomics, epigenomics, proteomics, metabolomics, radiomics, and microbiome profiling with these outcome phenotypes. Building on this foundation, we synthesize evidence for composite biomarkers of primary and acquired resistance, delineate emerging multi-omics signatures of HPD, and examine host- and tumor-derived multi-omics correlates of organ-specific and systemic irAEs. We further propose an efficacy-risk quadrant framework to guide clinical decision-making when favorable efficacy predictors coexist with elevated risk of severe adverse outcomes, and outline a three-step approach for high-efficacy/high-risk patients: joint probability reporting, multi-omics guided mitigation, and dynamic reassessment. Finally, we evaluate translational strategies that integrate multi-omics scores into baseline risk stratification, dynamic monitoring with attention to technical challenges such as distinguishing true progression from ctDNA pseudoprogression, and biomarker-driven trial design, while assessing the evidence level and translational readiness of candidate assays from retrospective discovery to clinical implementation. A clinical case illustrates how multi-omics can link baseline risk stratification, regimen selection, and longitudinal monitoring into a coherent action plan, while acknowledging that artificial intelligence-driven models remain investigational and real-world application still relies on clinician judgment. Collectively, this review defines how integrated multi-omics biomarkers can be leveraged to predict resistance, HPD, and immune-related toxicity, and to refine patient selection and management during PD-1/PD-L1 therapy in lung cancer.},
}

Humans
*Lung Neoplasms/drug therapy/immunology/metabolism/genetics
*Immune Checkpoint Inhibitors/adverse effects/therapeutic use
*Biomarkers, Tumor/genetics
*Drug Resistance, Neoplasm/genetics
*B7-H1 Antigen/antagonists & inhibitors/immunology
*Programmed Cell Death 1 Receptor/antagonists & inhibitors
Genomics/methods
Disease Progression
Proteomics
Immunotherapy/adverse effects
Multiomics

@article {pmid42183282,
year = {2026},
author = {Huang, CF and Wang, JY and Karmaus, WJJ and Wang, IJ},
title = {Paradoxical enrichment of Akkermansia in children with poorly controlled asthma: a longitudinal study.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1807949},
pmid = {42183282},
issn = {1664-3224},
mesh = {Humans ; *Asthma/microbiology/diagnosis ; Child ; Male ; Female ; *Gastrointestinal Microbiome ; Longitudinal Studies ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; Immunoglobulin E/blood ; Prospective Studies ; Taiwan ; Feces/microbiology ; Severity of Illness Index ; },
abstract = {INTRODUCTION: Gut dysbiosis is increasingly recognized as a factor in asthma pathogenesis, yet its relationship with disease severity and specific clinical phenotypes remains unclear. This longitudinal study investigated the dynamic changes in gut microbiota composition associated with asthma control and severity in children.

METHODS: We identified asthmatic children and matched them with healthy controls within the prospective Taiwan Childhood Environment and Allergic Diseases Cohort Study. Phenotypic data, including childhood asthma control test (C-ACT) scores, clinical severity, serum immunoglobulin E (IgE) levels, and peak expiratory flow (PEF) rates, were collected at the time of fecal sample collection. Gut microbiota composition was assessed using 16S rRNA sequencing and compared between groups. Subgroup analyses and longitudinal paired case comparisons were conducted to track microbial shifts between exacerbation and remission phases.

RESULTS: A total of 173 children, including 82 children with asthma (mean age: 6.9 ± 4.1 years) and 91 age- and gender-matched healthy controls (mean age: 7.5 ± 2.6 years), were recruited. Generally, children with asthma exhibited a lower relative abundance of Akkermansia, Anaerostipes, and Escherichia compared to controls. The relative abundance of Escherichia showed a significant negative correlation with C-ACT scores (β = -0.337, p = 0.016), whereas Akkermansia exhibited a significant negative correlation with PEF (β = -0.325, p = 0.032). Notably, longitudinal paired case comparisons distinguished asthma attack from remission phases, demonstrating a paradoxical enrichment of Akkermansia during exacerbations (LDA = 3.66, p = 0.023).

CONCLUSION: In contrast to the prevailing view of Akkermansia solely as a beneficial microbe, our study identifies a specific severe asthma-associated gut profile characterized by an unexpected enrichment of Akkermansia in children with poor control. This finding suggests a complex interaction between the gut microbiome and asthma severity, potentially influenced by high-intensity corticosteroid therapy. These results challenge the one-size-fits-all probiotic approach and highlight the need for precision microbiome-based interventions considering asthma phenotypes and medication history.},
}

Humans
*Asthma/microbiology/diagnosis
Child
Male
Female
*Gastrointestinal Microbiome
Longitudinal Studies
Child, Preschool
RNA, Ribosomal, 16S/genetics
*Dysbiosis/microbiology
Immunoglobulin E/blood
Prospective Studies
Taiwan
Feces/microbiology
Severity of Illness Index

@article {pmid41865792,
year = {2026},
author = {Do, QL and Malau, IA and Nguyen, HT and Liu, J and Chang, JP and Su, KP},
title = {Circulating Short-Chain Fatty Acid (SCFA) profiles as a biomarker of gut-brain axis dysfunction: A meta-analysis for the SCFA signature in major depression.},
journal = {Biomedical journal},
volume = {49},
number = {3},
pages = {100968},
doi = {10.1016/j.bj.2026.100968},
pmid = {41865792},
issn = {2320-2890},
abstract = {BACKGROUND: Major Depressive Disorder (MDD) is increasingly viewed through the lens of the neuroinflammatory hypothesis and gut-brain axis dysfunction. Short-Chain Fatty Acids (SCFAs), the primary metabolites produced by the gut microbiota, are vital signaling molecules that maintain intestinal barrier integrity, modulate peripheral immunity, and influence microglial function. While individual studies suggest altered SCFAs levels in MDD, a definitive, quantitative synthesis establishing a robust biomarker signature is currently lacking. This meta-analysis aimed to precisely characterize the signature of SCFAs (acetic, propionic, butyric, and isobutyric acid) in MDD patients compared to healthy controls.

METHODS: We systematically searched major databases across PubMed, Embase, and Web of Science databases for studies quantifying SCFAs levels up to September 15, 2025. Studies examining SCFAs levels in depressed patients and depressive-like murine models, as well as studies investigating SCFAs interventions for depressive-like behavior, were selected for synthesis. Risk of bias was evaluated using the Newcastle-Ottawa Scale. The effect sizes were synthesized using a random-effects model and presented as standardized mean differences.

RESULTS: Eight human and 52 murine studies were included in the meta-analyses. Depressed patients showed significantly lower concentrations in blood (plasma and serum) of propionic (SMD = -0.60, p-value = 0.007), butyric (SMD = -0.50, p-value = 0.006), isobutyric (SMD = -0.72, p-value = 0.020), valeric (SMD = -0.43, p-value = 0.040) and isovaleric acids (SMD = -0.75, p-value = 0.002). Secondary analysis of MDD patients confirmed consistent reductions. High heterogeneity was observed. In murine models, SCFAs depletion was frequently observed, while supplementation improved depressive-like behaviors.

CONCLUSION: MDD is characterized by a significant, quantifiable deficit in the circulating SCFAs metabolome, which provides strong empirical validation for the gut-brain axis hypothesis in depression. We advocate for the investigation of SCFAs as novel, measurable peripheral biomarkers and targeted therapeutic agents (e.g., butyrate supplementation) for precision nutritional psychiatry.},
}

@article {pmid42031071,
year = {2026},
author = {Ramirez-Posada, M and Guillen-Burgos, HF},
title = {Skin-Brain Axis: Biological Foundations and Clinical Implications.},
journal = {Journal of the Academy of Consultation-Liaison Psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaclp.2026.04.006},
pmid = {42031071},
issn = {2667-2960},
abstract = {BACKGROUND: The skin-brain axis has emerged as a novel conceptual framework describing bidirectional neuroimmune, neuroendocrine, and microbial communication between the skin and the central nervous system. Shared inflammatory pathways, hypothalamic-pituitary-adrenal axis dysregulation, neurotransmitter signaling, neurotrophins, and microbiome-related mechanisms may contribute to the overlap between dermatologic and psychiatric disorders.

OBJECTIVE: To review the biological and clinical implications of the skin-brain axis in dermatologic and psychiatric disorders.

METHODS: This perspective review summarizes current evidence regarding the biological foundations and clinical implications of the skin-brain axis. The article integrates findings related to inflammatory skin disorders, psychiatric symptoms, immune signaling, microbial composition, and therapeutic approaches relevant to psychodermatology.

RESULTS: Evidence from psoriasis, atopic dermatitis, acne vulgaris, chronic urticaria, and prurigo nodularis demonstrates substantial overlap between inflammatory skin diseases and symptoms of depression, anxiety, stress, and suicidality. Emerging data further support the role of cutaneous immune signaling and microbial composition in modulating emotional and cognitive processes. The review also highlights therapeutic convergence between dermatology and psychiatry, including biologic therapies, psychopharmacology, cognitive behavioral therapy, and neuroimmune-targeted interventions.

CONCLUSIONS: Understanding the skin-brain axis may improve recognition of the bidirectional relationship between dermatologic and psychiatric disorders and support more comprehensive, integrated approaches to patients with complex inflammatory and neuropsychiatric conditions.},
}

@article {pmid42169289,
year = {2026},
author = {Li, Y and Liu, X and Li, C and Xu, X and Tang, C and Zhou, G and Liu, Y and Blank, I},
title = {Elucidating microbial succession and aroma-active metabolite formation in hybrid dry-fermented sausage analogues with texturized pea protein: Integrating flavoromics, metabolomics, and metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {237},
number = {},
pages = {119324},
doi = {10.1016/j.foodres.2026.119324},
pmid = {42169289},
issn = {1873-7145},
mesh = {*Metabolomics/methods ; *Meat Products/microbiology/analysis ; *Odorants/analysis ; Fermentation ; *Metagenomics/methods ; Volatile Organic Compounds/analysis ; *Pea Proteins/metabolism ; Animals ; Gas Chromatography-Mass Spectrometry ; Taste ; Food Microbiology ; Humans ; Microbiota ; Swine ; Tandem Mass Spectrometry ; },
abstract = {Hybrid dry-fermented sausage analogues with texturized pea proteins (TPPs) are emerging, yet flavor formation mechanisms remain unclear. We combined quantitative descriptive analysis with complementary HS-SPME-GC-MS/HS-GC-IMS volatilomics, UHPLC-MS/MS untargeted metabolomics, and marker-gene microbiome sequencing across sausages with different fermentation and ripening stages to map key aroma and their potential microbial and metabolic drivers. Sensory data showed rising fruity, cocoa-chocolate and nutty notes. In total, 47 volatiles were identified by GC-MS and 40 by GC-IMS. Screening of odorants based on relative odor activity value (rOAV) consistently highlighted seven odorants, with a shift from hexanal-dominated raw profiles to linalool-dominated processed profiles, indicating suppression of aldehyde-derived off-notes and enrichment of terpene/ester notes. Metabolomics detected 2467 metabolites, dominated by lipids and organic acids, and short-peptide enrichment suggested intensified proteolysis supplying aroma precursors. Bacterial succession exceeded fungal variation, with Latilactobacillus and Staphylococcus as core taxa. The integrated dataset provides practical markers and microbial/process cues to enhance flavor quality of sustainable hybrid fermented meats.},
}

*Metabolomics/methods
*Meat Products/microbiology/analysis
*Odorants/analysis
Fermentation
*Metagenomics/methods
Volatile Organic Compounds/analysis
*Pea Proteins/metabolism
Animals
Gas Chromatography-Mass Spectrometry
Taste
Food Microbiology
Humans
Microbiota
Swine
Tandem Mass Spectrometry

@article {pmid42169344,
year = {2026},
author = {Song, H and Xue, S and Zhao, W and Yu, Z},
title = {Food-derived bioactive peptides in gut-muscle Axis regulation: Potential and challenges from microbiota homeostasis to muscle metabolism remodeling.},
journal = {Food research international (Ottawa, Ont.)},
volume = {237},
number = {},
pages = {119392},
doi = {10.1016/j.foodres.2026.119392},
pmid = {42169344},
issn = {1873-7145},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Peptides/metabolism ; Animals ; *Muscle, Skeletal/metabolism ; *Sarcopenia/metabolism ; Homeostasis ; Bioactive Peptides, Dietary ; },
abstract = {The global population is aging at an accelerating pace, and sarcopenia has emerged as a central challenge to elderly health. Food-derived bioactive peptides, as natural functional compounds, can interact significantly with the gut microbiota, thereby indirectly influencing muscle metabolism and function. This review systematically summarizes the pathological mechanisms of sarcopenia and its associated complications. Moreover, it reveals the complex interactions between food-derived bioactive peptides and the gut microbiome, and innovatively summarizes the multi-level mechanisms by which these peptides regulate the gut-muscle axis. Furthermore, we discuss current research limitations, including the limited translational potential of animal models, insufficient precision of detection techniques, and lack of clinical validation. Future research directions are proposed, including leveraging multi-omics and artificial intelligence approaches for peptide-microbiota-metabolite functional prediction, employing organoid and organ-on-a-chip platforms for mechanistic validation, and advancing systematic translation through high-quality clinical trials. This review aims to provide a comprehensive theoretical framework and offer direction for the application of food-derived bioactive peptides based on gut-muscle axis interventions.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Peptides/metabolism
Animals
*Muscle, Skeletal/metabolism
*Sarcopenia/metabolism
Homeostasis
Bioactive Peptides, Dietary

@article {pmid42169943,
year = {2026},
author = {Chittilla, M and Nagdev, P},
title = {A systematic review of artificial intelligence and machine learning for gut microbiome-based CRC screening.},
journal = {Journal of gastrointestinal oncology},
volume = {17},
number = {2},
pages = {95},
pmid = {42169943},
issn = {2078-6891},
abstract = {BACKGROUND: Over the last decade, ample evidence has shown that gut microbiome dysbiosis is significantly associated with colorectal cancer (CRC). More recently, studies have shown that artificial intelligence (AI) and machine learning (ML) models paired with gut microbiome data can detect CRC. The objectives for this systematic review are: (I) to systematically evaluate the diagnostic performance of AI/ML models using gut microbiome data for CRC detection; (II) to compare AI/ML-based microbiome screening approaches; (III) to identify microbial genera consistently associated with CRC across included studies; (IV) to assess study quality and risk of bias using QUADAS-2 and use the GRADE approach to assess certainty.

METHODS: A systematic review was conducted across PubMed, MEDLINE, Scopus, Embase, and The Cochrane Library including studies from January 1, 2023 to November 1, 2025. Studies applying AI/ML models to human gut microbiome data for CRC screening and reporting diagnostic performance metrics and significant genera were included. Risk of bias was assessed with QUADAS-2 and used the GRADE approach to assess certainty. Primary outcomes included area under the receiver operating characteristic curve (AUC). Secondary outcomes include balanced accuracy, sensitivity, specificity, examine AI/ML approaches used, and identify significant microbial genera associated with CRC detected by AI/ML models. No meta-analysis was done due to the heterogeneity, which came from various microbiome methods, AI/ML/microbiome models used, and validation strategies applied. Thereby the data was synthesized narratively.

RESULTS: Twelve studies met inclusion criteria. AI/ML models demonstrated moderate diagnostic performance, with internal validation sets AUC values ranging from 0.61 to 0.98 and external validation sets AUC ranging from 0.70-0.87. Random forest and XGBoost models showed consistent performance, with multi-omics approaches achieving the highest AUC of 0.98. Porphyromonas (e.g., P. asaccharolytica), Peptostreptococcus (e.g., P. stomatis), Fusobacterium (particularly F. nucleatum subspecies: animalis, vincentii, polymorphum, sensu stricto), Parvimonas micra, Gemella morbillorum, Bacteroides (B. fragilis), and Streptococcus species were significantly enriched in CRC as predicted the selected AI/ML/microbiome models.

CONCLUSIONS: AI/ML-based gut microbiome models demonstrate moderate AUC for CRC detection and may enhance noninvasive screening strategies pending prospective validation. Limitations include heterogeneity in AI/ML/microbiome models, microbiome methodologies, and model validation, with predominantly retrospective case-control studies and limited external validation.},
}

@article {pmid42170025,
year = {2026},
author = {Higashi, K and Ishikawa, H and Kurokawa, K and Mori, H},
title = {PZLAST-MAG: full length protein sequence similarity search server of large-scale MAG proteins.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag129},
pmid = {42170025},
issn = {2635-0041},
abstract = {MOTIVATION: Metagenome-assembled genomes (MAGs) provide access to novel protein sequences from uncultured microbes, offering invaluable resources for studying protein diversity, structure prediction, and evolutionary analysis. However, despite the explosive growth of MAG-derived protein data, tools enabling fast and accurate similarity searches against large-scale MAG protein datasets remain limited.

RESULTS: We present PZLAST-MAG, a web server for ultra-fast sequence similarity searches against 0.4 billion MAG-derived protein sequences (0.1 trillion amino acids) from over 210 000 MAGs indexed in Microbiome Datahub. Implemented on PEZY-SC3 MIMD many-core processors, PZLAST-MAG achieves high accuracy and speed, with performance comparable to widely used tools such as DIAMOND and MMseqs2 based on our benchmark analyses. In addition to tabular alignments, PZLAST-MAG provides interactive visualizations of phylogenetic and environmental distributions and co-occurrence patterns of homologous proteins across MAGs. This combination enables rapid homolog mining of functionally important genes across diverse microbial lineages while simultaneously revealing their taxonomic and ecological contexts. Two use case analyses indicate its utility for homolog mining of metabolic enzyme genes and plasmid-derived genes.

PZLAST-MAG is provided as a web-based service and is freely available at https://pzlast.nig.ac.jp/pzlast/mag without requiring registration.},
}

@article {pmid42170578,
year = {2026},
author = {Brodsky, M and Lalla, M and Oh, S and Anampa, JD},
title = {Chemotherapy-induced peripheral neuropathy in breast cancer: a narrative review.},
journal = {Translational breast cancer research : a journal focusing on translational research in breast cancer},
volume = {7},
number = {},
pages = {18},
pmid = {42170578},
issn = {2218-6778},
abstract = {BACKGROUND AND OBJECTIVE: Chemotherapy-induced peripheral neuropathy (CIPN) remains a major, unresolved complication of breast cancer therapy, often leading to treatment modifications and enduring functional impairment. This review addresses the complex pathogenesis of CIPN, as well as the clinical presentation and impact of CIPN on patient quality of life. The primary objective of this review is to highlight the pathophysiology and pathogenesis of CIPN, as well as detail current strategies and future targets to prevent and treat CIPN in breast cancer patients.

METHODS: We conducted a narrative review using the PubMed/Medline, Cochrane, and Embase databases from database inception to July 2025. We used keyword searches including 'breast cancer', 'chemotherapy-induced peripheral neuropathy/CIPN', 'taxane', 'taxane induced peripheral neuropathy/TIPN', 'platinum', 'alkaloids', 'antibody drug conjugates', 'CIPN prevention', 'CIPN treatment', 'biomarkers', 'microbiome', 'racial disparities', 'genetics', 'quality of life', 'inflammation'. Inclusion criteria included clinical and translational English-language studies addressing CIPN in breast cancer, CIPN biomarkers, and the microbiome in oncology research. Exclusion criteria included non-English language studies and clinical studies unrelated to breast cancer.

KEY CONTENT AND FINDINGS: In this paper, we synthesize the pathophysiology of CIPN and the growing body of research implicating systemic inflammation and gut microbiome composition in modulating CIPN pathogenesis, suggesting a biological basis for interindividual variability in susceptibility. We also summarize emerging evidence on the role of racial disparities in CIPN. Finally, we explore commonly studied biomarkers that have shown promise as potential predictive markers of CIPN onset as well as potential therapeutic strategies.

CONCLUSIONS: CIPN remains a common, dose-limiting toxicity in breast cancer care. Preventive strategies and symptomatic management with consistent clinical benefits are lacking. Duloxetine has strongest scientific evidence for pain reduction; other pharmacologic and non-pharmacologic approaches are promising but heterogeneous and should be framed as adjunctive. Biomarker driven trial designs that test anti-inflammatory strategies, as well as microbiome-targeted interventions, may accelerate treatment breakthroughs. Finally, attention to race as a factor in CIPN susceptibility can help to identify high-risk patients and reduce disparities in CIPN burden.},
}

@article {pmid42170678,
year = {2026},
author = {Yadav, S and Sharma, N and Yadav, M and Sharma, N and Tripathi, G and Bhat, SH and Pandey, S and Mathew, B and Bindal, V and Saifi, R and Sharma, V and Falari, S and Pamecha, V and Maras, JS},
title = {Distinct bile mycobiome signature identifies fungal peptide panel predictive for gallbladder carcinoma.},
journal = {Molecular therapy. Oncology},
volume = {34},
number = {2},
pages = {201220},
pmid = {42170678},
issn = {2950-3299},
abstract = {Carcinoma of the gallbladder (CAGB) carries a poor prognosis. While alterations in the bile microbiome and lipidome have been linked to CAGB development, the contribution of the fungal microbiome remains unexplored. We investigated fungal microbiome alterations and identified key fungal peptides capable of segregating CAGB patients. Bile samples from gallstone (GS) patients (n = 10), CAGB patients (n = 16), and healthy controls (n = 16) underwent fungal peptide-based diversity analysis and metabolomic profiling. Findings were cross-validated in plasma, correlated with clinical parameters and analyzed using machine learning. Six phyla and 24 fungal species were differentially regulated (p < 0.05). Alpha/beta diversity was higher in CAGB compared to GS and controls (p < 0.05). Ninety-three fungal peptides were upregulated and 63 downregulated in CAGB (p < 0.05, fold change [FC] > 1.5). CAGB patients showed significant enrichment of Aspergillus wentii (log2FC > 12.21), Nosema bombycis (FC > 11.25), Saccharomyces (FC > 10.89), Saccharomyces cerevisiae (FC > 10.68), and Schizosaccharomyces pombe (FC > 10.38). Fungal-metabolite correlations (r[2] > 0.5, p < 0.05) linked these taxa to lysine biosynthesis, taurine and hypotaurine metabolism, fatty acid metabolism in bile, and cysteine/methionine, ascorbate, and purine metabolism in plasma. Fungal peptide panel achieved 96% diagnostic efficiency for mortality prediction with>90% accuracy, sensitivity, and specificity. Bile fungal diversity correlates with CAGB development and identifies fungal peptide panel capable of segregation of CAGB patients.},
}

@article {pmid42170832,
year = {2026},
author = {Shorr, AF and Zilberberg, MD},
title = {Ventilator-associated pneumonia: newer insights that can drive improved outcomes.},
journal = {Current opinion in critical care},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCC.0000000000001390},
pmid = {42170832},
issn = {1531-7072},
abstract = {PURPOSE OF REVIEW: Ventilator-associated pneumonia (VAP) results in substantial morbidity and results in high crude mortality rates. Many recent studies address multiple aspects of VAP ranging from its evolving epidemiology and microbiology to novel means for prevention and treatment.

RECENT FINDINGS: The true incidence of VAP remains difficult to assess given definitional issues, which confound accurate diagnostic conclusions. The lack of a clear gold standard for identifying VAP makes comparisons across different studies difficult, as it remains unclear if like syndromes are actually being described. Nonetheless, VAP remains a clinical and costly challenge. Earlier discussion of achieving 'zero' VAP were clearly misplaced. Furthermore, the microbiology of VAP continues to evolve with the spread of antimicrobial resistance. New attention on the microbiome, though, may prove helpful and enhance our understanding of the pathogenesis of VAP. Simple interventions such a toothbrushing appear to successfully reduce rates of VAP and should be more broadly adopted. Rapid diagnostic tools, which are increasingly utilized to identify the causative pathogen in VAP, appear to have more limitations than previously thought. Several novel antibiotics are now available for treating multidrug-resistant organisms (MDROs) often encountered in VAP. With respect to antibiotic treatment more generally, it appears that shorter durations of therapy are well tolerated and effective, even in cases of VAP caused by MDROs.

SUMMARY: Although our knowledge and understanding of VAP continues to advance, many of the general questions of the last decade remain unresolved. We continue to lack a clear and simple means for defining VAP and have yet to identify the optimal approach for prevention. Likewise, despite the availability of newer antimicrobials, we continue to lack rapid diagnostics that can clearly be shown to improve patient-centered endpoints. The availability of newer antibiotics may allow us to more easily and safely treat MDROs, but they have not revolutionized outcomes or been shown to reduce mortality.},
}

@article {pmid42170966,
year = {2026},
author = {Luo, Y and Xu, H and Ye, X},
title = {Effects of nifuratel-based therapy combined with vaginal lactobacillus probiotics on microecological restoration in pregnant women with abnormal vaginal flora: A retrospective cohort study.},
journal = {Pakistan journal of pharmaceutical sciences},
volume = {39},
number = {7},
pages = {1993-2002},
doi = {10.36721/PJPS.2026.39.7.REG.189.1},
pmid = {42170966},
issn = {1011-601X},
mesh = {Female ; Humans ; Pregnancy ; *Probiotics/administration & dosage/therapeutic use/adverse effects ; Retrospective Studies ; Adult ; *Lactobacillus ; *Vagina/microbiology/drug effects ; Treatment Outcome ; *Microbiota/drug effects ; Young Adult ; Hydrogen-Ion Concentration ; },
abstract = {BACKGROUND: Imbalances in the vaginal flora during pregnancy elevate risks for adverse outcomes. While nifuratel targets pathogens, probiotics restore acidity, and robust cohort evidence supporting their combined safety and efficacy in restoring the microbiome remains limited.

OBJECTIVES: This retrospective cohort study assessed nifuratel-nystatin therapy plus Lactobacillus probiotics for restoring vaginal flora in pregnancy.

METHODS: Employing a retrospective cohort design, this study enrolled pregnant women diagnosed with vaginal microecological abnormalities between March 2023 and 2024. Participants were allocated via 1:1 propensity score matching (PSM) into two groups (n=58 each): a combination group receiving nifuratel-nystatin therapy combined with vaginal Lactobacillus probiotics and a monotherapy group receiving nifuratel-nystatin alone. All received a 7-day treatment. The primary endpoint was clinical effectiveness assessed one week post-treatment. Secondary outcomes included vaginal pH, Lactobacillus and bacterial diversity normalization rates, recurrence, adverse pregnancy outcomes and drug-related adverse events, monitored until delivery. Multivariate logistic regression identified independent predictors of treatment efficacy.

RESULTS: After PSM, baseline characteristics were balanced (P>0.05). The comparative analysis indicated a superior overall efficacy for the combination therapy (93.1%) over monotherapy (77.6%), with statistical significance (P<0.01) Both groups exhibited reduced vaginal pH and increased rates of normalized Lactobacillus and bacterial diversity, with greater improvements observed in the combination group (P<0.01). The recurrence rate was significantly lower in the combination group (8.6% vs. 22.4%; P<0.05), as was the total incidence of adverse pregnancy outcomes (6.9% vs. 20.7%; P<0.01). No significant difference in adverse drug reactions was found. Multivariate analysis identified combination therapy as an independent protective factor for clinical efficacy (aOR=4.25, 95% CI: 1.42-12.71, P<0.05).

CONCLUSIONS: In pregnant women with vaginal dysbiosis, combining nifuratel-nystatin with Lactobacillus probiotics safely enhances clinical efficacy, normalizes pH and flora and reduces adverse pregnancy outcomes.},
}

Female
Humans
Pregnancy
*Probiotics/administration & dosage/therapeutic use/adverse effects
Retrospective Studies
Adult
*Lactobacillus
*Vagina/microbiology/drug effects
Treatment Outcome
*Microbiota/drug effects
Young Adult
Hydrogen-Ion Concentration

@article {pmid42171003,
year = {2026},
author = {Pashaki, PA and Niepokny, TD and Khalilzadehsabet, T and Dumais, E and Flamand, N and Di Marzo, V and Mintz, EM and Silvestri, C},
title = {Circadian disruption elicits sex-specific gut microbiota, endocannabinoidome, and lipid mediator responses.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.70592},
pmid = {42171003},
issn = {1742-4658},
support = {R15GM134528/GF/NIH HHS/United States ; //Canadian Tri-Agency/ ; },
abstract = {Circadian disruption is a pervasive environmental stressor associated with increased risk of metabolic and inflammatory disease, yet sex-specific physiological responses remain poorly defined. Here, we investigated how constant light (LL) exposure, used as a circadian stressor, is associated with changes in the fecal microbiome and short-chain fatty acids (SCFAs), tissue-specific bioactive lipid mediator and systemic cytokine levels in female and male mice. Mice were kept under standard light/dark (LD; 12 : 12) or LL (24 : 0) conditions for 10 days before feces collection and for 5 more days before tissue collection. Females exhibited broader microbiota restructuring along with decreases in oxylipins within the jejunum. In the brain pronounced increases of N-acylethanolamine levels in the cerebellum and hypothalamus were observed when male and female mice were analyzed together, though these changes were largely driven by increased levels in the hypothalamus of females. Changes in muscle lipids were associated with the predominant muscle fiber type, with the soleus showing increases in a broad variety of lipid classes in both females and males. Adipose tissues also showed divergent responses to LL, with subcutaneous white adipose tissue having significantly decreased oxylipin levels specifically in males. Within plasma, females generally showed a more inflammatory profile than males. Together, these findings suggest that sex strongly shapes microbial, lipidomic, and immune pathways changes under circadian stress, highlighting divergent physiological strategies in response to light-cycle perturbation, which may contribute to sex-specific vulnerability at the level of metabolic and inflammatory dysregulation.},
}

@article {pmid42171373,
year = {2026},
author = {Schroer, HW and Beghini, F and Raygoza Garay, JA and Christakis, NA and Bosch, DE},
title = {Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0030526},
doi = {10.1128/msystems.00305-26},
pmid = {42171373},
issn = {2379-5077},
abstract = {Bacteria use antagonistic interbacterial weapons, such as polymorphic toxin secretion systems (TSS), to compete for niches in the human gut microbiome. We hypothesized that TSS influence gut microbiome development and disease-related dysbiosis. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including ~200 effector and immunity genes and applied it to ~15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states and enabled the construction of highly accurate linear regression classifier machine learning models. Elastic net machine learning models integrating bacterial taxonomy with PolyProf had strong predictive value for 12 disease states, outperforming models utilizing taxonomy alone. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, TSS genes strongly correlate with microbiome development and interpersonal strain sharing, suggesting roles for interbacterial antagonism. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.IMPORTANCEPrevious research has demonstrated that bacteria compete within the gut microbiome using toxin secretion systems (TSS). How TSS contribute to human microbiome development and the microbiome alterations observed in human diseases is not known. This study develops a new bioinformatic tool for profiling TSS-related genes in metagenomic data. Application of this approach to large-scale human fecal metagenomic data demonstrates the dynamic association of TSS during microbiome development, including the exchange of strains among social contacts. TSS gene abundance patterns are highly predictive of 12 disease states. This study advances the field by enabling TSS profiling in metagenomes and by identifying disease and microbiome development biomarkers that provide hypotheses for future mechanistic studies and may be useful for disease diagnosis.},
}

@article {pmid42171627,
year = {2026},
author = {Ribas, MP and Tort, C and Jasso, MV and Migura-Garcia, L and Cabezón, O},
title = {Skin Microbiome Variation Among Hosts and Batrachochytrium dendrobatidis Infection in Hyla meridionalis and Pelophylax perezi.},
journal = {Molecular ecology},
volume = {35},
number = {10},
pages = {e70393},
doi = {10.1111/mec.70393},
pmid = {42171627},
issn = {1365-294X},
support = {//Fundació Barcelona Zoo/ ; FI_B 00171//Departament de Recerca i Universitats, Generalitat de Catalunya, Spain/ ; //CERCA Program/ ; },
mesh = {Animals ; *Microbiota/genetics ; *Skin/microbiology ; *Batrachochytrium/pathogenicity ; RNA, Ribosomal, 16S/genetics ; *Ranidae/microbiology ; *Anura/microbiology ; Bacteria/genetics/classification ; *Mycoses/microbiology/veterinary ; Spain ; Chytridiomycota ; Skin Microbiome ; Animal Diseases ; },
abstract = {Chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), is a key driver of global amphibian declines. The amphibian skin microbiome, which may include Bd-inhibitory bacteria, plays a crucial role in defence against infection, influencing host susceptibility and disease outcome. In this study, we investigated the skin microbiota and Bd infection in two frog species, Hyla meridionalis (Hm) and Pelophylax perezi (Pp), from northeastern Spain using full-length 16S rRNA gene sequencing. We found that microbiota composition differed significantly between frog species, with Pp harbouring greater bacterial richness and a community composition more similar to the aquatic environment than Hm. Asymptomatic Bd infection did not significantly alter microbiota diversity or community composition in either species. Nonetheless, differential abundance analyses revealed distinct bacterial taxa associated with host species and, to a lesser extent, with Bd infection. The composition of putative Bd-inhibitory bacteria also differed between frog species but was not influenced by Bd, suggesting that the microbiome's protective role may not be straightforward. Lower pathogen loads in Pp suggest a potential link between microbial richness and disease resistance. Our findings indicate that amphibian skin microbiota do not necessarily shift in response to Bd infection in asymptomatic hosts but may play a role in species-specific mechanisms of tolerance and resistance. Additionally, we detected potentially pathogenic bacteria of public and animal health concern on amphibian skin, highlighting amphibians as potential reservoirs and sentinels of ecosystem and public health. Overall, our findings indicate that amphibian skin microbiomes are shaped primarily by host species identity rather than asymptomatic Bd infection, emphasizing the importance of baseline microbiome variation in understanding host-pathogen dynamics and informing probiotic bioaugmentation strategies.},
}

Animals
*Microbiota/genetics
*Skin/microbiology
*Batrachochytrium/pathogenicity
RNA, Ribosomal, 16S/genetics
*Ranidae/microbiology
*Anura/microbiology
Bacteria/genetics/classification
*Mycoses/microbiology/veterinary
Spain
Chytridiomycota
Skin Microbiome
Animal Diseases

@article {pmid42171661,
year = {2026},
author = {Goodall, T and Busi, SB and Jones, B and Thorpe, A and Griffiths, RI and Redhead, J and Hulmes, L and Hulmes, S and Ridding, L and Peyton, J and Pereira, G and Gweon, HS and Read, DS and Pywell, R},
title = {Taxonomic filtering accompanies functional expansion during long-term soil restoration.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag131},
pmid = {42171661},
issn = {1751-7370},
abstract = {The restoration of species-rich calcareous grasslands is a critical conservation objective, yet the recovery of the invisible below-ground microbiome remains poorly quantified compared to above-ground vegetation. Using a unique 143-year land-use chronosequence on Salisbury Plain, UK, we investigated the trajectory of ecosystem reassembly across arable, regenerating (23 and 67 years), and ancient grasslands. By integrating vegetation surveys with soil physiochemistry, microbial profiling, and shotgun metagenomics, we identified a decoupling between floral and edaphic recovery. While the diversity of vegetation recovered relatively rapidly, approaching ancient grassland levels within 23-67 years, soil properties exhibited persistent legacy effects and slow convergence. Bacterial richness decreased with restoration age; this taxonomic contraction was conversely matched by an expansion in inferred metagenomic functional potential. This was reflected in increased functional gene richness and shifts in the relative abundance of specific SEED-annotated functions toward metabolic pathways associated with complex carbon cycling and stress tolerance. These shifts were congruent with the emergence of specific, unnamed genera belonging to Pseudomonadota and Actinomycetota, and the Bacillota species Pristimantibacillus. The soil ecosystem remained distinct from the 143-year stage even after 67 years of recovery, characterised by persistent legacy phosphorus and a slow accumulation of soil organic matter. These findings suggest that passive regeneration alone may be insufficient for full soil functional recovery, and that strategies targeting microbial assembly and long-term carbon dynamics warrant further evaluation.},
}

@article {pmid42171783,
year = {2026},
author = {Rivera, DA and Lara-Guzmán, OJ and Villota-Salazar, NA and Sierra, JA and Muñoz-Durango, K and Escobar, JS},
title = {Analytic attributes of the 16S rRNA gene sequencing methodology for human gut microbiota characterization.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-026-13844-8},
pmid = {42171783},
issn = {1432-0614},
abstract = {Gut microbiota is crucial for human health. While 16S rRNA gene sequencing is most used for characterizing this community, the validation and standardization of the technique are often overlooked. This study analyzes critical factors influencing the repeatability and intermediate precision of 16S rRNA gene sequencing methodology for human gut microbiota characterization, examining the impact of key analytical factors. Our investigation evaluated the effects of the DNA extraction protocol, sample homogenization, thawing, library preparation, and sequencing on measurements of precision. This established a standardized operating procedure (SOP) whose variability was assessed within a single laboratory (intermediate precision) by analyzing DNA extraction kit lot variations and the laboratory analyst handling the samples. We discovered that the DNA extraction protocol and sample thawing were the most significant drivers of variability in gut microbiota profiles. At the same time, the intermediate precision of the method was high. We determined the method's limit of quantification, revealing an impressive sensitivity down to just 11 to 18 rarefied read counts (with coefficients of variation of 30% and 20%, respectively). Beyond technical considerations, we also quantified the variation in gut microbiota profiles among individuals and over time. Our findings confirm substantial inter-individual differences while demonstrating that changes within individuals over a week are relatively small. This research illuminates some critical factors influencing the precision and consistency of 16S rRNA gene sequencing for gut microbiota analysis. By incorporating these insights into standardized protocols, we can significantly improve best practices in DNA sequencing methodologies, strengthening the reliability and comparability of human microbiome studies. KEY POINTS: • DNA extraction and sample thawing critically affect the method's precision. • We established an SOP with high repeatability, intermediate precision, and a specific limit of quantification. • Gut microbiota profiles substantially vary among individuals but remain stable over a week.},
}

@article {pmid42171841,
year = {2026},
author = {Gómez-Montañez, E and Rojas-Salazar, YL and Rojas-Salazar, JG},
title = {Microbiome in Gastrointestinal Tumors: Implications in Oncogenesis and Therapeutic Response : Microbiome in Gastrointestinal Tumors.},
journal = {Current oncology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42171841},
issn = {1534-6269},
mesh = {Humans ; *Gastrointestinal Neoplasms/microbiology/therapy/pathology ; *Gastrointestinal Microbiome ; *Carcinogenesis ; *Dysbiosis/microbiology ; Tumor Microenvironment ; *Microbiota ; },
abstract = {PURPOSE OF REVIEW: To provide an updated overview of the role of the human microbiome in the initiation, progression, and therapeutic response of gastrointestinal tumors, emphasizing molecular, immunological, and metabolic mechanisms, as well as its potential as a target for novel therapeutic strategies.

RECENT FINDINGS: Emerging evidence demonstrates that microbiome dysbiosis contributes to carcinogenesis across gastrointestinal malignancies, including colorectal, gastric, hepatic, and pancreatic cancers. Microbial-derived metabolites, such as short-chain fatty acids and secondary bile acids, modulate key signaling pathways involved in cell proliferation, apoptosis, and genomic stability. In addition, the microbiome influences the tumor microenvironment and immune responses, shaping variability in treatment outcomes. Both preclinical and clinical studies have shown that microbiome composition affects the efficacy and toxicity of chemotherapy and immunotherapy. Notably, specific microbial signatures are being explored as non-invasive biomarkers for early detection and prognostic stratification, while microbiome modulation strategies, such as diet, probiotics, antibiotics, and fecal microbiota transplantation, have demonstrated potential to enhance therapeutic response. The bidirectional interaction between the microbiome and the host plays a central role in gastrointestinal tumorigenesis and treatment response. Although this field holds significant promise for precision oncology, its clinical translation remains limited by interindividual variability, methodological heterogeneity, and insufficient longitudinal evidence. Future efforts should focus on standardization, validation of microbiome-based biomarkers, and integration of multi-omics and artificial intelligence approaches to enable clinically actionable applications.},
}

Humans
*Gastrointestinal Neoplasms/microbiology/therapy/pathology
*Gastrointestinal Microbiome
*Carcinogenesis
*Dysbiosis/microbiology
Tumor Microenvironment
*Microbiota

@article {pmid42172047,
year = {2026},
author = {Delgado, LF and Sunyer, JO and Laczny, CC and Hickl, O and May, P and Wilmes, P},
title = {PathoFact 2.0: An Integrative Pipeline for the Prediction of Antimicrobial Resistance Genes, Virulence Factors, Toxins and Toxin-associated Proteins, and Biosynthetic Gene Clusters in Metagenomes.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giag062},
pmid = {42172047},
issn = {2047-217X},
abstract = {BACKGROUND: Antimicrobial resistance genes (ARG) and virulence factors (VFs) are central contributors to the global health crisis surrounding drug-resistant infections.

FINDINGS: We introduce PathoFact 2.0, an enhanced pipeline for improved ARG, VF, toxin, and biosynthetic gene clusters (BGC) prediction. Key improvements include an updated machine learning (ML) model for VF identification, expanded hidden Markov model profiles for VFs and toxin-associated proteins, a new ML model for toxin and toxin-associated proteins identification, and the integration of antiSMASH 7.0 for predicting biosynthetic gene clusters.

CONCLUSIONS: Our upgrades make PathoFact 2.0 a more powerful and user-friendly platform for predicting microbiome-based pathogenicity and resistance, providing a crucial tool for better understanding and addressing the challenges posed by antimicrobial resistance and infectious diseases.PathoFact 2.0 is available at https://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2. It is compatible with Linux operating systems.},
}

@article {pmid42172181,
year = {2026},
author = {Gomes, JV and Ribeiro, SPO and Nascimento, GMCD and Santos, DOD and Paula, DJG and Lima, SCS and Simão, TA},
title = {The human microbiome in cancer: Not just a sidekick anymore.},
journal = {Genetics and molecular biology},
volume = {49Suppl 1},
number = {Suppl 1},
pages = {e20250236},
pmid = {42172181},
issn = {1415-4757},
abstract = {The human microbiome is increasingly recognized as a dynamic element in cancer biology. Studies across breast, prostate, lung, colorectal, and cervical tumors reveal that microbial communities influence carcinogenesis, immune regulation, and treatment outcomes. When the balance of these microorganisms is altered, inflammation becomes chronic, metabolism is disrupted, and signaling pathways such as NF-κB, IL6-STAT3, and β-catenin are activated. Bacterial metabolites and genotoxins, including colibactin and bile acids, may damage DNA and reshape the epigenetic landscape. Distinct microbial profiles have been linked to prognosis and to patient responses to chemotherapy and immunotherapy. The presence of beneficial taxa, such as Akkermansia muciniphila and Ruminococcus, has been associated with improved response to immune checkpoint inhibitors. At the same time, antibiotic-induced depletion of gut microbiome can reduce therapeutic efficacy. Strategies that help restore microbial balance, including probiotics, dietary interventions, and fecal microbiota transplantation, are being explored as complementary therapies. Although methodological differences and contamination remain challenges, the growing body of evidence indicates that the microbiome is a measurable and modifiable component of tumor ecosystems with strong potential for diagnostic, prognostic, and therapeutic applications in precision oncology.},
}

@article {pmid42172659,
year = {2026},
author = {Liu, C and Yin, X and Yuan, X},
title = {Gut microbiota dysbiosis and osteoporosis: pathogenesis and novel intervention strategies.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/17460913.2026.2678122},
pmid = {42172659},
issn = {1746-0921},
abstract = {Osteoporosis represents a major global public health challenge, with current pharmacological treatment often limited by substantial side effects. Recent research identifies the gut-bone axis as a key regulatory pathway linking gut microbiota to bone metabolic homeostasis. This review synthesizes findings from PubMed, Web of Science, and Scopus (up to March 2026) to elucidate how gut microbiota dysbiosis drives osteoporosis pathogenesis through interconnected mechanisms: aberrant immune modulation, altered microbial metabolites, impaired nutrient absorption, endocrine disruption, and systemic inflammation stemming from intestinal barrier failure. Consequently, these pathways disrupt the delicate balance of bone remodeling. Based on these insights, we outline novel microbiota-targeted therapeutic strategies, including probiotics, prebiotics, fecal microbiota transplantation, natural bioactive compounds, traditional Chinese medicine, and nanomaterials. These interventions aim to prevent and manage osteoporosis by reshaping the intestinal microecology via multi-target modulation. Future endeavors should prioritize in-depth mechanistic exploration, personalized precision interventions, and enhanced clinical translation to integrate these strategies into comprehensive osteoporosis care frameworks.},
}

@article {pmid42172767,
year = {2026},
author = {Jin, X and Wu, D and Tong, Y and Weng, S and Jiang, Y and Zhang, J},
title = {The mechanism of rumen microorganisms regulating fatty acid and lipid metabolism in brown adipose tissue of sheep analyzed by multi-omics analysis.},
journal = {Food chemistry},
volume = {519},
number = {},
pages = {149670},
doi = {10.1016/j.foodchem.2026.149670},
pmid = {42172767},
issn = {1873-7072},
abstract = {Brown Adipose Tissue (BAT), a thermogenic fat in mammals that consumes energy rather than storing it, possesses unique characteristics. This study sought to clarify the specific mechanism and role of mutton in lipid deposition and nutritional quality. Using gas chromatography, lipidomics, and 16S rRNA gene sequencing, researchers found that BAT exhibited more active lipid metabolism, accompanied by increased abundance of the Firmicutes and Proteobacteria phyla. This activity manifested as a rise in beneficial DHA and EPA levels, along with a significant accumulation of key active lipids, such as cardiolipin and phosphatidylcholine. Further WGCNA and HCA analysis demonstrated that phyla including Verrucomicrobiota, Firmicutes, and Proteobacteria collectively enhanced BAT's nutritional value by regulating the biosynthesis of unsaturated fatty acids. This research successfully constructed a preliminary multi-dimensional interaction network of lipids and fatty acids within the "fat-rumen axis", providing a new theoretical framework for the accurate improvement of mutton's nutritional value.},
}

@article {pmid42172829,
year = {2026},
author = {Yang, H and Xie, Y and Wang, H and Sun, H and Li, X and Yao, X and Ding, J and Wang, Q and Lv, H and Turner, BL and Sun, S and Wang, J},
title = {Multi-omics association analysis of the toxicity mechanism differences of typical veterinary antibiotics on tomatoes: From physiological inhibition to metabolic reprogramming.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142457},
doi = {10.1016/j.jhazmat.2026.142457},
pmid = {42172829},
issn = {1873-3336},
abstract = {Widespread application of veterinary antibiotics is contaminating soil via animal feces, leading to uptake by plants and environmental damage. Currently, research on the toxicological mechanisms associated with various classes of antibiotics remains inadequate. Therefore, this study utilized tomato as the test species and selected three representative antibiotics-chlortetracycline (CTC), enrofloxacin (ENR), and tylosin (TYL)-to systematically evaluate their differential toxicity and associated metabolic mechanisms through 14 and 28 days exposure experiments. At the individual level, antibiotics significantly suppressed biomass accumulation and photosynthesis in tomato seedlings, the ENR exhibited maximum inhibition rates of 37.4% for fresh weight and 26.7% for plant height. In contrast, the CTC recorded peak values of 28% for leaf area and 25.1% for SPAD measurements. Furthermore, exposure to antibiotics induced oxidative stress in tomato seedlings, with SOD demonstrating its highest activation rate of 18.3% in the TYL. Within the rhizosphere microenvironment, there was a notable decrease in the abundance of the dominant phylum Bryobacter, which was accompanied by alterations in bacterial community structure, an increase in network complexity, and a reduction in modularity. Under antibiotic stress, microbial communities demonstrated distinct metabolic responses: enhanced lipid metabolism in CTC, elevated carbohydrate metabolism with ENR, and activated nucleotide metabolism associated with TYL. In summary, antibiotics present global ecological risks by inhibiting plant growth and disrupting the rhizosphere microbiome. The class-specific toxicity of these substances necessitates the implementation of targeted risk management strategies.},
}

@article {pmid42172872,
year = {2026},
author = {Yu, M and Wang, Z and Han, X and Ge, Y and Geng, Z and Wang, J and Wang, D and Lian, S},
title = {Parvimonas micra is a specifically enriched bacterium in advanced canine periodontal disease and its effects are ameliorated using ADSCs-exosomes.},
journal = {Veterinary microbiology},
volume = {318},
number = {},
pages = {111078},
doi = {10.1016/j.vetmic.2026.111078},
pmid = {42172872},
issn = {1873-2542},
abstract = {Canine periodontitis is a prevalent chronic inflammatory disease, with its pathological progression closely associated with oral microbiome dysbiosis and dysregulated host immune responses. This study aimed to characterize oral microbiome changes across different stages of canine periodontitis, identify bacteria associated with advanced disease and evaluate the immunomodulatory potential of adipose-derived stem cell exosomes (ADSCs-exosomes). We analyzed pooled subgingival and supragingival plaque samples collected from multiple oral sites in 60 dogs with clinical stages S0-S4 using 16S rRNA sequencing, and performed in vitro cell assays, ADSCs-exosomes isolation and characterization. Alpha-diversity analysis showed that, in this cohort and under our pooled oral sampling design, advanced periodontitis was associated with increased community richness and altered evenness at the subject level, while beta-diversity analysis confirmed marked structural differences among study groups (R[2] = 0.161, P = 0.001). P. micra showed significantly higher abundance in severe periodontitis (S4) and was identified by linear discriminant analysis effect-size (LEfSe), random forest, and analysis of variance (ANOVA) analyses (linear discriminant analysis (LDA) > 3.5, P < 0.01), suggesting an association with advanced disease. In vitro, P. micra reduced canine macrophage cell (DH82) (P < 0.05) viability and promoted a pro-inflammatory phenotypes. ADSCs-exosomes were internalized by canine macrophages and significantly downregulated pro-inflammatory cytokines (IL-1β, IL-6, iNOS) and upregulated anti-inflammatory markers (Arg-1, CD163, and IL-10) (P < 0.05), thereby partially reversing the inflammatory imbalance induced by P. micra. Together, these findings identify P. micra as a candidate bacterium associated with advanced canine periodontitis and suggest that ADSCs-exosomes may have potential as a host-modulatory therapeutic strategy in this disease.},
}

@article {pmid42172920,
year = {2026},
author = {Maria van Eijk, A and Quinn-Savory, A and Zulaika, G and Skinner, A and Mason, L and Green, SJ and Phillips-Howard, PA and Mehta, SD},
title = {Effect of menstrual cups on vaginal health, reproductive tract and urogenital infections: a systematic review and meta-analysis.},
journal = {EBioMedicine},
volume = {128},
number = {},
pages = {106307},
doi = {10.1016/j.ebiom.2026.106307},
pmid = {42172920},
issn = {2352-3964},
abstract = {BACKGROUND: The menstrual cup is a device inserted into the vagina during menstruation to collect blood. Evidence of its effect on the vaginal microbiome and associations with laboratory-confirmed infections is limited. We compiled existing information to assess associations between menstrual cups and reproductive tract infections (RTIs), sexually transmitted infections (STIs), and the vaginal microbiome.

METHODS: We searched four databases (PubMed, CINAHL, Global Health, and Scopus, from inception to January 23, 2026) for trials or observational studies reporting on menstrual cup use and laboratory-confirmed RTIs, STIs and the vaginal microbiome. Study quality was assessed using the Cochrane Collaboration tool for trials and the Joanna Briggs Institute Critical Appraisal Checklist for Cohort Studies. Outcomes of interest between cup-users and users of alternative menstrual products (non-cup users) were compared using prevalence ratios (PR). Meta-analyses were conducted using fixed-effects models to generate pooled estimates. PROSPERO registration: CRD42024559595.

FINDINGS: Eleven studies involving 10,268 participants were included. Only three studies were considered of good quality. In two randomised controlled studies in Kenya, menstrual cups reduced the risk of STIs relative to non-cup users (adjusted PR [aPR] 0.74, 95% CI 0.60-0.91, p = 0.037, n = 695, I[2] = 0.0%). The association with bacterial vaginosis was 0.81 (aPR, 0.63-1.04, p = 0.0963, n = 695, I[2] = 0.0%). When combining observational and randomised studies, a protective effect on bacterial vaginosis persisted (PR 0.79, 95% CI 0.69-0.90, p = 0.0004, five studies, n = 2103, I[2] = 0.0%, 3 continents). One trial showed an association between menstrual cups and HSV-2 of 0.71 (aPR, 95% CI 0.50-1.01, p = 0.057, n = 1451). Optimal vaginal community state type-1 (CST-I) was more likely among cup users compared to non-cup users (PR 1.18, 1.10-1.27, p < 0.0001, n = 2639, 5 studies in Kenya and Europe). No increased infection risks were noted among menstrual cup users across the infections evaluated. Main limitations included the low number and quality of existing studies.

INTERPRETATION: Menstrual cups reduced the risk of STIs in Kenya. For bacterial vaginosis, the association was consistent with a protective effect and supportive for a healthy vaginal microbiome composition in studies from different geographies. These data strengthen evidence on the value of menstrual cups as a global multipurpose menstrual product solution.

FUNDING: UK-Medical Research Council, Medical Research Foundation, USA-National Institutes of Health; National Institute of Child Health and Human Development, and the Gates Foundation.},
}

@article {pmid42173308,
year = {2026},
author = {Kumar Samanthapudi, VS and Ostos Mendoza, KC and Puvvala, S and Kamma, S and Kotla, S},
title = {Trimethylamine-N-oxide (TMAO) in multiorgan disease: mechanisms, translational insights, and therapeutic opportunities.},
journal = {Drug discovery today},
volume = {},
number = {},
pages = {104703},
doi = {10.1016/j.drudis.2026.104703},
pmid = {42173308},
issn = {1878-5832},
abstract = {Trimethylamine-N-oxide (TMAO), a gut microbe-derived metabolite, acts as a key mediator linking diet, microbial metabolism, and disease across multiple organs. Beyond cardiovascular and metabolic disorders, TMAO has also been implicated in a variety of pathological processes. It influences endothelial, immune, neuronal, and cancer cells, as well as platelets, through mechanisms including oxidative stress, inflammation, and organelle dysfunction. Systemic TMAO levels are influenced by hepatic metabolism, renal clearance, and hormonal factors, offering opportunities for targeted therapies. Approaches to reduce TMAO levels, including pharmacological inhibitors, dietary or microbiome-based interventions, and multiorgan strategies, could slow disease progression. Thus, TMAO shows promise as a diagnostic biomarker and therapeutic target, supporting avenues for drug discovery and precision medicine.},
}

@article {pmid42173442,
year = {2026},
author = {Venter, C and Ryczaj, K and Hicks, AG and Mack, DP and O'Mahony, L and Smith, PK and Brough, HA},
title = {Nutritional, Growth, and Microbiome Implications of Oral Immunotherapy: Unintended Consequences and Clinical Considerations.},
journal = {Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anai.2026.05.024},
pmid = {42173442},
issn = {1534-4436},
abstract = {Food allergy management has changed significantly, with oral immunotherapy (OIT) emerging as a widely adopted strategy to increase reaction thresholds and reduce the risk of severe allergic reactions. Alongside its immunological effects, OIT has important implications for nutrition, growth, and the gut microbiome. Traditional management of food allergy relies on strict allergen avoidance, which may compromise dietary adequacy and growth, particularly in children avoiding nutrient-dense foods such as cow's milk and eggs. OIT offers an opportunity to reintroduce these foods in controlled amounts, potentially improving nutrient intake and supporting growth trajectories. Emerging evidence highlights the role of the gut microbiome in modulating immune tolerance. Microbial diversity, metabolite production, and early-life colonization patterns influence regulatory immune pathways and epithelial barrier integrity. During OIT, microbiome changes appear modest and variable, with some studies suggesting taxon-specific or functional shifts rather than global restructuring. Importantly, dietary factors, particularly the use of ultra-processed foods as dosing vehicles, may confound microbiome outcomes and influence treatment responses. From a nutritional perspective, OIT presents both opportunities and risks. While allergen reintroduction may improve protein and micronutrient intake, reliance on energy-dense masking foods may increase the risk of excessive calorie intake and suboptimal diet quality. Growth outcomes during OIT appear generally favorable, particularly in younger children and those with lower baseline growth. This article summarizes current evidence on OIT, focusing on its interactions with diet, growth, and the gut microbiome, and highlights the need for integrated, multidisciplinary approaches to optimize both clinical and nutritional outcomes.},
}

@article {pmid42173447,
year = {2026},
author = {Harvey, HJ and Corrigan, S and Baiocco, D and Zhang, Z and Iqbal, TH and Teughels, W and Chapple, I and Horniblow, RD},
title = {Promicrobial mucoadhesive micro-composites enable delivery of beneficial oral bacteria to restore and modulate oral biofilm communities.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {115044},
doi = {10.1016/j.jconrel.2026.115044},
pmid = {42173447},
issn = {1873-4995},
abstract = {Imbalances within the oral microbiome, composed of over 700 phylotypes, drive both local diseases, including periodontitis, and systemic conditions, such as rheumatoid arthritis and cardiovascular disease. Given the overuse of conventional antimicrobial agents to manage oral diseases and the relapsing nature associated with current intervention strategies, innovative promicrobial approaches to oral biofilm community restoration are needed. Importantly, there is a critical unmet clinical need for active restoration and sustained delivery of beneficial oral commensals rather than continued disruption of already-imbalanced communities. We have developed a promicrobial formulation encapsulating live, health-associated, oral bacteria within mucoadhesive micro-composites to promote the establishment of beneficial biofilms under simulated oral flow conditions. We encapsulated and characterised a five-species bioactive consortia of oral bacteria in alginate micro-composites, surface modified with poly-l-lysine to enhance their adhesion to artificial saliva-coated surfaces in vitro. Dissemination of the encapsulated bacteria from the micro-composites led to the formation of stable oral biofilms. Notably, biofilm composition could be modulated by altering the encapsulated bioactive composition, enabling a tailored and targeted pathway to biofilm restoration. Under representative saliva flow, delivery of bioactives following their bioencapsulation resulted in strong biofilm-forming capacity, even in the presence of pre-existing oral bacterial communities containing pathobionts, highlighting their potential clinical applications in dental biofilm bioengineering. In experiments designed to simulate periodontal pocket debridement, we observed immunomodulation following treatment with bioactive formulations and pathobiont reduction when Limosilactobacillus reuteri was also incorporated into the consortia. These findings establish a framework for using sustained-release encapsulated probiotics to modulate the oral microbiome, offering a paradigm shift towards biofilm-promoting therapies for oral healthcare and paving the way for oral microbiome transplantation.},
}

@article {pmid42173626,
year = {2026},
author = {Sarkar, D},
title = {Artificial intelligence in multi-omics analysis of gastrointestinal diseases.},
journal = {Progress in molecular biology and translational science},
volume = {222},
number = {},
pages = {111-128},
doi = {10.1016/bs.pmbts.2026.02.003},
pmid = {42173626},
issn = {1878-0814},
mesh = {Humans ; *Artificial Intelligence ; *Gastrointestinal Diseases/genetics/microbiology/metabolism ; Precision Medicine ; *Genomics ; Multiomics ; },
abstract = {The assessment and treatment of gastrointestinal diseases face numerous obstacles, including inadequate diagnostic methods, limited therapeutic alternatives, and unequal access to medical services across different regions. However, advancements in technology such as artificial intelligence, personalized medicine, and microbiome analysis offer promising avenues to address these difficulties. An interdisciplinary and patient-centered approach can significantly improve health outcomes and reduce the overall impact of these conditions on both patients and healthcare systems. To effectively utilize AI while safeguarding patient interests, it is essential to establish ethical standards, adopt patient-oriented regulations, and provide strong support structures for spreading awareness among both healthcare providers and recipients.},
}

Humans
*Artificial Intelligence
*Gastrointestinal Diseases/genetics/microbiology/metabolism
Precision Medicine
*Genomics
Multiomics

@article {pmid42173629,
year = {2026},
author = {Roy, P and Saha, S},
title = {AI in multi-omics analysis in obstructive lung diseases.},
journal = {Progress in molecular biology and translational science},
volume = {222},
number = {},
pages = {165-206},
doi = {10.1016/bs.pmbts.2026.01.025},
pmid = {42173629},
issn = {1878-0814},
mesh = {Humans ; *Artificial Intelligence ; *Lung Diseases, Obstructive/genetics/microbiology/metabolism ; Pulmonary Disease, Chronic Obstructive/genetics ; *Genomics ; Multiomics ; },
abstract = {The reports of obstructive lung diseases (OLDs) like asthma, chronic obstructive pulmonary disease (COPD), and bronchiectasis show increasing global prevalence. The available treatment options for these diseases are limited to antibiotics and steroids. Different multi-omics integration approaches have been applied in studying host, microbiome, and host-microbiome interactions in these diseases to get better insights. Artificial intelligence (AI)-based, as well as statistical and other approaches, are used for multi-omics analyses, specifically the integration of multi-omics data in OLDs. This chapter discusses various aspects of multi-omics integration studies in asthma, COPD, and bronchiectasis. Overall, these studies focused on disease subtype classification, risk assessment, association with genetic factors, and several other aspects.},
}

Humans
*Artificial Intelligence
*Lung Diseases, Obstructive/genetics/microbiology/metabolism
Pulmonary Disease, Chronic Obstructive/genetics
*Genomics
Multiomics

@article {pmid42173637,
year = {2026},
author = {Rajalakshmi, SG and Sreehari, E and Viswanathan, P},
title = {Artificial intelligence-driven multi-omics analysis of gut-kidney axis in chronic kidney disease.},
journal = {Progress in molecular biology and translational science},
volume = {222},
number = {},
pages = {85-110},
doi = {10.1016/bs.pmbts.2026.01.015},
pmid = {42173637},
issn = {1878-0814},
mesh = {*Renal Insufficiency, Chronic/microbiology/metabolism ; Humans ; *Artificial Intelligence ; *Gastrointestinal Microbiome ; *Kidney/metabolism/pathology ; Animals ; *Metabolomics ; Proteomics ; Multiomics ; },
abstract = {The complex interactions between gut microbiota and kidney function in chronic kidney disease (CKD) present a challenging phenomenon in nephrology research. This comprehensive review explores how artificial intelligence (AI) is utilised for our understanding of the gut-kidney axis through multiomics analysis, offering a new platform for disease management and therapeutic interventions. Recent advances in multi-omics technologies have generated unprecedented volumes of data across microbiomics, metabolomics and proteomics platforms, necessitating sophisticated AI-driven approaches for meaningful interpretation. So, we substantially examined how machine learning methods integrate the omics data to establish the relationship between the gut-kidney axis for a more accurate predictive model and biomarker discovery. In addition, we explained the overview of molecular routes that relate microbiome changes to uremic toxin generation and inflammatory cascades in CKD patients. This timely review offers significant basic insights into using AI to better understand the pathogenesis of CKD progression in early stages via the gut-kidney route.},
}

*Renal Insufficiency, Chronic/microbiology/metabolism
Humans
*Artificial Intelligence
*Gastrointestinal Microbiome
*Kidney/metabolism/pathology
Animals
*Metabolomics
Proteomics
Multiomics

@article {pmid42173692,
year = {2026},
author = {Ambachew, S and Ramezanpour, M and Cooksley, CM and Shaghayegh, G and Burdon, I and Barry, EF and Fenix, KA and Wormald, PJ and Psaltis, AJ and Vreugde, S},
title = {Staphylococcus aureus and Staphylococcus lugdunensis Act in Concert to Disrupt the Nasal Epithelial Barrier.},
journal = {Clinical and translational allergy},
volume = {16},
number = {5},
pages = {e70177},
doi = {10.1002/clt2.70177},
pmid = {42173692},
issn = {2045-7022},
support = {Grant No. 0006008606//Australian National Health and Medical Research Council/ ; },
abstract = {INTRODUCTION: Chronic rhinosinusitis (CRS) pathophysiology and its link to microbiome is an area of ongoing investigation. Certain pathogens, in particular Staphylococcus aureus described to contribute to recalcitrant CRS. In addition, different species of coagulase negative staphylococci (CoNS) are frequently isolated from the sinonasal cavity of CRS patients. However, the influence of Staphylococcal species coexisting in the same niche on the inflammatory process remains unclear. The aim of this study was to explore the impact of exoproteins from various Staphylococcus species isolated from the same patients on the mucosal barrier.

METHODS: Staphylococcal species isolated from CRS and control patients were cultured from sinus swabs in planktonic and biofilm forms, and their exoproteins extracted. Primary human nasal epithelial cells (HNECs) from CRS patients were cultured at an air-liquid interface (ALI) and exposed to 20 μg/mL exoproteins or control. Barrier disruption and cytotoxicity were assessed by measuring the transepithelial electrical resistance (TEER), passage of fluorescein labeled dextrans and lactate dehydrogenase (LDH) levels. IL- 6 concentration was measured employing ELISA. Patient's matched sinonasal tissue samples were analyzed with flow cytometry to detect and quantify immune cells.

RESULTS: Forty-four Staphylococcal species were isolated from 22 CRS and control patients including: 22 S. aureus, 12 S. epidermidis, and 10 S. lugdunensis. 15 out of 22 S. aureus exoproteins significantly enhanced cytotoxicity, reduced TEER values and increased paracellular permeability compared to control (p < 0.05). By contrast, S. epidermidis and S. lugdunensis exoproteins caused either mild or negligible effects on the TEER values, cell viability, and paracellular permeability. However, S. lugdunensis exoproteins induced significantly higher IL-6 compared to control. Correlation analysis indicated S. aureus and S. lugdunensis from the same patient acted in concert to disrupt the nasal epithelial barrier and induce toxicity.

CONCLUSION: This study shows the significant and detrimental impact of the presence of S. aureus exoproteins on nasal epithelial cell barrier function. S. aureus and S. lugdunensis isolated from the same patients acted in concert to affect the nasal barrier and inducing toxicity.},
}

@article {pmid42173824,
year = {2026},
author = {Alanazi, HH},
title = {Immune discrimination between commensals and pathogenic bacteria.},
journal = {Virulence},
volume = {17},
number = {1},
pages = {2677297},
doi = {10.1080/21505594.2026.2677297},
pmid = {42173824},
issn = {2150-5608},
mesh = {Humans ; *Bacteria/immunology/pathogenicity ; *Symbiosis/immunology ; Gastrointestinal Microbiome/immunology ; Animals ; Dysbiosis/immunology/microbiology ; *Bacterial Infections/immunology/microbiology ; *Host-Pathogen Interactions/immunology ; Immune Tolerance ; *Bacterial Physiological Phenomena ; Gastrointestinal Tract/microbiology/immunology ; },
abstract = {Interaction with various bacteria is essential for the development of various components of the immune system. To prevent disease, the immune system must continuously discriminate between commensal and pathogenic bacteria. The immune system employs several mechanisms to discriminate between beneficial and harmful bacteria. This ensures selective immune tolerance toward commensals, especially in the gastrointestinal tract. Both commensal and pathogenic bacteria contain features that provoke immune responses. However, how the immune system reacts to or eliminates bacterial infections while preserving commensals is not fully understood. This review aims to explore the underlying mechanisms used by the immune system to distinguish between commensals and pathogenic bacteria. The review also addresses how commensals interact with immune system components to facilitate immune discrimination and host protection. Finally, dysbiosis and therapeutic interventions used to restore microbial balance are also discussed in this review.},
}

Humans
*Bacteria/immunology/pathogenicity
*Symbiosis/immunology
Gastrointestinal Microbiome/immunology
Animals
Dysbiosis/immunology/microbiology
*Bacterial Infections/immunology/microbiology
*Host-Pathogen Interactions/immunology
Immune Tolerance
*Bacterial Physiological Phenomena
Gastrointestinal Tract/microbiology/immunology

@article {pmid42173935,
year = {2026},
author = {Yang, J and Park, Y and Jang, SG and Park, MJ and Moon, SJ and Choi, HK and Kwok, SK},
title = {Clinical significance of gut microbiota-derived metabolite trimethylamine N-oxide in patients with systemic lupus erythematosus.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-53011-7},
pmid = {42173935},
issn = {2045-2322},
support = {RS-2023-00224099//National Research Foundation of Korea/ ; },
abstract = {Trimethylamine N-oxide (TMAO), a gut microbiota-derived metabolite, is associated with cardiovascular disease (CVD) via pro-inflammatory and pro-atherogenic mechanisms. Systemic lupus erythematosus (SLE) is a systemic autoimmune disease with a significantly increased risk of CVD, however, the role of TMAO in SLE remains unclear. This study aimed to assess the clinical significance of TMAO in patients with SLE, including analyses of precursor metabolites and gut microbiome. A total of 207 participants were enrolled, including 157 patients with SLE and 50 healthy controls. Serum TMAO levels were measured using ELISA, fecal precursor metabolites including trimethylamine (TMA) were quantified by [1]H-NMR spectroscopy, and gut microbiota composition was assessed using 16S rRNA sequencing. SLE patients with CVD had significantly higher TMAO levels than HC (P = 0.028) and SLE patients without CVD (P = 0.004). Serum TMAO (P = 0.025) and fecal TMA (P = 0.032) levels were positively correlated with the Systemic Lupus International Collaborating Clinics/American College of Rheumatology (SLICC/ACR) damage index. Serum TMAO was negatively correlated with steroid dose (P = 0.038). Distinct gut microbiota compositions were observed between SLE patients with and without CVD. TMAO is associated with cardiovascular disease and cumulative organ damage in SLE, potentially mediated by gut microbiome alterations and modulated by steroid therapy.},
}

@article {pmid42173975,
year = {2026},
author = {Liu, Y and Sun, C and Liu, H and Shu, X and Yu, T and Gong, Y and Li, J},
title = {Gut microbiota dysbiosis and altered fecal metabolome in patients with age-related cataract.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-53261-5},
pmid = {42173975},
issn = {2045-2322},
support = {CSTB2022NSCQ-MSX1274//Natural Science Foundation Project of Chongqing, Chongqing Science and Technology Commission/ ; CSTB2023NSCQ-MSX0194//Natural Science Foundation Project of Chongqing, Chongqing Science and Technology Commission/ ; NSFC; 32300778//National Natural Science Foundation of China/ ; W015//CQMU Program for Youth Innovation in Future Medicine/ ; },
abstract = {Age-related cataract (ARC) is a leading cause of vision loss with incompletely understood mechanisms. Emerging evidence suggests the gut microbiota can influence ocular health, yet the gut-eye connection in cataract remains unexplored. We characterized gut microbial communities and fecal metabolic profiles in 30 ARC patients and 30 healthy controls using 16S rDNA gene sequencing, untargeted LC-MS metabolomics, and targeted GC-MS for short-chain fatty acids (SCFAs). While alpha- and beta-diversity were comparable between groups, ARC patients exhibited significant dysbiosis, including reduced Gut Microbiome Health Index, increased Microbial Dysbiosis Index, higher relative abundance of Bifidobacterium and Klebsiella, and depletion of butyrate-producing taxa (Faecalibacterium, Clostridia). Fecal metabolomic profiles distinctly separated ARC patients from controls, with pathway analysis highlighting disruptions in glycerophospholipid and choline metabolism. Targeted analysis confirmed significant depletion of acetate, propionate, and butyrate in ARC patients (all P< 0.01), which positively correlated with beneficial genera abundance. This integrative study reveals that ARC patients harbor gut microbial dysbiosis and distinct fecal metabolomic signatures, notably a loss of SCFA-producing bacteria and anti-inflammatory SCFAs. These findings support a novel gut-eye axis in cataract pathogenesis and suggest that gut-derived microbial and metabolic biomarkers may aid in non-invasive risk assessment, while microbiome-targeted interventions could offer new preventive or therapeutic avenues.},
}

@article {pmid42174008,
year = {2026},
author = {de Mel, R and Al Khafaji, AH and Muthusamy, S and Xu, J and Håkansson, Å},
title = {Changes in gut microbiota composition following water kefir consumption in healthy adults.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42174008},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome ; Adult ; Male ; *Kefir/microbiology ; Female ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Healthy Volunteers ; Middle Aged ; Bacteria/genetics/classification/isolation & purification ; Water ; },
abstract = {Fermented foods have gained increasing scientific interest for their potential to modulate gut microbiota and provide probiotic microorganisms with possible health benefits. This intervention trial examined the impact of daily consumption of water kefir, a sustainable plant-based fermented beverage, on gut microbiota composition in 40 healthy adults. Participants consumed 200 mL of homemade water kefir daily for 14 days, with fecal samples collected before and after the intervention. Some participants reported mild, transient gastrointestinal effects such as flatulence (32%) and bloating (24%), which are common when introducing live microorganisms, while others experienced reduced abdominal pain (28%), and most (66%) reported no noticeable change in symptoms. 16S rRNA sequencing revealed significant shifts in microbial composition, including a 6.5% decrease in Firmicutes and increases in Bacteroidetes (+ 21.6%) and Actinobacteria (+ 14.8%). At the species level, beneficial taxa such as Blautia spp. and Roseburia faecis increased, along with commensals including Bacteroides fragilis, Bacteroides uniformis, Gemmiger formicilis, Prevotella copri, and Parabacteroides distasonis (p < 0.01). Although α-diversity remained unchanged, β-diversity differed significantly between pre- and post-intervention samples (p = 0.025). By comparing the relative abundance of dominant genera in participants' gut microbiota and in water kefir, overlapping genera such as Lactobacillus, Bifidobacterium, Prevotella, Coprococcus, and Faecalibacterium were identified. Among these, Bifidobacterium and Prevotella increased, Coprococcus decreased, and Lactobacillus and Faecalibacterium remained stable. Genera exclusive to the gut microbiota also exhibited differential changes. These findings suggest that water kefir consumption is associated with modulation of the gut microbiota, including increases in saccharolytic and short-chain fatty acid (SCFA)-producing taxa, potentially influenced by its exopolysaccharides and microbial community. Some genera from water kefir may transiently affect the gut microbiome, and the concurrent increase in Bifidobacterium and Prevotella may suggest a potential probiotic-like effect. However, causality cannot be established, and further studies are needed to assess the persistence of these changes and their long-term clinical relevance.},
}

Humans
*Gastrointestinal Microbiome
Adult
Male
*Kefir/microbiology
Female
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Young Adult
Healthy Volunteers
Middle Aged
Bacteria/genetics/classification/isolation & purification
Water

@article {pmid42174021,
year = {2026},
author = {Min, U and Kim, J and Kim, J and Jin, H and Oh, H and Ahn, S and Shin, H and Lee, W},
title = {Spicy food intake and dietary factors shape the gut microbiome and metabolism of mucin and short-chain fatty acids in healthy adults.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-53556-7},
pmid = {42174021},
issn = {2045-2322},
abstract = {Whether spicy food intake independently modulates mucin metabolism and short-chain fatty acid (SCFA) production or depends on co-ingested factors such as alcohol remains poorly understood. Herein, shotgun metagenomics characterized gut microbial composition, functional pathways, and their relationship with spicy food intake, alcohol consumption, and intestinal fatty acid-binding protein (I-FABP) and liver fatty acid-binding protein (L-FABP) levels in 229 healthy Korean adults. Alcohol intake was positively correlated with urinary I-FABP levels indicating mild epithelial stress, whereas spicy food intake was not associated with either FABP biomarker. Consumption of highly spicy foods resulted in increased abundance of SCFA-producing and mucin-metabolizing taxa, along with mucin degradation and SCFA production. Individuals with high alcohol intake showed stronger enrichment of mucin-degrading taxa with reduced SCFA flux and increased abundance of Proteobacteria and Fusobacteria. The cross-classified dietary groups exhibited distinct mucin and SCFA activity patterns. The Drink-High-Spicy-High (DHSH) group displayed elevated mucin turnover and SCFA production with dysbiosis. These findings suggest that spicy food may modulate mucus layer metabolism in a context-dependent manner, whereas alcohol more consistently perturbs mucin-SCFA networks and epithelial integrity.},
}

@article {pmid42174097,
year = {2026},
author = {Ali, A},
title = {Comment on "Gut microbiome impact on systemic therapy outcomes in metastatic renal cell carcinoma: a systematic review" by Gavi et al.},
journal = {World journal of urology},
volume = {44},
number = {1},
pages = {},
pmid = {42174097},
issn = {1433-8726},
}

@article {pmid42174231,
year = {2026},
author = {Schiele, J and Tsai, PL and Schimmele, T and Beck, S and Meyer, M and Mannes, M and Desmond, LW and Noschka, R and Huber-Lang, M and Haffner-Luntzer, M and Jarczok, MN and Lowry, CA and Reif, A and Langgartner, D and Stenger, S and Slattery, DA and Reber, SO},
title = {Microbial Legacy: Mycobacterium vaccae ATCC 15483[T] intergenerationally diversifies the microbiome and enhances stress resilience in male mice.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {42174231},
issn = {1476-5578},
support = {RE 2911/ 23-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; German Research 251293561//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; German Research 251293561//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SL 141/ 6-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {According to the "Old Friends" hypothesis, the increased prevalence of stress-associated disorders in urban concrete landscapes of high-income countries is at least in part due to a reduced exposure to immunoregulatory microorganisms. The latter is particularly impactful when occurring during early prenatal and postnatal life. Accordingly, our own preclinical studies demonstrate that non-pathogenic rapid-growing mycobacteria, including Mycobacterium (M.) vaccae NCTC 11659 and M. vaccae ATCC 15483[T], have immunoregulatory and stress-protective effects when administered repeatedly prior to or during stressor exposure. Here, we advance these findings by showing that repeated intragastric (i.g.) administration of a heat-killed preparation of M. vaccae ATCC 15483[T] to female C57BL/6 N mice provides intergenerational stress protection. Their male offspring, despite never directly receiving administration of rapid-growing mycobacteria, were protected against multiple adverse consequences of chronic stress in adulthood. Moreover, correlational analyses implicate the fecal microbiome as a potential mediator of these effects, with M. vaccae ATCC 15483[T] intergenerationally facilitating α-diversity and increasing the relative abundance of bacterial taxa known to be potent short-chain fatty acid producers. Repeated intragastric (i.g.) administration of a heat-killed preparation of Mycobacterium (M.) vaccae ATCC 15483[T] (MvacATCC)vs. its vehicle borate-buffered saline (BBS) to adult nulliparous female C57BL/6N mice was intergenerationally protective against multiple negative physiological and immunological consequences of chronic subordinate colony housing (CSC; compared with respective single-housed control (SHC) mice), including adrenal hypertrophy, splenomegaly, thymus involution, and tibia growth reduction as well as increased splenic toll-like receptor (TLR) 2 and TLR4 protein concentrations and splenocyte ex vivo (re)activity, but also decreased splenic ex vivo glucocorticoid sensitivity, regulatory T cell (Treg) counts and Treg suppression capacity in their male offspring. In contrast, CSC-induced increase in splenic myeloid cell counts as well as of neutrophilic chemotactic activity was not affected intergenerationally by MvacATCC. Moreover, fecal microbiome analyses before and after CSC showed that MvacATCC intergenerationally facilitated α-diversity and relative abundance of bacterial taxa known to be potent short-chain fatty acid (SCFA) producers. Of note, we abstained from showing respective data of female offspring in the graphical abstract (*), as the intergenerational resilience effects of MvacATCC on female offspring were difficult to interpret. The latter was due to the fact that chronic adult stressor exposure (i.e., social instability paradigm, SIP) per se did not affect any of the physiological and immunological readouts reported in females. The graphical abstract was created with Biorender.com.},
}

@article {pmid42174303,
year = {2026},
author = {Kim, CH and Ciloglu, A and Yan, J and Mackay, A and Noel, KR and Cooper, M and Oluoch, A and Canam, T and Stone, CM},
title = {Habitat Type and Locality Structure the Midgut Microbiota of Aedes albopictus.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02792-5},
pmid = {42174303},
issn = {1432-184X},
abstract = {The mosquito midgut microbiome plays a crucial role in nutrition, reproduction, and immunity, yet how locality and urban development shape these communities and their potential relevance to mosquito-pathogen interactions remains poorly understood. Here, we investigated bacterial community composition and diversity in the midguts of adult female Aedes albopictus collected from residential and woodland habitats of Champaign-Urbana and Charleston in Illinois, USA. We sequenced the V4 region of the 16 S rRNA gene from 160 samples and analyzed the data using QIIME 2. After quality and feature filtering, 112 samples were retained, yielding 2,531 unique amplicon sequence variants assigned to 34 bacterial phyla, 246 families, and 404 genera. Because formal contaminant assessment was not possible, findings should be interpreted with appropriate caution. Woodland habitats showed significantly higher Shannon diversity, observed ASV richness, and phylogenetic diversity than residential habitats, with Charleston woodland samples exhibiting the highest richness and phylogenetic diversity. Factorial analyses showed significant associations of both city and habitat type with Shannon diversity, observed richness, and Faith's phylogenetic diversity, with significant interaction terms also detected. Beta diversity analyses revealed distinct clustering of Charleston woodland samples, and factorial PERMANOVA indicated significant associations of both city and habitat type across all four beta diversity metrics, with the strongest interaction effect observed for unweighted UniFrac. In conclusion, these results show that habitat type and locality are strongly associated with the composition and diversity of the Ae. albopictus midgut microbiota, underscoring the importance of habitat-specific microbial patterns in mosquito biology.},
}

@article {pmid42174322,
year = {2026},
author = {Tan, Y and Peng, G and Abudouwanli, A and Zhao, W and Sun, Q and Yang, M and Ogawa, H and Okumura, K and Niyonsaba, F},
title = {Tryptophan Metabolism at the Crossroads of Immunity, Barrier Function, and the Microbiome in Atopic Dermatitis.},
journal = {Clinical reviews in allergy & immunology},
volume = {69},
number = {1},
pages = {},
pmid = {42174322},
issn = {1559-0267},
support = {24K23469//Japan Society for the Promotion of Science/ ; 24K11459//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Tryptophan/metabolism ; *Dermatitis, Atopic/metabolism/immunology/therapy/microbiology/etiology ; *Microbiota/immunology ; Animals ; *Skin/immunology/metabolism/microbiology ; Melatonin/metabolism ; Kynurenine/metabolism ; Immunity ; Probiotics/therapeutic use ; Serotonin/metabolism ; },
abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by complex interplay among immune imbalance, impaired barrier function, and alterations in host‒microbiome interactions. Accumulating evidence indicates that tryptophan (TRP) metabolism is associated with these core pathological processes. This review summarizes the major TRP metabolic pathways, including the kynurenine pathway, microbial indole production, and the serotonin-melatonin axis, and outlines how their respective metabolites influence cutaneous inflammation, immune regulation, and barrier integrity in the context of AD. We integrate findings from preclinical and clinical studies to describe disease-associated alterations in TRP metabolism in AD and their potential relevance to disease activity. In addition, we examine both existing and emerging therapeutic strategies aimed at correcting TRP metabolic imbalance, including pharmacological agents, dietary interventions, and probiotic supplementation. Overall, elucidating the multifaceted role of TRP metabolism in AD pathophysiology provides a rational foundation for developing more precise diagnostic tools and targeted therapeutic approaches.},
}

Humans
*Tryptophan/metabolism
*Dermatitis, Atopic/metabolism/immunology/therapy/microbiology/etiology
*Microbiota/immunology
Animals
*Skin/immunology/metabolism/microbiology
Melatonin/metabolism
Kynurenine/metabolism
Immunity
Probiotics/therapeutic use
Serotonin/metabolism

@article {pmid42174554,
year = {2026},
author = {Xing, X and Meng, W and Chen, W and Shi, X and Wei, D and Lu, Q},
title = {Causal effects of oral microbiome traits on female reproductive diseases: a two-sample Mendelian randomization study.},
journal = {BMC women's health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12905-026-04547-3},
pmid = {42174554},
issn = {1472-6874},
support = {CYDXK202203//Multidisciplinary Clinical Research Innovation Team Project of Beijing Chao-Yang Hospital/ ; },
abstract = {OBJECTIVE: Female reproductive diseases (FRDs) impose a substantial health burden. Observational studies suggest links between oral dysbiosis and systemic conditions, but whether oral microbial traits causally influence FRDs remains unclear. We used two-sample Mendelian randomization (MR) to evaluate potential causal effects of genetically predicted oral microbiome traits on FRDs.

METHODS: Genome-wide association study (GWAS) summary statistics for 44 salivary microbial traits were obtained from a publicly available oral microbiome GWAS based on the Danish ADDITION-PRO cohort (16 S rRNA profiling; European ancestry; n = 610). Outcome GWAS summary statistics for six FRDs were obtained from FinnGen (R12). The inverse-variance weighted (IVW) method was the primary analysis, complemented by MR-Egger, weighted median, and weighted mode. Sensitivity analyses included Cochran's Q, MR-Egger intercept, MR-PRESSO, leave-one-out, and Steiger directionality tests. Multiple testing for primary IVW analyses was addressed using Benjamini-Hochberg false discovery rate (FDR) correction.

RESULTS: In primary IVW analyses, several oral taxa showed nominal associations (P < 0.05) with uterine leiomyoma (class Bacilli: OR = 1.0303, 95% CI 1.0012-1.0602; genus Veillonella: OR = 1.0291, 95% CI 1.0075-1.0512) and tubal infertility (family Veillonellaceae: OR = 0.8640, 95% CI 0.7824-0.9541; genus Veillonella: OR = 0.8900, 95% CI 0.8167-0.9699). However, none of these associations remained statistically significant after Benjamini-Hochberg FDR correction for the primary IVW analyses (all q > 0.05). In sensitivity analyses, MR-PRESSO outlier correction suggested a nominal association between Rothia mucilaginosa and uterine leiomyoma (OR = 1.0228, 95% CI 1.0069-1.0391; P = 0.0202). Overall, sensitivity analyses and Steiger directionality tests did not indicate that the main signals were driven by strong directional pleiotropy or reverse causation.

CONCLUSION: This two-sample MR study provides suggestive, exploratory genetic evidence that specific oral microbiome traits may be linked to uterine leiomyoma and tubal infertility, but the evidence did not remain statistically significant after multiple-testing correction. Larger oral microbiome GWAS, independent outcome datasets, and functional studies are needed to validate these signals and clarify biological mechanisms.},
}

@article {pmid42174615,
year = {2026},
author = {Buddhasiri, S and Muangplod, T and Panathiwat, P and Chandrasrimuang, P and Jitjumnong, J and Boonyayatra, S and Singhla, T},
title = {Seasonal particulate matter exposure is associated with upper respiratory microbiota restructuring in dairy heifers.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05580-y},
pmid = {42174615},
issn = {1746-6148},
support = {R66IN00536, 2023//CMU Mid-Career Research Fellowship program, Chiang Mai University/ ; },
abstract = {BACKGROUND: Particulate matter (PM), particularly PM2.5 and PM10, is a major environmental health concern linked to respiratory diseases in humans and animals. Northern Thailand, especially Chiang Mai, experiences recurrent seasonal air pollution from biomass burning, exposing outdoor-housed livestock to elevated ambient PM levels. The bovine upper respiratory tract (URT) harbors both commensal and opportunistic microorganisms, and disruption of this microbiota may influence susceptibility to bovine respiratory disease (BRD). However, the impact of natural PM exposure on the bovine URT microbiota remains poorly understood.

RESULTS: Nasopharyngeal swabs from 25 clinically healthy dairy heifers were analyzed during low-PM and high-PM periods. During the high-PM period, peak PM2.5 levels exceeded 30 times the WHO 24-hour guideline. Alpha diversity, including observed features, Shannon diversity, and Simpson index, was significantly higher during the high-PM period than during the low-PM period. Beta diversity analysis showed significant differences in Bray-Curtis dissimilarity and Jaccard distance, indicating changes in both relative abundance-based community structure and presence-absence-based community membership. The high-PM period was characterized by altered taxonomic profiles, including higher proportions of Proteobacteria, Firmicutes, Gammaproteobacteria, and Bacilli, and lower proportions of Actinobacteriota, Bacteroidota, Actinobacteria, and Bacteroidia. Among selected dominant genera, Moraxella and Fusobacterium were significantly reduced during the high-PM period. BRD-associated genera, including Mycoplasma, Pasteurella, Mannheimia, and Histophilus, showed higher average relative abundances during the high-PM period; however, paired comparisons were not statistically significant.

CONCLUSIONS: Seasonal high-PM exposure in Chiang Mai was associated with measurable changes in the nasopharyngeal microbiota of clinically healthy dairy heifers, including increased alpha diversity, altered beta diversity, changes in taxonomic profiles, and reductions in selected dominant genera. These findings suggest that ambient air pollution may contribute to respiratory microbiota restructuring in dairy heifers. Further longitudinal studies integrating microbiota composition, host immune responses, farm-level environmental monitoring, and clinical respiratory outcomes are needed to clarify whether PM-associated microbiota changes contribute to BRD susceptibility.},
}

@article {pmid42174668,
year = {2026},
author = {Zhang, Z and Ma, X and Zhang, J and Wu, S and Zhang, X and Yang, C},
title = {Intratumoral microbiota exhibiting varied responses to neoadjuvant chemotherapy in triple-negative breast cancer revealed by 2bRAD-M.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08187-x},
pmid = {42174668},
issn = {1479-5876},
abstract = {BACKGROUND: Neoadjuvant chemotherapy (NACT) is the conventional therapy for early-stage and locally advanced triple-negative breast cancer (TNBC). Pathological complete response (pCR) serves as an essential indicator for predicting the effectiveness of NACT; however, a limited percentage of patients benefit from NACT. This research examined variations in the tumor microbiota between the pCR and non-pCR groups via 2BRAD sequencing for microbiome (2bRAD-M) technology and assessed the potential of the microbiota as a biomarker for predicting the NACT response.

METHODS: A total of 44 TNBC patients were enrolled, of whom 25 achieved pCR and 19 were classified as non-pCR patients. Clinical data were collected, tumor tissue was biopsied as sample, and DNA was extracted. The 2bRAD-M sequencing method was used to analyse the microbial communities and community structures of tumor tissues in both groups, conduct microbial diversity and differential analyses, and perform qualitative and quantitative studies on the microbes inside the tissues.

RESULTS: A total of 1,896 microbial species were identified. The microbial diversity in non-pCR tissue exceeded that in pCR patient tissue. The microbial composition of the tumor tissues in both groups was comparable. In the non-pCR group, there were significantly more gram-negative bacteria, such as Klebsiella, Escherichia, Acinetobacter, Vibrio, and Meiothermus, than in the pCR group. Calidithermus chliarophilus, Meiothermus sp.003226535, and Escherichia coli were identified as the three principal species distinguishing the two groups. Seven species were identified as markers to distinguish between non-pCRs and pCRs, with an AUC value of 90.3%. Validation in an independent cohort via qPCR indicated the potential predictive value of this seven-species model, yielding an AUC of 84%. Functional annotation analysis revealed 3,207 differentially expressed COGs and 230 differentially enriched signalling pathways across the non-pCR and pCR microbiomes. In vitro experiments suggested that lipopolysaccharide may contribute to doxorubicin and paclitaxel resistance in MDA-MB-231 cells, a process potentially linked to the reactivation of the PI3K/AKT signaling pathway.

CONCLUSION: This exploratory 2bRAD-M microbiome study of pCR and non-pCR tissues from TNBC patients receiving NACT identified significant differences in microbial environments between the two groups. Based on these findings, we developed a predictive model for chemotherapy effectiveness and highlighted the microbiome's potential as a biomarker for the efficacy of NACT in TNBC patients, offering novel insights that may inform future clinical diagnostic strategies.},
}

@article {pmid42174754,
year = {2026},
author = {Chen, Y and Zhao, J and Zhao, J and Chen, Q and Dong, S and Jia, S and Zhao, Y and Hao, D and Yin, Y and Lin, S and Chen, Y and Zhuang, Y and Peng, H},
title = {Effects of fecal microbiota transplantation and probiotics on the gut microbiome in antibiotic-treated septic patients: A pilot randomized controlled trial.},
journal = {Virulence},
volume = {17},
number = {1},
pages = {2668764},
doi = {10.1080/21505594.2026.2668764},
pmid = {42174754},
issn = {2150-5608},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration & dosage/therapeutic use ; *Fecal Microbiota Transplantation ; Pilot Projects ; Male ; Middle Aged ; Female ; *Sepsis/therapy/microbiology/drug therapy ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; Aged ; Prospective Studies ; Critical Illness ; Dysbiosis/therapy ; Treatment Outcome ; Feces/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Broad-spectrum antibiotics, essential for sepsis management in critically ill patients, cause significant gut dysbiosis. Restoring gut microbiota may improve outcomes, but the efficacy of interventions like fecal microbiota transplantation (FMT) and probiotics in this setting remains underexplored. This study aims to evaluate the feasibility and potential efficacy of FMT versus probiotics on gut microbiome restoration and inflammatory markers in critically ill, antibiotic-treated sepsis patients. In this single-center, prospective, exploratory pilot RCT, 40 sepsis patients were were randomized 2:1:1 to: Control (n = 20, antibiotics treatment), Probiotics (n = 10, antibiotics treatment combined one week of probiotics), and FMT (n = 10, antibiotics treatment combined one week of FMT) groups. Gut microbiota composition was analyzed using 16S rDNA sequencing, and clinical inflammatory markers were assessed at baseline, one week, and two weeks post-treatment. FMT significantly mitigated antibiotic-induced reductions in microbial diversity. At 2 weeks, the FMT group exhibited higher alpha-diversity (Chao1 index, p = 0.0125; Shannon/Simpson trends p = 0.06) compared to Control and Probiotics groups. FMT increased beneficial Bacteroides abundance and reduced Enterobacteriaceae. BugBase analysis revealed FMT significantly lowered pathogenic potential of gut microbiota (p = 0.021). Donor-recipient analysis showed FMT shifted recipient microbiomes toward donor enterotype. This study provides preliminary evidence that FMT, but not the probiotic regimen, effectively restores gut microbiome diversity and composition, reduces pathogenic potential, and may improve clinical outcomes in critically ill sepsis patients after broad-spectrum antibiotics. This study was registered on ClinicalTrials.gov (NCT05578196).},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Probiotics/administration & dosage/therapeutic use
*Fecal Microbiota Transplantation
Pilot Projects
Male
Middle Aged
Female
*Sepsis/therapy/microbiology/drug therapy
*Anti-Bacterial Agents/therapeutic use/adverse effects
Aged
Prospective Studies
Critical Illness
Dysbiosis/therapy
Treatment Outcome
Feces/microbiology
Adult
RNA, Ribosomal, 16S/genetics

@article {pmid42175400,
year = {2026},
author = {Wang, D and Zhang, F},
title = {Associations of bowel movements and stool types with risk of chronic kidney disease.},
journal = {Medicine},
volume = {105},
number = {21},
pages = {e48888},
doi = {10.1097/MD.0000000000048888},
pmid = {42175400},
issn = {1536-5964},
mesh = {Humans ; *Renal Insufficiency, Chronic/epidemiology/etiology/physiopathology ; Female ; Male ; Cross-Sectional Studies ; Middle Aged ; Glomerular Filtration Rate ; Adult ; Aged ; Risk Factors ; Nutrition Surveys ; *Feces ; *Defecation/physiology ; *Diarrhea/complications/epidemiology ; },
abstract = {The gut-kidney axis is increasingly recognized in chronic kidney disease (CKD) pathophysiology. Although stool frequency and consistency reflect gut microbiome status, their association with CKD remains underexplored. This study aimed to examine the relationship between bowel habits and CKD risk. In this cross-sectional analysis of 11,760 adults from National Health and Nutrition Examination Survey 2005 to 2010, stool frequency (weekly) and consistency (Bristol Stool Form Scale) were assessed. CKD was defined as estimated glomerular filtration rate (eGFR) < 60 mL/min/1.73m2 and/or urine albumin-to-creatinine ratio (uACR) ≥ 30 mg/g. Weighted logistic regression adjusted for multiple confounders was used; subgroup and mediation analyses were performed. Diarrhea-like stool (Bristol Stool Form Scale types 6/7) was independently associated with higher CKD risk (odds ratio [OR] = 1.57, 95% confidence interval [CI]: 1.14-2.27), consistent across eGFR < 60 (OR = 1.42, 95% CI: 1.01-1.99) and uACR ≥ 30 mg/g (OR = 1.55, 95% CI: 1.03-2.23). Mediation analysis indicated that systemic inflammation (C-reactive protein) explained 10.1%, 8.5%, and 15.3% of these associations for eGFR decline, elevated uACR, and overall CKD, respectively. Subgroup analyses supported robustness across demographic and clinical strata. Bowel movement frequency was not significantly associated with CKD. Diarrhea-like stool consistency, partly mediated by systemic inflammation, is associated with increased CKD risk.},
}

Humans
*Renal Insufficiency, Chronic/epidemiology/etiology/physiopathology
Female
Male
Cross-Sectional Studies
Middle Aged
Glomerular Filtration Rate
Adult
Aged
Risk Factors
Nutrition Surveys
*Feces
*Defecation/physiology
*Diarrhea/complications/epidemiology

@article {pmid42175487,
year = {2026},
author = {Liu, D and Wu, L and Liu, X and Liu, Z and Kuang, L and Wu, S},
title = {The causal role of skin microbiota in rheumatoid arthritis via gut microbiota and immune cell mediation: A Mendelian randomization study.},
journal = {Medicine},
volume = {105},
number = {21},
pages = {e48847},
doi = {10.1097/MD.0000000000048847},
pmid = {42175487},
issn = {1536-5964},
support = {20231A010042, 20251A010040//Science and Technology Project of Guangzhou Municipal Health Commission/ ; 2023A03J0976, 2023A03J0492,2024A03J0499, 2025A03J3440//Science and Technology Program of Guangzhou City/ ; },
mesh = {Humans ; *Arthritis, Rheumatoid/immunology/microbiology/genetics ; Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/immunology ; *Skin/microbiology/immunology ; *Microbiota/immunology ; Genome-Wide Association Study ; Skin Microbiome ; },
abstract = {Emerging evidence suggests that disturbances in skin microbiota homeostasis may contribute to rheumatoid arthritis (RA) development through systemic immunomodulatory pathways. However, the causal relationships and underlying intermediary mechanisms remain to be clarified. We utilized summary-level data from large-scale genome-wide association studies and the FinnGen database, including 150 skin microbiota taxa, 731 immune cell phenotypes, 473 gut microbiota taxa, and RA cases. Two-sample Mendelian randomization (TSMR) was applied to evaluate potential causal associations with RA. Mediation analysis was further performed to identify the intermediary roles of immune cells and gut microbiota. Multiple sensitivity analyses were conducted to ensure the robustness of the findings. We identified significant causal associations between 6 skin microbiota, 25 immune cell phenotypes, and 19 gut microbiotas with RA. Mediation analysis indicated that certain immune cell traits and gut microbes may act as intermediaries in these relationships. Specifically, 20.3% of the protective effect of phylum Proteobacteria_Dry on RA risk was mediated by species Eubacterium F sp000434115. In contrast, genus Photobacterium accounted for 21.1% of the risk effect mediated by family Micrococcaceae_Dry. Additionally, immune phenotypes such as CD3+ Tregs and CX3CR1+ monocytes partially offset microbial risks, underscoring a novel "skin-gut-immune" axis in RA etiology. This Mendelian randomization study provides robust genetic evidence supporting the causal role of skin microbiota in rheumatoid arthritis pathogenesis via dual mediation pathways involving gut microbiota and immune cells. Our results suggest that targeting the skin and gut microbiota could represent a novel preventive or adjunctive therapeutic strategy for RA. For instance, probiotics or prebiotics aimed at enriching protective taxa (e.g., Proteobacteria, Fournierella massiliensis) or suppressing risk-associated microbes (e.g., Photobacterium, Brachyspira) might help restore immune homeostasis. Additionally, immunomodulatory approaches focusing on Treg enhancement or CX3CR1+ monocyte regulation could be informed by the identified immune phenotypes. Future studies should validate these mechanisms in longitudinal cohorts and explore microbiome-based precision medicine for RA.},
}

Humans
*Arthritis, Rheumatoid/immunology/microbiology/genetics
Mendelian Randomization Analysis
*Gastrointestinal Microbiome/immunology
*Skin/microbiology/immunology
*Microbiota/immunology
Genome-Wide Association Study
Skin Microbiome

@article {pmid42175520,
year = {2026},
author = {Zeng, J and Ding, Z and Dai, Z},
title = {Dietary patterns supportive of gut microbiota and bacterial vaginosis: A cross-sectional analysis from NHANES 2001 to 2004.},
journal = {Medicine},
volume = {105},
number = {21},
pages = {e48863},
doi = {10.1097/MD.0000000000048863},
pmid = {42175520},
issn = {1536-5964},
mesh = {Humans ; Female ; Cross-Sectional Studies ; Adult ; *Vaginosis, Bacterial/epidemiology/microbiology ; Middle Aged ; Nutrition Surveys ; *Gastrointestinal Microbiome/physiology ; Young Adult ; Prevalence ; United States/epidemiology ; *Diet/statistics & numerical data ; },
abstract = {Bacterial vaginosis (BV) is the leading form of vaginal microbiome imbalance in women of reproductive age and has been associated with dietary patterns and gut microbial profiles. This study investigated the association between a literature-based dietary index for gut microbiota (DI-GM) and BV prevalence in US women. We conducted a cross-sectional analysis of 1169 nonpregnant women aged 20 to 49 years from the National Health and Nutrition Examination Survey 2001 to 2004 with Nugent score measurements and complete dietary data. BV was defined as a Nugent score ≥ 7. Dietary intake was assessed via two 24-hour recalls, and DI-GM was computed based on 14 food groups classified as beneficial or unbeneficial for gut microbial health. Multivariable survey-weighted logistic regression models were used to estimate odds ratios and 95% confidence intervals. BV prevalence was 31.2%. Higher DI-GM scores were associated with lower odds of BV; women with scores ≥6 had reduced odds compared with those with scores of 0 to 3 (adjusted odds ratio = 0.75; 95% confidence interval: 0.60-0.94; P = .015; P-trend = .013). In conclusion, higher DI-GM scores were inversely associated with BV prevalence in this cross-sectional study. These findings should be interpreted cautiously, and prospective studies are needed to confirm causality.},
}

Humans
Female
Cross-Sectional Studies
Adult
*Vaginosis, Bacterial/epidemiology/microbiology
Middle Aged
Nutrition Surveys
*Gastrointestinal Microbiome/physiology
Young Adult
Prevalence
United States/epidemiology
*Diet/statistics & numerical data