@article {pmid41764831,
year = {2026},
author = {Peng, X and Zhang, L},
title = {Advances and challenges in the application of metagenomic sequencing for the diagnosis and treatment of infectious diseases: from pathogen spectrum identification to personalized antimicrobial strategies.},
journal = {Diagnostic microbiology and infectious disease},
volume = {115},
number = {2},
pages = {117321},
doi = {10.1016/j.diagmicrobio.2026.117321},
pmid = {41764831},
issn = {1879-0070},
abstract = {Infectious diseases remain a major global public health concern, demanding rapid and accurate identification of pathogens. Although conventional diagnostic methods such as culture, PCR, and immunological assays are widely used, they are limited by long processing times, narrow detection scopes, and poor capability for identifying unknown pathogens. untargeted shotgun metagenomic sequencing (mNGS), as a non-targeted, high-throughput detection technology, enables broad-spectrum identification of diverse microorganisms and functional gene annotation, making it an increasingly important complement in infectious disease diagnostics. This review summarizes the clinical value of mNGS in key scenarios such as neurological, respiratory, and bloodstream infections. It also discusses its utility in antimicrobial resistance (AMR) monitoring and personalized therapy, highlights current challenges in sensitivity, bioinformatics analysis, and result interpretation, and briefly explores future directions involving artificial intelligence (AI), multi-omics integration, and healthcare information system integration. The goal is to provide a reference for the standardized application of mNGS in infectious disease diagnosis and treatment.},
}

@article {pmid41764596,
year = {2026},
author = {Yao, W and Du, H and Kulyar, MF and Pan, H and Ren, H and Luo, Q and Bhutta, ZA and Liu, S and Fang, R and Li, J},
title = {Probiotic efficacy of Bacillus amyloliquefaciens TL106 from Tibetan pigs in metabolic syndrome: modulation of gut microbiota and metabolic in sows and suckling piglets.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02328-y},
pmid = {41764596},
issn = {2049-2618},
abstract = {BACKGROUND: Metabolic syndrome disrupts metabolic resilience in periparturient sows and compromises piglet growth. As intestinal microbes govern host energy homeostasis, microbiome-directed feed additives represent a practical solution. We therefore evaluated the Tibetan‑pig isolate Bacillus amyloliquefaciens TL106, previously validated in weanlings for its capacity to alleviate sow-associated metabolic syndrome.

RESULTS: In a 43‑day trial (20 sows per group), dietary TL106 (5 × 10[9] CFU kg[-1]) increased digestibility of crude fiber (+ 12.5%, p < 0.05) and crude fat (+ 9.3%, p < 0.01), lowered serum IL‑1β (- 34%) and TNF‑α (- 28%), and boosted antioxidant enzymes and immunoglobulins (all p < 0.05). Litter performance improved, with a two‑thirds reduction in diarrhea and heavier piglets at 21 days (+ 15%, aggregate n = 300). Multi‑omics profiling revealed higher cecal α‑diversity, enrichment of butyrate‑producing Ruminococcus and Butyricicoccus (log2C 2.1 and 1.8; FDR < 0.05), and activation of histidine‑metabolism and ABC‑transporter pathways (q ≤ 0.03) in piglets, while pathways for amino‑acid biosynthesis, lipid utilization, and steroidogenesis were favored in sows.

CONCLUSIONS: Bacillus amyloliquefaciens TL106 simultaneously enhanced maternal metabolic health and neonatal development by reshaping gut microbiota and host metabolism, positioning it as a micro‑ecological tool for managing metabolic syndrome in Landrace × Yorkshire sows and Duroc × Landrace × Yorkshire suckling piglets. Video Abstract.},
}

@article {pmid41764594,
year = {2026},
author = {Geng, M and Zheng, Y and Tang, S and Fang, Z and Wang, T and Li, K and Chen, H and Zhang, J and Zhou, N and Wei, X and Yang, J},
title = {Gut T cell-microbiota crosstalk orchestrates antibacterial immunity and mucosal homeostasis in teleost.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02370-4},
pmid = {41764594},
issn = {2049-2618},
support = {2025T180854//China Postdoctoral Science Foundation/ ; 24ZR1419700//Natural Science Foundation of Shanghai Municipality/ ; 32373165//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: T cells cooperate with the intestinal microbiota to coordinate antimicrobial defense, but whether this crosstalk arose as an independent innovation in mammals or represents an evolutionarily conserved feature of vertebrate immunity remains unknown.

RESULTS: Using the teleost Nile tilapia as a model, we demonstrate that both systemic and localized infection with Edwardsiella piscicida induce enteritis, correlated with robust intestinal T cell responses. Selective T cell depletion triggered excessive expression of proinflammatory cytokines, impaired mucosal architecture, and diminished host resistance to infection, underscoring the essential role of T cells in gut immunity. Strikingly, T cell depletion also caused profound alterations in gut microbial composition, characterized by a sharp decline in beneficial taxa such as Cetobacterium and the expansion of opportunistic pathogens including Klebsiella and Acinetobacter, indicating that T cells are required to maintain microbiome homeostasis. Conversely, broad-spectrum antibiotic eradication of the microbiota provoked hyperproliferation of intestinal T cells and barrier disruption, revealing reciprocal regulation between T cells and commensals. From the gut content, we isolated a C. somerae strain SH518, whose dietary supplementation for 6-8 weeks enhanced the activation, proliferation, and effector function of intestinal T cells, preserved mucosal homeostasis during E. piscicida challenge, and even boosted systemic T cell immunity in the spleen.

CONCLUSIONS: Collectively, these findings demonstrate that teleost T cells engage in bidirectional interactions with gut microbiota to orchestrate both antimicrobial defense and mucosal homeostasis. We therefore propose that T cell-microbiota cooperation represents an evolutionarily ancient strategy predates terrestrial adaptation, offering new insights into the coevolution of mucosal T cell immunity and microbiome. Video Abstract.},
}

@article {pmid41764576,
year = {2026},
author = {Li, J and Ren, J and Xu, J and He, J and Xu, J and Yin, Q and Yao, J and Wu, S},
title = {Ability of the Chinese herbal residue to alleviate short-distance transportation stress in sheep through the remodeling of the rumen microbiome-metabolism axis.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {41764576},
issn = {1674-9782},
support = {2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; 32573272//National Natural Science Foundation of China/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; },
abstract = {BACKGROUND: Transportation is a common stressor in sheep production that is capable of inducing oxidative stress and impairing sheep health and production performance. This study aimed to investigate the alleviating effects of the traditional formula Siji Antiviral Mixture residue after water extraction, which still contains active ingredients, including fiber, polyphenols, and flavonoids, on short-distance transport stress in sheep, as well as its mechanism of action in regulating oxidative stress through the rumen microbiota‒metabolism axis.

RESULTS: Twenty first-lambing East Friesian × Hu sheep hybrids weighing 54.49 ± 7.94 kg were randomly assigned to a control group (CON, basal diet) or a Chinese herbal residue group (CMR, basal diet + 50 g/d CMR) feeding at 4 h after approximately 300 km of short-distance transport. Results indicated that 4 h of short-distance transport significantly elevated serum reactive oxygen species (ROS) levels in sheep. Supplementation with Chinese herbal medicine residues markedly reduced serum ROS and lactate dehydrogenase levels while increasing glutathione peroxidase and immunoglobulin G levels. Metagenomic results revealed significantly increased abundance of bacteria such as Selenomonas ruminantium in the rumen of the CMR group, along with substantial increases in CAZymes, including AA7, GH113, and GH84. Metabolomic analysis revealed differentially expressed metabolites in plasma and rumen fluid that were enriched in metabolic pathways such as glycerophospholipid metabolism, α-linolenic acid metabolism, and drug metabolism-cytochrome P450. Correlation network analysis further revealed that Selenomonas ruminantium was significantly negatively correlated with ROS and positively correlated with ruminal LysoPC (16:1(9Z)/0:0), plasma phosphatidylcholine, and key glycerophospholipid metabolism enzymes (e.g., EC 3.1.4.3, PLC). Glycerophospholipid metabolism exhibited synergistic regulatory interactions with arachidonic acid metabolism and drug metabolism-cytochrome P450 pathways.

CONCLUSION: This study confirmed that 4 h of short-distance transport can induce oxidative stress in sheep. Supplementing feed with Siji Antiviral Mixture herbal residue effectively alleviated transport stress and enhanced immune function. The mechanism of action involved rumen microbial conversion of the herbal residue, which substantially increased the abundance of Selenomonas ruminantium. Related metabolites then regulated host arachidonic acid metabolism and cytochrome P450 drug metabolism indirectly through the glycerophospholipid metabolic pathway and the rumen microbiota-metabolism axis, thereby synergistically exerting antioxidant effects.},
}

@article {pmid41764274,
year = {2026},
author = {ElNaggar, S and Chen, WC and Prodehl, LM and Marumo, TK and Khan, MU and Mathew, CG and Ruff, P and Jin, Z and Neugut, AI and Rustgi, AK and Uhlemann, AC and Korem, T and Abrams, JA},
title = {A generalizable cross-continent prediction of esophageal squamous cell carcinoma using the oral microbiome.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-026-01468-y},
pmid = {41764274},
issn = {2730-664X},
abstract = {BACKGROUND: Esophageal squamous cell carcinoma (ESCC) has a poor prognosis and limited tools for early detection. Saliva is easily accessible and its microbiome composition can serve as a marker for upper gastrointestinal tract disease. This study aims to evaluate the potential of an oral microbiome signature for classifying ESCC.

METHODS: In a cross-sectional study of 48 ESCC patients and 110 controls from South Africa, a region with high ESCC incidence, we studied the potential utility of an oral microbiome signature for the disease. We built models using nested cross-validation to evaluate whether this signature is generalizable to held-out samples and further evaluated generalizability in studies from China, a distinct geographic region.

RESULTS: We find significant alterations in the oral microbiome in patients with ESCC including significantly reduced α diversity and increased abundance of Fusobacterium nucleatum. We also find that logistic regression models based on microbiome data can better classify ESCC in held-out samples (auROC=0.96) compared to clinical and demographic data (auROC = 0.69; DeLong p < 1 x 10[-8]). Lastly, we find that microbiome-based models trained across multiple studies can generalize well to geographically distinct studies.

CONCLUSIONS: Our results show that the oral microbiome in individuals with ESCC is distinct from controls and that this signal can generalize across unseen samples, suggesting the potential of saliva to serve as a non-invasive screening tool for ESCC.},
}

@article {pmid41764142,
year = {2026},
author = {Brayley, ODM and McCready, K and Liu, S and Convey, P and Chen, Y and Ullah, S and Teets, N and Hayward, SAL},
title = {The Microbiome of an Invasive Antarctic insect, Eretmoptera Murphyi (Diptera: Chironomidae), and its Potential Role in Nutrient Cycling.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02706-5},
pmid = {41764142},
issn = {1432-184X},
support = {NE/S007350/1//NERC CENTA2/ ; NE/S007350/1//NERC CENTA2/ ; NE/T009446/1//NSFGEO-NERC/ ; NE/T009446/1//NSFGEO-NERC/ ; NE/T009446/1//NSFGEO-NERC/ ; OPP-1850988//National Science Foundation/ ; 700545//USDA National Institute of Food and Agriculture Hatch Project/ ; RF-2024-396/2//Leverhulme Research Fellowship/ ; },
}

@article {pmid41764137,
year = {2026},
author = {Zhao, S and Zou, Y and Wang, Z and Ye, L and Chen, Y and Cao, Z and Xu, X and Gao, A and Ying, X and Chen, M and Qin, K and Zhang, Y and Gu, W and Wang, J and Ning, G and Wang, W and Liu, R and Jin, J and Hong, J},
title = {Gut Microbiota and Bile Acid Profiles as Predictors of PCOS Remission: Findings from a Sleeve Gastrectomy Treatment Study.},
journal = {Obesity surgery},
volume = {},
number = {},
pages = {},
pmid = {41764137},
issn = {1708-0428},
}

@article {pmid41764092,
year = {2026},
author = {Kurbanova, DI and Gurov, AV and Romanenko, SG and Pavlikhin, OG and Lesogorova, EV and Krasilnikova, EN and Zemlyanov, VA and Eliseev, OV and Teplykh, EA and Safyannikova, EA},
title = {[Features of the laryngeal mucosa microbiota in patients with chronic hyperplastic laryngitis (literature review)].},
journal = {Vestnik otorinolaringologii},
volume = {91},
number = {1},
pages = {64-69},
doi = {10.17116/otorino20269101164},
pmid = {41764092},
issn = {0042-4668},
abstract = {The literature review analyzed the data concerning studies of the microbiome of the laryngeal mucosa in patients with chronic hyperplastic laryngitis. It remains a matter of discussion whether the inflammatory process in the larynx is primary with subsequent dysbiosis and excessive growth of pathogenic microorganisms, or whether changes in the structure of the normal microbial landscape become an inducer of the disease. The article reflects the results of basic research on the role of bacterial, fungal, and viral pathogens detected on the mucous membrane of the larynx in patients with chronic hyperplastic laryngitis, conducted by Russian and foreign scientists using various technological approaches.},
}

@article {pmid41764036,
year = {2026},
author = {Salaün, C and Huré, M and Guérin, C and Bôle-Feysot, C and Valentin, A and Léon, F and Lenoir, S and do-Rego, JL and do-Rego, JC and Langlois, L and Ribet, D and Achamrah, N and Coëffier, M},
title = {Intestinal epithelial TLR4 knock out induces sex-specific effects on gut barrier and microbiome in an activity-based anorexia model.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2637316},
doi = {10.1080/19490976.2026.2637316},
pmid = {41764036},
issn = {1949-0984},
abstract = {The role of the microbiota‒gut‒brain axis in the pathophysiology of anorexia nervosa has emerged in recent decades. Increased expression of Toll-like receptor 4 (TLR4) has been reported in the intestinal epithelial cells (IEC) of activity-based anorexia (ABA) mice. The inducible TLR4 knockout in IEC (TLR4[IEC][-/-]) was subsequently associated with behavioral and energy balance changes in ABA mice. Our study aimed to assess the intestinal response to TLR4[IEC][-/-] in both male and female ABA mice by focusing on three components: inflammation, the gut barrier, and the gut microbiota composition. After 12 d of undernutrition with free wheel access, the colonic expression of 43 markers was measured by RT-qPCR. The gut microbiota composition was analyzed by Illumina sequencing of the 16S rRNA gene. First, TLR4[IEC][-/-] was associated with more marked alterations in male control mice compared to females. Indeed, a reduction in the mRNA expression of eight inflammatory factors, seven tight junction proteins and fecal calprotectin levels was observed in males. Control TLR4[IEC][-/-] females showed increased expression of four inflammatory markers and one target involved in the gut barrier. The levels of the Bacillota phylum and the Deltaproteobacteria class and their subdivisions, up to the Desulfovibrio genus, increased in the control TLR4[IEC][-/-] males compared to wt. In females, only an increase in the Alcaligenaceae genus, which ranks from the Betaproteobacteria phylum, was observed. Interestingly, in both males and females, these alterations were not observed in response to ABA model in TLR4[IEC][-/-] mice. Similarly, ABA increased Tjp1 expression and Lactobacillus abundance, both of which were decreased by TLR4[IEC][-/-]. Our study shows for the first time the impact of inducible TLR4[IEC][-/-] on the intestinal response. TLR4[IEC][-/-] induced sex-specific colonic alterations and changes in the gut microbiota, which disappeared after the ABA model. Further studies are warranted to decipher the underlying mechanisms.},
}

@article {pmid41763984,
year = {2026},
author = {Amirsultan, S and Odunayo, A},
title = {From Diagnosis to Resolution: A Practical Guide to Acute Diarrhea in Veterinary Patients.},
journal = {The Veterinary clinics of North America. Small animal practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cvsm.2025.12.003},
pmid = {41763984},
issn = {1878-1306},
abstract = {This review emphasizes that most cases of acute diarrhea (AD) in dogs and cats are self-limiting and primarily managed with supportive care, including hydration and nutrition. Diagnostic testing should be tailored to individual cases, focusing on ruling out systemic illness or infectious causes. Recent evidence advocates against routine antibiotic use in uncomplicated AD to prevent antimicrobial resistance and microbiome disruption. Instead, targeted therapy is reserved for systemic or bacterial infections. Additional treatments such as antiemetics and careful hygiene are discussed. Clinicians should prioritize supportive care and judicious diagnostics, adhering to antimicrobial stewardship principles to optimize patient outcomes and combat resistance.},
}

@article {pmid41763967,
year = {2026},
author = {Boix-Amorós, A and Bu, K and Blank, RB and Cantor, A and Gutiérrez-Casbas, A and Rodríguez-Lago, I and Marin-Jimenez, I and Sanz, J and Masmitja, JG and Trujillo, E and Muñoz, MC and Vivar, MLG and Carrillo, M and Hernández, MVH and Calvet, X and Salaet, MA and Romero, MI and García, AB and Pérez, S and Llorente, JFG and Gonzalez-Lama, Y and Argumánez, CM and Plaza, Z and Domínguez, M and Cañete, JD and Diaz-Gonzalez, JF and Scher, JU and Clemente, JC},
title = {Microbial signatures in psoriatic arthritis distinguish disease phenotypes and newly diagnosed inflammatory bowel disease independent of faecal calprotectin.},
journal = {Annals of the rheumatic diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ard.2026.01.018},
pmid = {41763967},
issn = {1468-2060},
abstract = {OBJECTIVES: There is growing evidence of microbial involvement in immune-mediated inflammatory diseases, including psoriatic arthritis (PsA) and inflammatory bowel disease (IBD). However, it remains unclear whether different PsA phenotypes exhibit distinct microbial profiles. Furthermore, up to 4% of patients with PsA have comorbid IBD, which often remains undiagnosed. We hypothesised that the gut microbiome distinguishes PsA subphenotypes and serves as a biomarker of IBD in patients with PsA independent of faecal calprotectin (fCAL).

METHODS: We obtained samples from 192 patients with axial or peripheral PsA and no prior diagnosis of IBD enrolled in the EISER study. Patients with elevated fCAL and subclinical IBD symptoms underwent colonoscopy with intestinal biopsy. Stool samples were used to measure fCAL, and gut microbiome was characterised using shotgun metagenomics. Serum samples were used for cytokine profiling.

RESULTS: Axial PsA had lower alpha diversity and loss of several commensals compared with peripheral PsA, as well as a depletion of microbial biotin and arginine metabolism and higher levels of IL-23, IL-17F, and IL-8. Five subjects had newly diagnosed IBD which was characterised by a depletion of tryptophan and vitamin B6 metabolism. They also showed significant enrichment of several taxa compared to non-IBD and with a larger effect size than fCAL.

CONCLUSIONS: Our results identify a distinct microbiome and immune profile in axial PsA, with lower microbiome diversity, a depletion of commensals and protective microbial mechanisms, and higher levels of some proinflammatory cytokines. In patients with newly diagnosed IBD, we identified microbial taxa associated with the condition yet independent of fCAL, the current clinical standard.},
}

@article {pmid41763775,
year = {2026},
author = {Li, S and Liu, S and Yu, Y and Huang, X and Yang, M and Tian, L and Zhang, T and Liu, J and Li, Y and Du, Z},
title = {Bifunctional nanoparticles based on esterified hydroxypropyl β-cyclodextrin/quaternary ammonium chitosan for ulcerative colitis intervention.},
journal = {Food research international (Ottawa, Ont.)},
volume = {229},
number = {},
pages = {118450},
doi = {10.1016/j.foodres.2026.118450},
pmid = {41763775},
issn = {1873-7145},
abstract = {Developing oral nanoparticles (NPs) that combine anti-inflammatory effects with gut microbiome modulation enables an effective strategy for integrated ulcerative colitis (UC) therapy. Yet, the complex and dynamically evolving nature of the gastrointestinal milieu presents formidable challenges to the consistency and specificity of NP interventions. To address this challenge, this study designed and developed gastrointestinal microenvironment-adaptive NP via self-assembly, utilizing curcumin (Cur) for anti-inflammatory effects and anthocyanin (Cy) for microbiome regulation to achieve dual functional therapeutic outcomes. Employing the esterification strategy, hydroxypropyl-β-cyclodextrin (HPCD) was modified using citric acid (CA) and sulfonic acid (SA) to synthesize CACD (CA-modified HPCD) and SACD (SA-modified HPCD), respectively, which self-assembled in the presence of quaternary ammonium chitosan (HTCC), Cur, and Cy to yield NPs. NPs demonstrated high Cur encapsulation efficiency (EE) and encapsulation capacity (EC) across pH 2.0-7.0, highlighting their high gastrointestinal adaptability. In vivo experiments showed clear amelioration of colitis symptoms, including downregulation of pro-inflammatory cytokines and attenuation of tissue damage. HTCC-Cy-CACD-Cur NPs enriched Eubacterium siraeum_group and Prevotellaceae, HTCC-Cy-SACD-Cur NPs favored Peptococcus expansion, potentially contributing to improved immune regulation and attenuation of UC. These bifunctional NPs offer innovative UC therapy and precision nutrition interventions.},
}

@article {pmid41763459,
year = {2026},
author = {Xu, X and Wei, X and Yang, X and Lin, S},
title = {Inflammaging in Geriatric Liver Disease: Mechanistic Insights and Therapeutic Frontiers.},
journal = {Mechanisms of ageing and development},
volume = {},
number = {},
pages = {112165},
doi = {10.1016/j.mad.2026.112165},
pmid = {41763459},
issn = {1872-6216},
abstract = {The rising prevalence of chronic liver disease in older adults necessitates a deeper understanding of the mechanisms driving hepatic vulnerability to aging. This review proposes a mechanistic framework positioning hepatic "inflammaging"-a chronic, low-grade inflammatory state-as a key driver of geriatric liver pathology. This review synthesizes evidence linking three interconnected processes: hepatocellular senescence, innate immune dysregulation, and gut-liver axis impairment. Senescent hepatocytes secrete senescence-associated secretory phenotype (SASP) factors that activate Kupffer and stellate cells, forming self-sustaining inflammatory loops. The NLRP3 inflammasome functions as a central integrator of stress and metabolic dysfunction, while age-related intestinal barrier decline continuously supplies inflammatory stimuli such as lipopolysaccharides. These converging pathways perpetuate a pathological hepatic microenvironment characterized by oxidative stress, fibrogenesis, and impaired regeneration. Emerging therapeutics-validated primarily in preclinical murine models-include senolytic CAR-T cells, inflammasome inhibitors, and microbiome-targeted interventions, illustrating the translational potential of this paradigm. However, clinical validation in human cohorts remains a critical next step. This mechanistic framework redefines geriatric liver disease as an active, targetable pathology rather than a passive consequence of chronological aging, highlighting new avenues for precision therapies.},
}

@article {pmid41763351,
year = {2026},
author = {Murillo-Saich, JD and Mannochio-Russo, H and Sala-Climent, M and Argel, N and Quan, A and Hose, MK and Paz-Gonzalez, R and Akkati, M and Chang, E and Cutuk, A and Gentry, E and Coras, R and Lane, NE and Dorrestein, PC and Guma, M},
title = {Potential Role of Bile Acids as a Microbiome-Derived Mechanism in Synovitis of Knee Osteoarthritis Synovitis.},
journal = {Osteoarthritis and cartilage},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joca.2026.02.011},
pmid = {41763351},
issn = {1522-9653},
abstract = {OBJECTIVE: To evaluate the relationship between bile acids (BAs) and synovitis in knee osteoarthritis (KOA).

METHODS: Radiographic KOA patients with complete datasets were included. WOMAC total and subscores were calculated. Synovitis was assessed by ultrasound or Krenn score. BAs were profiled in plasma (N=28) or synovial fluid (SF, N=29) using liquid chromatography-tandem mass spectrometry. OA synovial explants, OA fibroblast-like synoviocytes (FLS), and bone marrow-derived macrophages (BMDM) were used for in vitro experiments. Data analysis was performed using R and MetaboAnalyst.

RESULTS: Sixteen KOA participants had low-grade (0-1) and twelve had high-grade synovitis (2-3). Glycohyodeoxycholic acid (1.198 ± 0.983 vs. 1.954 ± 0.686, 0.76[95% CI: 0.04 to 1.89]) and lithocholic acid (0.19 ± 0.53 vs. 0.825 ± 0.866, 0.63[95% CI: 0.00 to 1.58]) were elevated in subjects with high-grade synovitis. LPS-binding protein (LBP) (rho = 0.58, p = 0.037, [95% CI: -0.807 to 0.46]) correlated with synovitis but only in obese participants (BMI ≥ 30). LBP, lithocholic acid, and glycohyodeoxycholic acid predicted high synovitis (92% sensitivity, 75% specificity, AUC = 0.875[95% CI: 0.99 to 1.05], p < 0.001). In SF, taurodeoxycholic and glycohyodeoxycholic acids correlated positively with WOMAC pain and stiffness subscores and the total WOMAC score. The BA receptors, TGR5 and LXR, were present in synovial tissue. In vitro, BAs reduced cytokine secretion in FLS and BMDM.

CONCLUSION: Detection of BAs and their receptors in synovial tissue, together with their modulatory effects on synovial cells, supports a potential biological role for BAs in KOA.},
}

@article {pmid41763194,
year = {2026},
author = {Chi, F and Han, S and Yilmaz, ÖH},
title = {Purified diets enable experimental rigor through compositional control in animal research.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2026.01.010},
pmid = {41763194},
issn = {1932-7420},
abstract = {Purified diets offer compositionally defined platforms that improve causal inference in nutrition studies. When aligned with the biological question, they enable targeted nutrient loss- and gain-of-function experiments, systematic lipid-source swaps, and the discovery of diet-microbiome-drug interactions. We recommend complementary validation in grain-based chow or human-relevant diets to maximize translational relevance.},
}

@article {pmid41762976,
year = {2026},
author = {Hao, D and Han, H and Li, D and Sun, Y and Wang, Y and Yan, H and Li, G and Liu, H and Li, B and Li, F and Liu, W},
title = {Lactobacillus salivarius SNK-6 improves egg quality, yolk nutrient composition, and yolk flavor profile in laying hens via modulation of tissue metabolites and Cecal microbiomes.},
journal = {Poultry science},
volume = {105},
number = {5},
pages = {106649},
doi = {10.1016/j.psj.2026.106649},
pmid = {41762976},
issn = {1525-3171},
abstract = {This study aimed to investigate the effects of Lactobacillus salivarius SNK-6 (L.a-SNK-6) supplementation on the laying performance, egg quality and yolk nutrition composition, including amino acid (AAs), fatty acids, and flavor profile, of Wenshang Barred hens. A total of 432 healthy 40-week-old hens were randomly assigned to three groups with 6 replicates each: control group (CON), a group supplemented with 2.0 × 10[8] CFU/kg L.a-SNK-6 (T1), and a group supplemented with 2.0 × 10[9] CFU/kg L.a-SNK-6 (T2). Compared with the CON group, both the T1 and T2 groups showed a reduction in the broken egg rate and increases in serum alkaline phosphatase, calcium (Ca) and calcitonin levels (P < 0.05). These groups also exhibited higher Haugh unit, eggshell strength and eggshell Ca content (P < 0.05). Furthermore, egg yolks from the T1 and T2 groups contained higher levels of α-linolenic acid, and oleic acid than those of the CON group. Total AAs content in the egg yolks was markedly elevated in both T1 and T2 groups, particularly the glutamic acid and aspartic acid (P < 0.05). Twenty volatile compounds that differed significantly among the three groups were identified, including d-limonene and β-pinene. Metabolomic analyses revealed 326, 237, and 108 differential metabolites in plasma, liver, and cecal content, respectively, between the T1 and CON group. These metabolites were significantly enriched in the tryptophan metabolism (map00380) pathway in both plasma and cecal content. 16S rRNA sequencing indicated that cecal microbiome diversity and abundance were higher in T1 group compared with the CON group, although the differences were not statistically significant. Combined analysis showed seventy-five host metabolite-microbiota pairs were significantly correlated (P-adjust < 0.05). Collectively, L.a-SNK-6 supplementation modulated metabolites across multiple host tissues and the cecal microbiome, leading to improved egg quality, enhanced yolk nutrient composition, and alterations in yolk volatile compounds.},
}

@article {pmid41762973,
year = {2026},
author = {Vanderghinste, P and Bautil, A and Simmonds, SJ and Apajalahti, J and Bedford, MR and González-Ortiz, G and Courtin, CM},
title = {Extensive particle size reduction of wheat bran increases the broiler's caecal fermentative capacity, but not bran fermentability ex vivo.},
journal = {Poultry science},
volume = {105},
number = {5},
pages = {106695},
doi = {10.1016/j.psj.2026.106695},
pmid = {41762973},
issn = {1525-3171},
abstract = {The inclusion of fibre-rich fractions such as wheat bran in broiler feed can increase the production of short-chain fatty acids (SCFA) in the broiler's gut, improving performance, gut health and immunity. Benefits of fine fibre additions (< 300 µm) on caecal fibre fermentation in broilers have been reported, but it is unclear if further reduction in bran particle size continues to stimulate caecal fermentation, and if the ideal particle size for such fermentation is driven by its effects in the gastrointestinal tract or by microbial size preference. To separate these effects, the caecal inocula of 198 Ross 308 male broilers (d 21 and d 35) which received a 0.5% dietary inclusion of 452 µm bran (WB452), 27 µm bran (WB27) or no bran (control) were combined with the same bran fractions in a 3 × 3 ex vivo fermentation simulation design (n = 8). Gas production, pH, SCFA, branched-chain fatty acid (BCFA) content and total bacteria count were measured to assess the effect of bran particle size on the fermentation of the added bran, the fermentative capacity of the bran-fed caecal inocula and their interaction. Both sizes of added bran increased SCFA content (P < 0.05) and lowered the pH (P < 0.05) and tended to increase SCFA-to-BCFA ratio (P < 0.10) and gas production (P < 0.10), while bran particle size had little effect on these parameters during the ex vivo fermentation. The size of the in vivo-fed bran altered the fermentative capacity of the caecal inocula, based on decreased total gas production (P = 0.010) and increased acetic acid content (P = 0.005) for the WB452-fed inoculum, in contrast to tendencies towards a higher total bacteria count (P = 0.075) and SCFA-to-BCFA ratio (P = 0.059) for the WB27-fed inoculum. This shows that bran size does not directly control microbial fermentation but mainly affects the fibre-fermenting capacity of the caecal inocula through its presence in vivo. The lack of an interaction effect between the bran additions and the bran-fed inocula indicates that bran size does not play a major role in priming the fibre-fermenting microbiome. These results highlight the importance of selecting fibre size in feed additions to stimulate broilers' caecal fibre-fermenting capacity.},
}

@article {pmid41762911,
year = {2026},
author = {Abdel Jaleel, GA and Ammar, NM and Shabaan, A and El Hotaby, W and Elshamy, AI and El-Gendy, ZA},
title = {Metabolite-rich Saccharomyces cerevisiae cell wall extract counter diabetic tissue damage via AMPK activation and microbiome modulation in rats.},
journal = {Tissue & cell},
volume = {101},
number = {},
pages = {103414},
doi = {10.1016/j.tice.2026.103414},
pmid = {41762911},
issn = {1532-3072},
abstract = {Saccharomyces cerevisiae cell wall extract (SCCWE) contains a variety of bioactive compounds, yet its antidiabetic action mechanisms remain unclear. The current work aimed to characterize the chemical components using GC-MS of SCCWE along with its antidiabetic, hepatoprotective, antioxidant, and microbiome-modulating properties in streptozotocin (STZ)-induced diabetic rats. The rats were treated with glibenclamide, SCCWE (25, 50, or 100 mg/kg), or non-diabetic normal rats as a control. Key regulators (P-AMPK, HMGR, SREBP-1c, and LXRα) as well as metabolic parameters, oxidative and inflammatory indicators, and histopathology and FTIR analysis were evaluated. Trehalose (16.03%), turanose (15.05%), glycerol (12.24%), and mannobiose (7.38%) were found to be the primary constituents by GC-MS profiling. STZ elevated fasting glucose 1.5-fold and reduced lactic acid bacteria 6.6-fold. SCCWE lowered glucose by 27.4-30.4% and restored lactic acid bacteria by 266.7-711.6%. Serum ALT, increased 2.1-fold in diabetic rats, decreased by 35.3-55.6% with SCCWE. Dyslipidemia improved markedly, with total lipids, cholesterol, and triglycerides reduced by up to 45.6%, 63.9%, and 46%. SCCWE decreased hepatic MDA by 56.5% and increased GSH up to 607.2%. It elevated P-AMPK while suppressing HMGR (18.9-154.6%), SREBP-1c (29.7-92.6%), and LXRα mRNA (21.3-87.6%). Histopathology and FTIR confirmed tissue and membrane restoration. SCCWE demonstrates potent antidiabetic and hepatoprotective activities, supporting its potential as a natural therapeutic for diabetes.},
}

@article {pmid41762838,
year = {2026},
author = {Li, D and Diao, Z and Shu, A and Gan, S and Zhang, W and Zhang, Y and Xiong, L and Wei, D and He, L and Shi, W and Sun, G and Yuan, F and Liu, Z and Gao, Z},
title = {Deinococcus sp. NH1 enhances cadmium tolerance in rice by modulating rhizosphere microbiome and plant metabolism.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141623},
doi = {10.1016/j.jhazmat.2026.141623},
pmid = {41762838},
issn = {1873-3336},
abstract = {Cadmium stress threatens rice safety and farmland management. To investigate the role of high‑cadmium‑tolerant Deinococcus in alleviating plant cadmium stress, this study identified a strain, Deinococcus sp. NH1, with highly cadmium-tolerant and growth-promoting potential, via 16S rRNA gene sequencing and whole-genome average nucleotide identity analysis. Under cadmium stress conditions, inoculation with NH1 significantly alleviated growth inhibition in rice, resulting in notable increases in plant height, fresh weight, and root density. In soil containing 10 mg/kg cadmium, NH1 inoculation downregulated originally elevated genes related to cadmium detoxification and stress response, while upregulating biosynthesis and energy metabolism genes. Cadmium reduced rhizobacterial diversity, but NH1 restored diversity and induced community restructuring, significantly enriching beneficial microorganisms, such as Massilia and Haliangium. At the metabolic level, NH1 treatment altered the rhizosphere metabolome, in which terpenoids, and shikimates and phenylpropanoids such as 5-O-methylembelin and linoleate that showed significant positive correlations with the enriched microorganisms may play key roles. In summary, NH1 enhances rice tolerance to cadmium stress by regulating host gene expression, restoring and reshaping the rhizosphere microbial community structure, and driving beneficial microbe‑metabolite interactions. This study offers new insights into plant-microbe interactions in heavy metal stress mitigation.},
}

@article {pmid41762502,
year = {2026},
author = {Lei, J and Wu, Z and Liu, Z and Yang, R and Cheng, L and Wang, J and Liu, Y and Chen, R},
title = {Predicting aerobic granular sludge structural instability: An intelligent early-warning framework integrating convolutional neural network and fluorescence fingerprint features.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129115},
doi = {10.1016/j.jenvman.2026.129115},
pmid = {41762502},
issn = {1095-8630},
abstract = {Aerobic granular sludge (AGS) was recognized as an innovative alternative superior to activated sludge processes, yet its development has been constrained by structural instability and the lack of early-warning methods for critical states. To address this limitation, an intelligent early-warning model (EPS-ResNet) based on multi-view convolutional neural networks was developed. This model achieved a 6±1-day advance prediction of AGS structural destabilization (accuracy:97.6%) by analyzing fluorescence characteristics in Excitation-Emission-Matrix Spectra (EEMs) of loosely/tightly bound extracellular polymeric substances (LB-EPS/TB-EPS). Through occlusion sensitivity analysis and fluorescence region segmentation, Region I (tyrosine-like proteins) of TB-EPS, Region IV (soluble microbial metabolites) of TB-EPS, and Region IV of LB-EPS were identified as the top three contributors to early-warning efficacy. Integrated microbiome analysis revealed that the superior early-warning performance of the model was primarily attributed to the capacity of key EEMs regions (I, IV, and V) of EPS to sensitively capture dynamic succession of dominant phyla and functional genera in AGS following shocks. Correlation analysis conducted through the Mantel test demonstrated that key dominant phyla responding to the model included Bacteroidota and Patescibacteria, while critical functional genera comprised Flavobacterium, Pseudazoarcus, Thauera, and Candidatus_Competibacter. An early-warning framework for abnormal states of AGS integrating scalability and mechanistic interpretation was developed in this study. This framework was demonstrated to be applicable not only for the early warning of AGS structural destabilization, but also extensible to the early detection of anomalies in biological treatment systems, thereby promoting the transformation of water treatment process operation and maintenance toward digitalization and intelligentization.},
}

@article {pmid41762333,
year = {2026},
author = {Pavan, JS and Deeksha, PM and Rajarushi, CN and Paschapur, AU and Rishika, KS and Ramakrishnan, B and Subramanian, S},
title = {Gut microbiota-mediated nitrogen recycling in the white Grub Holotrichia longipennis: A model for microbiome-targeted pest control.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {3},
pages = {},
pmid = {41762333},
issn = {1573-0972},
}

@article {pmid41762294,
year = {2026},
author = {Joda, JF and Raji, RO and Nmadu, ME and Oyewole, OA},
title = {The Interactions of Emergent Contaminants (ECs) with Soil Microbiome.},
journal = {Ecotoxicology (London, England)},
volume = {35},
number = {4},
pages = {},
pmid = {41762294},
issn = {1573-3017},
}

@article {pmid41762172,
year = {2026},
author = {Ghahari, AA and Nourizadeh, M and SalekShahabi, M and Davari, S and Mohammadzadeh Mounesyar, S},
title = {Psychobiotics and the microbiota-gut-brain axis: Emerging paradigms in mental health modulation.},
journal = {Experimental physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/EP093301},
pmid = {41762172},
issn = {1469-445X},
abstract = {The global rise in mental health conditions has prompted interest in interventions that act beyond conventional psychopharmacology. Psychobiotics, broadly understood as live microorganisms or microbe-derived products that interact with the microbiota-gut-brain axis, have been suggested to exert neuroactive effects through neural, immune, endocrine and metabolic routes. This narrative review synthesizes recent preclinical, mechanistic and early clinical observations. Experimental studies show that selected strains can modulate cytokine signalling, influence stress-responsive systems such as the hypothalamic-pituitary-adrenal axis, and support synaptic plasticity via factors such as brain-derived neurotrophic factor. A limited number of human trials using well-characterized Lactobacillus and Bifidobacterium strains have reported improvements in affective and stress-related outcomes, but these effects are generally small to moderate, more apparent in adjunctive than stand-alone use, and dependent on strain, dose, population and intervention length (typically 4-12 weeks). Evidence on neurodevelopmental conditions (e.g., autism spectrum disorder, attention-deficit/hyperactivity disorder) remains preliminary, based on small and heterogeneous samples. Across studies, key constraints include methodological heterogeneity, incomplete strain-level reporting, and gaps in mechanistic resolution that make it difficult to link microbial shifts to psychiatric benefit. Emerging microbiome- and metabolomics-informed approaches may help identify likely responders and improve translational precision, but they are not yet ready for routine clinical application. Overall, psychobiotics should currently be viewed as a promising adjunct within integrative mental health care, warranting larger, standardized trials with clearly defined strains, doses and mechanistic endpoints.},
}

@article {pmid41762163,
year = {2026},
author = {Lu, Y and Nguyen, KN and Xia, J},
title = {Interpreting Microbiome Signatures with MicrobiomeNet.},
journal = {Current protocols},
volume = {6},
number = {3},
pages = {e70338},
pmid = {41762163},
issn = {2691-1299},
abstract = {MicrobiomeNet (https://microbiomenet.com) is a web-based platform developed to provide functional insights into microbiome signatures using genome-scale metabolic models (GEMs). It currently hosts 12,400 GEMs and around 6 million microbial signatures. Users can start by searching microbes, metabolites, genes, or enzymes, and perform common tasks such as to characterize the metabolic capacity for a given microbe, to explore known microbial associations, as well as to understand potential metabolic interactions. This book chapter provides practical, step-by-step instructions for navigating MicrobiomeNet to obtain functional insights into individual microbes or microbial association networks. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Characterizing the Metabolic Profile of a Microbe of Interest Basic Protocol 2: Elucidating Metabolic Interactions from Microbial Associations Basic Protocol 3: Analyzing Carbohydrate-Utilization Pathways to Explain Co-Responsive Taxa Basic Protocol 4: Identifying Novel Deoxycholic Acid-Producing Gut Microbes Basic Protocol 5: Assessing the Faecalibacterium prausnitzii-Coprococcus Relationship.},
}

@article {pmid41762159,
year = {2026},
author = {Zhang, Y and Liu, Q and Jing, L and Li, D},
title = {Suppressive microbiome protects against mulberry wilt by safeguarding host glycosylphosphatidylinositol-anchor biosynthesis.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag060},
pmid = {41762159},
issn = {1365-2672},
abstract = {AIMS: Soil-borne pathogens pose a significant threat to global agriculture. While certain soils naturally suppress disease, the complex interplay between different microbial kingdoms and their metabolic functions in orchestrating this suppression remains poorly understood.

METHODS AND RESULTS: We integrated 16S/ITS/18S rRNA amplicon sequencing with non-targeted LC-MS/MS metabolomics to elucidate the multi-kingdom microbial drivers and metabolic profiles of rhizosphere soils from healthy (HS) and diseased (DS) mulberry (Morus alba L.) orchards. The HS orchard, under long-term organic fertilization, exhibited strong disease suppression (12% incidence), whereas the DS orchard, under chemical fertilization, was highly susceptible (85% incidence) to wilt disease. The HS soils harbored a more complex and stable microbial co-occurrence network. This community was significantly enriched in putative beneficial taxa, including the bacteria Stenotrophomonas and Pseudomonas, the fungus Mortierella, and the predatory protist Colpoda. In contrast, the pathogen Fusarium was enriched in DS soils. Functional profiling predicted that the HS microbiome possessed a higher potential for antibiotic biosynthesis and stress tolerance. Metabolomic analysis revealed a striking divergence in metabolic pathways. Diseased plants mounted a massive but ineffective defense, characterized by the accumulation of phytoalexins. We identified a significant downregulation of the glycosylphosphatidylinositol-anchor biosynthesis pathway in DS soils, a fundamental process for anchoring functional proteins to the plant cell surface.

CONCLUSIONS: Our findings reveal a novel pathogenic strategy of targeting host cell-surface architecture and the corresponding community-level defense mechanism.},
}

@article {pmid41761982,
year = {2026},
author = {Yan, L and Hu, J and Feng, Q and Sun, J and Huang, X and Xu, C},
title = {A Unique Perspective on Auto-reactive Antibody Production in Autoimmune Disease Induced by Microbiome.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {2},
pages = {45424},
doi = {10.31083/FBL45424},
pmid = {41761982},
issn = {2768-6698},
support = {2023-JC-QN-0855//Natural Science Basic Research Program of Shaanxi/ ; 2021JY-17//Shaanxi Provincial People's Hospital Science and Technology Talent Support Program Project/ ; },
abstract = {Activation of autoreactive lymphocytes leads to cellular and tissue damage, which results in the development of autoimmune diseases. External environmental changes, such as chronic microbial infections, can alter the immune homeostasis and disrupt the balance of autoreactive T and B cells. In this review, we first summarize immune tolerance mechanisms of T and B cells, and then describe the breakthroughs of immune tolerance in T and B cells, followed by related autoimmune diseases. Furthermore, we explore how microbial infections can induce the production of autoreactive antibodies via carrier effects when the balance of autoreactive T and B cells is disrupted. These kinds of antibodies can lead to autoimmune diseases through molecular mimicry mechanisms. Our perspective provides a theoretical framework and novel insights into the mechanism of autoreactive antibodies in the pathogenesis of autoimmune diseases associated with microbial infections. This analysis may offer novel directions for drug discovery of autoimmune diseases.},
}

@article {pmid41761881,
year = {2026},
author = {Jin, X and Luo, X and Shen, W and Lv, G and Jiang, X and Jin, C and Feng, B and Che, L and Xu, S and Lin, Y and Zhuo, Y and Wu, D and Hua, L},
title = {Nicotinamide Riboside Alleviates Heat Stress-Induced Intestinal Dysfunction by Enhancing Antioxidant Capacity, Restoring Immune Homeostasis, and Modulating Gut Microbiota in a Boar Model.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {5},
pages = {e70418},
doi = {10.1002/mnfr.70418},
pmid = {41761881},
issn = {1613-4133},
support = {2023YFD1300804/5//National Key R&D Program of China/ ; NCTIP XD/B04//Strategic Priority Research Program of the National Center of Technology Innovation for Pigs/ ; 32472948//National Natural Science Foundation of China/ ; U21A20255//National Natural Science Foundation of China/ ; 2023NSFSC1139//Sichuan Science and Technology Program/ ; CARS-35//earmarked fund for China Agriculture Research System/ ; },
abstract = {Heat stress (HS) induces adverse intestinal effects, including morphological damage, immune dysfunction, and microbial dysbiosis. Nicotinamide riboside (NR) supplementation has shown promise in protecting against intestinal injury. This study aimed to investigate the efficacy of NR in alleviating HS-induced intestinal damage in a porcine model. Eighteen boars were randomized into three groups (n = 6): control (CON, thermoneutral), heat stress (HS), and HS with NR supplementation (HS-NR). After an initial feeding phase, the HS and HS-NR groups were exposed to an HS environment (35 ± 1°C) for 2 weeks, while the CON group remained thermoneutral. Intestinal injury was assessed via histomorphology, biochemical parameters, transcriptomics, and microbiome sequencing. We found that NR supplementation significantly restored intestinal morphology and attenuated colonic oxidative stress compared to the HS group. Moreover, NR ameliorated HS-induced immune dysfunction and corrected gut microbial dysbiosis. These results suggest the therapeutic potential of NR as a nutritional intervention to mitigate HS-induced intestinal damage.},
}

@article {pmid41761700,
year = {2026},
author = {Pepke, ML and Hansen, SB and Limborg, MT},
title = {The ageing holobiont: crosstalk between telomere dynamics, oxidative stress and the gut microbiome.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {},
number = {},
pages = {},
doi = {10.1002/brv.70152},
pmid = {41761700},
issn = {1469-185X},
support = {DNRF143//Danmarks Grundforskningsfond/ ; CF21-0356//Carlsbergfondet/ ; },
abstract = {The gut tissue is at the frontline of early onset of ageing. It exhibits high cell turnover rates and rapid telomere shortening, which can have systemic effects on the developing or senescing organism. We conducted a literature review of studies on the crosstalk between telomere length dynamics, telomerase activity, oxidative stress, and gut microbiota composition and activity in animals. Studies mainly on humans and animal models include correlations between telomere dynamics and gut microbiome components, particularly under pathogenic conditions, but also manipulations of either the gut microbiome through faecal microbiota transplantations or of telomere dynamics using telomerase knockout models. This synthesis reveals that components of the gut microbiome including microbial metabolites and pathogenic bacteria can affect telomere dynamics through oxidative-stress-inducing processes, and that telomere maintenance is critical in maintaining gut barrier and tissue integrity, which link inflammation and gut dysbiosis. Some of the interactions between the gut microbiome and host telomere dynamics are bidirectional and important in maintaining intestinal homeostasis. However, many of the causal molecular or cellular mechanisms - and how they translate into organismal senescence - remain to be identified. Furthermore, we highlight how recent advances in whole genome sequencing capacities and bioinformatic tools represent an often-unexploited resource for measuring telomere lengths and may be particularly valuable tools within the hologenomic framework outlined here. Investigating the role of telomere dynamics in mediating gut microbiota-host interactions in different species will improve our understanding of how crosstalk between these hallmarks of ageing shape holobiont physiology in general and the ageing phenotype in particular.},
}

@article {pmid41761590,
year = {2026},
author = {Matera, MG and Calzetta, L and De Biase, A and Parente, V and Cazzola, M},
title = {Emerging pharmacotherapies in chronic rhinosinusitis with nasal polyps.},
journal = {Expert opinion on pharmacotherapy},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/14656566.2026.2638480},
pmid = {41761590},
issn = {1744-7666},
abstract = {INTRODUCTION: Chronic rhinosinusitis with nasal polyps (CRSwNP) is a chronic, heterogeneous inflammatory disorder of the sinonasal mucosa that substantially impairs quality of life. It is characterized by T2 or non-T2 inflammatory endotypes and often coexists with asthma or aspirin-exacerbated respiratory disease, complicating management due to high recurrence rates and limited disease-modifying options.

AREAS COVERED: This review evaluates emerging pharmacotherapies for CRSwNP, emphasizing targeted biologics developed from mechanistic understanding of inflammatory pathways. Approved monoclonal antibodies, dupilumab, omalizumab, and mepolizumab, are discussed regarding their effects on nasal polyp size, symptom relief, and patient-reported outcomes, with reference to comparative efficacy and safety. Evidence is drawn from RCTs, meta-analyses, and real-world studies, highlighting both clinical benefits and current limitations. Emerging therapies targeting upstream epithelial cytokines (TSLP, IL-33) and complementary strategies, including small-molecule inhibitors, microbiome modulation, and advanced topical delivery systems, are also addressed.

EXPERT OPINION: Biologics have transformed CRSwNP treatment, but challenges remain in cost, treatment duration, and patient selection. Integrating endotype characterization, biomarkers, and comparative effectiveness data is crucial for personalized management. Future advances are expected from upstream immune modulation, restoration of epithelial barrier integrity, and optimized local drug delivery, enabling mechanism-based, adaptive approaches that maximize efficacy while minimizing systemic exposure.},
}

@article {pmid41761576,
year = {2026},
author = {Amancio, BR and Magnani, E and T Nunes, A and Silva, TH and Cortinhas, C and Carvalho, VV and Tamassia, LFM and Zihlmann, R and Berndt, A and Marcatto, JOS and Consolo, NRB and Benedeti, PDB and Branco, RH and Paula, EM},
title = {Effect of two-doses of 3-Nitrooxypropanol (3-NOP) on methane emissions, performance, rumen microbiome, and metabolomics in Nellore cattle.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag068},
pmid = {41761576},
issn = {1525-3163},
abstract = {This study evaluated the effects of two doses of 3-nitrooxypropanol (3-NOP) on methane (CH4) emissions, performance, dry matter (DM) intake, apparent digestibility, rumen microbiome and metabolomic profile of Nellore cattle fed a high concentrate finishing finishing diet. Seventy-five 20-month-old Nellore bulls, 361.6 ± 30.08 kg body weight (BW) were individually housed with ad libitum access to feed and water. Animals were distributed in a completely randomized study design, with three treatments and 25 animals per treatment, which were: 1) CON, control (basal diet + mineral premix without 3-NOP), 2) 3-NOP65 (Basal diet + mineral premix + 65 mg 3-NOP/kg of DM), 3) 3-NOP85 (Basal diet + mineral premix + 85 mg 3-NOP/kg of DM). The 115-day trial included a 3-week adaptation period with increasing dietary concentrate levels from 50% to 88%. Enteric CH4 emissions were measured using the sulfur hexafluoride (SF6) tracer gas technique. Supplementation with 3-NOP had no detrimental effect on final BW (P = 0.89) and average daily gain (ADG; P = 0.94), but DM intake increased linearly with 3-NOP inclusion (P = 0.05). Methane emissions (g/d) were reduced by 13.2% and 26.7% in the 3-NOP65 and 3-NOP85 groups, respectively (P < 0.05), without adverse effects on animal health. Rumen microbiome analysis revealed a quadratic response in the relative abundance of the phylum Euryarchaeota (P = 0.01). Metabolomic analysis indicated significant changes in amino acid and energy metabolism, with proline, arginine, and threonine identified as key discriminant metabolites (VIP > 1) in the 3-NOP85 group. These findings demonstrate that 3-NOP supplementation effectively reduces CH4 emissions in a dose-dependent manner, while maintaining animal performance and health.},
}

@article {pmid41761296,
year = {2026},
author = {Ye, H and Yang, X and Zheng, M and Dong, W and Chen, X and Chen, J and Hu, M and Zhou, M and Zheng, P and Shen, L and Wu, Y and Zheng, K and Huang, XF and Yu, Y},
title = {Early risperidone exposure impairs cognitive function by perturbation of the gut microbiome and bile acids/tyrosine-PTP1B axis.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02358-0},
pmid = {41761296},
issn = {2049-2618},
abstract = {BACKGROUND: Second-generation antipsychotics (SGAs) are increasingly being utilized in children and adolescents. Risperidone, one of the most commonly prescribed SGAs in this population, has been found to adversely affect cognitive function; however, limited knowledge exists regarding the impact of risperidone on the gut microbiome-brain axis. We hypothesized that the cognitive impairment induced by risperidone is mediated by alterations in the gut microbiome and its metabolites.

RESULTS: In this study, we found that early-life risperidone exposure impaired cognition in mice, including deficits in behavior tests and hippocampal dendritic architecture. The risperidone-exposed mice also exhibited gut microbiota dysbiosis along with damage to the intestinal barrier. Fecal microbiota transplantation (FMT) from treated donors to recipients demonstrated the causal role of the gut microbiome in risperidone-induced cognitive deficits. Of note, risperidone increased the abundance of species Escherichia coli, Eggerthella lenta, Ruminococcus gnavus, Clostridium perfringens, Clostridium difficile, and Blautia hydrogenotrophica. These altered species are identified to encode 7α-HSDH, 3β/α-HSDH, TyrB, and porA, the key enzymes in secondary bile acid metabolism and tyrosine metabolism. Furthermore, a significant reduction in tauroursodeoxycholic acid (TUDCA, the metabolite of bile acid metabolism) and accumulation of p-cresol (the metabolite of tyrosine metabolism) were observed in the brains of mice exposed to risperidone. Mechanically, TUDCA prevented cognitive impairment and endoplasmic reticulum (ER) stress in the hippocampus induced by risperidone, while p-cresol induced neuronal ER stress. Knockout of protein tyrosine phosphatase 1B (PTP1B, ER stress-associated protein) in neurons ameliorated cognitive impairment and neurological damage induced by risperidone.

CONCLUSIONS: This study, for the first time, reveals that early risperidone exposure induces gut microbiome dysbiosis and disturbs the bile acids/tyrosine-PTP1B axis to impair cognitive function. These findings alert the risk of gut and neurological side effects of SGAs treatment and highlight that it is crucial to maintain gut homeostasis during the brain developmental phases of children and adolescents with SGAs exposure. Video Abstract.},
}

@article {pmid41761226,
year = {2026},
author = {Zhao, X and Weng, Y and Huang, R and Hu, Y},
title = {From mouth to muscle: mechanistic and interventional perspectives on the tongue-coating microbiome in sarcopenia.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-07874-z},
pmid = {41761226},
issn = {1479-5876},
support = {U22A20287; 82571011//National Natural Science Foundation of China/ ; 202140058//Shanghai Municipal Health Commission/ ; 202240042//Shanghai Municipal Health Commission/ ; },
abstract = {BACKGROUND: Sarcopenia, the progressive loss of skeletal muscle mass and function, needs upstream, low-burden tools for early detection and high-frequency monitoring, especially in older adults. Conventional assessments such as handgrip strength and gait speed mainly capture downstream impairment and may miss early physiological change. The tongue-coating microbiome is an emerging, measurable niche on the oral-gut-muscle axis that may provide proximal signals of metabolic, inflammatory, and circadian status.

METHODS: We performed a narrative summary of recent evidence on tongue-gut coupling, mapped plausible mechanisms to muscle regulation, and evaluated the feasibility of tongue-based measurement. We propose a minimal methods set (fixed pre-breakfast sampling, strict low-biomass quality control, AI-assisted standardized tongue imaging, saliva assays integrated with multi-omics) and a three-tier metric structure aligned to the minimal clinically important difference (MCID) for functional endpoints.

RESULTS: Evidence supports links across three axes: metabolic (microbial metabolites such as short-chain fatty acids and niacin that modulate mitochondrial energetics and anabolism), inflammatory (oral dysbiosis and barrier disruption amplifying systemic inflammation via lipopolysaccharide, Toll-like receptor 4, and NF-κB signaling), and circadian (microbiome rhythms coupled to eating and sleep timing). The tongue coating forms a stable niche suitable for frequent follow-up. An upstream-midstream-downstream metric stack enables MCID-anchored interpretation. Current data are limited and heterogeneous, so tongue-derived metrics should complement stool testing and functional standards.

CONCLUSIONS: Tongue-based monitoring is a practical adjunct for earlier risk signaling and community-level follow-up. Priorities are multicenter validation, interpretable and device agnostic models, and axis-stratified trials to define when and for whom tongue-derived signals add MCID-level clinical value. Because direct longitudinal human evidence linking tongue-coating signals to clinically meaningful sarcopenia outcomes remains limited, we frame the tongue-coating microbiome primarily as a hypothesis-driven, upstream monitoring niche and outline testable priorities for validation and translation.},
}

@article {pmid41761093,
year = {2026},
author = {Qureshi, A and Wahid, A and Qazi, S and Shahzad, MK and Kiani, HM and Asif, MDA},
title = {DynaBiome: interpretable unsupervised learning of gut microbiome dysbiosis via temporal deep models.},
journal = {BMC bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12859-026-06400-8},
pmid = {41761093},
issn = {1471-2105},
}

@article {pmid41760891,
year = {2026},
author = {Song, B and Zeb, J and Sparagano, OA},
title = {Reactive oxygen species-producing genes regulate mosquito midgut bacteria colonization, transcriptomic changes and cell repair.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {41760891},
issn = {2399-3642},
abstract = {The mosquito midgut uses ROS (Reactive Oxygen Species)-producing pathway to control midgut bacteria and maintain cell regeneration. However, it is not clear what are the functional and mechanistic differences between the two components, NOX (NADPH oxidase) and DUOX (Dual Oxidase) enzymes. In this study, we characterize the different roles of Nox and Duox gene in eliminating ECC15 (Erwinia carotovora 15) after oral infection and controlling the microbiome by counting CFU (Colony-forming unit) and 16S rRNA sequencing after RNA interference-mediated knockdown. We also determined the different transcriptomic changes by RNA-sequencing and cell regeneration by immunostaining after knocking down the genes upon ECC15 infection. Here, we report that Nox but not Duox was necessary for eliminating ECC15 and suppressed more rare species in the microbiome. Transcriptionally, we found that Nox controls more gene responses than Duox upon ECC15 infection; the heat shock protein pathway may be the main stress pathway induced by ECC15 that discriminates Nox (highly-related) and Duox. The MAPK pathway was robustly induced in control (LacZ) and Duox-knockdown mosquitoes, but not in Nox-knockdown mosquitoes. AMP gene induction was also suppressed only in Nox-knockdown mosquitoes. We also found that ECC15 infection induced strong cell regeneration, while Nox RNAi suppressed it strongly. Although, Duox was highly related to metalloexopeptidase activity genes comparing to Nox.},
}

@article {pmid41760847,
year = {2026},
author = {Eilers, T and Delanghe, L and De Boeck, I and Van Rillaer, T and Van Malderen, J and Bakelants, S and Van Beeck, W and Wittouck, S and Lebeer, S},
title = {Pangenome-based design of strain-specific primers enables precise monitoring of bacteria in human microbiome intervention trials.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-41449-8},
pmid = {41760847},
issn = {2045-2322},
support = {HBC.2022.1000//Agentschap Innoveren en Ondernemen/ ; HBC.2020.2873//Agentschap Innoveren en Ondernemen/ ; 12S4222N//Fonds Wetenschappelijk Onderzoek/ ; 1S08523N//Fonds Wetenschappelijk Onderzoek/ ; 1224923N//Fonds Wetenschappelijk Onderzoek/ ; 12AZ624N//Fonds Wetenschappelijk Onderzoek/ ; 852600//Horizon 2020 Framework Programme/ ; },
}

@article {pmid41760690,
year = {2026},
author = {Sammons, SL and Kuntz, TM and DiLullo, M and Morgan, XC and Martin, A and Hughes, ME and Rahman, T and Barroso-Sousa, R and Ogayo, ER and Giordano, J and Ryan, S and Waks, AG and Schlam, I and Ligibel, J and Lin, NU and Garrido-Castro, AC and Mittendorf, EA and Tolaney, SM},
title = {The landscape of the intestinal microbiome among patients with newly diagnosed invasive breast cancer and ductal carcinoma in situ (DCIS).},
journal = {NPJ breast cancer},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41523-026-00922-3},
pmid = {41760690},
issn = {2374-4677},
support = {P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; Dana-Farber Cancer Institute project number 6395601//Massachusetts Life Sciences Center/ ; },
abstract = {The intestinal microbiome shapes immune responses and is associated with patient outcomes in cancer following immunotherapy. We evaluated differences between the intestinal microbiome profiles of patients with early-stage invasive breast cancer (BC) and ductal carcinoma in situ (DCIS) by subtype using whole genome metagenomic sequencing. There were no significant differences in microbiome composition between DCIS and invasive BC as measured by alpha diversity (p = 0.20, ANOVA) or beta diversity (p = 0.52, PERMANOVA). Within invasive BC, patients with hormone receptor-positive (HR +)/HER2 + BC differed significantly in beta diversity relative to other subtypes (p < 0.05), with differences in six species (q < 0.25). Bacteroides ovatus was significantly more abundant in patients with stage III BC vs. stage I (p = 0.0003). Functional pathway analysis using HUMAnN3 revealed stage-specific enrichment of amino acid biosynthesis and nucleotide-related pathways. Altogether, these findings highlight potential microbial signatures associated with BC subtype and stage.},
}

@article {pmid41760491,
year = {2026},
author = {Fu, X and Jang, YF and Dang, D and Hu, X and Wu, H},
title = {Decrease in intestinal microbiome diversity at birth is related to moderate and severe bronchopulmonary dysplasia in premature infants.},
journal = {Pediatrics and neonatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pedneo.2025.03.012},
pmid = {41760491},
issn = {2212-1692},
abstract = {BACKGROUND: Bronchopulmonary dysplasia (BPD) is a prevalent respiratory disorder in premature infants. Recent studies have revealed an association between the intestinal microbiome and respiratory diseases. This study aims to explore the characteristics of the gut microbiome of premature infants with moderate and severe BPD.

METHODS: The study population consisted of preterm infants with a gestational age of ≤34 weeks. Infants with moderate and severe BPD were selected as the case group. Stool samples were collected at birth and 28 days after delivery. The obtained samples were processed using 16sRNA technology for diversity analysis, taxonomic composition, and LEfSe analysis.

RESULTS: In this study, 15 infants were enrolled in the BPD group, while 15 infants were included as controls. At birth, the alpha diversity of the BPD group was significantly lower compared to the control group. Infants with severe BPD had even lower diversity. The relative abundance of Staphylococcus in the BPD group was higher, whereas Sphingomonas and Veillonella were the predominant species in the control group. Additionally, the severe BPD group exhibited a higher abundance of Bacillales and Oscillospiraceae compared to the moderate BPD group. At 28 days after birth, there was an increase in the abundance of Escherichia, Klebsiella, and Bifidobacterium compared with previous levels, and a decrease in the abundance of Herbaspirillum.

CONCLUSIONS: The diversity of intestinal microbiota in infants with moderate and severe BPD appears to be relatively lower, and specific microbial species such as Staphylococcus and Bacillales may contribute to the pathogenesis and progression of BPD. The intestinal microbiota in infants with BPD interacts with the oxygen environment in the gut, and its early formation is influenced by maternal factors. These findings regarding the diversity and specific flora of gut microbiota could potentially offer insights into the pathogenesis of BPD.},
}

@article {pmid41759957,
year = {2026},
author = {Pinar, I and Nielsen, TSS and Brach, T and Moll, JM and Nielsen, BH and Hvistendahl, MK and Berner-Hansen, M and Jeppesen, PB},
title = {Investigation of the stool microbiome of Short Bowel Syndrome patients before and after a 24-week treatment with the Glucagon-like Peptide 2 analog glepaglutide.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {102989},
doi = {10.1016/j.clnesp.2026.102989},
pmid = {41759957},
issn = {2405-4577},
abstract = {BACKGROUND AND AIMS: Glepaglutide is a long-acting glucagon-like peptide 2 (GLP-2) analog under development for the treatment of short bowel syndrome (SBS). Glepaglutide enhances intestinal absorption, which may hypothetically lead to changes in the intestinal microbiota, mainly by slowing gastrointestinal transit time. This study evaluated whether glepaglutide affects bacterial load and composition of the intestinal microbiota in SBS patients enrolled in a phase 3b trial assessing its 24-week efficacy on intestinal wet weight and energy absorption.

METHODS: In this single-center, open-label, EASE SBS-4 phase 3b study, 10 patients with SBS (8 of the 10 with intestinal failure and 8 of the 10 without colon-in-continuity) were treated with glepaglutide 10 mg by subcutaneous injection once weekly for 24 weeks. While the primary trial findings demonstrated increased intestinal wet weight and energy absorption assessed by metabolic balance studies, this study investigated whether these adaptations were associated with changes in bacterial load and composition of the intestinal microbiota. Samples were obtained from either stool or ostomy effluent at baseline and after 24 weeks of treatment with glepaglutide. Bacterial load was quantified using a spike-in approach, and microbiota composition was assessed by V3V4 16S rRNA gene sequencing.

RESULTS: No major changes in bacterial load or microbiota composition were observed following glepaglutide treatment. Bacterial load showed distinct differences between patients with and without a colon-in-continuity; in patients without a colon, most samples had values below 10[9] cells per gram, whereas those with a colon-in-continuity had bacterial loads within the physiological range observed in healthy individuals, ranging from 10[10] to 10[11] cells per gram feces. Microbiota composition also differed markedly by intestinal anatomy: patients without a colon-in-continuity had higher abundances of genera mainly associated with the upper gastrointestinal tract, such as Streptococcus, while those with a colon-in-continuity exhibited greater abundance of genera more commonly found in the lower gastrointestinal tract, including Bifidobacterium.

CONCLUSIONS: Treatment with the GLP-2 analog glepaglutide increased intestinal wet weight and energy absorption without altering the intestinal bacterial microbiota in the majority of the SBS patients participating in this study. Differences in bacterial load and composition were influenced by intestinal anatomy.

CLINICALTRIALS: gov no: NCT04991311; ClincalTrialsRegister.eu EudraCT no: 2020-005194-27.},
}

@article {pmid41759953,
year = {2026},
author = {Liu, X and Huang, Z and Liu, L and Wang, S and Huang, Y and Liu, X},
title = {Gut unclassified Ruminococcaceae reweights cortical functional gradients and small-world topology with links to mood and diet.},
journal = {NeuroImage},
volume = {329},
number = {},
pages = {121830},
doi = {10.1016/j.neuroimage.2026.121830},
pmid = {41759953},
issn = {1095-9572},
abstract = {The microbiota-gut-brain axis is a key conduit linking metabolism, mood, and cognition; however, its position within the continuous functional hierarchy of the cortex and the underlying mechanisms are unclear. In this study, a cross-modal brain-gut dataset from 88 healthy male participants was utilized. By integrating functional magnetic resonance imaging (fMRI) gradient analysis, microbiome sequencing, and dietary behavioral information, this study systematically evaluated the relationships between the abundance of unclassified Ruminococcaceae (Ruminococcaceae_unc), cerebral functional hierarchy, network topology, and emotional symptoms. The results demonstrated that increased abundance of this bacterial group was associated with a functional shift in the brain from unimodal to transmodal hubs, accompanied by a drift of the small-world network toward randomization. Functional gradient values were significantly negatively correlated with depression and anxiety scores and were tightly coupled with latent components in the dietary behavioral dimension, including education, physical activity, and nutrient intake. Transcriptomic analysis further revealed that the GPCR-Rho/integrin-vesicular trafficking pathway may serve as the key molecular mechanism. In conclusion, this study proposes a multiscale coupling framework encompassing the gut microbiota, functional gradients, and emotional health, thereby providing a theoretical basis for the development of microbiota-targeted intervention strategies for modulating transmodal emotions and cognition.},
}

@article {pmid41759950,
year = {2026},
author = {Yang, J and Shi, L and Jin, X and Shi, D and Cui, J and Wang, K and Xing, X and Qin, X and Dong, C},
title = {Multi-dimensional dynamic monitoring of gut microbiota-emotion axis and precision exercise intervention in compulsory drug rehabilitation: A 24-week randomized controlled trial.},
journal = {Psychology of sport and exercise},
volume = {},
number = {},
pages = {103095},
doi = {10.1016/j.psychsport.2026.103095},
pmid = {41759950},
issn = {1878-5476},
abstract = {BACKGROUND/OBJECTIVES: Substance use disorders (SUDs) present a global health challenge with high relapse rates. Emerging evidence implicates gut microbiota dysbiosis in SUD pathophysiology via the gut-brain axis. This 24-week randomized controlled trial investigated whether precision exercise interventions could modulate the gut microbiota-emotion axis to improve psychological outcomes in individuals undergoing compulsory drug rehabilitation.

METHODS: Thirty male participants were randomized to a precision exercise group (n=15; individualized aerobic + resistance training, 4-5 sessions/week) or control group (n=15; standard rehabilitation activities). Multi-dimensional assessments included weekly fecal (16S rRNA sequencing), urine (SCFAs via GC-MS), and saliva samples (cortisol, serotonin, BDNF via ELISA), alongside psychological evaluations (SCL-90-R, POMS) and physiological measures.

RESULTS: The exercise group exhibited significant increases in gut microbial diversity (Shannon index: +18.2%, p<0.001; Cohen's d = 2.14) and enrichment of beneficial taxa (e.g., Faecalibacterium, Bifidobacterium; LDA >3.5). Urinary SCFAs increased markedly (butyrate: 3.12-fold, p<0.001), correlating with elevated salivary BDNF (+82%, p<0.001) and reduced cortisol (-41.1%, p<0.001). Psychological outcomes improved substantially: SCL-90-R Global Severity Index decreased by 43.3% (p<0.001), and 78.6% of exercise participants achieved clinically meaningful improvement. Machine learning models predicted treatment response (AUC = 0.91) using baseline microbiome features.

CONCLUSIONS: Precision exercise restores gut microbiota homeostasis, enhances neuroactive metabolite production, and improves emotional regulation in SUD recovery. The gut microbiota-emotion axis represents a viable target for non-pharmacological interventions, with microbiome profiles enabling personalized treatment strategies.},
}

@article {pmid41759875,
year = {2026},
author = {Nuranindita, R and Natanegara, S and Wusono, AD and Amirudin, FA and Hitipeuw, D and Rahayu, AA and Daud, MM and Yuwanita, MR and Qanita, NG and Saputra, EY and Jun, H and Jeon, BY and Lee, MR and Ju, JW and Malik, MDA and Garjito, TA and Han, JH and Muh, F},
title = {Metatranscriptomic Analysis of Anopheles Species from Menoreh Hills Endemic Area in Central Java, Indonesia.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {108033},
doi = {10.1016/j.actatropica.2026.108033},
pmid = {41759875},
issn = {1873-6254},
abstract = {BACKGROUND: The mosquito microbiome plays a crucial role in vector competence and disease transmission dynamics, yet comprehensive metatranscriptomic analyses of Anopheles species microbiomes remain limited, particularly in malaria-endemic regions like the Menoreh Hills of Central Java, Indonesia. This study aimed to characterize the microbial and viral community compositions of five Anopheles species and their potential implications for vectorial capacity.

METHODS: Metatranscriptomic analysis was performed on five Anopheles species (An. barbirostris, An. flavirostris, An. kochi, An. maculatus, and An. vagus) collected from the Menoreh Hills endemic area using RNA sequencing, taxonomic classification, and functional annotation approaches.

RESULTS: Proteobacteria emerged as the dominant bacterial phylum across all species, with variations in relative abundance of other taxa. Baculoviridae emerged as the overwhelmingly dominant viral family across all species, with other families including Bunyavirales, Herpesvirales, and Nucleocytoviricota present at much lower abundances. Diversity indices revealed An. vagus with the highest microbial diversity and An. barbirostris with the lowest. Adherence-related virulence factors were predominant, particularly in An. maculatus and An. vagus, while carbohydrate-active enzymes AA1 and GT35 were abundant across all species.

CONCLUSIONS: This study examines microbiome and virome across five Anopheles species from Menoreh Hills. Betabaculovirus dominated virome, while bacterial and fungal communities showed species-specific patterns. Analyses revealed virulence differences. Study limitations include pooled samples. The results provide data for malaria research.},
}

@article {pmid41759844,
year = {2026},
author = {Leghari, A and Khand, FM and Laghari, S and Lakho, SA},
title = {Engineering bioavailability: Polysaccharide-protein-lipid delivery platforms for postbiotic therapeutics in gastrointestinal and systemic disorders.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {151123},
doi = {10.1016/j.ijbiomac.2026.151123},
pmid = {41759844},
issn = {1879-0003},
abstract = {Postbiotics, inanimate microorganisms and their components that confer health benefits, represent a promising therapeutic class with superior stability and safety profiles compared to live probiotics. However, their clinical translation is hindered by a critical bioavailability paradox such as physiological barriers, compound-specific instability, and the need for precise spatiotemporal release limit their efficacy at target sites. This review provides the first systematic analysis of how advanced pharmaceutical and food-grade delivery platforms can be engineered to overcome these challenges and unlock the clinical potential of postbiotics across gastrointestinal, metabolic, autoimmune, and neurological disorders. We critically evaluate a spectrum of technologies including micro/nanoencapsulation, smart hydrogels, lipid-based nanocarriers, and fermented food matrices and establish a rational framework for matching these platforms to disease-specific pathophysiology and delivery goals. Our analysis demonstrates that targeted strategies, such as pH-sensitive nanoparticles for colonic delivery in inflammatory bowel disease or brain-targeted carriers for gut-brain axis disorders, are essential for effective intervention. Furthermore, we identify and discuss key translational hurdles, including scalable manufacturing, regulatory ambiguity, and economic viability, while forecasting future trends toward personalized, microbiome-responsive smart systems. We conclude that the therapeutic success of postbiotics is intrinsically tied to the efficiency of their delivery. Bridging the gap between their documented biological activity and the engineered platforms designed to ensure targeted, sustained release is the decisive next step in transforming postbiotics from compelling concepts into cornerstone therapeutics of precision medicine.},
}

@article {pmid41759744,
year = {2026},
author = {Waghmare, PV and Kolekar, KA and Bashir, B and Kumbhar, PS and Patil, KS and Gupta, G and Prasher, P and Jha, SK and Disouza, J and Gurav, SS and Dua, K and Singh, SK},
title = {Advocating gut-retina connection and microbiota mediated pathways in management of age-related macular degeneration: Preclinical to clinical perspective.},
journal = {Ageing research reviews},
volume = {117},
number = {},
pages = {103071},
doi = {10.1016/j.arr.2026.103071},
pmid = {41759744},
issn = {1872-9649},
abstract = {Age-related macular degeneration (ARMD) is the primary manifestation of permanent vision loss internationally. Different factors that contribute to ARMD involve ageing, genetic predisposition, oxidative stress, immunological imbalances, aberrations in the breakdown of lipids, and persistent inflammation. Gut microbiota has emerged as the significant cause of ARMD by disrupting systemic immune and inflammatory responses and metabolic homeostasis. Age-related changes in gut microbiota (dysbiosis) cause lowered microbial diversity, enhanced gut permeability, and pro-inflammatory species, leading to macular damage. The healthy gut microbiota containing Lactobacillus casei, Lactobacillus plantarum, Lactobacillus rhamnosus, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium longum, and Faecalibacterium prausnitzii, are responsible for maintaining gut homeostasis, protecting the retina, and preventing ARMD progression. In contrast, the elevated population of pathogenic species such as Escherichia coli, Prevotella, Desulfovibrio, Enterococcus faecalis, and Streptococcus salivarius in gut dysbiosis is involved in ARMD progression. This review explores gut microbiota and their dynamics in ageing. The age-dependent gut microbiota variations and potential biological implications for the progression of ARMD are discussed. The review also discusses observations from experimental animals and explores potential microbiome-centered treatment avenues, covering probiotics, synbiotics, dietary remedies, metabolite-based treatment, and fecal microbiota transplantation for managing ARMD. Furthermore, various challenges in the management of gut microbiota-driven ARMD are also briefed with future directions. Thus, a gut microbiota-focused paradigm can offer novel choices for ARMD prevention and treatment.},
}

@article {pmid41759737,
year = {2026},
author = {Ju, T and Wang, Y and Nishio, H and Kudelka, MR and Sun, X and Wang, J and Zeng, J and Song, L and Akkas, G and Adsay, V and Parkos, CA and Cummings, RD},
title = {Deletion of Core 1 β3GalT-specific Molecular Chaperone (Cosmc) in murine intestinal epithelia leads to major alterations in glycocalyx and tumorigenesis.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {111319},
doi = {10.1016/j.jbc.2026.111319},
pmid = {41759737},
issn = {1083-351X},
abstract = {Intestinal mucins have extended O-glycans comprised primarily of the common Core 1 O-glycan (Galβ1-3GalNAcα1-Ser/Thr/Tyr) and its modifications. Expression of such glycans is under control of Cosmc (C1GalT1C1) that encodes a key ER molecular chaperone required for formation of active T-synthase, a Golgi enzyme that modifies the Tn antigen (GalNAcα1-Ser/Thr/Tyr - CD175) to generate a Core 1 O-glycan. We previously observed that targeted deletion of Cosmc in murine intestinal epithelial cells (IEC-Cosmc-KO mice) resulted in dysbiosis and alteration of the microbiome. Here we report a detailed description of these mutant mice and find that IEC-Cosmc-KO mice, but not WT mice, express CD175 throughout the intestinal epithelia. CD175 expression is accompanied by loss of glycocalyx, shortening of microvilli, compromised MUC2, thickening of the epithelial layer, as well as generation of high levels of reactive oxygen species. The majority of IEC-Cosmc[-/y] mice beginning at ∼3-9 months spontaneously developed colorectal adenocarcinomas, some with invasive features evidenced by mesenteric metastases, which were potentially associated with activation of TGFβ signaling. Thus, deletion of Cosmc results in expression of CD175 and loss of extended O-glycans in IEC, which is associated with dysregulation of epithelial cell surfaces, leading to spontaneous tumor development. SIGNIFICANCE: Extended O-glycans from the Tn antigen GalNAcα1-Ser/Thr/Tyr (CD175) have many biological functions but roles are poorly understood. Here we show that targeted deletion of Cosmc (C1GalT1C1) in murine intestinal epithelial cells leads to CD175 expression and a loss of extended O-glycans, dysregulation of multiple pathways, and spontaneous colorectal tumors.},
}

@article {pmid41759557,
year = {2026},
author = {Yang, W and Shi, L and Li, X and Rao, F and Luo, R and Huang, C},
title = {Alterations in the gut virome of children with allergic rhinitis: enrichment of pro-inflammatory bacteriophages and depletion of fungal viruses.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0327625},
doi = {10.1128/spectrum.03276-25},
pmid = {41759557},
issn = {2165-0497},
abstract = {This study aimed to characterize the gut virome in children with allergic rhinitis (AR) and explore its interactions with immune markers and allergens. Metagenomic sequencing was performed on fecal samples from 16 AR and 17 healthy control (HC) children. Viral genes (VGs) were identified and taxonomically annotated using BLASTP against the NCBI NR database. Virome diversity, differential abundance, and correlations with IgE were analyzed using LEfSe, random forest, and Spearman correlation. While alpha diversity did not differ, beta diversity revealed subtle compositional trends. Taranisvirus was enriched in AR and positively correlated with total IgE (ρ = 0.4647, P = 0.045). Mitovirus and Duamitovirus were depleted in AR and negatively correlated with allergens. Virus-bacteria co-occurrence network analysis revealed a reconfigured ecological interactome in AR, characterized by pro-phage-centric associations that may disrupt mucosal immune homeostasis. Random forest identified total IgE, milk, and dust mite as top discriminators. This first study of the gut virome in pediatric AR reveals a pro-inflammatory phage enrichment and protective fungal virus depletion, implicating the virome in modulating Th2 immunity. These findings suggest a potential correlation between virome alterations and allergic diseases, which may inform future research on virome-targeted interventions.IMPORTANCEAllergic rhinitis is a prevalent childhood condition with a significant impact on quality of life, yet its pathogenesis is not fully understood. While the bacterial microbiome has been studied, the role of the gut virome remains largely unexplored. Our study provides the first evidence of gut virome dysbiosis in children with allergic rhinitis. We identified specific pro-inflammatory bacteriophages that are enriched and correlated with IgE levels, as well as protective fungal viruses that are depleted. These findings offer new perspectives on allergic disease pathogenesis by suggesting a potential role of the virome in modulating host immunity. This work not only opens a new avenue for understanding the environmental and microbial drivers of allergic diseases but also suggests the potential for novel virome-based diagnostics and therapeutic strategies, such as phage therapy, which could have a broad impact on clinical practice.This study is registered with ClinicalTrials.gov as ChiCTR2400085982.},
}

@article {pmid41759554,
year = {2026},
author = {Dai, X and Liu, H and Bai, X and Li, D and Wang, T and Zhong, H and Xu, H and Sun, J},
title = {Insights into antibiotic resistomes from gut metagenome-assembled genomes of the free-range pigs.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0240725},
doi = {10.1128/spectrum.02407-25},
pmid = {41759554},
issn = {2165-0497},
abstract = {The pig gut microbiome serves as a reservoir for antibiotic resistance genes (ARGs), which pose a threat to public health and environmental safety. To investigate the presence of ARGs carried by free-range pigs, which have frequent contact with humans and their environment, we characterized the resistome of the pig gut microbiome through metagenomic sequencing of fecal samples from 120 pigs across four provinces in China (Yunnan, Guizhou, Sichuan, and Jiangsu). By constructing metagenome-assembled genomes (MAGs) and gene catalogs, we explored the microbial community structure and ARG distribution. Our analysis revealed a highly diverse array of ARGs, particularly those conferring resistance to multidrug, glycopeptide, peptide, and tetracycline antibiotics. Bacillota A and Actinomycetota were the dominant phyla across samples. However, notable regional differences in microbiota composition and resistance profiles were observed. These differences were likely influenced by local farming practices and environmental conditions. Guizhou harbored 11 unique ARG types, followed by Sichuan (seven), which showed region-specific resistome signatures. Escherichia coli and other microbial taxa were closely linked with ARG abundance, suggesting potential vectors for horizontal gene transfer. Analysis of mobile genetic elements (MGEs) further supported this, revealing a strong linear correlation between MGE and ARG abundance, with transposase elements particularly associated with multidrug ARGs. These findings highlight the central role of MGEs in ARG dissemination and underscore the need for targeted strategies to curb antibiotic resistance in livestock systems. Regional variation in resistome profiles further emphasizes the influence of local agricultural practices on resistance dynamics.IMPORTANCEThe growing prevalence of antibiotic resistance poses a significant global health threat, making it imperative to trace the origins and transmission routes of ARGs. This study delivers a comprehensive genomic reference for the porcine gut microbiota and clarifies how regional farming practices shape distinct resistome profiles. Integrating these data with analyses of mobile genetic elements and microbial hosts reveals the complex interplay among host, microbiota, and environment, thereby extending current knowledge of the pig gut ecosystem. These findings provide an evidence-based foundation for targeted surveillance and intervention strategies to curb antibiotic resistance in livestock and safeguard public health.},
}

@article {pmid41759472,
year = {2026},
author = {Wang, Q and Zhai, Y and Zhang, Y and Li, Z and Wang, Q and Liu, S},
title = {Assessing links between dental fluorosis and oral/systemic health via salivary microbiome in Chinese young adults.},
journal = {International dental journal},
volume = {76},
number = {3},
pages = {109461},
doi = {10.1016/j.identj.2026.109461},
pmid = {41759472},
issn = {1875-595X},
abstract = {OBJECTIVES: This study utilized dual control groups, caries patients (a representative bacterial infectious disease) and healthy individuals, to identify the core microbiome specific to dental fluorosis and elucidate the potential associations with systemic health and diseases from the perspective of the oral-gut-lung axis.

METHODS: Initially, 1001 volunteers were recruited, among whom 959 provided complete questionnaire data. In subsequent omics analyses, saliva samples from 387 participants (HC: n = 117; DC: n = 138; DF: n = 132) were included, and background confounders were controlled via partial correlation analysis. Multidimensional analyses based on 16S rRNA sequencing revealed significant intergroup separation of microbial communities.

RESULTS: By comparing differentially abundant taxa across pairwise comparisons (HC vs DC, HC vs DF, DC vs DF), 24 key DF-associated microorganisms were identified. These microbial markers exhibited high diagnostic accuracy, with area under the receiver operating characteristic curve values of 92.6% and 89.3% for distinguishing DF from HC and DF from DC, respectively. t-SNE dimensionality reduction further confirmed that the microbial signature clearly separated the DF group from both HC and DC groups. Microbial co-occurrence network analysis revealed significant positive correlations between Enhydrobacter and Caulobacter, Mycobacterium and Enhydrobacter, and Mycobacterium and Caulobacter.

CONCLUSIONS: This study provides evidence at the transmissible microecological level that dental fluorosis possesses a distinct microbiome profile compared to dental caries. In addition, the long-term periodontal status of patients with dental fluorosis and its potential link to periodontitis, intestinal and respiratory system diseases merit further investigation.},
}

@article {pmid41759374,
year = {2026},
author = {Zhou, H and Huang, Y and Chen, C and Song, M and Hylemon, PB},
title = {Gut microbiome and bile acid metabolism in liver disease: Mechanisms, clinical implications, and therapeutic opportunities.},
journal = {Pharmacological reviews},
volume = {78},
number = {2},
pages = {100120},
doi = {10.1016/j.pharmr.2026.100120},
pmid = {41759374},
issn = {1521-0081},
abstract = {The intricate interplay between the gut microbiome and bile acid metabolism via the gut-liver axis is fundamental to hepatic homeostasis. Perturbations in this axis are increasingly implicated in the pathogenesis of diverse liver diseases, including metabolic dysfunction-associated steatotic liver disease, alcohol-associated liver disease, cholestatic liver diseases, and hepatocellular carcinoma. This review integrates current understanding of hepatic bile acid synthesis, enterohepatic circulation, and gut microbial bile acid transformations, detailing how bile acids function as signaling molecules through nuclear receptors including farnesoid X receptor, pregnane X receptor, vitamin D receptor, constitutive androstane receptor, and G-protein-coupled receptors; G protein-coupled bile acid receptor 1 (also known as Takeda G protein-coupled receptor 5), and sphingosine-1-phosphate receptor 2. We explore disease-specific alterations in gut microbiota composition and bile acid profiles in metabolic dysfunction-associated steatotic liver disease, alcohol-associated liver disease, cholestatic liver diseases, and liver cancers, focusing on mechanisms linking gut dysbiosis, impaired intestinal barrier function, altered bile acid signaling, inflammation, and immune modulation to liver injury and progression. Furthermore, we discuss the clinical implications, highlighting the potential of microbiome signatures and bile acid profiles as diagnostic and prognostic biomarkers. Therapeutic strategies targeting the gut-liver axis, including probiotics, fecal microbiota transplantation, farnesoid X receptor agonists, and fibroblast growth factor 19 analogs, are reviewed. Finally, we address current challenges and future directions, emphasizing the need for multiomics integration, functional studies, and personalized medicine approaches to leverage the gut-liver axis for improved liver disease management. SIGNIFICANCE STATEMENT: Disruption of the gut microbiome-bile acid-liver axis is now recognized as a unifying mechanism driving multiple liver diseases, including metabolic dysfunction-associated steatotic liver disease, alcohol-associated liver disease, cholestatic liver diseases, and hepatocellular carcinoma. Unraveling the molecular and microbial interactions within this axis offers fundamental insights into disease pathogenesis and reveals novel therapeutic opportunities. Integrating multiomics technologies with artificial intelligence-based analytics will accelerate the discovery of predictive biomarkers and personalized interventions, advancing the field toward precision-based liver disease treatment protocols.},
}

@article {pmid41759241,
year = {2026},
author = {Myers, PN and van Beijsterveldt, IALP and Snowden, SG and Eriksen, C and Nielsen, HB and Hughes, IA and Ong, KK and Hokken-Koelega, ACS and Koulman, A and Brix, S},
title = {Breastfed infants receiving formula supplementation show altered lipid and gut microbiota profiles at 3 months of age.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {59},
number = {},
pages = {106602},
doi = {10.1016/j.clnu.2026.106602},
pmid = {41759241},
issn = {1532-1983},
abstract = {BACKGROUND & AIMS: Exclusive breastfeeding offers numerous health benefits. Despite advancements in formula, significant differences compared with breast milk remain. We aimed to assess how milk feeding type and volume at 3 months affect the infant plasma lipidome and gut microbiota.

METHODS: Infants were classified into exclusive breastfeeding (EBF), mixed feeding (MF), or exclusive formula feeding (EFF) groups based on feeding data collected prospectively across two European cohorts (n = 519). Lipidomics and shotgun metagenomics were applied to plasma and stool samples, respectively.

RESULTS: Feeding type explained major variation in both lipidomic and microbial profiles. Plasma lipids showed distinct signatures across groups, particularly in sphingomyelins and diacylglycerols. Microbiota diversity and species richness increased with formula exposure. Formula rich in intact whey protein was linked to higher S. thermophilus abundance in the infant gut. Random forest classification of feeding type using either lipidomic or gut microbiota features achieved high discriminatory accuracy (AUROC >0.90) in training and validation datasets.

CONCLUSION: Early nutrition is a critical determinant of the lipidome and gut microbiome during the breastfeeding phase.},
}

@article {pmid41759031,
year = {2026},
author = {Gudi, CR and Neilson, WJ and Mansell, TJ},
title = {An Engineered Variant of E. coli Nissle 1917 with Enhanced Transformation Efficiency and Robustness.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00852},
pmid = {41759031},
issn = {2161-5063},
abstract = {The gut microbiome and its effects on human health have generated considerable scientific, veterinary, and medical interest in recent years. Several gut bacterial species have emerged as potential chassis organisms for the delivery of therapeutics in this milieu. Among these, E. coli Nissle 1917 (EcN), a nonpathogenic gut isolate bacterium, is quickly gaining popularity. However, a bottleneck in harnessing EcN's potential has been its poor transformation efficiency relative to other bacterial strains. In this study, we present the use of adaptive laboratory evolution to increase EcN's transformation efficiency by subjecting the strain to repeated cycles of electroporation and recovery. This new strain has been comprehensively characterized in comparison to the wild-type EcN, including assessments of growth under gut-mimicking duress conditions, permeability, motility, hydrophobicity, and plasmid replication. Since EcN is known to compete with pathogenic strains in the gut for iron, the competition dynamics and iron consumption of the strain were also significant factors to consider. Furthermore, we conducted genome sequencing and gene ontology enrichment analysis to identify affected genes and pathways to probe the potential mechanisms of the improved phenotype. Overall, the strain shows improved transformation efficiency and robustness while preserving its key biological functionality.},
}

@article {pmid41758920,
year = {2026},
author = {Sakaguchi, N and Kusamoto, A and Harada, M and Shashni, B and Komura, A and Teshima, A and Tanaka, T and Koike, H and Xu, Z and Kawahara, Y and Tsuchida, C and Kunitomi, C and Takahashi, N and Urata, Y and Wada-Hiraike, O and Hirota, Y and Nagasaki, Y and Osuga, Y},
title = {Butyric acid-based self-assembling nanoparticles: a potential strategy to prevent development of polycystic ovary syndrome.},
journal = {Molecular human reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1093/molehr/gaag013},
pmid = {41758920},
issn = {1460-2407},
abstract = {Polycystic ovary syndrome (PCOS) is the most common endocrine disorder affecting women of reproductive age and cannot currently be cured or prevented fundamentally. Prenatal androgen exposure is a key factor in PCOS development, and both PCOS patients and animal models exhibit gut microbiota alterations. We previously demonstrated that prenatally androgenized (PNA) model mice display changes of gut microbiota before the manifestation of PCOS phenotypes, suggesting that an intervention targeting gut microbiota from the early stage of life can prevent development of PCOS. Butyric acid, a short-chain fatty acid produced by bacteria in the intestines, has various physiological effects. We investigated whether butyric acid could prevent PCOS phenotypes in PNA mice when administered from the early stage of life as a nanoparticle-based donor. We have developed butyric acid-based self-assembling nanoparticles (BNP), which release butyric acid in a sustained manner when exposed to digestive enzymes so that butyrate is delivered to the intestines. Control and PNA offspring were administered water containing or lacking BNP from just after weaning until 20 weeks of age. Reproductive and metabolic phenotypes were compared among these offspring (n = 10-14 for each group). Administration of BNP normalized irregular estrus cyclicity and improved the polycystic ovarian morphology, as evidenced by smaller numbers of atretic follicles in PNA offspring. Regarding metabolic phenotypes, administration of BNP improved hypertrophy of adipocytes and insulin resistance. Furthermore, analysis of the gut microbiota suggested that these primary effects were caused by butyrate itself, with an increase in certain butyrate-producing bacteria supporting this mechanism. The present findings indicate that administration of butyric acid to PNA offspring, which are at high risk of developing PCOS, from the early stage of life effectively prevents development of PCOS phenotypes at reproductive ages. Further exploration is necessary to clarify the mechanism by which butyric acid prevents development of PCOS.},
}

@article {pmid41758783,
year = {2026},
author = {Dimmers, F and Reichert, D and Nguyen, T and Lück, N and Ramachandran, H and Bremges, A and Schild, J and Humbek, M and Grether-Beck, S and Rossi, A and Staerk, C and Esser, C and Krutmann, J},
title = {Monocentric, vehicle-controlled, double-blind study to assess the short- and long-term effects of a Ceramide NP C15-containing emollient on the skin microbiome and the skin barrier function in sensitive skin.},
journal = {Skin pharmacology and physiology},
volume = {},
number = {},
pages = {1-30},
doi = {10.1159/000551043},
pmid = {41758783},
issn = {1660-5535},
abstract = {INTRODUCTION: Sensitive skin is a common skin condition that impairs quality of life and is characterised by unpleasant sensations to normally non-irritating stimuli. Restoration of skin barrier integrity can relieve symptoms, and accumulating evidence indicates a contributory role of the skin microbiome not only in barrier function but also as a potential modulator in sensitive skin. Ceramide-containing emollients improve barrier function and may modulate microbial communities via restoration of stratum corneum lipids, hydration, and immune regulation.

METHODS: In this randomized, double-blind, vehicle-controlled trial, an emollient containing Ceramide NP C15 was evaluated for its effects on sensitive skin symptoms and skin barrier function. Fifty participants applied the study products in a split-body design for six weeks. Primary assessments included skin physiology and symptom burden. Furthermore, skin microbiota changes were explored using flow cytometry (FC)-based bacterial profiling and 16s rRNA gene sequencing.

RESULTS: Both the Ceramide NP C15 formulation and the vehicle were associated with improvements in subjective symptoms. In participants with impaired skin barrier, treatment with the ceramide formulation was associated with a significant reduction in transepidermal water loss. FC- and 16S-based analyses indicated modest, treatment-associated changes in skin microbiota composition including an early and sustained increase in microbial evenness and a significant enrichment of Bifidobacterium.

CONCLUSION: In this exploratory, randomized controlled study, a Ceramide NP C15-containing emollient was associated with improvements in skin barrier function. Exploratory microbiome analyses suggested treatment-associated changes in microbial community characteristics, which should prompt further investigations in their clinical relevance for sensitive skin.},
}

@article {pmid41758690,
year = {2026},
author = {Yin, S and Cheng, L and Hu, E and Li, J and Wu, G and An, J and Nunez, L and Kawachi, N and Zhu, J and Rosenblatt, G and Segall, JE and Ostrer, H and Augustine, S and Song, EZ and Ow, TJ and Smith, RV and Prystowsky, MB and Verma, A and Deng, W},
title = {Association of Intratumoral Microbiota with Prognosis in Head and Neck Squamous Cell Carcinoma.},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
volume = {},
number = {},
pages = {},
doi = {10.1158/1078-0432.CCR-25-4420},
pmid = {41758690},
issn = {1557-3265},
abstract = {PURPOSE: To evaluate whether intratumoral bacterial load and diversity are associated with survival outcomes in HNSCC and to examine their relationship with HPV status.

EXPERIMENTAL DESIGN: This retrospective cohort study included 312 adults with surgically treated, primary HNSCC at Montefiore Einstein Cancer Center (2000-2023). Intratumoral bacterial load was quantified by qPCR, and microbial diversity was assessed by 16S rRNA sequencing in 312 tumor and 34 paired normal tissues. HPV status was determined by p16 immunohistochemistry and qPCR. Overall survival was the primary outcome.

RESULTS: HNSCC tumors showed higher bacterial load and lower bacterial diversity compared to adjacent normal tissues. High bacterial load (HR, 1.85; 95% CI, 1.31-2.61; P<0.001) and low bacterial diversity (HR, 1.65; 95% CI, 1.19-2.28; P=0.003) were independently associated with reduced OS, with the greatest risk in patients carrying both features (HR, 3.00; 95% CI, 1.76-5.09; P<0.001). The high-risk bacterial features were less frequent in HPV-positive than in HPV-negative tumors (high load: OR, 0.46; 95% CI, 0.29-0.73; P=0.001; low diversity: OR, 0.51; 95% CI, 0.32-0.81; P=0.004), and their prognostic significance was more pronounced in HPV-negative cases. Taxonomic profiling revealed marked depletion of predominant bacterial taxa in HNSCC, especially in HPV-negative tumors. Notably, loss of the class TM7-3 and the orders Actinomycetales and Burkholderiales was specifically associated with poor HNSCC survival, including early mortality.

CONCLUSIONS: High intratumoral bacterial load and low diversity are prognostic factors associated with survival in HNSCC, particularly in HPV-negative patients. Incorporating microbiome assessment into risk stratification may enhance prognostic precision and inform microbiota-directed therapeutic approaches.},
}

@article {pmid41758194,
year = {2026},
author = {Chen, J and Wang, Y and Xu, L and Li, X and Zhao, L},
title = {Exploring the gut microbiome and metabolomic interactions of antimetabolite drugs to optimize therapy.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2638009},
doi = {10.1080/19490976.2026.2638009},
pmid = {41758194},
issn = {1949-0984},
abstract = {Antimetabolite drugs are cornerstones in treating various cancers and autoimmune diseases; however, their clinical utility is often hampered by systemic toxicity caused by drug-induced gut microbiota dysbiosis. Predicting patient responses remains a significant challenge. Several studies have highlighted the influence of gut microbiota on antimetabolite treatment outcomes, revealing complex bidirectional interactions between the drugs and microbial communities. This review synthesizes the effects of common antimetabolites (including 5-fluorouracil, methotrexate, gemcitabine, capecitabine, 6-mercaptopurine, and thioguanine) on gut microbial communities and outlines a framework (pharmacokinetics, endogenous metabolite production, immune modulation, and apoptotic pathway modulation) for assessing chemotherapy-microbiota interactions. Additionally, potential microbial biomarkers for predicting treatment responses and strategies for manipulating the gut microbiota to enhance therapeutic efficacy are discussed. Therefore, advances in methodologies such as metagenomics and real-time microbial monitoring will be essential for unraveling these interactions and promoting the precise application of antimetabolite drugs.},
}

@article {pmid41758122,
year = {2026},
author = {Madushani, GRDS and Wu, X and Jayasinghe, WH and Wang, Q and Vinit, K and Hao, GF},
title = {Harnessing eCISs for precision phytomicrobiome engineering and biocontrol.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuag006},
pmid = {41758122},
issn = {1574-6976},
abstract = {Plant microbiome disruption often increases vulnerability to crop diseases, endangering worldwide food production, while chemical pesticides become increasingly less viable and continue to damage ecosystems. To safeguard plant microbiome health, several biological control strategies offer alternatives, yet many operate through broader or weakly defined target mechanisms. In recent years, bacterial contractile injection systems (BCISs) have emerged as a promising class of naturally evolved nanomachines that translocate molecular payloads directly into target cells. Subsets of these systems, extracellular contractile injection systems (eCISs), are distinguished by their specific narrow host range and receptor-dependent specificity. Recent studies have demonstrated that eCISs provide a transformative approach for targeted microbial manipulation, enabling the delivery of specialized molecules into particular microbes with higher precision. However, despite their potential, the integration of these engineered injection systems with microbial modulation for phytomicrobiome remains largely underexplored. Here, we explore the capabilities of eCISs as an advanced approach for the biocontrol, leveraging their tailored mechanisms for targeted payload delivery in plant-associated microbial communities with enhanced host specificity. This study aims to address the potential of engineered injection systems in facilitating sustainable phytomicrobiome engineering strategies that enhance biocontrol, aiming to reduce environmental harm while improving agricultural productivity.},
}

@article {pmid41757979,
year = {2026},
author = {Zhang, X and Luo, Q and Gong, Z and Yang, H and Chen, X and Wang, B and Yuan, M and Chen, Y and Jia, Y and Guo, S},
title = {Nano-selenium mitigates antibiotic resistance in paddy ecosystems via microbiome remodeling and environmental filtering shifts.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0223125},
doi = {10.1128/aem.02231-25},
pmid = {41757979},
issn = {1098-5336},
abstract = {UNLABELLED: The dissemination of antibiotic resistance genes (ARGs) in paddy ecosystems poses a serious threat to environmental health. A pot experiment was conducted to assess the efficacy of alkyl glycoside-stabilized selenium nanoparticles (AG-SeNPs) in mitigating ARG abundance within the soil, phyllosphere, and rice grains. Functional prediction, null model analysis, variance partitioning, and structural equation modeling were employed to identify ARG hosts, key metabolic pathways, and environmental drivers of ARG dynamics. Results showed that foliar application of AG-SeNPs (30 g ha[-1]) reduced ARGs by 5.13 × 10[6] copies g[-1], 2.28 × 10[7] copies g[-1], and 1.25 × 10[6] copies g[-1] in the rhizosphere soil, phyllosphere, and grains, respectively. TetPA and tetGF were dominant ARGs, predominantly associated with Mariniphaga anaerophila, Sediminibacter magnilacihabitans, and Limnospira fusiformis. ARG attenuation was linked to enhanced ABC transporter activity and suppressed purine metabolism and ribosome function, thereby reducing intracellular antibiotic pressure and limiting ARG expression in soil microbes. In the phyllosphere, activation of two-component systems modulated stress responses and antimicrobial resistance pathways, constraining horizontal gene transfer. Nano-selenium increased heterogeneous selection in the phyllosphere, enhancing deterministic filtering of ARG hosts and restructuring microbial communities. Environmental factors explained 42.81% of ARG variation, wherein selenium accumulation in leaves directly reduced ARG abundance, and soil pH, electrical conductivity, and organic matter indirectly influenced ARG dynamics through microbial community restructuring. These findings highlight that AG-SeNPs mitigate ARGs through an environmentally mediated, microbially driven cascade, offering a promising strategy for antibiotic resistance control in agricultural systems.

IMPORTANCE: The dissemination of antibiotic resistance genes within agricultural soil-plant systems poses a severe threat to food safety and public health. This study demonstrates that foliar application of nano-selenium fertilizer effectively reduces ARG abundance in the soil, phyllosphere, and rice grains. We found that nano-selenium functions not by direct bactericidal action but by beneficially reshaping the microbial communities in both the leaves and soil, thereby suppressing the pathways for ARG transmission. Our findings provide a novel and sustainable strategy to mitigate antibiotic resistance in agricultural ecosystems, potentially reducing the risk of these genes entering the human food chain via rice.},
}

@article {pmid41757954,
year = {2026},
author = {Ke, Y and Sun, Y and Wu, J and Ye, L and Zhu, Z},
title = {Association of vaginal microbiome, cytokines, and spontaneous preterm birth among Chinese women: a nested case-control study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0260725},
doi = {10.1128/spectrum.02607-25},
pmid = {41757954},
issn = {2165-0497},
abstract = {An imbalance of the vaginal microbiome and dysregulation of cytokines are associated with spontaneous preterm birth (sPTB). To date, the relationship between the vaginal microbiome, cytokines, and sPTB remains unclear in the Chinese population. Herein, we conducted a nested case-control study using data from a prospective cohort of 749 Chinese women with a singleton pregnancy who were enrolled between 16 and 28 weeks of pregnancy. Cases consisted of individuals experiencing sPTB (n = 38), while controls were selected randomly at a 4:1 ratio to cases (n = 152). Compared to the term group, the sPTB group exhibited significantly increased abundance of vaginal Aerococcus christensenii, Gardnerella swidsinskii, and Lactobacillus iners, along with elevated levels of interleukin (IL)-1β, IL-6, and IL-12p70 in vaginal fluid (P < 0.05). Least absolute shrinkage and selection operator (LASSO) regression identified L. iners, G. swidsinskii, and IL-6 as significant risk factors for sPTB, with adjusted odds ratios (ORs) (95% CI) of 1.57 (1.06-2.34), 1.45 (1.03-2.05), and 2.05 (1.43-2.93), respectively. Finally, a logistic regression model for sPTB was established incorporating L. iners, G. swidsinskii, and IL-6, which yielded an area under the receiver operating characteristic curve (AUC) of 0.73. These findings suggest that alterations in the vaginal microbiome and cytokine levels may contribute to sPTB in the Chinese population.IMPORTANCEPreterm birth (PTB) is the leading cause of death in children under 5 years of age, of which about 70% were spontaneous ones (sPTB); while genitourinary infections are implicated in 25-40% of sPTB cases. Previous studies have revealed some features of vaginal microbiome and cytokines related to sPTB: increased richness and diversity, increased levels of Lactobacillus iners, BV-associated bacteria, low abundance of L. crispatus, and high levels of pro-inflammatory cytokines. However, there were also some inconsistent findings, and little is known in the Chinese population. This study confirmed the correlations between vaginal microbiome, cytokines, and sPTB in Chinese pregnant women. Specifically, elevated vaginal L. iners, G. swidsinskii, and IL-6 levels were significantly associated factors, which may help to identify women at high risk of sPTB.},
}

@article {pmid41757945,
year = {2026},
author = {Surve, SV and Valls, RA and Barrack, KE and Gwilt, LL and Gardner, TB and O'Toole, GA},
title = {The regional landscape of the human colon culturome in health and cystic fibrosis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0312625},
doi = {10.1128/spectrum.03126-25},
pmid = {41757945},
issn = {2165-0497},
abstract = {UNLABELLED: Cystic fibrosis (CF) alters gut physiology, yet its impact on microbial communities across colonic regions (ascending, transverse, descending colon) and microhabitats (lumen, mucosa) remains incompletely understood. Here, we applied culturomics to characterize gut microbiota in a small cohort of 32 individuals (22 non-CF, 10 CF). Persons with CF (pwCF) exhibited significantly higher viable bacterial loads than non-CF individuals, particularly in mucosal samples. Anaerobes predominated overall, with relative enrichment of aerobes in the mucosa of pwCF. Alpha diversity was reduced in mucosal samples and aerobic cultures for pwCF, whereas beta diversity was influenced by all the tested variables except the colonic region. Phylum-level analyses revealed enrichment of Proteobacteria and depletion of Actinobacteria, Bacteroidota, and Firmicutes in samples from pwCF, consistent with stool analysis. Random forest models identified selected oral-associated microbes as key predictive taxa and accurately classified polyp status within this cohort. Whole-genome sequencing of Bacteroides fragilis (n = 21) and Escherichia coli (n = 15) isolates, representing a subset of 109 gut bacterial genomes sequenced from this cohort, revealed minimal genomic variation across colonic regions and sample types, indicating intra-individual strain stability. The understandings from this pilot culturome study, after future validation, may help in developing targeted microbial therapeutic approaches to address the gut dysbiosis of CF.

IMPORTANCE: This pilot study of a small cohort represents the first culturome analysis of the cystic fibrosis colon. Our preliminary findings demonstrate that cystic fibrosis (CF)-associated gut dysbiosis is spatially specific, with mucosal bacterial communities showing pronounced alterations while luminal communities show comparatively subtle phylum-specific shifts. This spatial specificity suggests the mucosal microenvironment as a potential therapeutic target and indicates that interventions focused solely on luminal bacteria may be insufficient. The promising predictive accuracy of culturome-based machine learning models in this small cohort suggests these viable bacterial signatures could serve as biomarkers for CF management pending larger validation studies. Additionally, our initial observations of CFTR modulator effects on gut microbial communities provide insight for future studies optimizing combination therapies.},
}

@article {pmid41757889,
year = {2026},
author = {El Hafi, B and Jean-Pierre, F and Taub, L and Hampton, TH and O'Toole, GA},
title = {Streptococcus sanguinis antagonizes Prevotella melaninogenica in the context of the cystic fibrosis respiratory microbiome.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0000526},
doi = {10.1128/jb.00005-26},
pmid = {41757889},
issn = {1098-5530},
abstract = {The latest generation of cystic fibrosis transmembrane conductance regulator-targeted modulator therapy, Elexacaftor/Tezacaftor/Ivacaftor (ETI), has significantly improved the clinical outcomes of persons with cystic fibrosis (pwCF) but does not appear to completely eliminate CF respiratory microbial colonization. Here, we analyzed over 4,200 publicly available respiratory microbiomes spanning pre- and post-ETI treatment periods and further stratified by age and type of sample. Our analyses reveal that despite reshaping of community composition by ETI, classical CF pathogens such as Pseudomonas and Staphylococcus spp. persist in sputum and sinonasal samples, while Streptococcus spp. drastically increase in prevalence and relative abundance post-ETI treatment. Obligate anaerobes such as Prevotella spp., Fusobacterium spp., Porphyromonas spp., and Veillonella spp. were readily detected post-ETI. We observed changes in the sputum samples from pwCF post-ETI, with an increase in the relative abundance of Streptococcus spp. and prevalence of Prevotella and a decline in Pseudomonas spp. Analysis of co-occurrence networks revealed mostly positive correlations between the different genera pre- and post-ETI; however, these correlations were reduced in number following ETI treatment, suggesting a disruption of community connectivity. To test one of the hypotheses raised by the computational analyses, we experimentally investigated the relationship between Streptococcus sanguinis and Prevotella melaninogenica in a CF sputum-like medium. Our data suggest that S. sanguinis uses reactive nitrogen species, and likely other factors, to antagonize P. melaninogenica, while Pseudomonas aeruginosa protects P. melaninogenica in CF-like culture conditions. Our findings implicate polymicrobial interactions, rather than individual species abundance, in determining microbial persistence and adaptation within the CF airway post-ETI.IMPORTANCEThe introduction of the latest cystic fibrosis transmembrane conductance regulator (CFTR)-targeted Elexacaftor/Tezacaftor/Ivacaftor (ETI) therapy represents a major therapeutic advance for persons with cystic fibrosis (pwCF); however, this therapy does not completely negate respiratory infections and colonization. We leverage large-scale publicly available microbiome data to demonstrate that while ETI therapy alters the respiratory microbial landscape, canonically prevalent and abundant CF pathogens persist in many pwCF and likely maintain ecological relevance through adaptive interactions with other taxa. Our in vitro findings also reveal that Streptococcus sanguinis can antagonize Prevotella melaninogenica, and that Pseudomonas aeruginosa can provide selective protection to quell this antagonism. These insights highlight the need to consider microbial interactions and community dynamics when evaluating long-term responses to CFTR modulators.},
}

@article {pmid41757865,
year = {2026},
author = {Hu, X and Shi, Z and Gao, Y and Zheng, H and Lin, L and Chen, JP and Chen, Y and Zhang, CX and Li, Y},
title = {Characterization of the dynamic microbiome evolution across thrips species.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70265},
pmid = {41757865},
issn = {1744-7917},
support = {2023J06040//Natural Science Foundation of Fujian Province/ ; //Ningbo Yongjiang grant/ ; 32472657//National Natural Science Foundation of China/ ; 32570491//National Natural Science Foundation of China/ ; },
abstract = {The insect microbiome profoundly influences host physiology and ecology, yet its composition and evolutionary dynamics in thrips remain poorly understood. Here, we present a systematic characterization of thrips-associated microbiomes through integrated metagenomic and culture-based approaches. Our analysis reveals that thrips microbiomes are dominated by both intracellular symbionts (e.g., Wolbachia and Spiroplasma) and extracellular taxa (e.g., Serratia, Pantoea, and Acinetobacter), with species-specific compositions exhibiting frequent gains and losses of bacterial lineages. We demonstrate that thrips microbiomes exhibit low interspecific microbial sharing, forming host-specific bacterial communities with minimal overlap between species. To address methodological challenges in microbiome research, we developed a dual-sequencing framework combining short-read sequencing (for comprehensive taxonomic detection) and long-read sequencing (for genomic verification), enabling the reconstruction of high-quality metagenome-assembled genomes that validated short-read findings. Furthermore, we isolated and sequenced the complete genomes of two dominant extracellular symbionts-Pantoea dispersa and Serratia marcescens-and performed pan-genome analyses. These revealed small core gene sets and expansive accessory genomes, including host-specific functional genes (e.g., hydrolases and neurotoxic N-acetyltransferases) likely involved in host adaptation. Our study provides a foundational genomic resource and a robust analytical pipeline for dissecting thrips microbiome evolution, with implications for understanding insect-microbe interactions and symbiont-mediated adaptations.},
}

@article {pmid41757862,
year = {2026},
author = {Zhang, Y and Zhang, R and Wang, G and Liu, Y},
title = {Antibiotic-Mediated Microbiota Depletion Suggests an Association Between Gastric Juice Dysbacteriosis and Abnormal Bile Acid Metabolism in Chronic Atrophic Gastritis Rats.},
journal = {Biomedical chromatography : BMC},
volume = {40},
number = {4},
pages = {e70404},
doi = {10.1002/bmc.70404},
pmid = {41757862},
issn = {1099-0801},
support = {82374025//National Natural Science Foundation of China/ ; 82073988//National Natural Science Foundation of China/ ; 202403021221327//Fundamental Research Program of Shanxi Province/ ; zyytd2024020//Traditional Chinese Medicine Innovation Team of Shanxi Province/ ; },
abstract = {Current research on chronic atrophic gastritis (CAG) has primarily focused on intestinal flora, while the role of gastric juice microecology remains poorly understood. This study investigated whether alterations in gastric juice microbiota and bile acid (BA) profiles are associated with CAG under microbiota perturbation. A CAG rat model was designed by a multifactor modeling method, and an antibiotic cocktail (Abx) was administered to deplete gastrointestinal microbiota. Full-length 16S rRNA gene sequencing and LC-MS technology were conducted to characterize microbial composition and metabolite profiles in gastric juice. An integrated strategy combining microbiome and metabolome data was employed to validate associations between microbiota and metabolites. CAG rats exhibited elevated proinflammatory cytokines and lipopolysaccharide (LPS) levels in gastric juice, accompanied by dysbacteriosis and aberrant BA profiles. After antibiotic treatment, LPS level and bile salt hydrolase (BSH) activity were reduced, along with the lower abundances of LPS-producing bacteria and multiple BA levels. Correlation analysis demonstrated a positive association between deoxycholic acid (DCA) and LPS-producing bacteria (Escherichia coli). These findings revealed that gastric juice dysbacteriosis and abnormal BA metabolism were relevant to the inflammatory status of CAG. This study provided multi-omics evidence supporting a potential involvement of gastric juice microecological imbalance in CAG progression.},
}

@article {pmid41757733,
year = {2026},
author = {Rau, SR and Kalkuhl, A and van Esch, E and Hahn, C and Nolte, T and Hempel, K},
title = {NPY2R Agonist-Induced Gastric Effects Leading to Intestinal Dysbiosis and Secondary Intestinal Pathology in CD1 Mice.},
journal = {Toxicologic pathology},
volume = {54},
number = {2},
pages = {167-180},
doi = {10.1177/01926233251392878},
pmid = {41757733},
issn = {1533-1601},
abstract = {Obesity research has identified several drug targets, including the neuropeptide Y receptor 2 (NPY2R), which causes anorexigenic effects and delays gastric emptying. Test Peptide, an NPY2R agonist, was tested for toxicity in CD1 mice. Following unexpected mortality in a 4-week study, a 4-day study was conducted to determine the cause. The examination included clinical observations, pathology, and microbiome analysis of jejunal samples. Histopathologic lesions were primarily observed in animals showing clinical signs of toxicity ("responders"), including vacuolation of gastric parietal cells, inflammation, ulcers, and bacterial overgrowth in the small intestine. Occasionally, vacuolation of parietal cells was noted in clinically asymptomatic animals ("non-responders") terminated after 4 days, but not in nonresponders treated for 4 weeks. Microbiome analysis revealed in responders a significantly increased abundance of pathogenic bacteria like Shigella and a significant decrease in probiotic bacteria like Lactobacillus. The altered intestinal microflora resulted in overt dysbiosis, leading to intestinal inflammation, sepsis, and death. The intestinal microbiome appears to be an important factor determining differences in the interindividual susceptibility of mice to Test Peptide treatment. The human relevance of these murine findings is considered low, owing to substantial anatomical and physiological gastrointestinal differences, and the absence of comparable observations in nonhuman primates.},
}

@article {pmid41757159,
year = {2026},
author = {Zhang, L and Ding, Z and Yi, N},
title = {BCGLMs: Bayesian modeling for disease prediction using compositional microbiome features.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag041},
pmid = {41757159},
issn = {2635-0041},
abstract = {MOTIVATION: BCGLMs is a freely available R package that provides functions for setting up and fitting Bayesian compositional models for continuous, binary, ordinal and survival responses. It also includes models with random effects to capture sample-related accumulated small effects, improving prediction accuracy. The package includes tools for summarizing results from fitted models both numerically and graphically. Built on top of the widely used brms package, BCGLMs enable users to incorporate phylogenetic relationships between microbiome taxa into the modeling framework. Overall, BCGLMs package offers a flexible and powerful set of tools for analyzing compositional microbiome data.

The package is publicly available via GitHub https://github.com/Li-Zhang28/BCGLMs.},
}

@article {pmid41757098,
year = {2026},
author = {Duan, L and Baumgartner, WA and Wanyama, JW and Okyere, L and Alvarado, DA and Minhas, BF and Gaulke, CA},
title = {Sex-stratified Gut Microbiome Disruption is Associated with Altered Hepatic Gene Expression during Acute Azoxystrobin Exposure.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.18.706612},
pmid = {41757098},
issn = {2692-8205},
abstract = {UNLABELLED: Azoxystrobin is a widely used fungicide that has been associated with to reproductive, neurological, and developmental defects. This chemical also disrupts gut microbial communities; however, if these perturbations contribute to the harms associated with exposure to azoxystrobin, this remains unclear. In this study, we investigated the effects of acute exposure to a series of concentrations (5-500 mg/kg) of azoxystrobin on the host and gut microbiota in zebrafish. Fecal amplicon and shotgun metagenomic sequencing was integrated with liver gene expression to quantify associations between microbiome disruption azoxystrobin toxicity in the host. Azoxystrobin exposure resulted in significant alteration in microbiome composition and functional potential in a dose- and sex-dependent manner. Microbial communities in exposed animals exhibited an increased abundance of xenobiotic metabolism pathways and decreased bacterial motility and lipopolysaccharide biosynthesis pathway metabolism. At the host level, histopathology identified increased biliary proliferation, most evident in medium- and high-dose fish. We also observed hepatic transcriptional changes consistent with a stress response, including altered redox-associated genes and reduced expression of lipid and small-molecule metabolic genes, with sex-stratified differences. Importantly, alterations in host transcriptional programming correlated with the compositional changes in exposed microbiota. Together, these results suggest concurrent impacts of azoxystrobin on gut microbiota and the liver implicate the microbiome as a potential contributor to changes in liver gene expression during exposure.

IMPORTANCE: Widespread fungicide use contaminates ecosystems worldwide, but the biological pathways underlying their effects on humans and other animals are not well understood. Using zebrafish (Danio rerio), we found that short-term exposure to the fungicide azoxystrobin was associated with changes in the gut microbiome, liver gene activity, and liver changes. Exposure produced dose- and sex-dependent shifts in microbial communities, including changes in predicted microbial functions involved in chemical metabolism, bacterial motility and defense. Compositional changes in the microbiome correlated with gene-expression changes consistent with stress and altered metabolism in exposed fish, suggesting that exposure induced disruption may contribute to exposure impact to the host. These results highlight a potential role for the microbiome in mediation of the impacts of azoxystrobin on host physiology. As such microbial based interventions could be a viable strategy to mitigate exposure impacts on health.},
}

@article {pmid41757095,
year = {2026},
author = {Wang, F and Holmes, AJ and Browne, GV and He, X and Bockmann, MR and Davis, KM and Hughes, TE and Adler, CJ},
title = {Ecological and evolutionary dynamics of the oral microbiome across childhood.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.13.705642},
pmid = {41757095},
issn = {2692-8205},
abstract = {Childhood represents a critical period for oral microbiome development, yet evolutionary trajectories and the relative roles of host and environment remain unclear. Using a large longitudinal metagenomic dataset of 920 samples from a twin cohort spanning the first decade of life, we characterised microbial shifts and population dynamics of key bacterial groups. Microbiome diversity was initially reduced and highly heterogeneous and became increasingly complex and convergent with age. Microbial community state was associated with developmental age, environment and in late childhood was surprisingly strongly associated with host genotype. Strain-level analyses revealed species-specific temporal patterns of genetic variation particularly within Streptococcus , reflecting adaptive responses to host and environmental pressures. Fusobacterium exhibited consistently high replication rates, indicating sustained growth dynamics. Phylogenetic reconstruction further revealed host and niche specific genomic diversification of Saccharibacteria lineages. These findings establish childhood as a decisive period of oral microbial evolution and highlight the role of host-microbiome and epithelial interactions in shaping community structure, providing guidance for oral management strategies that promote lifelong oral health.},
}

@article {pmid41757041,
year = {2026},
author = {Tschang, MA and Vuong, RD and Eilers, B and Chac, D and Waalkes, A and Penewit, K and Easton, A and Schuessler, B and Daniels, R and Weil, AA and Salipante, SJ and Gibbons, SM and Schindler, AG},
title = {If you give a mouse a poopsicle: a novel fecal microbiota transplant method for exploring the role of the gut microbiome in stress-related outcomes in mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.16.705192},
pmid = {41757041},
issn = {2692-8205},
abstract = {The microbiome-gut-brain axis is a mediator of stress-related disorders. The number of preclinical studies exploring the potential causal mechanism of this connection using fecal microbiota transplantation (FMT) is growing. However, the most common method for delivering fecal transplants in rodent models is still oral gavage, which creates an adverse experience that may confound stress-related outcomes. Here, we establish an alternative methodology for FMT that decreases stress induced by traditional experimental procedures. We first used preference and anxiety behavior assays to identify antibiotic therapies having maximal tolerability and minimal anxiolytic properties. We then collected feces from donor mice and homogenized them with a microbe-stabilizing buffer to create a slurry, which was frozen into pellets ("poopsicles") for subsequent FMT. Recipient mice voluntarily consumed the pellets, and blood was collected to compare corticosterone levels relative to traditional gavage FMT. Plasma corticosterone levels were found to be significantly lower in mice receiving FMT via pellets compared to oral gavage. Furthermore, relative to gavage FMT, microbial signatures of mice receiving FMT via pellets were more similar to those of the donor pellets at one week following final FMT and were sustained for up to six weeks, as assessed by comparing Bray-Curtis beta-diversity distances. Together, these results establish effective antibiotic and FMT methods that minimize treatment-induced stress, while effectively transplanting fecal microbes between murine conspecifics.},
}

@article {pmid41757006,
year = {2026},
author = {Tran, HN and Kirven, KJ and Davenport, ER},
title = {SCiMS: Sex Calling in Metagenomic Sequences.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.17.705110},
pmid = {41757006},
issn = {2692-8205},
abstract = {BACKGROUND: Host sex is a critical determinant of microbial community structure, influenced by hormonal profiles, physiology, and sex-stratified behaviors. Despite its importance, sex metadata is frequently missing or mislabeled in microbiome studies. Existing genomic sex-calling tools often fail in low-host-biomass samples (e.g., stool) because they require high read depths to achieve reliability.

RESULTS: Here, we present SCiMS (Sex Calling in Metagenomic Sequences), a bioinformatic tool that leverages host-derived DNA within metagenomic datasets to accurately predict host sex, even at low host coverage. SCiMS uses sex-chromosome read density ratios within a Bayesian classifier to provide high-accuracy sex calls. In simulations, SCiMS achieves >85% accuracy with as few as 450 host reads. When applied to 1,339 samples from the Human Microbiome Project, SCiMS outperforms existing tools, showing higher accuracy and more balanced precision-recall tradeoffs across body sites. SCiMS also generalizes effectively to non-human hosts, achieving 100% accuracy in a murine dataset and outperforming alternatives in a chicken dataset with a ZW sex determination system.

CONCLUSIONS: SCiMS provides an accurate, scalable, and cross-species generalizable solution for host sex classification in metagenomic datasets, even when host DNA is minimal. By enabling the recovery of missing sex metadata, it serves as a quality-control tool for ensuring the integrity of analyses in microbiome research. SCiMS is freely available at http://github.com/davenport-lab/SCiMS .},
}

@article {pmid41756980,
year = {2026},
author = {Park, H and Shen, X and Perelman, D and Berry, P and Lu, Y and Battersby, R and Rose, SMS and Celli, A and Bejikian, C and Snyder, M},
title = {Insulin resistance modifies longitudinal multi-omics responses to habitual diet.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.17.706440},
pmid = {41756980},
issn = {2692-8205},
abstract = {How habitual diet influences the gut microbiome and plasma metabolome across insulin resistance states remains unclear. We conducted year-long multi-omics profiling of 71 deeply phenotyped adults, integrating repeated assessments of diet, metabolome, gut microbiome, clinical laboratory measures, and inflammatory markers. Using gold-standard insulin suppression tests and machine learning-derived dietary patterns, we examined how dietary patterns relate to metabolic and microbial landscapes by insulin resistance status. Insulin-sensitive individuals exhibited stronger and more numerous diet-omics associations than insulin-resistant individuals, identifying metabolic flexibility as a central determinant of dietary responsiveness. Parabacteroides emerged as a candidate microbial mediator between refined carbohydrate-rich dietary patterns and host metabolic signatures. Integrated into a cardiovascular risk prediction model, diet, metabolites, microbial taxa, and immune markers each contributed to 10-year atherosclerotic cardiovascular disease risk. These findings show that inter-individual variation in cardiometabolic risk partly reflects differences in molecular responsiveness to habitual diet, informing precision nutrition and cardiovascular prevention.},
}

@article {pmid41756930,
year = {2026},
author = {Yuan, L and Qin, Y and West-Roberts, J and Anantharaman, K and Wang, H and Zou, Y and Duan, Y and Camargo, AP and Koonin, EV and Chen, L},
title = {A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.21.707213},
pmid = {41756930},
issn = {2692-8205},
abstract = {Closely related prophages are frequently found in phylogenetically distant bacteria in the human gut, despite limited evidence of productive phage infections across broad host ranges. Thus, it remains unclear how the wide distribution of prophages could emerge. Here, we identify a potential mechanism of prophage dissemination. We describe two deeply diverged groups of conjugative megaplasmids (>300 kilobases) in the human gut microbiome, which we term Hodors. Hodors encode conserved replication, partitioning, and type IV secretion systems, together with a complex surface-associated gene module. A subset of Hodors harbor complete, intact prophage genomes, and closely related prophages are detected across phylogenetically distant Bacillota lineages, including both Bacilli and Clostridia. Further analysis indicates that Hodor-associated prophages can exist as extracellular particles and demonstrate their transcriptional activity. Our findings support a model in which conjugative megaplasmids act as composite mobile platforms that disseminate prophage genomes across bacterial lineages, providing a mechanistic explanation for the widespread occurrence of closely related prophages in phylogenetically distant gut bacteria and effectively decoupling lysogenic host range from infective host range.},
}

@article {pmid41748722,
year = {2026},
author = {Hanz, U and Mueller, B and Bart, MC and Busch, K and Reichart, GJ and Rapp, HT and de Goeij, JM and Mienis, F},
title = {Unveiling in situ oxygen, carbon and nutrient cycling of a sponge-driven biological hotspot in the arctic.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41748722},
issn = {2045-2322},
abstract = {UNLABELLED: Deep-sea sponge grounds are habitat-forming benthic communities characterized by high biomass and structural complexity. Despite their ecological significance, their role for the deep-sea environment remains poorly understood and their functioning is often inferred from ex situ studies. We hypothesized that deep-sea sponge grounds exhibit substantially higher respiration and nutrient turnover than surrounding soft sediments, making them hotspots of carbon and nutrient cycling in the deep sea. Integrated respiration and nutrient cycling were quantified in a sponge ground on the summit of an Arctic seamount (Schulz Bank, ~ 580 m depth). We used in-situ incubation chambers measuring oxygen consumption, prokaryotic cell removal, and inorganic nutrient fluxes. Respiration rates ranged from 0.13 to 0.93 mmol O2 m[-2] h[-1], which is comparable to cold-water coral reefs and up to 7–21 times higher than reported for soft sediments of the Arctic deep sea. This indicates a high organic carbon demand exceeding surface-derived supply, suggesting the uptake of additional food resources. All incubations showed net release of ammonium, phosphate, nitrite and nitrate, with fluxes correlating with sponge biomass. Our results demonstrate that deep-sea sponge grounds function as hotspots of carbon and nutrient cycling and suggest distinct functional contributions of sponge groups and their microbiome.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41798-4.},
}

@article {pmid41756883,
year = {2026},
author = {Wirbel, J and Saber, W and Martens, MJ and Peled, JU and Andermann, TM and Fei, T and Brooks, EF and Doyle, B and Pincus, NB and Jenq, RR and Bar, M and Bolaños-Meade, J and Bratrude, B and Chhabra, S and Choi, SW and Clark, W and Das, S and Elmariah, H and Gooptu, M and Holtan, SG and Jones, RJ and Levine, JE and Logan, BR and Al Malki, MM and Murthy, HS and Rashidi, A and Rezvani, AR and Riches, ML and Runaas, L and Sandhu, K and Spahn, A and Sung, AD and van den Brink, MRM and Horowitz, MM and Hamadani, M and Kean, LS and Perales, MA and Bhatt, AS},
title = {Differential effects of two common GVHD prophylaxis regimens on the gut microbiome: Results from the BMT CTN 1801 study.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.19.706769},
pmid = {41756883},
issn = {2692-8205},
abstract = {Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative treatment for many hematological malignancies, but graft-versus-host disease (GVHD) is a common complication. Low gut microbiome diversity is associated with higher GVHD risk and shorter survival in multiple studies. Recently, the BMT CTN 1703 clinical trial demonstrated superiority of a GVHD-prophylaxis regimen including post-transplant cyclophosphamide (PTCy) compared to the standard prophylaxis (tacrolimus and methotrexate, Tac/MTX) in terms of GVHD-free, relapse-free survival at one year among reduced intensity conditioning allo-HCT recipients. However, the effect of PTCy on the gut microbiome and its association with clinical outcome have not been described. Here, we report on a companion randomized clinical controlled trial (BMT CTN 1801), which collected 2575 longitudinal stool samples from 304 study participants. Samples were obtained up to weekly up to day 84 post allo-HCT and at less frequent intervals thereafter, up to 2 years. Microbiome diversity and absolute microbial load were lower in the PTCy group compared to the Tac/MTX group on days 14-28 post-HCT. However, diversity at the timepoint closest to neutrophil engraftment was not significantly associated with non-relapse mortality after one year or other clinical outcomes, contrary to expectations from previous studies. Microbial domination events, when a single species exceeds 30% relative abundance, were comparable across treatment arms and reflected both pathogen blooms as well as less severe disruptions of the microbial community. Clostridium scindens and secondary bile acid metabolism pathways were less prevalent in the PTCy arm than in the Tac/MTX arm post-HCT, yet presence of secondary bile acid metabolism pathways was associated with a lower risk of chronic GVHD. Given that PTCy was associated with a greater disruption of the microbiome as measured by diversity, absolute microbial abundance, and bile acid metabolism capability, but better clinical outcomes overall, these data suggest that the importance of the microbiome in modulating the host immune systems after allo-HCT is specific to different types of GVHD prophylaxis.},
}

@article {pmid41756881,
year = {2026},
author = {Krieger, M and Kerns, KA and Palmer, EA and McLean, JS and Kreth, J and Yardimci, GG and Merritt, JL},
title = {Paired oral clinical specimens reveal the underlying ecology supporting the emergence of inflammophilic microbiome communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.20.706901},
pmid = {41756881},
issn = {2692-8205},
abstract = {BACKGROUND: Inflammatory oral diseases are associated with reproducible shifts from commensal-dominated microbiota toward pathobiont-enriched communities, yet the ecological mechanisms underlying the emergence of inflammophiles remain poorly understood. This study aims to investigate if host-derived inflammatory environments act as selective pressures that restructure microbial metabolism and community organization during disease progression.

METHODS: We performed 16S rRNA gene sequencing of patient-matched pediatric dental plaque and odontogenic abscess specimens to capture microbial community transitions across an inflammatory ecological gradient. Community ecology modeling and inferred metagenomic analyses were used to identify taxa and functional programs associated with commensal and inflammophilic states.

RESULTS: Patient-matched comparisons revealed a reproducible ecological selection gradient linking inflammatory environments to expansion of metabolically specialized inflammophiles and depletion of carbohydrate-utilizing commensals. Commensal-dominated plaque communities exhibited anabolic, carbohydrate-centered metabolic capacity, whereas abscess microbiota were enriched for catabolic metabolism, amino acid fermentation, and antimicrobial resistance, consistent with adaptation to inflammation-driven nutrient landscapes and immune pressure.

CONCLUSIONS: These findings support a model in which host inflammation drives ecological restructuring of the oral microbiome toward metabolically adapted inflammophilic communities. Defining the metabolic requirements and selective pressures governing these transitions provides a framework for microbiome-directed therapeutic strategies aimed at restoring ecological stability during inflammatory dysbiosis.},
}

@article {pmid41756820,
year = {2026},
author = {Trang, KT and Gulick, DA and Truell, J and Tian, J and Bodkhe, R and Hiseni, P and Gravdal, K and Kirubakaran, TG and Casén, C and Singh, R and Ziegler, TR and Reimer, RA and Kraft, CS},
title = {Diet-Microbiome Analysis in a Healthy Cohort Reveals Potential Role of Intestinal Microbiota in Metabolism.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.17.706416},
pmid = {41756820},
issn = {2692-8205},
abstract = {UNLABELLED: Both preclinical and clinical studies have revealed the indisputable importance of intestinal bacterial community composition in pathogenesis of various disease states, from obesity to neurodegeneration. Diet remains one of the most important factors shaping human intestinal microbiota composition. In this study, we investigated diet-microbiome interactions in a healthy cohort of 88 participants from Atlanta and Calgary. We examine microbial composition (16S rRNA sequencing) with dietary records using Spearman Correlation tests with Benjamini-Hochberg multiple hypothesis correction to make community-level comparisons between dietary scores and microbial diversity index scores. Predictive models were used for molecular-level comparisons between microbial gene pathways and molecules. Among generalized dietary and microbial indices, we identified a negative association between dietary whole grain consumption and a microbial dysbiosis score. Comparisons between dietary food groups and bacterial family abundance reveal significant associations between dairy consumption and Lactobacillaceae abundance, dietary unsaturated to saturated fatty acid ratio and Clostridia Cluster Family XIII, salt intake and Lachnospiraceae , and consumption of 'greens and beans' and Veillonellaceae . Predictive models of microbial gene pathways and molecules reveal significant positive associations between several dietary fatty acids and microbial short-chain fatty acid fermentation pathways, and between dietary lignans and archaeal methanogenesis pathways. Overall, these associations may inform future explorations on specific dietary interventions to impact the gut microbiome.

IMPORTANCE: In this study, we compare dietary records and composition of intestinal microbes in a cohort of 88 participants. We identified associations between dietary consumption of dairy and the presence of dairy-consuming bacteria called Lactobacteriaceae and between consumption of dietary fats and the presence of fat-consuming bacteria called Clostridia . Using predictive analysis, we identify specific fatty acids associated with specific biochemical pathways found in Clostridia that might underlie these associations, in addition to an association between archaeal microbes and dietary consumption of estrogen-binding molecules called lignans, which are commonly found in whole grains and vegetables. Overall, our study generates useful associations between diet and intestinal microbes that can be tested in experiments that may help scientists use diet to control intestinal microbes in order to improve human health.},
}

@article {pmid41756623,
year = {2026},
author = {Szilagyi, A and Galiatsatos, P and Margolese, N},
title = {There may be a differential mechanistic impact on colorectal cancer of lactose-containing foods between lactase persistent and lactase non-persistent populations.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1671166},
pmid = {41756623},
issn = {2296-861X},
abstract = {It is generally suggested that milk and milk products reduce the risk of colorectal cancer (CRC). While there is some controversy over specific sites affected throughout the colon and the benefits of specific dairy foods (DFs), there is a general consensus that calcium intake is the main mechanism of the cancer-reducing effects. This opinion may be sidelined by several other mechanisms. There is also a potentially important compensatory mechanism in populations with adult genetic lactase deficiency. The microbiome changes occur through a process of adaptation to continued lactose consumption. The bacterial blooms consist largely of Bifidobacterial species. These bacteria may exert anti-neoplastic effects and also increase the capacity of persons with adapted lactase insufficiency to consume dairy products. Bacterial metabolism thus provides a second pathway for lactose digestion. Since the use of Mendelian randomization (MR) accuracy disallow two different pathways for the genetic variable, this process constitutes a horizontal pleiotropy. This narrative review using articles from PubMed and Google Scholar will discuss different nutrients and mechanisms in milk and milk products that are involved in anti-neoplastic effects. The impact of adult lactase deficiency and continued dairy consumption on the microbiome, and its contribution to colorectal cancer reduction, is highlighted. The conclusions from this review are that calcium has multifaceted mechanisms of anti-carcinogenesis, but other nutrients, such as conjugated linoleic acid (CLA), lactoferrin, and folate in the dairy matrix, could also contribute. In lactase non-persistent (LNP) populations adapted to dairy foods, a bifidogenic bloom in the microbiome may add additional anti-neoplastic effects and /or increase dairy food consumption. We argue that predictions of colon cancer effects from dairy foods may be inaccurate, and that evaluating both populations together may confound outcomes.},
}

@article {pmid41756428,
year = {2026},
author = {Li, J and Bu, E and Lian, A and Li, Y and Tao, C},
title = {Polarity-Aware Knowledge Graph Reveals Diet-Microbiome-Health Mechanisms with Relevance to Muscle, Immune and Metabolic Aging.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8771108/v1},
pmid = {41756428},
issn = {2693-5015},
abstract = {Diet profoundly influences gut microbial composition and metabolism, yet mechanistic pathways linking dietary exposures to human health remain fragmented across the literature. To systematically organize and integrate this evidence, we constructed an evidence-weighted Diet-Microbiome-Health Knowledge Graph (DMH-KG) from 1,309 curated PubMed abstracts (2023-2025), using a standardized schema spanning 11 entity categories and 12 relationship types with explicit polarity labels. Entities and relationships were identified through manual annotation, yielding 10,270 entity mentions and 4,866 relationships. Expert-guided consolidation of synonymous and lexically variant terms, along with pruning of disconnected concepts, resulted in 4,766 unique entities connected by 4,772 polarity-weighted edges. To prioritize robust biological signals, a composite edge-weighting function was applied, integrating both relationship frequency and polarity. Network analysis revealed a modular small-world structure centered on microbial and inflammatory mediators. High-confidence pathways emerged, including the probiotic-SCFA-immunity axis (34 supporting documents) and the high-fat diet-LPS-endotoxemia cascade (8 documents), both of which are central to age-related immune modulation and metabolic health. Quantitative validation against five KEGG and Reactome pathways demonstrated high biological fidelity: the DMH-KG recovered all reference diet-microbiome-outcome edges for Butanoate metabolism and Secondary Bile Acid biosynthesis (100% coverage) and achieved a mean pathway-level entity coverage of 92.0%, measured as the proportion of predefined pathway components represented in the graph. A comparative pilot study further demonstrated that DMH-KG augmentation improves mechanistic specificity inference across Diet-Microbiome-Health interactions. These features position the DMH-KG as a scalable platform for mechanistic inference across Diet-Microbiome-Health interactions, with direct relevance to immune regulation, muscle health, metabolic aging, and chronic disease prevention. The framework preserves evidence provenance, relationship polarity, and biological direction, supporting both discovery science and AI-driven nutritional reasoning.},
}

@article {pmid41756197,
year = {2026},
author = {Li, F and Anyaso-Samuel, S and Yano, Y and Chang, VC and Hua, X and Wan, Y and Dagnall, CL and Jones, K and Hicks, BD and Hutchinson, A and Liao, LM and Huang, WY and Freedman, ND and Beane Freeman, LE and Sandler, DP and Abnet, CC and Sinha, R and Shi, J and Loftfield, E and Vogtmann, E},
title = {Association between diet quality and the oral microbiome in three US cohort studies.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2635238},
pmid = {41756197},
issn = {2000-2297},
abstract = {BACKGROUND: The oral microbiome has been associated with overall health, but the contribution of dietary habits to oral microbial composition is not well understood.

OBJECTIVE: We evaluated the association between diet quality (Healthy Eating Index [HEI] 2015) and the oral microbiome in the Agricultural Health Study, NIH-AARP Diet and Health Study, and Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial within 5,546 participants.

METHODS: Individual HEI components were scored from FFQ data and summed. Alpha and beta diversity and genus-level presence and relative abundance were estimated. The proportion of variability in the beta diversity matrices explained by diet quality and other covariates were calculated. Linear, logistic, and zero-inflated negative binomial regression models with adjustment for confounders were used and cohort-specific estimates were meta-analyzed.

RESULTS: Age explained the largest variability in beta diversity (Bray-Curtis), followed by smoking, education, and the HEI component for added sugar. Although overall diet quality was not associated with alpha diversity overall, the added sugar component was consistently inversely associated with alpha diversity. At the genus-level, most of the identified associations were with added sugar.

CONCLUSIONS: Consumption of added sugars was consistently associated with oral microbial diversity and specific genera.},
}

@article {pmid41756132,
year = {2026},
author = {Bamrung, V and Sitthicharoenchai, P},
title = {The evolving story of Streptococcus gallolyticus: classification, pathogenesis, role in human and animal disease, and laboratory diagnostics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1765252},
pmid = {41756132},
issn = {1664-302X},
abstract = {Streptococcus gallolyticus, formerly known as S. bovis, belongs to the Streptococcus bovis/Streptococcus equinus complex (SBSEC). Besides being a part of the gut microbiome, this organism has gained interest due to its association with infective endocarditis and its strong correlation with colorectal cancer in humans. In veterinary medicine, systemic infection caused by S. gallolyticus has been reported in various animal populations, including porcine, ruminant, and avian species. Despite its clinical importance in humans and animals, two key challenges persist: the limited understanding of the pathogenesis due to its ubiquitous nature and inconsistencies in diagnostic laboratory reporting of the bacteria in SBSEC. This review summarizes the taxonomic characterization of the SBSEC, its clinical manifestations across species, current understanding of the bacterial pathogenesis, and the laboratory diagnostic assays used for its detection. We will further discuss the importance of SBSEC speciation and subspeciation, highlighting their distinct clinical implications and potential impact on human and animal health.},
}

@article {pmid41756131,
year = {2026},
author = {Liu, Z and Deng, W and Xu, W and Ye, L and Rao, Z},
title = {Probiotic supplementation modulates the gut microbiome and improves clinical outcomes in pediatric refractory asthma.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1756436},
pmid = {41756131},
issn = {1664-302X},
abstract = {BACKGROUND: Refractory asthma in children remains a clinical challenge despite conventional therapies, with emerging evidence linking gut microbiome dysbiosis to persistent inflammation via the gut-lung axis. This study investigated whether multi-strain probiotic supplementation could improve asthma control and restore microbial balance when added to standard treatment.

METHODS: This prospective randomized controlled trial enrolled 88 children aged 4-8 years with refractory asthma. Participants were allocated into two groups (n = 44 each): a conventional treatment group (bronchodilators and glucocorticoids) and a combination treatment group, which received conventional therapy plus a multi-strain probiotic (Bifidobacterium, Lactobacillus acidophilus, Streptococcus thermophilus) for 4 months. Primary outcomes were asthma control level, Asthma Control Test (ACT) scores, and pulmonary function (FEV₁, FVC, PEF). Secondary outcomes included gut microbiota changes, assessed by 16S rRNA gene sequencing.

RESULTS: Combination therapy achieved complete asthma control in 68.18% of patients versus 36.36% with conventional therapy (Z = 2.415, p < 0.05). Post-treatment ACT scores were higher in the combination group (22.45 ± 1.20 vs. 19.78 ± 1.45; p < 0.05), with superior improvements in FEV1 (2.65 ± 0.10 L vs. 2.30 ± 0.08 L; p < 0.001), FVC (3.10 ± 0.18 L vs. 2.80 ± 0.15 L; p < 0.001), and PEF (4.00 ± 0.25 L/s vs. 3.50 ± 0.20 L/s; p < 0.001). Symptoms resolved faster with combination therapy (e.g., cough: 5.60 ± 1.50 vs. 10.45 ± 2.30 days; p < 0.05). Microbiome analysis showed increased alpha diversity (e.g., Shannon index: p < 0.05) and beneficial shifts in the combination group, including higher Bifidobacterium (25.00 ± 15.31% vs. 0.98 ± 1.92%; p < 0.001) and reduced Bacteroides, with distinct beta diversity clustering (PERMANOVA p < 0.05).

CONCLUSION: Adjunctive multi-strain probiotics enhance clinical outcomes and gut microbiome health in pediatric refractory asthma, supporting microbiome-targeted therapies via the gut-lung axis. Larger, double-blind randomized controlled trials are warranted to confirm long-term benefits.},
}

@article {pmid41756119,
year = {2026},
author = {Cai, L and Sun, J and Li, H and Wang, C and Zhang, M and Shao, Q and Wang, Z},
title = {A novel internal reference microorganism-based method reveals wild-enriched Penicillium for enhancing growth and disease resistance in Fritillaria thunbergii.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1746815},
pmid = {41756119},
issn = {1664-302X},
abstract = {INTRODUCTION: Fritillaria thunbergii Miq. is an important traditional Chinese medicinal herb, but bulb rot disease causes severe losses during its cultivation. Screening and reintroducing beneficial microorganisms from the wild rhizosphere is an effective strategy to increase disease resistance in cultivated plants. However, the absolute quantitative characteristics of microorganisms cannot be reflected by traditional methods based on relative abundance analysis due to compositional bias.

METHODS: In this study, we identified Clavatospora as a host-specific internal reference microorganism (IRM) and established an IRM-based relative abundance differential microorganism analysis (IRMRADMA) method.

RESULTS: Application of this method revealed that wild F. thunbergii possesses greater potential than cultivated plants for mining beneficial rhizosphere microorganisms. Specifically, Penicillium was identified as a key wild-enriched genus. Subsequently, two strains, Penicillium korosum and Penicillium aculeatum, were isolated from the rhizosphere of wild F. thunbergii. Functional tests confirmed that these strains demonstrated dual functions in disease suppression and plant growth promotion by solubilizing phosphate, producing siderophores, antagonizing pathogens, and upregulating defenserelated genes.

CONCLUSION: This study established the IRM-RADMA method and identified key Penicillium strains from the wild Fritillaria thunbergii rhizosphere. Their confirmed dual functions in growth promotion and disease suppression validate the 'plant microbiome rewilding' strategy, offering a new paradigm for the biological control of F. thunbergii diseases.},
}

@article {pmid41755783,
year = {2026},
author = {Kim, KS and Cho, JY and Park, YC and Hong, JH and Jung, JG and Sunwoo, J},
title = {Exploring LEPR-Linked Metabolic Diversity through Gut Microbiome-Metabolome Network Analysis in Non-Obese Adults.},
journal = {Biomolecules & therapeutics},
volume = {34},
number = {2},
pages = {448-460},
doi = {10.4062/biomolther.2025.161},
pmid = {41755783},
issn = {1976-9148},
abstract = {Genetic variation in the leptin receptor (LEPR) gene has been implicated in metabolic regulation, while the gut microbiome and circulating metabolites are increasingly recognized as mediators of host metabolic phenotype. However, the systems-level interactions among LEPR genotypes, gut microbial composition, and serum metabolomic profiles remain poorly understood, particularly in healthy individuals. We conducted a cross-sectional study involving 37 healthy Korean adults. Three LEPR single nucleotide polymorphisms (rs1137101, rs1173100, rs790419) were genotyped. Untargeted metabolomics of fasting serum was performed using gas chromatography-time-of-flight mass spectrometry, and gut microbiome composition was profiled by 16S rRNA gene sequencing. Statistical analysis included principal component analysis, Mann-Whitney U tests, and Spearman correlations. Network analysis integrating microbiome, metabolomic, and clinical phenotype data was conducted using Cytoscape. A total of 54 serum metabolites were identified. LEPR genotypes, particularly rs1137101 and rs1173100, were associated with differences in metabolites such as pimelic acid, malonic acid, and 2,4-dihydroxybutyric acid. Firmicutes negatively correlated with saturated fatty acids and organic acids, whereas Actinobacteria positively correlated with cholesterol and amino acids. Network analysis revealed indole-3-acetate and cholesterol as central nodes linking microbial taxa with body mass index and leptin levels. However, no direct molecular pathways connecting leptin or its receptor were identified. LEPR genetic variation is associated with distinct serum metabolomic patterns and microbiome-host networks in healthy adults. Although no direct leptin signaling links were found, network-level associations suggest indirect genetic influences on metabolic states through microbiome-metabolome interactions. These findings advance understanding of personalized metabolic regulation and gene-microbiome interplay.},
}

@article {pmid41755580,
year = {2026},
author = {Mendoza, ADG and Nuncio-Mora, L and Sánchez, V and Gonzalez, V and Nicolini, H},
title = {Dysbiosis in the Family nucleus of Children Diagnosed With Autism Spectrumin Mexico City.},
journal = {Actas espanolas de psiquiatria},
volume = {54},
number = {1},
pages = {121-127},
pmid = {41755580},
issn = {1578-2735},
abstract = {BACKGROUND: The relationship between the gut microbiome and Autism Spectrum Disorder (ASD) has been the subject of growing interest in scientific research. Research into the relationship between the gut microbiome and ASD has gained relevance in recent years as recent studies have identified significant differences in the gut microbiome abundance and composition in ASD children compared to neurotypical ones. However, little is known about the microbiome interplay, changes and relationship in parents and children with ASD, considering that they share a consistent environment. Charactering the microbiota of trio-type families with a child diagnosed with autism.

METHODS: The hypervariable region of the 16s ribosomal gene was sequenced from stool samples from adolescents with ASD and their parents. The analysis was performed using various software programs, including QIIME2 and DADA2.

RESULTS: In this paper, we discuss this relationship in three families, and observed that the gut microbiome of the offspring with ASD is more similar to the mother's than the father's microbiome.

CONCLUSIONS: These observations could lead to the understanding of the potential heritability of the disorder through parental connectedness of the gut microbiome and eventually to the development of interventions aimed at modulating the gut microbiota to improve symptoms associated with ASD.},
}

@article {pmid41755545,
year = {2026},
author = {Song, Z and Song, C and Yi, X and Shao, Y and Zhang, Y},
title = {Targeting the transferrin receptor in breast cancer: nanotechnology-based drug delivery strategies.},
journal = {Nanomedicine (London, England)},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/17435889.2026.2628237},
pmid = {41755545},
issn = {1748-6963},
abstract = {Breast cancer remains a leading cause of cancer-related morbidity and mortality worldwide, with treatment efficacy often limited by systemic toxicity, poor tumor selectivity, and multidrug resistance. Nanotechnology-based drug delivery systems offer a promising strategy to enhance therapeutic precision, particularly through active targeting of tumor-associated receptors. The transferrin receptor (TfR), which is frequently overexpressed in breast cancer cells, has emerged as an attractive target due to its role in receptor-mediated endocytosis. This review critically summarizes recent advances in transferrin-functionalized nanocarriers for breast cancer therapy, including liposomal, polymeric, dendrimeric, metallic, and hybrid platforms. Key design parameters influencing cellular uptake, biodistribution, and therapeutic efficacy - such as particle size, surface charge, ligand density, and release behavior - are discussed. We highlight progress in multifunctional and stimuli-responsive systems designed to overcome tumor microenvironment barriers and multidrug resistance. In addition, emerging evidence on the role of the gut microbiota in modulating breast cancer progression and treatment response is examined, with a focus on its potential impact on targeted nanomedicine efficacy. Finally, current translational challenges and future directions, including personalized and microbiome-informed nanotherapeutic strategies, are outlined. Literature was identified through systematic searches of PubMed, Web of Science, Scopus, and Google Scholar from January 2005 to March 2025.},
}

@article {pmid41755503,
year = {2026},
author = {Li, J and Will, I and Silva, LM and Travers-Cook, TJ and Blackwood, PE and King, KC},
title = {Integrating the Microbiome Into Infection Ecology and Evolution in Wild Animals.},
journal = {Molecular ecology},
volume = {35},
number = {5},
pages = {e70281},
pmid = {41755503},
issn = {1365-294X},
support = {//Canada Excellence Research Chairs, Government of Canada/ ; },
abstract = {Parasites are a ubiquitous force in nature threatening wildlife populations and ecosystems. Interactions between hosts and their parasites are impacted by host-associated microbiomes, which are essential for host development, physiology and immunity. We synthesise current understanding of the ecological interactions between host microbiomes and parasites, ranging from competitive to facilitative, and explore their potential evolutionary consequences for parasite virulence and transmission in the wild. We highlight recent mechanistic insights that support integrating a microbiome perspective into wildlife parasitology, with examples across diverse animal taxa including amphibians, bats, insects and corals, particularly within the context of climate change. Adopting such a holistic approach can open new avenues whereby host microbial shifts can be used to predict and mitigate infectious diseases in wild populations. Finally, we propose a conceptual framework to guide future research on microbiome-parasite-host interactions, aiming to better reflect natural ecological complexities and advance both fundamental understanding and conservation applications.},
}

@article {pmid41755380,
year = {2026},
author = {Lee, Y and Mustakim, KR and Eo, MY and Cho, YJ and Kim, SM},
title = {Peri-implantitis as a potential risk factor for peri-implant oral malignancy.},
journal = {Journal of the Korean Association of Oral and Maxillofacial Surgeons},
volume = {52},
number = {1},
pages = {27-33},
doi = {10.5125/jkaoms.2026.52.1.27},
pmid = {41755380},
issn = {2234-7550},
abstract = {Peri-implant oral malignancy (PIOM) refers to malignant tumors arising around dental implants and is an increasingly reported complication of implant therapy. PIOM may follow distinct pathophysiological mechanisms, including chronic peri-implant inflammation and implant-related factors that contribute to carcinogenesis. This current review aims to explore the potential role of peri-implantitis (PI) as a risk factor for PIOM, discussing the proposed pathogenic mechanisms, histological findings, and clinical implications. A comprehensive literature search was conducted in PubMed, Scopus, and Web of Science databases. Relevant case reports, clinical studies, and reviews on the keywords "PIOM" and "PI" published from 2019 up to 2025 were included and qualitatively analyzed. Clinicopathologic characteristics are summarized as location and morphology, disease progression, histopathology, and degree of differentiation, and pathophysiological hypotheses involve inflammatory and electrochemical pathways, epithelial barrier dysfunction, molecular alterations, microbiome dysbiosis, and immune dysregulation. Current evidence remains limited and primarily anecdotal. Several studies suggest that chronic inflammation, titanium particle exposure, corrosion byproducts, and sustained tissue damage in peri-implant tissues may contribute to oncogenesis. While a direct causal link between PI and PIOM remains unproven, chronic peri-implant inflammation may contribute to malignancy development in predisposed individuals. Clinicians should consider a biopsy when peri-implant lesions exhibit atypical features, promptly.},
}

@article {pmid41754858,
year = {2026},
author = {Bertin, L and Facchin, S and Barberio, B and Maniero, D and Lorenzon, G and Cesaroni, F and Zanconato, M and Romanelli, G and Francini-Pesenti, F and Busetto, L and Cananzi, M and Gaio, P and Bosa, L and Zingone, F and Gianolio, L and Damas, OM and Savarino, EV},
title = {Diet and Gut Microbiota in Inflammatory Bowel Disease: A Clinical and Nutritional Perspective.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {2},
pages = {},
pmid = {41754858},
issn = {1424-8247},
abstract = {Inflammatory bowel diseases, comprising Crohn's disease and ulcerative colitis, represent chronic inflammatory disorders with rising global incidence, underscoring the pivotal role of modifiable environmental factors in disease pathogenesis. Diet and intestinal microbiota have emerged as critical bidirectional therapeutic targets through complex interactions with host immune responses. Epidemiological evidence demonstrates that healthy and high fiber diets reduce disease risk, while ultra-processed foods and inflammatory dietary patterns increase susceptibility. Therapeutic nutritional interventions, including exclusive enteral nutrition, the Crohn's Disease Exclusion Diet combined with partial enteral nutrition, and the Mediterranean diet can induce and maintain clinical remission while promoting favorable microbiome modifications characterized by the enrichment of butyrate-producing taxa such as Faecalibacterium prausnitzii and Roseburia species, alongside a reduction in pathogenic Proteobacteria. Micronutrient deficiencies affect up to 78% of patients through malabsorption, chronic blood losses, dietary restrictions, and drug-nutrient interactions. Nutritional status significantly impacts surgical outcomes, with preoperative malnutrition and sarcopenia associated with increased postoperative complications, and it reciprocally influences biologic therapy response. Integration of personalized, microbiome-informed dietary strategies as complementary components of comprehensive treatment plans represents a promising therapeutic frontier, requiring multidisciplinary collaboration, rigorous clinical trials with standardized microbiome analyses, and precision nutrition algorithms accounting for disease phenotype, baseline microbial composition, and individual patient characteristics to optimize outcomes and improve quality of life.},
}

@article {pmid41754809,
year = {2026},
author = {Krakowska, A and Skiba-Kurek, I and Zontek-Wilkowska, J and Koczurkiewicz-Adamczyk, P and Muszyńska, B and Skalski, T},
title = {The Use of Biomass from In Vitro Fungal Cultures as a Bioactive Ingredient with Antimicrobial Activity in Hydrogel Dressings.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {2},
pages = {},
pmid = {41754809},
issn = {1424-8247},
support = {NCN 2024/08/X/NZ7/01059//National Science Centre/ ; },
abstract = {Background/Objectives: Chronic wounds represent a significant clinical burden and require multimodal treatment strategies targeting inflammation, infection, moisture balance, and tissue remodeling, as defined by the TIME framework. This study aimed to evaluate the therapeutic potential of innovative hydrogel dressings enriched with fungal biomass, designed to exploit natural bioactive compounds-such as antimicrobial peptides and proteolytic enzymes-to enhance wound healing while maintaining high biocompatibility. Methods: Hydrogel dressings incorporating selected fungal biomasses were fabricated and characterized for physicochemical and biological performance. Key material properties relevant to wound care, including hydrophilicity and porosity, were analyzed to assess exudate management capacity and maintenance of a moist wound environment. Antimicrobial activity was tested against common wound pathogens, and species-pathogen interactions were evaluated using generalized linear modeling. In vitro biocompatibility was assessed using human keratinocytes and compared with conventional silver nanoparticle-based dressings. Results: The developed hydrogels demonstrated properties suitable for clinical application, including superhydrophilicity and high porosity, supporting effective exudate control and moisture retention. Significant broad-spectrum antimicrobial activity was observed, particularly against Staphylococcus aureus and Pseudomonas aeruginosa, with effects dependent on fungal species. Statistical modeling revealed highly significant interactions between fungal species and pathogens in inhibition zones (p < 0.001). Hydrogels containing Pleurotus ostreatus and Agaricus bisporus showed broad activity against Escherichia coli, P. aeruginosa, and S. aureus, whereas Enterococcus faecalis exhibited resistance. Fungal biomass-based dressings displayed superior keratinocyte biocompatibility compared to silver nanoparticle controls. Conclusions: Fungal biomass-reinforced hydrogels offer a promising, safer, multifunctional alternative for infected chronic wound management, supporting both antimicrobial action and tissue regeneration.},
}

@article {pmid41754522,
year = {2026},
author = {Atkins, H and Stegman, N and Putonti, C},
title = {Diverse Temperate Coliphages of the Urinary Tract.},
journal = {Viruses},
volume = {18},
number = {2},
pages = {},
pmid = {41754522},
issn = {1999-4915},
support = {1R15AI171873-05/NH/NIH HHS/United States ; },
abstract = {While Escherichia coli can be found in the bladders of females without lower urinary tract symptoms, its presence is often associated with urinary tract infections (UTIs). The genomic plasticity of E. coli, including urogenital strains, is largely shaped by the integration of prophages. Although genomic and metagenomic analyses of urinary E. coli and the urinary microbiome suggest that prophages are abundant, many represent uncharacterized species. Sequence analysis suggests that these prophages represent temperate phages. This study aimed to fill this gap, isolating and characterizing temperate phages from urinary E. coli strains. We assessed phage host range across a panel of urinary isolates, providing a critical first step for future work investigating their putative role in shaping E. coli populations within the urinary community. In total, 20 temperate urinary phages were evaluated. Phage morphology and genic content of these phages were determined via transmission electron microscopy (TEM) and whole-genome sequencing, respectively. Together, these analyses provide insight into the diversity, infectivity, and genomic composition of temperate coliphages from the female urinary tract.},
}

@article {pmid41754473,
year = {2026},
author = {Vilela, C and Mendoza, L and Vilela, R and Moreira Jardilino, FD and Brilhante Bhering, CL and Moreno, A},
title = {Microbial Diversity and Composition Uncovered on Obturator Prosthesis Biofilms: Exploratory Findings from a Pilot Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754473},
issn = {2076-0817},
abstract = {Microbial communities on obturator prosthesis biofilms have yet to be investigated. This pilot study explores eukaryotes, prokaryotes, and viruses present on obturator prosthesis biofilms using metagenomics. The prostheses of the selected patients (n = 3) were collected and their biofilms were physically removed. The total genomic DNA was extracted, followed by metagenomic analysis. The microbial diversity in each of the investigated biofilms was exceptionally abundant. Between 2616 to 3024 species were detected in the three biofilms. The highest percentage included prokaryotes and unclassified species, followed by low percentages of fungi, viruses, and archaea. Unusual pathogens rarely reported in oral biofilms, such as Mycobacterium and other species, were also found at very low percentages. Unigenes for functional pathways related to metabolism, cellular processes, human disease, and other microbial unigenes were abundant. In addition, unigenes for several antibiotic-resistance mechanisms were also detected. This study reveals, for the first time, that biofilm formation on obturator prostheses comprises a variety of dynamic microbial communities, suggesting a putative role in health and disease in patients following maxillofacial surgery.},
}

@article {pmid41754458,
year = {2026},
author = {Anderson, JG and Scarsella, E and Soltero-Rivera, M and Goldschmidt, S and Rojas, CA and Ganz, HH},
title = {First Description of Oral Microbiota in Domestic Cats Affected by Oral Squamous Cell Carcinoma.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754458},
issn = {2076-0817},
support = {annual grant 2022//Foundation for Veterinary Dentistry/ ; 5K12-CA138464//National Cancer Institute/National Institutes of Health/ ; UL1 TR001860/TR/NCATS NIH HHS/United States ; },
abstract = {Oral squamous cell carcinoma (OSCC) accounts for the majority of feline oral neoplasms and carries a poor prognosis; however, the oral microbiome in affected cats remains poorly characterized. This study aimed to preliminarily describe the oral bacterial communities of cats with OSCC and compare them with those of clinically healthy cats using DNA amplicon sequencing. Oral swabs were collected from cats with OSCC, including tumor surfaces, tumor cut surfaces, and clinically normal mucosa distant from the tumor (n = 20 total samples), and from the gingival margin of healthy cats (n = 12). DNA was extracted and full-length 16S rRNA gene sequencing was performed to assess microbial composition and diversity. Cats with OSCC exhibited significant alterations in oral microbiota compared with healthy controls, including reduced alpha diversity, distinct beta-diversity clustering, and consistent taxonomic shifts. Healthy cats displayed a relatively conserved core microbiome dominated by Porphyromonas spp., Bacteroides, Pasteurellaceae, Helcococcus, and Moraxella. In contrast, OSCC-associated samples showed increased relative abundances of anaerobic and disease-associated taxa, including Filifactor villosus, Bacteroides pyogenes, Odoribacter denticanis, Porphyromonas circumdentaria, and members of the Pasteurellaceae. These findings provide the first description of the oral microbiota associated with feline OSCC and demonstrate exploratory microbial differences between health and disease.},
}

@article {pmid41754428,
year = {2026},
author = {Ugwu, CE and Akinsulie, OC and Ayandokun, TF and Ajibade, FA and Shahzad, S and Aliyu, VA and Oladoye, MJ and Idris, I and Obasi, KO and Edeh, JK and Olojede, AA and Ukauwa, CB and Adeyemi, MI and Ugwu, CC and Ugorji, LC},
title = {Mechanisms and Therapeutic Potential of Nutritional Immunity.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754428},
issn = {2076-0817},
abstract = {Nutritional immunity is a major facet of host defense, wherein the host immune system strategically limits pathogen access to critical nutrients, including iron, zinc, vitamins, lipids, and amino acids, to repress microbial proliferation and virulence. This review provides a comprehensive synthesis of the molecular mechanisms that power nutrient immunity, including metal homeostasis, nutrient competition, transporter modulation, hormonal regulation, and direct antimicrobial actions. We examine nutrient-specific strategies employed by the host, such as iron-withholding mechanisms, vitamin deprivation, and copper-mediated toxicity. We also explore how diverse pathogens, including extracellular, intracellular, and eukaryotic pathogens, adapt to these hostile nutritional landscapes through siderophore diversification, regulatory integration, and metabolic rewiring. Comparative genomic analyses reveal convergent evolution in nutrient acquisition systems, illuminating the dynamic arms race between host restriction and microbial evasion. We examine the immunological mechanisms that regulate nutritional immunity. Further, we discuss the translational potential of nutritional immunity, cutting across nutrient-based therapies, host-directed interventions, and emerging diagnostic biomarkers. Finally, we suggest future directions that synergize nutritional immunity with microbiome ecology, global malnutrition, and personalized medicine. By elucidating the interconnection between metabolism and immunity, this review highlights the therapeutic promise of starving or toxifying the pathogen to save the host.},
}

@article {pmid41754400,
year = {2026},
author = {Wang, X and Duan, R and Ming, A and Zhang, Y and Liu, T and Wang, X and Diao, M},
title = {Age-Dependent Dynamics of the Biliary Microbiome in Children with Choledochal Cysts: Functional Remodeling Underlying Taxonomic Conservation.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754400},
issn = {2076-0817},
abstract = {Choledochal cyst (CC), a congenital biliary anomaly, is associated with recurrent infections, chronic inflammation, and an increased risk of malignancy. Although emerging evidence implicates the biliary microbiome in disease pathophysiology, its developmental dynamics in pediatric CC remain unclear. Using deep metagenomic sequencing and comprehensive functional annotation, this study characterized age-dependent changes in the biliary microbiome of 201 pediatric CC patients stratified into infancy (<1 year), early childhood (1-5 years), and later childhood (5-12 years). We found that while the taxonomic composition and alpha diversity of the microbiota remained conserved across age groups, profound functional remodeling occurred with host development. A core set of microbial species(Bacteroidota, Actinomycetota, Bacillota, and Pseudomonadota) and functional pathways was shared across all ages; however, early childhood (1-5 years) exhibited the greatest number of unique functional genes, metabolic pathways, and carbohydrate-active enzymes, identifying this period as a critical window for microbial metabolic adaptation. Age-specific patterns were also evident in clinically relevant traits: infants (<1 year) harbored the most unique antibiotic resistance and virulence factor genes, whereas the resistome and virulome became more streamlined in older children. These findings establish a paradigm of "taxonomic conservation coupled with functional remodeling" in the CC microbiome and highlight age as a key determinant of microbial community function. This study offers novel insights into the microbial dynamics underlying CC progression and suggests potential age-specific targets for future therapeutic strategies.},
}

@article {pmid41754336,
year = {2026},
author = {Haidri, I and Ullah, Q and Qasim, M and Amir, MA and Haider, W and Nguyen, HH and Promwee, A},
title = {Microbiome-Mediated Cd Stabilization in Chilli Pepper: Roles of Capsaicinoids and Cultivar Genetics Under Environmental Stress.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {41754336},
issn = {2223-7747},
support = {WU-CIA0 5205/2025//Walailak University under the international research collaboration scheme/ ; },
abstract = {Chilli pepper agroecosystems (Capsicum annuum L.) are increasingly threatened by cadmium (Cd) contamination, with emerging climatic stressors such as drought further exacerbating risks to food safety and crop productivity. This review synthesizes current evidence on microbiome-mediated Cd phytostabilisation in chilli pepper, with a particular focus on the roles of capsaicinoids and cultivar-specific genetic regulation in shaping rhizosphere microbial communities. Existing studies demonstrate that capsaicinoid-rich cultivars selectively recruit specialized rhizosphere microbes, enhancing root-level Cd sequestration and achieving Cd retention efficiencies of approximately 40-55%, thereby substantially restricting Cd translocation to edible fruit tissues. Multi-strain plant growth-promoting rhizobacteria (PGPR) consortia, especially when combined with structured organic amendments, have been reported to reduce fruit Cd and nickel (Ni) accumulation by more than 87% in contaminated soils. These responses are regulated by pungency-associated genetic loci, including Pun1 (pungency locus 1) and Pun4 (pungency locus 4) genes, which influence secondary metabolism and microbial assembly under metal stress conditions. The review highlights key knowledge gaps regarding the long-term stability of engineered rhizobiomes, the in situ dynamics of the Capsicum volatilome as a microbial recruitment signal, and the interactive effects of Cd contamination and drought in field environments. Overall, this synthesis provides a mechanistic framework for deploying high-pungency cultivars and microbiome-based strategies to improve Cd phytostabilisation, with important implications for sustainable chilli production in drought-prone, metal-contaminated agroecosystems.},
}

@article {pmid41754214,
year = {2026},
author = {Churin, AA and Sokolyanskaya, LO and Lukina, AP and Karnachuk, OV},
title = {Current Concepts in Probiotic Safety and Efficacy.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040696},
pmid = {41754214},
issn = {2072-6643},
support = {25-24-00493//Russian Science Foundation/ ; },
abstract = {Background/Objectives: Advances in molecular biology, genetics, and microbiome research have significantly expanded our understanding of probiotic microorganisms and their interactions with human health, stimulating the development of both traditional and next-generation probiotic products. Although probiotics are widely used and generally considered safe for healthy individuals, accumulating evidence indicates that their safety profile varies significantly depending on the strain, dose, host, and context, with rare but clinically significant adverse events reported in vulnerable populations. Methods: This review summarizes current knowledge on the efficacy and safety of probiotics, analyzes limitations in clinical safety reporting, and compares regulatory frameworks governing the use of probiotics as dietary supplements, medicinal products, and live biotherapeutics. Particular attention is given to new genomic and computational approaches to safety assessment. Conclusions: Overall, the review emphasizes the need for coordinated regulation, rigorous clinical evidence, and integrated, modern safety assessment strategies to support the responsible expansion of probiotic use.},
}

@article {pmid41754202,
year = {2026},
author = {Reytor-González, C and Sarno, G and Montalvan, M and Verde, L and Annunziata, G and Barrea, L and Muscogiuri, G and Simancas-Racines, D},
title = {Obesity, Bariatric Surgery, and Cancer Risk: Nutritional Perspectives and Long-Term Clinical Implications.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040685},
pmid = {41754202},
issn = {2072-6643},
abstract = {Obesity is recognized as a causal risk factor for the development of multiple cancers, with risk magnitude varying by tumor site, sex, life stage, and adipose tissue distribution. This narrative review synthesizes recent epidemiological evidence linking excess body fatness with cancer incidence and mortality and integrates the biological mechanisms that explain this association. Chronic low-grade inflammation, insulin resistance with compensatory hyperinsulinemia, dysregulation of adipose-derived hormones and sex steroids, impairment of anti-tumor immune responses, alterations in the gut microbiota, and remodeling of the tumor microenvironment collectively create conditions that favor tumor initiation and progression. Bariatric surgery is the most effective clinical intervention for achieving substantial and sustained weight loss in individuals with severe obesity, and growing evidence indicates that it is associated with a reduction in overall cancer risk and cancer-related mortality, particularly for malignancies strongly linked to obesity. However, the extent of this benefit differs by surgical technique and remains less consistent for colorectal cancer. Beyond metabolic improvements, bariatric surgery produces long-term changes in nutritional physiology that may also influence oncologic outcomes. Persistent deficiencies of micronutrients such as iron, folate, vitamin B12, vitamin D, and calcium can affect DNA synthesis, methylation, oxidative balance, and cellular repair. Altered protein and energy intake may contribute to loss of lean mass and reduced metabolic resilience, while changes in alcohol absorption and metabolism can increase systemic exposure to ethanol and its carcinogenic metabolites. In addition, bariatric surgery induces sustained remodeling of the gut microbiome and bile acid metabolism, which may further modulate tumorigenic signaling. Overall, the oncological impact of bariatric surgery reflects a balance between metabolic improvement and long-term nutritional management, underscoring the need for structured follow-up and targeted nutritional strategies to optimize cancer risk reduction.},
}

@article {pmid41754199,
year = {2026},
author = {Arabi, T and Akbar, A and Yaqinuddin, A and Khan, MI and Arora, I},
title = {Cross-Cultural Nutritional Epigenomics: Diet and Microbiome Interactions Shaping Type 2 Diabetes in Arab and Western Populations.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040681},
pmid = {41754199},
issn = {2072-6643},
abstract = {In the Middle East and North Africa (MENA) region, the prevalence of Type 2 Diabetes (T2D) is 17-18%, substantially higher than the ~9-10% reported in Western populations, with some Gulf states approaching 25% in adults. Historically, Arab diets, characterized by high fiber intake from whole grains, legumes, and fermented dairy products, have contrasted markedly with the Western dietary pattern increasingly prevalent among urbanized Arab populations. These nutritional shifts have been associated with changes in gut microbial composition, including lower representation of short-chain fatty acid-producing bacteria and higher abundance of dysbiosis-associated taxa. Concurrently, diet-derived compounds and microbial metabolites have been associated with changes in DNA methylation, histone modifications, and non-coding RNA expression. Epigenome-wide association studies revealed both shared and population-specific methylation signatures in patients with T2D. However, integrated multi-omics studies remain limited in Arab populations, where the disease burden is highest. This review integrates emerging evidence on diet-linked epigenetic alterations, microbiome-associated metabolic pathways, and their intersection in potentially contributing to T2D risk and progression. Given the heterogeneity of T2D across populations, there is a pressing need for culturally contextualized precision medicine frameworks that integrate population-specific diet-microbiome-epigenome dynamics rather than extrapolating findings across populations. Additionally, this review synthesizes evidence that dietary patterns are associated with T2D-relevant pathways through the diet-microbiome-epigenome axis, with emphasis on Arab/MENA populations and Western comparator cohorts.},
}

@article {pmid41754197,
year = {2026},
author = {Zhu, A and Bonja Geleto, F and Mohammed Ali, M and Ashenafi, H and Erko, B and Taye, B},
title = {Household Food Insecurity Alters Gut Microbiome Composition and Enriches Sutterella in Ethiopian Schoolchildren.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040680},
pmid = {41754197},
issn = {2072-6643},
support = {Picker ISI//Colgate University/ ; },
abstract = {Background: Household food insecurity (HFI) adversely affects child development by restricting caloric intake, dietary diversity, and food quality. Since diet is a key factor influencing the gut microbiome, HFI may negatively impact health by altering microbial communities. However, direct evidence linking HFI to changes in the gut microbiome is limited. Therefore, we investigated the effects of HFI as a composite variable and used individual HFI assessment questions as specific proxies for dietary deprivation on the gut microbiome in a group of Ethiopian schoolchildren. Methods: Fecal samples were collected from 57 school-aged children in Ethiopia, and microbial profiles were established using 16S rRNA amplicon paired-end sequencing. Food insecurity was assessed using the Household Food Insecurity Access Scale (HFIAS). Results: We observed no significant differences in alpha diversity across food security status (Wilcoxon p > 0.05). However, beta diversity analysis revealed a significant shift in microbiome composition between food-secure and food-insecure individuals (Bray-Curtis dissimilarity; PERMANOVA, p < 0.05). Further analyses of individual HFIAS questions as specific proxies for dietary deprivation showed that limited dietary variety, consumption of disliked foods, and reduced meal size were each associated with significant changes in microbial compositions (PERMANOVA; all q < 0.05). Differential abundance analyses consistently identified Sutterella as significantly more abundant among food-insecure participants (composite model q = 0.11; component-specific models q < 0.05). Additionally, a microbial feature-based machine learning model accurately predicted food security status (AUC = 0.81), with Sutterella emerging as the top predictive feature. Conclusions: Our findings suggest that food insecurity metrics are associated with alterations in gut microbial composition. The consistent enrichment of Sutterella in food-insecure children in this study suggests the need for future mechanistic studies to explore its role in mediating the effects of food insecurity.},
}

@article {pmid41754196,
year = {2026},
author = {Qiu, Y and Laguna, JC and Alegret, M and Vilà, L},
title = {A Global Perspective on Metabolic Dysfunction-Associated Steatotic Liver Disease: From Molecular Mechanisms to Therapeutic Strategy Innovation.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040679},
pmid = {41754196},
issn = {2072-6643},
support = {PID2023-146140OB-I00//MICIU/AEI/10.13039/501100011033 and FEDER, UE/ ; 2021SGR-00345//Generalitat de Catalunya/ ; 202406910009//China Scholarship Council/ ; },
abstract = {Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) is a prevalent global health issue driven by metabolic syndrome, with cardiovascular disease being the leading cause of mortality. This review synthesizes current knowledge on its multifactorial pathogenesis, the impact of sexual dimorphism, and key experimental models. The progression of MASLD involves interconnected pathways including dysregulated de novo lipogenesis, insulin resistance, mitochondrial dysfunction, gut dysbiosis, ferroptosis, and genetic and epigenetic predispositions. These mechanisms not only promote hepatic injury but also accelerate atherosclerosis. Notably, MASLD exhibits significant sexual dimorphism, influenced by physiological differences, sex hormones, genetic factors, and the microbiome. The study of these complex processes relies mostly on dietary-induced animal models, particularly in rats, which effectively recapitulate features of the human disease. Given the multifaceted nature of MASLD, the therapeutic focus is shifting from monotherapies to combination or dual-target strategies. To enable this transition, refinement of preclinical models is essential to better understand and target this complex disorder.},
}

@article {pmid41754185,
year = {2026},
author = {Alessa, H and Quinn, ME and Alhomidan, L and Ross, C and Kainadas, S and Brownson, E and MacDonald, J and Seenan, JP and Nichols, B and Koutsos, A and Gerasimidis, K},
title = {In Vitro Effects of Twelve Food Additives on Gut Microbiome and Its Fibre Fermentation Capacity in Adults with Crohn's Disease in Remission and Healthy Controls.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040668},
pmid = {41754185},
issn = {2072-6643},
support = {N/A//The Ministry of Education in Saudi Arabia, and Imam Abdulrahman Bin Faisal University in Dammam, Saudi Arabia, funded Hanoof Alessa's PhD/ ; },
abstract = {Background/Objectives: Animal studies have shown that food additives may adversely affect the gut microbiome. However, the effect of food additives on the microbiome in adults with Crohn's disease (CD) remains less explored. This study investigated the impact of food additives on gut microbiome and fibre fermentation capacity in adults with CD and healthy controls (HCs) using in vitro faecal fermentations. Methods: Faeces from 6 HCs and 6 patients with CD in clinical remission (Harvey Bradshaw Index < 5) were used for in vitro fermentation of a fibre mix with one of 12 food additives (calcium propionate, carboxymethylcellulose, carrageenan kappa, cinnamaldehyde, maltodextrin, polysorbate-80, potassium sorbate, sodium benzoate, sodium sulphite, titanium dioxide, turmeric, and xanthan gum). Short-chain fatty acids (SCFAs) were measured using gas chromatography, the microbiome was profiled with 16S rRNA amplicon sequencing and total bacterial load was measured with qPCR. Results: Maltodextrin increased acetate production in both groups. In HCs, turmeric increased acetate and butyrate production, sodium sulphite reduced acetate production, and maltodextrin reduced butyrate production. Microbiome Shannon α-diversity increased with titanium dioxide (both groups), and with carrageenan kappa only in patients with CD. In both groups, the addition of maltodextrin and polysorbate-80 induced significant shifts in microbiome structure (β-diversity). Significant shifts were seen with maltodextrin (HC: R[2] = 6.8%, p = 0.001; CD: R[2] = 5.1%, p = 0.004) and sodium sulphite (HC: R[2] = 6.9%, p = 0.001). Maltodextrin significantly decreased the estimated absolute abundance of Escherichia-Shigella in patients CD; sodium benzoate, potassium sorbate, and calcium propionate did so in HCs. Faecalibacterium decreased in the presence of polysorbate-80 in the HC and CD groups, as well as in the presence of maltodextrin in the CD group. Total bacterial load decreased with polysorbate-80, potassium sorbate, maltodextrin and calcium propionate in both groups. Xanthan gum decreased total bacterial load in HCs. Conclusion: Certain food additives significantly affected fibre fermentation capacity and microbiome structure, with only modest differences observed according to participants' health status.},
}

@article {pmid41754156,
year = {2026},
author = {Carvalho, PA and Paciência, I and Moreira, A and de Castro Mendes, F},
title = {Air Pollution, Asthma and Diet: From Mechanisms to Prevention Strategies.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040639},
pmid = {41754156},
issn = {2072-6643},
abstract = {BACKGROUND/OBJECTIVES: Air pollution is a major environmental determinant of asthma morbidity and lung function impairment across the life course. Both outdoor and indoor exposures contribute to asthma development and exacerbations, impaired lung function growth, and accelerated decline, with heightened susceptibility during pregnancy and childhood. In this narrative review, we aimed to: (i) synthesize evidence on outdoor and indoor air pollution in asthma and lung function decline; (ii) describe key modulators of pollution-related risk; (iii) evaluate diet and supplementation as effect modifiers; and (iv) outline strategies and recommendations to mitigate pollution-related asthma burden.

METHODS: A narrative synthesis was conducted based on a comprehensive PubMed literature search through 2025, integrating evidence from observational and interventional studies evaluating habitual diet and nutritional supplementation as potential modifiers of the respiratory effects of indoor and outdoor air pollution.

RESULTS: We synthesized human observational and interventional studies associating outdoor and indoor air pollution with asthma and lung function outcomes, highlighted major susceptibility modulators and mechanistic pathways, and appraised emerging evidence that habitual diet and nutritional supplementation might modify pollutant-related respiratory effects. Mechanistic evidence supported dietary modulation through redox buffering, epithelial-immune pathways, lipid-mediated inflammatory balance, and microbiome-immune crosstalk. However, human evidence remained heterogeneous across pollutants, settings, dietary metrics, and endpoints.

CONCLUSIONS: Emissions reduction at source remained the cornerstone of prevention. Effective mitigation should be multi-level and equity-focused, combining structural air-quality improvements with pollution-aware asthma care and feasible household practices. Diet should be framed as a supportive, food-first resilience strategy, improving overall diet quality, fat quality, and fiber intake rather than a substitute for emissions reduction or guideline-based asthma management.},
}

@article {pmid41754155,
year = {2026},
author = {He, J and Shan, L and Yu, L and Yu, L and Jiang, X and Shen, Y and Du, Z and Yu, R and Zhao, C and Du, X and Wang, H and Yang, R and Fang, C},
title = {Structural Insights and Metabolic Profiles of Oxidized Green Coffee Extract, and Its Impact on Obesity and Gut Microbiota in High-Fat Diet-Fed Mice.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040638},
pmid = {41754155},
issn = {2072-6643},
support = {Yunnan Internstion Joint Laboratory of Green Health Food (China & Thailand) (202203AP140011)//Chongye Fang/ ; },
abstract = {Background: Obesity is a severe chronic disease impacting health, closely linked to intestinal microbiota. Gut microbiome significantly contributes to obesity and metabolic issues. This study aims to explore the structural characterization of two coffee extracts and their effects on gut microbiota disturbances caused by a high-fat diet (HFD). Methods: Male C57BL/6J mice were divided into four groups-normal diet (ND), high-fat diet (HFD), HFD supplemented with unroasted coffee extract (UC), and HFD supplemented with oxidized green coffee extract (GCE). Results: Structural characterization revealed that both extracts are polymeric phenolic compounds rich in hydroxyl and carboxyl groups. Full-target metabolomic analysis revealed significant metabolic differences between the extracts, with 499 differential metabolites identified: a total of 247 metabolites were upregulated and 252 were downregulated in GCE compared to UC. Supplementation with GCE reduced body weight gain and adipose tissue accumulation, improved dyslipidemia and insulin sensitivity, and enhanced hepatic antioxidant capacity in high-fat model mice. Gut microbial analysis showed that GCE significantly (p < 0.05) increased the growth of beneficial bacteria such as Prevotella, Butyricimonas, and Parabacteroides. Conclusions: Oxidized green coffee extract has the effect of lowering lipids and increasing intestinal beneficial bacteria.},
}