@article {pmid42326530,
year = {2026},
author = {Robinson, S and Price, C and Nicklin, A and Kujawska, M and Koev, T and Liu, T and Ilker, N and Lumreras-Perales, C and Teng, N and Fowler, W and McKee, A and Mitchell, L and Rowe, M and Taylor, J and Benwell, C and Dreger, S and Mueller, J and Kumar, A and Singh, P and Heiss, C and Azadi, P and Beraza, N and Hall, L},
title = {Bifidobacterium pseudocatenulatum capsular exopolysaccharide enhances systemic anti-tumour immunity in pre-clinical breast cancer.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {42326530},
issn = {2693-5015},
abstract = {Gut microbes have emerged as powerful regulators of cancer responses, with Bifidobacterium species and strains playing a key role in promoting anti-tumour immunity. While they represent promising candidates for cancer therapeutics, the specific underlying microbial mechanisms driving their efficacy remains poorly understood. In this study, we demonstrate the broad potential of Bifidobacterium species to inhibit breast cancer progression across multiple pre-clinical mouse models. We identify a novel strain, Bifidobacterium pseudocatenulatum 210, which induces systemic anti-tumour immunity and enhances responses to standard-of-care therapies via its cell surface capsular exopolysaccharide (EPS). 210 EPS remains predominantly gut local after oral administration and promotes dendritic cell activation, including preferential activation of small intestinal cDC1, leading to robust CD8[+] T cell-mediated anti-tumour activity. Comparative structural analyses further support that EPS function is strain dependent. Our findings position Bifidobacterium EPS as a novel class of therapeutic compounds with significant potential for cancer treatment.},
}

@article {pmid42479691,
year = {2026},
author = {Xie, J and Lian, T},
title = {Enrichment is not necessarily recruitment in root microbiome assembly.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag192},
pmid = {42479691},
issn = {1751-7370},
abstract = {Rhizosphere enrichment is often interpreted as evidence that plants recruit beneficial microorganisms from soil, but enrichment and recruitment describe different levels of inference. Enrichment is a compositional pattern, whereas root association is a broader outcome produced by distinct processes through which microorganisms reach, attach to, colonize, and persist on roots. Within this outcome, recruitment in a narrower, directional sense denotes cases in which host-derived cues promote microbial attraction to, and/or specific attachment on, roots. Recruitment in this sense is independent of benefit, because recruited microbes may be beneficial, neutral, or harmful. This distinction is often blurred when differential abundance alone is used to infer host-driven recruitment. Recruitment claims should instead be evaluated through microbial traits and host physiological, immune, and metabolic states that jointly determine root association. Motile bacteria with flagella, chemotaxis systems, and extracellular polysaccharides can respond directionally to root-derived cues and stabilize attachment on root surfaces. Many root-associated fungi lack comparable active motility, and their enrichment more often reflects contact opportunity, surface compatibility, and host immune permissiveness. Recent work further shows that enrichment can be uncoupled from plant benefit, because host physiological states may create permissive niches whereas strain-level competition determines functional outcomes. We therefore propose a framework that separates microbe-driven attraction and attachment from host-mediated accommodation and persistence. Rhizosphere enrichment is thus an observable outcome, not a default signature of recruitment or benefit. Precise recruitment language requires trait-based, spatial, temporal, and functional evidence linking microbial presence to the mechanisms that generate and maintain root association.},
}

@article {pmid42479725,
year = {2026},
author = {Wright, SL and Joslin, M and Kim, Y and Olson, M and Hall, A and Peter, B and Whisner, CM},
title = {Distinct gut and oral microbiome patterns associated with dyslexia in a family-based cohort: A preliminary exploratory study.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0353463},
pmid = {42479725},
issn = {1932-6203},
mesh = {Humans ; *Dyslexia/microbiology ; Female ; Male ; Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Cohort Studies ; *Microbiota ; Child ; *Mouth/microbiology ; *Gastrointestinal Microbiome ; Family ; Adolescent ; },
abstract = {BACKGROUND: Many neurodevelopmental disorders, including dyslexia and childhood apraxia of speech (CAS), have genetic predispositions that are understood to varying degrees. However, the microbiome in individuals with dyslexia and CAS remains underexplored. The goal of this exploratory study was to determine whether fecal and saliva microbiome diversity and composition are associated with dyslexia or CAS.

METHODS: To this end, we examined the fecal and saliva microbiota of individuals with dyslexia, CAS, and their neurotypical family members using 16S rRNA gene amplicon sequencing in a family-based cohort composing of 7 individuals with dyslexia, 11 with CAS, and 10 neurotypical family members (n = 28). Participants with dyslexia and CAS were drawn from separate families, with neurotypical relatives serving as within-family controls. A total of 19 fecal and 29 saliva samples were collected, with paired fecal-saliva samples available for 19 individuals. Taxonomic classification was performed using four 16S rRNA reference databases, and microbial diversity, composition, and functional potential were analyzed.

RESULTS: Individuals with dyslexia consistently showed distinct fecal microbiome alpha and beta diversity patterns at the species level compared to neurotypical family members and participants with CAS histories, irrespective of taxonomic database employed. Both fecal and saliva datasets identified key taxa associated with dyslexia, but not with CAS. Predicted functional profiling further identified dyslexia-associated pathways in the fecal microbiome, whereas no functional differences were detected in saliva.

CONCLUSION: Although these results suggest that individuals with dyslexia may harbor distinct fecal and saliva microbiomes, the findings are exploratory and should be considered as hypothesis-generating. Future studies leveraging larger, independent cohorts will be essential to validate these findings and to more rigorously examine the oral-gut-brain axis in language-based syndromes.},
}

Humans
*Dyslexia/microbiology
Female
Male
Saliva/microbiology
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Cohort Studies
*Microbiota
Child
*Mouth/microbiology
*Gastrointestinal Microbiome
Family
Adolescent

@article {pmid42479812,
year = {2026},
author = {Jia, Y and Yan, Y and Chen, B and Shu, WS and Lu, H},
title = {Revealing Dual Synergistic Strategies in Sulfate-Reducing Microbiomes for Sulfamethoxazole Biodegradation via DNA-SIP and Metagenomics.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c05921},
pmid = {42479812},
issn = {1520-5851},
abstract = {Sulfate-reducing microbiomes (SRMs) have shown strong potential for antibiotic remediation, yet the active microorganisms and community-level strategies associated with sulfamethoxazole (SMX) biotransformation remain poorly understood. In this study, long-term bioreactor operation (269 days; 500-1500 μg/L SMX), DNA-stable isotope probing (DNA-SIP), and metagenomic analyses were integrated to investigate the microbial contributors and functional organization underlying SRM-driven SMX biotransformation. Desulfobacterium, a key SRM member, was co-enriched with Geobacter and Leptolinea in the [13]C-labeled heavy fraction, suggesting potential metabolic complementarity during community-level SMX biotransformation. Genome-resolved analyses further revealed structured patterns of inferred horizontal gene transfer (HGT) and predicted metabolite exchange among keystone taxa. The transferred genes were mainly associated with energy conservation, transport, sulfur-associated metabolism, and stress-response functions, whereas the predicted exchanged metabolites included carbon metabolites, amino acid-related sulfur compounds, purine-related intermediates, and cofactor-associated metabolites. Together, these findings suggest that HGT-associated functional redistribution and metabolic complementarity may contribute to the persistence and coordinated activity of sulfate-reducing microbiomes under high SMX stress. This study links SIP-identified active populations with genome-inferred interaction patterns in a sulfate-reducing system and provides new insight into microbiome-based anaerobic strategies for antibiotic-containing wastewater treatment.},
}

@article {pmid42479871,
year = {2026},
author = {Gong, EJ and Bang, CS and Lee, JJ and Baik, GH},
title = {Post-Marketing Safety Signals of Microbiota-Based Live Biotherapeutic Products for Recurrent Clostridioides difficile Infection: A FAERS Pharmacovigilance Study.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ajg.0000000000004133},
pmid = {42479871},
issn = {1572-0241},
abstract = {BACKGROUND: REBYOTA and VOWST are the first FDA-approved live biotherapeutic products (LBPs) for recurrent Clostridioides difficile infection (rCDI). Prior FDA safety alerts (2019-2020) regarding invasive infections from investigational fecal microbiota transplantation underscore the need for post-marketing surveillance of these novel products.

AIMS: To characterize the real-world safety profiles of REBYOTA and VOWST using the FDA Adverse Event Reporting System (FAERS) and compare them against established CDI therapeutics.

METHODS: We performed disproportionality analysis of FAERS data (Q1;2020-Q4;2025). REBYOTA and VOWST were identified as primary suspect drugs using BLA numbers and drug name matching. Comparators included fidaxomicin, bezlotoxumab, and vancomycin (CDI-filtered). Four methods were applied: reporting odds ratio (ROR), proportional reporting ratio, information component, and empirical Bayes geometric mean. Signals required ≥2 methods agreement.

RESULTS: We identified 231 REBYOTA and 813 VOWST primary suspect reports, yielding 18 and 54 disproportionality signals, respectively. Both products' signals were consistent with known gastrointestinal adverse events. No signals were detected for bacteremia, septic shock, or anaphylaxis. Death was reported at lower-than-expected frequency for VOWST (ROR 0.29; 95% CI 0.15-0.53). A VOWST-specific UTI cluster (Klebsiella UTI ROR 405.73; Pseudomonal UTI ROR 168.54) was identified; head-to-head comparison showed no significant UTI difference versus REBYOTA (ROR 1.39, NS), suggesting stimulated reporting bias rather than a biological signal. Route-dependent adverse event profiles differed between oral VOWST and rectal REBYOTA.

CONCLUSIONS: FDA-approved LBPs demonstrate reassuring post-marketing safety profiles without transmitted infection signals. The extreme VOWST UTI signal is likely attributable to FDA-mandated expedited reporting obligations rather than a causal drug effect.},
}

@article {pmid42480125,
year = {2026},
author = {Wei, J and Xu, F and He, Z and Xie, J and Feng, X},
title = {Reuterin drives osteogenic and suppresses adipogenic differentiation of bone marrow mesenchymal stem cells via BMP/SMAD signaling to ameliorate osteoporosis.},
journal = {Tissue & cell},
volume = {104},
number = {Pt 1},
pages = {103791},
doi = {10.1016/j.tice.2026.103791},
pmid = {42480125},
issn = {1532-3072},
abstract = {Osteoporosis, a prevalent skeletal condition defined by diminished bone density and disrupted microarchitecture, dramatically elevates fracture risk. Its pathophysiology is now understood to extend beyond classic remodeling imbalances to include a pivotal shift in bone marrow mesenchymal stem cell (BMSC) differentiation, where adipogenesis is favored over osteogenesis-a key feature of aging and estrogen deficiency. The emerging "gut-bone axis" suggests that microbiota-derived metabolites can systemically influence skeletal homeostasis, presenting new therapeutic possibilities. This research uncovers the direct osteoanabolic and anti-adipogenic properties of Reuterin (3-hydroxypropionaldehyde, Reut), a principal antimicrobial metabolite from Lactobacillus reuteri. In vitro, Reut (5-20 μM) showed excellent cytocompatibility, dose-dependently boosting osteogenic differentiation (increased ALP activity and mineralization) while effectively suppressing adipogenic differentiation (decreased lipid accumulation) in BMSCs. Mechanistically, Reut specifically activated the canonical BMP-Smad pathway, demonstrated by the rapid phosphorylation and nuclear translocation of Smad1/5/9 and the upregulated expression of its direct targets (ID1, ID2). This activation was crucial, as the BMP receptor inhibitor LDN-193189 completely negated Reut's effects. In an ovariectomized (OVX) rat model, systemic Reut administration (10 mg/kg, every other day for 8 weeks) not only mitigated trabecular bone loss and enhanced biomechanical properties but also markedly reversed the OVX-induced expansion of marrow adipose tissue (MAT). Remarkably, the bone-preserving efficacy of Reut was statistically equivalent to that of teriparatide (TPTD), a clinically approved anabolic agent, while both treatments similarly and significantly countered the pathological marrow adiposity. These results establish Reut as a novel, gut microbiome-derived therapeutic metabolite that rectifies the fundamental lineage imbalance in osteoporosis by directly engaging the BMP-Smad pathway, offering a distinct postbiotic strategy for anabolic bone therapy.},
}

@article {pmid42480175,
year = {2026},
author = {Braga, AS and Dos Santos Araujo, KC and Alves da Silva, LR and de Paula Almeida, G and de Castro Rocha, AF and Pessôa, AS and Saldanha, LL and Kim, RR and de Souza, BM and de Oliveira, RC and Esteves-Oliveira, M and Ribeiro, AA and Magalhães, AC},
title = {Antimicrobial and anticaries effects of Malva sylvestris associated or not with fluoride/xylitol under a microcosm biofilm model.},
journal = {Archives of oral biology},
volume = {190},
number = {},
pages = {106695},
doi = {10.1016/j.archoralbio.2026.106695},
pmid = {42480175},
issn = {1879-1506},
abstract = {OBJECTIVE: This study evaluated the effects of different combinations of Malva sylvestris on colony-forming unit (CFU) counts and microbiome in a microcosm biofilm, fibroblast cytotoxicity, and reduction of tooth demineralization.

DESIGN: Samples were assigned to nine groups (n = 12): Malva sylvestris (2.5%); M. sylvestris + 5% xylitol; M. sylvestris + fluoride (0.0225%); M. sylvestris + xylitol + fluoride; xylitol; fluoride; M. sylvestris in a commercial product (Malvatricin Plus®); chlorhexidine (0.12%); and PBS. Plant metabolites were extracted by percolation. A microcosm biofilm model was applied, and from the 2[nd] to the 5[th] day, samples were treated with the solutions for 1 min. CFU counts were performed for Streptococcus mutans/S. sobrinus, Lactobacillus spp., and Candida albicans. Biofilm samples were analyzed by 16S rRNA gene sequencing (Illumina MiSeq) and QIIME. Cytotoxicity of M. sylvestris (0.08-2%) was assessed on human gingival fibroblasts, and demineralization was quantified by transverse microradiography.

RESULTS: M. sylvestris (2%) showed lower cytotoxicity than chlorhexidine. The combination of M. sylvestris and xylitol reduced S. mutans counts in dentin biofilm by 1 log10/mL compared with PBS (p = 0.03), but not in enamel biofilm. Biofilms treated with M. sylvestris showed microbial communities similar to the negative control. However, the extract combined with fluoride and xylitol significantly reduced enamel demineralization compared with PBS (p < 0.0001), but not dentin demineralization.

CONCLUSION: Malva sylvestris extract combined with fluoride and xylitol showed some antimicrobial and anticaries effects in vitro.},
}

@article {pmid42480345,
year = {2026},
author = {Kim, HW and Hayashi, RM and Mendez-Garcia, C and Gering, E and Cann, I and Rehberger, TG and Smith, AH and Santin, E and Mackie, RI},
title = {Microbiota profiles and intestinal immunity in Bermuda feral chickens: A comparison with commercial broilers.},
journal = {Poultry science},
volume = {105},
number = {10},
pages = {107440},
doi = {10.1016/j.psj.2026.107440},
pmid = {42480345},
issn = {1525-3171},
abstract = {Domestication for production and captive rearing may alter the chicken gut microbiome and compromise immune function in modern broiler chickens. In this study, we compared microbiota, Toll-like receptor (TLR) gene expression, and intestinal health between feral chickens from Bermuda (BFC, n = 21) and commercial Cobb 500 broilers (BC, n = 12). Microbiota analysis showed that feral chickens harbored greater microbial diversity with higher proportions of Gram-negative bacteria in BFC (31%) vs. BC (8.2%). RT-qPCR analysis, followed by ANOVA and Tukey's test, revealed higher ileal expression of TLR in BFC and hepatic expression in BC (P < 0.05) indicating enhanced mucosal innate immunity in feral chickens and systemic immune activation in broiler chickens, respectively. The upregulation of ileal TLR4 and TLR5 in feral chickens correlated with Gram-negative and flagellated Proteobacteria, respectively. Histological evaluation showed higher Intestinal Scoring Index (ISI) scores in BFC (Kruskal-Wallis test, P < 0.05) with increased lamina propria thickness, goblet cell proliferation, and a robust mucosal inflammatory response, while BC showed minimal mucosal inflammation but significant hepatic lymphocytic aggregation and congestion (P < 0.05). These findings suggest that feralization and free-living conditions are associated with a high mucosal immune surveillance that effectively limits systemic antigen translocation, while commercial broilers show reduced intestinal immune activation and increased susceptibility to hepatic inflammation. This indicates that selection for intensive production may compromise gut barrier function and shift the site of immune activation from the mucosa to the liver.},
}

@article {pmid42480437,
year = {2026},
author = {Zhou, X and Sun, G and Jiang, Q and Liu, S and Shi, K and Wang, B and Xue, J and Wang, F and Gao, Y and Feng, Y},
title = {Electron transfer mechanisms and microbiome stability of mixed-SRB-assembled Bio-FeS hybrids for enhanced chromium remediation.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143051},
doi = {10.1016/j.jhazmat.2026.143051},
pmid = {42480437},
issn = {1873-3336},
abstract = {While biogenic iron sulfide nanoparticles (Bio-FeS NPs) exhibit exceptional efficacy in hexavalent chromium (Cr(VI)) remediation, their broader application is severely constrained by an overreliance on pure-culture synthesis that oversimplifies complex environmental realities, and a limited understanding of the underlying electron transfer and synergistic removal mechanisms within mixed microbial consortia. To bridge these knowledge gaps, we synthesized a biohybrid material (Bio-FeS@SRB) in situ using a mixed consortium of sulfate-reducing bacteria (SRB). Response surface analysis identified the optimal synthetic conditions (640.31 mg L[-1] SO4[2-], 202.77 mg L[-1] Fe[2+], pH 7.22), under which FeS NPs (24.46 ± 4.30 nm) formed evenly on the cell surface. Electrochemical analysis demonstrated a significantly greater electron transfer capacity for Bio-FeS@SRB compared to SRB alone, as evidenced by a 67.20% reduction in charge transfer resistance, an increased direct electron transfer ratio, and doubled electron transport system activity (ETSA). Consequently, Bio-FeS@SRB achieved > 99% removal of Cr(VI) at high concentrations (50 mg L[-1]). The reaction followed first-order kinetics and also substantially promoted sulfate reduction. Mechanism investigations revealed that FeS NPs could substitute coenzyme Q, establishing an alternative high-efficiency intracellular electron transfer conduit. The in-situ formed FeS NPs protected key sulfate-reducing genera (e.g., Humidesulfovibrio), enriched Cr(VI) resistant groups (e.g., Enterococcus), and increased the abundance of functional genes involved in sulfur metabolism (e.g., sat, aprA, aprB) and Cr(VI) tolerance (chrA, yieF). Partial Least Squares Path Modeling (PLS-PM) identified ETSA as the key internal driver for the bio-mineral synergy, and the synergistic effect increased with initial Cr(VI) concentration (from 7.82 ± 0.51% at 50 mg L[-1] to 18.52 ± 0.75% at 100 mg L[-1]). Our study provided systematic insights into the synergies between biogenic FeS and complex microbial communities, providing a robust foundation for efficient bioremediation technologies.},
}

@article {pmid42480452,
year = {2026},
author = {Shan, X and Shi, L and Zhu, T and Liang, X and Yang, J and Zhou, G and He, L and Mei, B and Wang, S and Li, F},
title = {Microbial tryptophan-IPA axis mediates 6:2 chlorinated polyfluorinated ether sulfonate (6:2Cl-PFESA)-induced gut-brain dysfunction and neurobehavioral impairments.},
journal = {Environment international},
volume = {214},
number = {},
pages = {110422},
doi = {10.1016/j.envint.2026.110422},
pmid = {42480452},
issn = {1873-6750},
abstract = {Chlorinated polyfluoroalkyl ether sulfonic acids (Cl-PFESAs) are widely used substitutes for perfluorooctane sulfonate (PFOS) and are increasingly detected in environmental and human matrices, yet their neurobehavioral risks during early life remain poorly defined. Here, male C57BL/6J mice were orally exposed to F-53B (6:2Cl-PFESA; 0.1 or 1 mg/kg/day) during juvenility for four weeks. F-53B selectively impaired recognition memory and social novelty preference, whereas locomotor activity, anxiety-like behavior, and Y-maze working memory were largely preserved. Mechanistically, F-53B compromised intestinal barrier integrity, as evidenced by reduced occludin expression and disrupted ZO-1 continuity, accompanied by elevated circulating lipopolysaccharide (LPS) and a systemic pro-inflammatory cytokine shift. In parallel, the hippocampus exhibited microglial activation, enhanced inflammatory signaling, and reduced PSD95 expression, consistent with neuroinflammatory stress and synaptic vulnerability. Shotgun metagenomics revealed pronounced microbiome restructuring and network rewiring, while widely targeted metabolomics converged on a marked disruption of tryptophan metabolism, characterized by depletion of microbiota-derived indole metabolites, including indole-3-propionic acid (IPA), together with altered serotonin-related signatures. Notably, oral IPA supplementation rescued behavioral deficits and attenuated gut-brain inflammatory alterations, restoring intestinal aryl hydrocarbon receptor (AhR) nuclear translocation, reducing LPS and cytokine levels, and ameliorating hippocampal inflammatory phenotypes. Collectively, these findings provide mechanistic evidence that a microbiota-tryptophan metabolite-gut barrier-inflammation axis links exposure to substitute PFAS with selective neurobehavioral dysfunction, highlighting microbiota-derived metabolites as potential modulators of PFAS-associated neurotoxicity.},
}

@article {pmid42480622,
year = {2026},
author = {Ren, X and Ma, J and Zhao, Y and Yang, M and Li, Y and Song, W and Wang, N},
title = {Microbiome Remodeling During Aging: Integrative Multi-Omics and Spatiotemporal Perspectives on Immune and Metabolic Regulation.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {103269},
doi = {10.1016/j.arr.2026.103269},
pmid = {42480622},
issn = {1872-9649},
abstract = {Changes in the gut microbiota occur throughout the human lifespan, and maintaining microbial homeostasis plays a critical role in promoting healthy aging. In recent years, substantial progress has been made in elucidating the mechanistic links between aging and microbiota remodeling, highlighting the central role of microbiota-host interactions in regulating immune responses and maintaining metabolic homeostasis. These findings provide new potential targets for the precision prevention and treatment of age-related diseases. This review systematically summarizes the patterns of gut microbiota succession across different stages of the human life cycle, including infancy, adolescence, adulthood, and old age, as well as the mechanisms through which the microbiota regulates immune and metabolic functions. Furthermore, the role of the gut microbiota as a key mediator linking aging with an increased risk of chronic inflammation, cardiovascular disease, cognitive impairment, neurodegenerative disorders, and cancer was explored. In addition, this review evaluates the therapeutic potential of microbiota-targeted interventions, such as dietary modification, probiotic and prebiotic supplementation, fecal microbiota transplantation (FMT), and lifestyle interventions-in maintaining microbiome homeostasis and mitigating age-related diseases. The feasibility of personalized microbiota-based intervention strategies is also discussed. Finally, we highlight the current challenges and limitations in this field and outline future research directions. In particular, integrating multi-omics approaches with metagenomic sequencing, including emerging spatial and spatiotemporal multi-omics technologies, is crucial for advancing our understanding of the complex interactions within the gut microbiome. These insights provide a theoretical framework for optimizing anti-aging therapeutic strategies and promoting healthy lifespan extension.},
}

@article {pmid42480723,
year = {2026},
author = {Bottaro, F and Enrico, P and Cabasino, C and Caprioli, F and Brambilla, P and Delvecchio, G},
title = {Gut microbiome variability and brain structure and function in unipolar and bipolar depression: A review.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {122287},
doi = {10.1016/j.jad.2026.122287},
pmid = {42480723},
issn = {1573-2517},
abstract = {INTRODUCTION: Depression is a multifactorial disorder with significant global health impact. Neuroimaging advances have provided insights into neural mechanisms underlying depression, while gut microbiome alterations have been linked to brain structure and function. This review summarizes evidence on the association between gut microbiome variability and brain structural and functional changes in Major Depressive Disorder (MDD) and Bipolar Depression (BD).

METHODS: A bibliographic search was conducted on PubMed, Scopus and Web of Science for original studies investigating correlations between gut microbiome and brain structure and function.

RESULTS: Three studies investigated probiotic interventions in MDD, showing significant associations with increased gray matter volume (GMV) in the calcarine sulcus, reduced putamen and hippocampal activation, and altered fronto-limbic functional connectivity, especially within the precuneus and superior parietal lobule. Also, observational studies in MDD showed that specific microbial taxa or alpha diversity were positively correlated with limbic and basal ganglia GMV, whereas other taxa negatively correlated with frontal connectivity or GMV in regions involved in memory, somatosensory integration, and emotional regulation. Finally, although no interventional studies were available for BD, the available observational studies in this disorder exhibited gut-brain imbalance associations with immune activation and prefrontal dysfunction, with gut microbes linked to neuroactive metabolites correlated with altered connectivity in thalamus, striatum, and language and limbic regions.

CONCLUSIONS: From the available literature emerged that gut microbiome variations seem to be associated with brain structural and functional alterations in both MDD and BD, with preliminary evidence also suggesting significant neurobiological effects of probiotics in MDD. Nonetheless, further studies are needed to confirm the role of gut microbiome modulation as part of personalized approaches.},
}

@article {pmid42480770,
year = {2026},
author = {Zhang, Q and Wang, D and Qin, K and Fan, W and Wan, Y and Zhuo, G and Ji, L and Liu, G and Pan, Y},
title = {Intratumoral Pseudomonas fragi inversely correlates with Jab1/COPS5 expression and improves prognosis in breast cancer.},
journal = {Biochimica et biophysica acta. Molecular basis of disease},
volume = {},
number = {},
pages = {168378},
doi = {10.1016/j.bbadis.2026.168378},
pmid = {42480770},
issn = {1879-260X},
abstract = {OBJECTIVE: This study aimed to characterize the differential composition of intratumoral microbiota in breast cancer tissues with varying Jab1/COPS5 expression, evaluate their impact on tumor prognosis, progression, and immune cell infiltration.

METHODS: Jab1 expression was quantified via immunohistochemistry. Differential analysis of 2bRAD-M sequencing data was performed to screen and identify target bacterial species. Kaplan-Meier survival analysis was applied to evaluate the prognostic value of bacterial abundance. Integrative analysis of 2bRAD-M microbiome data and Digital Spatial Profiler (DSP) transcriptomic data was further conducted to dissect microbial regulation of immune cell infiltration. In vitro experiments validated the effects of target bacteria on tumor cell proliferation and neutrophil chemotaxis. In vivo, murine models of breast cancer were inoculated with target bacteria to assess tumor growth and neutrophil infiltration.

RESULTS: Pseudomonas fragi (P. fragi) and Ralstonia pickettii emerged as key taxa, with P. fragi abundance significantly associated with improved patient prognosis. In vitro, co-culture with P. fragi markedly reduced the proliferation and migration of breast cancer cells while attenuating neutrophil chemotaxis. In vivo, P. fragi inoculation in murine models suppressed tumor growth and decreased neutrophil infiltration in the tumor microenvironment, consistent with in vitro findings.

CONCLUSION: P. fragi within breast cancer tissues is inversely correlated with Jab1 expression, inhibiting tumor cell proliferation and suppressing neutrophil chemotaxis, and reducing tumor progression.},
}

@article {pmid42480908,
year = {2026},
author = {Farz, S and Ashrafi, SN and Mohebifar, M and Ansarian, MA},
title = {Oral Microbiome Dysbiosis and Innate Immune Dysregulation as Determinants of Oronasal Fistula After Primary Cleft Palate Repair.},
journal = {Journal of stomatology, oral and maxillofacial surgery},
volume = {},
number = {},
pages = {102915},
doi = {10.1016/j.jormas.2026.102915},
pmid = {42480908},
issn = {2468-7855},
abstract = {Oronasal fistula complicates 15-55% of primary cleft palate repairs, with recurrence rates approaching 43% after secondary closure, and global fistula rates have risen despite decades of iterative technical refinement, a trend that mechanical closure quality alone cannot explain. This narrative review synthesizes evidence from PubMed/MEDLINE, Scopus, and Web of Science from inception through April 2026 to argue that ONF is increasingly recognizable as a biologically mediated complication in which oral microbiome dysbiosis and innate immune dysregulation are primary, historically underrecognized determinants of palatal wound failure that act in synergy with, rather than independently of, mechanical and technical factors. Children with cleft lip and palate harbor a preoperative dysbiotic oral microbiome characterized by reduced alpha diversity, enrichment of Gram-negative anaerobes, and elevated proportions of pathobionts, including Porphyromonas gingivalis, Fusobacterium nucleatum, and Prevotella spp., establishing an unfavorable immunological baseline before the first surgical incision. Perioperative broad-spectrum antibiotic prophylaxis compounds this trajectory by depleting commensal communities, while suture-associated polymicrobial biofilms sustain a persistent antigenic depot at the healing flap margin. Unremitting pathogen-associated molecular pattern exposure drives sustained TLR4-NF-κB signaling, NLRP3 inflammasome activation, macrophage M1 polarization arrest, neutrophil extracellular trap-mediated matrix degradation, and complement-coagulation amplification at the wound interface. Failure of the specialized pro-resolving mediator class switch leaves the wound frozen in a self-sustaining inflammatory state, precluding re-epithelialization and adequate collagen deposition. Direct human biopsy evidence for these pathways at palatoplasty wound margins remains limited; the causal temporal relationship between dysbiosis and wound breakdown remains unresolved; and all translational proposals require prospective validation in cleft-specific cohorts. Reducing ONF burden demands a conceptual shift from purely mechanical closure paradigms toward precision perioperative strategies that pair preoperative microbiome profiling, targeted immune modulation, and resolution-phase biomarker monitoring with sound surgical fundamentals.},
}

@article {pmid42480928,
year = {2026},
author = {Liu, R and Zhang, Y and Guan, X and Zhang, X and Xu, Y and Liu, C and Yang, H and Yang, X and Liu, J and Li, S and Tian, W and Li, C and Li, Y},
title = {New insights into the improvement of milk performance in lactating cows: A novel fermented liquid feed strategy that modulates fermentation profile and microbiome of the rumen and feces.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-28262},
pmid = {42480928},
issn = {1525-3198},
abstract = {This study evaluated the effects of replacing a concentrate supplement with fermented liquid feed (FLF) on gross feed efficiency (GFE), production performance, and blood parameters in lactating dairy cows. Twenty-four lactating Chinese Holstein cows with comparable body weight (657 ± 32.6 kg), milk yield (38.7 ± 4.7 kg/day), parity (2.8 ± 1.2), and days in milk (104 ± 10.8 d) were randomly assigned to either a control group (CON, total mixed ration without fermented products) or a treatment group (FLF, total mixed ration supplemented with FLF) in a randomized complete block design. Compared with the CON group, feeding FLF increased GFE, energy-corrected milk yield, milk fat and protein percentages, milk nitrogen efficiency, apparent total-tract digestibility of dry matter, crude protein, neutral detergent fiber, and acid detergent fiber, as well as fecal score. Additionally, compared with the CON group, ruminal total volatile fatty acid (VFA) concentration, microbial crude protein yield, and the molar proportion of propionate increased significantly in the FLF group, whereas ruminal pH, acetate proportion, and acetate-to-propionate ratio were decreased. Total VFA concentrations and the molar proportion of butyrate in the feces increased significantly, whereas pH was decreased. In addition, in the FLF group, the relative abundance of unclassified_Clostridia_UCG_014, Prevotella_7, and Lachnospiraceae_NK3A20_group in the rumen and the relative abundance of Bifidobacterium, Candidatus_Saccharimonas, unclassified_Clostridia_UCG_014, and unclassified_[Eubacterium]_coprostanoligenes_group in the feces increased significantly, whereas the relative abundance of NK4A214 group, Rikenellaceae_RC9_gut_group, Treponema, Succiniclasticum, and Isotricha in the rumen and UCG_005, Rikenellaceae_RC9_gut_group, and Bacteroides in the feces decreased. Compared with the CON group, supplement of FLF activated the secondary bile acid pathways, upregulating ursodeoxycholic acid, taurocholic acid, glycocholate, while downregulating deoxycholic acid, lithocholic acid, and chenodeoxycholate in the feces. Additionally, plasma glucose levels, total antioxidant capacity, and total superoxide dismutase activity significantly increased in the FLF group, while β-hydroxybutyric acid, nonesterified fatty acids, and malondialdehyde were significantly decreased. In conclusion, FLF effectively regulated the microbiota in the rumen and feces, improved lactation performance, GFE, and health condition of dairy cows, and provided a novel and promising nutritional regulation strategy for high-yielding dairy cows.},
}

@article {pmid42480933,
year = {2026},
author = {Wang, P and Zhang, B and Shi, Y and Wang, Z and Wen, S and Sethi, G and Zhao, L and Zhao, M and Xing, H},
title = {Tumor-specific mechanisms and therapeutic strategies for overcoming immunotherapy resistance in advanced urological tumors.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.07.035},
pmid = {42480933},
issn = {2090-1224},
abstract = {BACKGROUND: Advanced urological tumors, particularly renal cell carcinoma (RCC), urothelial carcinoma (UC), and prostate cancer, remain a major source of cancer morbidity and mortality. Although immune checkpoint inhibitors (ICIs) have reshaped the management of advanced disease, most patients experience limited or non-durable clinical benefit due to primary or acquired resistance.

AIM: of the review. To summarize the major phenotypes and mechanisms of immunotherapy resistance in advanced urological tumors, and outline mechanism-based strategies that may restore sensitivity and improve the durability of response. Key scientific concepts of the review. Immunotherapy resistance is the result of the interplay between tumor-intrinsic alterations, the tumor microenvironment (TME), and host-related systemic determinants. Tumor-intrinsic mechanisms include low tumor antigenicity, defects in antigen processing and presentation pathways, and lineage-specific oncogenic programs such as the von Hippel-Lindau-hypoxia-inducible factor (VHL-HIF) signaling axis in RCC, fibroblast growth factor receptor (FGFR) pathway activation in UC, and androgen receptor (AR)-driven immune suppression in prostate cancer. Microenvironmental resistance is driven by suppressive myeloid and regulatory lymphoid populations, inhibitory cytokine and metabolic circuits, abnormal vasculature, fibrosis, and adaptive upregulation of alternative immune checkpoints. Host factors, including baseline immune competence, human leukocyte antigen (HLA) diversity, and the gut microbiome, further shape treatment efficacy. On this basis, current reversal strategies include multi-checkpoint blockade, rational combinations with targeted agents, chemo-/radio-immunotherapy, TME reprogramming, and microbiome-directed interventions, ideally guided by biomarkers and multi-omics stratification.

CONCLUSION: Overall, immunotherapy resistance in urological malignancies is a multifactorial and dynamic process involving tumor, microenvironmental, and host determinants. A comprehensive, mechanism-driven approach integrating biomarker-guided strategies and combination therapies is essential to improve clinical outcomes and achieve durable responses.},
}

@article {pmid42480964,
year = {2026},
author = {Wang, JM and Zhou, Y and Li, F and Ding, Y},
title = {Recent Advances in Immunotherapy for Breast Cancer: An Updated Review.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105498},
doi = {10.1016/j.critrevonc.2026.105498},
pmid = {42480964},
issn = {1879-0461},
abstract = {Immunotherapy has revolutionized the treatment landscape of breast cancer, particularly for triple-negative breast cancer (TNBC), yet primary and acquired resistance remain formidable obstacles limiting durable clinical benefit. This review provides a comprehensive update on recent advances in breast cancer immunotherapy, with a focused emphasis on the molecular and cellular mechanisms driving treatment resistance and emerging strategies to overcome them. We dissect tumor-intrinsic resistance pathways, including loss of tumor antigens, defects in antigen processing and presentation machinery, insensitivity to interferon-γ signaling, metabolic reprogramming, and epigenetic dysregulation. Tumor-extrinsic mechanisms, such as infiltration of immunosuppressive cells, abnormal angiogenesis, extracellular matrix remodeling, and FGF/FGFR genomic amplification, are highlighted as key barriers to effective immune checkpoint blockade. Emerging evidence implicates novel resistance mediators, including the DUSP22-LGALS1 axis, THSD4-driven T cell exclusion, and the MTDH-SND1 complex impairing antigen presentation, etc. We critically evaluate current strategies to surmount resistance, encompassing combination regimens with chemotherapy, targeted therapies, radiotherapy, and novel immunomodulators. The review also addresses challenges in managing immune-related adverse events, controversies surrounding patient selection biomarkers, and the urgent need for optimized efficacy evaluation systems beyond RECIST criteria. Finally, we discuss future directions, including novel immune checkpoints, microbiome modulation, artificial intelligence-assisted decision-making, and innovative trial designs. By integrating mechanistic insights with clinical evidence, this review provides a framework for understanding and overcoming immunotherapy resistance, advancing the paradigm from "effective" to "precise" immuno-oncology in breast cancer.},
}

@article {pmid42481097,
year = {2026},
author = {Ha, A and Yuen, AT and Song, C},
title = {Current Management of Food Allergies in Pediatric Patients.},
journal = {Advances in pediatrics},
volume = {73},
number = {1},
pages = {283-294},
doi = {10.1016/j.yapd.2025.12.003},
pmid = {42481097},
issn = {1878-1926},
mesh = {Humans ; *Food Hypersensitivity/diagnosis/therapy/immunology ; Child ; Epinephrine/therapeutic use ; Immunotherapy/methods ; },
abstract = {Food allergy is a growing public health concern affecting up to 8% of children. The underlying pathophysiology involves a complex interplay of genetic predisposition, microbiome dysbiosis, and environmental factors disrupting epithelial barrier integrity, leading to a spectrum of immune reactions. Diagnosis is a clinical process integrating a detailed patient history with sensitization tests, with the oral food challenge serving as the definitive tool. While strict avoidance and emergency epinephrine form the foundation of management, the paradigm is shifting toward proactive immunomodulatory therapies, including oral immunotherapy.},
}

Humans
*Food Hypersensitivity/diagnosis/therapy/immunology
Child
Epinephrine/therapeutic use
Immunotherapy/methods

@article {pmid42481112,
year = {2026},
author = {Delgado-Noguera, LA and Hernandez, C and Garcia-Thomas, ME and Colmenarez, A and Hernandez, U and Mogollon, O and Pereira, I and Rivero, A and Colmenarez, K and Gomez, M and Suarez, JA and Cordon-Cardo, C and Balzano-Nogueira, L and Paniz-Mondolfi, AE},
title = {Molecular detection of Fonsecaea pedrosoi in Rhipicephalus sanguineus and Rhipicephalus microplus ticks from Venezuela.},
journal = {Fungal biology},
volume = {130},
number = {5},
pages = {101790},
doi = {10.1016/j.funbio.2026.101790},
pmid = {42481112},
issn = {1878-6146},
mesh = {Animals ; Venezuela ; *Ascomycota/isolation & purification/genetics/classification ; *Rhipicephalus sanguineus/microbiology ; *Rhipicephalus/microbiology ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Chromoblastomycosis, caused primarily by Fonsecaea pedrosoi, is traditionally associated with traumatic environmental inoculation. We analyzed 50 Rhipicephalus sanguineus/R. microplus ticks from chromoblastomycosis-endemic Venezuelan states (Lara and Portuguesa) using Oxford Nanopore amplicon sequencing. Remarkably, F. pedrosoi dominated the tick eukaryotic microbiome, comprising 78% and 75% of fungal communities in Lara and Portuguesa, respectively. This unexpected high abundance across geographically distinct endemic foci suggests a previously unrecognized ecological association between ticks and the pathogen. While environmental transmission remains established, these findings provide first molecular evidence of F. pedrosoi in tick microbiomes, warranting investigation into potential carrier, vector or reservoir roles that may reshape chromoblastomycosis epidemiology understanding.},
}

Animals
Venezuela
*Ascomycota/isolation & purification/genetics/classification
*Rhipicephalus sanguineus/microbiology
*Rhipicephalus/microbiology
Phylogeny
Sequence Analysis, DNA

@article {pmid42481122,
year = {2026},
author = {Chhetri, S and Debnath, S and Yonzone, R and Singh, S and Mukherjee, S},
title = {Comprehensive analysis of southern corn rust (Puccinia polysora): morphology, host interactions, and molecular identification in maize.},
journal = {Fungal biology},
volume = {130},
number = {5},
pages = {101801},
doi = {10.1016/j.funbio.2026.101801},
pmid = {42481122},
issn = {1878-6146},
mesh = {*Zea mays/microbiology ; *Plant Diseases/microbiology ; *Puccinia/genetics/classification/cytology/isolation & purification/physiology ; Phylogeny ; DNA, Fungal/genetics/chemistry ; Sequence Analysis, DNA ; Spores, Fungal/cytology ; DNA, Ribosomal Spacer/genetics/chemistry ; Hyphae/growth & development ; *Host-Pathogen Interactions ; Microscopy, Electron, Scanning ; *Basidiomycota/genetics/classification ; Cluster Analysis ; },
abstract = {Puccinia polysora, the causal agent of southern corn rust (SCR), poses a major threat to maize production, yet comprehensive studies under Indian conditions remain limited. This study provides an integrated analysis of the morphology, infection biology, molecular identity, and associated fungal microbiome of P. polysora. Microscopic investigations using stereoscopic, light, and scanning electron microscopy revealed detailed spore morphology and infection structures, including appressoria formation and intercellular colonization. Notably, hyphal anastomosis was observed, suggesting a potential mechanism for genetic exchange and pathogen adaptability. Molecular identification using basidiomycete-specific ITS primers (ITS1-F and ITS4-B) confirmed pathogen identity, supported by phylogenetic analysis. These findings significantly enhance our understanding of SCR pathogenesis and provide new insights into the biology and adaptability of P. polysora, opening new avenues for research on pathogen evolution and the development of effective strategies for disease management.},
}

*Zea mays/microbiology
*Plant Diseases/microbiology
*Puccinia/genetics/classification/cytology/isolation & purification/physiology
Phylogeny
DNA, Fungal/genetics/chemistry
Sequence Analysis, DNA
Spores, Fungal/cytology
DNA, Ribosomal Spacer/genetics/chemistry
Hyphae/growth & development
*Host-Pathogen Interactions
Microscopy, Electron, Scanning
*Basidiomycota/genetics/classification
Cluster Analysis

@article {pmid42481191,
year = {2026},
author = {Meinderts, JR and Berger, SP and Bakker, SJL and de Jong, MFC and , },
title = {Rationale and design of a prospective cohort study and biobank of the offspring born to mothers with a solid organ transplant: protocol for the TransplantLines Next Generation study.},
journal = {BMJ open},
volume = {16},
number = {7},
pages = {e115736},
doi = {10.1136/bmjopen-2025-115736},
pmid = {42481191},
issn = {2044-6055},
mesh = {Humans ; Female ; Prospective Studies ; *Organ Transplantation ; Pregnancy ; *Biological Specimen Banks ; Netherlands ; Research Design ; Adolescent ; Male ; Adult ; Infant, Newborn ; Health Status ; },
abstract = {INTRODUCTION: Successful pregnancies with healthy newborns have been reported after all types of solid organ transplantation (SOT). Limited data in young children suggest similar development and health compared with the general population. However, fetal development may be influenced by factors such as immunosuppressive medication and the increased incidence of pregnancy complications, and forthcoming health problems may only become apparent later in the life of the offspring. To allow for better investigation of the long-term health of offspring born after SOT, we designed the Transplantlines Next Generation biobank and cohort study. This study will be the first with detailed data on overall health status at later age in offspring born to mothers after kidney, liver, pancreas (including pancreas islet), heart and lung transplantation (KTx, LiTx, PTx, HTx and LuTx, respectively).

METHODS AND ANALYSIS: Transplantlines Next Generation is a descriptive, prospective cohort study and biobank. It includes offspring aged≥16 years born after KTx or LiTx. Because of the scarcity of pregnancies after (solo) PTx, HTx and LuTx worldwide, and as a consequence the lack of information about these pregnancies, we want to include all offspring, at any age, born after (solo) PTx, HTx and/or LuTx in the Netherlands. Participants will attend a one-time visit for questionnaires, physical tests (for participants≥16 years including kidney ultrasound and 24-hour ambulatory blood pressure) and biological sample collection (urine, blood, faeces) for participants≥16 years of age for biobanking. Reference values and values from existing birth cohorts will serve as controls. Primary endpoints are cardiovascular and kidney health, assessed through growth charts, physical tests (eg, body composition, blood pressure, kidney ultrasound) and metabolic and kidney function biomarkers. Secondary aims include immunological status, microbiome analysis, quality of life and overall development.

ETHICS AND DISSEMINATION: Ethical approval has been obtained from the local medical ethical committee; the Institutional Review Board METc UMC Groningen (METc 2023/610). The study will be conducted according to the Declaration of Helsinki and in accordance with the Medical Research Involving Human Subjects Act and other guidelines, regulations and Acts including the General Data Protection Regulation (GDPR). All participants will give written informed consent upon enrolment. TransplantLines Next Generation is designed to deliver pioneering insights into the health of offspring born after SOT. This knowledge will help optimise care and available information for families with a pregnancy wish after SOT and provide a rationale for future studies. The results of this study are planned to be submitted for publication in relevant peer-reviewed journals and will be presented at national and international conferences.

TRIAL REGISTRATION NUMBER: NCT07291258.},
}

Humans
Female
Prospective Studies
*Organ Transplantation
Pregnancy
*Biological Specimen Banks
Netherlands
Research Design
Adolescent
Male
Adult
Infant, Newborn
Health Status

@article {pmid42481224,
year = {2026},
author = {Dini-Andreote, F and de Lima Brossi, MJ},
title = {Predicting plant microbiomes through complexity.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2026.07.002},
pmid = {42481224},
issn = {1878-4372},
abstract = {Predicting how microbiota composition determines functional outputs remains a major challenge in rhizosphere ecology. Moran et al. show that physiological or environmental constraints organize high-diversity communities along dominant ecological axes, allowing microbiome functioning to become increasingly predictable. This perspective suggests that rhizosphere complexity itself may generate a predictable ecological organization.},
}

@article {pmid42481422,
year = {2026},
author = {Li, J and Xiao, Y and Yang, T and Hunter, DJ and Zhang, W and Doherty, M and Zhang, Y and Yang, Z and Wang, Y and Xie, D and Li, C and Zhao, K and Li, W and Wen, Z and Zeng, C and Lei, G and Wei, J},
title = {Oral microbiome dysbiosis and oral-gut microbial network disruption in hand osteoarthritis: data from the Xiangya Osteoarthritis Study.},
journal = {RMD open},
volume = {12},
number = {3},
pages = {},
doi = {10.1136/rmdopen-2026-006962},
pmid = {42481422},
issn = {2056-5933},
mesh = {Humans ; *Dysbiosis/complications ; *Osteoarthritis/etiology/epidemiology/microbiology/diagnosis ; Male ; Female ; Middle Aged ; Aged ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; *Mouth/microbiology ; *Microbiota ; Bacteria/classification/genetics ; Case-Control Studies ; },
abstract = {OBJECTIVES: The oral microbiome plays a critical role in modulating systemic inflammation, partly through its interactions with the gut microbiome. Although gut microbiome dysbiosis has been implicated in symptomatic hand osteoarthritis (SHOA), the role of oral microbiome dysbiosis in SHOA and its relationship with gut microbiome dysbiosis remain unclear. Elucidating these associations could provide novel insights into SHOA pathogenesis.

METHODS: Participants were recruited from the Xiangya Osteoarthritis (XO) Study, an ongoing community-based observational study. Saliva samples were analysed using 16S ribosomal RNA gene sequencing. Oral microbial richness, composition and relative abundance of specific taxa were compared between SHOA participants and controls without SHOA. Correlations within the oral-gut microbiome network were also assessed and compared between groups.

RESULTS: Compared with controls (n=712), participants with SHOA (n=52) exhibited significantly lower oral microbial richness (p=0.007) and altered composition (p=0.007). The relative abundance of the genus Trichococcus was significantly higher in SHOA participants (β=0.437 (95% CI 0.174 to 0.699), p=0.001, Q=0.073) and positively associated with SHOA severity. Furthermore, the number of significant correlations within the oral-gut microbiome network was markedly reduced in SHOA participants compared with controls. Notably, Trichococcus abundance in the oral microbiome correlated positively with the gut microbial KEGG pathway of tyrosine metabolism (r=0.137, p=0.001, Q=0.047), both linked to SHOA.

CONCLUSION: Oral microbiome dysbiosis and disruption of the oral-gut microbiome network are associated with prevalent SHOA. These findings suggest a potential role of the oral-gut microbiome axis in SHOA pathogenesis. Larger studies are needed to confirm these associations.

TRIAL REGISTRATION NUMBER: NCT04033757.},
}

Humans
*Dysbiosis/complications
*Osteoarthritis/etiology/epidemiology/microbiology/diagnosis
Male
Female
Middle Aged
Aged
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
*Mouth/microbiology
*Microbiota
Bacteria/classification/genetics
Case-Control Studies

@article {pmid42481505,
year = {2026},
author = {Song, W and Wang, Z and Liu, Y and Wang, Q and Li, M and Shi, W and Gao, Z and Chen, Y},
title = {Kocuria rosea LAT6 enhances wheat salt tolerance via modulation of rhizosphere microbial function and nitrogen cycling.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01103-7},
pmid = {42481505},
issn = {2055-5008},
support = {ZR2025QC186//Natural Science Foundation of Shandong Province/ ; SYS202206, ZR2021MC190//Natural Science Foundation of Shandong Province/ ; 2021YFF1000403//National Key R&D Program of China/ ; SKL81103//Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; No. 2022KJ333//Youth Innovation Team of Shandong Provincial Department of Science and Technology/ ; tsqn202103162//Taishan Scholars Program/ ; 2024CXPT072//Key R&D Program of Shandong Province, China/ ; },
abstract = {Pioneer plants in saline-alkali soils support unique rhizosphere microbial communities. Some of these microbes promote plant salt tolerance and growth, although the underlying mechanisms are not yet fully understood. In this study, we isolated Kocuria rosea LAT6 from the rhizosphere of pioneer plants in saline-alkali soils. Genome sequencing revealed genes associated with plant growth promotion and stress adaptation. Inoculation with LAT6 markedly reshaped the rhizosphere microbiota, and metagenomic analysis indicated that specific microbial taxa contributed to enhanced nitrogen-cycling functions. Transcriptome profiling further demonstrated that LAT6 promotes nitrate transport and stimulates phenylpropanoid biosynthesis in wheat. It reveals how microbial reorganization and plant-microbiome interactions enhance nitrogen use under salt stress, highlighting the potential of salt-tolerant consortia for saline-alkaline crops.},
}

@article {pmid42481530,
year = {2026},
author = {Gonzales, G and Malka, R and Miar, S and Ong, JL and Bizios, R and Dion, GR and Guda, T},
title = {Therapeutic-delivering endotracheal tubes heal intubation injury via mucosal remodeling and disrupting the inflammation-microbiome-fibrosis triad.},
journal = {NPJ Regenerative medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41536-026-00497-4},
pmid = {42481530},
issn = {2057-3995},
support = {AC20COV10//U.S. Department of Defense/ ; AC20COV10//U.S. Department of Defense/ ; AC20COV10//U.S. Department of Defense/ ; AC20COV10//U.S. Department of Defense/ ; T2 Grant//University of Texas at San Antonio/ ; },
abstract = {Endotracheal intubation is essential in clinical care but often exacerbates airway inflammation, fibrosis, and microbial dysbiosis, contributing to long-term complications. This study investigates how newly developed, coated endotracheal tubes (ETTs) modulate airway healing through localized therapeutic delivery in a swine model of laryngotracheal injury. Animals were intubated with uncoated, dexamethasone-coated, or composite-coated (dexamethasone + PEG hydrogel delivering siRNA against smad3) ETTs for 3, 7, or 14 days. Tissues were analyzed via mechanical testing, immunohistochemistry, ELISA, cytokine profiling, 16S rRNA sequencing, and microscopy. Therapeutic coatings induced region- and time-dependent alterations in airway stiffness and extracellular matrix composition, including remodeling of collagen IV, laminin, and elastin. Reduced nuclear pSMAD3 staining in composite-treated airways relative to uninjured controls provided supportive, indirect evidence of altered SMAD3 pathway activity following smad3-targeting siRNA delivery, although downstream TGF-β1 and collagen I expression did not significantly differ across treatment groups or over the time course. Composite-coated ETTs also promoted a temporal shift from pro-inflammatory (M1) toward reparative (M2) macrophage phenotypes and altered local cytokine profiles. Microbial community composition varied by coating type and duration, with treatment-associated changes in bacterial taxa and predicted metabolic pathways. Mucin composition also shifted over time, reflecting evolving epithelial responses during prolonged intubation. These findings demonstrate that localized therapeutic delivery influences interconnected mechanical, inflammatory, and microbial responses during airway healing and supports the development of multifunctional ETT coatings as a strategy to modulate post-intubation airway remodeling.},
}

@article {pmid42481690,
year = {2026},
author = {Kabir, T and Lawler, ZK and Gates, LA},
title = {The impact of microbial metabolites on host chromatin and epigenetic regulation.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {42481690},
issn = {2522-5812},
support = {R00GM1433550//U.S. Department of Health & Human Services | NIH | Center for Information Technology (Center for Information Technology, National Institutes of Health)/ ; },
abstract = {The chemical diversity of histone post-translational modifications (PTMs), or histone marks, has been greatly expanded with the discovery of understudied and emerging modifications. The microbiome and microbial metabolites have been identified as crucial regulators of these novel PTMs, many of which have key roles in gene regulation. Thus, select histone marks represent a mechanism of host-microbe interaction via chromatin. This Perspective details the emerging roles of histone marks in gene regulation and host physiology. We discuss how these PTMs are regulated by microbial metabolism and the molecular mechanisms of how these microbiota-dependent histone PTMs affect host gene expression. We also highlight examples of the functional roles of these histone marks in physiology and disease, with a focus on the intestine and associated tissues. Understanding the mechanistic link between the microbiota and the host epigenome, particularly emerging histone marks, provides new avenues of how microbial metabolites influence host physiology.},
}

@article {pmid42482070,
year = {2026},
author = {Zachariassen, LF and Mortensen, FUF and Mentzel, CMJ and Jiang, PP and Lopez, PA and Krych, L and Canibe, N and Kirk, RK and Vegge, A and Rasmussen, MA and Stokholm, J and Hansen, CHF},
title = {Cesarean section-induced changes in the gut microbiota facilitate metabolic disease in high-fat diet-induced obese mice.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02468-9},
pmid = {42482070},
issn = {2049-2618},
abstract = {BACKGROUND: The global rate of cesarean section (CS) births is increasing. Growing evidence suggests that CS birth may alter the gut microbiota (i.e., dysbiosis) and increase the risk of immune and metabolic disorders, although confounding factors make causality difficult to establish. The studies presented here aimed to investigate the causal relationship between CS-induced gut dysbiosis and obesity in a diet-induced obese mouse model and explore potential microbiota-targeted therapies.

RESULTS: In the first study, male C57BL/6 mice were delivered via CS or vaginally (VD) and fed a high- or low-fat diet (HFD, LFD) for 12 weeks. In the second study, male germ-free BALB/c mice were transplanted with fecal microbiota from 1-month-old infants born by CS or VD and fed a HFD or HFD + human milk oligosaccharides (HMOs) for 16 weeks. CS in mice induced only minor differences in weight gain and had no effect on other metabolic endpoints, likely because there was no difference in the gut microbiota between the CS and VD mice. In contrast, mice colonized with the human CS microbiota weighed significantly more and developed greater insulin resistance than mice colonized with the VD microbiota. These phenotypic changes were accompanied by alterations in serum cytokines, adipokines and metabolic hormones as well as differential gene expression across multiple metabolic tissues. Notably, these manifestations were partially ameliorated by HMO supplementation and by administration of Bacteroides fragilis, a taxon depleted in the CS donor microbiota, which directly reduced circulating FGF-21 levels, implicating this bacterium in host metabolic regulation.

CONCLUSIONS: CS-induced gut dysbiosis can increase the risk of developing obesity and insulin resistance, but without dysbiosis, the metabolic effects of CS birth in isolation are minimal, suggesting that promising therapeutic targets may be identified in the gut microbiome. Video Abstract.},
}

@article {pmid42482090,
year = {2026},
author = {Folch, BA and Pérez-Prieto, I and Salas-Espejo, E and Sola-Leyva, A and Canha-Gouveia, A and Molina, NM and Vargas, E and Leonés-Baños, I and Gámiz-Aguilera, M and Tenorio, CM and Sáez-Lara, MJ and Ruíz-Durán, S and Sánchez-Ruíz, R and Romero, B and Castilla, JA and Altmäe, S},
title = {Assessing the female urogenital-rectal axis microbiome: focus on endometriosis and recurrent implantation failure.},
journal = {Reproductive biology and endocrinology : RB&E},
volume = {24},
number = {1},
pages = {},
pmid = {42482090},
issn = {1477-7827},
abstract = {BACKGROUND: Emerging evidence suggests microbial dysbiosis may contribute to gynaecological pathologies, including endometriosis and recurrent implantation failure (RIF). The vaginal microbiome is well-characterised, with Lactobacillus-dominance as a hallmark of health, yet interactions between vaginal, cervical, and endometrial microbiomes remain inconclusive. The adjacent sites to the vagina, rectal and urinary environments in infertile women are scarcely studied.

METHODS: This cross-sectional study included 136 reproductive-aged women, enrolled at the Reproductive Unit of the University Hospital Virgen de las Nieves (Granada, Spain) between March 2019 and March 2024. Each participant provided five samples during the mid-secretory phase: vaginal and cervical swabs, endometrial brushing, urine, and rectal swabs. The microbiome was analysed using 16S rRNA gene sequencing (V4 region) with functional profiles inferred using PICRUSt2. Diversity and bacterial abundance were compared between endometriosis, RIF, and controls, adjusting for age, body mass index, and antimicrobial use.

RESULTS: In total, 520 samples from 104 women were analysed and revealed shared microbial profiles across the vagina, cervix, endometrium, and urine. The rectal microbiome differed significantly from urogenital sites (Global PERMANOVA, adj p-value = 0.001, R[2] = 0.259). A Lactobacillus gradient in the reproductive tract was observed, with dominance > 98% in the lower tract, 69.72% in urine, and 46.25% in the endometrium. Moreover, Lactobacillus negatively correlated with all other genera within the reproductive tract. Significant differential abundance was detected between body sites: 15 bacteria between vagina-cervix, 166 vagina-uterus and 172 cervix-uterus (all adj p-values < 0.05). Diversity comparisons between the condition groups (endometriosis and RIF) and controls at each anatomical sites revealed no significant differences in microbial communities and functional pathways. However, four bacterial genera showed a significantly different abundance between the endometriosis and controls in the vagina.

CONCLUSIONS: Our study results provide knowledge about the microbial composition throughout the female urogenital tract and rectum, highlighting the interindividual variability rather than the site-specificity. The vaginal bacteria that associated with endometriosis should be investigated further for clarifying their potential as non-invasive biomarkers of the disease. Microbiomes of other urogenital sites do not seem to associate with endometriosis, and microbiomes of the urogenital-rectal axis do not seem to correlate with RIF.

TRIAL REGISTRATION: N/A.},
}

@article {pmid42482126,
year = {2026},
author = {Zhai, Y and Kim, Y and Ban, GH and Kim, YM and Kim, SC and Bae, D and Jeong, KC and Kim, SA},
title = {Environmental reservoirs and transmission pathways of antimicrobial resistance across the pork production continuum.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02444-3},
pmid = {42482126},
issn = {2049-2618},
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a major One Health challenge linking human, animal, and environmental health, yet the contribution of food production environments to resistance transmission remains poorly understood.

RESULTS: We conducted a longitudinal shotgun metagenomic study across the pork production continuum from farm to retail to identify environmental AMR reservoirs and transmission pathways of antimicrobial resistance genes (ARGs). Assembly-based, genome-resolved, and source-tracking analyses were integrated to characterize resistomes, microbial communities, and horizontal gene transfer dynamics. ARG abundance and diversity were highest at farms, slaughterhouses, and processing plants and declined toward retail, although clinically relevant resistance determinants persisted throughout processing. Slaughterhouse environments emerged as major contributors to ARG contamination on carcasses, highlighting the importance of environmental exposure at intermediate stages. Resistome structure was closely linked to microbial community composition, with persistent taxa such as Acinetobacter and Pseudomonas serving as key ARG carriers, including genes conferring resistance to tetracycline, aminoglycosides, macrolide-lincosamide-streptogramin, and β-lactams, multidrug efflux. Co-localization of ARGs with mobile genetic elements demonstrated ongoing potential for horizontal transfer across production stages, and genome-resolved metagenome-assembled genome analyses revealed overlapping resistance and virulence profiles between slaughterhouse- and processing plant-associated bacteria, indicating adaptive persistence within pork production environments.

CONCLUSIONS: Resistome composition across the pork production chain is largely shaped by stage-specific environmental sources, highlighting potential intervention points to mitigate AMR transmission. Video Abstract.},
}

@article {pmid42482155,
year = {2026},
author = {Sun, C and Wang, S and Zhang, Q and Liu, R and Du, Y},
title = {mBatchNet: an interactive web server for diagnosis, correction, and benchmarking of batch effects in microbiome data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag538},
pmid = {42482155},
issn = {1367-4811},
abstract = {SUMMARY: Batch-effect diagnosis and correction are important for reproducible microbiome analysis and cross-study integration. Several batch-correction algorithms are available, but applying and comparing established methods in practice remains nontrivial because they differ in assumptions, accepted inputs, parameters, and evaluation outputs. Here, we present mBatchNet, an interactive web server for applying established batch-correction methods to processed microbiome feature tables and evaluating their effects within a single workflow. The server supports correction methods spanning recent microbiome-oriented approaches and established general-purpose baselines, validates uploaded feature tables and metadata, flags batch-target association, applies matched pre- and post-correction diagnostics, and exports corrected matrices, statistical summaries, run logs, and reproducibility records. In a 16S ribosomal RNA (rRNA) anaerobic digestion case study, mBatchNet revealed method-dependent differences in batch attenuation and phenotype preservation, highlighting its utility for comparing correction strategies.

mBatchNet is freely available without login at https://mbatchnet.com/. The latest source code is available at https://github.com/gilmore307/mBatchNet, and is archived at https://doi.org/10.5281/zenodo.20767444. The server is implemented with a Python/Dash front end and coordinated Python/R back-end analysis scripts.

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

@article {pmid42482202,
year = {2026},
author = {Kamel, AHM and El-Tantawy, N and Ahmed, S and Wadan, AS and AbuBakr, N},
title = {The oral microbiota in oral squamous cell carcinoma: unravelling mechanisms and clinical potential.},
journal = {Cancer cell international},
volume = {26},
number = {1},
pages = {},
pmid = {42482202},
issn = {1475-2867},
abstract = {Originating in the mucosal lining of the mouth, oral squamous cell carcinoma is the most common malignancy of the head and neck regions. Its pathogenesis is multifactorial, involving environmental exposures, genetic susceptibility, and lifestyle-related risk factors. Increasing evidence indicates that oral microbial dysbiosis contributes to the initiation and progression of OSCC. Under healthy conditions, the oral cavity harbors a diverse and functionally balanced microbial ecosystem that maintains mucosal integrity, supports immune homeostasis, and prevents colonization by pathogenic species. Disruption of this equilibrium, known as oral dysbiosis, is increasingly recognized as a key event in oral carcinogenesis. In OSCC, a shift toward pathogenic and pro-inflammatory microbial communities has been consistently observed, particularly involving periodontal bacteria such as Porphyromonas gingivalis, Treponema denticola, and Fusobacterium nucleatum. These organisms contribute to tumor progression by activating inflammatory and oncogenic signaling pathways, including NF-κB, STAT3, and PI3K/Akt; suppressing apoptosis; inducing epithelial-mesenchymal transition; and immune evasion, thereby creating a tumor-promoting microenvironment. In addition to bacterial dysbiosis, viral and fungal components of the oral microbiome may act as important cofactors in OSCC. High-risk Epstein-Barr virus (EBV) and human papillomavirus (HPV) have been implicated in disrupting tumor suppressor pathways, causing genomic instability, and modulating the immune response. Fungal species, particularly Candida albicans, may further contribute by producing carcinogenic metabolites and inducing chronic inflammation. This review provides an integrated overview of the oral microbiome in OSCC, focusing on the composition and protective roles of the core microbiota, factors influencing microbial stability, and mechanisms by which dysbiosis contributes to carcinogenesis. It also highlights the oral microbiome as a potential source of non-invasive biomarkers and discusses microbiome-targeted strategies, including prebiotics, probiotics, and postbiotics, as promising adjunctive approaches to restore microbial balance and reduce tumor-promoting inflammation.},
}

@article {pmid42482345,
year = {2026},
author = {Liu, Y and du Rand, E and Pirk, C and Zheng, H},
title = {Symbiont-Mediated Detoxification of Xenobiotics in Honey Bees.},
journal = {Microbial biotechnology},
volume = {19},
number = {7},
pages = {e70415},
doi = {10.1111/1751-7915.70415},
pmid = {42482345},
issn = {1751-7915},
support = {32072798//National Natural Science Foundation of China/ ; CARS-44//China Agriculture Research System of MOF and MARA/ ; //National Research Foundation of South Africa/ ; },
mesh = {Animals ; *Xenobiotics/metabolism ; Bees/microbiology/metabolism ; *Symbiosis ; Inactivation, Metabolic ; *Gastrointestinal Microbiome ; },
abstract = {The active foraging behaviour of honey bees frequently exposes them to various xenobiotics. Honey bees rely primarily on endogenous enzymatic detoxification systems to metabolise these compounds; however, this capacity is constrained by limitations in their genomic detoxification repertoire. The gut microbiota may partially compensate for this deficiency through two complementary mechanisms: directly transforming or sequestering xenobiotics, and modulating host detoxification pathways. We therefore propose that the gut microbiota should be regarded as an extended detoxification organ in honey bees. This perspective also points to a microbial biotechnology agenda for pollinator protection, including precision probiotics, microbiome-informed breeding and engineered symbionts. Viewing detoxification as a holobiont trait provides a more comprehensive framework for understanding bee resilience and for developing microbiome-based interventions under real-world chemical stress.},
}

Animals
*Xenobiotics/metabolism
Bees/microbiology/metabolism
*Symbiosis
Inactivation, Metabolic
*Gastrointestinal Microbiome

@article {pmid42482460,
year = {2026},
author = {van den Berg, FF and van Santvoort, HC},
title = {Antibiotics in severe acute pancreatitis: from routine prophylaxis to targeted use.},
journal = {Expert review of anti-infective therapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14787210.2026.2708163},
pmid = {42482460},
issn = {1744-8336},
}

@article {pmid42482485,
year = {2026},
author = {Ruting, W and Jiale, L and Hongxi, W and Zhenjin, H and Ruohan, Z and Yuanbo, S and Rongxin, Z and Hongzhen, T and Feng, J},
title = {Intestinal Organoids as Models to Study Viruses: Current Application and Future Perspective.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2603016},
doi = {10.4014/jmb.2603.03016},
pmid = {42482485},
issn = {1738-8872},
mesh = {*Organoids/virology ; Humans ; Animals ; *Intestines/virology ; *Viruses/growth & development ; Virology/methods ; Intestinal Mucosa/virology ; Host Microbial Interactions ; Models, Biological ; Microphysiological Systems ; Host-Pathogen Interactions ; Coculture Techniques ; },
abstract = {Intestinal organoids have emerged as a transformative model system in virology, bridging the gap between conventional cell lines and animal models by recapitulating the complex cellular diversity, three-dimensional architecture, and key functions of the human intestinal epithelium. This review highlights how this technology has enabled groundbreaking studies of enteric viruses, including the successful cultivation of previously uncultivable human norovirus, and has provided critical insights into the infection mechanisms of rotavirus, enterovirus A71, and Severe Acute Respiratory Syndrome Coronavirus 2. We discuss how emerging technologies, such as co-culture systems for host-microbiome interactions, vascularization techniques, and CRISPR/Cas9 gene editing, are being integrated with organoids to create more physiologically relevant microphysiological systems. Despite challenges related to immune component integration and model standardization, intestinal organoids offer a promising platform for elucidating virus-host interactions, advancing antiviral drug screening, and promoting personalized infectious disease research.},
}

*Organoids/virology
Humans
Animals
*Intestines/virology
*Viruses/growth & development
Virology/methods
Intestinal Mucosa/virology
Host Microbial Interactions
Models, Biological
Microphysiological Systems
Host-Pathogen Interactions
Coculture Techniques

@article {pmid42482573,
year = {2026},
author = {Pacheco, AP and Benedict, C},
title = {Can the gut microbiome help 'digest' insomnia? A novel target in sleep medicine.},
journal = {Journal of internal medicine},
volume = {},
number = {},
pages = {},
doi = {10.1111/joim.70131},
pmid = {42482573},
issn = {1365-2796},
}

@article {pmid42482748,
year = {2026},
author = {Zhou, B and Wang, Z and Cao, Z and Liao, R and Xiong, W},
title = {Integrative analysis of GEO data on the microbial community in colorectal cancer tissues and its impact on the tumor immune microenvironment.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1808851},
pmid = {42482748},
issn = {2234-943X},
abstract = {OBJECTIVE: Colorectal cancer (CRC) development is closely associated with gut microbiota dysbiosis and disruption of the tumor immune microenvironment. This study aimed to characterize and independently validate the cross-dataset associations of the "microbiome-immune axis" in CRC through multi-omics integration analysis and independent large-scale cohort validation methods.

METHODS: A multi-stage strategy was applied. The microbiome cohort GSE163366 was analyzed to identify gut dysbiosis in CRC. Single-cell transcriptomic data from GSE132465 characterized tumor immune remodeling. Cross-dataset association analysis linked microbial abundances (GSE163366) with immune cell proportions (GSE132465), and bulk transcriptomics explored underlying pathways. Independent validation cohort GSE237523 rigorously tested the robustness of core bacterial genera.

RESULTS: CRC patients exhibited significantly reduced α diversity (Shannon index, P = 1.29×10[-7]) and altered community structure (PERMANOVA, P = 0.001). The discovery set identified seven key differentially abundant genera, including pathogenic bacteria such as Fusobacterium nucleatum and Bacteroides fragilis, which were enriched in CRC, whereas beneficial bacteria such as Akkermansia muciniphila and Roseburia intestinalis were depleted. The tumor microenvironment exhibited features of reduced adaptive immune infiltration, including a significant reduction in B-cell proportion (11.5% decrease). Cross-dataset association analysis revealed that pathogenic bacteria showed positive associations with myeloid cells but negative associations with B-cells, whereas beneficial bacteria exhibited the opposite pattern. KEGG pathway enrichment analysis demonstrated that differentially expressed genes were significantly enriched in key immune signaling pathways, including the Toll-like receptor and NF-κB signaling pathways. Within the independent validation dataset GSE237523, all seven core bacterial genera identified in the discovery cohort were detected with significant abundance changes. Among these, six genera (85.7%) exhibited completely consistent directions of abundance change in the independent cohort. Notably, core pathogenic bacteria, including Fusobacterium nucleatum and Bacteroides fragilis, demonstrated high cross-cohort consistency.

CONCLUSION: This study provides systematic characterization and independent validation of gut microbiota dysbiosis and its cross-dataset association with the immunosuppressive microenvironment of CRC. The reproducible abundance changes of six out of seven core microbial genera (85.7%) confirm cross-cohort robustness, offering a validated reference for understanding the microbiota-immune axis in tumor progression and developing microbiome-based diagnostic strategies.},
}

@article {pmid42482833,
year = {2026},
author = {Suzuki, E and Deleray, V and Zemlin, J and Kousha, A and Nonoguchi, H and Sun, D and Tsai, CM and Zuffa, S and Kvitne, KE and Dorrestein, PC and Tsunoda, SM and Nizet, V and Liu, GY and Askarian, F},
title = {Effect of perinatal ampicillin or amoxicillin/clavulanate exposure on maternal and infant gut microbiome, metabolome, and infant responses to the 20-valent pneumococcal conjugate vaccine.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2705707},
pmid = {42482833},
issn = {2993-3935},
abstract = {Emerging studies suggest that antibiotics can disrupt the gut microbiome and alter vaccine-induced immune responses. However, the specific consequences of early-life exposure on neonatal immune development remain poorly understood. Here, we examined how two antibiotics frequently used in perinatal care, broad-spectrum ampicillin (AMP) and the extended-spectrum combination amoxicillin/clavulanate (AMOX/CLAV), administered during gestation and lactation, influence neonatal gut microbiome composition, fecal metabolome profiles, and responses to the 20-valent pneumococcal conjugate vaccine (PCV20). Maternal treatment with AMOX/CLAV, but not AMP, significantly reduced PCV-specific IgG titers at 4 and 6 weeks post-prime immunization compared to untreated controls. Exclusive exposure to AMOX/CLAV also impaired neutrophil-mediated opsonophagocytic killing, indicating reduced antibody functionality. These effects were transient, with immune parameters normalizing by 8 weeks post-prime immunization. Metabolomic and microbiome profiling revealed that maternal AMP and AMOX/CLAV differentially perturbed specific metabolite classes, including bile acids, N-acyl lipids, and indole derivatives. Key commensal taxa, including Bacteroidales and Coriobacteriales were also impacted within the gut microbiota. Together, these findings reveal a previously underappreciated maternal-offspring route of antibiotic influence that is transiently associated with neonatal vaccine responsiveness and microbiome and metabolome alterations. These results highlight maternal antibiotic exposure as a possible modifiable factor shaping early-life immunity.},
}

@article {pmid42482927,
year = {2026},
author = {Sebouai, M and Kumar, P},
title = {A comprehensive review of advances in probiotic encapsulation for improved gastrointestinal delivery and health benefits.},
journal = {3 Biotech},
volume = {16},
number = {8},
pages = {343},
pmid = {42482927},
issn = {2190-572X},
abstract = {Probiotics, predominantly lactic acid bacteria (LAB), play an important role in modulating the human gastrointestinal microbiota, particularly the intestinal microbiome. These microorganisms produce a range of bioactive compounds with demonstrated pharmacological activities, including anticancer, antioxidant, and anti-inflammatory effects, whose production and release may be influenced by encapsulation conditions. Owing to these health-promoting properties, LAB have been extensively applied as functional ingredients in food formulations and as therapeutic agents in pharmaceutical products. However, their inherent sensitivity and susceptibility to adverse conditions within the gastrointestinal tract pose a significant challenge to ensuring their survival and delivery in sufficient viable counts to confer health benefits. Encapsulation has emerged as a promising strategy to enhance probiotic stability, protect against harsh gastrointestinal environments, and enable controlled and site-specific release through physicochemical and biological triggers. This review covers literature published primarily between 2010 and 2024, focusing on experimentally validated studies related to probiotic encapsulation and gastrointestinal delivery. The scope includes both established encapsulation techniques (e.g., extrusion, emulsification, and spray drying) and emerging approaches such as electrospinning, layer-by-layer assembly, and nanostructured delivery systems. While numerous in vitro and in vivo studies demonstrate improved probiotic stability and functionality through encapsulation, clinical evidence remains limited, highlighting the need for well-designed human trials to validate therapeutic efficacy.},
}

@article {pmid42482932,
year = {2026},
author = {Yan, Z and Zhou, F and Lin, D and Ruan, D and Liu, Y and Yang, M and Meng, F and Huang, S and Liu, L and Zheng, E and Cai, G and Yang, J and Zhang, Z},
title = {Domestication reshapes the swine gut microbiome: metagenomic insights into taxonomic and functional divergence across wild and domestic populations.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1854568},
pmid = {42482932},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiota constitutes a highly diverse, complex, and dynamically evolving ecosystem within the host. However, the domestication process may alter microbial community composition and function. Here, we investigate these shifts using metagenomic analysis.

METHODS: Microbial diversity was evaluated using alpha and beta-diversity analysis. Furthermore, LEfSe and Functional analyses were employed to delineate significant disparities in microbial abundance and functional potential between wild boars (WB), Chinese domestic pigs (CDP), and Western domestic pigs (WDP).

RESULTS: Our analysis revealed distinct microbial signatures across populations. WB exhibit greater diversity differentiation from WDP, while showing higher similarity to CDP. WB were significantly enriched in the genera Treponema, Oscillibacter, and Pseudoflavonifractor. In contrast, Chinese domestic breeds were characterized by Lactobacillus, Prevotella and Ruminococcus, while WDP retained high abundances of Alistipes, Bacteroides and Clostridium. Functionally, the wild boar microbiome showed significantly higher activity in pathways related to plant secondary metabolite degradation and nutrient biosynthesis. Conversely, domestic pig microbiomes showed significant enrichment in antimicrobial resistance genes and DNA damage repair pathways.

CONCLUSIONS: These findings indicate that domestication has influenced the swine gut microbiota, contributing to distinct compositional and functional divergences. Future research may explore the potential of reintroducing wild-derived probiotics to enhance domestic pig health.},
}

@article {pmid42482937,
year = {2026},
author = {Xie, L and Chen, X and Wan, X and Li, B},
title = {Gut microbiota and pre-competitive anxiety in high-performance taekwondo athletes during pre-competition training: an exploratory pilot study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1845485},
pmid = {42482937},
issn = {1664-302X},
abstract = {OBJECTIVE: Gut microbiota has been implicated in exercise adaptation and emotional regulation, but evidence from high-performance athletes during closed pre-competition training remains limited. This exploratory pilot study examined changes in gut microbiota and competition anxiety across an 8-week pre-competition training period in high-performance taekwondo athletes and explored their associations.

METHODS: Eleven high-performance taekwondo athletes (6 men and 5 women) preparing for the 31st FISU World University Games were assessed before training and again at week 8. Stool samples were analyzed using 16S rRNA V3-V4 sequencing, and competition anxiety was measured with the Competitive State Anxiety Inventory-2 (CSAI-2). Given the small single-group repeated-measures design, all microbiome analyses were treated as exploratory. Paired Wilcoxon signed-rank tests were used for displayed pre-post comparisons, and PERMANOVA was applied to the reconstructed beta-diversity coordinate set.

RESULTS: Shannon alpha diversity showed no clear pre-post difference (Wilcoxon p = 0.278), and the reconstructed PCoA coordinate set showed no significant overall separation (PERMANOVA R2 = 0.028, p = 0.647). Exploratory differential-abundance screening highlighted several candidate taxa, with the strongest signals in the reconstructed dataset observed for Lactobacillus, Enterococcus, norank_f__Muribaculaceae, and Bosea. According to the archived CSAI-2 analysis, cognitive anxiety and somatic anxiety were higher after the preparation period, whereas state self-confidence did not differ significantly. Additional taxa-anxiety associations were observed in the originally reported association subset, but these should be interpreted as nominal exploratory findings only.

CONCLUSION: In this small single-group pilot cohort, the pre-competition period was accompanied by shifts in selected gut microbiota features and by higher pre-competition anxiety-related responses, particularly in the cognitive and somatic domains.},
}

@article {pmid42482993,
year = {2026},
author = {García, G and Díaz, A and Fernández, LT and Bernal, M and Soto, J and Núñez, G and Fleites, V and Arteaga, E and Sichel, L and Cano, RJ},
title = {Del immune V and microbiome restructuring in colorectal cancer surgery: a randomized double blind placebo controlled trial.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1853373},
pmid = {42482993},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/surgery/microbiology ; Double-Blind Method ; Female ; Male ; Aged ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Probiotics/administration & dosage/therapeutic use ; Interleukin-6/blood ; *Lacticaseibacillus rhamnosus ; C-Reactive Protein/analysis ; },
abstract = {INTRODUCTION: The gut microbiome is increasingly recognized as a central factor in carcinogenesis. Dietary components and therapeutic interventions, including probiotics, may influence microbial composition and function, thereby modulating cancer risk. Del-Immune V, a metabiotic supplement derived from Lactobacillus rhamnosus, has demonstrated immunomodulatory properties. This study investigates its role in microbiome restructuring and patient-reported outcomes in colorectal cancer patients during the perioperative period.

MATERIALS AND METHODS: A randomized, controlled, double-blind Phase I trial was conducted in 39 colorectal cancer patients undergoing elective resection, assigned to Del-Immune V (n=22) or placebo (n=17). Participants received two capsules daily (100 mg each), starting 7-15 days before surgery and continuing until 15 days postoperatively. Blood and fecal samples were collected at baseline and day 60 to assess IL-6, CRP, CEA, and microbiome composition. Patient-reported outcomes were measured using the EORTC QLQ-C30 questionnaire. Microbiome profiling was performed using 16S rRNA gene sequencing with PICRUSt-based functional inference.

RESULTS: Del-Immune V significantly reduced IL-6 (p=0.012) and supported CRP decline, while quality-of-life scores improved across multiple domains. Microbiome analyses revealed enrichment of short-chain fatty acid-producing genera (Bifidobacterium, Agathobacter, Gemmiger, Phocaeicola) and decline of CRC-associated taxa (Fusobacterium), with a significant improvement in the dysbiosis index (p=0.024).

CONCLUSIONS: Del-Immune V demonstrated immunomodulatory activity, evidenced by reductions in IL-6 and CRP, alongside improvements in patient-reported quality of life. These effects were accompanied by restructuring of the gut microbiome, characterized by enrichment of protective commensals and reduction of CRC-associated taxa. Collectively, findings support Del-Immune V as a safe adjunctive therapy in colorectal cancer surgery, with potential to enhance recovery and long-term outcomes.},
}

Humans
*Colorectal Neoplasms/surgery/microbiology
Double-Blind Method
Female
Male
Aged
*Gastrointestinal Microbiome/drug effects
Middle Aged
RNA, Ribosomal, 16S/genetics
Feces/microbiology
*Probiotics/administration & dosage/therapeutic use
Interleukin-6/blood
*Lacticaseibacillus rhamnosus
C-Reactive Protein/analysis

@article {pmid42482995,
year = {2026},
author = {Titusson, C and Lundmark, A and Soares, RRG and Damdimopoulos, A and Johannsen, G and Naseem, U and Yucel-Lindberg, T},
title = {Integration of periodontal pathogens and inflammatory mediators in saliva as biomarkers for periodontitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1846125},
pmid = {42482995},
issn = {2235-2988},
mesh = {Humans ; *Saliva/microbiology/chemistry ; *Biomarkers/analysis ; *Periodontitis/microbiology/diagnosis ; Female ; Cross-Sectional Studies ; *Inflammation Mediators/analysis ; Adult ; Male ; Middle Aged ; *Bacteria/genetics/classification/isolation & purification ; Microbiota ; },
abstract = {BACKGROUND/OBJECTIVE: Periodontitis pathogenesis is driven by oral microbiome dysbiosis and dysregulated host immune responses. This cross-sectional study characterized salivary microbiome and inflammatory mediator profiles to identify candidate biomarkers distinguishing periodontal health from periodontitis (PD) using hyperplex PCR, multiplex assay and exploratory machine learning.

MATERIALS AND METHODS: Stimulated saliva samples from 57 participants (28 periodontally healthy, 29 with PD stage III/IV) were collected and analyzed using Hyperplex PCR (simultaneously amplifying multiple targets in a single assay) for oral bacteria and a multiplex immunoassay including 37 inflammatory mediators. Random forest modeling explored the discriminatory performance of individual and combined biomarkers.

RESULTS: Individuals with PD stage III/IV showed elevated relative abundance of Filifactor alocis, Fretibacterium spp., Parvimonas micra (P < 0.05) compared to periodontally healthy individuals. Among determined inflammatory mediators, the levels of Chitinase 3-like 1, sIL-6Rβ, sIL-6Rα, IL-19, pentraxin-3, sTNF-R1 and TWEAK were elevated in PD stage III/IV. Exploratory modeling identified Fretibacterium spp. as the strongest individual discriminator (AUC = 0.82), a performance that was not improved by two- or three-marker combinations incorporating additional bacteria or inflammatory mediators.

CONCLUSION: In exploratory unadjusted analyses, salivary Fretibacterium spp. showed the highest discriminatory performance (AUC = 0.82), although this association was not statistically significant after adjustment for age, smoking, and cardiovascular disease. These exploratory findings require further validation in larger, diverse cohorts to assess their potential clinical utility.},
}

Humans
*Saliva/microbiology/chemistry
*Biomarkers/analysis
*Periodontitis/microbiology/diagnosis
Female
Cross-Sectional Studies
*Inflammation Mediators/analysis
Adult
Male
Middle Aged
*Bacteria/genetics/classification/isolation & purification
Microbiota

@article {pmid42483182,
year = {2026},
author = {Zhu, JX and Huang, GJ},
title = {The microbiota-metabolite-immune axis in the olfactory cleft microenvironment: mechanisms and therapeutic implications for dysbiosis-driven olfactory dysfunction in chronic rhinosinusitis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1841979},
pmid = {42483182},
issn = {1664-3224},
mesh = {Humans ; *Rhinosinusitis/immunology/microbiology/metabolism/complications/therapy ; *Dysbiosis/immunology ; Chronic Disease ; *Microbiota/immunology ; Animals ; *Olfaction Disorders/immunology/etiology/metabolism/therapy ; *Olfactory Mucosa/immunology/metabolism/microbiology ; },
abstract = {Chronic rhinosinusitis is the leading cause of olfactory dysfunction in adults. Although mechanical obstruction and type 2 inflammation remain important explanations for smell loss in chronic rhinosinusitis, emerging multi-omics studies suggest that disruption of the olfactory cleft microenvironment may also contribute to olfactory dysfunction. In this review, we propose the microbiota-metabolite-immune (MMI) axis as an integrative framework linking microbial dysbiosis, metabolite perturbation, and local immune remodeling in CRS-associated olfactory dysfunction. We systematically examine four interconnected domains. First, several studies have reported dysbiosis within the olfactory niche, including enrichment of Acinetobacter johnsonii in one CRS-OD cohort together with depletion of putative commensals. Second, altered metabolite profiles in CRS-OD have been associated with disturbed purine metabolism, uric acid accumulation, and reduced levels of the potentially protective metabolite indole-3-acetic acid. These changes may contribute to innate inflammatory signaling, including Toll-like receptor 4/nuclear factor kappa-light-chain-enhancer of activated B cells (TLR4/NF-κB)-related pathways. Third, Staphylococcus aureus superantigens may promote T helper 2 (Th2) polarization, alter regulatory T-cell function, disrupt tight junction integrity, and impair olfactory neurogenesis, thereby sustaining bidirectional immune-microbial crosstalk. Fourth, emerging microbiota-targeted therapeutics, including xylitol irrigation, probiotics, and Interleukin-4 receptor alpha (IL-4Rα) blockade, offer novel intervention strategies. Throughout this review, we distinguish olfactory cleft-specific evidence from broader sinonasal data and acknowledge the current predominance of association studies over causal validation. Taken together, the MMI axis provides a useful framework for understanding CRS-associated OD and for identifying testable therapeutic hypotheses.},
}

Humans
*Rhinosinusitis/immunology/microbiology/metabolism/complications/therapy
*Dysbiosis/immunology
Chronic Disease
*Microbiota/immunology
Animals
*Olfaction Disorders/immunology/etiology/metabolism/therapy
*Olfactory Mucosa/immunology/metabolism/microbiology

@article {pmid42483439,
year = {2026},
author = {Tien, PT and Wei, CC and Lin, SC and Meng, PP and Huang, YT and Chen, JJ and Wu, MY and Shih, YH and Hsu, TJ and Tsai, FJ and Wang, YC and Lin, HJ and Wan, L},
title = {Early-life exposure to antibiotics increases the risk of myopia: A retrospective cohort study.},
journal = {BioMedicine},
volume = {16},
number = {2},
pages = {75-86},
pmid = {42483439},
issn = {2211-8020},
abstract = {BACKGROUND: The prevalence of myopia is increasing worldwide and is projected to affect nearly half of the global population by 2050. Although genetic susceptibility plays an important role, early-life environmental exposures are increasingly recognized as modifiable contributors to myopia development. Antibiotics are frequently prescribed during infancy and early childhood and can alter gut microbiota composition, which has been implicated in ocular disorders.

METHODS: We conducted a retrospective cohort study using data from a national health insurance database. Children aged three years or younger who received systemic antibiotics were included, while those with pre-existing myopia or retinopathy were excluded. Antibiotic-exposed children were matched with non-exposed controls by age, sex, and relevant comorbidities. Cox proportional hazards regression models were used to estimate adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs) for incident myopia.

RESULTS: Early-life antibiotic exposure was associated with a significantly increased risk of myopia compared with non-exposed controls (aHR = 1.03; 95% CI: 1.02-1.04), accompanied by a higher cumulative incidence of myopia (log-rank test, p < 0.001). The elevated risk was observed in both females (incidence rate [IR] = 66.98 vs. 64.10; aHR = 1.05; 95% CI: 1.04-1.07) and males (IR = 61.53 vs. 59.66; aHR = 1.04; 95% CI: 1.02-1.05). Urbanization level, parental monthly income, and comorbidities were independently associated with antibiotic exposure. The increased risk of myopia persisted irrespective of antibiotic treatment duration (<11 days; aHR = 1.19; 95% CI: 1.15-1.23) or cumulative dose (defined daily dose <2833; aHR = 1.31; 95% CI: 1.28-1.33).

CONCLUSIONS: Early-life exposure to antibiotics is associated with a higher incidence of myopia in children. These findings underscore the importance of cautious and judicious antibiotics prescribing during early childhood to mitigate potential long-term ocular health risks.},
}

@article {pmid42483512,
year = {2026},
author = {Wei, Q and Duan, G and Sui, L and Anwar, S and Ao, J and Liu, G and Xu, Z and Zhang, C and Qi, M and Li, X and Zhao, M and Wang, B and Ge, Y},
title = {Coffee endophytes: diversity, ecological functions, and application prospects in sustainable production.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1884416},
pmid = {42483512},
issn = {1664-462X},
abstract = {Coffee production is increasingly constrained by climatic variability, unstable yields, major pests and diseases, and growing demand for consistent bean quality. Endophytic microorganisms that colonize internal coffee tissues may contribute to plant growth, stress tolerance, disease and pest suppression, and postharvest quality-related processes. However, current knowledge remains fragmented because confirmed endophytes, rhizosphere microorganisms, phyllosphere taxa, and fermentation-associated microbiota are often discussed together. This review synthesizes coffee endophyte diversity, tissue-specific distribution, colonization routes, host-selection filters, ecological functions, and application prospects, while explicitly separating direct endophyte evidence from coffee-associated and indirect evidence. We show that coffee endophytes are shaped by host genotype, tissue niche, altitude, shade, management system, developmental stage, and microbial source pools, rather than representing a fixed list of ubiquitous taxa. Mechanistically, coffee endophytes may influence nutrient acquisition, phytohormone balance, stress physiology, salicylic acid- and jasmonic acid/ethylene-mediated defense signaling, reactive oxygen species regulation, PR proteins, lignification, antimicrobial metabolites, and multitrophic plant-microbe-insect interactions. Current evidence is strongest for isolation, community description, in vitro screening, and short-term greenhouse or pot studies, whereas field persistence, functional stability, biosafety, and formulation remain insufficiently validated. We propose an application-oriented pipeline linking tissue-specific isolation, evidence-level classification, host reinoculation, colonization tracking, multi-omics, synthetic consortia, multi-environment trials, and product development. This synthesis clarifies how coffee endophyte research can move from descriptive microbiome inventories towards reliable microbial tools for sustainable coffee cultivation, integrated pest and disease management, and quality-oriented processing.},
}

@article {pmid42483640,
year = {2026},
author = {Huang, Y and Liu, X and Lin, C and Li, Y and Zhou, A and Huang, Y and Wang, Y and Liu, X},
title = {Dietary index for gut microbiota and risk of incident gastroesophageal reflux disease: a prospective cohort analysis integrating plasma proteomics in the UK Biobank.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1880631},
pmid = {42483640},
issn = {2296-861X},
abstract = {OBJECTIVES: Gastroesophageal reflux disease (GERD) is a common chronic digestive disorder, and diet is an important modifiable risk factor. The Dietary Index for Gut Microbiota (DI-GM) reflects dietary patterns considered favorable to the gut microbiota; however, the gut microbiome itself was not measured, and evidence on whether DI-GM is associated with GERD risk is limited. We aimed to evaluate the association between DI-GM and incident GERD and to explore potential intermediate pathways using mediation analysis and plasma proteomics.

METHODS: We included 133,915 UK Biobank participants free of GERD at baseline. DI-GM scores (range 0-14) were calculated from the Oxford WebQ 24-h dietary recall and grouped into four categories (0-3, 4, 5, ≥6). Incident GERD was identified from the UK Biobank first-occurrence records (ICD-10 K21). Cox proportional hazards regression was complemented by restricted cubic spline (RCS), subgroup, and Cox weighted quantile sum (WQS) analyses, counterfactual mediation analysis, integrated plasma proteomics (Olink Explore 3072), and a range of sensitivity analyses.

RESULTS: During a median follow-up of 13.6 years, 12,271 incident GERD cases occurred. In the fully adjusted model, each 1-point increase in DI-GM was associated with an approximately 4% lower hazard of GERD [hazard ratio (HR) 0.956, 95% CI 0.947-0.965; P < 0.001], and the highest DI-GM group (≥6) had a lower hazard than the lowest (0-3) (HR 0.812, 95% CI 0.774-0.851; P for trend < 0.001). RCS analysis showed a modest inverse dose-response relationship that was most apparent at higher DI-GM scores, and WQS analysis indicated that the association was driven by a few key components rather than shared equally across the index. BMI (proportion mediated 21.43%) and phenotypic age acceleration (7.53%) both significantly mediated the association (both P < 0.001). Integrated proteomic analysis identified 13 shared proteins; the nine positively associated with DI-GM and inversely associated with GERD showed exploratory enrichment in neurodevelopment- and cell-adhesion-related processes.

CONCLUSIONS: Higher DI-GM was associated with a lower incidence of medically attended GERD, with mediation analysis suggesting that BMI and biological aging may partly account for this association. Exploratory proteomic analyses identified shared protein correlates, including adiposity-related and, tentatively, neurodevelopment- and cell-adhesion-related proteins; these are hypothesis-generating and require confirmation. Because the gut microbiome was not measured, the diet-microbiota link remains inferential, and these findings should be interpreted as associations rather than established mechanisms.},
}

@article {pmid42483643,
year = {2026},
author = {Xie, Y and Lu, Y and Jiang, Z and Dong, W and Liu, Y and Wang, Y and Shao, J and Yan, W and Chai, Z},
title = {Dynamics and drivers of the human breast milk microbiome across lactation stages.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1861294},
pmid = {42483643},
issn = {2296-861X},
abstract = {INTRODUCTION: Human breast milk (HBM) not only provides all the nutrients and microbiota for the initial development of infants but is also the source of gut microbes in infants and is essential for establishing a healthy gut microbiota and immune system. In this study, we enrolled 188 healthy Uyghur mothers from Xinjiang, China, analysed the structure and diversity of the human breast milk microbial community from 0 to 856 days after delivery, and explored the characteristics of the human breast milk microbiome and potential influencing factors at each lactation stage.

METHODS: By constructing microbial cooccurrence relationship networks at various stages of lactation and random forest models, we adopted large sample collection and combined multiple models to largely avoid individual differences.

RESULTS: We showed that the human breast milk microbiota is a dynamic and complex ecosystem, and we found the network central nodes that change during the transition from human colostrum to human mature milk and various stage specific microbial markers. In addition, we also found that the mode of delivery and intrapartum antibiotic prophylaxis during delivery affected the structure and diversity of the microbial community of colostrum, but the degree of influence decreased as the human colostrum transitioned to mature milk.

DISCUSSION: We determined the change trends for microbial community structure and diversity during the transition from human colostrum to human mature milk, provided evidence for the temporal dynamics of the microbial community in human breast milk, and evaluated the impact of potential factors, such as mode of delivery on the microbes in human breast milk. These findings have potential implications for the health and development of infants.},
}

@article {pmid42483733,
year = {2026},
author = {Pyrsopoulos, NT and Gunn, N and Jalal, PK and Catinis, GE},
title = {Reducing the Risk of Overt Hepatic Encephalopathy Recurrence: A Narrative Review.},
journal = {Journal of clinical and translational hepatology},
volume = {14},
number = {6},
pages = {674-686},
pmid = {42483733},
issn = {2310-8819},
abstract = {Hepatic encephalopathy (HE) is a neurologic complication of advanced liver disease (e.g., cirrhosis) resulting in impaired functioning and reduced quality of life. This condition is associated with a substantial burden for patients and their caregivers and carries a poor prognosis and increased risk of hospitalization and mortality. This narrative review discusses the burden of HE, precipitating risk factors, and clinical considerations for reducing the risk of overt HE (OHE) recurrence in adults with cirrhosis. Key precipitating factors include certain medications, constipation, dehydration, uncontrolled diabetes mellitus, electrolyte imbalances, gastrointestinal bleeding, infection, and sarcopenia, among others. Identification and treatment of precipitating factors are critical steps in the management of HE. Components of ongoing care include patient and caregiver education, nutritional supplementation and sleep management, pharmacotherapy, and nonpharmacologic interventions (e.g., spontaneous portosystemic shunt embolization and liver transplantation in appropriate patients). Clinical guidelines recommend lactulose therapy as secondary prophylaxis after an initial episode of OHE. Rifaximin is recommended as add-on therapy to lactulose when an additional OHE episode occurs. Polyethylene glycol has been investigated as an alternative to lactulose in patients with acute HE and in those with chronic HE and a poor response to lactulose. Oral L-ornithine-L-aspartate may reduce the risk of OHE recurrence in patients with cirrhosis. Investigational agents include nitazoxanide, fecal microbiota transplantation, and the use of artificial intelligence, app-based technology, and wearable devices to facilitate acute and prophylactic management of HE.},
}

@article {pmid42483952,
year = {2026},
author = {Oyama, LB},
title = {From sequence space to ecological function: microbiome-derived antimicrobial peptides as community effectors and therapeutic leads.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20250036},
pmid = {42483952},
issn = {1744-1358},
support = {BB/X012794/1//UKRI | Biotechnology and Biological Sciences Research Council (AFRC)/ ; BB/Z515346/1//UK Research and Innovation (UKRI)/ ; },
abstract = {Antimicrobial peptide research has long centred on host defence molecules, yet microbiomes themselves encode a diverse and increasingly important repertoire of peptide-based antimicrobials. These microbiome-derived antimicrobial peptides include bacteriocins, ribosomally synthesised and post-translationally modified peptides, cryptic short open reading frame-encoded peptides, embedded antimicrobial regions within larger proteins, and selected peptide antibiotics recovered from human, animal, plant and environmental microbiomes. Recent advances in genome mining, metagenomics, and machine learning have greatly expanded the scale of discovery, moving the field from a handful of landmark exemplars to large candidate catalogues spanning the global microbiome. In the clearest cases, these molecules are not only anti-infective leads but ecological effectors: they mediate microbial competition, enforce colonisation resistance, and influence community structure within densely occupied niches. The present review synthesises the field across discovery classes, microbiome sources, ecological roles, and translational bottlenecks, emphasizing a central limitation of the field: candidate catalogues are expanding at extraordinary scale, while evidence for native expression, producer assignment, ecological function, and in vivo relevance remains limited for the vast majority of predicted molecules. Progress will depend on workflows that connect sequence level prediction to biological context through expression support, producer assignment, community level validation, and perturbation-based approaches that distinguish ecological association from causal function. Microbiome-derived antimicrobial peptides are best understood not only as promising therapeutic leads, but also as molecular mediators of microbial social life whose ecological origins are central to their interpretation and future application.},
}

@article {pmid42484062,
year = {2026},
author = {Zhang, X and Gan, D and Shi, Y and Liu, W and Yin, H and Fu, Q and Huang, X},
title = {Disruption of mucosal immune homeostasis in food allergy: a convergence of genetic, barrier, microbiome, and environmental triggers.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo02631a},
pmid = {42484062},
issn = {2042-650X},
abstract = {Food allergy is a pathological immune response to food antigens. Its global prevalence continues to rise, making it a significant public health and food safety concern. This review describes the pathogenesis of food allergy, proposing that its development results from the interplay of multiple factors, including genetic background, disruption of the intestinal barrier, breakdown of oral tolerance, gut microbiome dysbiosis, and early-life environmental exposures. Genetic background establishes a baseline risk for the disease. Compromised intestinal barrier integrity facilitates abnormal allergen translocation and alarmin release, thereby initiating a type 2 immune response. The collapse of oral tolerance is marked by impaired regulatory T cell function and a dominant Th2 response. Gut microbiome dysbiosis, by altering key metabolites such as short-chain fatty acids, further exacerbates immune dysregulation. Dietary and environmental factors program these processes during critical early-life windows. Together, these elements form a dynamic, interactive pathogenic network. Future research should integrate multi-omics and systems biology approaches to better elucidate the interaction mechanisms within this network, thereby advancing the development of precise preventive and therapeutic strategies for food allergy.},
}

@article {pmid42484341,
year = {2026},
author = {Sato, Y and Uda, Y and Nagao, Y},
title = {Maternal contact and age-dependent succession influence the assembly of the calf rumen microbiome and virome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0167726},
doi = {10.1128/spectrum.01677-26},
pmid = {42484341},
issn = {2165-0497},
abstract = {Early-life colonization of the rumen is particularly important; however, the processes by which microbial and viral communities are transmitted and developed remain poorly understood. Here, we present a genome-resolved investigation of the effects of maternal contact and age-dependent succession on the calf rumen microbiome and DNA virome by comparing calves raised with or without maternal contact across early life using the metagenome-assembled genomes (MAGs) and viral operational taxonomic units (vOTUs) reconstructed from whole- and virus-like particle metagenomes. Across longitudinal samples from calves and their mothers, we identified 694 MAGs and 30,479 vOTUs, substantially expanding current genome databases and revealing extensive microbial and viral novelty. Our analyses demonstrated that both prokaryotes and DNA viruses are shared between dams and calves, with greater sharing observed in calves raised with maternal contact than in calves raised without maternal contact. Notably, viral sharing between cow-calf pairs was markedly lower compared to prokaryotes, suggesting high turnover and rapid viral diversification. Age-associated analyses further revealed coordinated shifts in prokaryotes and their viruses, with dominant genera such as Prevotella, Ruminococcus, and Fibrobacter, and their corresponding viruses increasing after day 40. These findings indicate that the early-life rumen microbiome and DNA virome undergo substantial age-dependent succession and are associated with maternal contact, providing new insights into host-microbe-virus interactions during rumen development.IMPORTANCEThis study provides one of the first genome-resolved views of DNA viral community development during early rumen colonization in calves (from 1 week to 70 days of age) and reveals how maternal contact and age influence the establishment of the calf rumen microbiome and virome. By analyzing longitudinal samples from calves raised with or without their mothers, we show that prokaryotes and their viruses undergo coordinated, age-dependent succession. Our results demonstrate that maternal separation alters the assembly of the calf rumen microbiome, highlighting the influence of maternal contact during early-life rumen development. These findings underscore the high plasticity of the early-life rumen ecosystem and suggest that early management practices, such as maternal separation, can have lasting effects on rumen development. This work provides fundamental insights into the establishment and succession of the calf rumen microbiome and DNA virome during early life and may contribute to future microbiome manipulation studies.},
}

@article {pmid42484355,
year = {2026},
author = {McDermott, JE and Nelson, WC and Zimmerman, AE and Anthony, W and Coleman-Derr, D and Elmore, JR and Nitka, T and McClure, RS and Handakumbura, PP and Guss, AM and Wheeler, TJ and Egbert, RG},
title = {Describing the persistence landscape for introducing microbes into complex communities.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0093026},
doi = {10.1128/aem.00930-26},
pmid = {42484355},
issn = {1098-5336},
abstract = {Introducing non-native organisms into natural or designed microbial communities holds enormous potential but faces challenges in establishment, persistence, and containment. We propose the "persistence landscape"-the functional composition of a target microbiome that promotes or discourages engineered organism persistence. Building on existing ecological concepts, this framework predicts the fitness of introduced organisms. Application of this concept would enable controlled introduction of desired taxa and phenotypes, addressing pressing challenges in agronomy, biomanufacturing, and human health.},
}

@article {pmid42484379,
year = {2026},
author = {Basting, CM and Anderson, J and Escandón, K and Wieking, G and Guerrero, C and Reichel, J and Cromarty, RT and Swanson, E and Schroeder, T and Creagan, E and Barrett, M and Torres-Ruiz, F and Soto-Nava, M and Carvajal-Ruiz, L and Ordaz-Candelario, KK and Briceño, O and Funderburg, N and Graham, M and Hunt, P and Avila-Rios, S and Salgado Montes de Oca, G and Schacker, TW and Klatt, NR},
title = {Multi-omics links microbial dysbiosis, systemic inflammation, and metabolomic disruptions to SNAE risk in treated HIV.},
journal = {JCI insight},
volume = {11},
number = {14},
pages = {},
doi = {10.1172/jci.insight.205379},
pmid = {42484379},
issn = {2379-3708},
mesh = {Humans ; *HIV Infections/drug therapy/complications/microbiology/immunology ; *Dysbiosis/microbiology ; *Inflammation/metabolism/microbiology ; Male ; Multiomics ; Female ; Adult ; Metabolomics ; Middle Aged ; Gastrointestinal Microbiome ; CD4-CD8 Ratio ; },
abstract = {Serious non-AIDS events (SNAEs), including non-AIDS malignancies, cardiovascular disease, and hepatic complications, remain major causes of mortality in treated HIV infection. These outcomes are driven by persistent immune activation, systemic inflammation, and metabolic dysfunction despite effective viral suppression with antiretroviral therapy (ART). To investigate mechanisms underlying SNAE pathogenesis, we performed a cross-site multi-omic analysis integrating plasma proteins, plasma metabolites, and mucosal microbiomes in 82 ART-treated people with HIV (PWH) and 10 people without HIV from the United States and Mexico. Geography was the dominant source of variation, particularly across lipid classes. However, individuals at high risk for SNAEs, defined by low CD4+ T cell counts and low CD4/CD8 ratios, shared a consistent signature of systemic inflammation, mitochondrial dysfunction, and microbial dysbiosis, including elevated plasma IL-6 and ω-oxidation products (adipic and suberic acids) and depletion of short-chain fatty acid-producing commensals in the gut mucosa, including Akkermansia muciniphila, Bacteroides uniformis, and Ruminococcus. A. muciniphila abundance correlated with lower IL-6 levels, fewer HIV RNA-producing cells in lymph nodes, and higher CD4/CD8 ratios. These findings identify a shared inflammatory and metabolic phenotype in PWH and implicate A. muciniphila as a potential microbiome-based target to mitigate immune activation and SNAE risk in treated HIV.},
}

Humans
*HIV Infections/drug therapy/complications/microbiology/immunology
*Dysbiosis/microbiology
*Inflammation/metabolism/microbiology
Male
Multiomics
Female
Adult
Metabolomics
Middle Aged
Gastrointestinal Microbiome
CD4-CD8 Ratio

@article {pmid42484460,
year = {2026},
author = {Cabral, CD and Apaza-Castillo, GA and Lorenzi, AS and Mattiuzzi, PHP and de Alencar, AA and Quecine, MC and de Moraes, MT and Rabêlo, FHS and Mazzafera, P and Tezotto, T},
title = {Temperature-Dependent Root Responses to Water Deficit Modulate Biological Nitrogen Fixation and Rhizosphere Dynamics in Soybeans.},
journal = {Physiologia plantarum},
volume = {178},
number = {4},
pages = {e71029},
doi = {10.1111/ppl.71029},
pmid = {42484460},
issn = {1399-3054},
support = {88887.906771/2023-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 1185 PIB//Fundação de Estudos e Pesquisas Agrícolas e Florestais/ ; 7867//Fundação de Apoio à Univesidade de São Paulo/ ; },
mesh = {*Glycine max/physiology/metabolism/microbiology ; *Nitrogen Fixation/physiology ; *Rhizosphere ; *Plant Roots/physiology/metabolism ; Temperature ; *Water/metabolism ; Soil Microbiology ; Soil/chemistry ; Plant Root Nodulation ; Nitrogen/metabolism ; Root Nodules, Plant ; },
abstract = {Although soil warming and water scarcity are frequently associated with reductions in soybean productivity and biological nitrogen fixation (BNF), their combined effects remain poorly understood. This study evaluated how soil temperature and water regime influence nodulation, BNF efficiency, plant physiology and metabolism, soil enzymatic activity, and rhizosphere microbial communities in soybean plants grown at two soil temperatures (24°C and 36°C) under two water regimes: well-watered (WW) and water deficit (WD). The WD treatment was the main limiting factor, reducing plant growth, nodule number, and biomass, ureide accumulation, and integrated BNF indices. Surprisingly, nodular efficiency and photosynthetic rate were higher under WD. Root-zone warming under adequate water availability promoted greater plant and nodule biomass, higher ureide accumulation, and increased integrated BNF efficiency despite a reduction in nodule number. In addition, soil warming increased malondialdehyde and citrate concentrations in shoots as well as nodular concentrations of N, P, K, S, and B. Soil enzymatic activities and rhizosphere bacterial community structure varied among treatments, whereas fungal communities remained relatively stable. Overall, water deficit structured BNF limitation, while soil warming modulated metabolic responses. These results indicate that water availability and soil temperature jointly regulate biological nitrogen fixation and soil-plant-microbe interactions in soybeans, highlighting the importance of considering these factors together when developing management strategies under climate change scenarios.},
}

*Glycine max/physiology/metabolism/microbiology
*Nitrogen Fixation/physiology
*Rhizosphere
*Plant Roots/physiology/metabolism
Temperature
*Water/metabolism
Soil Microbiology
Soil/chemistry
Plant Root Nodulation
Nitrogen/metabolism
Root Nodules, Plant

@article {pmid42484622,
year = {2026},
author = {Soler-Sáez, I and Galiana-Roselló, C and Grillo-Risco, R and Falony, G and Tepavčević, V and Vieira-Silva, S and García-García, F},
title = {Integrative multicohort analysis reveals consistent sex differences in gut microbiota of multiple sclerosis patients.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0041626},
doi = {10.1128/msystems.00416-26},
pmid = {42484622},
issn = {2379-5077},
abstract = {UNLABELLED: Biological sex is a key determinant in the onset and progression of multiple diseases. In multiple sclerosis (MS), females exhibit higher disease prevalence, earlier onset, and more pronounced inflammatory activity, whereas males tend to experience a more severe neurodegenerative course, characterized by accelerated central nervous system damage and increased brain atrophy. The gut microbiome has emerged as a critical factor in MS, as its composition can either ameliorate or exacerbate disease progression. In this study, we aimed to identify reproducible sex-associated differences in gut microbial composition across independent cohorts of MS patients. Through a systematic search, we identified six independent studies based on 16S rRNA gene sequencing, comprising a total of 337 samples. Despite substantial interstudy variability, sex-associated differences were more pronounced in MS patients than in healthy controls. We identified 11 microbial taxa showing significant sex-associated differences in MS, nine enriched in females, and two in males. Notably, the female-enriched taxa Eggerthella and Eisenbergiella were associated with specific MS subtypes and higher disability. To facilitate the use of our findings by the scientific community, we developed a freely accessible web-based tool that provides full access to our results. Thus, in this work, we identified consistent and reproducible sex differences in the gut microbiota of MS patients, highlighting the importance of incorporating sex as a critical variable in microbiome research, with potential implications for understanding disease heterogeneity in MS.

IMPORTANCE: Multiple sclerosis (MS) affects females and males differently, but the biological reasons behind these differences are not fully understood. One potential factor is the gut microbiome (i.e., the community of microorganisms living in our intestines), which can influence immune function and disease progression. In this study, we analyzed data from multiple independent cohorts and found consistent differences in gut microbial composition between female and male MS patients. Notably, certain bacteria were more abundant in females and were linked to more severe disease features. We also developed a freely accessible web tool where researchers can explore the complete findings in detail. Our results highlight the importance of considering sex as a key factor in microbiome research and may help guide more personalized approaches to understanding and treating MS.},
}

@article {pmid42484632,
year = {2026},
author = {Vernon, JJ and Lynch, J and Yu, X and Do, T},
title = {Clostridioides difficile in the oral microbiome: an in silico analysis.},
journal = {Journal of medical microbiology},
volume = {75},
number = {7},
pages = {},
doi = {10.1099/jmm.0.002188},
pmid = {42484632},
issn = {1473-5644},
mesh = {Humans ; *Clostridioides difficile/genetics/isolation & purification/classification ; Saliva/microbiology ; *Dental Plaque/microbiology ; *Microbiota ; *Clostridium Infections/microbiology/epidemiology ; Periodontitis/microbiology ; *Mouth/microbiology ; Computer Simulation ; Computational Biology ; Metagenomics ; Female ; Male ; },
abstract = {Introduction. High rates of recurrent Clostridioides difficile infection (CDI) and environmental contamination are attributed to its ability to form spores. Periodontal diseases are characterized by gingival inflammation, caused by dental plaque accumulation.Hypothesis. Periodontal plaque could harbour C. difficile spores, acting as a reservoir for reinfection.Aim. Compare the prevalence and abundance of C. difficile in metagenomic sequences of saliva and dental plaque from healthy and periodontal disease patients.Methodology. Publicly available metagenomic reads from oral samples of healthy (n=80) and periodontitis (n=204) patients were analysed for C. difficile presence through an in-house bioinformatic pipeline. Briefly, reads underwent quality control (cutadapt/fastQC) prior to subsampling of 3 million reads (seqtk). Reads and MEGAHIT-assembled contigs were aligned to a C. difficile reference genome (ASM1888508v1) or a full non-redundant protein DIAMOND database. Outputs were filtered, annotated (Entrez Direct) and top hits identified via National Center for Biotechnology Information blast. Abundance and prevalence were compared between cohorts.Results. Low levels of C. difficile sequences were observed, with significantly higher prevalence in periodontitis (7.4%, n=15/204) vs. healthy cohorts (5.0%, n=4/80) (P=0.0087) with reference genome alignment. Using the full non-redundant database, prevalence was also higher in periodontitis (14.2% vs. 3.8%; P=0.012), along with significantly greater average C. difficile sequence counts (0.608 vs. 0.075; P=0.018) and relative abundance (0.00029% vs. 0.0000003%; P=0.009).Conclusion. Sequences pertaining to C. difficile were detected in oral samples, with significantly more observed in periodontal disease compared to healthy cohorts. This highlights the possibility for dental plaque to act as a reservoir, potentially contributing to reinfection in CDI patients.},
}

Humans
*Clostridioides difficile/genetics/isolation & purification/classification
Saliva/microbiology
*Dental Plaque/microbiology
*Microbiota
*Clostridium Infections/microbiology/epidemiology
Periodontitis/microbiology
*Mouth/microbiology
Computer Simulation
Computational Biology
Metagenomics
Female
Male

@article {pmid42484738,
year = {2026},
author = {Mendez, AC and Alalhareth, FK and Kydd, L and Hohn, ME and Radunskaya, A and Jaworski, J and Kojouharov, HV},
title = {Who wins? Analysis and Simulation of a Batch Culture Model of Bacterial Competition in the Presence of Plasmids.},
journal = {Bulletin of mathematical biology},
volume = {88},
number = {8},
pages = {},
pmid = {42484738},
issn = {1522-9602},
support = {2230790//Division of Mathematical Sciences/ ; },
mesh = {*Plasmids/genetics ; *Escherichia coli/growth & development/genetics ; *Models, Biological ; Computer Simulation ; Mathematical Concepts ; Batch Cell Culture Techniques/statistics & numerical data ; Conjugation, Genetic ; },
abstract = {Bacteria are essential in research and commercial processes for producing DNA, proteins, and converting raw materials into high-value molecules, often using batch culture systems. These systems provide controlled conditions for bacterial growth, which is influenced by factors like temperature, oxygen, and nutrients. This study introduces a mathematical model of plasmid dynamics, including loss, uptake, and transfer by conjugation, within batch cultures. The model helps optimize E. coli cultures for product formation and predict plasmid-carrying bacteria levels, offering insights into plasmid dynamics in "one-pot" systems. Our findings show that plasmid retention is influenced by selection pressures which can be an important consideration in probiotic dosing regimens. The model aligns with experimental data and highlights the importance of understanding plasmid dynamics for controlling bacterial growth processes, with implications for research, commercial applications, and gut microbiome stability. Future work will explore temporal changes in plasmid dynamics, requiring advanced instrumentation for precise bacterial population quantification.},
}

*Plasmids/genetics
*Escherichia coli/growth & development/genetics
*Models, Biological
Computer Simulation
Mathematical Concepts
Batch Cell Culture Techniques/statistics & numerical data
Conjugation, Genetic

@article {pmid42484923,
year = {2026},
author = {Chen, J and Gan, L and Zhang, S and Liao, S and Lv, L},
title = {FUT2-mediated α1,2-fucosylation in inflammatory bowel disease: mechanisms and translational potential.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42484923},
issn = {1573-4978},
support = {2022CQBSHTB2064//Special support for postdoctoral of Chongqing/ ; CSTB2024NSCQ-MSX0403//Chongqing Natural Science Foundation/ ; 82173360//National Natural Science Foundation of China/ ; 2022M720606//China Postdoctoral Science Foundation/ ; 2024QNXM053//Chongqing Science and Health Joint Medical Research Project/ ; },
mesh = {*Fucosyltransferases/metabolism/genetics ; Humans ; *Inflammatory Bowel Diseases/metabolism/genetics ; Galactoside 2-alpha-L-fucosyltransferase ; Animals ; Glycosylation ; Fucose/metabolism ; Gastrointestinal Microbiome ; Intestinal Mucosa/metabolism ; Genetic Predisposition to Disease ; Trisaccharides/metabolism ; },
abstract = {Inflammatory bowel disease (IBD) arises from complex interactions among genetic susceptibility, immune dysregulation, the intestinal microbiota and environmental factors. Fucosyltransferase 2 (FUT2) regulates mucosal α1,2-fucosylation and the expression of histo-blood group antigens (HBGAs), thereby shaping host-microbe interactions at the intestinal surface. Loss-of-function FUT2 variants define the non-secretor phenotype and have been linked to IBD susceptibility and altered microbial communities. This review summarizes current evidence on FUT2 in IBD, including epithelial glycosylation-microbiota crosstalk, immune and barrier regulation, metabolite-related inflammatory pathways, intestinal stem-cell biology, and enteric nervous system/VIP-related signaling. We also evaluate translational strategies, including functional compensation with the FUT2-dependent human milk oligosaccharide 2'-fucosyllactose (2'-FL), secretor-status-stratified interventions, and preclinical approaches such as L-fucose and D-serine. Overall, FUT2 is an important node connecting host glycosylation, microbial ecology and intestinal immune homeostasis, but its value as a direct therapeutic or biomarker target in IBD remains exploratory. Most mechanistic and causal evidence currently derives from mouse models. Although human genetic and microbiome association data are relatively robust, interventional clinical evidence remains limited, which represents a major barrier to clinical translation.},
}

*Fucosyltransferases/metabolism/genetics
Humans
*Inflammatory Bowel Diseases/metabolism/genetics
Galactoside 2-alpha-L-fucosyltransferase
Animals
Glycosylation
Fucose/metabolism
Gastrointestinal Microbiome
Intestinal Mucosa/metabolism
Genetic Predisposition to Disease
Trisaccharides/metabolism

@article {pmid42485280,
year = {2026},
author = {K V, S and Thaha, N and Dehury, B},
title = {In silico identification and biophysical characterization of candidate antimicrobial peptides from the Indian marine microbiome targeting multidrug-resistant ESKAPE pathogens.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0353985},
doi = {10.1371/journal.pone.0353985},
pmid = {42485280},
issn = {1932-6203},
mesh = {*Antimicrobial Peptides/pharmacology/chemistry ; Molecular Dynamics Simulation ; *Microbiota ; *Drug Resistance, Multiple, Bacterial/drug effects ; Acinetobacter baumannii/drug effects ; India ; Computer Simulation ; *Anti-Bacterial Agents/pharmacology/chemistry ; Klebsiella pneumoniae/drug effects ; Pseudomonas aeruginosa/drug effects ; Machine Learning ; },
abstract = {The global health crisis of antimicrobial resistance necessitates the discovery of new antibacterial agents. Underexplored marine microbiomes, particularly from the biodiverse Indian coast, represent a rich potential source of antimicrobial peptides (AMPs). Targeting the urgent threat of multidrug-resistant ESKAPE pathogens, the present study aimed to computationally identify novel, membrane-active AMPs from these unique metagenomic datasets, with a focus on inhibiting Gram-negative bacteria. In this study, we computationally mined Indian marine high-resolution shotgun metagenomic datasets through quality filtering, de novo assembly, and small open reading frame prediction. An ensemble of six machine learning-based AMP prediction tools identified over 51,000 high-confidence candidate AMPs. Subsequent filtering based on physicochemical properties and AlphaFold3-predicted structures prioritized ten peptides with favourable membrane-active characteristics. Two lead candidates, c_AMP_1 and c_AMP_2, were subjected to all-atom molecular dynamics simulations within Gram-negative membrane mimetic models of Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae. Our simulations indicated distinct membrane interaction modes: c_AMP_1 adopted a stable, surface-associated α-helical orientation, while c_AMP_2 displayed a more flexible, membrane-inserting orientation in the simulations. Analysis of the MD simulations revealed distinct predicted peptide-membrane interaction profiles, characterized by specific hydrogen bonding patterns, peptide tilt angles, and membrane thinning, which collectively suggest differing biophysical interaction modes. Taken together, our work suggests the Indian marine microbiome as a promising reservoir for novel AMP candidates and suggests that an integrated computational pipeline - combining machine learning, structural biology, and biophysical simulation - may help prioritize candidate peptides for future experimental validation against critical pathogens.},
}

*Antimicrobial Peptides/pharmacology/chemistry
Molecular Dynamics Simulation
*Microbiota
*Drug Resistance, Multiple, Bacterial/drug effects
Acinetobacter baumannii/drug effects
India
Computer Simulation
*Anti-Bacterial Agents/pharmacology/chemistry
Klebsiella pneumoniae/drug effects
Pseudomonas aeruginosa/drug effects
Machine Learning

@article {pmid42485324,
year = {2026},
author = {Scully, S and Earley, B and Smith, PE and Finnie, MSJ and McAloon, C and Kenny, DA and Waters, SM},
title = {Characterisation of the bacterial and archaeal microbiota in processed colostrum collected from a spring-calving dairy herd.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0353693},
doi = {10.1371/journal.pone.0353693},
pmid = {42485324},
issn = {1932-6203},
mesh = {*Colostrum/microbiology ; Animals ; *Archaea/genetics/classification/isolation & purification ; Cattle ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; Female ; RNA, Ribosomal, 16S/genetics ; Dairying ; },
abstract = {Colostrum feeding is critical for neonatal calf health, providing immunoglobulins (Ig) and other bioactive compounds that support immune function and early microbiome development. While the microbiota of fresh colostrum has been characterised, colostrum on commercial dairy farms is often refrigerated and reheated prior to feeding - practices that may alter its microbial composition. Therefore, the objective of this study was to characterise the prokaryotic community of refrigerated and reheated (processed) colostrum collected immediately before calf feeding. Twenty-one processed colostrum samples were collected from a single, primi- and multiparous Holstein-Friesian and Jersey, spring-calving dairy herd with no more than two donors contributing to each sample. Colostrum samples were refrigerated for no more than 24h and then re-heated in a 38°C water bath for 60 minutes. Colostrum samples were collected immediately prior to being fed to the calf. Microbial DNA was extracted and16S rRNA gene amplicon libraries were sequenced using the Illumina platform. Raw sequencing data were processed in R via the DADA2 pipeline, and an amplicon sequence variant (ASV) table was generated. Taxonomy was assigned using the SILVA database (v. 138.1) and data were subjected to α- and β-diversity analysis using Phyloseq, Microbiome and Vegan. Breed and parity had no effect (P ≥ 0.05) on α- and β-diversity. The mean Shannon index score (α-diversity) was 2.26 (SE 0.18), indicating unevenness and low levels of richness. Microbial community composition varied considerably between samples. Five archaeal ASV genus groups were identified, with Methanobrevibacter dominating this community(relative abundance (RA) of 85.19%). Four bacterial phyla were identified as the major contributors to the bacterial component of processed colostrum. Only 39 ASV genus groups were identified as having a RA > 0.05%. Processed colostrum was dominated by Pseudomonas (RA = 20.97%) and Acinetobacter (RA = 18.65%). These genera, along with 11 others, including Romboutsia, Flavobacterium. Lachnospiraceae NK3A20 group and Clostridium sensu stricto 1 were present across all samples and thus considered core bacteria. Overall, these findings indicate that refrigeration and reheating may significantly alter the natural colostrum microbiota, reduce diversity and increase heterogeneity of the community composition. Further research is needed to determine how these changes influence microbial seeding and calf health outcomes.},
}

*Colostrum/microbiology
Animals
*Archaea/genetics/classification/isolation & purification
Cattle
*Bacteria/genetics/classification/isolation & purification
*Microbiota/genetics
Female
RNA, Ribosomal, 16S/genetics
Dairying

@article {pmid42477438,
year = {2026},
author = {Liu, L and Wang, Q and Zhang, Y and Zhai, Y and Liu, S and Chen, W},
title = {Associations of self-reported toothbrushing frequency with salivary microbiome in caries, fluorosis, and healthy subjects.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-62911-7},
pmid = {42477438},
issn = {2045-2322},
support = {No. 2025byyfyjq04//the First Affiliated Hospital of Bengbu Medical University Science Fund for Outstanding Young Scholars/ ; No. YQZD2023060//the Anhui Province Key Cultivation Project for Excellent Young Teachers in Universities/ ; No. LH250304001//the Longhu Project of Bengbu Medical University/ ; No. GXXT-2021-056//the University Synergy Innovation Program of Anhui Province, China/ ; No. BYYFY2022TD001//the high-level scientific and technological innovation team of the First Affiliated Hospital of Bengbu Medical University/ ; },
abstract = {Toothbrushing is a fundamental oral hygiene behavior associated with differences in the composition of salivary microbiome, yet whether its relationship with microbial profiles differs across oral conditions remains unclear. In this study, 300 participants were initially enrolled, including healthy controls and patients with dental caries or dental fluorosis (100 per group). After exclusion of one fluorosis sample that failed sequencing, 299 unstimulated saliva samples were analyzed. Based on questionnaire data, participants were classified as high-frequency (≥ 2 times/day) or low-frequency (< 2 times/day) brushers. Salivary microbiota were characterized using 16 S rRNA gene sequencing, and microbial diversity and taxonomic composition were compared both across oral conditions within each brushing cohort and between brushing-frequency subgroups within each condition. No significant differences in α- or β-diversity were observed between brushing-frequency subgroups in the healthy or fluorosis groups. In contrast, among patients with dental caries, high-frequency brushing was associated with greater α-diversity, distinct β-diversity, and characteristic taxonomic shifts, with nine genus-level markers identified by random forest analysis (AUC = 0.7688); at the species level, Serratia marcescens, Mobiluncus mulieris, and Neisseria bacilliformis were significantly enriched in the high-frequency brushing subgroup, showing higher mean relative abundance and detection rates than in the low-frequency brushing subgroup. Across oral conditions, clear microbial separation was observed only in the low-frequency brushing cohort. These findings suggest that the association between self-reported toothbrushing frequency and the salivary microbiome is oral condition-dependent and most evident in dental caries.},
}

@article {pmid42477483,
year = {2026},
author = {Shalev, O and Ye, X and Kilian, J and Stahl, M and Ratzke, C},
title = {Increased nutrient diversity can induce loss of microbial diversity through enhanced resource uptake.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {42477483},
issn = {2397-334X},
support = {948753//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 468972576//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 540605007//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Cluster of Excellence//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 516931136//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {The origin of biodiversity is a central question in ecology, particularly how numerous microbial species co-exist within a single community. A prevailing hypothesis holds that microbial species co-exist by specializing on different resources, thereby reducing competition. Accordingly, increasing resource diversity is expected to promote species co-existence and boost biodiversity. By integrating high-throughput experiments, ecological analysis of global microbiome data, metabolic profiling and theoretical modelling, we find that the relationship between resource diversity and microbial biodiversity is not consistently positive and can even decline with increasing resource diversity. This unexpected result emerges from a widespread physiological response across diverse microbial taxa, in which more complex environments trigger higher overall resource uptake. This intensifies competition and can lead to biodiversity loss. Updating a central ecological model to include this physiological trait accurately reproduces the observed decline. Our findings suggest that physiological changes at the individual level can substantially alter predicted diversity patterns and scale up to influence community structure.},
}

@article {pmid42477518,
year = {2026},
author = {Shi, F and Wang, KK and Luo, C and Jin, PJ and Liu, HJ and Wang, S},
title = {High soil fertility supports greater soil quality, microbial network complexity, and keystone taxa in arable black soil.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05412-x},
pmid = {42477518},
issn = {1471-2180},
support = {LBH-Z25279//Heilongjiang Postdoctoral Financial Assistance/ ; ZY04JD05//the central government guides the special project of local scientific and technological development - scientific and technological innovation base project/ ; 2021YFD1500300//the National Key R&D Program of China/ ; JQ2024D005//the Natural Science Foundation of Heilongjiang Province of China/ ; },
abstract = {The depletion of soil organic matter (SOM) represents one of the most conspicuous hallmarks of Mollisol degradation in Northeast China. This study focuses on typical black soil with high, medium, and low fertility levels to investigate the responses of soil properties and microbial communities to varying soil fertility. We observed a significant decline in the Soil Quality Index (SQI) and key enzyme activities from high to low fertility levels, which mirrored the synchronous depletion of soil carbon fractions (SOM, POC, and MBC). Our results indicated that while microbial alpha diversity peaked in soils with medium fertility, overarching network complexity was highest in environments with high fertility. Compositionally, this robust community structure was primarily associated with significant increases in the abundance of Actinobacterota and Mortierellomycota. Furthermore, network analysis identified specific keystone taxa, including Gemmatimonadaceae, Roseiflexaceae, Penicillium, and Trichoderma, which are closely associated with efficient nutrient cycling and enhanced disease resistance. This study elucidates the microbial taxa associated with high-fertility soils. And by elucidating these underlying microbial associations, this study provides a solid theoretical foundation for restoring degraded black soils through targeted microbiome regulation. Ultimately, our findings highlight promising avenues for developing novel soil conservation technologies centered on core functional microorganisms.},
}

@article {pmid42477600,
year = {2026},
author = {Xing, C and Lu, Z and Guo, X and Zhu, X},
title = {Healthy Eating Index-2020 and post-stroke depression (PSD): cross-sectional analysis of NHANES data.},
journal = {BMC psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12888-026-08402-5},
pmid = {42477600},
issn = {1471-244X},
support = {MS2025001//Jiangsu Provincial Traditional Chinese Medicine Science and Technology Development Program Project/ ; 2025PSPT0906100, 2025PSPT0906101, 2025PSPT0906102, 2025PSPT0906103, 2025PSPT0906104//Key Projects for Science and Technology Response to Stroke Prevention and Treatment/ ; MS2024029//Research Project of Nantong Municipal Health Commission/ ; },
abstract = {BACKGROUND: Post-stroke depression (PSD) is a common complication after stroke and contributes to poor functional recovery and reduced quality of life. Dietary quality has been associated with depression in the general population, but evidence in individuals with stroke remains limited. This study examined the cross-sectional association between the Healthy Eating Index-2020 (HEI-2020) and PSD.

METHODS: This study included 962 adults with a history of stroke from seven cycles of the National Health and Nutrition Examination Survey from 2005 to 2018. Depressive symptoms were assessed using the Patient Health Questionnaire-9, with a score ≥ 10 indicating probable depression. Dietary quality was evaluated using HEI-2020 and categorized into tertiles. Multivariate logistic regression, restricted cubic spline analysis, and mediation analysis were used to assess associations and the statistical indirect association of the Dietary Index for Gut Microbiota (DI-GM).

RESULTS: After multivariate adjustment, each one-point increase in HEI-2020 score was associated with 2% lower odds of probable depression (PHQ-9-defined) (OR = 0.98). Compared with the low dietary quality group, the high dietary quality group had 59% lower odds (OR = 0.41). The dose-response relationship was nonlinear, with a significant inverse association observed only when HEI-2020 scores exceeded 57. This exploratory threshold may serve as a reference for future prospective studies but requires validation before clinical application. Furthermore, a significant interaction with race or ethnicity was identified (P for interaction = 0.033). DI-GM showed a significant indirect association (P = 0.04), but the direct and indirect components were in opposite directions, indicating an inconsistent mediation pattern. Given that DI-GM is a dietary proxy, these findings reflect statistical associations with a dietary pattern, not biological mediation. Future studies with direct microbiome measurements are needed to verify gut-brain axis involvement in PSD.

CONCLUSIONS: In this cross-sectional study, HEI-2020 was inversely associated with PSD, with nonlinear and race-specific patterns. DI-GM showed a significant but inconsistent indirect association, suggesting a suppressive rather than mediating role. Findings are associational, not causal.},
}

@article {pmid42477662,
year = {2026},
author = {Chao-Chao, Q and Zhi-Ruo, L and Xiao-Qing, L and Yan-Hong, M and Yue-Ying, Z and Ning, P and Ji-Chan, S and Xian-Gao, J},
title = {Exploring differences in alveolar microbiome between pulmonary tuberculosis patients with different treatment outcomes: a metagenomic study from China.},
journal = {BMC pulmonary medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12890-026-04500-y},
pmid = {42477662},
issn = {1471-2466},
abstract = {This study aimed to investigate differences in the composition and functional characteristics of alveolar microbiota in patients with pulmonary tuberculosis (PTB) exhibiting differential therapeutic responses. Thirty-two patients with drug-sensitive PTB who had completed standard anti-tuberculosis therapy were enrolled and classified into good-response (n = 16) and poor-response (n = 16) groups. Bronchoalveolar lavage fluid (BALF) samples were collected and analysed using metagenomic sequencing to characterize microbial community and functional pathways. No significant differences were observed in α-diversity between the two groups; however, β-diversity analysis demonstrated moderate but significant in microbial community structure (ANOSIM, R = 0.381, P < 0.001). The good efficacy group was characterized by enrichment of Prevotella, Staphylococcus, and oral commensal bacteria including Fusobacterium and Rothia, together with significantly increased pathways related to peptidoglycan biosynthesis, glutathione metabolism, energy production, and DNA repair. In contrast, the poor efficacy group was characterised by enrichment of Microbacterium and activation of functional pathways associated with biofilm formation. These findings suggest that both the taxonomic composition and functional activity of the pulmonary microbiome are closely associated with anti-tuberculosis treatment outcomes.},
}

@article {pmid42477714,
year = {2026},
author = {Zhang, Y and Chang, ZH and Gan, S and Wang, SH and Luo, JX and Jin, L and Zhai, XF and Sun, YB},
title = {Hologenomic rewiring facilitates dietary adaptation to chitin-rich marine resources in the crab-eating frog.},
journal = {Frontiers in zoology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12983-026-00626-1},
pmid = {42477714},
issn = {1742-9994},
support = {XNYB24-07//Foundation of Key Laboratory of Southwest China Wildlife Rsources Conservation (Ministry of Education)/ ; 2022YFF0802300//National Key Research Development Program of China/ ; 202401BC070011//Yunnan Fundamental Research Projects/ ; },
abstract = {BACKGROUND: Secondary adaptation of amphibians to marine environments is exceptionally rare. The crab-eating frog, Fejervarya cancrivora, is the only known amphibian capable of completing its life cycle in intertidal zones, where it faces dual challenges: high salinity stress and a diet rich in chitinous crab exoskeletons. While osmoregulatory adaptations have been well documented, the synergistic roles of the host's digestive system and its gut microbiota in this dietary specialization remain unclear.

RESULTS: Here, we integrated histological analysis, comparative transcriptomics, chitinase activity assays, and gut metagenomics to compare F. cancrivora with its freshwater congener, F. multistriata. We found that F. cancrivora has evolved a thicker gastric muscularis and longer gastric villi, consistent with enhanced processing of hard prey. Comparative transcriptomic analysis revealed an expanded repertoire of putative chitinase encoding transcripts (15 vs. 8 non-redundant transcripts), and both gastric and intestinal tissues exhibit significantly higher and more pH-tolerant chitinase activity. In contrast, the gut microbiota of F. cancrivora is not enriched for microbial chitin degradation genes, but instead is functionally specialized for lipid metabolism and DNA repair pathways. A controlled feeding experiment confirmed that the microbial enrichment in lipid metabolism is diet-driven, while the DNA repair pathways is largely independent of diet and likely reflects microbiome-intrinsic adaptation to chronic saline stress.

CONCLUSIONS: Together, these findings suggest a partially partitioned host-microbiome strategy in which host manages chitin breakdown, while the microbiota optimizes energy harvest and intrinsic stress tolerance. Our findings provide a new paradigm for amphibian marine adaptation, and highlights host-microbiome functional differentiation during niche expansion.

CLINICAL TRIAL NUMBER: Not applicable.},
}

@article {pmid42477746,
year = {2026},
author = {Jiang, P and Zhou, M and Wen, Y and Hu, Z and Hu, Y and Liu, M},
title = {Genome-resolved gut microbial guild and fecal metabolic signatures associated with post-weaning estrus return in sows.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00601-5},
pmid = {42477746},
issn = {2524-4671},
support = {2022YFA1304204//National Key R&D Program of China/ ; },
abstract = {Post-weaning estrus return is critical for sow reproductive efficiency. The gut microbiota is associated with post-weaning estrus of sows, potentially through effects on nutrient utilization and metabolic regulation. However, current microbial signatures associated with estrus return remain poorly resolved at the strain-level. Here, we explored the relationship between the gut microbiome and post-weaning estrus in sows using metagenomics and metabolomics profiling of 85 fecal samples. From 2,704 non-redundant metagenome-assembled genomes (MAGs), 608 estrus-associated MAGs were identified by LEfSe analysis. Among these, 48 high-quality MAGs were selected for co-abundance network analysis, which revealed two competing microbial functional guilds. Guild 1 was significantly enriched in the normal group, harboring more β-glucosidase and folate biosynthesis genes, but fewer antibiotic resistance genes and virulence factors than Guild 2. A random forest model based on these 48 MAGs demonstrated excellent performance in distinguishing between the normal and non-return sows (AUROC = 0.946) and was validated in an independent dataset (n = 29, AUROC = 0.818). Additionally, the guild-level microbiome index (GMI) derived from abundance differences between the two guilds also showed good discriminatory power (AUROC = 0.799). Integrated multi-omics analysis revealed alterations in fecal bile acid metabolism in non-return sows, characterized by a significantly increased ratio of secondary to primary bile acids and the accumulation of specific secondary bile acids. Notably, the enrichment of the Clostridia strain SFHK01 sp016296675, a member of Guild 2, and its encoded 12α-HSDH gene was positively associated with specific secondary bile acids, suggesting that this specific strain is involved in the distinct metabolic alterations observed in non-return sows. These findings provide the genome-resolved and guild-based insights into the gut microbial signatures associated with post-weaning estrus return, offering a basis for potential microbiota-targeted interventions to improve sow reproductive performance.},
}

@article {pmid42477864,
year = {2026},
author = {Lakamp, AD and Adams, S and Kuehn, LA and Snelling, WM and Wells, J and Hales, K and Neville, B and Fernando, SC and Spangler, ML},
title = {Influence of host genetics on the functional composition of the rumen metagenome in beef cattle1.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag224},
pmid = {42477864},
issn = {1525-3163},
abstract = {Cattle rely on the microorganisms in their rumen to break down plant matter into useable nutrients. Studies have demonstrated that the rumen microbiome plays a critical role in economically important traits. One factor that impacts rumen microbial community assembly is the host genome. Previous studies have demonstrated host genetics affect rumen microbial community composition and the association of microbiome features with production traits. However, gaps exist relative to the underlying host genetic influence on functional features of the rumen metagenome. Here we elucidated the relationship between host genetics and functional composition of the rumen metagenome while identifying metagenomic features which may provide targets for genetic selection. Rumen samples were collected via esophageal tubing from 717 beef cattle on four diets and were subjected to shotgun sequencing from which open reading frames (ORFs) were predicted. Animal genotypes were generated from imputation based on low-pass sequencing and array data. The log-transformed relative abundance of 16,350 ORFs were used as phenotypes in linear mixed models with the random effect of host genotype. In this population of 717 animals, approximately 4% of the ORFs had heritability estimates larger than twice their standard error and more than 10% of the ORFs had estimates greater than 0.20. Functions of highly heritable ORFs included aromatic amino acid biosynthesis and genome regulation. Additionally, some ORFs were genetically correlated with production traits. Eleven host genes were associated with more than one ORF. The functionality of these candidate host genes can be generally classified as either immune-related, metabolism-related, or possibly involved in host-microbiome crosstalk. Host genetics influence the rumen microbiome function making genetic selection of the host an avenue to alter rumen microbiome functionality. Associations between host genes and rumen metagenome composition indicate multiple potential biological mechanisms underlie these associations. Moreover, a portion of the highly heritable ORFs are genetically correlated with feed efficiency traits making them potential selection targets to increase productivity. The functions of the candidate host genes show the rumen metagenome is influenced by multiple complex biological systems of the host.},
}

@article {pmid42477874,
year = {2026},
author = {Oyewole, OA and Oyegbade, SA and Albaqami, A},
title = {Nanotechnology and Plant-Microbe Interactions: Enhancing Symbiotic Relationships for Crop Resilience.},
journal = {Integrated environmental assessment and management},
volume = {},
number = {},
pages = {},
doi = {10.1093/inteam/vjag117},
pmid = {42477874},
issn = {1551-3793},
abstract = {The integration of nanomaterials (NMs) with plant-beneficial microorganisms has emerged as a promising strategy to improve crop resilience to abiotic stresses. Evidence from multiple studies indicates that NM-microbe co-application often enhances plant growth, nutrient uptake, biomass accumulation, and stress tolerance more effectively than either approach alone. Under drought and salinity stress, these combinations help maintain ionic balance, particularly higher K+/Na+ ratios, sustain photosynthesis, and reduce oxidative damage by increasing the activities of antioxidant enzymes such as superoxide dismutase, catalase, and peroxidase. Nanoparticles, including ZnO, Fe3O4, and SiO2, when combined with plant growth-promoting rhizobacteria (PGPR) or arbuscular mycorrhizal fungi (AMF), stimulate root development, increasing water and nutrient acquisition. Additionally, NMs can reshape rhizosphere microbial communities by enriching beneficial taxa such as Pseudomonas, Bacillus, and Trichoderma while suppressing certain phytopathogens. Nanoformulated fertilizers and micronutrients further enhance nutrient use efficiency and may reduce dependence on conventional agrochemicals, supporting sustainable agricultural practices. However, the benefits of NM-microbe integration are not universal. Several studies report that some nanomaterials can inhibit beneficial microorganisms, including nitrogen-fixing bacteria and AMF, at concentrations only slightly above stimulatory levels, highlighting a narrow safety margin. Concerns also remain regarding NM persistence, soil-dependent mobility, trophic transfer through food webs, and potential disruption of soil microbial communities. This review evaluates both the advantages and risks of NM-microbe interactions, emphasizing the importance of dose, soil characteristics, and microbial strain selection. Current evidence, largely derived from short-term laboratory studies, remains insufficient to support widespread field application without long-term ecological monitoring, standardized assessment protocols, and evaluation of economic feasibility for smallholder farming systems.},
}

@article {pmid42478053,
year = {2026},
author = {Feng, K and Wang, J and Wang, S and Sun, Z and Qiu, M and Zhou, Z and Li, Y and Chen, K},
title = {Harnessing the microbiome: a new frontier in lung cancer immunotherapy.},
journal = {Cancer biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.20892/j.issn.2095-3941.2025.0177},
pmid = {42478053},
issn = {2095-3941},
support = {Z240013//Beijing Natural Science Foundation/ ; L234002//Beijing Natural Science Foundation/ ; L222021//Beijing Natural Science Foundation/ ; BRWEP2024W034080200//Beijing Research Ward Excellence Program/ ; BRWEP2024W034080204//Beijing Research Ward Excellence Program/ ; 2021RU002//Chinese Academy of Medical Sciences/ ; 92259303//National Natural Science Foundation of China/ ; 82388102//National Natural Science Foundation of China/ ; 82450111//National Natural Science Foundation of China/ ; 82373416//National Natural Science Foundation of China/ ; 82573950//National Natural Science Foundation of China/ ; 2021-I2M-5-002//CAMS Medical and Health Science and Technology Innovation Project/ ; RZG2024-02//Peking University People's Hospital Research and Development Funds/ ; },
abstract = {Lung cancer is a fatal and the most common malignancy globally. Despite the significant therapeutic benefits of immune checkpoint inhibitors (ICIs), 60%-80% of patients respond poorly to immunotherapy. The identification of reliable predictive biomarkers is essential for implementing precision medicine strategies. In recent years the microbiome has emerged as a promising predictor of immunotherapy outcomes. The influence of the microbiome on lung cancer immunotherapy was systematically and comprehensively reviewed. Moreover, the distinctive microbiome profiles among patients with lung cancer and the correlation with treatment effectiveness are discussed. We investigated the core mechanisms of the interactions between the microbiome and the tumor microenvironment, assessed the usefulness of microbial metabolites as predictive biomarkers, and discussed strategies for microbiome-targeted interventions. Furthermore, we evaluated the current limitations in research methodology and highlighted future research directions, offering novel insights, including multi-site integrated biomarker approaches, site-specific intervention strategies, metabolite-based functional biomarkers, and lung cancer-specific microbiome considerations for developing personalized immunotherapy.},
}

@article {pmid42478074,
year = {2026},
author = {Kumar, N and Yarlagadda, V},
title = {Microbes and Microbial Chemical Matter in the Seeding of Alzheimer's Disease: Prospects for Orthogonal Therapies.},
journal = {ACS chemical neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschemneuro.6c00255},
pmid = {42478074},
issn = {1948-7193},
abstract = {Alzheimer's disease (AD) remains the leading cause of dementia, with mortality rates having doubled over the past two to three decades and projected to rise with continued population aging. Despite its profound health and economic impact, effective therapeutic and preventive interventions remain limited, largely owing to an incomplete understanding of its etiopathogenesis. Emerging evidence indicates that microbes, including viruses, bacteria, and fungi, as well as their associated metabolites, toxins, and structural components, are involved in the development of AD. Microbial invasion, through dysbiosis or infection, can trigger neuroinflammation that drives overproduction of amyloid β peptide (AβP). AβP functions as a broad-spectrum antimicrobial agent, and its accumulation, a key pathological hallmark of AD, is promoted by microbial presence as part of the immune response. Maintaining microbial eubiosis, preventing infections that impact the nervous system (e.g., herpes zoster), supporting gut microbiome homeostasis through prebiotics, and the judicious use of antimicrobial interventions may mitigate AD onset and progression. This Review delineates the involvement of microbes and their components in the initiation of AD and presents the prospects of orthogonal therapies to control AD.},
}

@article {pmid42478626,
year = {2026},
author = {Gardemeister, S and Saarikivi, A and Rautava, S and Mälkönen, J and de Vos, WM and Korpela, K and Kolho, KL},
title = {Association of Elevated C-Reactive Protein in Term Newborns With Neonatal Factors and Gut Microbiota.},
journal = {Acta paediatrica (Oslo, Norway : 1992)},
volume = {},
number = {},
pages = {},
doi = {10.1111/apa.70693},
pmid = {42478626},
issn = {1651-2227},
support = {//Lastentautien Tutkimussäätiö/ ; //Tekes/ ; },
abstract = {AIM: Plasma C-reactive protein (CRP) is widely used to assess neonatal infection, although mild, unexplained elevations are common in healthy newborns. We examined relationships between non-infectious CRP levels and neonatal factors, and early gut microbiota composition in term infants.

METHODS: This study was conducted within the prospective Finnish HELMi birth cohort. We included 105 full-term infants with plasma CRP levels measured during the first four postnatal days. Perinatal data were retrieved from medical records. Faecal samples collected at 3 weeks underwent 16S rRNA gene sequencing.

RESULTS: Initial CRP level was elevated (≥ 3 mg/L) in 57% of infants, with no diagnosis of an infection. CRP levels were not associated with maternal group B Streptococcus status, intrapartum antibiotics, early neonatal complications or delivery mode, except for higher levels on day three after spontaneous versus induced vaginal delivery. Gut microbiota composition at 3 weeks differed according to CRP status, with family Acidaminococcaceae being less prevalent when CRP was elevated. Birth mode, antibiotic exposure and umbilical artery pH in the asphyxia range (≤ 7.1) were associated with distinct microbial profiles.

CONCLUSIONS: Mild CRP elevations in term newborns were associated with differences in early gut microbiota composition but poorly explained by perinatal clinical factors.},
}

@article {pmid42478782,
year = {2026},
author = {Weinberg, J and Jeon, J and Crandall, WJ and Lee, CM and Jarrell, ZR and Lim, G and Lee, HY and Go, YM and Jones, DP},
title = {Microbiome-associated metabolites, valerobetaine and homocarnitine, inhibit carnitine transport via OCTN2.},
journal = {American journal of physiology. Cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpcell.00317.2026},
pmid = {42478782},
issn = {1522-1563},
support = {R21 AG080247/AG/NIA NIH HHS/United States ; R21 AG080247/AG/NIA NIH HHS/United States ; },
abstract = {The intestinal microbiome-derived metabolite, valerobetaine (δ-valerobetaine), promotes obesity, hepatic steatosis, and impaired cognition in mice and is associated with obesity, fatty liver disease, diabetes, and cardiovascular disease in humans. Mechanistic studies show that valerobetaine decreases systemic carnitine and inhibits mitochondrial fatty acid oxidation. Valerobetaine and its mammalian hydroxylation product, homocarnitine, share close structural homology with carnitine, which is mainly transported by the organic cation transporter OCTN2. To determine whether reductions in systemic carnitine induced by valerobetaine and homocarnitine result from interactions with OCTN2, we performed in vitro uptake studies using HEK293 cells overexpressing human OCTN2 coupled with metabolite measurement by mass spectrometry. OCTN2 overexpression increased the uptake rates of both homocarnitine and valerobetaine relative to control cells. Meldonium, an OCTN2 substrate and inhibitor, reduced uptake of both metabolites in a concentration-dependent manner. Saturating uptake kinetics were observed for valerobetaine whereas homocarnitine exhibited linear uptake across the concentration range tested (1-100 μM). Both metabolites exhibited lower transport efficiency compared to the carnitine precursor γ-butyrobetaine and showed relatively lower potency in inhibition of carnitine uptake. Together, these findings identify homocarnitine and valerobetaine as modulators of carnitine transport and provide a mechanistic basis by which these microbiome-derived metabolites lower systemic carnitine levels and impair mitochondrial fatty acid oxidation.},
}

@article {pmid42478812,
year = {2026},
author = {Henige, M and Anklam, K and Yoon, I and Wheeler, J and Dawson, G and Döpfer, D},
title = {Effect of Saccharomyces cerevisiae fermentation postbiotic supplementation on metagenomics of digital dermatitis lesions in lactating Holstein cows.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0030426},
doi = {10.1128/spectrum.00304-26},
pmid = {42478812},
issn = {2165-0497},
abstract = {Digital dermatitis (DD) is the leading cause of lameness in cattle, posing major animal welfare and economic concerns. Effective prevention strategies are increasingly important given emerging antimicrobial resistance associated with common DD treatments. Supplementation with Saccharomyces cerevisiae fermentation postbiotics (SCFP) has been shown to enhance innate immunity and reduce DD lesion development. This study evaluated the effect of a commercial SCFP supplement on the microbial composition of DD lesions using shotgun metagenomic sequencing to characterize microbial communities and associated antimicrobial resistance genes. Beta diversity analysis revealed that stage M4 DD lesions from SCFP-supplemented cows had a trend for different microbial compositions compared with controls (P = 0.051). At the genus level, M2 lesions were found to have statistically significant lower abundance of the genera Desulfovibrio, Pseudomonas, Staphylococcus, Anaerotignum, Caproicibacterium, and Bacteroides in the SCFP treatment group compared with the control (P < 0.05). M2 lesions from the SCFP treatment group were also found to have statistically significant higher abundance of the genera Fusobacterium, Citricoccus, Listeria, and Fundicoccus as compared with the control (P < 0.05). M4 lesions were found to have statistically significant lower abundance of the genera Blautia and Petrimonas in the SCFP treatment group compared with the control (P < 0.05). At the species level, M2 lesions were found to have statistically significant lower abundance of the species Desulfovibrio sp. G11, Anaerotignum sp. MB30-C6, Caproicibacterium argilliputei, and Prevotella intermedia in the SCFP treatment group compared with the control (P < 0.05). M2 lesions from the SCFP treatment group were also found to have statistically significant higher abundance of the species Fundicoccus culcitae and Helcococcus ovis as compared with the control (P < 0.05). Metagenomic analysis identified antimicrobial resistance genes associated with multiple antibiotics commonly used for DD treatment, including tetracyclines, lincosamides, and pleuromutilins. These findings demonstrate the potential for SCFP supplementation to alter the microbial composition of DD lesions while highlighting the ongoing concerns regarding antimicrobial resistance in DD management.IMPORTANCEDigital dermatitis (DD) causes substantial economic loss and welfare concerns in cattle production systems worldwide. Our findings show that dietary supplementation with Saccharomyces cerevisiae fermentation postbiotics (SCFP) has the potential to alter the microbial ecology of DD lesions. Importantly, this work identifies antimicrobial resistance genes within DD lesions, underscoring the limitations of antibiotic-based control strategies. By linking nutritional supplementation to changes in microbial communities and resistance gene profiles, this study advances understanding of non-antibiotic approaches to disease mitigation and supports the development of sustainable, microbiome-informed management practices in food animal production.},
}

@article {pmid42478878,
year = {2026},
author = {Davis, EC and Jackson, CM and Diaz, NS and Susana, J and Nelson, A and Insel, R and Seppo, AE and Järvinen, KM},
title = {Maternal Perinatal Gut Microbiome Is Shaped by Traditional Farming Lifestyle and Associated With Early Childhood Atopic Disease.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70446},
pmid = {42478878},
issn = {1398-9995},
support = {U01 AI131344/AI/NIAID NIH HHS/United States ; //University of Rochester University Research Award/ ; NIFA 67012-35010//U.S. Department of Agriculture/ ; T32 ES007026/ES/NIEHS NIH HHS/United States ; P30 ES001247/ES/NIEHS NIH HHS/United States ; T32 HL066988/HL/NHLBI NIH HHS/United States ; },
abstract = {Maternal exposure to a traditional farming lifestyle during pregnancy is associated with protection against allergic disease in childhood; however, the mechanism remains unclear. Pre-clinical work has demonstrated a role for the maternal gut microbiome in fetal immune programming. Given the diverse microbial exposure on farms, we sought to assess whether the maternal gut microbiome may mediate the relationship between maternal farm exposure and protection against offspring allergic disease. Deep shotgun metagenomic analysis of the perinatal fecal microbiome showed that women from an Old Order Mennonite traditional farming community (OOM, n = 68) harbored a more diverse gut microbiome relative to women from urban/suburban Rochester, NY (ROC, n = 55). We identified several bacterial species differentially abundant between lifestyle groups, including those from Dorea, Anaerobutyricum, Bifidobacterium, and Bacteroides genera, which translated to marked differences in microbiome functional capacity. These differences in the gut microbiome composition were accompanied by targeted metabolite findings indicating higher serum acetate and isobutyrate levels in OOM women that were positively correlated with cord plasma levels and infant systemic IgA concentrations. Among urban women, maternal microbiome composition was associated with early childhood atopic disease outcomes. Specifically, Dorea longicatena and Segatella copri were least abundant in urban mothers whose infants developed atopic disease (atopic dermatitis) or IgE-mediated food allergy alone, respectively, and were most abundant in the OOM mothers. Together, these findings highlight the maternal gut microbiome and metabolites as potential contributors to prenatal farming lifestyle protection against early childhood allergic disease.},
}

@article {pmid42479017,
year = {2026},
author = {Xiong, C and Liu, Q and Sun, X and Xue, Y and Zhang, Y and Li, J and Shen, G and Wang, L},
title = {Integrated multi-omics analysis of resistant and susceptible Brassica napus roots reveals phenylpropanoid biosynthesis associated with clubroot resistance.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-04-26-0668-RE},
pmid = {42479017},
issn = {0191-2917},
abstract = {Clubroot is a soil-borne disease caused by the obligate biotrophic pathogen Plasmodiophora brassicae, severely affecting cruciferous crops worldwide, especially Brassica napus. However, cultivar-dependent features associated with contrasting clubroot phenotypes under natural field conditions remain poorly understood. To investigate these multi-omics features at the late disease stage, an integrated transcriptomic, untargeted metabolomic, and root endophytic microbiome analysis was performed using resistant and susceptible B. napus cultivars collected from a naturally infested field. Comparative analysis revealed significant multi-omics differences between the two cultivars. Among the enriched pathways, phenylpropanoid biosynthesis was identified as a major resistance-associated feature, supported by the upregulation of multiple structural genes involved in lignin and phenolic compound biosynthesis, including PAL, 4CL, CCR, POD, CAD, and F5H, together with the increased accumulation of phenylpropanoid-related metabolites such as Caffeic acid, Coniferyl aldehyde, and Sinapyl alcohol. In addition, resistant roots showed elevated levels of glucosinolate-derived metabolites, particularly isothiocyanate-related compounds. Hormone signaling-related genes, especially those associated with jasmonate and auxin pathways, also displayed differential expression patterns between resistant and susceptible cultivars and were further supported by RT-qPCR validation. Microbiome analysis further revealed differences in root endophytic bacterial community composition between the two cultivars, with several bacterial genera showing positive correlations with metabolites enriched in resistant roots. Overall, these findings reveal cultivar-dependent multi-omics differences accompanying contrasting clubroot phenotypes under natural field infection conditions and provide a basis for future studies of clubroot resistance in B. napus.},
}

@article {pmid42479179,
year = {2026},
author = {Brealey, JC and Davey, ML and Pedersen, B},
title = {Bacterial and Green Algal Communities of Norwegian Birch Tree Bark.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02841-z},
pmid = {42479179},
issn = {1432-184X},
abstract = {Tree bark hosts a unique community of microorganisms, distinct from that of other plant tissues and from the microbial associates of macrophytic epiphytes. These corticolous communities are important components of tree-associated food webs. However, the factors influencing corticolous microbial diversity are understudied. We used amplicon sequencing to characterise and compare the bacterial and aerophytic algal communities colonising the bark of birch trees at three sites in southern Norway with differing histories of nitrogen deposition. Within each site, we investigated associations between the corticolous community and variation in placement on the trunk, including north-facing vs. south-facing aspect, height and trunk diameter. While the most abundant bacterial and algal taxa were similar across the three sites, there were clear differences among sites. Aspect had a strong effect at the most oceanic and open site, with increased abundance of cyanobacteria at northern compared to southern aspects. We observed a higher abundance of nitrogen-fixing cyanobacteria at the site where historical nitrogen deposition had been lowest and correspondingly higher abundance of non-diazotrophic green algae where historical nitrogen deposition had been highest. Generally, the bacterial and algal communities followed similar patterns and co-occurrence network analysis revealed that algal taxa were interspersed among bacterial clusters. Our study provides the first characterisation of both the bacterial and aerophytic algal bark-associated communities of birch, one of the most common and ecologically important trees in Norway. Our results add to the growing body of literature demonstrating that tree bark supports a complex microbial community that varies among sites.},
}

@article {pmid42479266,
year = {2026},
author = {Mori, P and Chauhan, M and Khan, ZH and Kumar, N and Goswami, S and Kumar, V},
title = {Preliminary study on the modulation of diet-induced malnutrition in BALB/c mice using a probiotic consortium: a physiological, biochemical, histopathological, and gut microbiota evaluation.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {8},
pages = {},
pmid = {42479266},
issn = {1573-0972},
mesh = {Animals ; *Probiotics/administration & dosage/therapeutic use ; Male ; Mice, Inbred BALB C ; Mice ; *Protein-Energy Malnutrition/therapy ; *Gastrointestinal Microbiome/drug effects ; Diet, Protein-Restricted/adverse effects ; Bacillus/physiology ; RNA, Ribosomal, 16S/genetics ; Liver/pathology ; Body Weight ; },
abstract = {Protein-energy malnutrition (PEM) remains a major global health challenge that adversely affects growth, metabolism, immune function, and organ integrity. This study evaluated the efficacy of a food-derived Bacillus-based probiotic consortium in alleviating PEM and investigated its effects on gut microbial composition in BALB/c mice. Forty-eight male mice were allocated to Control (C), Disease Control (DC), Treatment (TG), Preventive (PG), and Healthy + Probiotic (HPG) groups. Malnutrition was induced using a 4% low-protein diet (LPD) for six weeks. The TG received probiotic supplementation during the recovery phase (weeks 6-9), whereas PG and HPG received probiotics throughout the study. The consortium consisted of Bacillus spizizenii, Bacillus tequilensis, and Bacillus rugosus (1 × 10[9] CFU/mL each).LPD feeding significantly reduced body weight, total protein, albumin, cholesterol, and alkaline phosphatase activity while increasing C-reactive protein, serum glutamic oxaloacetic transaminase (SGOT), and serum glutamic pyruvic transaminase (SGPT), indicating metabolic impairment, systemic inflammation, and hepatic stress. Probiotic supplementation during nutritional rehabilitation significantly improved body weight gain, restored protein and albumin levels, normalized alkaline phosphatase activity, and reduced inflammatory and hepatic injury markers compared with dietary rehabilitation alone. Histopathological analyses demonstrated improved intestinal architecture, hepatocyte morphology, splenic organization, and renal integrity in the treatment group, whereas preventive supplementation under continued protein restriction resulted in only limited protection.Gut microbiota profiling using 16 S rRNA amplicon sequencing revealed that all groups were dominated by the phyla Bacteroidetes and Firmicutes. The treatment group exhibited increased relative abundance of beneficial taxa, including Barnesiella and Lactobacillus, together with reduced Proteobacteria abundance compared with the preventive group. Microbial community composition in the treatment group more closely resembled that of healthy animals, suggesting partial restoration of gut microbial homeostasis during nutritional rehabilitation.Collectively, these findings indicate that probiotic supplementation is most effective when combined with adequate nutritional support and may serve as a valuable adjunct strategy for improving physiological recovery, tissue regeneration, and gut microbial balance during protein-energy malnutrition.},
}

Animals
*Probiotics/administration & dosage/therapeutic use
Male
Mice, Inbred BALB C
Mice
*Protein-Energy Malnutrition/therapy
*Gastrointestinal Microbiome/drug effects
Diet, Protein-Restricted/adverse effects
Bacillus/physiology
RNA, Ribosomal, 16S/genetics
Liver/pathology
Body Weight

@article {pmid42479269,
year = {2026},
author = {Zou, J and Cai, L and Geng, Y and Yin, M and Mu, Y and Guo, J and Wang, H and Zhang, F},
title = {Integrated biological and chemical strategies for sustainable management of Nigrospora coryli-induced tobacco leaf spot.},
journal = {Archives of microbiology},
volume = {208},
number = {10},
pages = {},
pmid = {42479269},
issn = {1432-072X},
support = {Qiankehe Talent Platform - CXTD[2023]021//Guizhou Science Technology Foundation/ ; GCC[2022]028-2, GCC[2023]108//"Hundred" Level Innovative Talent Foundation of Guizhou Province/ ; 110202101048(LS-08)//China National Tobacco Corporation/ ; ZDYF2023XDNY034//Key Research and Development Program of Hainan Province/ ; BZ2024056//Jiangsu Provincial Basic Research Special Fund for Soft Science Research/ ; 32460698//National Natural Science Foundation of China/ ; 2024XM06//Guizhou Tobacco Company Project/ ; 2022YFD1700300 and 2022YFD1700200//National Key Research and Development Program of China/ ; },
mesh = {Plant Leaves/microbiology ; *Ascomycota/drug effects/growth & development/physiology/genetics ; *Nicotiana/microbiology ; *Fungicides, Industrial/pharmacology ; *Plant Diseases/microbiology/prevention & control ; China ; Antibiosis ; Microbiota ; },
abstract = {Tobacco (Nicotiana tabacum) leaf spot disease caused by fungal pathogens poses a major threat to crop yield and quality worldwide. Recently, Nigrospora coryli was identified as a novel causal agent of tobacco leaf spot in China, yet its biology, ecological interactions, and management strategies remained largely unexplored. In this study, we characterized N. coryli through growth physiology, phyllosphere microbiome analysis, microbial interaction assays, and fungicide sensitivity tests. The pathogen exhibited optimal growth on PDA at 28 °C and pH 6.0, with broad pH tolerance from 4 to 11 and a lethal temperature of 57 °C. Soluble starch and peptone were the preferred carbon and nitrogen sources, respectively. High-throughput sequencing revealed disease-associated phyllosphere shifts, including enrichment of Stenotrophomonas and reduced relative abundance of Pseudomonas in symptomatic leaves, as well as detection of Nigrospora and Sarocladium only in symptomatic samples. Functional screening identified multiple antagonistic microbes, with Aspergillus niger MGM reducing lesion size by 87.6% in planta, whereas co-inoculation with Pseudomonas syringae pv. angulata SLB-5-3 was associated with increased lesion size under controlled conditions. Among eight commercial fungicides, fludioxonil was the most potent (EC50 = 0.0057 µg/mL), followed by the prochloraz-manganese chloride complex, difenoconazole, and fenaminstrobin. Synergistic interactions were observed in binary mixtures: fludioxonil + difenoconazole (1:4, SR = 1.7360), fludioxonil + fenaminstrobin (1:1, SR = 1.5365), and difenoconazole + fenaminstrobin (1:2, SR = 2.0219). These findings provide a basis for further evaluating candidate microbial antagonists and fungicide combinations for the management of N. coryli-induced tobacco leaf spot.},
}

Plant Leaves/microbiology
*Ascomycota/drug effects/growth & development/physiology/genetics
*Nicotiana/microbiology
*Fungicides, Industrial/pharmacology
*Plant Diseases/microbiology/prevention & control
China
Antibiosis
Microbiota

@article {pmid42479457,
year = {2026},
author = {You, J and Khan, RM and Reji, N},
title = {Gut microbiome profiles as predictors of response to chemoradiotherapy in locally advanced rectal cancer.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2026.02874},
pmid = {42479457},
issn = {1588-2640},
abstract = {This prospective cohort study investigates the predictive role of gut microbiota composition in determining the therapeutic response to neoadjuvant chemoradiotherapy (CRT) in patients with locally advanced rectal cancer (LARC) at Qiqihar Jianhua Hospital. A total of 178 patients underwent standardized CRT protocols and were stratified into responders and non-responders based on pathological tumor regression grades. Gut microbiome profiling was conducted via 16S rRNA amplicon sequencing and shotgun metagenomics at three treatment stages (pre-, mid-, and post-CRT). Responders exhibited significantly higher alpha diversity (Shannon, Chao1) at baseline and maintained greater microbial richness throughout treatment. Taxonomic analysis identified Faecalibacterium, Akkermansia, and Bifidobacterium as enriched in responders, while non-responders showed elevated Clostridium, Escherichia, and Streptococcus. Multivariate regression confirmed Faecalibacterium (OR = 1.16, P = 0.0002) and Akkermansia (OR = 1.27, P = 0.0146) as independent predictors of CRT response. Functional profiling revealed enrichment of anti-inflammatory pathways (butyrate synthesis, tryptophan metabolism) in responders and pro-inflammatory, stress-related functions (lipopolysaccharide biosynthesis, oxidative stress) in non-responders. Exploratory microbiome modulation using probiotics or fecal microbiota transplantation (FMT) targeting Faecalibacterium and Akkermansia demonstrated increased responder rates by 12.5 and 18.2%, respectively. These findings highlight the potential of gut microbiome signatures as non-invasive biomarkers for CRT response prediction and as targets for adjunctive therapeutic strategies. Personalized microbiome-informed treatment may enhance CRT efficacy and reduce unnecessary exposure in non-responders, paving the way for precision oncology in rectal cancer.},
}

@article {pmid42479464,
year = {2026},
author = {Cabral da Silva, A and Flantzer, L and Weinberg, J and Kyu, S and Daley-Bauer, LP and Godoy, A and Santana, AC and Talla, A and Rittgers, A and Welbourn, S and Gordon, DE and Tomalka, JA and Marconi, VC and Jones, DP and Younes, SA},
title = {Microbiome-Derived Metabolites Shape CD4[+] T-Cell Differentiation and Immune Aging in HIV-1 Infection.},
journal = {JCI insight},
volume = {},
number = {},
pages = {},
doi = {10.1172/jci.insight.204383},
pmid = {42479464},
issn = {2379-3708},
abstract = {The role of aromatic gut-derived bacterial metabolites (GDBMs) in shaping immune cell metabolism and function remains poorly explored. Using ex vivo metabolomic profiling of paired plasma and CD4[+] T-cells from people living with HIV-1 (PLWH), we identified a network of aromatic GDBMs whose cell-associated abundance, rather than systemic levels, was linked to broad alterations in CD4[+] T-cell metabolic and functional states. Among these, p-cresol sulfate (PCS) emerged as a mechanistic prototype. Ex vivo flow cytometry and single-cell RNA sequencing of CD4[+] T-cells stratified by cell-associated PCS levels revealed dose-dependent enrichment of transcriptional programs associated with impaired differentiation, regulatory-like identity, and cellular senescence. In vitro transcriptomic and proteomic analyses of PCS-exposed CD4[+] T cells demonstrated induction of cell-cycle arrest, mitochondrial dysfunction, and senescence-associated programs, including upregulation of p16 and p21. Integration of these immunometabolic findings with HIV-1 reservoir measurements revealed that CD4[+] T-cell states defined by cell-associated GDBMs track with intact proviral DNA levels in vivo. These findings define a microbiome-derived axis that reshapes CD4[+] T-cell metabolism and fate, promotes immune aging in PLWH, and may foster immunometabolic states linked to long-term HIV-1 reservoir persistence.},
}

@article {pmid42479497,
year = {2026},
author = {Ansari, U and Mallat, J},
title = {Can We Identify Severe Dysbiosis at the Bedside?.},
journal = {Critical care explorations},
volume = {8},
number = {7},
pages = {e1456},
doi = {10.1097/CCE.0000000000001456},
pmid = {42479497},
issn = {2639-8028},
}

@article {pmid42213629,
year = {2026},
author = {Gosavi, R and Bell, S and Ooi, G and McMurrick, PJ and Warrier, S and Narasimhan, V},
title = {Early-Onset Colorectal Cancer in Australia: Environmental, Microbial, and Policy Implications.},
journal = {Digestive diseases (Basel, Switzerland)},
volume = {},
number = {},
pages = {1-7},
doi = {10.1159/000552644},
pmid = {42213629},
issn = {1421-9875},
abstract = {BACKGROUND: Early-onset colorectal cancer (EOCRC; age <50 years) is rising in Australia despite improving outcomes in older adults. EOCRC shows a strong birth cohort effect, disproportionate growth in left-sided and rectal tumours, and more frequent stage III-IV presentation. Most cases occur without a family history, suggesting that environmental and biological pressures are accelerating carcinogenesis in otherwise average-risk hosts.

SUMMARY: Traditional risk factors such as obesity, metabolic syndrome, sedentary behaviour, alcohol, and smoking likely contribute through insulin resistance, chronic inflammation, and insulin-like growth factor 1-mediated signalling, but they do not fully explain the recent acceleration or distal predominance of EOCRC. Hereditary syndromes account for only a minority of cases, and tumour driver mutation patterns broadly resemble those of later-onset colorectal cancer, supporting earlier triggering rather than novel genetics. Emerging evidence implicates gut dysbiosis and exposures that disrupt mucosal defences or cause direct DNA damage. Colibactin-producing Escherichia coli may induce distinctive mutational signatures enriched in early and distal tumours. Microplastics and plasticisers may impair barrier function and promote low-grade inflammation, while per- and polyfluoroalkyl substances and related endocrine-disrupting chemicals are linked to metabolic and immune perturbation and altered bile acid biology. Antibiotic exposure, particularly early in life, may reduce microbial diversity and favour pathobionts. Inflammatory phenotypes, including inflammatory bowel disease, provide an additional model of inflammation-driven carcinogenesis relevant to EOCRC.

KEY MESSAGES: EOCRC in Australia is a growing clinical and public health challenge that cannot be explained by inherited predisposition alone. A unifying exposome model may help integrate dietary, microbial, inflammatory, and environmental drivers of risk. Clinicians should promote earlier participation in the National Bowel Cancer Screening Program, including the 45-49 opt-in pathway, expedite investigation of rectal bleeding, altered bowel habit, and iron deficiency anaemia in younger adults, and embed lifestyle counselling into routine and survivorship care. Research priorities include prospective cohorts with early-life exposure data, integrated exposomics, microbiome profiling, and mutational signature analysis to clarify modifiable drivers and guide prevention.},
}

@article {pmid42472546,
year = {2026},
author = {Upadhyay, SK},
title = {Plant-microbiome-based biostimulants: Mechanistic insights into disease suppression and sustainable crop productivity under biotic stress.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {},
number = {},
pages = {113332},
doi = {10.1016/j.plantsci.2026.113332},
pmid = {42472546},
issn = {1873-2259},
abstract = {Plant-associated microbiomes are becoming widely accepted as being part of the regulation of crop health, productivity and resilience to growing biotic stress. This review aims to synthesize current knowledge on the ecological organization, mechanistic basis, and engineering potential of plant microbiomes in disease suppression and sustainable crop productivity under biotic stress. In this context, microbiome-derived biostimulants, bioinoculants and bioactive compounds are emerging as promising eco-friendly strategies to enhance plant health and stress resilience. The review is a synthesis of current progress in the composition, functional properties, and ecological processes of plant microbiomes in the rhizosphere, phyllosphere, and endosphere. Mechanistically, microbiome-mediated disease suppression works via nutrient competition (e.g., siderophore-mediated iron binding), generation of antimicrobial metabolites (e.g., DAPG, lipopeptides, VOCs), niche exclusion by biofilm production, and regulation of plant defense responses via induced systemic resistance (ISR) and defense priming. These activities include the stimulation of pattern-stimulated defense system, such as Ca[2+] influx, reactive ROS build-up, MAPK signaling, and regulation of defense-associated genes. Multi-omics studies have shown that the functionality of microbiomes is too specific to a situation, and it depends on host genotype, environmental factors, and networks of microbial interactions. New approaches like synthetic microbial consortia and microbiome engineering have potential to improve disease control but are limited by ecological variability and field variability. Further development of mechanistic insights and predictive models will be critical in the ability to apply microbiome-based interventions to scalable and robust agricultural systems.},
}

@article {pmid42472554,
year = {2026},
author = {Gao, Z and Shen, Y and Zhang, W and Jian, Y and Li, H and Feng, L and Zhuang, WQ and Zhou, L},
title = {Community reconfiguration in hydrogen-driven denitrification under oxidized co-contaminants: Shift or shuffle.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135452},
doi = {10.1016/j.biortech.2026.135452},
pmid = {42472554},
issn = {1873-2976},
abstract = {Low-carbon nitrogen removal requires H2-driven microbiomes that remain stable under oxidized co-contaminant stress. We compared hydrogenotrophic communities exposed to Cr(VI), Se(VI), and As(V) + perfluorooctanoic acid (PFOA) in membrane biofilm reactors (MBfRs) and sequencing batch reactors (SBRs), using 16S rRNA profiling and compositional data analysis. Cr(VI) and Se(VI) served as single-inorganic-oxyanion references, while As(V) + PFOA represented a complex co-stress scenario to test backbone persistence under dual toxicity. We defined Shift as directional taxonomic turnover and Shuffle as abundance reweighting within a conserved core. Although α-diversity and genus-level dominance varied with dose, neither Bray-Curtis nor Aitchison ordination showed significant global separation among stressors (permutational multivariate analysis of variance, PERMANOVA: Bray-Curtis R[2] = 0.201, p = 0.356; Aitchison R[2] = 0.182, p = 0.796; Permutational analysis of multivariate dispersion, PERMDISP: p > 0.05 for both), a pattern consistent with shuffle-dominant change rather than wholesale community replacement. Set-overlap and Sankey analyses revealed conserved family- and phylum-level backbones centered on Comamonadaceae, Rhodocyclaceae, and Proteobacteria-centered routes. An integrated Stability-Ubiquity-Abundance (SUA) scoring framework with leave-one-sample-out sensitivity analysis prioritized ten candidate cross-contaminant generalists, including Pseudomonas, Stenotrophomonas, Azospira, Acinetobacter, Hydrogenophaga, Flavobacterium, Bradyrhizobium, Reyranella, Mycobacterium, and Sphingomonas. Localized shift signals were most evident under dichromate and in PFOA-sensitive niches. Reactor-configuration sensitivity analyses indicated that reactor configuration alone was unlikely to account for the conserved-backbone pattern. These findings support operating H2-driven denitrification as a generalist-centered, shuffle-resilient process, with stepwise contaminant loading, stable H2 supply, and early-warning monitoring of nitrate removal, oxyanion reduction, and conserved core taxa.},
}

@article {pmid42472578,
year = {2026},
author = {Beyoğlu, D and Idle, JR},
title = {Molecular signatures of the gut microbiota that affect longevity.},
journal = {Biochemical pharmacology},
volume = {},
number = {},
pages = {118267},
doi = {10.1016/j.bcp.2026.118267},
pmid = {42472578},
issn = {1873-2968},
abstract = {The human colonic microbiota has been estimated to contain 38 trillion bacteria whereas the total human somatic cells constitute 30 trillion. The mutualistic relationship between host and microbiome is ancient and believed to have evolved over 600 million years ago. Other than a digestive function and provision to the host of certain vitamins, the gut microbiome has a single important and overarching purpose, which is maintenance of homeostasis by regulation of host metabolism and immune function. Consuming a diet that maintains gut microbial eubiosis and avoids dysbiosis is essential for a long healthy life. Dysbiosis contributes to noncommunicable illnesses, including hypertension, cardiovascular disease, obesity, diabetes, inflammatory bowel disease, and cancer, any of which can reduce lifespan. The combined impact of diabetes and heart disease alone potentially shortens lifespan by up to 15-23 years. Although there has been considerable research on the bacterial abundance and diversity of the human gut microbiota, relatively little detailed attention has been given to the metabolites it produces, especially in relation to morbidity and mortality. By a thorough analysis of the gut bacterial species associated with longevity, we have identified a number of their metabolites that are beneficial to the host in this regard. The action of these metabolites underlines an important principle - that what is generated by the intestinal microbiota from a wholesome diet determines healthy aging and ultimately longevity. Future research on gut microbiota function should focus on the detailed mechanisms of action of beneficial bacterial metabolites that prolong both healthspan and lifespan.},
}

@article {pmid42472606,
year = {2026},
author = {Akgun, Y},
title = {The Circulating Senosome: Blood as the Therapeutic Interface of Aging.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {103264},
doi = {10.1016/j.arr.2026.103264},
pmid = {42472606},
issn = {1872-9649},
abstract = {Aging is commonly framed as a progressive accumulation of cellular and tissue-level damage. However, the aged organism does not decline as a collection of isolated organs. Aging is communicated systemically through blood-borne signals that connect senescent cells, immune remodeling, vascular dysfunction, metabolic stress, dysbiosis, and chronic inflammation. I propose the concept of the circulating senosome to describe the composite network of age-associated circulating mediators, including senescence-associated secretory phenotype proteins, extracellular vesicles, inflammatory cytokines, lipids, metabolites, complement and coagulation mediators, autoantibodies, cell-free nucleic acids, and microbiome-derived products. This framework positions blood as both a biomarker compartment and a therapeutic interface in aging biology. The circulating senosome does not replace established hallmarks of aging; rather, it provides a systemic layer through which multiple hallmarks interact. Defining, measuring, and therapeutically remodeling this circulating network may create new opportunities for translational geroscience.},
}

@article {pmid42472852,
year = {2026},
author = {Yuan, M and Qin, F and Wu, L and Jiang, N and Du, J and Yang, B and Zhang, W},
title = {Gut microbiota-driven metabolites modulate the development of stress-related mental disorders.},
journal = {Translational psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41398-026-04154-8},
pmid = {42472852},
issn = {2158-3188},
support = {82401769//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Stress-related mental disorders, including depression, anxiety, and post-traumatic stress disorder, represent a major global health burden, yet their underlying biological mechanisms and effective therapeutic strategies remain incompletely understood. Growing evidence from both preclinical and clinical studies indicates that alterations in gut microbiota composition and function are closely associated with the onset and progression of these disorders. A central role of the gut microbiota is the biotransformation of dietary and host-derived substrates into diverse metabolites that enter systemic circulation and influence host physiology. In this review, we highlight gut microbiota-driven metabolites. short-chain fatty acids, amino acid-related metabolites, bile acids, and monoamine-related metabolites, as key mediators of gut-brain communication that influence neural, immune, epigenetic, and endocrine processes involved in stress-related mental disorders. We summarize emerging microbial and metabolic signatures identified in animal models and human studies. Furthermore, we discuss microbiome-targeted strategies for the prevention and treatment. However, the complexity of the gut microbiota and pronounced inter-individual variability limit causal inference from current clinical studies. Consequently, translating these findings into clinical practice will require standardized study designs, longitudinal clinical investigations, and the integration of multi-omics approaches to advance precision microbiome-based interventions for psychiatric disorders.},
}

@article {pmid42472976,
year = {2026},
author = {Buday, T and Brozmanova, M and Jakusova, J and Burjanivova, T and Mokra, D and Kolomaznik, M and Gondas, E and Franova, S and Kovalska, M and Biringerova, Z and Martvon, L and Plevkova, J},
title = {Microbial load perturbation model identifies commensal-dependent control of cough sensitivity in health and disease.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-63067-0},
pmid = {42472976},
issn = {2045-2322},
support = {1/0041/23//Vedecká Grantová Agentúra MŠVVaŠ SR a SAV/ ; APVV-22-0052//Agentúra na Podporu Výskumu a Vývoja/ ; },
abstract = {The cough reflex is a fundamental airway defence mechanism regulated by interactions among epithelial, immune, and neuronal pathways. Recent evidence suggests that the low-biomass respiratory microbiome provides tonic signals essential for maintaining airway defence. Antibiotics (ATB) reduce microbial load in the airways, yet their impact on cough regulation under physiological and pathological conditions remains insufficiently understood. The aim of the present study is to investigate how ATB-induced perturbation of airway microbial load affects cough reflex sensitivity in naïve and allergen-sensitised airways, and to assess associated immune, cellular, and structural changes. Male and female Dunkin Hartley guinea pigs were studied under naïve or ovalbumin (OVA)-sensitised conditions. Animals received saline or sulfadoxine/trimethoprim pretreatment for 14 days. Cough was induced by inhalation of 0.4 M citric acid and quantified using whole-body plethysmography. Airway microbial load in bronchoalveolar lavage fluid (BALF) was measured by droplet digital PCR targeting the 16 S rRNA gene in naïve animals. Blood leukocyte counts, BALF cellularity and viability, and airway remodelling were assessed using automated cell analysis and histological staining (H&E and Sirius Red). ATB pretreatment significantly reduced airway microbial load in naïve animals, markedly suppressing cough counts and prolonging cough latency without major changes in blood cell counts or airway structure. In OVA-sensitised animals, cough latency was also significantly prolonged, whereas the number of provoked coughs showed a non-significant decrease. ATB treatment did not affect collagen deposition or peribronchiolar inflammatory infiltrates in either group. Immune responses were context-dependent: sensitised animals exhibited increased circulating neutrophils, eosinophils, and monocytes following ATB treatment, whereas naïve animals showed no systemic cellular changes. BALF cell viability decreased in naïve animals but increased in sensitised animals after ATB treatment. ATB-induced depletion of airway microbial load suppresses cough reflex sensitivity in both healthy and inflamed airways, independent of airway remodelling. These findings identify microbial-derived tonic signalling as a possible regulator of airway sensory excitability and demonstrate that immune effects of ATB depend on baseline inflammatory status. Excessive ATB use may therefore compromise airway defence in clinical practice.},
}

@article {pmid42473050,
year = {2026},
author = {Yang, ZK and Zou, X and Smagghe, G and Shen, XX and Zhang, QQ and Ji, XY and Bai, XQ and Han, ZY and Shen, ZJ and Wang, FR and Huang, Y and Yang, MF},
title = {Associations between endophytic entomopathogenic fungi and Myzus persicae-tobacco-natural enemy interactions: links to volatile organic compound profiles and microbiome structure.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.71134},
pmid = {42473050},
issn = {1526-4998},
abstract = {BACKGROUND: Myzus persicae is a major tobacco pest that causes severe economic losses through rapid reproduction and virus transmission. Integrating endophytic entomopathogenic fungi with natural enemies offers a promising, sustainable management strategy. However, the mechanisms underlying four-trophic-level interactions (endophyte-plant-pest-natural enemy) are still poorly understood.

RESULTS: Beauveria bassiana GL-5 and Cordyceps cateniannulata H8 both significantly inhibited aphid growth and reproduction. Strain-specific effects were observed: GL-5 enhanced parasitism by Aphidius gifuensis, whereas H8 reduced it. Fungal inoculation increased the female-to-male ratio in Aphidoletes aphidimyza but decreased it in Aphidius gifuensis. Furthermore, fungal inoculation reduced the emergence rates of both natural enemies and decreased the predation capacity of Aphidoletes aphidimyza. Fungal colonization also increased the diversity of tobacco volatile organic compounds (VOCs), and several tentatively identified VOCs may be linked to oviposition preference in Aphidoletes aphidimyza. Fungal treatments significantly reshaped microbial community composition and network complexity in aphid guts and tobacco leaves, altering dominant taxa (Buchnera, Acinetobacter, Pseudomonas, and Bradyrhizobium). Redundancy analysis suggested potential correlations among VOC profiles, microbial community shifts, aphid performance, and natural enemy behavior.

CONCLUSION: Entomopathogenic fungi affect the M. persicae-tobacco-natural enemy system, potentially through simultaneous changes in VOCs and microbiomes; however, the underlying causal mechanisms remain unclear. GL-5 demonstrated superior aphid suppression and merits further evaluation for sustainable aphid management. This study advances our understanding of multitrophic regulation and lays the groundwork for integrating fungal endophytes into environmentally friendly pest control strategies. © 2026 Society of Chemical Industry.},
}

@article {pmid42473133,
year = {2026},
author = {Cui, H and Ding, A and Ma, W and Qiu, W and Zhao, Y and Van der Bruggen, B and Tang, CY},
title = {Salinity-Driven Microbial Community Engineering for Safer Ultrafiltration Water Reuse.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c05538},
pmid = {42473133},
issn = {1520-5851},
abstract = {Ultrafiltration is central to water reclamation but faces two critical challenges: microbial regrowth that threatens biostability and pathogen invasion that undermines biosafety. Here, we proposed an ecological strategy that transformed backwash from a cleaning procedure into a microbiome engineering tool, thereby simultaneously addressing both challenges. Our findings provided evidence for the major microbial sources in permeate, including membrane breakthrough, detachment from the membrane permeate side, and from downstream pipeline surfaces. High-salinity backwash (100 mM NaCl) suppressed the latter two dominant sources, reducing permeate total cell counts (TCC) by more than 50%. It also enhanced the removal of assimilable organic carbon (AOC), thereby limiting microbial regrowth in the permeate by 32% during 40 day storage. Under pathogen shock loading, the salinity-driven biocake layer accelerated pathogen inactivation, reduced pathogen accumulation by 86.9%, and thereby prevented pathogen leakage into the permeate. The mechanism analysis revealed that NaCl reshaped the biocake microbiome, enhancing deterministic assembly. This functionally specialized consortium showed strengthened cooperation and upregulated key metabolic pathways, enabling synergistic AOC degradation. In addition, it suppressed pathogen invasion through superior carbon competitiveness and secretion of antimicrobial metabolites. This work provided an ecological engineering approach to enhance both biostability and biosafety in ultrafiltration-based water reuse systems.},
}

@article {pmid42473148,
year = {2026},
author = {Wang, M and Chen, P and Pei, S and Wang, R and Liu, S and Hou, Z and Liu, Z},
title = {Panax ginseng Extract Alleviates Qi Deficiency Liver Cancer via the Gut-Liver Axis: Insights from Metabolomics and Microbiome.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c00814},
pmid = {42473148},
issn = {1520-5118},
abstract = {Panax ginseng (PG), a valuable functional food known as the "King of Herbs," demonstrates therapeutic potential in the treatment of Qi deficiency liver cancer (QDLC). Regulating the gut-liver axis (GLA) may be an important mechanism of action of PG in the treatment of QDLC; however, its detailed mechanism remains unclear. This study aimed to elucidate this mechanism in QDLC rats using metabolomics and microbiome analysis. Metabolomics and microbiome experiments demonstrate that PG alleviates QDLC by modulating the composition of the gut microbiota, restoring its diversity, improving metabolic disorders, and increasing short-chain fatty acid levels. Antibiotics cocktail treatment, fecal microbiota transplantation, and probiotic colonization experiments further confirmed that PG's role in alleviating QDLC is gut microbiota-dependent. Additionally, PG alleviated GLA damage in QDLC rats by inhibiting the TLR4/MyD88/NF-κB signaling pathway. Collectively, our study provides a novel interpretation of the natural intervention mechanisms for QDLC and confirms the potential value of PG as a functional food.},
}

@article {pmid42473164,
year = {2026},
author = {Sangkham, S and Ta, AT},
title = {Nano- and Microplastics and Gastrointestinal Toxicity.},
journal = {Chemical research in toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.chemrestox.6c00274},
pmid = {42473164},
issn = {1520-5010},
abstract = {Increasing global plastic production has intensified human exposure to nano- and microplastics (NMPs) through food, water, and air. Emerging evidence links NMP exposure to oxidative stress, inflammation, microbiome disruption, and metabolic dysfunction, although human exposure and health risk data remain limited.},
}

@article {pmid42473187,
year = {2026},
author = {Li, Q and He, R and Wang, X and Long, C and He, Z and Zhang, S and Liu, Y and Zhang, Z and Wu, J and Sun, G and Cui, B and Zhao, F and Zhang, F},
title = {Akkermansia muciniphila enhances washed microbiota transplantation in the treatment of epilepsy.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
pmid = {42473187},
issn = {2542-5641},
abstract = {BACKGROUND: Refractory epilepsy remains a global clinical challenge. This first-in-human cohort study aimed to evaluate the efficacy and safety of washed microbiota transplantation (WMT) in the treatment of epilepsy.

METHODS: A prospective, single-center, open-label study of WMT in patients with epilepsy was conducted at the Second Affiliated Hospital of Nanjing Medical University from November 2016 to November 2023. The primary outcome was the clinical response rate (≥50% reduction in seizure frequency) at one month post-WMT. Parallel experiments using a pentylenetetrazole-induced epileptic mouse model were performed to validate clinical findings and investigate the role of specific core bacterial species.

RESULTS: Among 21 patients (mean age, 18.9 years), including 18 with refractory epilepsy, the clinical response rates were 43% (9/21), 57% (12/21), and 38% (8/21) at one, three, and six months post-WMT, respectively. A second maintenance WMT course at three months was associated with a higher response rate at six months compared to no maintenance therapy (odds ratio [OR] >999, 95% confidence interval [CI]: [1.12, +infinity], P = 0.080). WMT significantly increased Akkermansia muciniphila (A. muciniphila) levels in responders (P = 0.038). A higher baseline A. muciniphila abundance was associated with improved clinical outcomes (Z = 3.28, P = 0.001). The preclinical study confirmed that A. muciniphila augmented the effects of WMT against seizures, significantly reducing seizure severity and duration, and prolonging seizure latency.

CONCLUSIONS: Integrating clinical and preclinical findings, this study demonstrates that A. muciniphila synergistically enhances the effects of WMT against epileptic seizures. This study provides evidence for a new concept of microbiome-based therapeutics in epilepsy treatment.

TRIAL REGISTRATION: Clinicaltrials.gov, NCT02889627.},
}

@article {pmid42473450,
year = {2026},
author = {Li, Y and Zhang, S and Xu, K and Zhang, J and Dong, M and Lu, H and Fan, Y},
title = {Microbial diversity and functional analysis in wastewater and sludge of wastewater treatment plants.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21546},
pmid = {42473450},
issn = {2167-8359},
mesh = {*Sewage/microbiology ; *Bacteria/classification/isolation & purification/genetics ; *Fungi/classification/isolation & purification/genetics ; *Wastewater/microbiology ; Biodiversity ; China ; *Microbiota ; },
abstract = {BACKGROUND: The efficiency of wastewater treatment plants (WWTPs) relies heavily on microbial communities. However, the microbial characteristics of different treatment units in the Qian'an WWTP (Hebei, China) remain unclear. This study investigates its microbial diversity and functions to provide a basis for process optimization.

METHODS: Samples were collected in October 2024 from four representative units were selected: sludge (group A), sedimentation tank water (group C), aeration tank water (group E), and raw wastewater (group F). Bacterial and fungal communities were analyzed via Illumina NextSeq 2000 PE300 platform sequencing, with functional potentials predicted using PICRUSt2 and FUNGuild, respectively.

RESULTS: Bacterial richness was highest in groups A, C, and E and lowest in group F, whereas fungal richness was highest in groups C and E and lowest in group F. The microbial community structures of groups C and E were highly similar in terms of richness and diversity patterns, but both differed markedly from groups A and F. At the phylum level, bacteria in group A were significantly enriched in Chloroflexi and Firmicutes, and fungi by Rozellomycota; bacteria in groups C, E and F were mainly Proteobacteria and Bacteroidetes. Fungal composition varied significantly, with Rozellomycota in A, Blastocladiomycota in C/E, and Ascomycota in F. Predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed 25 differential metabolic pathways (e.g., amino acid and carbohydrate metabolism). Furthermore, 24 predicted functional genes related to nitrogen metabolism (nitrification, nitrogen fixation) were inferred, suggesting strong nitrogen cycling potential. Fungal functional groups differed significantly among groups: Ectomycorrhizal fungi dominated in group A, Insect Parasite-Undefined Saprotroph in groups C and E, and Animal Pathogen was predicted to account for up to 54.41 ± 4.75% in group F.

CONCLUSIONS: This study clarifies the microbial characteristics across treatment units and highlights the nitrogen cycling potential of the WWTP microbiome, providing a scientific basis for optimizing treatment processes.},
}

*Sewage/microbiology
*Bacteria/classification/isolation & purification/genetics
*Fungi/classification/isolation & purification/genetics
*Wastewater/microbiology
Biodiversity
China
*Microbiota

@article {pmid42473587,
year = {2026},
author = {Fu, X and Xia, Y and Han, J and Wang, W and Zhang, B and Liu, H and Yang, X and Han, S and Zhang, C},
title = {Effects of Gut Microbiome and Metabolic Pathways on Obesity: A Two-Sample Mendelian Randomization and Case-Control Study.},
journal = {Iranian journal of biotechnology},
volume = {24},
number = {3},
pages = {},
pmid = {42473587},
issn = {1728-3043},
abstract = {OBJECTIVES: We employed Mendelian randomization (MR) and case-control studies to identify causal associations and validate biological relevance.

MATERIALS AND METHODS: Two-sample MR using genome-wide association studies (GWAS) summary statistics prioritized inverse variance-weighted analysis, supplemented by weighted median and MR-Egger regression. Sensitivity analyses included leave-one-out cross-validation, MR-PRESSO global test, and Cochran's Q test for heterogeneity/pleiotropy. False Discovery Rate (FDR) correction identified robust associations. Clinical validation involved 16S rRNA sequencing and untargeted metabolomics in obese and case-control cohorts.

RESULTS: MR identified two microbiota (Streptococcus thermophilus, OR = 0. 98, 95% CI: 0.96-0.99, P < 0.01; Lachnospiraceae bacterium 5_1_63FAA, OR = 0.98, 95% CI: 0.97-0.99, P < 0.001) and two pathways (4-aminobutanoate degradation V, OR = 0.95, 95% CI: 0.92-0.97, P < 0.001; Pyridoxal 5 phosphate biosynthesis I (OR = 0.96, 95% CI: 0.94-0.98, P < 0.001) significantly associated with reduced obesity risk. Sensitivity analyses confirmed no heterogeneity/pleiotropy. Clinical data validated these findings: obese participants exhibited lower abundances of Streptococcus thermophilus and Lachnospiraceae bacterium 5_1_63FAA, reduced serum 4-aminobutanoate and pyridoxal 5-phosphate levels.

CONCLUSION: Lachnospiraceae bacterium 5_1_63FAA and Streptococcus thermophilus, alongside 4-aminobutanoate degradation and pyridoxal 5-phosphate biosynthesis, represent protective factors against obesity. Targeted modulation of these targets may exert beneficial effects on the prevention and treatment of obesity.},
}

@article {pmid42473684,
year = {2026},
author = {Banerjee, B and Dolai, TK and Ghosh, K},
title = {Hydroxyurea and Gut Microbiome Interactions in Sickle Cell Disease: Toward Adjunctive Microbiome-based Therapy.},
journal = {Hemoglobin},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/03630269.2026.2702342},
pmid = {42473684},
issn = {1532-432X},
abstract = {Sickle cell disease (SCD) is a monogenic disorder marked by hemoglobin S polymerization, resulting in chronic hemolysis, vaso-occlusion, systemic inflammation, and progressive multiorgan damage. Despite major therapeutic advances, SCD remains a complex inflammatory condition with significant morbidity. Hydroxyurea is the cornerstone of treatment, primarily by inducing fetal hemoglobin and reducing vaso-occlusive crises and hemolysis. It also exerts anti-inflammatory effects by decreasing leukocyte activation and endothelial adhesion. However, hydroxyurea does not fully reverse microvascular injury, persistent immune activation, or organ dysfunction, particularly renal and endothelial damage. This review aims to synthesize current evidence on the interactions between hydroxyurea and the gut microbiome in SCD and to evaluate the potential role of microbiome-directed therapies as adjunctive strategies to control inflammation and organ damage. Recent evidence highlights the gut microbiome as a critical regulator of immune homeostasis and inflammation in SCD. Dysbiosis, marked by reduced microbial diversity and diminished short-chain fatty acid (SCFA) production, drives cytokine activation, endothelial dysfunction, and pain sensitization. Emerging studies suggest that hydroxyurea may partially restore microbial balance, yet residual dysbiosis persists. Microbiome-directed therapies, including probiotics and microbial metabolites, show promise for reducing pro-inflammatory cytokines, strengthening gut barrier integrity, and modulating immune responses. Probiotic strains such as Lactobacillus and Bifidobacterium, together with SCFA-mediated pathways, may enhance anti-inflammatory effects and address therapeutic gaps left by hydroxyurea. A combined strategy targeting both hematologic and microbiome pathways may offer superior control of inflammation and organ damage. Integrating microbiome-based interventions with conventional therapy represents a promising, patient-centered approach to improving long-term outcomes and quality of life in SCD.},
}

@article {pmid42473781,
year = {2026},
author = {Jang, LK and Robertson, C and Triplett, MG and Hinckley, A and Moya, M and Kok, CR and Mohagheghi, MV and Weisenberger, TM and Bourguet, FA and Bowers, E and Morrison, M and Wang, Y and Noy, A and Park, JA and Be, NA and Hynes, WF},
title = {Development of a gut-on-a-chip microfluidic device with three-dimensionally printed human intestinal tissue for studying human-microbe interactions.},
journal = {Biofabrication},
volume = {},
number = {},
pages = {},
doi = {10.1088/1758-5090/ae8ccc},
pmid = {42473781},
issn = {1758-5090},
abstract = {The human small intestinal epithelium features villi protruding into the gut lumen, and crypts invaginating toward the gut exterior, forming a microarchitecture critical for intestinal homeostasis and renewal. Reproducing this complex geometry at physiological dimensions and pliability, while achieving cell compatibility, remains challenging. Here, we developed three-dimensionally (3D) printed gelatin methacryloyl (GelMA) crypt-villus scaffolds and a gut-on-a-chip microfluidic device integrating dynamic fluid flow control, oxygen/pH regulation, and continuously sampled gut effluent collection. Using our custom biological projection micro-stereolithography (BioPμSL) system, we fabricated physiologically relevant crypt-villus scaffolds with physiological dimensions and softness within 30 minutes. We demonstrated that microbial transglutaminase (TG) enzyme could stably link proteins to GelMA, significantly improving Caco-2 cell adhesion to the GelMA surface. Moreover, we show stable protein density gradients could be created by allowing the mixture of TG and proteins to diffuse into hydrogels. Human intestinal cells seeded on 3D printed intestinal tissues exhibited robust adhesion, proliferation, and maturation into an apico-basal polarized monolayer. By integrating the crypt-villus scaffolds into the microfluidic platform, we demonstrated its potential for co-culturing epithelial cells with gut-relevant microbes, enabling monitoring of oxygen and pH levels and analysis of microbial growth during co-culture and assessment of cell viability afterward. This innovative platform holds promise for investigating human-microbiome interactions, advancing disease diagnosis/prevention, and facilitating drug screening applications.},
}

@article {pmid42473946,
year = {2026},
author = {Ali, B and Khan, M and Osama, M and Iftikhar, H and Zaman, P and Khan, MN and Imran, A and Imin, N and Khan, Z},
title = {Phages as Metabolic Switches in Plant-Associated Microbiomes: Implications for Climate-Smart Agriculture.},
journal = {Journal of basic microbiology},
volume = {66},
number = {7},
pages = {e70186},
doi = {10.1002/jobm.70186},
pmid = {42473946},
issn = {1521-4028},
mesh = {*Bacteriophages/physiology/genetics/metabolism ; Rhizosphere ; Soil Microbiology ; Agriculture/methods ; *Microbiota/physiology ; *Plants/microbiology/virology ; *Bacteria/virology/metabolism ; Plant Roots/microbiology ; Stress, Physiological ; Lysogeny ; },
abstract = {Bacteriophages constitute a regulatory layer in plant-associated microbiomes that has been systematically under-characterized relative to their ecological importance. This review advances the hypothesis that phages function as metabolic switches, alternating between lytic nutrient release and lysogenic host-fitness enhancement to govern the microbial metabolic states that determine nutrient cycling, stress responses, and microbiome stability in the rhizosphere and phyllosphere. During lytic infection, phage-driven cell lysis releases dissolved organic carbon, ammonium, and phosphate through the viral shunt, redistributing microbial biomass into forms directly accessible to plant roots and surviving microbial taxa. Lysogenic integration, by contrast, delivers prophage-encoded auxiliary metabolic genes that reprogram bacterial hosts with enhanced metabolic capacity across multiple generations without immediate cell death. Environmental stressors, include drought, salinity, temperature extremes, heavy metal contamination, and pathogen pressure remodel root exudation profiles, alter microbial metabolic bottlenecks, and shift phage life-cycle decisions through quorum-sensing-responsive and SOS-dependent switching mechanisms. These phage-mediated processes have cascading consequences for plant-relevant outcomes including nutrient uptake efficiency, oxidative stress management, phytohormone signaling, and growth-defense trade-offs mediated by plant growth-promoting rhizobacteria. By integrating mechanistic evidence across abiotic and biotic stress contexts, this review proposes a phage-microbe-plant metabolic axis as a unifying framework for understanding how soil virome dynamics translate into plant physiological outcomes. Practical implications for engineering phage-informed microbiomes and developing climate-resilient agricultural systems are evaluated alongside ecological risks, knowledge gaps, and priorities for field validation, virome mapping, and predictive modeling that must be addressed before phage-based interventions can be reliably deployed in crop production.},
}

*Bacteriophages/physiology/genetics/metabolism
Rhizosphere
Soil Microbiology
Agriculture/methods
*Microbiota/physiology
*Plants/microbiology/virology
*Bacteria/virology/metabolism
Plant Roots/microbiology
Stress, Physiological
Lysogeny

@article {pmid42474008,
year = {2026},
author = {Khan, F and Barve, K},
title = {Marine Products as Therapeutics for Atherosclerosis Through Modulation of Gut-heart Axis.},
journal = {Cardiovascular & hematological disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/011871529X473049260710110225},
pmid = {42474008},
issn = {2212-4063},
abstract = {INTRODUCTION: A bidirectional relationship between cardiovascular health and gut microbiota, established by the gut-heart axis, is a major contributor to the development or prevention of atherosclerosis. Chronic immune-inflammatory and fibro-proliferative atherosclerosis remains a significant global cause of morbidity and death. Bile acids, Short-Chain Fatty Acids (SCFAs), and trimethylamine-N-oxide (TMAO) are examples of gut-derived metabolites that majorly impact inflammation, endothelial dysfunction, and plaque formation.

METHODS: Data were collected using keywords like 'marine', 'atherosclerosis', 'gut dysbiosis', 'short-chain fatty acids', and 'gut-heart axis' from databases such as PubMed, ScienceDirect, and Scopus. Relevant studies were analysed to evaluate mechanisms linking gut dysbiosis, metabolite modulation, and prevention of atherosclerosis.

RESULTS: Marine-derived bioactive compounds include peptides, carotenoids (Fucoxanthin), polysaccharides (Fucoidan, Alginate), and sterols (Fucosterol), which have anti-inflammatory, lipidlowering, and microbiome-balancing properties, making them promising therapeutic options. These bioactive compounds prevent the progression of atherosclerosis by lowering TMAO levels, increasing SCFA synthesis, improving lipid metabolism, and regulating genes associated with cholesterol metabolism.

DISCUSSION: The gut-heart axis is a critical contributor to the development and progression of atherosclerosis. Marine natural products have therapeutic potential in the management of atherosclerosis since they act as modulators of gut microbiota and cardiovascular health.

CONCLUSION: Marine-derived natural products offer a novel therapeutic strategy for prevention and management of atherosclerosis by targeting the gut-heart axis.},
}