@article {pmid42931362,
year = {2026},
author = {Deleemans, JM and Mina, R and Spiropoulos, A and Lawal, OA and Reimer, RA and Karim, S and Richardson, B and Carlson, LE},
title = {The Chemo-Gut Probiotic Trial Protocol: A Double-Blind Randomized Controlled Trial Investigating the Effects of a Multi-Strain Probiotic on Gut Microbiota, Gastrointestinal Symptoms, and Psychosocial Health Among Cancer Survivors.},
journal = {Methods and protocols},
volume = {9},
number = {5},
pages = {},
pmid = {42931362},
issn = {2409-9279},
support = {//Alberta Cancer Foundation/ ; },
abstract = {Background: Survivors of cancer experience chronic gastrointestinal (GI) and psychosocial health symptoms and reduced gut microbial diversity. This may compromise their long-term health and wellbeing. No studies have investigated probiotics for managing both GI and psychosocial symptoms together, or their effects on the composition of the gut microbiota in post-treatment cancer survivors. Aims: To investigate the effects of a probiotic vs. placebo on (i) abdominal pain and depressive symptoms (primary outcomes); (ii) (a) GI (i.e., gas/bloating, diarrhea, and constipation), and psychosocial (i.e., anxiety, cognitive function, and fatigue) symptoms and (b) gut microbiota composition; and (iii) relationships between bacteria and GI and psychosocial symptoms. Methods: This double-blind, placebo-controlled, two-arm, randomized trial will recruit N = 66 participants allocated 1:1 to the probiotic or placebo group for a 12-week trial. Adult survivors diagnosed with a solid tumor or blood cancer who have completed chemotherapy within the last 5 years and show elevated GI or psychosocial symptoms will be included. The probiotic capsule contains a blend of Lacticaseibacillus rhamnosus, Lactobacillus helveticus, and Bifidobacterium animalis subsp. lactis strains, ingested orally once daily. Stool samples will be collected at baseline and week 12 and analyzed using 16S rRNA gene sequencing. GI and psychosocial surveys will be completed at baseline and at weeks 6 and 12. Descriptive statistics, frequencies, paired-samples t-tests, linear mixed models, and Spearman's correlational analyses will be used. Conclusions: We explore a novel, microbiota-based intervention for chronic GI and psychosocial symptoms following cancer treatment. Our findings and commitment to person-centered knowledge translation via creating informational materials will enable people to make informed decisions about their health.},
}

@article {pmid42931636,
year = {2026},
author = {Wang, Y and Yu, W and Kanda, K and Iwata, H and Guo, J},
title = {In Ovo Exposure to Phenanthrene Promotes Antimicrobial Resistance Genes and Hemolysin Virulence Factor in Guts of Chicken Embryos.},
journal = {Toxics},
volume = {14},
number = {10},
pages = {},
pmid = {42931636},
issn = {2305-6304},
support = {42571089//National Natural Science Foundation of China/ ; 2026JC-YXQN-119//Natural Science Basic Research Program of Shaanxi/ ; },
abstract = {Antimicrobial resistance genes (ARGs) are increasingly recognized as emerging environmental contaminants that threaten ecological integrity and animal health. Polycyclic aromatic hydrocarbons (PAHs) are widespread pollutants that accumulate in the environment and have been detected in wild bird eggs. Although PAHs have been shown to accelerate ARG dissemination in environmental matrices, their influence on ARG dynamics in birds is unclear. Therefore, it is hypothesized that exposure to elevated levels of PAHs promotes the propagation and enrichment of ARGs in the avian gut. In this study, chicken embryos at Hamburger-Hamilton Stage 1 (HHS 1) were exposed in ovo to phenanthrene (PHE; 1, 100, and 400 nmol/g egg), and the toxic effects were evaluated. High PHE exposure significantly reduced embryonic tarsus length by 14.81% and increased the liver somatic index (LSI) by 26.97%. Functional annotation based on the Virulence Factor Database (VFDB) showed that the relative abundance of hemolysin, a microbial virulence factor associated with gastrointestinal microorganisms, was significantly elevated in the high-PHE group. In a Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, genes involved in nucleotide excision repair (NER) and basal transcription factor (BTF) pathways showed significantly lower relative abundance following high-dose exposure. Additionally, ARGs related to polymyxin and pleuromutilin resistance were significantly enriched in the high-exposure group. Partial least squares path modeling (PLS-PM) indicated that ARG enrichment was jointly shaped by multiple factors. PHE may be directly associated with ARG proliferation or may act indirectly through mobile genetic elements (MGEs), whereas bacterial community abundance might be linked to the potential dissemination of ARGs given its significant positive association with MGEs. Collectively, these findings provide correlative evidence that PHE exposure is associated with increased ARG abundance in avian organisms and highlight the need for an integrated evaluation of PAH-associated hazards to avian health.},
}

@article {pmid42931684,
year = {2026},
author = {Miao, Z and Yuan, F and Zou, Q and Yuan, C and Zheng, Y and Wang, K and Lyu, B and Luo, Z and Jiang, M},
title = {Stage-Associated Plant-Soil-Microbiome Patterns and Rhizosphere Pb-Zn Stabilization in Indocalamus decorus at a Mining Site.},
journal = {Toxics},
volume = {14},
number = {10},
pages = {},
pmid = {42931684},
issn = {2305-6304},
support = {Grant No. 32371976//National Natural Science Foundation of China/ ; grant numbers 202611KY0005//Funding for the Construction of the Chengdu National Botanical Garden System/ ; },
abstract = {Indocalamus decorus is a perennial bamboo with potential for phytomanagement, but its Pb-Zn partitioning and associated microbiome under field co-contamination remain unclear. Parallel plantings were established at a Pb-Zn mining site and the provenance site. Plant nutrients, rhizosphere properties, Pb-Zn concentrations and soil fractions, and bacterial and fungal communities were evaluated across four developmental stages at the mining site; shoot initiation was also evaluated at the provenance site. At shoot initiation, mine-site plants had lower organ P concentrations, whereas root N was maintained. Rhizosphere nutrient availability was relatively high during shooting. Pb accumulated mainly in roots, while Zn was transferred more readily to culms; organ-specific bioconcentration factors for both metals remained below 1. Compared with bulk soil, rhizosphere soil contained lower DTPA-extractable Pb and Zn, smaller acid-soluble/exchangeable fractions, and larger residual fractions. Sample compartment explained 60.8% and 66.9% of bacterial and fungal community variation, respectively. Rhizosphere fungi were associated with a broader range of metal fractions and plant metal-distribution indices than other microbial compartments. These results indicate root-dominated Pb retention, reduced rhizosphere Pb-Zn lability, and compartment-specific microbial associations, supporting further evaluation of I. decorus as a candidate for phytostabilization-oriented management of Pb-Zn-contaminated mine soils.},
}

@article {pmid42931886,
year = {2026},
author = {Zeber-Lubecka, N and Ciebiera, M},
title = {cFrom microbiota to microbiome - how should gynecologists interpret cervicovaginal microbial studies?.},
journal = {Ginekologia polska},
volume = {},
number = {},
pages = {},
doi = {10.5603/gpl.115313},
pmid = {42931886},
issn = {2543-6767},
}

@article {pmid42931891,
year = {2026},
author = {Zhou, Z and Zhang, C and Yin, L},
title = {IgA nephropathy: gut microbiome insights and unmet needs in pediatrics.},
journal = {Pediatric nephrology (Berlin, Germany)},
volume = {},
number = {},
pages = {},
pmid = {42931891},
issn = {1432-198X},
abstract = {Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulopathy worldwide and a leading cause of chronic kidney disease and kidney failure in children and young adults. Well-established pathogenic pathways include genetic susceptibility, intrinsic B-cell glycosylation abnormalities, complement activation, and immune dysregulation, and accumulating evidence further places the gut microbiome at the center of IgAN pathogenesis via the gut-kidney axis. A critical evidence gap defines the field: no prospective cohort has characterized the gut microbiome in pediatric primary IgAN. This conceptual narrative review synthesizes well-validated mechanistic data from adult cohorts-most notably microbial-mediated IgA1 deglycosylation-and extrapolates these findings to pediatric populations through the lens of the developmental entanglement framework, which accounts for the synchronized maturation of the gut microbiome, mucosal immunity, and renal structure in early life. Using an adapted Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach, we separately rate evidence quality for adult and pediatric populations, explicitly mark all pediatric extrapolations as unvalidated, and cautiously appraise indirect evidence from pediatric IgA vasculitis with nephritis (IgAVN). We further evaluate the translational potential of microbiome-guided strategies, and conclude with a pragmatic, stepwise research agenda centered on foundational cohort studies and emerging technologies to address the evidence gap. Closing this deficit will enable the development of non-invasive biomarkers and safe, mechanism-targeted therapies to prevent progressive renal failure in children with IgAN.},
}

@article {pmid42932086,
year = {2026},
author = {Chawda, D and Tyagi, N and Mubashra, and Srivastava, A and Shukla, A and Srivastava, S},
title = {Gut microbiome in colorectal cancer: a dual regulator of tumor biology and therapeutic response.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {42932086},
issn = {1874-9356},
abstract = {Colorectal cancer is one of the most prevalent malignancies and a major cause of cancer-related mortality worldwide. It remains a significant health concern, with an alarming rise in early-onset colorectal cancer cases in younger populations. Many factors are reported to have been responsible for its onset, progression, and metastasis, among which the gut microbiome is found to be a crucial one. Dysbiosis among these gut microbes impacts normal cellular functions and homeostasis, which may lead to cancer. Under unfavourable conditions biological processes such as cell differentiation, proliferation, migration, and apoptosis get disrupted and give rise to pathological traits such as invasion and metastasis. Emerging evidence indicates a rather significant role of the gut microbiome in this transition, influencing both onset and progression. Over the past few decades, our understanding of microbiome-cancer interaction has evolved considerably, yet effective microbiome-based therapies remain limited. This review highlights how these microbes modulate normal biological functions to pathological ones, and we further discuss current microbiome-based therapies along with their future prospects.},
}

@article {pmid42932096,
year = {2026},
author = {Latif, MZ and Deng, M and Asghar, N and Kong, L and Kousar, S and Zhang, H and Rehman, SU and Jiang, Y and Humza, M and Lu, C and Ding, X},
title = {Plant resilience: harnessing bioactive compounds for sustainable disease protection.},
journal = {Stress biology},
volume = {6},
number = {1},
pages = {},
pmid = {42932096},
issn = {2731-0450},
support = {32272557//National Natural Science Foundation of China/ ; 32072500//National Natural Science Foundation of China/ ; ZR2022ZD23//Natural Science Foundation of Shandong Province/ ; ZR2024ZD07//Natural Science Foundation of Shandong Province/ ; Y20240208//National Foreign Expert Program/ ; },
abstract = {Plants have evolved complex phytochemical and immune defense mechanisms in response to pathogen invasion. Plants deploy phytochemical defense system-signaling molecules, secondary metabolites, antimicrobial proteins and peptides-to mitigate the pathogens they encounter. Pathogens have developed strategies-effector proteins, efflux pumps and detoxification mechanisms-to manipulate or overcome plant defenses. This review offers insights into how these bioactive compounds are biosynthesized and activated following pathogen recognition. We provide an overview of the dynamic crosstalk between PTI and ETI and their role in optimizing plant defense. Additionally, we discuss the potential of advanced genetic engineering approaches, nanocarrier-mediated elicitor delivery, and microbiome engineering to enhance these natural defenses. Finally, we address the technical bottlenecks of engineering plant immunity and provide a roadmap for future research directions. This review provides a stronger mechanistic foundation for breeding crops with durable, broad-spectrum resilience for sustainable crop protection.},
}

@article {pmid42932263,
year = {2026},
author = {Mogey, R and Goodacre, R and Curtis, F and Maden, M and Edwards, KL},
title = {Metabolomics in the wild: A scoping review of non-invasive methods for understanding vertebrate wildlife health and success.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0359720},
pmid = {42932263},
issn = {1932-6203},
mesh = {Animals ; *Metabolomics/methods ; *Animals, Wild/metabolism ; *Vertebrates/metabolism ; Conservation of Natural Resources ; },
abstract = {An increase in metabolomics research over the last decade has expanded species-specific knowledge of biological processes, but has primarily focused upon humans, domesticated and model animal species. Recent advances, particularly around data management pipelines for untargeted studies, make the field more accessible to disciplines outside those embedded in analytical chemistry, including wildlife conservation. To establish the breadth of existing wild vertebrate animal metabolomic research, specifically utilising non-invasive sampling, this scoping review establishes: (1) general trends in publication numbers; (2) coverage of wildlife taxonomic groups and species; (3) subject numbers and sample size; (4) non-invasive sample types; (5) metabolomic techniques utilised; (6) the context of current literature and (7) conservation implications. This scoping review was conducted following the JBI methodology and reported in accordance with PRISMA-ScR; searches were conducted using PubMed, Scopus, Web of Science and supplemented with Google Scholar; following screening, 83 peer-reviewed original research papers were identified using predefined criteria and data extracted. The most popular areas of research were physiology and reproduction (30%) and diet and nutrition (27%). Although most publications focused on a single species, there were 11 multi-species publications, resulting in metabolomics data for 93 species. A large proportion of which, 72%, were mammalian, and of these, 52% are currently listed at risk of extinction on the IUCN Red List. With over 60% of all publications published between 2022-2025, non-invasive vertebrate wildlife metabolomics appears to be gaining traction as a tool in wildlife physiology research. However, future research would benefit from alignment with model animal metabolome research experimental design, as few studies included the consideration of metabolite extraction optimisation, storage conditions, the use of integrated omics platforms beyond microbiome analysis and consideration of statistical power, particularly in respect to intra-individual variation and the characterisation of species-specific metabolomes.},
}

Animals
*Metabolomics/methods
*Animals, Wild/metabolism
*Vertebrates/metabolism
Conservation of Natural Resources

@article {pmid42932302,
year = {2026},
author = {Hiratsuka, D and Iki, A and Kinoshita, M and Doi, Y and Kato, O and Oshima, K and Hiraoka, T and Matsuo, M and Ichinose, M and Makabe, T and Izumi, G and Harada, M and Hirota, Y and Nabeta, M},
title = {Oral versus vaginal Lactobacillus supplementation for endometrial dysbiosis: A paired pre and post-endometrial microbiome study.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0360619},
pmid = {42932302},
issn = {1932-6203},
mesh = {Female ; Humans ; *Dysbiosis/microbiology/therapy/drug therapy ; *Lactobacillus/physiology ; *Endometrium/microbiology ; Administration, Oral ; *Microbiota ; *Probiotics/administration & dosage/therapeutic use ; *Vagina/microbiology ; Retrospective Studies ; Adult ; Administration, Intravaginal ; },
abstract = {Infertility is a global health challenge, and impaired endometrial receptivity remains an important contributor to treatment failure. Endometrial dysbiosis, characterized by a low proportion of Lactobacillus in the endometrial microbiota, has been proposed as a potentially modifiable factor that may affect endometrial receptivity and fertility, and treatment with Lactobacillus-containing probiotics is emerging as a promising therapeutic approach. However, the optimal route of Lactobacillus supplementation remains unclear. We compared oral versus vaginal supplementation using the same Lactobacillus-containing formulation as an adjunct to standardized doxycycline/metronidazole therapy and continued oral lactoferrin in patients with baseline endometrial Lactobacillus <10%, based on paired microbiome profiling of endometrial samples (aspirated intrauterine fluid and endometrial tissue). In this single-center retrospective cohort study, thirty-two patients underwent paired endometrial microbiome testing before and after 30 days of supplementation (oral, n = 18; vaginal, n = 14). In the vaginal group, the median endometrial Lactobacillus proportion increased from 0.05% [0.00-0.20] to 99.15% [70.45-100.00] (p = 0.001), whereas in the oral group it increased from 0.00% [0.00-0.18] to 0.30% [0.03-66.33] (p = 0.005). The median change was greater with vaginal versus oral supplementation (+98.90% [70.45-99.80] vs + 0.25% [0.03-66.33], p < 0.001). Post-treatment Lactobacillus ≥80%, used as an exploratory marker of marked microbiota improvement, was observed in 9/14 patients (64%) in the vaginal group and 3/18 (17%) in the oral group (p = 0.010). Exploratory reproductive outcomes were limited by the small sample size and did not define a reliable clinical threshold. These findings suggest that, within this combined treatment regimen, vaginal Lactobacillus supplementation may provide a greater route-associated additional improvement in endometrial microbiota profiles than oral administration.},
}

Female
Humans
*Dysbiosis/microbiology/therapy/drug therapy
*Lactobacillus/physiology
*Endometrium/microbiology
Administration, Oral
*Microbiota
*Probiotics/administration & dosage/therapeutic use
*Vagina/microbiology
Retrospective Studies
Adult
Administration, Intravaginal

@article {pmid42932307,
year = {2026},
author = {Li, J and Özkurt, AG and Baertschi, I and Wang, J and Aeschlimann, L and Goepfert, C and Misselwitz, B and Sokollik, C and Yilmaz, B},
title = {Baseline microbial ecology encodes probiotic responsiveness through distinct metabolic and network configurations.},
journal = {Cell reports},
volume = {45},
number = {11},
pages = {118228},
doi = {10.1016/j.celrep.2026.118228},
pmid = {42932307},
issn = {2211-1247},
abstract = {Probiotic efficacy in inflammatory bowel disease varies widely between individuals, and the sources of that variability remain poorly understood. D-lactate is a microbiota-derived metabolite that accumulates during intestinal inflammation and is associated with epithelial barrier dysfunction, which motivated our use of a consortium selected to contribute none of it. Here we show that its benefit is not an intrinsic property of the administered strains but is determined by the pre-existing ecological state of the recipient microbiome. Across three independent mouse resources, preventive administration reduced disease severity and histopathological damage only where baseline communities carried higher diversity and more complex co-occurrence architecture; in those animals the consortium preserved community structure and metabolic output, restoring disease-disrupted metabolites, and selectively raising butyrate and propionate. Sustained exogenous D-lactate did not abolish protection, placing D-lactate as a tractable readout of ecological restoration rather than its effector. Responsiveness is encoded in the baseline microbiota and predictable before intervention, establishing probiotic efficacy as a stratifiable property of the host microbiome.},
}

@article {pmid42932319,
year = {2026},
author = {Perry, NS and Cavalcanti, ARO and Hayes, KA and Yeung, NW and Sischo, DR and Shizuru, SH and Antonsen, AK and Haubner, ML and Ah Cook, AN and Hee, CE and Hill, MMY and Krenteras, CT and Maruno, TMB and Nakasone, RH and Rosenbush, HK and Stiefel, SM and Sullivan, AJ and Meyer Iii, WM},
title = {Examining microbial assemblage differences on plants preferred and avoided by threatened Hawaiian land snails to identify important food resources.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0361108},
pmid = {42932319},
issn = {1932-6203},
mesh = {Animals ; *Snails/microbiology/physiology ; Hawaii ; *Endangered Species ; Fungi/classification/isolation & purification ; Feeding Behavior ; Bacteria/classification/isolation & purification ; },
abstract = {The Hawaiian Islands, an isolated oceanic archipelago in the Pacific, had one of the world's most spectacular land snail radiations. Unfortunately, only 35% of the 759 Hawaiian snail species remain, with >100 species threatened with imminent extinction. Though many extant Hawaiian snails are arboreal and are known to eat microbes on the surface of plants, our current understanding of which microbes compose arboreal Hawaiian snails' diets remains rudimentary. Here, we examined microbial assemblages (bacterial and fungal) on plants previously identified as preferred and avoided by a diverse assemblage of arboreal snails at three sites in wet and mesic forests on O'ahu, Hawai'i, USA, to identify microbes that may form the foundation of Hawaiian arboreal snails' diets. At Mt. Ka'ala, we also investigated if microbial assemblages change across years. Across sites, microbial assemblages differed on preferred and avoided plants. While differences across sites can complicate the process of identifying key microbes, microbes with elevated abundances on preferred plants across sites are likely important food resources. Using this approach, we identified bacterial and fungal OTUs that we hypothesize form important components of Hawaiian arboreal snails' diets. While we found that microbial assemblages differed among years at Mt. Ka'ala, differences between preferred and avoided plants remained consistent across years. Expanding a snail plant preference-microbiome framework across multiple forest types is a crucial step in understanding arboreal snail diets as microbial taxa enriched on preferred plants across sites may be meaningful components of snail-associated microbial resources. Microbial taxa enriched on preferred plants are not presented here as confirmed dietary components, but as experimentally tractable candidates that should be further evaluated in laboratory trials. This information is foundational to improving captive rearing of critically endangered snails and informing habitat quality assessments for the many threatened Hawaiian snails.},
}

Animals
*Snails/microbiology/physiology
Hawaii
*Endangered Species
Fungi/classification/isolation & purification
Feeding Behavior
Bacteria/classification/isolation & purification

@article {pmid42932354,
year = {2026},
author = {Otto, M and Camus, L and Busche, T and Bünte, J and Hütten, A and Persicke, M and Klages, LJ and Kalinowski, J and Heilbronner, S and Rückert-Reed, C},
title = {Characterization of Corynebacterium species isolated from nasal swabs of healthy volunteers: description of Corynebacterium nasorum sp. nov., Corynebacterium tardum sp. nov., Corynebacterium tuingiense sp. nov., Corynebacterium limaceinasi sp. nov. and Corynebacterium kefirresidentii sp. nov.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {76},
number = {10},
pages = {},
doi = {10.1099/ijsem.0.007292},
pmid = {42932354},
issn = {1466-5034},
mesh = {*Corynebacterium/classification/genetics/isolation & purification/chemistry ; Humans ; Bacterial Typing Techniques ; *Phylogeny ; DNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Sequence Analysis, DNA ; Fatty Acids/chemistry ; Genome, Bacterial ; Healthy Volunteers ; Base Composition ; Adult ; *Nose/microbiology ; },
abstract = {Members of the genus Corynebacterium are common constituents of the human nasal microbiota but their cultivable diversity remains incompletely represented in taxonomic and diagnostic databases. Ten coryneform strains isolated from nasal swabs of seven healthy adults were characterized using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS), whole-genome sequencing, phylogenomic inference, overall genome relatedness indices, phenotypic testing and chemotaxonomic analyses. MALDI-TOF MS initially assigned most strains to Corynebacterium tuberculostearicum or Corynebacterium accolens, whereas genome-based analyses resolved the strains into five distinct species-level lineages. The lineages represented by strains LaCa116[T], LaCa142[T] and LaCa191[T] were clearly differentiated from their closest related type strains by average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values below accepted species-level thresholds. Strains LaCa7[T] and LaCa117[T] represented closely related but distinguishable genomic lineages, with an ANI value of 95.9% and a dDDH value of 66.4%. Strain LaCa117[T] was closely related to strain SB, to which the effectively but not validly published name 'Corynebacterium kefirresidentii' had previously been applied. Phenotypic and chemotaxonomic characteristics supported the genomic groupings and placement of the strains within the genus Corynebacterium. These findings reveal previously unrecognized diversity among cultivable nasal corynebacteria and demonstrate that routine MALDI-TOF MS identification may be unreliable when suitable reference spectra are absent. Based on the integrated taxonomic evidence, the names Corynebacterium nasorum sp. nov. (type strain LaCa7[T]=DSM 119349[T]=LMG 33882[T]), Corynebacterium kefirresidentii sp. nov. (type strain LaCa117[T]=DSM 119343[T]=LMG 33886[T]), Corynebacterium tuingiense sp. nov. (type strain LaCa142[T]=DSM 119342[T]=LMG 33884[T]), Corynebacterium limaceinasi sp. nov. (type strain LaCa191[T]=DSM 119341[T]=LMG 33883[T]) and Corynebacterium tardum sp. nov. (type strain LaCa116[T]=DSM 119344[T]=LMG 33885[T]) are proposed.},
}

*Corynebacterium/classification/genetics/isolation & purification/chemistry
Humans
Bacterial Typing Techniques
*Phylogeny
DNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Sequence Analysis, DNA
Fatty Acids/chemistry
Genome, Bacterial
Healthy Volunteers
Base Composition
Adult
*Nose/microbiology

@article {pmid42933036,
year = {2026},
author = {Shang, C and Zhu, Z and Liu, Y and Sun, S and Dong, K and Xu, C},
title = {Cascade-targeting elimination of tumor-resident intracellular bacteria with biomimetic nanomedicine for enhancing breast cancer immunotherapy.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {270},
number = {},
pages = {116257},
doi = {10.1016/j.colsurfb.2026.116257},
pmid = {42933036},
issn = {1873-4367},
abstract = {Fusobacterium nucleatum as a typical tumor-resident intracellular bacteria can colonize in breast cancer for promoting immunosuppression and inducing tumor metastasis. Herein, we developed a biomimetic nanomedicine (HM-GZNC) for cascade-targeting elimination of tumor-resident intracellular bacteria and enhancing breast cancer immunotherapy. HM‑GZNC was composed of a ZIF‑8‑derived nanozyme loaded with glycyrrhetinic acid (GA) and coated with a hybrid cell membrane. The hybrid cell membrane from Fusobacterium nucleatum-activated RAW264.7 macrophages and 4T1 breast cancer cells endowed HM‑GZNC with a cascade-targeting capability. Upon NIR irradiation, HM‑GZNC exhibited the enhanced peroxidase-like activity, controlled drug release, and excellent photothermal effects for synergistic killing intratumoral bacteria and breast cancer cells. In vivo experiments showed that HM‑GZNC could precisely localize within tumors for effectively eliminating Fusobacterium nucleatum and inducing immunogenic cell death (ICD). Moreover, HM‑GZNC could promote dendritic cell maturation and antigen presentation, improve the infiltration of CD8[+] and CD4[+] T cells along with the secretion of pro‑inflammatory cytokines for enhancing antitumor immune responses and inhibiting metastasis. The biomimetic nanomedicine provided a novel strategy for developing tumor-associated microbiome-targeted therapies against breast cancer.},
}

@article {pmid42933211,
year = {2026},
author = {Shah, OU and Shuchen, F and Jia, W and Hongfei, S and Luyao, C and Wenjie, Z and Wenping, X},
title = {Integrated multi-omics analysis reveals coordinated root and rhizosphere responses underlying AMF-mediated drought tolerance in kiwifruit.},
journal = {Microbiological research},
volume = {315},
number = {},
pages = {128791},
doi = {10.1016/j.micres.2026.128791},
pmid = {42933211},
issn = {1618-0623},
abstract = {Drought stress substantially restricts kiwifruit (Actinidia spp.) growth and productivity, yet the mechanisms through which arbuscular mycorrhizal fungi (AMF) promote drought tolerance remain insufficiently understood. To address this gap, root physiological and molecular analyses were integrated with multi-omics profiling of the rhizosphere microbiome to investigate AMF-mediated drought responses under well-watered and drought-stress conditions. Under drought stress, AMF inoculation improved plant growth, root development, cellular ultrastructure, and physiological performance. More importantly, root omics analysis revealed coordinated regulation of drought-responsive pathways involving glutathione metabolism, amino acid biosynthesis, phytohormone regulation, and energy metabolism. Beyond these plant responses, AMF inoculation altered bacterial and fungal community composition, enriched potentially beneficial taxa, and increased rhizosphere network connectivity under drought stress. Within the restructured microbiome, we identified an AMF-specific drought-responsive amplicon sequence variant (ASV) module composed primarily of bacterial taxa and associated with cross-kingdom microbial interactions. Integrated microbial-metabolite network analysis further identified a metabolite feature annotated as 1-piperideine as a candidate associated with selective microbial recruitment in AMF-colonized rhizospheres. Together, these findings suggest that AMF-associated drought tolerance in kiwifruit involves complementary changes in plant physiology, root molecular responses, and rhizosphere microbiome assembly. A mechanistic basis is thereby provided for developing AMF-based strategies to improve kiwifruit production under increasing water limitation.},
}

@article {pmid42933357,
year = {2026},
author = {Laila, U and Zeng, Y and Tan, C and Nazir, A and Abbas, T and Bareen, FE and Kammann, C and Farwa, U and Liang, Y},
title = {Zn-modified biochar coupled with biological nitrification inhibitors mitigates nitrous oxide emissions from alkaline soil through modulation of ammonia-oxidizing microorganisms.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131238},
doi = {10.1016/j.jenvman.2026.131238},
pmid = {42933357},
issn = {1095-8630},
abstract = {Biochar (BC) has generally been employed to mitigate the nitrous oxide (N2O) emissions from agricultural soils, but its response is soil-dependent. Thereby, in soil with proficient nitrification tendency, Zn-modified BC coupled with biological nitrification inhibitors (BNIs) could be more effective in mitigating N2O emissions. The effects of coupled application of Zn-modified biochar and BNIs on N2O emission and its underlying microbial mechanism remain largely unknown. In our study, a 24-day incubation experiment was established representing nine treatments; with three biochars amendments using three settings of BNIs, referred to as: 1) control (without amendment/inhibitor, 2) control with methyl 3-(4-hydroxyphenyl) acrylate -MHPA, 3) control with methyl 3-(4-hydroxyphenyl) Propionate-MHPP, 4) pristine BC without inhibitor, 5) pristine BC with MHPA, 6) pristine BC with MHPP, 7) Zn-modified BC without inhibitor, 8) Zn-modified BC with MHPA, 9) Zn-modified BC with MHPP, all at agronomically recommended dosage. N dynamics were evaluated following the addition of urea. The inclusion of Zn-modified BC in combination with MHPA and MHPP substantially reduced N2O emissions by 94.52% and 96.85% relative to control. Quantification of N-cycling genes indicated that the treatment without BC amendment stimulated the growth of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across the entire incubation period. The input of Zn-BC with MHPA and MHPP substantially inhibited the population of AOA and AOB. LEfSe cladogram elucidated the distinct shift in bacterial assemblage across the treatments. Overall, our results demonstrated that Zn-modified BC + MHPP played a key role in the dynamics of ammonia-oxidizing functional microbiome and N turnover, potentially considerably mitigating N2O emissions.},
}

@article {pmid42933395,
year = {2026},
author = {Pedersen, TK and Jain, T and Segerstolpe, Å and Lin, C and Shih, AR and Yuan, L and Ashenberg, O and Kaper, ME and Twardus, SW and Ricciardi, R and Lau, H and Moon, JJ and Brix, S and Xavier, RJ and Graham, DB},
title = {A microbiome-reactive TMIGD2[hi] Th17 subset is spatially enriched at the intestinal epithelium and expanded in inflammatory bowel disease.},
journal = {Immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.immuni.2026.09.026},
pmid = {42933395},
issn = {1097-4180},
abstract = {Subsets of intestinal CD4[+] T cells directly recognize commensal bacteria and coordinate tolerance versus protective immunity. Our limited understanding of CD4[+] T cell specificities and corresponding functional phenotypes has created a barrier to deciphering the mechanisms of mucosal homeostasis and inflammation mediated by the adaptive immune system. To address this, we leveraged an immunodominant Bacteroidetes epitope in SusC to perform single-cell profiling of the SusC-specific and total CD4[+] T cell landscapes in intestinal tissues of patients with inflammatory bowel disease (IBD). By analyzing phenotypes and T cell receptor specificities in parallel, we uncovered phenotypic diversification of T helper 17 (Th17) cells in IBD and identified an epithelial-localized, SusC-reactive Th17 subset that is BACH2[lo], GZMA[hi], and expresses the costimulatory receptor TMIGD2. Together, our results highlight the utility of tracking commensal-specific T cell responses to define specialized subsets of Th17 cells associated with loss of tolerance to the microbiome.},
}

@article {pmid42933401,
year = {2026},
author = {van Uden, AM and Zweers, H and Vasquez, AA and Wansink, DG and 't Hoen, PAC and Gusinac, A and de Baaij-Daalmeyer, A and Gerrits, K and Melchers, WJG and van Engelen, B and Ederveen, THA and Braakman, HMH},
title = {Exploring the gut microbiome in children and young adults with myotonic dystrophy type 1.},
journal = {Journal of neuromuscular diseases},
volume = {},
number = {},
pages = {22143602261496624},
doi = {10.1177/22143602261496624},
pmid = {42933401},
issn = {2214-3602},
abstract = {Myotonic Dystrophy type 1 (DM1) is a complex multisystem disorder, and affected children commonly present with gastrointestinal and neurodevelopmental challenges. Despite the high prevalence of these symptoms, their underlying mechanisms remain poorly understood. The gut microbiome is known to be involved in gastrointestinal and neurodevelopmental disorders, and emerging research suggests that it could also play a contributory role in various neuromuscular diseases. However, the gut microbiota of children with DM1 remains unexplored. This pilot study compared gut microbiota profiles of 10 children and one young adult with DM1, to that of their unaffected siblings (n=11). Three-day food records and faecal samples were collected, and bacterial taxa were analysed through 16S rRNA marker-gene sequencing. A within-family paired-sample design accounted for potential confounders, such as diet and lifestyle. Results revealed that overall microbial diversity and community structure were similar between groups. Moreover, participants with DM1 showed a significant lower relative abundance of the bacterial genus Faecalibacterium (mean 4.9% ± 2.1%) compared to their unaffected siblings (mean 9.1% ± 4.4%)(p=0.005). This finding should be considered exploratory, as its univariate analysis was uncorrected for multiple testing. Faecalibacterium is a key gut bacterium, and reduced abundance has been reported in several DM1-associated gastrointestinal and neurodevelopmental disorders. Although causality cannot be inferred from this exploratory study the observed reduction may be relevant to gastrointestinal and neurodevelopmental challenges frequently seen in DM1. If larger further studies confirm its role, targeting Faecalibacterium relative abundance could become a potential therapeutic strategy for alleviating gastrointestinal and neurodevelopmental symptoms in DM1.},
}

@article {pmid42933406,
year = {2026},
author = {Lee, JH and Kim, SH and Kim, EK and Lee, KA and Bhin, J and Hwang, D and Lee, DG and Bahn, YS and Lee, WJ},
title = {The antimicrobial peptide pileup promotes enterocyte shedding to maintain gut homeostasis in aging Drosophila.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2026.09.077},
pmid = {42933406},
issn = {1879-0445},
abstract = {Cellular turnover is a fundamental biological process that counteracts aging by activating stem cells to replace aging cells. This process is especially critical for maintaining the intestinal epithelium, one of the most rapidly renewing tissues in the body. However, the replacement of aging enterocytes cannot be explained solely by the generation of new cells from intestinal stem cells (ISCs); it also requires the complementary process of physically removing aging enterocytes through shedding. Compared with the well-characterized regulation of ISCs, the mechanisms governing enterocyte shedding remain poorly understood. Here, we identify pileup, a novel age-associated antimicrobial peptide (AMP) in Drosophila, as both a genetic marker and a key regulator of enterocyte shedding. Reactive oxygen species (ROS) generated through age-related mitochondrial dysfunction, a process facilitated by Autophagy-related gene 1 (ATG1) kinase, activate hypoxia-inducible factor 1α, which induces pileup expression specifically in aging enterocytes. Pileup then compromises the membrane of these cells and triggers c-Jun N-terminal kinase (JNK) activation, which we propose promotes their shedding. Notably, pileup has three homologs, and loss of all four genes leads to tumorous cell accumulation, gut barrier dysfunction, microbiome dysbiosis, and premature death. Our findings reveal a previously unrecognized role for AMPs in the turnover of aging host cells, extending their classical function beyond microbial defense. This work provides new mechanistic insights into enterocyte shedding and underscores its essential role in preserving gut homeostasis during aging.},
}

@article {pmid42933603,
year = {2026},
author = {Ahamed, F and Palepu, S and Pal, D and Bandyopadhyay, A and Sengupta, M and Hossain, CM and Das, S and Somashekara, J and Goswami, K},
title = {Impact of supplementation of a package of iron folic acid (IFA) with probiotics on haemoglobin levels in the elderly with mild to moderate anaemia: A double-blind, randomised controlled trial (PRobiotics in Anaemia Trial for Healthy Ageing Management - PRATHAM).},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {105208},
doi = {10.1016/j.clnesp.2026.105208},
pmid = {42933603},
issn = {2405-4577},
abstract = {INTRODUCTION: The growing geriatric population has increased the burden of age-related conditions such as anaemia, highlighting the need for effective strategies to promote healthy ageing. This study evaluated the effect of supplementation of iron and folic acid (IFA) with probiotics on haematological, inflammatory, and gut microbiome parameters among elderly individuals with mild-to-moderate anaemia.

METHODOLOGY: This community-based, placebo-controlled, double-blind, randomised controlled trial was conducted among individuals aged ≥60 years from the "AIIMS SBIMB Study on Healthy Ageing (ASTHA)" cohort. A total of 200 participants were randomised in a 1:1 ratio. The intervention group received daily IFA tablets containing 60 mg of elemental iron and 500 μg of folic acid, along with probiotic capsules containing Streptococcus faecalis, Bifidobacterium, and Lactobacillus (30 billion CFUs/capsule) for 12 weeks. The control group received IFA tablets with placebo capsules containing one milligram of oral rehydration solution (ORS). Haemoglobin, ferritin, hepcidin, CRP, acute infections, and gut microbiome diversity were assessed at baseline and 12 weeks. An intention-to-treat (ITT) analysis was performed as the primary analysis, with a per-protocol analysis conducted as a sensitivity analysis.

RESULTS: A total of 184 study participants completed follow-up; missing endline biochemical data for the remaining participants were imputed using the last observation carried forward approach. The mean change in haemoglobin in the intervention and control groups was 1.0 ± 1.1 g/dL and 1.2 ± 1.1 g/dL, respectively (p=0.439). Hepcidin increased in both groups, with no significant between-group difference (p=0.550). Ferritin increased significantly more in the control group than in the intervention group (20.6 ± 34.2 ng/mL vs 10.0 ± 20.4 ng/mL; p=0.033). Baseline alpha-diversity was higher in the intervention group, while most endline diversity measures were comparable between groups.

CONCLUSION: IFA with probiotics did not provide additional benefit in haemoglobin or ferritin responses compared with IFA alone over 12 weeks, and there were no significant between-group differences in hepcidin or most gut microbiota alpha-diversity measures at endline.

CTRI/2023/09/057830.},
}

@article {pmid42933652,
year = {2026},
author = {Liu, L and Wu, R and Gao, Z and Fang, F and Chang, C and Hou, Z and Wang, H and Zhang, D and Wang, Z},
title = {Hydroxyproline Enhances Branched-Chain Amino Acid Effects on Lifespan and Healthspan in Caenorhabditis elegans.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101898},
doi = {10.1016/j.tjnut.2026.101898},
pmid = {42933652},
issn = {1541-6100},
abstract = {Food-derived protein hydrolysates frequently contain both collagen-associated hydroxyproline (Hyp) and branched-chain amino acids (BCAAs), but the biological consequences of their combination remain unclear. This study tested whether Hyp changes the effects of leucine (Leu), isoleucine (Ile), and valine (Val) on lifespan and healthspan-related phenotypes in Caenorhabditis elegans and whether these treatment effects are accompanied by coordinated microbial and metabolic remodeling. Amino acid concentrations that did not strongly disrupt bacterial food clearance were selected for lifespan, stress-resistance, motility, muscle-integrity, biochemical, microbiome, metabolomic, and transcriptomic analyses. Hyp+BCAA combinations improved lifespan- and healthspan-related phenotypes in a BCAA- and dose-dependent manner. The strongest combined treatments enhanced resistance to thermal and oxidative stress, preserved age-associated motility and muscle structure, reduced oxidative and lipofuscin-associated markers, and increased ATP-related readouts. Multi-omics profiling showed that these direct treatment effects were accompanied by distinct C. elegans-associated microbiota signatures, altered NAD precursor-related metabolites including nicotinic acid ribonucleoside (NaR), and a Leu+Hyp transcriptional response enriched for energy metabolism, proteostasis, and extracellular-matrix remodeling. Integrated microbiome-metabolome analysis identified a positive association between Rhodococcus abundance and NaR levels. These findings demonstrate that, under the tested culture conditions, Hyp+BCAA exposure improves longevity-related phenotypes and identifies microbial composition, NAD precursor metabolism, and host energy homeostasis as candidate, testable mediators.},
}

@article {pmid42933673,
year = {2026},
author = {Turner, D and Kenigsberg, S and Plotkin, L and Aharoni-Frutkoff, Y and Sokolik, M and Focht, G and Gasasa, S and Turpin, W and Waslyk, AM and Ledder, O and Griffiths, AM and Martincevic, I and Huynh, HQ and Godny, L and Avni-Biron, I and Torres, J and Panaccione, R and Jacobson, K and Otley, A and Sharar-Fischler, T and Li, Q and Azulay, A and Sigall-Boneh, R and Lee, SH and Croitoru, K},
title = {TASTY AND HEALTHY DIET REDUCES FECAL CALPROTECTIN IN HIGH-RISK FIRST-DEGREE RELATIVES OF PATIENTS WITH CROHN'S DISEASE: PIONIR RANDOMIZED CROSSOVER TRIAL.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.10.376},
pmid = {42933673},
issn = {1528-0012},
abstract = {BACKGROUND: With the rising prevalence of inflammatory bowel disease (IBD), preventing new-onset disease becomes a priority. The PIONIR (Preventing IBD ONset in Individuals at Risk) randomized controlled trial explored whether the Tasty&Healthy (T&H) diet reduces inflammatory markers in high-risk first-degree relatives (FDRs) of patients with Crohn's disease (CD).

METHODS: FDRs with persistently elevated fecal calprotectin (FC, >70μg/g) and, at most, nonspecific mucosal abnormalities (edema or ≤10 aphthous ulcers) on video-capsule endoscopy or ileocolonoscopy were randomized to T&H or habitual diet (HD) for 8 weeks, followed by crossover for additional 8 weeks. Treatment effect on the primary outcome, FC response, was analyzed using generalized estimating equations for the two-period, two-sequence crossover design, following the intention-to-treat principle.

RESULTS: Twenty-nine FDRs were randomized (n=14 T&H-first, n=15 HD-first). At week 8, median FC was lower with T&H (64μg/g [IQR 44-127]) vs. HD (112μg/g [74-227]; P=.022). FC decreased by ≥50% in 71% on T&H versus 27% on HD (RR=2.68 [95%CI 1.09-6.60]; P=.016). Across both crossover periods, estimated marginal mean FC declined from 185μg/g [95%CI 144-237] by 61% to 72μg/g [95%CI 57-91] with T&H, versus 38% to 114μg/g [95%CI 93-140] with HD (ratio 0.63 [95%CI 0.51-0.80], translating to 37% overall decrease with T&H; P<0.001). Six microbial species differed between diets after FDR correction. By week 8, 79% rated T&H acceptable and 83% had good or complete adherence.

CONCLUSION: These findings demonstrate the modifiability of low-grade intestinal inflammation in healthy high-risk FDRs with persistent FC elevation but without diagnostic endoscopic evidence of CD, supporting long-term dietary prevention trials (ClinicalTrials.gov #NCT05211518).},
}

@article {pmid42933708,
year = {2026},
author = {Khan, S and Chen, M and Chen, Z and Liang, Z and Abbas, M and Ahmad, S and Hassan, MU and Xie, S and Chen, D},
title = {PFAS and microbiota dysbiosis: An emerging link to respiratory toxicity.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {},
number = {},
pages = {110732},
doi = {10.1016/j.cbpc.2026.110732},
pmid = {42933708},
issn = {1532-0456},
abstract = {Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants of increasing concern because of their widespread use, environmental mobility, bioaccumulation, and multisystem toxicity, including immunotoxicity, hepatotoxicity, neurotoxicity, reproductive toxicity, and endocrine disruption. Regulatory restrictions on legacy PFAS have accelerated the use of short-chain, ether-containing, and other replacement compounds, including GenX/HFPO derivatives, 6:2 Cl-PFESA, OBS, and ultrashort-chain PFAS; however, their respiratory and toxicological profiles remain incompletely characterized. Although ingestion through food and drinking water is the major exposure route for the general population, inhalation through indoor dust, aerosols, occupational emissions, and firefighting-related sources may be relevant in high-exposure settings, while the actual dose reaching human lung tissue remains poorly defined. Emerging evidence indicates that PFAS-induced toxicity may also involve disruption of host-microbiota interactions. The lung microbiome, despite its low biomass, contributes to mucosal immunity, epithelial homeostasis, and respiratory defense, while the gut-lung axis enables intestinal microbial signals to influence pulmonary inflammation. PFAS-associated gut dysbiosis can alter short-chain fatty acids, bile-acid metabolism, tryptophan-derived metabolites, and microbial products such as lipopolysaccharide, thereby providing plausible mechanistic links between intestinal disturbance and pulmonary immune responses. However, direct evidence that PFAS causally remodel the lung microbiota or that microbiota-derived signals mediate PFAS-induced lung injury remains limited. This review integrates current evidence from epidemiological, in vitro, and in vivo studies to evaluate PFAS-associated respiratory toxicity, with particular emphasis on emerging PFAS, exposure relevance, pulmonary inflammation and injury, and microbiota-mediated mechanisms along the gut-lung axis. By distinguishing established pulmonary effects from emerging microbiota-related hypotheses, this review identifies critical knowledge gaps and highlights priorities for future exposure assessment, mechanistic research, and risk evaluation.},
}

@article {pmid42933735,
year = {2026},
author = {Zhang, L and Wang, K and Chai, D and Mo, T and Jiang, W and Ma, W and Yu, B and Shi, Q and Ding, P and Deng, W and Wang, W and Zhao, K and Chen, C},
title = {Intestinal Candida albicans promotes HCC progression and anti-PD-1 resistance via IL-17A and Trem2[+] macrophages.},
journal = {Journal of hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhep.2026.10.018},
pmid = {42933735},
issn = {1600-0641},
abstract = {BACKGROUND & AIMS: Whether intestinal fungal dysbiosis contributes to hepatocellular carcinoma (HCC) progression and resistance to immune checkpoint inhibitors (ICIs) remains unclear. We investigated how gut Candida albicans influences HCC progression, immune remodeling, and response to ICI therapy.

METHODS: Fecal and tumor samples from patients with HCC, liver cirrhosis, and healthy controls were analyzed using ITS2 sequencing, immune profiling, and correlation analyses. Mechanistic studies focused on four complementary autochthonous murine HCC models and cell-based assays, integrating single-cell and bulk RNA sequencing, genetic and pharmacologic perturbations, Kaede photoconversion, fungal antigen recall assays, antifungal treatment, and anti-PD-1 therapy.

RESULTS: Fecal C. albicans abundance was higher in HCC patients and was associated with advanced disease, shorter overall survival, and reduced durable clinical benefit. Across HCC models, C. albicans gavage increased tumor burden and induced a Th17/IL-17A-skewed microenvironment characterized by Trem2[+] macrophage accumulation and impaired CD8[+] T cell infiltration and function. Antifungal treatment attenuated tumor progression, whereas IL-17A blockade or deficiency largely abrogated C. albicans-associated tumor promotion. Mechanistically, IL-17A induced tumor-derived MCP-1 through ACT1-TRAF6-TAK1 signaling to recruit macrophages and upregulated PAI-1, which activated TGF-β/Smad3 signaling to promote an immunosuppressive Trem2[+] macrophage state. These macrophages limited CD8[+] T cell recruitment and effector function through coordinated CXCL10 repression and GAL-1 induction, while potentially reinforcing Th17 responses through IL-1β and IL-6. Kaede photoconversion demonstrated enhanced mesenteric lymph node-to-liver Th17 trafficking, while fungal antigen recall assays revealed preferential Th17 responsiveness to C. albicans. C. albicans also impaired anti-PD-1 efficacy in vivo, whereas antifungal treatment partially restored therapeutic responsiveness.

CONCLUSIONS: Intestinal C. albicans promotes HCC progression and anti-PD-1 resistance through an IL-17A-Trem2[+] macrophage circuit, supporting its potential as a biomarker and therapeutic target.

IMPACT AND IMPLICATIONS: Intestinal fungal dysbiosis is increasingly recognized as a component of the gut-liver axis, but its functional contribution to HCC has remained poorly defined. Our study identifies intestinal Candida albicans as a promoter of HCC progression in experimental models and delineates an IL-17A-MCP-1/PAI-1-Trem2[+] macrophage circuit that links fungal exposure to impaired CD8[+] T-cell immunity and reduced response to PD-1 blockade. These findings are relevant to researchers and clinicians seeking microbiome-associated determinants of HCC progression and immunotherapy resistance. Fecal C. albicans abundance and components of this immune circuit may warrant evaluation as biomarkers for patient stratification and as potential targets for combination therapy. However, the clinical associations reported here are based on modest observational cohorts, and antifungal treatment was tested as a proof-of-concept intervention in mice. Larger prospective studies and more selective therapeutic approaches will therefore be required before these findings can inform clinical management.},
}

@article {pmid42933792,
year = {2026},
author = {Sun, Y and Stradner, MH and Fessler, J and Reisch, MK},
title = {Predictors of treatment response in rheumatoid arthritis: a narrative review.},
journal = {RMD open},
volume = {12},
number = {4},
pages = {},
pmid = {42933792},
issn = {2056-5933},
abstract = {Rheumatoid arthritis (RA) is a common autoimmune disease having diverse responses to disease-modifying antirheumatic drugs. Although treat-to-target strategies have improved disease management, therapeutic selection remains largely empirical and a substantial proportion of patients fail to achieve adequate clinical response to their therapies. Therefore, reliable biomarkers capable of predicting treatment response before therapy initiation are urgently needed to guide personalised treatment decisions. Current evidence suggests that multiple categories of biomarkers may contribute to the prediction of treatment responses across different therapeutic agents in RA, including clinical characteristics, serological markers, cytokine profiles, genetic and transcriptomic signatures, immune-cell phenotypes, synovial pathotypes and microbiome features. This review summarises current biomarker strategies for predicting therapeutic response in RA and discusses their potential utility in improving precision medicine. However, most individual biomarkers show limited predictive power, partly due to the complex and dynamic nature of RA pathogenesis. Combining biomarkers from multiple biological dimensions, together with the continued exploration of novel predictive markers, may improve the robustness and accuracy of treatment response prediction in RA.},
}

@article {pmid42933939,
year = {2026},
author = {O'Donnell, JEM and Zeef, DH and Gopan, A and Muise, AM},
title = {Genetics of Inflammatory Bowel Disease-What is Unsought Goes Undetected.},
journal = {Gastroenterology clinics of North America},
volume = {55},
number = {4},
pages = {653-672},
doi = {10.1016/j.gtc.2026.05.016},
pmid = {42933939},
issn = {1558-1942},
mesh = {Humans ; *Inflammatory Bowel Diseases/genetics ; Genetic Testing ; Genetic Predisposition to Disease ; Precision Medicine ; },
abstract = {Inflammatory bowel disease (IBD) affects nearly 1% of North Americans and arises from complex interactions between genetics, environment, and the gut microbiome. This article examines IBD's genetic architecture-spanning monogenic, oligogenic, and polygenic disease-and highlights that genetic evaluation should not be limited by age. A negative genetic screen does not exclude a genetic basis for disease, as emerging mechanisms like mosaicism and regulatory variants may go undetected. The authors advocate for immunogenetic pathway-based classification to enable precision therapeutics, improve treatment outcomes, and reduce adverse effects, emphasizing that what is unsought in genetic testing will inevitably go undetected.},
}

Humans
*Inflammatory Bowel Diseases/genetics
Genetic Testing
Genetic Predisposition to Disease
Precision Medicine

@article {pmid42934177,
year = {2026},
author = {Kanehisa, M and Furumichi, M and Sato, Y and Matsuura, Y and Ishiguro-Watanabe, M},
title = {KEGG for characterizing genomes and pathways in the biosphere.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkag1042},
pmid = {42934177},
issn = {1362-4962},
support = {JPMJND2203//NBDC Database Integration Coordination Program/ ; //Japan Science and Technology Agency/ ; //NBDC Program of the Japan Science and Technology Agency/ ; },
abstract = {The KEGG database (https://www.kegg.jp) has been developed as a model of the biological systems. By organizing knowledge of cellular and organism-level functions in the form of molecular wiring diagrams, the model enables generating new knowledge and finding practical applications. The KO (KEGG Orthology) dataset plays the basic role of organizing knowledge. KO is an ortholog with functional relevance, generalizing experimental evidence in specific organisms to other organisms. KEGG molecular networks, including pathway maps and modules, are generic networks with KOs as network nodes, and thus KEGG mapping from genomes to pathways can be applied to any organism. As the number of KOs increases and the KO annotation rate improves, KEGG mapping is further expanded. A set of KOs in the genome and a set of modules in the metabolic pathways are now used to characterize various data objects in the biosphere, including organisms, organism groups, microbiomes, viruses, and their combinations, such as endosymbiont-host, microbiome-host, and virus-host relationships. Furthermore, a simple measure of similarity either by KO compositions or module compositions is introduced to compare organism groups. The resulting similarity dendrograms possibly reflect similarity of cellular functions or, more specifically, metabolic functions, which can be compared with phylogenetic trees.},
}

@article {pmid42934212,
year = {2026},
author = {Short, I and Martínez-Pérez, C and Miravet-Verde, S and Sunagawa, S and Stocker, R and Alcolombri, U},
title = {Alteromonas macleodii breaches the diatom frustule triggering protoplast emergence and programmed necrosis-like death in Thalassiosira rotula.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42934212},
issn = {2041-1723},
support = {542395//Simons Foundation/ ; 542395//Simons Foundation/ ; LT0050/2023-L//Human Frontier Science Program (HFSP)/ ; LT0050/2023-L//Human Frontier Science Program (HFSP)/ ; GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {*Diatoms/microbiology/physiology/cytology ; *Alteromonas/physiology/genetics ; Necrosis ; },
abstract = {Diatom-bacteria interactions drive biogeochemical fluxes at the base of the marine food-web. Although bacteria are increasingly recognised as important drivers of algal mortality, the diversity of algicidal strategies remains understudied. Here we show that Alteromonas macleodii, a recurrent member of Thalassiosira rotula's microbiome, breaches the diatom's silica frustule, inducing >95% of cells to emerge from their shells within 72 h, exposing protoplasts to lysis and exploitation. Whilst protoplast formation was induced by diverse bacteria, A. macleodii uniquely caused population-wide collapse, used here to characterise this diatom stress response. Dual transcriptomics indicated the presence of a programmed necrosis-like cell death pathway in diatoms underpinning T. rotula's terminal morphological change, alongside upregulation of bacterial motility, chemotaxis and opportunistic metabolism. These findings reveal a potent algicidal strategy, recasting A. macleodii as an antagonist that exploits diatom mortality for its own benefit, removes the ballast provided by their frustules and thus reshapes oceanic carbon cycling.},
}

*Diatoms/microbiology/physiology/cytology
*Alteromonas/physiology/genetics
Necrosis

@article {pmid42934317,
year = {2026},
author = {},
title = {Laying the foundations for clinical microbiome research.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {23},
number = {11},
pages = {805},
pmid = {42934317},
issn = {1759-5053},
}

@article {pmid42934449,
year = {2026},
author = {Kolawole, O and van Diepeningen, AD and Martens, JG and Arrizabalaga-Larrañaga, A and Black, L and van Overbeek, L},
title = {Wheat Ear Microbiome State as a Transferable Indicator of Within-Season Mycotoxin Risk.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42934449},
issn = {1432-184X},
mesh = {*Triticum/microbiology/chemistry ; Seasons ; *Microbiota ; *Mycotoxins/analysis ; Bacteria/isolation & purification/genetics/classification ; *Fungi/genetics/isolation & purification/classification/metabolism ; Trichothecenes/analysis ; Weather ; RNA, Ribosomal, 16S/genetics ; Food Contamination/analysis ; },
abstract = {Weather based models are central to mycotoxin risk assessment, but field level discrimination can be limited when environmental training data are sparse and models must transfer to locations not used during training. We tested whether wheat ear microbiome state provides a transferable biological indicator for within season classification of trichothecene contamination under strict spatial holdout, with relevance for food and feed safety. Across three winter wheat trial locations within a single production year, ears were sampled at BBCH 77 to 83, corresponding to mid to late grain filling, and paired bacterial 16 S rRNA gene and fungal ITS profiles were analysed alongside LC-MS/MS measurements of DON and T-2 + HT-2. Under leave one location out evaluation, microbiome informed models achieved substantially higher discrimination of higher versus lower contamination than station level weather summaries under identical spatial holdout. Weather features added little in the single season dataset, but simulation analyses indicated that environmental predictors become more learnable with temporal replication, supporting a future two stage framework in which early season weather context is refined by within season microbiome state. Portability screening and drop one ablation prioritised microbial indicators with sign consistent associations across locations and non-redundant predictive value. Together, these findings provide proof of concept that wheat ear microbiome state can support spatially transferable within season mycotoxin risk classification and targeted surveillance when environmental training data are limited.},
}

*Triticum/microbiology/chemistry
Seasons
*Microbiota
*Mycotoxins/analysis
Bacteria/isolation & purification/genetics/classification
*Fungi/genetics/isolation & purification/classification/metabolism
Trichothecenes/analysis
Weather
RNA, Ribosomal, 16S/genetics
Food Contamination/analysis

@article {pmid42934450,
year = {2026},
author = {Gu, Z and Shen, Y and Li, Y and Mi, L and Shu, C and Zhang, J and Geng, L},
title = {Early phyllosphere remodeling in maize after herbivory uncovers candidate insecticidal bacteria from feeding-altered taxa.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {11},
pages = {},
pmid = {42934450},
issn = {1573-0972},
support = {2022ZD040150204//Major Project of Agricultural Biological Breeding/ ; 2024YFE0214100//National Key Research and Development Program of China/ ; },
mesh = {*Zea mays/microbiology ; Animals ; *Plant Leaves/microbiology ; *Herbivory ; Spodoptera/physiology/microbiology ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Larva/microbiology/physiology ; Microbiota ; Phylogeny ; Pest Control, Biological ; Insecticides ; DNA, Bacterial/genetics ; },
abstract = {The "cry for help" hypothesis suggests that herbivore-stressed plants reshape their microbiome for defense, yet the speed and systemic characteristics of the phyllosphere bacterial response to chewing herbivores remain poorly understood. To address this, we examined how larval feeding by fall armyworm (Spodoptera frugiperda) affects the phyllosphere bacterial community within undamaged maize (Zea mays) leaves. We combined 16S amplicon sequencing, culturomics, and machine learning to characterize microbial community dynamics and culture-dependent recover candidate biocontrol strains from herbivory-altered taxa. Localized larval feeding on a single leaf induced rapid changes in the phyllosphere bacterial community of distal undamaged leaves within 12 h. Herbivory modified bacterial cooccurrence network topology. A significantly enriched OTU7 was isolated and identified as Enterobacter strain P12A2, which exhibited high toxicity against S. frugiperda. This study indicates that herbivory-induced systemic changes in the phyllosphere bacterial community of undamaged leaves may serve as a source for identifying novel biological resources. These findings provide a promising basis for developing microbiome-based strategies for sustainable pest management.},
}

*Zea mays/microbiology
Animals
*Plant Leaves/microbiology
*Herbivory
Spodoptera/physiology/microbiology
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Larva/microbiology/physiology
Microbiota
Phylogeny
Pest Control, Biological
Insecticides
DNA, Bacterial/genetics

@article {pmid42934476,
year = {2026},
author = {Smith, C and Garza, K and Azari, H and Vellers, H and Abdelrahman, M and Dhanasekara, CS and Salmon, AB and Liang, H and Fernandez, E and Musi, N and Massett, MP and Albracht-Schulte, K},
title = {Aerobic exercise training alters gastrointestinal microbiota and enhances exercise capacity in UM-HET3 mice.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {42934476},
issn = {2509-2723},
support = {P30 AG013319/AG/NIA NIH HHS/United States ; },
abstract = {Aerobic exercise attenuates age-related physiological decline, potentially through favorable modulation of gut microbiota diversity. The purpose of this study was to characterize aerobic exercise training (ET)-induced alterations in the gut microbiome of aging, genetically heterogeneous UM-HET3 mice and examine associations between microbial shifts and changes in body composition (body weight, lean mass, and fat mass) and exercise capacity (total work, distance, and duration). Male UM-HET3 mice were assigned to sedentary (SED; n = 16) or ET (n = 17) groups. ET mice trained 5 days per week for 4 weeks at 65% of maximal work output. Body composition and exercise capacity were assessed before and after the intervention. Post-intervention fecal samples were analyzed by 16S rRNA gene sequencing (SED, n = 13; ET, n = 13). ASVs were taxonomically classified using QIIME2 with the SILVA 138.1 reference database. Alpha and beta diversity analyses were conducted in R, and Spearman's correlations assessed relationships between phylum-level abundances and physiological outcomes. ET mice exhibited greater alpha diversity, with a higher median richness (219.5), although differences were not statistically significant. Principal coordinate analysis of beta diversity demonstrated significant separation between groups (P = 0.01), indicating distinct microbial community composition. At the phylum level, ET was associated with modest shifts in gut microbial composition, characterized by higher relative abundances of Firmicutes and Verrucomicrobiota and lower abundances of Bacteroidota and Desulfobacterota compared to SED mice. Collectively, these findings indicate that aerobic exercise training induces distinct shifts in gut microbiota composition in middle-aged UM-HET3 mice despite underlying genetic heterogeneity.},
}

@article {pmid42934723,
year = {2026},
author = {Rungrojn, A and Chaisiri, K and Thaipadungpanit, J and Batty, EM and Taweethavonsawat, P and Thempachana, O and Kongkaew, W and Morand, S and Blacksell, SD},
title = {Environmental and host-associated determinants of microbiome variation in the brown dog tick Rhipicephalus linnaei in Thailand.},
journal = {Parasites & vectors},
volume = {19},
number = {1},
pages = {},
pmid = {42934723},
issn = {1756-3305},
support = {JCPET02//Royal Society of Tropical Medicine and Hygiene/ ; MOTIP-ECIA 2024/001//MOTIP/ ; 315982/Z/24/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Thailand/epidemiology ; *Microbiota ; Dogs ; RNA, Ribosomal, 16S/genetics ; Female ; *Rhipicephalus/microbiology ; Male ; *Tick Infestations/veterinary/parasitology/epidemiology ; *Bacteria/classification/genetics/isolation & purification ; *Dog Diseases/parasitology/microbiology/epidemiology ; Phylogeny ; Coxiella/isolation & purification/genetics ; },
abstract = {BACKGROUND: The brown dog tick, Rhipicephalus linnaei, is an important vector of veterinary and zoonotic pathogens worldwide. The composition of the tick-associated microbiome may influence tick physiology, adaptation, and vector competence; however, factors shaping the microbiome of R. linnaei in Southeast Asia remain poorly understood.

METHODS: A total of 131 R. linnaei ticks were collected from dogs across five provinces in Thailand, representing different geographical and ecological settings. Full-length bacterial 16S rRNA sequencing was performed using Oxford Nanopore Technology to characterise bacterial community composition. Microbiome diversity and structure were evaluated by geographical region, sampling area (urban versus rural), blood-feeding status, tick sex, and developmental stage using alpha diversity metrics, Bray-Curtis dissimilarities, principal coordinates analysis, PERMANOVA, and ANCOM-BC2 differential abundance analysis.

RESULTS: The microbiome of R. linnaei was dominated by Candidatus Coxiella mudrowiae, which was detected in all ticks. Significant differences in bacterial community composition were observed between geographical regions, sampling areas, and blood-feeding status. Urban ticks showed lower bacterial diversity than rural ticks, and engorged ticks showed altered microbial diversity compared with feeding ticks. Sex- and developmental stage-associated differences were less pronounced. Differential abundance analysis identified several bacterial taxa associated with ecological and host-related factors. Putative tick-associated bacterial taxa, including Anaplasma and Ehrlichia species, were identified at low frequency.

CONCLUSIONS: This study demonstrates that geography, habitat type, and blood-feeding status are associated with variation in the microbiome of R. linnaei in Thailand. The findings provide new insights into the ecological factors shaping tick-associated bacterial communities in Southeast Asia and highlight the utility of full-length 16S rRNA Nanopore sequencing for vector microbiome investigations.},
}

Animals
Thailand/epidemiology
*Microbiota
Dogs
RNA, Ribosomal, 16S/genetics
Female
*Rhipicephalus/microbiology
Male
*Tick Infestations/veterinary/parasitology/epidemiology
*Bacteria/classification/genetics/isolation & purification
*Dog Diseases/parasitology/microbiology/epidemiology
Phylogeny
Coxiella/isolation & purification/genetics

@article {pmid42934726,
year = {2026},
author = {Auguste, M and Bosi, E and Saad, J and Oliveri, C and Doni, L and Marchese, A and Travers, MA and Toulza, E and Boulo, V and Courtay, G and Petton, B and Koechlin, H and Montagnani, C and Di Cesare, A and Corno, G and Andree, KB and Gairin, I and Furones, D and Broquard, C and Wegner, KM and Destoumieux-Garzón, D and Vezzulli, L},
title = {The resistome of European coastal environments revealed by high-resolution targeted metagenomics in oysters.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42934726},
issn = {2049-2618},
mesh = {Animals ; *Metagenomics/methods ; Europe ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Ostreidae/microbiology ; Metagenome ; Anti-Bacterial Agents/pharmacology ; Microbiota ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Antimicrobial resistance is a major global health threat, and the environment is increasingly recognised as a key reservoir of antibiotic resistance genes (ARGs). In marine ecosystems, filter-feeding organisms such as oysters are sentinel species that reflect the microbiological diversity of their environment. Here, we investigated the ARG content of the Pacific oyster Magallana gigas across four European coastal sites, contrasting anthropogenically impacted aquaculture sites (Bay of Brest, Ebro Delta, Thau lagoon) with natural oyster reefs (Sylt island). ARGs sequencing was enriched using a targeted probe-and-capture metagenomic approach employing 37,826 RNA baits covering over 2000 ARG sequences. Moreover, a novel bioinformatic pipeline ARGifier was specifically designed for sensitive, high-resolution detection and classification of ARGs in metagenomic samples dominated by host DNA.

RESULTS: This strategy was able to overcome limitations of cultivation-based methods and whole metagenomic sequencing, enabling the detection of more than 33,000 ARG sequences in the oyster resistome spanning over 450 genes distributed over 23 resistance classes. Reads assigned to ARGs represented 0.23% of all raw reads and 25.02% of host-depleted reads. Accordingly, comparison of targeted metagenomics and pool-seq analysis of cultured isolates (culturomics) in specific pathogen-free oysters revealed that metagenomics captured dominant, community-wide resistance determinants, whereas culturomics recovered a broader diversity of ARGs due to their presence in genomes of cultivable strains. The oyster resistome across the four farming sites was dominated by multidrug efflux systems associated with intrinsic and housekeeping-related mechanisms, suggesting an environmentally shaped resistance profile. Clinically relevant ARGs, including extended-spectrum Beta-Lactamase, carbapenem, colistin, and vancomycin resistance genes, were detected in low abundance at all sites, with higher enrichment in anthropogenically impacted areas. In addition, several ARGs were associated with plasmids, indicating mobilization potential. Taxonomic analysis revealed that a limited subset of bacteria, particularly Betaproteobacteria and Actinomycetes, carried a disproportionately high number of ARGs despite their low relative abundance in the oyster microbiome.

CONCLUSIONS: Overall, this study delivers a comprehensive inventory of ecologically and clinically relevant ARGs in European coastal environments, positioning farmed and wild oysters as sentinel organisms for monitoring antimicrobial resistance in coastal waters. Our findings highlight the circulation of ARGs within coastal marine ecosystems, which may act as reservoirs and potential sources of mobilisable antimicrobial resistance. Video Abstract.},
}

Animals
*Metagenomics/methods
Europe
*Bacteria/genetics/classification/drug effects/isolation & purification
*Ostreidae/microbiology
Metagenome
Anti-Bacterial Agents/pharmacology
Microbiota
Sequence Analysis, DNA

@article {pmid42934733,
year = {2026},
author = {Nichols, HL and Brettell, LE and Saldaña, MA and Hegde, S and Heinz, E and Vaccaro, K and Hughes, GL and Coon, KL},
title = {Vertical transmission of mosquito microbiota and its effects on offspring development.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42934733},
issn = {2049-2618},
mesh = {Animals ; *Aedes/microbiology/growth & development ; Female ; Larva/microbiology/growth & development ; *Bacteria/classification/isolation & purification/genetics ; *Gastrointestinal Microbiome ; Infectious Disease Transmission, Vertical ; *Mosquito Vectors/microbiology ; },
abstract = {BACKGROUND: The mosquito's gut microbiota plays a crucial role in determining its capacity to transmit harmful viruses and parasites. Accordingly, manipulating mosquito gut microbiota is a promising avenue for reducing the transmission of mosquito-borne human pathogens. A successful microbial control campaign will require a thorough understanding of how bacteria are transmitted within mosquito populations. In two parallel but complementary studies using the yellow fever mosquito Aedes aegypti as a focal host species, we surveyed the vertical transmission of bacteria from individual mothers to cohorts of offspring maintained in a closed system.

RESULTS: Laboratory- and field-derived mothers deposited bacteria that support offspring development, and the relative abundances of commonly transmitted taxa correlated with offspring fitness. Maternally transmitted bacteria were detected in both larval and adult offspring, and the relative abundances of specific taxa differed between life stages. Microbiota composition in adult offspring closely resembled that of mothers, despite dramatic shifts in the relative abundance of specific community members during the larval stage. Variability in microbiota composition among offspring was also greater than variability across the population of egg-laying mothers. Eggs that underwent a period of desiccation before hatching produced larval communities dominated by endospore-forming bacteria that were rare in maternal samples.

CONCLUSIONS: Overall, our results demonstrate vertical transmission of mosquito-associated microbiota across generations, including bacterial taxa that could potentially be leveraged for mosquito and mosquito-borne disease control Video Abstract.},
}

Animals
*Aedes/microbiology/growth & development
Female
Larva/microbiology/growth & development
*Bacteria/classification/isolation & purification/genetics
*Gastrointestinal Microbiome
Infectious Disease Transmission, Vertical
*Mosquito Vectors/microbiology

@article {pmid42934758,
year = {2026},
author = {Skonieczna, B and Nazarko, N and Godlewska, E and Wasiluk, N and Czech, EK and Wilczewska, AZ and Regulska, E and Car, H and Niemirowicz-Laskowska, K},
title = {Nanoparticles and their significant risks: a comprehensive review of toxicological and regulatory perspectives.},
journal = {Journal of nanobiotechnology},
volume = {24},
number = {1},
pages = {},
pmid = {42934758},
issn = {1477-3155},
support = {NCN/2019/35/B/ST5/03391//Narodowe Centrum Nauki/ ; PRTR-C17.I1//Advanced Materials programme/ ; B.SUB.25.215//Uniwersytet Medyczny w Bialymstoku/ ; B.SUB.25.257//Uniwersytet Medyczny w Bialymstoku/ ; },
mesh = {Humans ; *Nanoparticles/toxicity/chemistry ; Animals ; Gastrointestinal Microbiome/drug effects ; Oxidative Stress/drug effects ; Tissue Distribution ; Drug Carriers/toxicity/chemistry ; Liver/drug effects ; },
abstract = {BACKGROUND: Nanoparticles are increasingly important as drug carriers due to their ability to enhance solubility, stability, and selective delivery of therapeutic agents, enabling accumulation at disease sites, interaction with cell-surface receptors, and penetration of biological barriers such as the blood-brain barrier. Despite these numerous advantages, their potential toxicity remains a key obstacle to safe clinical use. Emerging evidence suggests that nanoparticles may alter the composition of the gut microbiome, potentially affecting metabolism, immune homeostasis, neurobehavioral pathways, and reproductive function by influencing hormonal regulation and fertility.

AIM OF THE REVIEW: This review provides a detailed analysis of the toxicological aspects of nanoparticles, including cytotoxicity, oxidative stress, potential genotoxicity, and effects on immune responses such as inflammation and immunosuppression. In vivo biodistribution, organ accumulation, and effects on liver enzymes are also discussed, emphasizing the role of the liver in drug metabolism and the potential risk of impaired detoxification. Additionally, the review examines the effects of nanoparticles on the gut microbiome and reproductive system. It emphasizes their capacity to disrupt the microbial balance, the intestinal barrier integrity, and reproductive hormone homeostasis. We discuss regulatory issues for nanotechnology-based medicinal products, emphasizing the importance of standardized testing protocols and long-term safety assessments. Finally, future perspectives and developmental directions for nanoparticles have been highlighted.

CONCLUSION: This review highlights the need for a comprehensive understanding of nanoparticle toxicity mechanisms, which is crucial for their safe design and further development in nano-based therapy.},
}

Humans
*Nanoparticles/toxicity/chemistry
Animals
Gastrointestinal Microbiome/drug effects
Oxidative Stress/drug effects
Tissue Distribution
Drug Carriers/toxicity/chemistry
Liver/drug effects

@article {pmid42934845,
year = {2026},
author = {Li, Y and Wang, W and Liu, W},
title = {CNTN4: A Possible Candidate Gene for Microbiota-Gut-Brain Axis in Autism Spectrum Disorders and Attention-Deficit/Hyperactivity Disorder.},
journal = {Autism : the international journal of research and practice},
volume = {},
number = {},
pages = {13623613261493643},
doi = {10.1177/13623613261493643},
pmid = {42934845},
issn = {1461-7005},
abstract = {The gut microbiota plays a significant role in autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD), though findings vary substantially across studies. Using gut microbiome data from a genome-wide association study of 5,959 participants and summary statistics from 46,351 ASD and 55,374 ADHD cases, we conducted bidirectional Mendelian randomization (MR) analyses with inverse variance weighting as the primary method. Reverse MR analysis assessed potential reverse causality. We annotated single nucleotide polymorphisms (SNPs) with SNP-nexus to identify associated genes, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to characterize their functional roles. Seventeen gut microbial taxa showed causal associations with ASD risk, while 27 were linked to ADHD. Reverse MR analysis revealed associations between aSD and species Desulfovibrio piger as well as species Bacillus U, but no reverse causality was detected for ADHD. Biological annotation identified five novel conserved genes in host-microbiome interactions shared by ASD and ADHD, with CNTN4 emerging as a common candidate gene. These findings support a potential causal relationship between gut microbiota and ASD/ADHD risk while uncovering novel conserved genes implicated in host-microbiome interactions for both disorders.Lay AbstractDistinct gut microbiota profiles were observed in individuals with ADHD and ASD. Seventeen microbial species showed significant associations with ASD, while 27 were linked to ADHD. CNTN4 emerged as a potential candidate gene shared across both neurodevelopmental conditions and host-microbiome interactions.},
}

@article {pmid42934883,
year = {2026},
author = {Zhang, J and Li, P and Wu, H and Zhang, Z and Wang, Z and Liu, Y and Xu, M and Chen, F and Yang, Y},
title = {Oral Irrigation and Microbiome Remodeling after Oral Cancer Reconstruction.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345261489246},
doi = {10.1177/00220345261489246},
pmid = {42934883},
issn = {1544-0591},
abstract = {Patients with oral cancer undergoing free flap reconstruction face significant surgical trauma, making the prevention of postoperative wound infection and the maintenance of oral microecological balance critical. This study systematically evaluated oral microbiome changes before and after surgery and assessed the effectiveness of postoperative oral irrigation using 2 different regimens. In an exploratory randomized controlled trial, 60 patients were assigned to receive oral irrigation with either bipolar water or a combination of hydrogen peroxide and sodium bicarbonate solution. Saliva and irrigation samples were collected at 7 time points, preoperatively and before and 5 minutes after oral irrigation on postoperative days 1, 4, and 7, and analyzed using specialized sequencing techniques to determine microbial abundance and diversity. Clinical outcomes, including wound infection rates and patient comfort, were also recorded. The results indicated that surgical treatment reduced the diversity of the oral microbiota and altered its composition. Before surgery, the oral cavity was dominated by potentially pathogenic taxa, which shifted toward oral resident microorganisms postoperatively. Continued oral irrigation promoted a transition from an unstable, anaerobic-enriched state toward a relatively stable community structure dominated by facultative anaerobes. While no differences were observed between the 2 groups regarding wound infection rates or microbial composition, the bipolar water group reported higher patient comfort and required shorter irrigation times. Furthermore, the bipolar water group maintained more stable microbial diversity, whereas the hydrogen peroxide group exhibited more pronounced fluctuations and higher fungal detection rates. In conclusion, surgery induces early microbial imbalance, but staged oral irrigation facilitates the stabilization of the oral microecosystem. Bipolar water is an effective alternative for perioperative care, helping to maintain microbial stability while improving the patient experience.},
}

@article {pmid42935490,
year = {2026},
author = {Tomita, K and Nakano, T and Morozumi, S and Okahashi, N and Arita, M},
title = {Microbiome-dependent phytosterol sulfates production and tissue distribution in mice.},
journal = {iScience},
volume = {29},
number = {11},
pages = {117883},
pmid = {42935490},
issn = {2589-0042},
abstract = {Microbial biotransformation of dietary lipids, such as cholesterol, influences host homeostasis. Despite extensive studies on animal sterols in host-microbiota interactions, the role of phytosterols in homeostasis remains unclear. In this study, we characterized phytosterol sulfates as microbiota-derived metabolites using untargeted lipidomic data mining. The levels of sitosterol sulfate (SIS), campesterol sulfate, and stigmasterol sulfate, the three major phytosterol sulfates, along with coprostanol sulfate, were reduced in the feces of germ-free mice compared with those of specific pathogen-free mice. We characterized a series of Bacteroidota species and their sterol sulfotransferases that produced phytosterol sulfates more efficiently than mammalian enzymes. Furthermore, SIS significantly accumulated in host tissues in a microbiota- and age-dependent manner, whereas unconjugated phytosterols were mostly undetectable. Our work provides insights into host-microbiome interactions via gut bacterial phytosterol metabolism.},
}

@article {pmid42935576,
year = {2026},
author = {Lee, SH and Na, SI and Park, SC and Cho, BR and Lee, BK and Cho, YJ and Cho, H and Youk, HJ and Ryu, DR},
title = {Effect of a potassium-competitive acid blocker on the gut microbiota in patients undergoing percutaneous coronary intervention: a randomized pilot study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1942212},
pmid = {42935576},
issn = {2235-2988},
mesh = {Humans ; Pilot Projects ; Female ; *Percutaneous Coronary Intervention/adverse effects ; Male ; *Gastrointestinal Microbiome/drug effects ; *Proton Pump Inhibitors/administration & dosage/adverse effects/therapeutic use ; Prospective Studies ; Aged ; Middle Aged ; *Pantoprazole/administration & dosage/adverse effects/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Dysbiosis/chemically induced ; Gastrointestinal Hemorrhage/prevention & control ; },
abstract = {BACKGROUND AND AIM: Proton pump inhibitors (PPIs) are routinely used in patients undergoing percutaneous coronary intervention (PCI) to prevent gastrointestinal bleeding associated with dual-antiplatelet therapy (DAPT). However, long-term PPI use has been linked to gut microbiota dysbiosis. Tegoprazan, a potassium-competitive acid blocker (P-CAB), may exert distinct effects on the gut microbiome. This study compared the longitudinal effects of tegoprazan and pantoprazole on gut microbiota composition in patients with angina undergoing PCI.

METHODS: This prospective, randomized, controlled pilot study randomized 38 patients 1:1:1 to tegoprazan 50 mg once daily, pantoprazole 40 mg once daily, or no acid-suppressive therapy for 24 weeks. Five participants did not provide baseline fecal samples, and nine discontinued participation before week 24. Thus, 24 participants with paired baseline and week-24 fecal samples were included in the final analysis. Fecal samples were analyzed using 16S rRNA gene sequencing.

RESULTS: No drug-related adverse events or gastrointestinal bleeding occurred in any group. Observed amplicon sequence variant (ASV) richness was significantly higher at week 24 than at baseline in the overall cohort (p = 0.003) and P-CAB group (p = 0.016), whereas the Shannon index showed no significant changes. Paired PERMANOVA with permutations restricted by patient ID revealed significant differences in Bray-Curtis beta diversity between baseline and week 24 in the P-CAB group (R² = 0.070, p = 0.031) and PPI group (R² = 0.059, p = 0.008), but not in the no acid-suppressive therapy group (R² = 0.021, p = 0.691). In the formal cross-arm analysis, the treatment group-by-visit interaction was not significant for Bray-Curtis beta diversity (R² = 0.021, pseudo-F = 0.505, p = 0.270). Although nominal within-arm taxonomic changes were observed, no treatment group-by-visit interaction survived Benjamini-Hochberg correction in ANCOM-BC2.

CONCLUSION: Tegoprazan was well tolerated, with no drug-related adverse events or gastrointestinal bleeding during the 24-week follow-up. Both acid-suppressive treatment groups showed modest longitudinal microbiome changes. The taxon-level findings were exploratory and hypothesis-generating and should not be interpreted as definitive evidence of treatment-specific differential effects. Larger, adequately powered studies are required to confirm these observations.},
}

Humans
Pilot Projects
Female
*Percutaneous Coronary Intervention/adverse effects
Male
*Gastrointestinal Microbiome/drug effects
*Proton Pump Inhibitors/administration & dosage/adverse effects/therapeutic use
Prospective Studies
Aged
Middle Aged
*Pantoprazole/administration & dosage/adverse effects/therapeutic use
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Dysbiosis/chemically induced
Gastrointestinal Hemorrhage/prevention & control

@article {pmid42935596,
year = {2026},
author = {Kool, J and Konstanti, P and van Dijken, H and Chu, MLJN and Nanlohy, NM and Bijvank, E and van Woudenbergh, E and van Beek, J and van Baarle, D and Fuentes, S},
title = {Linking nasopharyngeal and oropharyngeal microbiota to immune responses during influenza-like illness in an aging population.},
journal = {iScience},
volume = {29},
number = {11},
pages = {117929},
pmid = {42935596},
issn = {2589-0042},
abstract = {Older adults are vulnerable to influenza-like illness (ILI). To study how infection shapes the respiratory microbiota, we profiled nasopharyngeal (NP) and oropharyngeal (OP) communities alongside local immune mediators in adults aged 60-88, comparing asymptomatic, ILI, and recovery states. NP communities clustered into three community state types (CSTs): Moraxella-dominated (CST-1), Haemophilus/Streptococcus/Staphylococcus-associated (CST-2), and Corynebacterium/Dolosigranulum-dominated (CST-3). During infection, compositional shifts were restricted to the NP niche, where CST-1 and CST-2 were more frequent. Streptococcus, Haemophilus and Moraxella were positively associated with inflammatory and interferon-related mediators, including IL-6, CXCL9 and CXCL10, while Corynebacterium showed negative associations. Immune activation was strong in the NP but limited in the OP, and stayed above healthy levels at follow-up, suggesting incomplete recovery. NP composition was also associated with symptom burden, viral and bacterial co-detection and smoking status. These site-specific microbiota-immune relationships identify the nasopharynx as the primary site of immune modulation during ILI in older adults.},
}

@article {pmid42935632,
year = {2026},
author = {Bae, YJ and Daily, JW and Park, S},
title = {Gut Microbiota as a Mechanistic Nexus between Type 2 Diabetes and Alzheimer's Disease: Insulin Resistance, Neuroinflammation, and Functional Food Strategies.},
journal = {Preventive nutrition and food science},
volume = {31},
number = {5},
pages = {},
pmid = {42935632},
issn = {2287-1098},
abstract = {Type 2 diabetes mellitus (T2DM) and Alzheimer's disease (AD) share substantial pathological overlap, including brain-specific insulin resistance driven by impaired insulin receptor substrate-1/phosphoinositide 3-kinase/protein kinase B signaling, glycogen synthase kinase-3β dysregulation, tau hyperphosphorylation, and amyloid-β accumulation. Brain-insulin resistance is a key mechanistic link between peripheral metabolic dysfunction and neurodegeneration, although the upstream regulatory pathways remain incompletely defined. Gastrointestinal depletion of butyrate-producing microbial taxa and enrichment of pro-inflammatory genera have been independently documented in T2DM and AD. Gut microbiota dysbiosis propagates insulin resistance through at least five pathways: short-chain fatty acid depletion, lipopolysaccharide (LPS)-mediated endotoxemia, bile acid dysregulation, tryptophan-kynurenine imbalance, and vagus nerve disruption. Critically, LPS translocation and kynurenine-driven neurotoxicity propagate AD-relevant neuroinflammation independently of peripheral metabolic dysfunction, implicating a bidirectional gut-brain mechanism. These risks are amplified in Asian populations, who exhibit a lower pancreatic β-cell mass and attenuated insulin secretion that confer disproportionate vulnerability to glucotoxic cycling and its neurological complications. Such a population-specific dimension remains largely absent from reviews. Against this backdrop, traditional Asian fermented foods (chungkookjang, kimchi, and natto) and plant-derived functional ingredients (Eucommia ulmoides, gooseberry, and black garlic) have a preclinical capacity to restore microbial balance, attenuate insulin resistance, and exert neuroprotection. This review integrates these strands into a unified mechanistic and translational framework, positioning gut microbiota modulation through culturally grounded dietary strategies as a tractable approach to reducing the converging burdens of T2DM and AD in Asians.},
}

@article {pmid42935770,
year = {2026},
author = {Wang, S and Chen, D and Yang, D and Gao, L and Zhang, Y},
title = {Modulation of Toll-like receptor signaling by intestinal bacteria in colorectal cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1963456},
pmid = {42935770},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/immunology/metabolism/pathology ; *Toll-Like Receptors/metabolism ; *Signal Transduction ; Tumor Microenvironment/immunology ; *Gastrointestinal Microbiome/immunology ; Animals ; *Bacteria/metabolism/immunology ; Dysbiosis ; },
abstract = {The gut microbiota contributes to intestinal homeostasis through dynamic interactions with epithelial, immune and stromal cells. Disruption of the balance, often termed dysbiosis, has been associated with colorectal cancer (CRC). At the same time, selected commensal bacteria have shown protective effects. Toll-like receptors (TLRs) provide an important molecular interface through which host cells detect bacterial components and initiate cellular responses. This Mini Review examines current evidence that intestinal bacteria and their products modulate TLR signaling in CRC, with effects that may promote or restrain tumor development. The reported mechanisms involve CRC cells as well as immune and stromal compartments within the tumor microenvironment. The available evidence does not support assigning a fixed biological effect to a bacterial species or TLR. Instead, the reported outcomes appear to vary with the nature of the bacterial stimulus, the responding cell and the disease setting. Resolving this context dependence may clarify how host cells translate bacterial stimuli through TLRs into responses that influence CRC progression and treatment response.},
}

Humans
*Colorectal Neoplasms/microbiology/immunology/metabolism/pathology
*Toll-Like Receptors/metabolism
*Signal Transduction
Tumor Microenvironment/immunology
*Gastrointestinal Microbiome/immunology
Animals
*Bacteria/metabolism/immunology
Dysbiosis

@article {pmid42935883,
year = {2026},
author = {Zhang, L and Jiang, T and Cao, R and Han, L and Ni, L},
title = {The liver-gut-bone axis in hepatic osteodystrophy: mechanisms, clinical evidence and therapeutic perspectives.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1935323},
pmid = {42935883},
issn = {2235-2988},
mesh = {Humans ; *Liver/pathology/metabolism ; *Bone and Bones/pathology/metabolism ; *Liver Diseases/complications ; Gastrointestinal Microbiome ; Animals ; Dysbiosis ; *Bone Diseases, Metabolic/etiology/therapy ; },
abstract = {Hepatic osteodystrophy (HOD) is an important but under-recognized complication of chronic liver disease (CLD), characterized by reduced bone mass, impaired bone microarchitecture and increased fragility fracture risk. Its skeletal phenotype and pathogenic mechanisms vary substantially according to CLD aetiology and disease stage. In metabolic dysfunction-associated steatotic liver disease (MASLD), skeletal risk is closely associated with metabolic dysfunction and hepatic fibrosis; alcohol-associated liver disease combines direct ethanol-related osteotoxicity with malnutrition and endocrine abnormalities; viral hepatitis-associated bone disease is influenced by persistent inflammation, disease stage and antiviral exposure; and cholestatic liver diseases are characterized by disrupted bile acid homeostasis, fat-soluble vitamin malabsorption and impaired bone formation. The liver-gut-bone axis provides an integrative framework linking these disease-specific features. Gut dysbiosis, intestinal barrier dysfunction, microbial translocation and altered metabolites, including short-chain fatty acids, bile acids and tryptophan-derived metabolites, may contribute to abnormal bone remodelling through inflammatory, metabolic and nutritional pathways. Cirrhosis further amplifies skeletal injury through sarcopenia, malnutrition and endocrine dysfunction. However, human evidence establishing a complete causal liver-gut-bone pathway remains limited. Current management should therefore focus on treatment of the underlying liver disease, fracture-risk assessment, nutritional and lifestyle interventions and evidence-based anti-osteoporotic therapy, while microbiota- and metabolite-targeted strategies remain investigational. Future prospective studies integrating microbiome and metabolomic profiling with bone turnover, microarchitecture and fracture outcomes are needed to clarify causal mechanisms and improve individualized management of CLD-associated HOD.},
}

Humans
*Liver/pathology/metabolism
*Bone and Bones/pathology/metabolism
*Liver Diseases/complications
Gastrointestinal Microbiome
Animals
Dysbiosis
*Bone Diseases, Metabolic/etiology/therapy

@article {pmid42936070,
year = {2026},
author = {Jiang, P and Yang, X and Zhang, C and Li, Y and Xu, C},
title = {Mendelian randomization of gut microbiota and exploratory testing of preventive effect of commercial Rothia mucilaginosa in constipated mice.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1941480},
pmid = {42936070},
issn = {1664-302X},
abstract = {Constipation is linked to gut microbiota dysbiosis, but causal microbial contributors and tractable bacterial interventions remain incompletely defined. This study first performed two-sample Mendelian randomization using Dutch Microbiome Project gut-microbiome Genome-Wide Association Study (GWAS) data (N = 7,738) and a European constipation GWAS (N = 411,623) to identify gut taxa linked to constipation. Then, in vitro metabolomics and a loperamide-induced constipation mouse model were used in male C57BL/6 mice to exploratorily test whether the commercial Rothia mucilaginosa strain BNCC363031 prevents loperamide-induced constipation. In an exploratory two-sample MR screen across 207 gut taxa, genetically predicted Rothia was nominally associated with lower constipation risk [odds ratio (OR) = 0.916, p = 0.0041], and the species-level Rothia mucilaginosa showed a concordant nominal protective association (OR = 0.921, p = 0.0232). In mice (n = 8 per group), preventive gavage partially restored loperamide-suppressed defecation: the cross-day mean fecal pellet count in the last 3 h per day was higher in the Rothia mucilaginosa group (RG) than in model controls (MCs) (7.94 vs. 4.41; p = 0.0306) but lower than in normal controls (NCs) (13.16; p = 0.00162), whereas body weight; small-intestinal transit; and immunohistochemical zonula occludens-1 (ZO-1), Claudin-1, and mucin 2 (MUC2) H-scores were unchanged. A fecal 16S V4 signal corresponding to R. mucilaginosa was detected at a very low abundance in only 2/8 RG mice; in vitro metabolomics identified candidates of secreted metabolites, including acetic acid. This study provides a reference for research on Rothia mucilaginosa in the context of constipation.},
}

@article {pmid42936086,
year = {2026},
author = {Gosain, M and Kaur, M and Talukdar, D and Tanwar, S and Jana, P and Karmakar, SP and Verma, J and Bakshi, S and Kamboj, K and Verma, P and Pareek, M and Raghavan, S and Kshetrapal, P and Bhatnagar, S and Bhattacharya, J and Garg, PK and Wadhwa, N and Das, B},
title = {Upper respiratory virome signatures reflect COVID-19 severity and post-recovery shifts.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1925299},
pmid = {42936086},
issn = {1664-302X},
abstract = {INTRODUCTION: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection profoundly affects the upper respiratory tract, yet the dynamics of the resident virome across different stages of Coronavirus Disease 2019 (COVID-19) and recovery remain poorly understood.

METHODS: This study profiled alterations in the virome and microbiome in 143 SARS-CoV-2-positive adults, stratified by disease severity (Non-Severe, Severe, Critical), compared with 96 RT-PCR-negative controls. Nasal and oral swabs underwent targeted viral enrichment and next-generation sequencing, followed by virome profiling.

RESULTS: The respiratory virome of SARS-CoV-2-positive individuals was dominated by SARS-CoV-2, with co-detected viruses such as Human Mastadenovirus C, which increased with disease severity and persisting post-recovery. Alpha diversity was highest in Non-Severe cases and declined in Severe and Critical groups, suggesting increasing disruption of the virome with disease severity. Beta diversity showed clear separation between controls and cases, and across severity levels. LEfSe identified distinct viral signatures differentiating infection status, and logistic regression of key viral taxa accurately classified Critical versus post-recovery samples (AUC = 0.91). Although the study focused on viruses, bacterial taxa including Rothia mucilaginosa and Haemophilus parahaemolyticus were also detected with severity-linked variation, highlighting viral-bacterial interactions. Longitudinal paired analysis revealed consistent post-recovery enrichment of Streptococcus-specific bacteriophages across all severity groups, suggesting restoration of Streptococcus-associated phage dynamics during convalescence.

DISCUSSION: Overall, this study reveals SARS-CoV-2-associated alterations in the respiratory virome and microbiome and highlights specific microbial taxa with potential as biomarkers for disease severity and post-infection recovery.},
}

@article {pmid42936144,
year = {2026},
author = {Zhang, Y and Bian, N and Dong, Z and Ren, B and Li, J},
title = {From correlation to causation: dissecting the detection methodologies of oral bacterial-fungal crosstalk in health and disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1937704},
pmid = {42936144},
issn = {1664-302X},
abstract = {In the oral microecosystem, cross-kingdom interactions between bacteria and fungi are pivotal ecological events that determine the equilibrium between oral health and disease. Historically, technical limitations have confined research to describing correlations in microbial community composition, hindering the elucidation of underlying pathogenic mechanisms. This review aims to systematically outline the evolution of detection technologies for oral bacterial-fungal interactions and critically discuss the paradigm shift from identifying "associative correlations" to deciphering "causal mechanisms." The literature search encompassed studies ranging from traditional culture and molecular identification to high-throughput sequencing for ecological network construction, as well as cutting-edge multi-omics integration and high-resolution imaging technologies. Beyond cataloguing technical advances, we critically evaluate the level of causal inference supported by each methodological class, with particular attention to temporality, confounding, ecological simplification, and the need for perturbational validation in disease-relevant models. Representative studies are used to illustrate how evidence can progress from co-occurrence and spatial proximity to functional dependency and mechanism.},
}

@article {pmid42936186,
year = {2026},
author = {Lahtinen, E and Hugerth, LW and Edfeldt, G and Säfholm, A and Kornfält, S and Strevens, H and Schuppe-Koistinen, I},
title = {Effect of pHyph, A novel antibiotic-free treatment, on bacterial vaginosis symptoms and vaginal microbiome composition.},
journal = {European journal of obstetrics & gynecology and reproductive biology: X},
volume = {32},
number = {},
pages = {100497},
pmid = {42936186},
issn = {2590-1613},
abstract = {BACKGROUND: Bacterial vaginosis (BV) is the most prevalent vaginal infection among reproductive-age women and is associated with increased susceptibility to gynecological complications. Current antibiotic treatments achieve high initial cure rates but show high rates of recurrence, partly due to their inability to remove persistent biofilms. pHyph is a novel, non-antibiotic treatment that lowers vaginal pH, promoting Lactobacillus growth and biofilm disruption.

OBJECTIVE: To evaluate the immediate and long-term effects of pHyph on the vaginal microbiome, BV resolution, and symptom reduction.

STUDY DESIGN: In a randomized, controlled, partially blinded study, 61 women with clinically diagnosed BV were randomized to immediate (IT, n = 35) or delayed (DT, n = 26) treatment. Vaginal swabs were collected before treatment, after 6 days, and during maintenance to Day 70. Microbiome composition was analyzed using a qPCR panel targeting 47 bacterial and 6 fungal species.

RESULTS: Compared to controls, pHyph reduced the abundance of multiple BV-associated species and increased Lactobacillus iners following 6-day treatment (median 8.96 ×10[3] [Q1-Q3: 3.10 ×10[3]-2.72 ×10[4]] vs. median 9.44 × 10² [Q1-Q3: 0.00-4.29 × 10 ³] normalized qPCR counts, p < 0.05). Additionally, pHyph reduced BV-related symptoms, particularly fishy odor (p < 0.05). Treatment promoted a shift to CST III microbiome composition, and maintenance dosing was associated with sustained Lactobacillus abundance up to Day 70.

CONCLUSIONS: pHyph shows potential as an alternative BV treatment by reducing BV-associated pathogens while promoting lactobacilli. Extended dosing may enhance microbiome stability.},
}

@article {pmid42936198,
year = {2026},
author = {Han, Y and Liu, J and Song, C and Fu, L and Gu, Y and Zeng, Y and Zou, Z},
title = {Multi-omics insights into immune dysregulation and candidate biological programs in kawasaki disease: toward precision immunomodulation.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1960681},
pmid = {42936198},
issn = {2296-2360},
abstract = {Kawasaki disease (KD) is an immune-mediated pediatric vasculitis characterized by dynamic interactions among genetic susceptibility, innate and adaptive immune activation, endothelial dysfunction, and vascular remodeling. Although intravenous immunoglobulin (IVIG) therapy substantially reduces coronary complications, 10%-20% of patients show persistent or recurrent fever after initial IVIG treatment, and reliable clinically validated molecular approaches for diagnosis, treatment-response prediction, and coronary-risk stratification remain unavailable. Recent advances in multi-omics technologies, including genomics, epigenomics, transcriptomics, single-cell sequencing, proteomics, metabolomics, and microbiome profiling, have expanded our understanding of KD-associated immune dysregulation. However, the clinical interpretation of these molecular findings remains challenging because of limited cohort sizes, heterogeneous control populations, treatment-related confounding, and insufficient external validation. In this review, we integrate evidence across multiple molecular layers and propose a framework in which current KD multi-omics findings converge into candidate biological programs rather than fixed molecular subtypes. These programs may represent temporally dynamic biological states along a shared inflammatory trajectory, influenced by disease phase, cellular composition, genetic background, and treatment exposure. Synthesized from convergent multi-omics evidence rather than derived from formal molecular classification, these candidate biological programs include myeloid inflammatory activation characterized by S100A8/A9 and IL-1/NF-κB signaling, interferon-associated immune responses, and vascular injury/remodeling responses involving endothelial activation and extracellular matrix regulation. Current evidence supports biologically meaningful molecular programs that may contribute to clinical heterogeneity, but prospective validation is required before molecular signatures can be applied as clinical classifiers or treatment-selection tools. Integrating multi-omics approaches with functional validation, longitudinal sampling, and multicenter studies may facilitate the development of precision immunomodulation strategies for Kawasaki disease.},
}

@article {pmid42936271,
year = {2026},
author = {Ben Said, M and Selmi, R and Belkahia, H},
title = {Vector-borne zoonotic bacteria in Tunisia: from fragmented data to an integrated One Health surveillance framework.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1951493},
pmid = {42936271},
issn = {1664-302X},
abstract = {Vector-borne and vector-associated bacterial zoonoses represent an important component of infectious disease epidemiology in Tunisia. This review synthesizes available evidence on major bacterial groups, including Rickettsia, Bartonella, Anaplasma, Ehrlichia, Borrelia, Coxiella burnetii, and other arthropod-associated bacteria, using a One Health framework integrating human, animal, vector, wildlife, and environmental compartments. The available evidence reveals heterogeneous levels of knowledge across bacterial taxa. Rickettsia represents the most established tick-associated zoonotic system, with Rickettsia conorii as the main confirmed human pathogen, while additional species have been detected mainly in arthropods or animal-associated settings. Bartonella has a significant clinical association with blood culture-negative endocarditis, whereas other bacterial groups show predominantly animal- or vector-associated evidence. Coxiella burnetii remains a major zoonotic concern linked to livestock, camels, reproductive materials, and environmental exposure. For Borrelia, Anaplasma, and Ehrlichia, substantial evidence of circulation exists in vectors and animals, but human clinical relevance remains incompletely characterized. Across bacterial groups, a recurrent limitation is the imbalance between molecular detection in vectors or animal hosts and confirmed evidence of transmission or human disease. Detection of bacterial DNA should therefore be interpreted cautiously and not considered equivalent to infection, reservoir competence, or vectorial transmission. Additional arthropod-associated bacteria identified through microbiome studies require further investigation to clarify their ecological significance. The Tunisian evidence base demonstrates active circulation of diverse vector-associated bacteria but remains fragmented across clinical, veterinary, entomological, and ecological domains. Strengthening integrated One Health surveillance through coordinated human diagnosis, animal sentinel systems, vector monitoring, environmental investigations, and advanced molecular approaches is essential to better assess zoonotic risks in Tunisia and the wider North African-Mediterranean region.},
}

@article {pmid42936295,
year = {2026},
author = {Yuan, H and Zhao, M and Wang, Y and Shen, C and Liu, D and Wang, C and Liu, J},
title = {Gut microbiota, microbial metabolites, and mucosal barrier dysfunction in benign anorectal disorders and ulcerative colitis: shared mechanisms, clinical links, and precision interventions.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1979206},
pmid = {42936295},
issn = {2296-858X},
abstract = {Benign anorectal disorders and ulcerative colitis (UC) are typically managed as separate clinical conditions, despite growing recognition of overlapping pathophysiological features. Constipation, hemorrhoidal disease, anal fistula and colonic mucosal inflammation may converge on partially shared molecular pathways involving microbial dysbiosis, altered microbial metabolite generation, epithelial barrier impairment, immune activation, stromal remodeling and dysregulated tissue repair, although the strength of mechanistic evidence varies substantially among these conditions. This review synthesizes advances from the past decade to propose a translational molecular medicine framework for investigating potential molecular connections among anatomically distinct anorectal and colonic disorders, without assuming shared causal origins. Clinical and pathological associations between disordered defecation, hemorrhoidal vascular remodeling, fistula persistence and UC are contextualized alongside current insights into gut and anorectal microbiota dysbiosis, short-chain fatty acid signaling, bile acid metabolism, tryptophan metabolite activity, gas-producing microbial communities, mucus biology, tight junction function, innate and adaptive immune responses, and fibro-inflammatory repair processes. Integrating microbiome profiling, metabolomics, transcriptomics, single-cell and spatial analyses with causal inference provides a cross-disease framework for resolving convergent molecular states associated with recurrence, healing and therapeutic response. By moving beyond disease-by-disease description, this strategy may uncover biomarkers and actionable pathways otherwise overlooked, supporting mechanism-informed prevention, perioperative optimization and individualized intervention across anorectal disorders and inflammatory bowel disease (IBD).},
}

@article {pmid42936303,
year = {2026},
author = {Kamijo, TC and Tsuji, M},
title = {Early life stress, lower urinary tract dysfunction, and respiratory disease: a proposed shared-mechanism framework.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1929695},
pmid = {42936303},
issn = {1664-042X},
abstract = {Early life stress (ELS) has been associated with persistent dysfunction across multiple physiological systems in humans, and maternal separation produces such dysfunction in rodent models. The respiratory and urinary tracts appear functionally distinct, yet both may be influenced by candidate overlapping neuro-endocrine, immune, and epigenetic consequences of ELS - a convergence that has received little attention because respiratory medicine, urology, and stress physiology have largely studied these effects in isolation. Our starting point is an experimental observation: in maternal separation rats, bladder-directed low-intensity extracorporeal shock wave therapy (Li-ESWT) reduced the elevated bladder weight and also improved anxiety-like behavior, showing that an intervention directed toward the bladder - regional rather than strictly organ-restricted - can be followed by change in a central behavioral endpoint, although the route, direction, and causality were not established. If peripheral-to-central communication of this kind is general, organs other than the bladder that may share elements of ELS-related programming could be similarly accessible. The airway is a plausible candidate: in mouse studies of maternal separation, ELS suppresses regulatory T-cell development and biases airway immunity toward Th2 responses, while separate rat studies report bladder overactivity, altered voiding, and anxiety-like behavior. The two have not been measured in the same animals. We review the candidate shared substrates - hypothalamic-pituitary-adrenal (HPA) axis dysregulation, chronic low-grade inflammation (e.g. IL-6, TNF), autonomic/vagal imbalance, microbiome-mediated immune programming along the gut-lung and gut-bladder axes, and epigenetic reprogramming - distinguishing throughout what has been shown in humans from what rests on rodent models. We propose a "psycho-neuro-immune-urinary-respiratory nexus" as a testable framework rather than an established entity, and outline the experimental models, biomarkers, and integrated therapeutic strategies needed to test it.},
}

@article {pmid42936305,
year = {2026},
author = {Akpor, OB and Ajinde, AO},
title = {Gut microbiota- and probiotic-derived bioactive metabolites: mechanisms, evidence, and therapeutic potential in metabolic disorders.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1953273},
pmid = {42936305},
issn = {2235-2988},
mesh = {Humans ; *Probiotics/therapeutic use ; *Metabolic Diseases/therapy/microbiology ; *Gastrointestinal Microbiome/physiology ; Animals ; Bacteria/metabolism ; },
abstract = {The gut microbiota is a taxonomically, genetically, and metabolically diverse and dynamic community of different microbial groups, including bacteria, archaea, fungi, and viruses, which are either in mutualistic or commensal relationships with their host, performing important metabolic regulation functions that bring a range of health benefits through the action of a wide range of bioactive compounds. These include short-chain fatty acids, secondary bile acids, exopolysaccharides, conjugated linoleic acids, tryptophan and indole derivatives, bacteriocins and antimicrobial peptides, and vitamins. Their health benefits include intestinal epithelial integrity, immunomodulation, metabolism, energy homeostasis, and host-gut microbiome interactions. A shift in the compositional and functional balance of the gut microbiota has been strongly linked to various metabolic disorders, including obesity, type 2 diabetes mellitus, metabolic syndrome, and non-alcoholic fatty liver disease. The use of these probiotic-derived metabolites as an alternative or complement to standard therapeutic procedures is gaining traction within the scientific community because of potential benefits such as improved stability, standardized dosing, minimal risks of genetic mutability through gene transfer, and pathogenicity. In this narrative review, we searched popular databases such as PubMed and Google Scholar for relevant materials, with emphasis on quality and rigor. This review discusses the current state of knowledge concerning the principal groups of gut microbiota- and probiotic-derived metabolites, their biosynthetic pathways, mechanisms of action, and origin. It presents a synthesized knowledge of the potential therapeutic benefits of these bioactive molecules in metabolic disorders. An attempt is made to critically evaluate their therapeutic benefits from available evidence. The review presents an interspersed discussion of the key constraints limiting the applicability of these metabolites in clinical metabolic therapy. It ends by highlighting key future research areas necessary for the eventual applicability of these metabolites as effective agents against metabolic diseases.},
}

Humans
*Probiotics/therapeutic use
*Metabolic Diseases/therapy/microbiology
*Gastrointestinal Microbiome/physiology
Animals
Bacteria/metabolism

@article {pmid42936388,
year = {2026},
author = {Zhong, D and Li, C and Xiao, Z},
title = {Nutritional regulation of the tumor immune microenvironment: metabolic mechanisms, immunotherapy response, and nursing implications.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1938564},
pmid = {42936388},
issn = {1664-3224},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Neoplasms/immunology/therapy/metabolism ; *Immunotherapy/methods ; Animals ; *Nutritional Status ; Gastrointestinal Microbiome/immunology ; },
abstract = {Nutrition is increasingly recognized as an active regulator of the tumor immune microenvironment rather than a passive supportive-care factor. Beyond maintaining body weight and treatment tolerance, dietary inputs and nutritional interventions can reshape systemic metabolism, gut microbial ecology, stromal barriers, immune-cell fitness, and response to immune checkpoint blockade. Recent experimental and translational studies indicate that fasting-mimicking diets, ketogenic interventions, carbohydrate-derived signals, amino acid availability, lipid mediators, artificial sweeteners, and microbiota-derived metabolites may either enhance or impair antitumor immunity depending on tumor type, host metabolic status, microbial composition, and treatment context. These effects involve multiple interconnected mechanisms, including CD8[+] T-cell activation or exhaustion, myeloid-cell reprogramming, cancer-associated fibroblast-mediated immune exclusion, adipocyte and hepatocyte metabolic signaling, and microbiome-dependent immune modulation. Importantly, the same nutritional factor may produce beneficial, neutral, or harmful effects across different models, indicating that nutrition should not be translated into universal anticancer dietary prescriptions. This review summarizes current evidence linking nutritional regulation to tumor immune remodeling and immunotherapy response, with particular attention to nursing implications. Oncology nurses play a key role in nutritional screening, patient education, monitoring of extreme dietary practices, assessment of supplement and artificial sweetener use, and multidisciplinary nutritional management during immunotherapy.},
}

Humans
*Tumor Microenvironment/immunology
*Neoplasms/immunology/therapy/metabolism
*Immunotherapy/methods
Animals
*Nutritional Status
Gastrointestinal Microbiome/immunology

@article {pmid42936501,
year = {2026},
author = {Yachanahalli Purushotham, A and Shilpa, BM and Sundaram, D},
title = {The mind-body connection in women's reproductive health: how psychological stress shapes gut and ovarian function - a narrative review.},
journal = {Frontiers in gastroenterology (Lausanne, Switzerland)},
volume = {5},
number = {},
pages = {1854862},
pmid = {42936501},
issn = {2813-1169},
abstract = {Psychological stress plays a critical role in modulating women's reproductive health through integrated neuroendocrine, immune, and microbiome-mediated pathways. Activation of the hypothalamic-pituitary-adrenal (HPA) axis leads to elevated secretion of corticotropin-releasing hormone (CRH), adrenocorticotropic hormone (ACTH), and cortisol, which suppress hypothalamic gonadotropin-releasing hormone (GnRH) pulsatility, thereby disrupting the hypothalamic-pituitary-gonadal (HPG) axis. This results in reduced secretion of luteinising hormone (LH) and follicle-stimulating hormone (FSH), impairing folliculogenesis, ovulation, and menstrual cyclicity. Chronic stress further induces oxidative stress, mitochondrial dysfunction, and apoptosis in ovarian cells, thereby reducing oocyte competence and diminishing ovarian reserve. Additionally, stress-induced gut microbiota dysbiosis alters the composition of key microbial taxa, including Lactobacillus, Bifidobacterium, and Clostridium, disrupting the estrobolome and impairing oestrogen metabolism. This dysregulation increases intestinal permeability and promotes systemic inflammation, as evidenced by biomarkers including interleukin-6 (IL-6), tumour necrosis factor-alpha (TNF-α), and C-reactive protein (CRP), which adversely affect endometrial receptivity and implantation success. Emerging evidence also indicates that microbial metabolites such as short-chain fatty acids (SCFAs), tryptophan metabolites, and serotonin play a crucial role in modulating neuroendocrine signalling and reproductive outcomes. Despite growing evidence, the lack of standardised biomarkers and well-designed clinical trials limits translation into clinical practice. Future research should focus on integrative, personalised therapeutic approaches combining psychological interventions, lifestyle modifications, and microbiome-targeted therapies to improve reproductive outcomes and overall well-being.},
}

@article {pmid42936527,
year = {2026},
author = {Jawad, M and Zhang, P and Yang, H and Shi, J and Mi, L and He, Y and Lu, S and Fu, P and Iftikhar, H and Song, X},
title = {Mulberry (Morus alba) leaves in sheep and goat nutrition: a critical narrative review of rumen function, performance, meat quality, and mechanistic evidence.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1986200},
pmid = {42936527},
issn = {2297-1769},
abstract = {Mulberry (Morus alba) leaves combine conventional nutrients with polyphenols and flavonoids and are increasingly evaluated as alternative feeds for sheep and goats. This critical narrative review examines how feed form, processing, inclusion level, replacement strategy, and dietary balance influence nutrient utilization, rumen function, productive performance, carcass traits, and meat quality. The review question, eligibility criteria, evidence hierarchy, and synthesis framework were defined and approved by the authors. Relevant literature was identified and verified across bibliographic databases, publisher and journal platforms, Chinese-language sources, regional scholarly indexes, and backward/forward citation chaining, with direct sheep and goat feeding trials assigned the greatest evidential weight. Mulberry generally maintains intake and growth when complete diets remain nutritionally adequate, whereas excessive replacement of nutrient-dense concentrate can depress performance. Carcass yield is commonly maintained. Several independent trials demonstrate diet-sensitive tenderness, water retention, muscle fatty-acid profiles, and amino-acid composition, although sensory and physicochemical responses remain heterogeneous. Rumen fermentation, microbial-community shifts, antioxidant responses, and tissue lipid or gene-expression pathways provide mechanistic plausibility, but microbiome and omics associations are not treated as causal unless mediation was directly tested. Mulberry should therefore be treated as a context-dependent feed resource rather than a universally beneficial additive.},
}

@article {pmid42936760,
year = {2026},
author = {Drobne, D and Ambrožič Avguštin, J and Kralj, MB and Čehovin Zajc, J and Čremožnik Zupančič, J and Dragoš, A and Ficko, A and Fišer, C and Bulc, TG and Heath, E and Hočevar, M and Hrovat, K and Istenič, D and Jovanovska, S and Kavčič, M and Klančnik, A and Zidar, Ž and Iglič, VK and Lukšič, AA and Mulec, IM and Novak, S and Perc, V and Pogačar, T and Smole Možina, S and Šunta, U and Trebše, P and Vogrinc, J and Vošnjak, M and Zupanc, V and Železnikar, Š and Pintar, M},
title = {Microbiome: A Nexus of One Health Strategies to Address Emerging Risks.},
journal = {Bioscience},
volume = {76},
number = {10},
pages = {1111-1127},
pmid = {42936760},
issn = {0006-3568},
abstract = {This paper positions microbiomes as pivotal to advancing the One Health framework, emphasizing their role in linking human, animal, and environmental health. Despite widespread support, implementation faces hurdles due to insufficient metrics, standardized indicators, and limited cross-sector collaboration. An interdisciplinary team investigates how climate change, pollution, and microbial contamination influence microbiome dynamics. Microbiome indicators like stress, resilience, and stability are proposed as proxies for health to guide evidence-based interventions. Key domains for microbiome assessment include the human and animal gut, soil, groundwater, and built environments, with food safety and water quality data serving as vital connectors. The paper introduces the nanostructurome to uncover microbial communication pathways and enable precision microbiome modulation. Integration of microbiological databases, microbiome literacy, citizen science, and social science perspectives is advocated to foster coordinated action. Ultimately, the microbiome is proposed as a strategic nexus for conceptual alignment, health indicator development, and targeted interventions.},
}

@article {pmid42936806,
year = {2026},
author = {Ji, M and Li, L and Gao, L and Xu, J and Liu, H and Yao, Y and Niu, G and Hao, B},
title = {From the rhizosphere to systemic circulation: cross-kingdom signaling and health effects of soil microbial metabolites.},
journal = {Open life sciences},
volume = {21},
number = {1},
pages = {20251393},
pmid = {42936806},
issn = {2391-5412},
abstract = {Plant roots and soil microorganisms engage in continuous, complex chemical dialogues at the rhizosphere-a highly dynamic interface. The rhizosphere not only serves as a "black box" where root exudates and microbial metabolites converge but also functions as a critical site for shaping microbial community structure. Small-molecule metabolites produced by either plant roots or microbes mediate plant-microbe interactions locally and can further influence shoot physiology through systemic signaling. Similarly, in animal and human systems, gut microbes produce bioactive metabolites - such as short-chain fatty acids, indole derivatives, and secondary bile acids - that enter systemic circulation and participate in host metabolic regulation, immune modulation, and even neural function. Although the rhizosphere and gut belong to distinct ecosystems, they exhibit remarkable parallels in metabolite-mediated cross-kingdom signaling mechanisms: microbial metabolites in both systems can traverse biological barriers, enter systemic circulation, and modulate host phenotypes. Thus, from the rhizosphere to systemic circulation, soil (or gut) microbial metabolites are being redefined as pivotal mediators linking environment, microbiota, and host health. Elucidating the chemical nature, transmission pathways, and biological effects of these metabolic signals will not only advance the development of green, microbiome-based inputs for sustainable agriculture but also offer novel ecological perspectives for understanding human metabolic and neurodegenerative diseases.},
}

@article {pmid42937050,
year = {2026},
author = {Jiang, Z and Xuan, L and Lock, EF and Cui, E},
title = {Bayesian multiple imputation for functional data.},
journal = {Biometrics},
volume = {82},
number = {4},
pages = {},
pmid = {42937050},
issn = {1541-0420},
support = {R01HL187193/NH/NIH HHS/United States ; R21LM014912/NH/NIH HHS/United States ; R35GM161467/NH/NIH HHS/United States ; },
mesh = {Bayes Theorem ; Computer Simulation ; Algorithms ; *Models, Statistical ; Humans ; Data Interpretation, Statistical ; Biometry/methods ; },
abstract = {Missing data are pervasive in modern functional datasets, where trajectories are often sparsely or irregularly observed. Although functional principal component analysis is widely used to reconstruct incomplete curves, existing approaches typically employ single imputation, leading to overly optimistic inferences in downstream analyses. To address these challenges, we develop a novel Bayesian multiple imputation framework for functional data (BAMIFun). For single-level functional data, we impose a Bayesian low-rank model that incorporates penalized spline representations to enforce smoothness of the functional domain and derive an efficient Gibbs sampler algorithm for posterior computation. In addition, we demonstrate and validate how to properly account for estimation uncertainties in downstream analysis. Furthermore, we extend the framework to multiway functional data using Functional Tensor Singular Value Decomposition model, enabling Bayesian multiple imputation in settings not supported by existing methods. Simulation studies show that BAMIFun achieves substantially improved coverage and more reliable downstream inference compared to existing methods, while maintaining similar imputation accuracy. Case studies using a physical activity dataset and an infant gut microbiome dataset further demonstrate the practical advantages of our proposed methods under severe missingness.},
}

Bayes Theorem
Computer Simulation
Algorithms
*Models, Statistical
Humans
Data Interpretation, Statistical
Biometry/methods

@article {pmid42937190,
year = {2026},
author = {Quinger, F and Klein, N and Steinhoff-Wagner, J and Camarinha-Silva, A and Rodehutscord, M and Seifert, J},
title = {Field Pea Variants affect Nutrient Digestibility and Gut Microbiome in Pigs.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag346},
pmid = {42937190},
issn = {1525-3163},
abstract = {The digestibility of nutrients in different field pea variants in pigs can vary due to characteristics such as anti-nutritional factors. Undigested nutrients can be fermented in the hindgut, and their amount and composition likely affect microbial composition. This study compared a spring field pea variant (SP) with two winter field pea variants (WP1, WP2) with higher trypsin inhibitor activity and a tannic spring forage pea variant (SFP) in terms of nutrient digestibility and effects on the gut microbiome in growing pigs. Four diets containing 40% of one of the four field pea variants were formulated and randomly assigned to 8 ileally cannulated barrows according to a 4 × 4 double Latin square design with the blocking factors animal and period. The experiment consisted of 4 periods, each lasting 11 days. Ileal digesta and feces were collected for 2 days each to determine nutrient digestibility. On the last day of every period, ileal digesta and feces were sampled and analyzed for digestive enzyme activity, metagenomics, metaproteomics, and metabolomics. The data was integrated using DIABLO. The winter field pea variants decreased the prececal digestibility of 16 amino acids (P ≤ 0.032) and increased the activity of carboxypeptidase A (P = 0.002). Pigs fed the SFP showed decreased hindgut disappearance of total dietary fiber (P < 0.001) and concentrations of acetate, propionate, and butyrate in the feces (P ≤ 0.026). More differentially abundant taxa in metagenomic and metaproteomic data were detected in the feces than in ileal digesta among field pea variants. The SFP increased the abundance of host proteins related to innate immune response in ileal digesta and feces (adjusted P ≤ 0.047). Integration of the acquired data layers revealed a negative association of ileal amino acid concentrations with the abundance of Prevotella and proteins related to starch degradation and propionate production in the ileal digesta for winter field pea variants. For SFP, reduced hindgut disappearance of total dietary fiber was associated with a reduction of proteins from Ruminococcus. In conclusion, field pea variants can affect the ileal and fecal microbiome in pigs, potentially due to anti-nutritional factors that either indirectly influence the microbiome by reducing nutrient digestibility or directly affect individual microbial taxa.},
}

@article {pmid42937224,
year = {2026},
author = {Srivastava, S and Misra, M and Gujrati, C},
title = {Vaginal-Endometrial Microbiome Synchrony as a Predictor of Implantation in Frozen Embryo Transfer Cycles: A Prospective Study.},
journal = {JBRA assisted reproduction},
volume = {},
number = {},
pages = {},
doi = {10.5935/1518-0557.20260081},
pmid = {42937224},
issn = {1518-0557},
abstract = {OBJECTIVE: To evaluate whether vaginal-endometrial microbiome synchrony is associated with biochemical and clinical pregnancy outcomes in frozen embryo transfer (FET) cycles.

METHODS: This prospective observational study included 100 women undergoing single Day 5 FET cycles. Vaginal and endometrial samples were collected during a mock FET cycle on progesterone day 5 and analyzed using a contamination-aware targeted 16S rRNA polymerase chain reaction (PCR) panel optimized for low-biomass reproductive tract samples. A Synchrony Index (SI), a similarity metric analogous to Jaccard-type indices, was calculated based on shared dominant microbial taxa between vaginal and endometrial compartments. An SI cutoff of ≥0.7 was pre-specified prior to outcome analysis based on biological plausibility and accepted similarity thresholds in microbiome research. Biochemical pregnancy (β-hCG positive) and clinical pregnancy rates were compared between high and low SI groups. A randomly selected subset underwent next-generation sequencing validation.

RESULTS: Baseline demographic, ovarian reserve, embryo quality, and endometrial parameters were comparable between groups. Biochemical pregnancy rates were significantly higher in women with high SI compared with low SI (65.5% vs. 28.9%, p<0.001), as were clinical pregnancy rates (61.8% vs. 26.7%, p<0.001). On multivariable logistic regression adjusting for clinical confounders, SI remained independently associated with biochemical pregnancy (adjusted odds ratio 1.20 per 0.1 increase; 95% CI 1.06-1.36; p=0.004). PCR-derived SI demonstrated substantial agreement with sequencing-based validation.

CONCLUSION: Vaginal-endometrial microbiome synchrony is independently associated with biochemical pregnancy in Day 5 FET cycles. The PCR-based Synchrony Index warrants further evaluation as an investigational biomarker of reproductive tract receptivity in larger and independent cohorts.},
}

@article {pmid42937468,
year = {2026},
author = {Zong, L and Zhang, Q and Sun, C and Cao, D and Ni, X and Chen, D and Ma, F and Peng, Y and Jin, P and Guan, M},
title = {Benzotriazole Ultraviolet Stabilizer UV-PS Exposure Induces Immune Hyperactivation and Metabolic Reprogramming in Drosophila in a Microbiota-Dependent Manner.},
journal = {Environmental science & technology},
volume = {60},
number = {42},
pages = {29911-29925},
doi = {10.1021/acs.est.6c07239},
pmid = {42937468},
issn = {1520-5851},
support = {BK20230762//Natural Science Foundation of Jiangsu Province/ ; 42307146//National Natural Science Foundation of China (NSFC)/ ; 42477288//National Natural Science Foundation of China (NSFC)/ ; 42677348//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Animals ; *Triazoles ; Male ; *Drosophila melanogaster ; Microbiota ; },
abstract = {Benzotriazole ultraviolet stabilizers (BUVSs) have raised ecological safety concerns due to their environmental persistence and bioaccumulation. Among them, 2-(2H-benzotriazol-2-yl)-4-tert-butylphenol (UV-PS) is frequently detected in various environments and biological media, with its aryl hydrocarbon receptor agonistic activity suggesting potential toxicity. However, its chronic toxic effects and underlying mechanisms remain unclear. This study employed male fruit fly (Drosophila melanogaster) as a model organism to explore chronic toxicity of UV-PS via a 14 day dietary exposure at 1-1000 μg/L. The results demonstrated that UV-PS induced phenotypic alterations in Drosophila, including weight loss, metabolic reprogramming, compromised intestinal barrier integrity, impaired locomotor activity, and decreased survival rates. Transcriptomic analysis revealed that response to oxidative stress and immune activation constitute the early molecular responses of toxic effects. Microbiome profiling further indicated that UV-PS altered gut microbial community structure, leading to shifts in specific bacterial family abundances that significantly correlated with immune pathway activation. In vitro S2 cells and in vivo germ-free fly experiments further confirmed that gut microbiota was essential for oxidative stress and immune hyperactivation. These findings provide novel evidence that UV-PS-induced chronic toxicity in male Drosophila involves a gut-immune-metabolic axis. Our work offers valuable insights into risk assessments of BUVSs.},
}

Animals
*Triazoles
Male
*Drosophila melanogaster
Microbiota

@article {pmid42937515,
year = {2026},
author = {Clark, RM and Palmer, LD},
title = {Sleeper agents: asymptomatic Acinetobacter colonization and underlying mechanisms.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0029026},
doi = {10.1128/iai.00290-26},
pmid = {42937515},
issn = {1098-5522},
abstract = {Acinetobacter baumannii and other Acinetobacter species are a growing public health concern because they commonly cause healthcare-associated infections. Acinetobacter spp. are often multi-drug resistant, leading to significant morbidity and mortality. Therefore, understanding the reservoirs for Acinetobacter spp. in healthcare settings is particularly important to infection control. Acinetobacter spp. are known to asymptomatically colonize the human gut, skin, and respiratory flora, and recent work has found the prevalence of Acinetobacter colonization is high in patients in healthcare environments, such as hospitals and long-term care facilities. Patients colonized by A. baumannii are at increased risk of developing clinical infections, including by the same strains. Additionally, multiple studies report transmission of A. baumannii strains to other patients in the same healthcare setting. Recent mechanistic studies on A. baumannii gut colonization have found that the microbiota, host immunity, and diet contribute to colonization resistance in animal models. Here, we review the epidemiologic evidence for asymptomatic colonization as a clinically important reservoir for A. baumannii and examine the nascent study of the molecular mechanisms of Acinetobacter colonization. We discuss future prospects for understanding Acinetobacter colonization that may help develop strategies to support colonization resistance and prevent infections.},
}

@article {pmid42937876,
year = {2026},
author = {Hioki, Y and Klapper, M and Ibrahim, A and Hübner, A and Steinacker, M and Willing, K and Nachawati, R and Hildebrandt, D and Reimer, L and Zimmermann, A and Mantke, J and Sato, M and Warinner, C and Stallforth, P},
title = {Reconstruction of a 30,000-Year-Old Biosynthetic Gene Cluster Reveals Lasso Peptides Formed by a Highly Tolerant Cyclase.},
journal = {Journal of the American Chemical Society},
volume = {148},
number = {38},
pages = {40629-40635},
pmid = {42937876},
issn = {1520-5126},
support = {NA//Werner Siemens-Stiftung/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; JP24KJ1884//Japan Society for the Promotion of Science/ ; NA//Astellas Foundation for Research on Metabolic Disorders/ ; },
mesh = {*Multigene Family ; *Peptides/chemistry/genetics/metabolism ; Humans ; *Actinomyces/genetics/enzymology ; Amino Acid Sequence ; Phylogeny ; },
abstract = {Microbial metagenomes preserved in prehistoric dental calculus samples provide access to past bacterial biodiversity and evolutionary dynamics across archeological time scales. Consequently, this sequence space represents a largely unexplored resource for natural product discovery. Phylogeny-guided genome mining of human dental calculus metagenomes spanning recent times to the Middle and Upper Paleolithic revealed a distinct lasso cyclase lineage associated with oral Actinomyces species. Heterologous expression of a biosynthetic gene cluster reconstructed from an approximately 30,000-year-old sample yielded two lasso peptides, palassoptides A1 and A2. Structure analyses established a canonical class II lasso topology with an eight-residue macrolactam ring. Notably, both palassoptides feature an unprecedented amino acid composition for lasso peptides. Mutational analysis of the PalA2 precursor further showed that PalC accepts all possible substitutions at core position 1 except for Pro, revealing the broadest respective tolerance reported for a lasso cyclase to date. Homologous gene clusters with highly conserved yet variable precursor sequences are widespread among modern oral Actinomyces, indicating long-term preservation of this biosynthetic lineage within the human oral microbiome. The two palassoptides exhibited combination-dependent antibacterial activity against selected Gram-positive bacteria. These findings demonstrate that ancient metagenomes can reveal chemically uncharacterized natural products and expand the known structural diversity of natural products.},
}

*Multigene Family
*Peptides/chemistry/genetics/metabolism
Humans
*Actinomyces/genetics/enzymology
Amino Acid Sequence
Phylogeny

@article {pmid42937952,
year = {2026},
author = {Colombano, HMA and Lüthy, L and Sieber, S and Frei, JM and Wolfrum, S and Gademann, K and Carreira, EM},
title = {Total Synthesis and Structure Determination of Mutanolins Detected in a Human Oral Microbiome Symbiont.},
journal = {Journal of the American Chemical Society},
volume = {148},
number = {39},
pages = {42351-42360},
doi = {10.1021/jacs.6c12634},
pmid = {42937952},
issn = {1520-5126},
support = {NA//Eidgen?ssische Technische Hochschule Z?rich/ ; NA//Swiss Chemical Industry/ ; },
mesh = {*Streptococcus mutans/chemistry/metabolism ; Humans ; *Mouth/microbiology ; *Microbiota ; *Peptides, Cyclic/chemical synthesis/chemistry ; Stereoisomerism ; },
abstract = {Mutanolins are macrocyclic lipopeptides produced in the human oral microbiome by Streptococcus mutans UA159, an etiological agent of caries. Putative structures have been published based on MS/MS analysis of bacterial extracts. Accordingly, the configuration of the natural products was not determined, and the constitutional assignment was not secured spectroscopically. Mutanolins share a common lipidated γ-amino acid fragment that incorporates a β-S-linked cysteine, which had been reported to be elongated at its N-terminus with Glu or Glu-Gly. Herein, we present streamlined total syntheses to elucidate the structures of mutanolins A-F. Regio- and diastereoselective sulfenylchlorinations were key to efficiently access the variable exocyclic peptidic side chains of these natural products. All four C24/C25 diastereomers of mutanolin A were synthesized. Coinjection experiments (UHPLC) of synthetic standards with crude extracts of S. mutans UA159 led to the configurational assignment of mutanolin A as C24(R)C25(R). Mutanolin B was synthesized and assigned as C24(R)C25(R) by analogy to mutanolin A. We then prepared nominal mutanolins C-F; however, the observed MS/MS fragmentation patterns of synthetic nominal mutanolins C-F did not match the reported data. Based on biosynthetic considerations, we speculated that all mutanolins are derived from intermediates in the glutathione biosynthesis. Accordingly, our proposed structures of mutanolins C-F were synthesized and characterized by NMR spectroscopy. The revised assignment was validated by MS/MS and coinjection experiments. By securing the structures of these metabolites, our work provides a starting point for exploring the biological function of the mutanolins as secondary metabolites within the human oral microbiome.},
}

*Streptococcus mutans/chemistry/metabolism
Humans
*Mouth/microbiology
*Microbiota
*Peptides, Cyclic/chemical synthesis/chemistry
Stereoisomerism

@article {pmid42938254,
year = {2026},
author = {Colobatiu, L and Mihaiu, R and Pusta, A and Mirel, S},
title = {Continuous Glucose Monitoring for Metabolic Phenotyping and Precision Nutrition: Current Evidence, Clinical Applications and Future Perspectives.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {20},
pages = {},
pmid = {42938254},
issn = {2075-4418},
abstract = {Continuous glucose monitoring (CGM) has evolved beyond conventional diabetes management into an enabling technology for metabolic phenotyping and precision nutrition by providing continuous, real-world assessment of individual glycemic responses to dietary and lifestyle exposures. This narrative review examines the principles and clinical utility of CGM and its emerging applications in metabolic monitoring and personalized nutrition, with particular emphasis on postprandial glycemic variability, computational prediction, dietary feedback, and behavioral interventions. A literature search was conducted in Web of Science, PubMed, Scopus, and Google Scholar using predefined combinations of terms related to CGM, precision and personalized nutrition, diet, postprandial glycemic responses, lifestyle, glycemic variability, artificial intelligence, machine learning, and computational nutrition, including English-language literature available up to June 2026. Current evidence demonstrates substantial interindividual variability in postprandial glycemic responses and supports the potential integration of CGM with dietary, clinical, anthropometric, behavioral, and microbiome-derived data to characterize individual metabolic responses and inform individualized prediction and nutritional guidance. However, the reproducibility and generalizability of CGM-derived metabolic phenotypes and predictive models remain incompletely established. CGM-supported nutritional and behavioral interventions have demonstrated improvements in glycemic and selected cardiometabolic outcomes, particularly in individuals with type 2 diabetes, whereas evidence of clinical benefit in populations without diabetes remains substantially more limited. Sustained engagement and psychological, technical, and accessibility-related limitations also remain important considerations. Emerging multi-analyte sensing technologies may further broaden continuous metabolic assessment and support more comprehensive, data-driven precision-nutrition strategies.},
}

@article {pmid42938279,
year = {2026},
author = {Wang, M},
title = {Genomics of the Genus Rhodiola: From Genome Assembly to High-Altitude Adaptation and Bioactive Compound Biosynthesis.},
journal = {Genes},
volume = {17},
number = {10},
pages = {},
pmid = {42938279},
issn = {2073-4425},
support = {2081921039//Chengdu University/ ; },
mesh = {*Rhodiola/genetics/metabolism ; Genomics/methods ; *Genome, Plant ; Altitude ; *Adaptation, Physiological/genetics ; Genome, Chloroplast ; Phylogeny ; Plants, Medicinal/genetics ; },
abstract = {Background/Objectives: The genus Rhodiola comprises alpine medicinal plants renowned for extreme high-altitude adaptability and valuable bioactive compounds. This narrative review synthesizes recent genomic advances to understand how genomic mechanisms contribute to both environmental adaptation and bioactive compound biosynthesis. Methods: This review is a narrative synthesis of genomic studies from the past decade, including chloroplast and nuclear assemblies, comparative genomics of transposable elements and gene families, and integrative multi-omics approaches for pathway elucidation. Results: Chloroplast genomes are structurally conserved but harbor sufficient variation for phylogenetic resolution. Nuclear genomes reveal dynamic patterns of expansion and contraction associated with transposable element bursts and lineage-specific gene family dynamics, although causal relationships remain to be established. Multi-omics integration has fully elucidated the salidroside pathway, identified candidate genes for rosavin biosynthesis, predicted transcriptional regulators, and suggested plant-microbiome contributions to specialized metabolism. Conclusions: These findings support Rhodiola as a promising model for studying coordinated high-altitude adaptation and bioactive compound biosynthesis. Future pan-genome construction, synthetic biology, and molecular breeding offer avenues for sustainable utilization and precision improvement of this medicinal genus.},
}

*Rhodiola/genetics/metabolism
Genomics/methods
*Genome, Plant
Altitude
*Adaptation, Physiological/genetics
Genome, Chloroplast
Phylogeny
Plants, Medicinal/genetics

@article {pmid42938335,
year = {2026},
author = {Lampsas, S and Agapitou, C and Chardalia, GM and Soulimiotis, D and Papastamopoulos, K and Theodossiadis, P and Chatziralli, I},
title = {Epigenetic Regulation and Gut Microbiota Dysbiosis in Age-Related Macular Degeneration.},
journal = {Genes},
volume = {17},
number = {10},
pages = {},
pmid = {42938335},
issn = {2073-4425},
mesh = {Humans ; *Macular Degeneration/genetics/microbiology/pathology ; *Epigenesis, Genetic ; *Gastrointestinal Microbiome/genetics ; *Dysbiosis/genetics/microbiology ; DNA Methylation/genetics ; Animals ; },
abstract = {Age-related macular degeneration (AMD) is a leading cause of visual impairment. Beyond the classical pathogenetic pathways, increasing evidence suggests that epigenetic regulation and the gut-retina axis may substantially contribute to AMD development and progression. This review synthesizes current evidence on two increasingly recognized and interconnected domains of AMD pathogenesis: epigenetic regulation and gut microbiota dysbiosis. Epigenetic processes, such as DNA methylation, histone modifications, and non-coding RNAs, can influence gene function involved in oxidative stress responses, complement regulation, angiogenesis, and inflammation, while several related markers have emerged as potential diagnostic and prognostic biomarkers. Moreover, growing evidence suggests a functional gut-retina axis, in which alterations in the gut microbiota impair intestinal barrier function and facilitate the systemic passage of bacteria and microbial metabolites, potentially affecting retinal inflammation and immune responses. Furthermore, several microbial metabolites, including short-chain fatty acids, lipopolysaccharide, bile acids, tryptophan derivatives, and trimethylamine-N-oxide, may have either protective or harmful effects on retinal and choroidal homeostasis, with altered circulating and fecal concentrations reported in patients with AMD compared with controls. These findings support AMD as a systemically and molecularly interconnected disorder, while further longitudinal, mechanistic, and multi-omics studies are required to establish causality, define interactions between epigenetic and microbiome-related pathways, and clarify their potential utility as biomarkers and therapeutic targets.},
}

Humans
*Macular Degeneration/genetics/microbiology/pathology
*Epigenesis, Genetic
*Gastrointestinal Microbiome/genetics
*Dysbiosis/genetics/microbiology
DNA Methylation/genetics
Animals

@article {pmid42938706,
year = {2026},
author = {Iaquinto, G and Picariello, E and Iaquinto, S and Melina, R and Sellitto, C and Sellitto, S and Cataldo, G and Pastore, R and Rotondi Aufiero, V},
title = {Novel Therapeutic Strategies for Active Crohn's Disease: Targeting Pathobionts and Host-Microbe Interactions.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42938706},
issn = {2079-6382},
abstract = {Crohn's disease (CD) is a chronic inflammatory disorder characterized by complex interactions among genetic susceptibility, environmental factors, dysregulated immune responses, and alterations of the intestinal microbiota. Although corticosteroids, immunomodulators, biologics, and advanced small-molecule therapies remain central to disease management, a substantial proportion of patients experience primary non-response, loss of response, or treatment-related adverse effects. This has stimulated interest in complementary therapeutic strategies targeting host-microbe interactions and intestinal microbial homeostasis. This review critically examines emerging microbiome-directed approaches for CD, with particular emphasis on pathobionts such as adherent-invasive Escherichia coli (AIEC). We discuss the available evidence for antibiotics, antimicrobial peptides (AMP), gut bacteriophages, fecal microbiota transplantation (FMT), and selected nutraceutical and dietary interventions. While some approaches show promising biological or clinical signals, the strength of evidence varies considerably, ranging from in vitro and animal studies to randomized clinical trials and meta-analyses. Antibiotic therapies targeting intestinal pathogens have shown heterogeneous results, suggesting the need for pathogen-guided and intracellularly active antimicrobial strategies. Novel approaches, including AIEC-specific phages and AMP-based interventions, represent promising microbiome-sparing alternatives capable of selectively modulating disease-associated microorganisms. Furthermore, FMT and nutraceuticals may contribute to restoring microbial balance and strengthening intestinal homeostasis, although their efficacy requires further validation in controlled clinical trials. Overall, these strategies support a transition toward precision medicine approaches integrating microbial profiling, host immune characterization, and targeted antimicrobial interventions to improve therapeutic outcomes in CD.},
}

@article {pmid42938711,
year = {2026},
author = {Ferrara, F and De Berardinis, F},
title = {Antimicrobial Stewardship During Lactation: Current Evidence on the Human Milk-Infant Microbiome Axis and Neurodevelopment.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42938711},
issn = {2079-6382},
abstract = {Human milk is increasingly recognized as a complex biological system that contributes to infant development through nutritional, immunological, and microbial pathways. Simultaneously, antimicrobial stewardship (AMS) has become a global healthcare priority because of rising antimicrobial resistance and concerns regarding the ecological consequences of antibiotic exposure during early life. This narrative review examines current evidence regarding the impact of anti-infective therapies during lactation on the maternal-infant microbiome axis and discusses the role of AMS in supporting appropriate maternal treatment while preserving breastfeeding. While previous reviews have independently described the biological properties of human milk or general antimicrobial resistance, this narrative review uniquely bridges these domains by framing the infant microbiome as a clinical endpoint for pharmacological governance. The primary objective is to synthesize current evidence on the relationships among human milk, the infant gut microbiome, and neurodevelopment, with a novel emphasis on how integrating Antimicrobial Stewardship (AMS) and microbiome-conscious prescribing during lactation actively safeguards these developmental trajectories. This work contributes to the existing literature by shifting the focus from observational biology to an actionable clinical framework for healthcare providers. A structured literature search was conducted in PubMed/MEDLINE, Scopus, and Web of Science. Studies addressing human milk biology, infant gut microbiota development, antimicrobial exposure during lactation, microbiota-gut-brain interactions, and stewardship strategies were reviewed. Available evidence indicates that breastfeeding promotes the establishment of a beneficial gut microbiota and supports immune maturation through the combined action of human milk oligosaccharides, immunological factors, and milk-associated microorganisms. Maternal and neonatal antibiotic exposure may alter microbial colonization patterns; however, the magnitude, persistence, and long-term clinical significance of these effects remain incompletely understood. Although mechanistic studies support biologically plausible links between microbiome alterations and neurodevelopmental pathways, direct evidence connecting maternal antibiotic use during lactation with adverse neurodevelopmental outcomes is limited. Current evidence supports continued breastfeeding during most maternal antibiotic treatments and highlights the importance of microbiome-conscious prescribing. AMS strategies based on diagnostic appropriateness, treatment optimization, and avoidance of unnecessary antibiotic exposure may help minimize microbial disruption while ensuring effective infection management.},
}

@article {pmid42938771,
year = {2026},
author = {Zawadzki, D and Libergal, N and Kisiała, M and Gwoździk, H and Ratajczyk, O and Hejnowicz, M and Misiąg, P and Nowak, Ł and Janczak, D and Krajewski, W and Szydełko, T and Małkiewicz, B},
title = {Novel Therapeutic Strategies for Preventing Recurrent Urinary Tract Infections in Women: A Narrative Review.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42938771},
issn = {2079-6382},
support = {SUBZ.C090.26.080//Wroclaw Medical University/ ; },
abstract = {Background: It is estimated that approximately 20-30% of women suffer from recurrent urinary tract infections (rUTIs). The disease is primarily bacterial, especially Escherichia coli, making antibiotics the standard treatment. Increasing antibiotic resistance of uropathogens reduces treatment effectiveness. Therefore, non-antibiotic approaches are increasingly being investigated for the management of rUTIs. This narrative review provides a comprehensive overview of currently available and emerging methods of treatment and prevention of rUTIs in women. Methods: This paper employs a narrative review with a structured literature search and synthesizes data from three major databases, including PubMed, Web of Science, and Scopus. The review was conducted in accordance with the Scale for the Assessment of Narrative Review Articles (SANRA) checklist. Scientific articles were searched using the following keywords: 'recurrent urinary tract infections in women', 'antibiotic prophylaxis', 'immunoprophylaxis', 'urinary microbiome'. Results: Observational evidence has reported an association between continuous antibiotic prophylaxis and severe outcomes, including pyelonephritis and septicemia; however, these findings are susceptible to confounding by indication and should not be interpreted as evidence of a causal relationship. Clinical studies suggest that immunomodulatory approaches, such as OM-89 bacterial lysate, next-generation polybacterial mucosal vaccines (e.g., MV140), and oral immunostimulants, have potential to reduce the frequency of rUTI recurrences in women, although the strength and certainty of evidence vary between interventions. Bacteriophage therapy is an emerging and exploratory targeted approach supported by early clinical and experimental evidence, but its efficacy for preventing recurrent uncomplicated UTIs remains uncertain, though rapid development of phage resistance remains a potential limitation. Prophylactic strategies, including Lactobacillus-based probiotics, low-dose estriol, and microbiota transplantation, have shown preliminary or variable results, with limited evidence for rUTI prevention. In particular, findings on vaginal dysbiosis and microbiota modulation should not be interpreted as a direct evidence of rUTI prevention. Conclusions: While antibiotic therapy remains essential, continuous prophylaxis may contribute to antimicrobial resistance and disrupt microbial balance. Therefore, novel therapeutic strategies are still being studied. Several non-antibiotic strategies, including immunoprophylaxis and microbiome modulation, represent potential preventive approaches, whereas bacteriophage therapy and vaginal microbiota transplantation remain exploratory and require further clinical validation. Their preventive efficacy against rUTIs remains unestablished. Moreover, antimicrobial peptides (AMPs), nanotechnology, molecularly targeted therapies, and precision medicine strategies are being investigated. Plant-based therapies may provide benefit, but their clinical efficacy remains to be established. Overall, further clinical studies are needed to confirm the preventive efficacy of these emerging approaches.},
}

@article {pmid42938781,
year = {2026},
author = {Shuvo, MSH and Ju-Young, W and Jo, S and Ahmed, I and Aziz, MT and Atashi, A and Raihan, MA and Yeji, P and Hyunhee, C and Kim, T and Yu, H and Bae, H and Kim, S and Seo, H and Song, HY},
title = {Hospital Drain Microbiomes as Distinct Microbial Signatures Within Urban Wastewater Networks in the Han River Watershed.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42938781},
issn = {2079-6382},
support = {RS-2023-00219563//Ministry of Science and ICT/ ; P0027492//Korea Institute for Advancement of Technology/ ; NA//Korea Bio Associations/ ; NA//Soonchunhyang University/ ; },
abstract = {Background: Hospital drainage systems represent an important interface between healthcare facilities and urban wastewater networks and may contribute distinct microbial inputs to downstream aquatic environments. This issue is particularly relevant in Seoul, Republic of Korea, where urban wastewater discharges into receiving waters within the Han River watershed. Methods: In this study, we characterized hospital drain microbiomes to evaluate their microbial and environmental signatures, using residential drains as a non-clinical comparison. Results: Hospital drains exhibited a distinct taxonomic profile, with greater relative abundances of Bacteroidota and Firmicutes and several genera of environmental or potential public health relevance, including Mycobacterium, Legionella, and Pseudomonas. Although microbial richness was comparable between the two environments, Simpson diversity was significantly lower in hospital drains, indicating reduced community evenness. Bray-Curtis and Jaccard analyses showed clear separation between hospital and residential microbial communities, and hierarchical clustering further supported environment-associated community structuring. LEfSe analysis identified distinct hospital-associated taxonomic biomarkers, and predicted functional profiling revealed substantial metabolic differentiation, with 19 of the 25 most significantly differentiated pathways enriched in hospital samples. Conclusions: These microbial and functional differences underscore the ecological uniqueness of hospital drains and support their inclusion in future wastewater-based microbial surveillance strategies. Collectively, these findings establish hospital drains as distinct microbial ecosystems within urban wastewater networks and provide a baseline for future studies examining the persistence of hospital-associated microbial signatures within the Han River watershed.},
}

@article {pmid42938969,
year = {2026},
author = {Nguyen, T and Woods, C and Liu, J and Wang, C and Lin, AL and Cheng, J},
title = {APOEFormer: A Multimodal AI Model for APOE4 Carrier Status Prediction and Phenotype Characterization in Alzheimer's Disease.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {13},
number = {10},
pages = {},
pmid = {42938969},
issn = {2306-5354},
support = {//University of Missouri/ ; },
abstract = {The apolipoprotein E ε4 (APOE4) allele is the strongest genetic risk factor for late-onset Alzheimer's disease (AD), the most common form of dementia. APOE4 carriers exhibit cerebrovascular and metabolic dysfunction, structural brain alterations, and gut microbiome changes decades before the onset of clinical symptoms. Better understanding of the early manifestation of these physiological changes is critical for development of timely AD interventions and risk reduction protocols. Multi-modal datasets encompassing a wide range of APOE ε4 and AD associated biomarkers provide a valuable opportunity to gain insight into the APOE4 phenotype; however, these datasets often present analytical challenges due to small sample sizes and high heterogeneity. Here, we propose a two-stage multimodal AI model (APOEFormer) that integrates blood metabolites, brain vascular and structural MRI, microbiome profiles, and other clinical and demographic data to predict APOE4 allele status. In the first stage, modality-specific encoders are used to generate initial representations of input data modalities, which are aligned in a shared latent space via self-supervised contrastive learning during pretraining. The contrastive learning objective encourages learning of informative and consistent representations across modalities through leveraging cross-modality relationships. In the second stage, the pretrained representations are used as inputs to a multimodal transformer that integrates information across modalities to predict a key AD-risk genetic variant (APOE4). Across 10 repeated experimental runs with different train-validation-test splits, APOEFormer predicts whether an individual carries an APOE4 allele with an average prediction accuracy of 75%, demonstrating robust performance under limited sample sizes. Post hoc perturbation analysis of the predictive model revealed valuable insights into the driving components of the APOE4 phenotype-including key blood biomarkers and brain regions strongly associated with APOE4.},
}

@article {pmid42939146,
year = {2026},
author = {Kunay, L and Fialkovičová, M and Benková, M and Tóthová, C and Kořená, N and Gomulcová, S and Vargová, M and Micháľová, A and Lukáč, B and Bielik, B and Staroňová, R},
title = {Comparison of Selected Therapies Within the Step-Up Therapeutic Approach in Canine Chronic Inflammatory Enteropathy.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {20},
pages = {},
pmid = {42939146},
issn = {2076-2615},
support = {VEGA 1/0381/25//Ministry of Education, Science, Research, and Sport of the Slovak Republic/ ; },
abstract = {Canine chronic inflammatory enteropathy (CIE) frequently requires a sequential therapeutic approach in which treatment is escalated according to clinical response. This prospective, open-label clinical study evaluates selected dietary, antimicrobial, microbiome-directed, and corticosteroid interventions used within a step-up treatment strategy in dogs with CIE under routine clinical conditions. Fifty-six dogs were enrolled. Clinical response was assessed using the Canine Chronic Enteropathy Clinical Activity Index (CCECAI), together with faecal calprotectin, serum folate, and serum cobalamin concentrations. In the dietary stage, both novel-protein and hydrolysed diets significantly reduced CCECAI and faecal calprotectin. Clinical remission, defined as a final CCECAI score ≤ 3, was achieved in 64% and 60% of dogs, respectively. Baseline-adjusted analyses likewise showed no significant between-group differences in CCECAI, faecal calprotectin, or cobalamin. In dogs receiving second-line treatment, both metronidazole and probiotics combined with fibre significantly reduced CCECAI and faecal calprotectin, while baseline-adjusted comparisons demonstrated no significant differences between treatments for the evaluated outcome. In dogs receiving corticosteroid-containing treatment, substantial numerical reductions in CCECAI and faecal calprotectin were observed in both the prednisone-containing and budesonide-containing regimens; however, the very small subgroup sizes and concomitant dietary, probiotic, and fibre interventions precluded definitive conclusions regarding the specific effects or comparative efficacy of the individual corticosteroids. These findings provide real-world clinical evidence supporting a structured step-up approach to canine CIE and provide a rationale for larger, adequately powered controlled studies to determine whether non-antibiotic microbiome-directed strategies and locally acting corticosteroid-containing therapy can reduce reliance on empirical antimicrobial treatment and systemic corticosteroids, thereby minimising the potential adverse consequences associated with these therapies.},
}

@article {pmid42939166,
year = {2026},
author = {Yorozui, Y and Inoue, S and Mu, Y and Matsuyama, S and Ohkura, S and Morita, Y},
title = {Rumen-Protected Niacin Supplementation Modulates Uterine Arterial Hemodynamics and Endometrial Microbiome Functional Potential in Postpartum Japanese Black Cattle.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {20},
pages = {},
pmid = {42939166},
issn = {2076-2615},
support = {KEN82//Ito Foundation of Japan/ ; 20K15647//Japan Society for the Promotion of Science/ ; 24K09209//Japan Society for the Promotion of Science/ ; },
abstract = {This study examined whether rumen-protected niacin (RPN) supplementation is associated with uterine hemodynamics and the postpartum uterine environment in Japanese Black cattle. Experiment 1 used a crossover design to evaluate acute uterine vascular responses to RPN in synchronized heifers (n = 6). Experiment 2 was an exploratory evaluation of postpartum cows (n = 6) during long-term RPN supplementation using uterine artery Doppler measurements, uterine inflammatory indicators, and endometrial microbiome analysis. In Experiment 1, high-dose RPN administration was associated with changes in uterine hemodynamic parameters (p < 0.05) and higher baseline-adjusted whole-blood NAD[+] concentrations across the post-administration period (p < 0.001). In Experiment 2, RPN supplementation was associated with time-dependent differences in uterine hemodynamic parameters, whereas uterine inflammatory indicators were not significantly affected. Although broad treatment-associated differences in overall endometrial microbial diversity and community structure were not detected, exploratory differences in specific bacterial taxa were observed between treatment groups, and predicted metabolic pathways showed treatment-dependent temporal changes. Exploratory integrated analysis further identified concurrent within-animal patterns across uterine hemodynamics, microbial community structure, and predicted microbial functional potential. These exploratory findings suggest that RPN may modulate uterine hemodynamics and be associated with selective changes in the postpartum uterine environment, providing a basis for further investigation of the relationships among nutritional intervention, uterine hemodynamics, the endometrial microbial ecosystem, and subsequent reproductive physiology.},
}

@article {pmid42939184,
year = {2026},
author = {Ho, ST and Chen, MJ},
title = {From Microbiome Associations to Deployable Precision Probiotics in Animals: A Critical Narrative Review and Proposed Causal Evidence Framework for Next-Generation Probiotic Development.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {20},
pages = {},
pmid = {42939184},
issn = {2076-2615},
support = {NSTC 115-2313-B-002-006-MY3//National Science and Technology Council/ ; },
abstract = {Next-generation probiotics (NGPs) are promoted as precision tools for animal health, yet the term is often applied to uncommon taxa before causality, safety and target-species efficacy are established. This critical narrative review reframes animal NGPs as a development pathway rather than a taxonomic category. A structured PubMed search was last run on 14 September 2026 with a publication date cutoff of 1 September 2026 and was supplemented by citation tracing and targeted searches of authoritative sources. From the screened literature, 45 representative and conceptually informative sources were purposively selected for the final narrative synthesis; the review was not intended to provide systematic or exhaustive coverage. The detailed synthesis focused on terrestrial farm and companion animals, whereas equine, rabbit and aquaculture studies were treated as boundary evidence. We evaluate how strain-resolved metagenomics, culturomics, metatranscriptomics, metaproteomics, metabolomics, host transcriptomics, machine learning, metabolic modeling and perturbation systems can move discovery beyond association. Studies across animal sectors show many biomarkers but limited causal validation, strain tracking, formulation data, multisite trials and ecological safety assessment. We propose an author-developed conceptual framework comprising a cumulative evidence ladder, from reproducible associations to field-ready deployment, and the ANIMAL-NGP reporting checklist (Animal endotype, Native ecological fit, Identity and genomic safety, Mechanism, Administration and manufacturing, and Longitudinal validation). These tools are intended to align claims with evidence and require prospective application and external validation. Multi-omics should therefore function as an evidence-navigation system, not as a substitute for causality.},
}

@article {pmid42939185,
year = {2026},
author = {Fu, L and Xue, Y and Wang, Y and Zhao, S and Wang, Q and Che, H},
title = {Potential Feasibility and Perspectives of Fecal Microbiota Transplantation for Restoring Gut Function in Giant Pandas.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {20},
pages = {},
pmid = {42939185},
issn = {2076-2615},
support = {//China Agricultural University-Sichuan Advanced Agricultural & Industrial Institute/ ; },
abstract = {Although the giant panda (Ailuropoda melanoleuca) relies almost exclusively on bamboo, its carnivore-like gastrointestinal tract has limited capacity for fiber digestion. The gut microbiota contributes to bamboo-derived nutrient utilization, although the extent of this contribution remains limited. Captivity-associated dietary and environmental changes frequently disrupt this microbial ecosystem, resulting in impaired digestive function and reduced physiological resilience. Conventional interventions, including antibiotics and single-strain probiotics, are generally insufficient to restore the complexity and stability of the gut microbiota. Fecal microbiota transplantation (FMT), which reconstructs the gut microbial ecosystem by transferring an intact microbial community, has demonstrated therapeutic potential in humans and various animal models. However, its feasibility in giant pandas remains unclear because their short intestinal tract, absence of fermentation chambers, rapid gastrointestinal transit, and host-mediated ecological filtering substantially limit donor microbiota engraftment. This review evaluates the biological rationale and technical feasibility of oral FMT in giant pandas by integrating evidence from gastrointestinal physiology, microbial ecology, and conservation medicine. This review identifies the principal barriers to microbial engraftment. It synthesizes a giant panda-specific framework from the available literature, encompassing function-oriented donor selection, optimized microbial delivery strategies, and multidimensional efficacy assessment. Collectively, this synthesis provides a theoretical foundation for future FMT research in giant pandas and offers a conceptual reference for microbiota-based interventions in the conservation of endangered wildlife.},
}

@article {pmid42939211,
year = {2026},
author = {Jin, X and Lu, Q and Zhang, Z and Liang, R and Zhang, T and Luo, Q},
title = {Salmonella Phage X5 Alleviates Salmonella pullorum-Induced Growth Impairment in Chickens: Associations with Reduced Salmonella Burden, Modulated Intestinal Microbiome and Attenuated Inflammatory Responses.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {20},
pages = {},
pmid = {42939211},
issn = {2076-2615},
support = {CARS-41//The China Agriculture Research System of MOF and MARA/ ; 2021CFA019//the Key Projects of Hubei Natural Science Foundation/ ; 2022BBA0055//the Key Research and Development Project of Hubei Province/ ; },
abstract = {Salmonella infection of chickens can cause persistent intestinal inflammation, intestinal microbiota disorder, and growth obstruction, which is an important bacterial disease causing significant economic losses in poultry farming. Phages, as an alternative to antibiotics as biological control agents, have advantages such as precise killing and no residue. This study aims to explore the effect and mechanism of the lytic Salmonella phage X5 in alleviating the growth impairment in chickens caused by S. pullorum. Oral administration of phages effectively prevents and controls S. pullorum infection in chickens. Phages can alleviate growth impairment caused by Salmonella, reduce Salmonella levels in the liver and ileum, lower serum concentrations of IL-1β, IL-6, and TNF-α, and decrease mRNA expression of inflammatory cytokines IL-1β and IL-6 in the ileum. They also enhance mRNA expression of tight junction proteins Claudin-3 and ZO-1 in the ileal mucosa, helping maintain intestinal barrier integrity, and modulate the microbial community composition in the cecum. In the context of reduced and restricted antibiotic usage in livestock production, this study initially verified the protective effect of phage X5 against Salmonella pullorum infection in chickens, providing an experimental basis for the application of phages in the prevention and control of this bacterial disease, and offering new clues for analyzing the potential pathways through which bacteriophages confer host protective effects.},
}

@article {pmid42939245,
year = {2026},
author = {Ma, C and Li, C and Li, H and Liu, J and Liao, K and Li, Y and Ren, J and Wei, G and Li, X},
title = {Effects of Thymol Supplementation in Health Care Sand on Growth Performance, Serum Biochemical Parameters, Fecal Microbial Diversity, and Fecal Metabolites in Squabs.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {20},
pages = {},
pmid = {42939245},
issn = {2076-2615},
support = {2026650005000075//The Horizontal Research Project of Xinjiang Agricultural University/ ; 2023B02036-2, 2023B02036-2-1, and 2023B02036-2-2//The Key Research and Development Program of the Xinjiang Uygur Autonomous Region/ ; },
abstract = {This study aimed to investigate the effects of thymol supplementation in health care sand on growth performance, serum biochemical parameters, fecal microbial diversity, and fecal metabolites in Grey King squabs. A total of 160 healthy 28-day-old Grey King squabs were selected and randomly assigned to four treatment groups: the CON, 2%Thy, 3%Thy, and 4%Thy groups. Each group consisted of 10 replicates with four squabs per replicate, resulting in a total of 40 squabs per group. Under identical feeding management conditions and dietary nutrient levels, squabs in the CON group received the basal diet plus 5 g of health care sand; those in the 2%Thy group received the basal diet plus 5 g of health care sand containing 2% thymol; those in the 3%Thy group received the basal diet plus 5 g of health care sand containing 3% thymol; and those in the 4%Thy group received the basal diet plus 5 g of health care sand containing 4% thymol. The experiment lasted for 30 days. During the experimental period, the pigeons were housed in cages measuring 45 cm × 50 cm × 60 cm. Each pigeon was provided with 40 g of diet and 5 g of health care sand daily and had free access to water. After Benjamini-Hochberg false discovery rate correction, no significant differences were observed in growth performance, body measurements, apparent nutrient retention, or energy metabolizability among treatments (q > 0.05). However, thymol-supplemented groups exhibited significantly increased serum total antioxidant capacity and superoxide dismutase, glutathione peroxidase, and catalase activities, together with decreased malondialdehyde levels (q < 0.05). Fecal microbiome and metabolomic analyses were restricted to the CON and 3%Thy groups, with the 3%Thy group selected after evaluation of the phenotypic and physiological responses rather than being prespecified before the experiment. These omics comparisons were therefore considered exploratory. No statistically significant difference in overall fecal microbial community composition was detected between the two groups, whereas 17 candidate differential fecal metabolite features were observed. These features were mainly putatively annotated as lipids and lipid-like molecules, organic acids and derivatives, organoheterocyclic compounds, and benzenoids. Among the supplementation levels evaluated, the 3%Thy group showed comparatively favorable numerical responses in several measured parameters and may be considered a candidate level for further investigation. However, the present findings do not establish an optimal thymol supplementation level, and the biological significance of the exploratory fecal omics results requires further validation.},
}

@article {pmid42939407,
year = {2026},
author = {Deryabin, D and Vlasenko, L and Karimov, I and Kosyan, D and Rakhmatullin, S and Duskaev, G},
title = {Microbiome-Related Amino-Acid Profiles of Liver and Muscle Tissues in Arbor Acres Broiler Chickens.},
journal = {Biology},
volume = {15},
number = {20},
pages = {},
pmid = {42939407},
issn = {2079-7737},
support = {22-16-00036//Russian Science Foundation/ ; },
abstract = {The study, designed as a group-level integrative data analysis, included homogeneous datasets obtained from 24 Arbor Acres chicken groups. Quantitative amino-acid analysis in chicken tissues was carried out using the capillary electrophoresis method. Gut microbial community analysis was performed using 16S rRNA gene-sequencing technology on the Illumina MiSeq platform. Amino-acid analysis of liver samples revealed 10 Arg-high and 14 Arg-low chicken groups, while for thigh samples, the ratio of Arg-high and Arg-low groups was 18/6, respectively. The gut microbiomes of chickens with an Arg-high amino-acid profile showed increased Chao1 and Shannon diversity index values, defined by a significant abundance of several members of the phylum Bacillota (formerly Firmicutes), including the genera Christensenella, Eisenbergiella, Dysosmobacter, Anaerotignum, Oscillibacter, unclassified Oscillospiraceae, and Lachnospiraceae. In contrast, the gut microbial communities of chickens with low Arg content showed decreased Chao1 and an increased Shannon dominance index, which was explained by the significant abundance of the genus Alistipes belonging to the phylum Bacteroidota (formerly Bacteroidetes). Prediction of amino-acid biosynthetic pathways in chicken-gut microbiomes revealed a general trend toward increased relative abundance of most KEGG orthologs in Arg-high groups, as well as a number of positive links with Arg and Val/Leu + Ile content in liver and thigh samples.},
}

@article {pmid42939437,
year = {2026},
author = {Xu, J and Liu, Y and Yun, J and Cheng, X and Wang, E and Tang, C},
title = {Keystone K-Strategists Shape Microbial Co-Occurrence Networks in Shale-Gas Wellpad Soils in the Field, Sichuan Basin, China.},
journal = {Biology},
volume = {15},
number = {20},
pages = {},
pmid = {42939437},
issn = {2079-7737},
support = {2024D107-01-06//PetroChina Southwest Oil and Gas Field Company (China)/ ; },
abstract = {Shale-gas extraction imposes persistent, low-intensity, multi-factor disturbances on terrestrial soil ecosystems, driven by flowback-fluid-derived salinization, drilling-residue deposition, and moderate petroleum hydrocarbon contamination. However, microbial community assembly mechanisms and the corresponding ecological strategies under such combined chronic perturbations remain insufficiently understood. This study employed 16S rRNA gene sequencing, quantitative PCR, and molecular ecological network (MEN) analysis to characterize the soil microbiome within the Changning shale-gas field, Sichuan Basin, China. The results revealed that microbial communities in shale-gas wellpad soils formed highly modular (M = 0.786), non-random "small-world" co-occurrence networks, indicating intrinsically stable microbial systems. Via Zi-Pi topological classification, six low-abundance (<0.63%) keystone taxa were identified: three module hubs (OTU11572, OTU14908, OTU11976) and three connectors (OTU8845, OTU13035, OTU8962), phylogenetically affiliated with Acidobacteriota, Chloroflexi, and Actinobacteriota. These keystone organisms exhibited typical K-strategy traits, including high network connectivity (degree = 21-24), metabolic stability, and dependence on inter-taxa cooperative interactions. Significant positive correlations were detected between these K-strategy keystone species and anaerobic functional genes (nirS, nirK, dsrAB) responsible for denitrification and sulfate reduction, highlighting their adaptation to fluctuating redox environments generated by drilling-cutting accumulation. Distance-based redundancy analysis (Db-RDA) further demonstrated that electrical conductivity (representing salinization stress from flowback-water intrusion) and soil organic matter acted as the dominant environmental filters shaping microbial community composition, outweighing the influence of labile inorganic nutrients. Overall, this work provides novel evidence that K-selection dominates microbial community assembly under chronic soil disturbance associated with shale-gas extraction. Keystone K-strategists sustain modular network stability through the combination of metabolic plasticity and anaerobic respiratory adaptation. These findings expand r/K-selection theory to anthropogenically disturbed soil habitats and offer theoretical guidance for soil ecological restoration and risk assessment for shale-gas exploiting regions.},
}

@article {pmid42939458,
year = {2026},
author = {Rizzo, S and Schiavone Panni, F and Di Vito, M and Garzoli, S and Coggiatti, D and Mariotti, M and Sanguinetti, M and Percio, A and Urbani, A and Greco, V and Bugli, F},
title = {In Vitro Study of the Antimicrobial and Prebiotic Activity of Origanum heracleoticum Hydrolates from Two Italian Crops and the Proteomic Response of Probiotic Bacteria.},
journal = {Biology},
volume = {15},
number = {20},
pages = {},
pmid = {42939458},
issn = {2079-7737},
support = {PE00000007, INF-ACT//Ministero dell'università e della ricerca/ ; //Università Cattolica del Sacro Cuore/ ; },
abstract = {This study explores the chemical composition and biological activities of essential oils (EOs) and hydrolates (Hys) from Origanum heracleoticum (OH), an aromatic plant with known applications in the food industry. While EOs have been widely studied, Hys (co-products of EO distillation) remain largely overlooked. OH was cultivated in the Lucanian and Casola areas, respectively in the regions of Basilicata and Emilia-Romagna, to evaluate the influence of geographic and climatic factors on product composition and activity. Gas chromatographic analysis showed significant variability between the EO and its related Hy. Carvacrol emerged as the dominant compound, ranging from 71% to 91% in both extracts followed by γ-terpinene and thymol in EOs and Hys, respectively. Both EOs and Hys exhibited antimicrobial activity against tested bacterial strains even if active compounds of Hys were relatively more effective than that of EOs. Notably, Lactobacillus rhamnosus (probiotic) showed greater resistance to EOs compared to Escherichia coli (pathogenic), whereas Hys inhibited L. rhamnosus at 25% v/v, while no MIC against E. coli was reached within the tested concentration range (>50% v/v). Interestingly, sub-inhibitory concentrations of Hys (especially those from Lucan area) stimulated L. rhamnosus growth, promoting earlier exponential phase entry and higher final cell densities. Proteomic analysis revealed associated changes in protein secretion, suggesting adaptive metabolic responses. These findings highlight the distinct chemical and biological properties of Hys obtained from a spice widely used in food, and their potential as functional agents. Their ability to influence L. rhamnosus growth in vitro supports further investigation of their potential microbiota-modulating properties and the development of food supplements and microbiome-friendly formulations.},
}

@article {pmid42939495,
year = {2026},
author = {Adam, SY and Husien, HM and Mathapo, MC and Ahmed, AA and Essa, MOA and Abdulrahman, MY and Tyasi, TL and Cai, D},
title = {Environmental Stress and Feed Intake in Chickens: Neuroendocrine Mechanisms and Mitigation Strategies.},
journal = {Biology},
volume = {15},
number = {20},
pages = {},
pmid = {42939495},
issn = {2079-7737},
abstract = {Environmental stresses negatively affect feed intake in chickens, leading to reduced growth rates and significant economic losses. This review examined the molecular mechanisms of stress-induced loss of appetite, focusing on the hypothalamic regulation of appetite-associated neuropeptides, the role of the HPA axis, elevated CORT levels, and stress-induced inflammatory cytokines that inhibit appetite-stimulating signals. Current mitigation strategies, such as cooling systems, nutritional supplements, early-life programs and genetic selection using QTL mapping, have been shown to provide varying levels of effectiveness. Limited understanding of how multiple stressors act in concert at the cellular level in natural environments is a major limitation. Furthermore, the majority of studies focus on acute stress, while low-grade chronic stress models are underrepresented despite their commercial importance. A significant shortcoming is the absence of validated non-invasive biomarkers to predict stress-induced feed reductions before production losses begin. This review examines the molecular neuroendocrine mechanisms of stress-induced anorexia and the available mitigation strategies, highlighting the disconnect between mechanistic understanding and current interventions, and emphasizing the need for mechanism-based proactive measures to sustainably improve feed intake and productivity in stressed chickens. Therefore, future research should focus on integrated multi-stress frameworks and the evaluation of the lasting epigenetic effects of early-life interventions in chickens.},
}

@article {pmid42939502,
year = {2026},
author = {Basave-Villalobos, E and Sigala, JA and Jacobo-Salcedo, MDR and Sánchez-Cohen, I and Constante-García, V and Sánchez-Ledesma, JA and Nava-Reyna, E},
title = {Grazing Management Regimen Shapes Soil Carbon Stocks and Associated Bacterial Community Composition in a Semi-Arid Rangeland.},
journal = {Biology},
volume = {15},
number = {20},
pages = {},
pmid = {42939502},
issn = {2079-7737},
support = {0265435769//Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias/ ; },
abstract = {Semi-arid rangelands are highly vulnerable to climate change and overgrazing, yet the functional coupling between soil carbon stabilization and microbial recovery remains largely unquantified. This study was carried out in Northern Mexico (24°0'33″ N, 104°42'28″ W, 1990 m.a.s.l.) and evaluated associations between a grazing management gradient comprising continuous grazing (CG), closed non-selective intensive grazing (GE), and open non-selective intensive grazing (SG) on soil carbon stocks and different labile fractions, bacterial community structures, and functional metabolic pathways in semi-arid soils. The results show that SG showed the highest observed organic and inorganic carbon stocks (SOC and SIC stocks, respectively), along with the labile carbon (LC) fraction. Conversely, GE favors the accumulation of stable, non-labile carbon (NLC). Although alpha diversity remained unaffected, grazing management induced differences in beta diversity. Redundancy and LEfSe analyses revealed a strong coupling between carbon fractions and microbial assembly, characterized by the exclusive enrichment of copiotrophic biomarker families (Burkholderiaceae and Sphingobacteriaceae) under SG. Furthermore, predictive functional profiling (PICRUSt2 and ANCOM) showed that pathways such as tRNA charging and nicotinate degradation were enriched under SG and GE, reflecting potential metabolic capacities and inferred microbial adjustments to heterogeneous, excreta-derived nutrient microenvironments during intermediate recovery states. Ultimately, the findings suggest that targeted rotational grazing may contribute to improved soil carbon stocks and microbial community recovery in semi-arid rangelands.},
}

@article {pmid42939512,
year = {2026},
author = {Yi, KH and Lee, HE and Kim, HS and Techapichetvanich, T},
title = {Deoxycholic Acid at the Interface of Bile Acid Metabolism and Adipose Tissue Remodeling: From Endogenous Signaling to Injectable Adipocytolysis.},
journal = {Current issues in molecular biology},
volume = {48},
number = {10},
pages = {},
pmid = {42939512},
issn = {1467-3045},
abstract = {Deoxycholic acid (DCA) occupies an unusual position at the boundary between endogenous metabolism and therapeutic tissue ablation. Under physiological conditions, DCA is a gut microbial secondary bile acid that enters the enterohepatic circulation, contributes to the composition of the bile-acid pool, and participates in receptor-dependent signaling. When delivered as a concentrated injectable drug into subcutaneous fat, however, DCA acts primarily as an amphipathic cytolytic molecule that disrupts cell membranes, initiates adipocyte death, and provokes an organized inflammatory and reparative response. These two biological identities are often conflated, leading to imprecise descriptions of injectable DCA as a lipolytic, receptor-targeted, or metabolically selective treatment. This critical review integrates evidence from bile-acid biochemistry, microbiology, membrane biophysics, adipose-tissue biology, human histology, pharmacokinetics, and clinical trials. We describe the microbial formation, transport, conjugation, and signaling actions of endogenous DCA; distinguish physiological receptor signaling from concentration-dependent detergent injury; and examine the temporal sequence of adipocytolysis, innate immune recruitment, lipid clearance, fibrovascular remodeling, and volume reduction after local injection. We also assess systemic exposure, clinical efficacy, anatomic determinants of safety, and the limitations of extrapolating submental data to large-volume or non-submental treatment. Finally, we propose a translational metabolomics and lipidomics framework that combines local interstitial sampling, plasma bile-acid profiling, lipid mediator analysis, imaging, and tissue phenotyping. The central conclusion is that injectable DCA is best understood as a controlled local cytolytic perturbation superimposed on a tightly regulated endogenous bile-acid system. Framing the intervention in this way clarifies terminology, identifies measurable biomarkers, and creates a rational path toward dose optimization, patient selection, and safer clinical translation.},
}

@article {pmid42939527,
year = {2026},
author = {Yang, G and Yang, W and Liu, Y and Wang, H},
title = {Exercise-Driven Remodeling of the Gut Microbiome: Reciprocal Regulation of Structural and Functional Adaptations in Elite Athletes.},
journal = {Current issues in molecular biology},
volume = {48},
number = {10},
pages = {},
pmid = {42939527},
issn = {1467-3045},
support = {No. ZL22018//Lingnan Normal University/ ; No. 2026JSJY29//Lingnan Normal University/ ; },
abstract = {The gut microbiome plays a critical role in training adaptation and athletic performance. Athletes exhibit elevated gut microbial α-diversity and enrichment of short-chain fatty acid (SCFA)-producing genera, although these associations may be confounded by dietary and lifestyle factors. Exercise regulates the gut microbiota in a non-linear, intensity-dependent manner: moderate-intensity training preserves intestinal barrier integrity, whereas high-intensity exercise exceeding 85% of maximal oxygen uptake may precipitate dysbiosis, although this remains to be directly validated. Periodized training drives sustained microbial remodeling, with adaptive changes persisting for months in ultra-endurance athletes. Mechanistically, exercise enhances SCFA synthesis, remodels bile acid and tryptophan metabolism, and modulates host energy homeostasis and inflammatory status through AMPK, FXR/TGR5, and epigenetic pathways. In turn, the microbiota exerts bidirectional effects on skeletal muscle mitochondrial function, central fatigue, and post-exercise recovery via the gut-muscle, gut-brain, and immune axes. Probiotic and dietary interventions show translational promise, yet their application is constrained by strain-specific efficacy and the absence of standardized protocols. Finally, we propose the Microbiota-Exercise Threshold-Adaptation-Reconsolidation (METAR) hypothesis framework, which stratifies putative microbiota responses into three intensity-defined zones and three athlete subtypes, providing a testable foundation for precision training that awaits empirical validation.},
}

@article {pmid42939546,
year = {2026},
author = {Cozma, D and Tudoran, C and Vacarescu, C},
title = {Metformin, SGLT2 Inhibitors, and Intermittent Fasting: Convergent Pathways to Healthspan Extension, Cardiovascular Longevity, and Cancer Prevention-A Narrative Review.},
journal = {Current issues in molecular biology},
volume = {48},
number = {10},
pages = {},
pmid = {42939546},
issn = {1467-3045},
abstract = {The biology of aging and the epidemiology of cardiovascular disease share a common molecular pathway expressed through nutrient-sensing kinases, mitochondrial redox state, and chronic inflammation. Three interventions have independently emerged as translators of that interconnection into clinical benefit: metformin, a biguanide that has evolved from a first-line anti-diabetic into the world's most extensively studied putative geroprotector; the sodium-glucose cotransporter-2 inhibitors (SGLT2is), pharmacological generators of a fasting-mimetic state that has reshaped heart failure outcomes across the ejection-fraction spectrum; and intermittent fasting (IF), the evolutionary archetype from which both agents partially derive their effects on longevity. Based on the synthetized evidence, we propose a stage-stratified clinical framework for integrated deployment. To find the manuscripts relevant for our narrative review, we searched the medical literature by using key words ("metformin"; "SGLT2i"; "intermittent fasting"; "health span"; "cardiovascular longevity"; "cancer chemoprevention"; "gut microbiome"; "geroprotection"; "heart failure") combined through Boolean operators (AND/OR). This narrative review integrates preclinical mechanistic evidence, landmark randomized controlled trial data, and emerging data on cancer chemoprevention and gut microbiome remodeling to provide a rigorous, side-by-side analysis of all three strategies. We delineate molecular convergence on adenosine monophosphate kinase (AMPK) activation, mechanistic target of rapamycin complex 1 (mTORC1) suppression, enhanced autophagy, mitochondrial renewal, inflammatory responses, and anti-cancer biology, while mapping critical divergences in specific populations, lifespan timing, combinability, and safety. Our proposed framework has to be treated with caution, as it is based on the current evidence base, which lacks dedicated outcome trials for IF and published randomized clinical trial data for metformin in non-diabetic adults.},
}

@article {pmid42939670,
year = {2026},
author = {Dawson, ZD and Martin, T and Ji, E and Lee, KE and Chen, X and Zhou, X and St Jean, S and Li, Y and Ma, J},
title = {PAD2 Deficiency Reveals Sex-Divergent Colonic Homeostasis, β-Catenin Remodeling, and Antibiotic-Sensitive Phenotypes.},
journal = {Biomolecules},
volume = {16},
number = {10},
pages = {},
pmid = {42939670},
issn = {2218-273X},
support = {R01AG071676/AG/NIA NIH HHS/United States ; R01AG072430/AG/NIA NIH HHS/United States ; R01EY036243/EY/NEI NIH HHS/United States ; R01HL157215//National Heart Lung and Blood Institute/ ; },
mesh = {Animals ; *beta Catenin/metabolism ; Female ; Male ; Mice ; Colitis/chemically induced/metabolism/genetics/pathology ; *Anti-Bacterial Agents/pharmacology ; Humans ; Homeostasis/drug effects ; *Protein-Arginine Deiminase Type 2/deficiency/genetics/metabolism ; Mice, Knockout ; *Colon/metabolism/pathology/drug effects ; Phenotype ; Intestinal Mucosa/metabolism ; Dextran Sulfate ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Peptidylarginine deiminase 2 (PAD2) catalyzes protein citrullination and is implicated in inflammatory bowel disease and colorectal cancer. However, its role in regulating the intestinal epithelium and the influence of biological sex and the microbiome remain poorly defined. This study investigated the relationships among PAD2 deficiency, sex-divergent epithelial states, β-catenin regulation, and the intestinal microbiome. Global PAD2 knockout and wild-type littermate mice of both sexes were characterized under basal conditions and following dextran sodium sulfate-induced colitis. Intestinal epithelial phenotypes were assessed by histology, immunofluorescence, immunoblotting, quantitative RT-PCR, and immunoprecipitation. Gut microbial communities were evaluated by shotgun metagenomics, while broad-spectrum antibiotic treatment, fecal protein immunoblotting, and recombinant human PAD2 exposure in vitro were used to examine relationships among antibiotic-sensitive factors, β-catenin regulation, and epithelial phenotypes. PAD2 deficiency was associated with distinct epithelial states in male and female colons before injury. Male KO mice displayed increased β-catenin phosphorylation and increased susceptibility to DSS colitis, whereas female KO mice demonstrated increased total β-catenin abundance and preservation of structural epithelial features following injury. Female KO microbiota exhibited genotype-associated differences in microbial community composition by exploratory Bray-Curtis PERMANOVA. Broad-spectrum antibiotic treatment altered the female epithelial phenotype, reduced active β-catenin, and progressively depleted luminal PAD2-immunoreactive proteins. Exogenous recombinant human PAD2 increased epithelial protein citrullination and altered active β-catenin abundance in HT29 cells. Collectively, these findings demonstrate both sex-specific and sex-divergent colonic phenotypes while supporting a framework connecting PAD2 biology, epithelial architecture, and the microbial environment during intestinal maintenance and injury.},
}

Animals
*beta Catenin/metabolism
Female
Male
Mice
Colitis/chemically induced/metabolism/genetics/pathology
*Anti-Bacterial Agents/pharmacology
Humans
Homeostasis/drug effects
*Protein-Arginine Deiminase Type 2/deficiency/genetics/metabolism
Mice, Knockout
*Colon/metabolism/pathology/drug effects
Phenotype
Intestinal Mucosa/metabolism
Dextran Sulfate
Gastrointestinal Microbiome/drug effects

@article {pmid42939680,
year = {2026},
author = {Akhtar, MS and Aslam, M and Beg, MMA},
title = {The Nuclear Damage-Response Code of Cutaneous Wound Repair: Mechanotransduction, cGAS-STING, Senescence, and Regenerative Interfaces.},
journal = {Biomolecules},
volume = {16},
number = {10},
pages = {},
pmid = {42939680},
issn = {2218-273X},
mesh = {Humans ; *Wound Healing ; *Mechanotransduction, Cellular ; cGAS-STING Signaling Pathway ; Animals ; *Nucleotidyltransferases/metabolism ; STING Protein ; *Cell Nucleus/metabolism ; Cyclic Guanosine Monophosphate-Adenosine Monophosphate Synthase ; *Skin/metabolism/injuries/pathology ; *Membrane Proteins/metabolism ; Cellular Senescence ; Regeneration ; },
abstract = {Chronic cutaneous wounds are often described as disorders of inflammation, infection, perfusion, or extracellular matrix turnover, yet these categories do not fully explain why a wound that initially detects injury fails to re-enter a coordinated program of repair. This Perspective proposes a unifying model in which the nucleus acts as a damage integrator at the wound edge. Mechanical strain, osmotic swelling, oxidative stress, chromatin fragmentation, and mitochondrial injury converge on nuclear-envelope tension, nuclear rupture, cytoplasmic deoxyribonucleic acid sensing, and senescence-associated transcription. When the signal is brief and spatially restricted, it can support leukocyte recruitment, keratinocyte migration, matrix remodeling, and early host defense. When it is amplified by diabetes, aging, tissue stiffness, biofilm-compatible inflammation, or defective autophagic and efferocytic clearance, the same pathway becomes a self-reinforcing loop that sustains interferon signaling, inflammasome activity, endothelial dysfunction, fibroblast memory, and impaired epidermal differentiation. The review integrates evidence from single-cell wound atlases, mechanobiology, innate immune deoxyribonucleic acid sensing, mitochondrial stress, macrophage biology, senescence, microbiome studies, and smart biomaterials. It argues that future wound therapeutics should not simply accelerate closure, but should classify and reset the temporal polarity of nuclear damage responses. Nucleus-aware dressings, local signal-gated inhibitors, senolytic or senomorphic interfaces, and biomaterials that reduce pathological mechanical memory may provide more precise ways to convert chronic wound fields into regenerative ones.},
}

Humans
*Wound Healing
*Mechanotransduction, Cellular
cGAS-STING Signaling Pathway
Animals
*Nucleotidyltransferases/metabolism
STING Protein
*Cell Nucleus/metabolism
Cyclic Guanosine Monophosphate-Adenosine Monophosphate Synthase
*Skin/metabolism/injuries/pathology
*Membrane Proteins/metabolism
Cellular Senescence
Regeneration

@article {pmid42939710,
year = {2026},
author = {Ascari, F and Baldelli, L and Scicchitano, D and Pellegrini, C and Ravaioli, F and De Fanti, S and Esposito, E and Porru, E and Di Laudo, F and Lodi, R and Bacalini, MG and Candela, M and Provini, F and Fiori, J and Interino, N},
title = {Exploratory Metabolomic and Metagenomic Profiling of Fecal Samples in Isolated REM Sleep Behavior Disorder.},
journal = {Biomolecules},
volume = {16},
number = {10},
pages = {},
pmid = {42939710},
issn = {2218-273X},
support = {//Ministero della Salute/ ; 2024.0058//Fondazione Del monte di Bologna e di Ravenna/ ; },
mesh = {Humans ; *REM Sleep Behavior Disorder/metabolism/microbiology/genetics ; *Feces/chemistry/microbiology ; *Metabolomics/methods ; Female ; Male ; Cross-Sectional Studies ; *Metabolome ; Middle Aged ; *Metagenomics/methods ; Multiomics ; Gastrointestinal Microbiome ; Aged ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Isolated REM sleep behavior disorder (iRBD) is among the most reliable prodromal markers of α-synucleinopathies. Under the body-first (gut-first) model of α-synuclein pathology, in which pathology may originate in the enteric nervous system and ascend to the brain, the gut is a biologically plausible compartment in which early and accessible molecular alterations might be detectable; however, the fecal metabolome remains poorly investigated in this population. In this exploratory, cross-sectional study of 21 iRBD patients and 15 healthy controls, we characterized fecal samples through an integrated multi-omics framework. The fecal metabolome was profiled on two complementary mass spectrometry platforms: HS-SPME GC-EI-high-resolution MS, used for both untargeted volatilomics and targeted quantification of linear and branched short-chain fatty acids, and untargeted LC-MS/MS for the non-volatile fraction. Gut microbial community composition was characterized on the same material by 16S rRNA gene sequencing, and the metabolomic and microbial layers were combined by DIABLO multi-omics integration. Linear short-chain fatty acids were preserved, whereas branched-chain fatty acids were selectively increased in iRBD, indicating a shift toward proteolytic fermentation. Volatile indole was reduced, while p-cresol and 2-octanone were increased, paralleled at the LC-MS/MS level by attenuation of the tryptophan-indole axis, class-level bile acid depletion, and increased acylcarnitines. The microbiome was depleted of Blautia and Faecalibacterium and enriched in Oscillospirales. Integration resolved a coherent host-microbe signature that discriminated iRBD patients from controls within this discovery cohort (84.8% cross-validated accuracy). These cross-sectional findings characterize candidate fecal signatures associated with iRBD; given the exploratory design and the limited sample size, they are hypothesis-generating, and their value for predicting phenoconversion remains to be established in prospective studies.},
}

Humans
*REM Sleep Behavior Disorder/metabolism/microbiology/genetics
*Feces/chemistry/microbiology
*Metabolomics/methods
Female
Male
Cross-Sectional Studies
*Metabolome
Middle Aged
*Metagenomics/methods
Multiomics
Gastrointestinal Microbiome
Aged
RNA, Ribosomal, 16S/genetics

@article {pmid42939738,
year = {2026},
author = {Gheri, CF and Luisi, MLE and Lucarini, L and Biffi, B and Madiai, S and Roccotelli, A and Zipoli, R and Sgambellone, S and Provensi, G and Macchi, C and Masini, E and Ceccherini, MT},
title = {An Exploratory Randomized Clinical Trial to Assess the Effects of Vitamin D and Leucine-Enriched Whey Protein Supplementation on Inflammaging and Gut Eubacterial Biomass in Cardiac Rehabilitation Patients.},
journal = {Biomolecules},
volume = {16},
number = {10},
pages = {},
pmid = {42939738},
issn = {2218-273X},
support = {2015/0885//Ente Cassa di Risparmio di Firenze/ ; },
mesh = {*Whey Proteins/pharmacology/administration & dosage ; Humans ; *Leucine/pharmacology/administration & dosage ; Dietary Supplements ; Female ; Male ; *Inflammation/drug therapy ; *Vitamin D/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Aged ; Interleukin-6/blood ; Middle Aged ; C-Reactive Protein/metabolism ; },
abstract = {Whey protein (WP) supplementation could affect low-grade inflammation (inflammaging) and gut microbiome dysbiosis, both of which play key roles in non-communicable diseases (NCDs). Twenty-seven cardiac rehabilitation patients were randomly allocated to two groups: the case group (CA) (n = 14) received 80 g/die vitamin D and leucine-enriched WP supplement, combined with a standard hospital diet, while the control group (CO, n = 13) received the standard hospital diet alone. Blood and stool samples were collected at baseline (T0) and after two weeks (T1). At T1, serum levels of interleukin 6 (IL-6) and C-reactive protein (CRP) significantly decreased in the CA group. Ferritin levels significantly decreased within both groups and between the two groups. No significant differences were observed for IL-1β, tumor necrosis factor-α (TNF-α), or IL-10. A clear difference in the bacterial intestinal microbiome composition between the case group at T1 (CAT1) and at T0 (CAT0), and control group at T0 (COT0) and at T1 (COT1), was observed. The eubacterial rpoB copy number, which was quantified by qPCR, significantly increased between CAT0 and CAT1, in contrast to the Lactobacillus spp. rpoB copy number. Our exploratory results showed that vitamin D and leucine-enriched WP supplementation could have a potential effect on chronic inflammation and gut microbiota composition in cardiac rehabilitation patients.},
}

*Whey Proteins/pharmacology/administration & dosage
Humans
*Leucine/pharmacology/administration & dosage
Dietary Supplements
Female
Male
*Inflammation/drug therapy
*Vitamin D/pharmacology/administration & dosage
*Gastrointestinal Microbiome/drug effects
Aged
Interleukin-6/blood
Middle Aged
C-Reactive Protein/metabolism

@article {pmid42939758,
year = {2026},
author = {Rose, SC and Rizvanov, AA and Haines, DD and Cowan, FM and Silverstein, RH and Mahmoud, FF and Solovyeva, VV and Kitaeva, KV and Hyo-Seok, S and Tosaki, A},
title = {Lifestyle-Associated Biomarkers of Cellular and Whole-Organism Aging: A Practical Roadmap for Human Geroscience Trials.},
journal = {Biomolecules},
volume = {16},
number = {10},
pages = {},
pmid = {42939758},
issn = {2218-273X},
support = {//University of Debrecen/ ; },
mesh = {Humans ; *Biomarkers/metabolism ; *Aging/metabolism/genetics ; *Geroscience/methods ; *Life Style ; Epigenesis, Genetic ; Cellular Senescence ; Oxidative Stress ; DNA Methylation ; },
abstract = {Aging is a multidimensional biological process that is not adequately captured by chronological age alone. Geroscience-the study of biological mechanisms that drive age-related functional decline and disease susceptibility-therefore requires biomarker frameworks that can identify biological aging trajectories and assess whether lifestyle-associated interventions meaningfully influence aging-related pathways. In this review, we propose a practical, mechanism-based framework for studying lifestyle-associated effects on cellular and whole-organism aging in humans. We examine major biomarker domains, including DNA-methylation-based epigenetic aging clocks, cellular senescence-associated measures, senescence-associated secretory phenotype factors, inflammaging mediators, oxidative stress indicators, mitochondrial function, metabolic and nutrient-sensing pathways, proteomic and metabolomic signatures, microbiome-associated markers, and functional measures of frailty, mobility, cognition, and resilience. We also discuss criteria for biomarker selection in exploratory and multicenter trials, emphasizing biological relevance, analytical validity, responsiveness to intervention, feasibility, reproducibility, and clinical interpretability. Finally, we outline a practical study-design roadmap integrating biospecimen collection, repeated assessments, core and exploratory biomarker panels, and functional endpoints. A biomarker-guided geroscience strategy may provide a practical route for connecting mechanistic aging biology with clinically relevant human studies designed to preserve healthspan and functional independence.},
}

Humans
*Biomarkers/metabolism
*Aging/metabolism/genetics
*Geroscience/methods
*Life Style
Epigenesis, Genetic
Cellular Senescence
Oxidative Stress
DNA Methylation

@article {pmid42939828,
year = {2026},
author = {Chen, S and Yin, Y and Yin, J and Zhou, X},
title = {Gut Microbiota-Host Redox Crosstalk: Molecular Mechanisms, Disease Pathogenesis, and Therapeutic Interventions.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42939828},
issn = {2076-3921},
support = {32341053//National Natural Science Foundation of China/ ; },
abstract = {The crosstalk between the gut microbiota and the host redox system is essential for maintaining intestinal homeostasis and systemic health. Disruption of this bidirectional interaction impairs redox balance, promotes oxidative stress, and contributes to the initiation and progression of a wide range of diseases, including inflammatory bowel disease, metabolic liver disease, neurodegenerative disorders, and chronic kidney disease. In this review, we comprehensively summarize the molecular mechanisms by which the gut microbiota regulates host redox homeostasis, focusing on microbial metabolites, immune signaling, and host antioxidant pathways. We also discuss emerging mechanisms underlying microbiota-host redox interactions, including extracellular vesicle (EV)-mediated interkingdom communication, microbiota-driven regulation of intestinal epithelial ferroptosis, and microbial metabolic reprogramming. Furthermore, we highlight how gut microbiota dysbiosis extends oxidative stress beyond the intestine through the gut-liver, gut-brain, and gut-kidney axes, thereby driving the development of multiple organ diseases. Finally, we summarize recent advances in microbiota-targeted therapies and engineered bacterial EVs as innovative strategies for restoring redox homeostasis, and discuss their potential for the precision prevention and treatment of oxidative stress-associated diseases as well as the development of next-generation microbiome-based therapeutics.},
}

@article {pmid42939838,
year = {2026},
author = {Liu, J and Jia, R and Wang, P and Liang, Y and Feng, F and Wang, F and Yang, Q},
title = {Limosilactobacillus mucosae LM410 Enhances Intestinal Barrier and Antioxidant Capacity in Weaned Piglets via Microbial Tyrosine Metabolism and AhR/STAT3 Pathway.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42939838},
issn = {2076-3921},
support = {32460845//the National Natural Science Foundation of China/ ; GSARS10//the Earmarked Fund for the Pig Industry of Gansu Provincial Modern Cold-Arid Characteristic Agricultural Technology Research System/ ; },
abstract = {Oxidative stress compromises intestinal barrier function and antioxidant defense in weaned piglets, causing substantial economic losses in the pig industry. Probiotic interventions to improve gut health are considered a highly promising solution; research indicates that certain Lactobacillus species can promote the proliferation of Lgr5[+] stem cells and activate the AhR/STAT3 pathway by modulating microbiota metabolism, thereby enhancing intestinal barrier and antioxidant function. Although Limosilactobacillus mucosae (L. mucosae) has demonstrated antioxidant properties in rodent models, its involvement in modulating intestinal stem cell (ISC) fate in piglets, as well as the associated mechanisms, remains unclear. We hypothesized that L. mucosae could alleviate oxidative stress in weaned piglets by modulating intestinal microbiota and activating the aryl hydrocarbon receptor/signal transducer and activator of transcription 3 (AhR/STAT3) signaling-mediated intestinal epithelial renewal. We compared the gut microbiota composition between Hezuo pigs (a subgroup of the plateau-type Tibetan breed) and Landrace × Yorkshire (LY) pigs, and isolated L. mucosae LM410 from Hezuo pigs. The strain was evaluated for acid and bile tolerance, antioxidant activity, and inhibitory properties. Subsequently, a 14-day animal trial was conducted using Duroc × Landrace × Yorkshire (DLY) weaned piglets orally administered with 1 × 10[9] CFU/mL L. mucosae LM410. Intestinal morphology, barrier integrity, immune responses, antioxidant capacity and cecal microbiota composition and metabolic pathways were assessed. We found that Hezuo pigs harbored a higher abundance of L. mucosae in the gut compared with LY pigs. The isolate L. mucosae LM410 from Hezuo pigs, demonstrated strong acid and bile salt tolerance, as well as antioxidant and antimicrobial activities, and effectively improved intestinal morphology, barrier integrity, immune responses, and antioxidant capacity in DLY weaned piglets. Mechanistically, L. mucosae LM410 reshaped the cecal microbiota by enriching short-chain fatty acid (SCFA)-producing bacteria and upregulating the tyrosine metabolic pathway. Concomitantly, L. mucosae LM410 activated the AhR/STAT3 signaling axis, which likely promoted ISC proliferation and differentiation into goblet cells. These findings demonstrate for the first time that L. mucosae may enhance piglet antioxidant defense through coordinated cecal microbiome remodeling, upregulation of tyrosine metabolism and AhR/STAT3-driven epithelial renewal, providing a theoretical foundation for developing L. mucosae LM410 as a candidate probiotic to improve piglet health.},
}

@article {pmid42939840,
year = {2026},
author = {Kőrösi, L and Hatem, O and Röckel, F and Schneider, G and Papp, S},
title = {Phenolic Profiling of Grapevine Leaves and the Protective Effect of a Polyphenol-Rich Vitis amurensis Extract on Lactiplantibacillus plantarum Under Oxidative Stress.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42939840},
issn = {2076-3921},
abstract = {Polyphenols are plant secondary metabolites widely recognized for their antioxidant properties and potential health benefits. Grapevine leaves are a rich yet underexplored source of these bioactive compounds. In this study, caftaric acid, and predominant flavonol glycosides were characterized in leaves of seventeen grapevine genotypes by high-performance liquid chromatography, while total phenolic content (TPC) was determined using the Folin-Ciocalteu assay. In addition, the growth-promoting effect of a polyphenol-rich Vitis amurensis leaf extract on Lactiplantibacillus plantarum and its protective effect under H2O2-induced oxidative stress were evaluated. Both TPC and phenolic composition were strongly genotype-dependent, with TPC ranging from approximately 20 to 100 mg gallic acid equivalents (GAE) g[-1] dry weight (DW). Quercetin and kaempferol glycosides were the predominant flavonols, and quercetin-3-O-glucuronide, one of the most abundant derivatives, varied nearly tenfold among genotypes (approximately 2100-20,000 mg kg[-1] DW). The leaf extract of V. amurensis, the genotype with the highest TPC, significantly promoted the in vitro growth of L. plantarum in a dose-dependent manner, resulting in higher viable cell counts after 24 h. The extract also markedly enhanced bacterial survival under H2O2-induced oxidative stress. At 2 mM H2O2, no bacterial growth was detected in the absence of the extract, whereas extract-supplemented cultures maintained substantial growth and reached a viable cell count of 1.8 × 10[8] colony-forming units (CFU) mL[-1] after 24 h. The phenolic patterns identified across the investigated genotypes provide a basis for selecting Vitis genotypes as sources of specific flavonol glycosides. Furthermore, our microbiological results provide preliminary evidence of the beneficial effects of V. amurensis leaf extract on L. plantarum and warrant further investigation of its potential functional applications.},
}

@article {pmid42939852,
year = {2026},
author = {Kim, JW and Lee, YJ and Kim, K and Ko, SH},
title = {Interplay Between the Gut Microbiome and Oxidative Stress in Type 2 Diabetes.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42939852},
issn = {2076-3921},
support = {No. RS-2024-00338024//National Research Foundation of Korea/ ; },
abstract = {Type 2 diabetes (T2D) develops when pancreatic beta cells progressively fail to compensate for insulin resistance in a host environment shaped by diet, adiposity, aging, medications, and genetics. Gut microbial dysbiosis and oxidative stress are often treated as parallel abnormalities; however, evidence increasingly supports a bidirectional microbiome-redox axis. Reduced butyrate production, altered bile-acid and amino-acid metabolism, intestinal barrier failure, and microbial products can promote mitochondrial dysfunction, NADPH oxidase activity, inflammation, and impaired insulin signaling. Conversely, hyperglycemia, lipotoxicity, inflammation, and reactive oxygen and nitrogen species remodel the intestinal habitat, favoring inflammation-adapted organisms and reinforcing dysbiosis. This review synthesizes evidence linking this circuit to insulin-responsive tissues, pancreatic islets, regulated cell death, and diabetic complications and critically examines dietary, microbiome-directed, antioxidant, glucose-lowering, and metabolic-surgical interventions. Human evidence is strongest for reproducible functional shifts, medication-microbiome interactions, and modest benefits of selected dietary and biotic interventions, whereas redox mediation and durable clinical efficacy remain heterogeneous. Future studies should integrate longitudinal metagenomics, metabolomics, validated redox biomarkers, strain-level and spatial sampling, and causal designs to identify patients with T2D most likely to benefit from microbiome-redox precision therapy.},
}

@article {pmid42939855,
year = {2026},
author = {Pan, M and Scarlata, E and Hui, F and Xia, J and O'Flaherty, C},
title = {Lipidomic Remodelling and Low Sperm Quality Associated with High-Fat Diet-Induced Gut Microbial Dysbiosis in Mice.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42939855},
issn = {2076-3921},
support = {11644//McGill Interdisciplinary Initiative in Infection and Immunity (MI4) Grant and Pathy Family Foundation/ ; },
abstract = {Infertility affects one in six couples worldwide, with male infertility contributing to ~50% of cases. Rising obesity rates have been linked to impaired male fertility, potentially through alterations in the gut microbiota; however, underlying mechanisms remain poorly understood. We characterized gut microbiome composition and lipidomic profiles in stool, serum, and testis samples. We assessed sperm quality in C57BL6 male mice fed a 45% fat diet (high-fat diet, HFD) or a 10% fat diet (normal diet, ND). We analyzed the gut microbiota by 16S rRNA sequencing. We measured short-chain fatty acids by gas chromatography. We performed untargeted lipidomic profiling of stool, serum, and testis using UPLC-MS/MS. CASA and cytochemical and immunocytochemical analyses assessed sperm quality and oxidative stress markers. HFD-fed mice exhibited gut microbiota dysbiosis characterized by an increased Bacillota/Bacteroidota ratio, altered bacterial community composition, increased acetic acid, and reduced butyric acid. Lipidomic analyses revealed distinct stool, serum, and testis lipid profiles, including increased abundance of gut microbiota-associated lipids containing odd-chain fatty acyl groups in HFD-fed mice. These alterations were accompanied by reduced sperm motility, impaired acrosomal integrity, epididymal sperm maturation and sperm capacitation, and elevated oxidative and nitrosative stress. Collectively, these findings support a gut-testis-epididymis axis in which altered gut microbiota-derived lipids contribute to oxidative stress and reduced sperm quality.},
}

@article {pmid42939857,
year = {2026},
author = {Kurhaluk, N and Kołodziejska, R and Tkaczenko, H},
title = {GLP-1 as a Regulator of Oxidative Signalling in Metabolic Health and Disease.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42939857},
issn = {2076-3921},
abstract = {Glucagon-like peptide-1 (GLP-1) has emerged as a key regulator of metabolic, inflammatory and oxidative homeostasis, extending beyond its traditional function as an incretin hormone. This narrative review summarises the latest evidence from two decades of research into the role of GLP-1 in redox biology and metabolic regulation in tissues affected by obesity, type 2 diabetes and metabolic dysfunction-associated steatotic liver disease. There is growing evidence that GLP-1 signalling modulates multiple oxidative pathways, including AMPK-dependent metabolic reprogramming, mitochondrial quality control, nitric oxide-cGMP signalling, the regulation of ferroptosis, and the suppression of inflammatory pathways such as the NLRP3 inflammasome. Through these mechanisms, GLP-1 contributes to maintaining cellular redox balance, mitochondrial resilience, and metabolic adaptation in conditions of chronic oxidative stress. The review also emphasises the complementary function of GLP-1 receptor agonists (GLP-1RAs) and natural bioactive compounds such as polyphenols, anthocyanins, terpenoids and omega-3 fatty acids. These compounds may reinforce antioxidant defences, reduce inflammatory signalling and support mitochondrial function. Particular attention is given to the role of the gut microbiota in determining GLP-1 responsiveness. Gut microbiota-derived metabolites, including short-chain fatty acids (SCFAs) and bile acid derivatives, contribute to incretin secretion, intestinal barrier maintenance, and systemic redox regulation. This review integrates endocrinology, oxidative stress biology, microbiome science and nutritional biochemistry to provide a comprehensive framework describing GLP-1 as a multi-organ metabolic signal that coordinates endocrine, immune, mitochondrial and redox pathways. These insights will inform the development of future therapeutic strategies that combine GLP-1-based pharmacology with precision nutrition and microbiome-targeted approaches, with the aim of improving metabolic resilience and addressing the oxidative dysregulation associated with chronic metabolic diseases.},
}

@article {pmid42939906,
year = {2026},
author = {Kareem, HA and Saleem, S and Hafeez, MB and Ahmad, N and Yin, DC},
title = {Nanobubble-Driven Precision Aeration: Deciphering Abiotic Hypoxia Responses via Multi-Omics for Next-Generation Smart Agriculture.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42939906},
issn = {2076-3921},
support = {32471230//National Natural Science Foundation of China (NSFC)/ ; },
abstract = {Soil salinity and drought can restrict oxygen availability in the root zone, adding hypoxic stress to the ionic, osmotic, and hydraulic constraints experienced by crops. Nanobubble (NB) water offers a chemical-free approach for delivering highly dispersed oxygen and sustaining dissolved oxygen during irrigation. This review connects the physicochemical behavior of NBs with plant responses to salinity- and drought-associated hypoxia. It examines restoration of aerobic respiration and ATP homeostasis, modulation of ethylene response factor group VII and hypoxia-responsive gene signaling, recovery of ion transport and aquaporin function, redox regulation, hormonal cross-talk, and rhizosphere microbiome responses. Evidence from rice, maize, wheat, cotton, and controlled-environment systems is evaluated alongside opportunities for nanoparticle co-delivery, nanofertilizers, seed priming, and sensor-guided irrigation. The review also outlines how transcriptomics, proteomics, metabolomics, epigenomics, ionomics, and phenomics can resolve NB-mediated mechanisms across the plant-soil continuum. Current evidence supports NB irrigation as a promising precision-aeration platform, but field-scale validation, standardized NB characterization, dose-response studies, energy and cost assessments, and long-term environmental safety analyses remain necessary before broad agricultural deployment.},
}

@article {pmid42939947,
year = {2026},
author = {Dyszkiewicz, M and Cudowska, B and Omeljaniuk, WJ and Marcinkiewicz-Rybołowicz, S and Lebensztejn, DM},
title = {Tryptophan Metabolism in Pediatric Atopic Dermatitis: Shared Mechanisms, Age-Specific Biomarkers, and Emerging Therapies.},
journal = {Biomedicines},
volume = {14},
number = {10},
pages = {},
pmid = {42939947},
issn = {2227-9059},
support = {B.SUB.26.107//Medical University of Białystok/ ; },
abstract = {Atopic dermatitis affects up to one in five children; however, most mechanistic evidence linking tryptophan metabolism to disease pathogenesis derives from adult cohorts and preclinical models. Whether these mechanisms operate similarly across pediatric developmental stages remains poorly characterized. Tryptophan metabolism, through the kynurenine, serotonin-melatonin, and microbiota-derived indole pathways, regulates immune homeostasis, epidermal barrier integrity, and gut-skin microbiome crosstalk, with disruptions implicated in pediatric and adult disease alike. This review synthesizes pediatric evidence on tryptophan metabolism in atopic dermatitis, benchmarked against the more extensive adult and preclinical literature, spanning aryl hydrocarbon receptor signaling, filaggrin regulation, gut and skin microbiome-derived metabolites, circulating biomarkers, and emerging therapeutics including tapinarof, melatonin, and dupilumab. Age-stratified evidence indicates that components of this pathway have clinical or translational feasibility in children; however, standardized, prospective studies directly contrasting age groups are still lacking. By mapping pediatric-adult differences, the review identifies mechanisms that may be shared across age groups while acknowledging the limited direct pediatric evidence, providing a hypothesis-generating framework for future age-appropriate, biomarker-informed precision medicine in pediatric atopic dermatitis (PAD).},
}

@article {pmid42939950,
year = {2026},
author = {Vijverman, L and Maddalena, T and Delrue, C and Speeckaert, MM},
title = {The Gut-Kidney Axis in Chronic Kidney Disease: Microbial Dysbiosis, Host-Microbial Metabolism, and Emerging Therapeutic Strategies.},
journal = {Biomedicines},
volume = {14},
number = {10},
pages = {},
pmid = {42939950},
issn = {2227-9059},
abstract = {Chronic kidney disease (CKD) appears linked to changes in the gut microbiota, intestinal barrier defects, and microbiota-driven changes in metabolite profiles. Experimental evidence links gut microbiota disturbances to kidney injury through pathways such as microbial metabolism, inflammation, immune signals, and epithelial barrier dysfunction. Still, applying this knowledge in clinical practice for patients with CKD remains difficult. For instance, one study on indoxyl sulfate and p-cresyl sulfate levels in a patient showed that, beyond being synthesized by the intestinal microbiota, the host can also metabolize or alter these metabolites. In addition, they undergo impaired renal clearance and can be secreted by the tubules. Moreover, most human microbiome-related studies are observational, making it difficult to determine the causal role of bacterial dysbiosis. Disease, dietary factors, medication, and other comorbid conditions are major confounders. Microbiota-directed means of altering the composition of the microbiota, such as changing diet, using prebiotics, probiotics, synbiotics, oral adsorbents, and even fecal microbiota transplantation, have, to varying degrees, affected the composition of the gut microbiota, levels of uremic toxins, short-chain fatty acids, and markers of inflammation. They have also been connected to leaky gut syndrome. However, evidence that these actions delay eGFR decline or prevent kidney failure, cardiovascular events, hospitalization, or mortality remains limited. Postbiotics and microbiota-derived metabolites in pure form are distinct experimental therapies and need to be assessed independently. This article reviews the gut kidney axis at different levels of evidence and distinguishes preclinical mechanisms, human associations, surrogate biomarker responses, and clinical outcomes. It points out why impressive mechanistic and biomarker results have not translated into better kidney or cardiovascular outcomes. Future research should use standardized methodologies, provide more detail on microbial functions and host metabolite metabolism, and test microbiome-targeted therapies in sufficiently powered randomized controlled trials with meaningful endpoints.},
}