@article {pmid42365622,
year = {2026},
author = {Carneiro, CLDS and Cruz, TPD and Monteiro, LCP and Glugoski, L and Feldhaus, MV and Lipinski, LC and Vicari, MR and Nogaroto, V and Barriviera, VR and Furuya, WM},
title = {L-Glutamine Plus L-Glutamic Acid Enhances Antioxidant Status and Ammonia Toxicity Resilience, Upregulates Interleukin IL-10 Gene, and Improves Gut Microbiota and Survival in Juvenile Nile Tilapia.},
journal = {Journal of animal physiology and animal nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpn.70086},
pmid = {42365622},
issn = {1439-0396},
support = {176820/2023-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {Glutamine (Gln) and glutamic acid (Glu) are the most abundant free amino acids (AAs) in the fish body. Although classified as non-essential AAs, their supplementation can be a strategy to optimize the growth performance and health of fish. This study aimed to investigate the effects of dietary Gln and Glu blend on growth performance, biochemical parameters, gut microbiota composition, short-chain fatty acids (SCFAs) production, digestive enzyme activity, histomorphometry, and liver mRNA levels of glutamine synthetase (GS), peroxisome proliferator-activated receptor alpha (PPAR-α), anti-inflammatory interleukin 10 (IL-10), pro-inflammatory interleukin 1β (IL-1β), and antioxidant status of juvenile Nile tilapia. Fish (n = 216; 0.99 ± 0.01 g) were randomly allocated into eight aquariums containing 27 fish each, in a four-replicate design. Fish were hand-fed a Glu + Gln unsupplemented basal diet (CON) or a basal diet supplemented with 20 g kg[-1] Glu + Gln (AMG) six times daily until apparent satiety for 60 days. Relative to fish fed CON diet, fish fed AMG diet exhibited enhanced feed conversion ratio (FCR; -5.6%), energy retention efficiency (+8.20%), and protein retention efficiency (+7.69%), and a trend towards a higher survival rate (+5.9%), suggesting improved nutrient utilization. Although the general structure of the microbiota of fish fed AMG diet remained similar to that of fish fed CON diet, it was observed that Gln + Glu supplementation promoted increased relative abundance of Enterococcus sp., a potential probiotic. Notably, fish fed AMG diet showed higher SCFA production than those fed CON diet, enhancing intestinal fold development. Fish fed AMG diet also exhibited higher liver activity of superoxide dismutase (SOD) and glutathione-S-transferase (GST), resulting in lower malondialdehyde (MDA) concentration and indicating a healthier intestinal mucosal state. Furthermore, fish fed AMG diet showed higher mRNA expression of IL-10 and GS, indicating enhanced anti-inflammatory responses and ammonia metabolism, respectively. In conclusion, 20 g kg[-1] dietary Gln plus Glu enhanced FCR, nutrient retention, and survival by favorably modulating the microbiota and improving intestinal function, thereby optimizing antioxidant responses and innate immunity in juvenile Nile tilapia. These findings highlight the potential of Gln and Glu blend to improve profitability and sustainability in Nile tilapia aquaculture.},
}

@article {pmid42365629,
year = {2026},
author = {Radikova, Z and Tibensky, M and Mosna, L and Penesova, A and Havranova, A and Vlcek, M and Imrich, R},
title = {Current perspectives on the pathogenesis of multiple sclerosis: A minireview.},
journal = {Endocrine regulations},
volume = {60},
number = {1},
pages = {72-85},
doi = {10.2478/enr-2026-0009},
pmid = {42365629},
issn = {1336-0329},
mesh = {Humans ; *Multiple Sclerosis/etiology/metabolism/physiopathology/immunology/pathology ; Oxidative Stress/physiology ; Animals ; Inflammation ; Disease Progression ; },
abstract = {Multiple sclerosis (MS) is a chronic immune-mediated demyelinating disease of the central nervous system characterized by inflammation, reactive gliosis, and progressive neuroaxonal damage resulting in heterogeneous clinical and histopathological manifestations. As MS often leads to disability at a young age, it represents a substantial socio-economic burden in developed countries. The etiopathogenesis of MS is multifactorial and incompletely understood, involving genetic, immunologic, and environmental factors. Recent research highlights immune responses to Epstein-Barr virus, blood-brain barrier disruption, microbiome-gut-brain axis alterations, oxidative damage, and mitochondrial dysfunction. Studying patients with newly diagnosed MS without significant comorbidities provides insight into early disease mechanisms before disability development or long-term treatment effects. This mini-review focuses on early vascular and metabolic alterations that may contribute to MS, including lipoprotein subfractions as markers of incipient atherosclerosis, endothelial dysfunction as an initiating vascular event, and autonomic nervous system imbalance during disease progression. It also addresses insulin sensitivity as a key metabolic factor alongside chronic inflammation and oxidative damage as interconnected mechanisms driving tissue injury. Metabolic changes reflecting neuronal impairment, mitochondrial dysfunction, and astroglial activation are detectable in both lesional and normal-appearing white matter in early stages. Reduced antioxidant capacity supports a role of oxidative damage in MS pathogenesis. Accelerated vascular aging, independent of traditional cardiovascular risk factors, may progress from endothelial dysfunction to structural atherosclerotic changes. Subtle alterations in lipoprotein profiles further suggest an increased risk of atherosclerosis, potentially influenced by inflammatory activity and oxidative damage, with possible sex-specific differences. Autonomic dysfunction appears to develop secondary to disease progression rather than as a primary driver of pathogenesis.},
}

Humans
*Multiple Sclerosis/etiology/metabolism/physiopathology/immunology/pathology
Oxidative Stress/physiology
Animals
Inflammation
Disease Progression

@article {pmid42365631,
year = {2026},
author = {Vargovic, P and Osacka, J and Horvathova, L and Tillinger, A and Mihalj, D and Bodorova, BB and Dziewiczova, L and Havranek, T and Bacova, Z and Bakos, J},
title = {Early life adversity influences brain development through neuroendocrine, immune, and microbiota-related mechanisms: A review.},
journal = {Endocrine regulations},
volume = {60},
number = {1},
pages = {86-97},
doi = {10.2478/enr-2026-0010},
pmid = {42365631},
issn = {1336-0329},
mesh = {Humans ; Animals ; *Brain/growth & development/immunology/metabolism ; *Hypothalamo-Hypophyseal System/metabolism/physiopathology ; *Pituitary-Adrenal System/metabolism/physiopathology ; *Adverse Childhood Experiences ; *Stress, Psychological/immunology/physiopathology/metabolism ; *Gastrointestinal Microbiome/physiology ; *Neurosecretory Systems ; Neurodevelopment ; *Immune System ; *Microbiota/physiology ; },
abstract = {The early life experiences have an important impact on the development of the brain and behavior and early life adversities (ELA) may affect several biological systems including the hypothalamic-pituitary-adrenal (HPA) axis, neurotransmitter and immune signaling systems, and microbiota composition. Dysregulation of these systems may result in an altered stress reactivity in both early life and the adulthood periods leading to maladaptive responses to the environmental stimuli. The activation of certain neuropeptides, including oxytocin, stimulation of the HPA axis, and increased glucocorticoid levels, may also play an important role in the early adaptive processes. In terms of brain maturation, ELA can directly or indirectly elicit structural changes in neurite growth, neurogenesis, neuronal connectivities, and signaling processes, which may contribute to the production of the long-term behavioral changes associated with an increased risk of the neuropsychiatric disorders' development in later periods of the life. In this review, we summarize the effect of ELA on the HPA axis function, stress-related hormonal balance, immune responses, and the gut microbiome indicating how these changes may affect the brain function and behavior in the early stages of the life and adulthood. We also provide insight into animal studies revealing the responses of corticotropin-releasing hormone, urocortins, and corticosterone in various neural circuits in response to ELA evoked by maternal separation and limited bedding paradigms.},
}

Humans
Animals
*Brain/growth & development/immunology/metabolism
*Hypothalamo-Hypophyseal System/metabolism/physiopathology
*Pituitary-Adrenal System/metabolism/physiopathology
*Adverse Childhood Experiences
*Stress, Psychological/immunology/physiopathology/metabolism
*Gastrointestinal Microbiome/physiology
*Neurosecretory Systems
Neurodevelopment
*Immune System
*Microbiota/physiology

@article {pmid42365641,
year = {2026},
author = {Gherman-Lencu, CC and Bud, MG and Perne, MG and Gavris, MD and David, LE and Alexescu, TG},
title = {Hepatocrinology: New Conceptual Frameworks Linking Endocrine Disorders to Chronic Liver Pathology.},
journal = {Journal of gastrointestinal and liver diseases : JGLD},
volume = {35},
number = {2},
pages = {286-295},
doi = {10.15403/jgld-6940},
pmid = {42365641},
issn = {1842-1121},
mesh = {Humans ; *Liver/metabolism/pathology/physiopathology ; *Endocrine System Diseases/metabolism/physiopathology/complications ; *Liver Diseases/metabolism/physiopathology ; *Endocrine System/metabolism/physiopathology ; Chronic Disease ; Animals ; Signal Transduction ; },
abstract = {Hepatocrinology is an emerging interdisciplinary field that examines the bidirectional interactions between the liver and the endocrine system, emphasizing how hepatic dysfunction influences hormonal regulation and how endocrine disorders, in turn, shape liver metabolism, inflammation, and disease progression. This review summarizes current theoretical frameworks, including hepato-endocrine axes, hepatokine signaling, and multi-organ communication models, highlighting the liver's role as a central endocrine hub. Key hepatic hormones, transport proteins, and hepatokines such as fetuin-A, fibroblast growth factor 21, and selenoprotein P are discussed in relation to metabolic disorders including metabolic dysfunction-associated steatotic liver disease, metabolic dysfunction-associated steatohepatitis, polycystic ovary syndrome, diabetes, and advanced chronic liver disease. The review further explores hormonal axes involving the thyroid, pancreas, adrenal glands, parathyroids, and gonads, illustrating their complex interplay with hepatic physiology. Current challenges, such as limited long-term studies and therapeutic controversies, are examined alongside emerging directions involving hepatokine-targeted therapies, precision medicine, and microbiome-driven modulation. Understanding these interconnected pathways is essential for improving diagnostic accuracy, risk stratification, and therapeutic strategies in hepato-endocrine disorders.},
}

Humans
*Liver/metabolism/pathology/physiopathology
*Endocrine System Diseases/metabolism/physiopathology/complications
*Liver Diseases/metabolism/physiopathology
*Endocrine System/metabolism/physiopathology
Chronic Disease
Animals
Signal Transduction

@article {pmid42366201,
year = {2026},
author = {Chen, Y and Gui, H and Ma, K and Zhang, Z and Zhao, T and Wang, M},
title = {Lifestyle-associated blood metabolic pathways and functional performance in cognitive aging.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-58782-7},
pmid = {42366201},
issn = {2045-2322},
abstract = {Functional decline is a major clinical feature of Alzheimer's disease (AD), yet the blood metabolic pathways associated with lifestyle factors and multidimensional functional performance across cognitive stages remain incompletely characterized. We applied a pathway-level blood metabolomics framework to harmonized, de-identified data from aging and dementia-related cohort resources spanning cognitively normal aging (CN), mild cognitive impairment (MCI), and AD. Metabolites were mapped to curated pathways and summarized into pathway activity scores across five domains: energy metabolism, amino acid metabolism, lipid metabolism, inflammation/oxidative stress, and microbiome-linked metabolism. We evaluated associations among physical activity, diet quality, pathway activity scores, and functional outcomes, including activities of daily living, gait speed, grip strength, global cognition, composite function, and frailty. To summarize pathway patterns jointly associated with physical activity and diet quality, we derived a lifestyle-modulated metabolic pathway score (LMPS) using elastic net regression with cross-validation, out-of-fold score estimation, and bootstrap stability assessment. Lifestyle-associated pathway activity showed coordinated patterns across metabolic domains and was associated with functional performance across cognitive groups. Higher LMPS values were associated with better physical and cognitive function and lower frailty, with graded differences observed across CN, MCI, and AD. Internal robustness analyses indicated greater stability at the pathway-domain level than at the individual-pathway coefficient level. Sensitivity analyses adjusting for cognitive group attenuated but did not eliminate the directionally consistent associations between LMPS and major functional outcomes. Convergent pathway patterns involved mitochondrial energy metabolism, lipid remodeling, inflammatory regulation, and microbiome-related metabolism. Pathway-level blood metabolomics identified lifestyle-associated metabolic patterns related to multidimensional functional outcomes across the cognitive aging spectrum. LMPS provides a data-driven summary of lifestyle-associated pathway variation in this cohort and may help generate hypotheses about metabolic correlates of functional performance. Independent and longitudinal validation will be required to determine its reproducibility, temporal relevance, and translational utility.},
}

@article {pmid42366210,
year = {2026},
author = {Sun, X and Wang, X and Jia, R and Tang, J and Zeng, X and Zhao, F and Zeng, F and Huang, N and Li, J and Cui, K},
title = {Biologics for cardiovascular diseases: from bench to bedside.},
journal = {Signal transduction and targeted therapy},
volume = {11},
number = {1},
pages = {},
pmid = {42366210},
issn = {2059-3635},
mesh = {Humans ; *Cardiovascular Diseases/genetics/therapy/pathology/metabolism ; Proprotein Convertase 9/genetics ; *Biological Products/therapeutic use ; Animals ; *Genetic Therapy ; Lipid Metabolism/genetics/drug effects ; },
abstract = {The rise of biologics, including recombinant proteins, gene therapies, and cell therapies, is reshaping the landscape of modern therapeutics, offering new strategies to address previously "undruggable" targets. Cardiovascular diseases (CVDs), the leading cause of mortality worldwide, remain inadequately managed by traditional therapies, but biologics offer a paradigm shift from symptom control to disease modification. This review provides a comprehensive analysis of biologics in cardiovascular medicine, focusing on five key biological processes: cardiac regeneration, cardiac reverse remodeling, genetic cardiomyopathy correction, vascular function modulation, and lipid metabolism modulation. Advances in cardiac regeneration are highlighted by the transplantation of pluripotent stem cells, direct reprogramming, stimulation of endogenous adult cardiomyocyte proliferation, and noncell strategies, all of which aim to restore cardiac tissue integrity. In reverse cardiac remodeling, therapies targeting key signaling pathways, metabolic processes, and contractility-enhancing agents offer promising new approaches for CVD management. The development of gene therapies targeting genetic cardiomyopathies, including gene replacement, genome editing, and gene silencing, is discussed. For vascular function modulation, therapies targeting angiotensinogen, natriuretic peptide receptor 1, and the gut microbiome have been explored as innovative approaches to regulate vascular tone and hemodynamics. Finally, lipid modulation therapies, including agents targeting proprotein convertase subtilisin/kexin type 9 (PCSK9) and atherogenic lipoproteins, have redefined the management of dyslipidemia and cardiovascular risk. Collectively, these advancements underscore the transformative potential of biologics to provide targeted, personalized, and disease-modifying treatments for CVD. By addressing both the pathophysiological roots and clinical manifestations of CVDs, biologics represent a promising frontier in cardiovascular medicine.},
}

Humans
*Cardiovascular Diseases/genetics/therapy/pathology/metabolism
Proprotein Convertase 9/genetics
*Biological Products/therapeutic use
Animals
*Genetic Therapy
Lipid Metabolism/genetics/drug effects

@article {pmid42366391,
year = {2026},
author = {Lai, T and Liu, Y and Duan, Z and Su, S and Ding, H and Dai, Y and Gao, M and Ji, M and Liao, L},
title = {Deep metagenomics uncovers functional adaptations and pathogenic risks in the gut microbiome of Antarctic fur seals (Arctocephalus gazella).},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00919-2},
pmid = {42366391},
issn = {2524-6372},
support = {2022YFC2807501//National Key Research and Development Program of China/ ; 42476264//National Natural Science Foundation of China/ ; },
abstract = {The Antarctic fur seal (Arctocephalus gazella) plays a key role in the Antarctic marine ecosystem by regulating krill, fish, and cephalopod populations through selective foraging, promoting Southern Ocean productivity via excretion, and influencing coastal island ecosystems during breeding season. Despite the importance of the gut microbiota in reflecting diet, health, and environmental adaptation, the gut microbiome of the Antarctic fur seal remains poorly characterized. To address this gap and evaluate its potential as a bioindicator of Antarctic marine environmental health, we employed shotgun metagenomics and 16S rRNA amplicon sequencing on fresh fecal samples collected from four Antarctic fur seals (designated S59, S62, S63, and S64) at King George Island, Western Antarctica. Despite inter-individual variation, both approaches identified Bacillota as the dominant phylum but showed genus-level discrepancies, with Fusobacterium prevailing in metagenomes and Clostridium in 16S amplicons. Viral communities constituted up to 5.3% of the microbiome, including an immunodeficiency-associated Lentivirus. Chitin-degrading capacity was ubiquitous, consistent with the host's krill-based diet. Metagenome-assembled genomes (MAGs) resolved distinct taxonomic contributions to discrete steps of chitin hydrolysis, suggesting that complete depolymerization requires metabolic cross-feeding among functionally complementary taxa. Notably, Helicobacter MAGs were abundant in individual S62, suggesting potential pathogenicity. Additionally, 16 antibiotic resistance gene types were detected, with bacitracin, polymyxin, and multidrug resistance dominating the resistome. These findings not only elucidate the community composition, functional potential, and ecological adaptation of the Antarctic fur seal gut microbiota but also establish a comprehensive baseline for assessing environmental change and human impacts on the Antarctic marine ecosystem, thereby offering valuable scientific data and methodological insights for the conservation of polar marine mammals.},
}

@article {pmid42366393,
year = {2026},
author = {Cheney, CV and Page, EC and Yeung, DT and White, DL},
title = {The gastrointestinal microbiome and constituent short-chain fatty acids: a narrative review of an underexplored axis in acute lymphoblastic leukemia.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00855-z},
pmid = {42366393},
issn = {1757-4749},
abstract = {Acute Lymphoblastic Leukemia (ALL) is an aggressive malignancy of lymphoid progenitors, and remains the most commonly diagnosed hematological cancer in the pediatric population. Although 5-year overall survival rates now exceed 90%, standard-of-care therapies are associated with substantial acute and long-term toxicities, underscoring the need for novel and supportive strategies that preserve treatment efficacy whilst reducing dose-limiting side effects. Increasing evidence linking the microbiome to therapeutic response and toxicity in oncology highlights the potential relevance of microbial-derived metabolites, particularly short-chain fatty acids (SCFAs), in hematological malignancies. This review critically examines the emerging, yet limited, evidence supporting a role for SCFAs in ALL, integrating mechanistic insights from metabolic, immunological, and oncological studies to propose biologically plausible pathways of involvement. Specifically, we suggest how SCFAs may influence treatment response, mitigate therapy-related toxicity, reduce treatment-related morbidity and modulate early-life factors associated with ALL risk. Whilst direct ALL-specific evidence remains sparse, we propose that SCFAs represent a compelling and underexplored axis for microbiome-ALL research, and we aim to stimulate targeted experimental and clinical investigations to define their therapeutic potential.},
}

@article {pmid42366510,
year = {2026},
author = {Bather, K},
title = {Comments on: The Biliary Multi-Omics Landscape: Integrating Microbiome and Metabolomics in Gallbladder Cancer: Biliary Stasis, Microbial Viability, and Host Antimicrobial Defenses.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70538},
pmid = {42366510},
issn = {1440-1746},
}

@article {pmid42366665,
year = {2026},
author = {Kuzbekov, SR},
title = {[Microbiota and microbiome of the lacrimal drainage system].},
journal = {Vestnik oftalmologii},
volume = {142},
number = {3},
pages = {91-100},
doi = {10.17116/oftalma202614203191},
pmid = {42366665},
issn = {0042-465X},
mesh = {Humans ; *Microbiota ; *Lacrimal Apparatus/microbiology/physiopathology/pathology ; *Dacryocystitis/microbiology/diagnosis/physiopathology ; *Lacrimal Duct Obstruction/diagnosis ; Anti-Bacterial Agents/pharmacology ; },
abstract = {This review analyzes current concepts of the role of the microbiota and microbiome in the physiology and pathology of the human lacrimal drainage system (LDS). The terms are clearly differentiated: microbiota is the collection of living microorganisms, whereas microbiome also includes their genetic material and habitat. The article describes anatomical features of the LDS and involutional changes in adults (atrophy of the lacrimal puncta, canalicular fibrosis, and nasolacrimal duct stenosis), which predispose to tear stagnation and inflammation. The review includes a comparative analysis of the microbiological spectrum in healthy individuals and patients with dacryocystitis and canaliculitis. The composition of the flora was found to differ substantially depending on age (predominance of S. pneumoniae in children versus Staphylococcus spp. in adults) and geographical region. Metagenomic sequencing data (16S rRNA) demonstrate significantly greater microbial diversity compared with conventional culture methods, revealing a broad spectrum of aerobes, anaerobes, and fungi. The work pays particular attention to regional resistance patterns, including the high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in several Asian countries. Based on the literature data this study proposes and algorithm for empirical antibacterial therapy, taking into account the likely pathogens, as well as the indications for surgical correction, and emphasizes the prospects for creating a national map of the LDS microbiome in the Russian Federation to optimize treatment strategies for dacryocystitis and dacryostenosis.},
}

Humans
*Microbiota
*Lacrimal Apparatus/microbiology/physiopathology/pathology
*Dacryocystitis/microbiology/diagnosis/physiopathology
*Lacrimal Duct Obstruction/diagnosis
Anti-Bacterial Agents/pharmacology

@article {pmid42366719,
year = {2025},
author = {Malik, P and Tyczkowska-Sieroń, E and Durczyński, A and Hogendorf, P and Strzelczyk, J and Wlaźlak, M and Grzegory, A},
title = {Microbiota and serum tumor markers in patients with pancreatic cystic neoplasm.},
journal = {Polski przeglad chirurgiczny},
volume = {97},
number = {3},
pages = {46-52},
doi = {10.5604/01.3001.0054.9921},
pmid = {42366719},
issn = {2299-2847},
mesh = {Humans ; Female ; *Pancreatic Neoplasms/blood/microbiology/pathology ; Male ; *Biomarkers, Tumor/blood ; Middle Aged ; Aged ; Adult ; *Microbiota ; *Pancreatic Cyst/blood/microbiology ; CA-19-9 Antigen/blood ; },
abstract = {Introduction: One of the main precursory lesions for pancreatic carcinoma is pancreatic cystic neoplasms (PCN). Differentiation between the various types of cysts is a clinical challenge.

Aim: The aim of the study was to assess the microbiological status and the serum tumor markers compared with biochemical parameters and histopathological results in patients with PCN.

Materials and methods: A total of 59 patients diagnosed with PCN and treated between 2022 and 2023 were included in the study. Preoperative levels of serum inflammatory and tumor markers were assessed. Bacterial culture samples were collected from the nasal vestibule, the skin of the groin, and from cyst fluid and bile (in the case of cholecystectomy), and histopathology reports were examined.

Results: Seven (41.18%) patients with positive culture had cancer compared with 12 (28.57%) negative patients (p = 0.35). In the cystic pancreatic cancer group CA19-9 level was higher (190.43 427.80 ng/ml) than among benign lesions (100.16 506.22 ng/ml) (p = 0.02). Among patients with positive culture, C-reactive protein (CRP) level was higher (31.84 70.91 mg/l) comparing with patients with negative culture (10.94 28.75 mg/l; p = 0.03). Serum alpha fetoprotein (AFP) levels were lower in patients with positive culture (2.34 1.13 vs. 4.08 2.44 ng/ml, respectively; p = 0.04). Furthermore, CRP level was positively correlated with CA19-9, and CA125 levels and negatively correlated with AFP level and hospitalization period.

Conclusions: Patients with positive cultures tended to have a higher incidence of cancers, CRP levels, and longer hospitalization periods. Further analyses of pancreatic cyst microbiome are definitely required.},
}

Humans
Female
*Pancreatic Neoplasms/blood/microbiology/pathology
Male
*Biomarkers, Tumor/blood
Middle Aged
Aged
Adult
*Microbiota
*Pancreatic Cyst/blood/microbiology
CA-19-9 Antigen/blood

@article {pmid42366944,
year = {2026},
author = {Tu, XM and Nguyen, PT and Nguyen, TN and Nguyen, LTT and Tran, DN and Huynh, PX},
title = {Full-length 16S rRNA metabarcoding characterization of facial skin microbiota in acne patients: a case study in the Mekong Delta of Viet Nam.},
journal = {Dermatology reports},
volume = {},
number = {},
pages = {},
doi = {10.4081/dr.2026.10643},
pmid = {42366944},
issn = {2036-7392},
abstract = {Acne vulgaris is a chronic inflammatory disorder of the pilosebaceous unit in which skin microbiome dysbiosis plays a key pathogenic role. This study, based on full-length 16S rRNA gene amplicon sequencing (V1-V9), characterized facial microbial diversity in 45 participants classified as healthy (n=15), mild acne (n=15), and moderate-severe acne (n=15), using pooled samples for downstream microbiome analyses. Samples from the skin surface and sebaceous follicles were analyzed by 16S rRNA (V1-V9) sequencing using Illumina MiniSeq and processed via QIIME2. Alpha diversity (observed taxa, Shannon index), beta diversity (Bray-Curtis dissimilarity, permutational multivariate analysis of variance [PERMANOVA]), and biomarker taxa (linear discriminant analysis effect size [LEfSe]) were assessed. Bacillota, mainly Staphylococcus spp., predominated on the skin surface, with relative abundance increasing with acne severity, whereas follicles were dominated by Cutibacterium acnes (Actinomycetota). Follicular samples showed lower richness and Shannon diversity than surface samples, though intergroup differences were not significant. Principal coordinates analysis (PCoA) explained >65% of variation, revealing greater dispersion among surface communities but no clear clustering by severity (PERMANOVA p>0.3). LEfSe identified distinct bacterial biomarkers across clinical groups. Overall, site-specific microbial shifts - particularly C. acnes and Staphylococcus dysbiosis - appear central to acne development, suggesting microbiome-targeted interventions as potential therapeutic strategies.},
}

@article {pmid42367109,
year = {2026},
author = {Jamei, M and Jamei, R},
title = {Engineered nanoparticles at the redox interface: Rewiring ROS signaling and stress responses in plants.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.70316},
pmid = {42367109},
issn = {1744-7909},
abstract = {Engineered nanoparticles (ENPs) are increasingly recognized as promising tools for modulating plant stress responses; however, their underlying mechanisms and associated risks remain under debate. This review integrates recent advances showing that ENPs can reprogram plant redox homeostasis through multiple pathways, including direct surface redox activity, nanozyme-like catalysis, ion release, and disruption of organellar electron transport. In addition, ENPs influence membrane physicochemical properties, transcriptional regulation, metabolic fluxes, hormonal crosstalk, epigenetic modifications, and the structure of the plant-associated microbiome. These processes produce distinct reactive oxygen and nitrogen species (ROS/RNS) signatures that activate Ca[2+] fluxes, mitogen-activated protein kinase (MAPK) cascades, and downstream transcriptional networks. We emphasize the importance of dose-dependent-often hormetic-responses, the critical role of the rhizosphere microbiome, and the application of spatially resolved techniques (e.g., μ-XRF, NanoSIMS, and spatial omics) to link NP fate with localized redox dynamics. Finally, we propose a safe-by-design framework that incorporates standardized NP characterization, appropriate ionic and inert controls, and predictive modeling approaches. This framework aims to facilitate the risk-informed and sustainable deployment of ENPs in agriculture.},
}

@article {pmid42367143,
year = {2026},
author = {Sengupta, A and Sahoo, RN and Sinharoy, S},
title = {Engineered diazotrophs with host-inducible nitrogen supply systems: Transforming rice farming through innovative nitrogen biofertilizers.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.70320},
pmid = {42367143},
issn = {1744-7909},
abstract = {Nitrogen pollution represents a critical challenge in the 21st century, highlighting the urgent need for sustainable alternatives to industrial nitrogen fixation. Diazotrophic bacteria, which uniquely convert dinitrogen (N2) into bioavailable forms, offer a promising solution through biological nitrogen fixation (BNF). These bacteria typically perform nitrogen fixation under nitrogen-limited conditions. Over the past 50 years, extensive research has elucidated the molecular mechanisms and regulatory pathways governing BNF. Recent microbiome studies have revealed that wild rice accessions harbor a greater abundance of diazotrophic bacteria, whereas a substantial proportion of these beneficial microbes have been lost in modern cultivated varieties. Advancements in synthetic biology have enabled the engineering of nitrogen‑exporting diazotrophs, potentially reducing dependence on industrial nitrogen fertilizers. This review emphasizes the importance of targeted research to develop customized diazotrophic microbes in conjunction with synthetic microbial community that can serve as nitrogen exporters for rice. Furthermore, it highlights the necessity of identifying rice cultivars that are particularly responsive to these microbial interventions. Finally, it provides a comprehensive roadmap addressing key challenges and opportunities in deploying BNF to supplement plant nitrogen nutrition and advance sustainable agriculture.},
}

@article {pmid42367188,
year = {2026},
author = {Montesanto, F and McCauley, M and Bedgood, SA and Miner, C and Steinworth, B and Sharp, V and Ohdera, AH and Oluokun, A and Fowowe, M and Oluokun, O and Mechref, Y and Xiang, T and Medina, M and Weis, VM and Martindale, MQ and Loesgen, S},
title = {Cnidarian-algal partnerships structure bacterial communities during strobilation in Cassiopea xamachana.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag147},
pmid = {42367188},
issn = {2730-6151},
abstract = {Cnidarian-algal (Symbiodiniaceae) symbioses rely on complex interactions among the cnidarian host, algal symbionts, and associated bacterial communities. In the upside-down jellyfish Cassiopea xamachana, the polyp-to-medusa transition (strobilation) requires the establishment of symbiosis with Symbiodiniaceae algal partners, yet bacterial community dynamics during this developmental process remain unknown. Here, we experimentally induced symbiosis in aposymbiotic polyps using four algal treatments: xenic Symbiodinium microadriaticum (native symbiont), xenic Breviolum minutum, antibiotic-treated B. minutum, and a photosynthetically impaired B. minutum mutant. We combined 16S rRNA gene sequencing with measurements of photosynthetic efficiency, asexual budding, and algal surface N-glycan profiles to characterize holobiont assembly during symbiosis onset and strobilation. Algal treatment structured bacterial communities in both algal cultures and polyp tissues. Our analyses identified a set of amplicon sequence variants that consistently distinguished strobilating polyps from non-strobilating aposymbiotic and mutant polyps, in addition to potential bacterial biomarkers associated with successful metamorphosis. Strobilation was associated with the enrichment of bacterial communities putatively involved in sulfur and nitrogen cycling, whereas non-strobilating aposymbiotic and mutant polyps were characterized by opportunistic bacteria and increased community variability. Together, these results reveal coordinated changes in algal physiology, surface glycan profiles, and bacterial community structure associated with successful strobilation in C. xamachana and support a model in which tripartite host-alga-bacteria interactions influence cnidarian life stage transitions.},
}

@article {pmid42367194,
year = {2026},
author = {Abaakil, K and Liu, Z and Wang, M and Kuznecova, E and Sung, MSC and Marchesi, JR and Mausz, MA and Li, JV},
title = {Antibiotic course frequency and recovery strategies alter gut microbial composition and metabolism.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag145},
pmid = {42367194},
issn = {2730-6151},
abstract = {Antibiotics profoundly alter the gut microbiome, but how exposure frequencies shape microbial recovery remains unclear. The effectiveness of post-antibiotic interventions, e.g. probiotics or autologous fecal microbiota transplantation, (aFMT) requires further exploration. This study investigated how antibiotic course timing and recovery strategies influence gut microbiome and metabolism in male Wistar rats. A single oral dose of vancomycin-ciprofloxacin (VC) caused rapid urinary and fecal metabolic shifts within 8-12 h and reduced bacterial α-diversity in cecal and colonic contents. When three VC courses were administered at regular (every 3 weeks; VCr) or irregular (1-3 weeks; VCi) intervals, VCr showed greater suppression of fecal α-diversity and stronger disruption of amino acid and host-microbial co-metabolism than VCi. Over the 3-week recovery period, VCr exhibited slower fecal α-diversity restoration; at week 3, β-diversity remained significantly different between groups, and cecal butyrate levels were persistently reduced in VCr. Both groups showed elevated levels of 5-aminovalerate in feces and colon compared with controls, whereas only VCi showed reductions in jejunal and ileal amino acids. Probiotics or aFMT had limited influence on small intestinal alterations, though aFMT accelerated fecal α-diversity recovery, and both interventions promoted partial normalization of fecal amino acids and 5-aminovalerate, without achieving complete restoration. Overall, shorter antibiotic intervals exerted stronger effects on the small intestinal luminal chemical environment, whereas longer intervals led to greater suppression of colonic and fecal microbial metabolism. Probiotics and aFMT supported selective metabolic recovery without fully reversing antibiotics-induced disturbances, highlighting the need for more targeted restoration strategies across gastrointestinal regions.},
}

@article {pmid42367298,
year = {2026},
author = {Mishra, SP and Jacobson, R and Wang, B and Prajapati, S and Sanberg, P and Brechot, C and Jain, S and Yadav, H},
title = {Microbiota-miR-101 interactions in obesity-associated colorectal cancer: from barrier dysfunction to precision therapeutic strategies.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1850919},
pmid = {42367298},
issn = {1663-9812},
abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related morbidity and mortality worldwide, with obesity recognized as a major modifiable risk factor. Obesity-associated CRC is characterized by systemic low-grade inflammation, altered lipid metabolism, and gut microbial dysbiosis, all of which converge to create a pro-inflammatory niche. Emerging evidence implicates murine miR-101a/b, an ortholog of the human miR-101 family, as a key molecular mediator linking metabolic dysfunction, promoting inflammation, endotoxemia, and affecting epithelial homeostasis. Traditionally, the miR-101 family is considered a tumor suppressor by repressing oncogenes such as EZH2, MCL-1, and COX-2; miR-101a appears to exhibit a paradoxical microenvironment-modulating role in obese colon. Recent studies demonstrate that elevated dietary and microbiota-derived ethanolamine induces miR-101a overexpression in colonic epithelial cells. Mechanistically, miR-101a directly destabilizes the mRNA encoding the tight junction protein (ZO-1; TJP1), thereby impairing epithelial barrier integrity, increasing intestinal permeability, and promoting chronic inflammation. The chronic inflammation promotes epithelial proliferation, generates mutagenic reactive oxygen species, and activates pro-survival pathways such as STAT3 and AKT, collectively contributing to a tumor-permissive microenvironment that may support adenoma initiation and progression. The resulting chronic inflammatory milieu promotes epithelial stress, proliferative signaling, and accumulation of DNA damage, contributing to conditions that favor colorectal carcinogenesis. Importantly, this ethanolamine-miR-101a axis represents a novel mechanistic link between diet, microbiota, and cancer biology. Translationally, miR-101a holds promise as a biomarker of early barrier dysfunction and CRC risk, as detectable in tissue, serum, or fecal samples. Furthermore, microbiome-targeted interventions, dietary modifications, or direct inhibition of miR-101a may offer innovative therapeutic strategies. Collectively, these findings support the development of precision microbiome-miRNA-based approaches and highlight the importance of context-dependent miRNA regulation in obesity-associated CRC.},
}

@article {pmid42367597,
year = {2026},
author = {Gilroy, R and Chaloner, G and Wedley, A and Richards-Rios, P and Pottenger, S and Wigley, P},
title = {Caecal microbiome transplant inhibits transmission and intestinal colonisation of Campylobacter jejuni in broiler chickens.},
journal = {Poultry science and management},
volume = {3},
number = {1},
pages = {13},
pmid = {42367597},
issn = {3005-0715},
abstract = {Campylobacter jejuni is the most frequent cause of foodborne bacterial gastroenteritis with poultry products the most frequent source of infection. C. jejuni can colonise the intestinal tract of the chicken and in particular the large blind caeca to a high level accompanied by faecal shedding and rapid transmission in flocks. As such, reducing transmission and intestinal colonisation in poultry meat production is considered a key target to reduce human infection. Whilst vaccines and feed-based approaches including modulation of the microbiome are considered most likely to reduce numbers in the chicken caeca, neither have yet shown the capacity to lead to significant reductions. We have previously shown that administration of a caecal microbiome transplant (CMT) at hatch acts to modify the microbiome, increasing diversity and reducing Enterobacteriacae levels associated with poor gut health and increased Campylobacter susceptibility. When challenged at 21 days old with C. jejuni M1 in a seeder bird infection model, birds in groups receiving CMT showed reduced transmission and significantly lower levels of C. jejuni at post-mortem examination at 35 days of age than control birds or birds treated with a commercial microflora competitive exclusion product (Aviguard). These data show that a microbiome-based intervention has the potential to inhibit C. jejuni transmission and decrease levels in the caeca at slaughter age. This is modelled to lead to a significant reduction in human cases. CMT offers a valuable tool to determine protective taxa in the chicken gut, aiding rational development of microbial interventions as well as a low-cost platform to help understand immunological development in the chicken gut.},
}

@article {pmid42367655,
year = {2025},
author = {Fleming, EG and Chen, J and Mohideen, S and Broder, A and Oladipo, AF},
title = {The fourth trimester and challenges for the lupus patient.},
journal = {EULAR rheumatology open},
volume = {1},
number = {4},
pages = {403-412},
pmid = {42367655},
issn = {3050-7081},
abstract = {Systemic lupus erythematosus (SLE) is a multisystem autoimmune disease that primarily affects persons of reproductive age. While SLE management during pregnancy has been previously studied, the unique challenges of the postpartum period, particularly the first 3 months after delivery, remain underexplored. The postpartum period is a time of significant physiological, social, and psychological change for both the birthing parent and infant. This review aims to summarise the available evidence regarding postpartum SLE flares, thrombosis, breastfeeding, perinatal microbiome, perinatal mood and anxiety disorders, maternal-infant bonding, and social support. Additionally, the review identifies significant knowledge gaps in postpartum SLE care and highlights priorities for future research to improve short-term and long-term outcomes for birthing parents with SLE and their infants.},
}

@article {pmid42367768,
year = {2026},
author = {Feng, M and Xu, W and Zhu, H},
title = {Autoimmune gastritis: a comprehensive review of pathophysiology, risk stratification, and management.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1878128},
pmid = {42367768},
issn = {1664-3224},
mesh = {Humans ; *Gastritis/therapy/diagnosis/immunology/etiology/physiopathology ; *Autoimmune Diseases/therapy/diagnosis/immunology/etiology ; Animals ; Risk Assessment ; Helicobacter Infections ; Disease Management ; Genetic Predisposition to Disease ; },
abstract = {Autoimmune gastritis (AIG) is a chronic, organ-specific autoimmune disease characterized by the immune-mediated destruction of gastric parietal cells, leading to impaired acid secretion, vitamin B12 deficiency, and an increased risk of gastric malignancies. The diagnosis of AIG relies on endoscopic findings combined with serological markers and histopathological confirmation. This review synthesizes current knowledge on the pathophysiology, diagnosis, and management of AIG, with a special focus on familial aggregation, polyglandular autoimmunity, and emerging therapeutic strategies. We discuss the diagnostic challenges posed by serological variability, the complex interplay with Helicobacter pylori infection, and the diagnostic pitfalls of macrocytic anemia. Furthermore, we explore precision risk stratification models for gastric neuroendocrine tumors (gNETs) and gastric adenocarcinoma, emphasizing the roles of endoscopic surveillance and molecular biomarkers. Finally, we review emerging therapeutic options, including novel immunomodulators and microbiome-targeted interventions. This review provides a comprehensive framework for clinicians to navigate the complexities of AIG, from early diagnosis to long-term management, with the goal of improving patient outcomes and mitigating the risk of malignant transformation.},
}

Humans
*Gastritis/therapy/diagnosis/immunology/etiology/physiopathology
*Autoimmune Diseases/therapy/diagnosis/immunology/etiology
Animals
Risk Assessment
Helicobacter Infections
Disease Management
Genetic Predisposition to Disease

@article {pmid42367778,
year = {2026},
author = {Fan, R and Zang, Q and Xu, Y and Gao, L and Zhou, J and Zang, Y},
title = {Metagenomic characterization of gut microbiota in rheumatoid arthritis-associated interstitial lung disease: taxonomic shifts and clinical correlations.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1868704},
pmid = {42367778},
issn = {1664-3224},
mesh = {Humans ; *Arthritis, Rheumatoid/complications/microbiology ; *Lung Diseases, Interstitial/microbiology/etiology ; Female ; *Metagenomics/methods ; Male ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Feces/microbiology ; Aged ; *Bacteria/classification/genetics ; Dysbiosis/microbiology ; *Metagenome ; },
abstract = {BACKGROUND: Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a severe extra-articular manifestation with limited diagnostic biomarkers. While gut microbiota dysbiosis contributes to rheumatoid arthritis (RA) pathogenesis, its specific role in RA-ILD remains poorly characterized.

METHODS: We performed shotgun metagenomic sequencing on fecal samples from 41 participants: 10 RA-ILD patients, 20 RA patients without ILD (RA-non-ILD), and 11 healthy controls (HCs). We assessed alpha and beta diversity, differential abundance (Wilcoxon rank-sum tests with FDR correction), Spearman correlations with clinical parameters, microbial co-occurrence networks, and random forest classification.

RESULTS: Alpha and beta diversity did not differ significantly among groups. After FDR correction, no genus differed significantly between RA-ILD and RA-non-ILD. Exploratory analysis (uncorrected P < 0.05) revealed enrichment of Escherichia/Shigella in RA-ILD (11.72% vs. 2.66%, P = 0.003) and depletion of Roseburia (1.05% vs. 3.77%, P = 0.005) and Ruminococcus (5.98% vs. 7.85%, P = 0.032), while Faecalibacterium showed a trend toward depletion without reaching nominal significance (4.45% vs. 4.66%, P = 0.409). Correlation analysis revealed a dichotomous pattern: pro-inflammatory genera correlated positively with disease activity, while butyrate-producing genera correlated negatively. Co-occurrence network analysis showed RA patients had a more complex network than HC and RA-ILD. Random forest classification identified Bifidobacterium, unclassified_ Oscillospiraceae, and unclassified_Lachnospiraceae as top discriminators between HC and RA, and unclassified_ Bacteroidaceae, Parabacteroides, and Blautia for RA-ILD vs RA.

CONCLUSIONS: RA-ILD is associated with specific gut microbial alterations-notably Escherichia/Shigella enrichment and depletion of Roseburia and Ruminococcus-despite preserved overall diversity. These changes correlate with systemic inflammation and suggest a role for the gut microbiota in RA-ILD pathogenesis via the gut-lung axis. The identified taxa warrant validation as candidate biomarkers in larger cohorts.},
}

Humans
*Arthritis, Rheumatoid/complications/microbiology
*Lung Diseases, Interstitial/microbiology/etiology
Female
*Metagenomics/methods
Male
*Gastrointestinal Microbiome/genetics
Middle Aged
Feces/microbiology
Aged
*Bacteria/classification/genetics
Dysbiosis/microbiology
*Metagenome

@article {pmid42367810,
year = {2026},
author = {Ismaili, N},
title = {Rethinking biomarker strategy in gastric cancer immunotherapy: from tumor to host.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1847526},
pmid = {42367810},
issn = {1664-3224},
mesh = {Humans ; *Stomach Neoplasms/immunology/therapy/genetics ; *Biomarkers, Tumor/immunology/genetics ; *Immunotherapy/methods ; Animals ; Immune Checkpoint Inhibitors/therapeutic use ; Autoantibodies/immunology ; },
abstract = {Immune checkpoint inhibitors (ICIs) have transformed advanced gastric cancer (GC) treatment, but durable responses remain rare, highlighting the need for better patient selection. Recent studies suggest that host-derived autoantibodies (e.g., ANA, ENA) may serve as prognostic markers in GC patients receiving immunotherapy. These hypothesis-generating observations indicate that pre-existing humoral immunity could reflect a clinically relevant axis of immune fitness. This review critically appraises these findings alongside established and emerging predictive biomarkers. We examine the strengths and limitations of PD-L1, MSI, TMB, and EBV status, and explore the clinical potential of dynamic tools like ctDNA and computational models. We also discuss emerging evidence on intrinsic resistance to PD-1 blockade in MSI-H GC, including PTEN mutations, low TMB within MSI-H tumors, and antigen presentation defects. Murine models have provided key insights into these resistance mechanisms and the immunomodulatory role of the gut microbiome. Collectively, the data support a shift from single-analyte biomarkers toward integrative, dynamic, systems-level models for patient selection, heralding a new era of precision immune-oncology in GC. However, most emerging biomarkers remain investigational and require prospective validation.},
}

Humans
*Stomach Neoplasms/immunology/therapy/genetics
*Biomarkers, Tumor/immunology/genetics
*Immunotherapy/methods
Animals
Immune Checkpoint Inhibitors/therapeutic use
Autoantibodies/immunology

@article {pmid42367844,
year = {2026},
author = {Johnson, D and Salman, T and Noorani, A and Benowitz, B and He, Y and Sundararaj, K and Shelley, H and Luo, Z and Wan, Z and Fitting, S and Penrod, RD and Jiang, W},
title = {Cocaine-Enriched Oral Streptococcus parasanguinis Promotes Neuroimmune Dysfunction and Memory Impairment.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.12.731966},
pmid = {42367844},
issn = {2692-8205},
abstract = {Chronic cocaine use is associated with neuroinflammation and cognitive dysfunction, but the underlying mechanisms remain unclear. We previously identified oral enrichment of Streptococcus parasanguinis (SP) and other species in individuals with cocaine use disorder (CUD), and here demonstrate that cocaine selectively enhanced SP growth in vitro . To investigate causality, antibiotic-pretreated wild-type C57BL/6 mice received chronic oral inoculation of SP, S. salivarius , Neisseria flavescens , or vehicle. SP-treated mice exhibited spatial memory impairment, increased brain IL-1β, and non-region-specific microglial activation, without detectable bacterial translocation into the brain. While amyloid-associated signaling changes were observed across all bacterial treatment groups, only SP induced cognitive deficits and neuroinflammation. Untargeted metabolomics identified distinct SP-associated oral-to-brain metabolite signatures, including cysteine S-sulfate (CSS) and altered histamine-associated metabolites. CSS and histamine induced neuroinflammatory and amyloid-associated responses in vitro . Together, these findings identify a cocaine-associated oral pathobiont that promotes neuroinflammation and neurodegeneration, suggesting a novel oral microbiome-brain axis in CUD.},
}

@article {pmid42367858,
year = {2026},
author = {Schäfer, JH and O'Neill, RT and Grotjahn, D and Powers, ET and Kelly, JW and Lander, GC},
title = {Siphoviridae phage tails co-enrich with ex vivo amyloids.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.17.733002},
pmid = {42367858},
issn = {2692-8205},
abstract = {Bacteriophages are ubiquitous in the environment and are part of the natural human microbiome. Despite their abundance, the role of the human phagome in health and disease remains poorly understood. Here, we identify phage tails in ex vivo amyloid extracts from patients with lysozyme amyloidosis (ALys) and light-chain amyloidosis (AL). Using cryo-EM analysis of the ALys dataset, automated model building, and database searches, we assigned the observed tubular assemblies to a phage tail tube protein (TTP). Although we cannot fully rule out the possibility of contamination, the presence of phage tails raises the question of whether they bind to and are co-purified with amyloid fibrils. These structures may provide further insight into the potential relationship between phage-derived assemblies and amyloid remodeling, with possible implications for future therapeutic strategies in human amyloidosis.},
}

@article {pmid42367889,
year = {2026},
author = {Bodkhe, R and Choi, R and Shapira, M},
title = {Environmental microbial extracts for longitudinal studies of gut microbiome assembly and maintenance.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.12.732002},
pmid = {42367889},
issn = {2692-8205},
abstract = {Animals harbor diverse gut microorganisms that influence host health and fitness. Synthetic microbial communities have been instrumental in enabling reductionist studies of host-microbiome interactions, but some questions require microbial communities with more natural-like complexity while preserving experimental tractability, in vivo monitoring, and quantitative analysis. Here, we describe a method optimized for longitudinal studies of host-microbiome-environment interactions in the nematode Caenorhabditis elegans . In this approach, complex microbial extracts (CMEs) are generated from environmental samples and applied to worm culture plates, providing a diverse yet experimentally convenient microbial environment. We show that CME composition remains stable during cold storage, enabling reproducible longitudinal experiments while minimizing confounding environmental drift over time. As a proof of principle, we apply this method to examine age-dependent changes in the worm gut microbiome, providing support for previous reports of age-dependent increase in the abundance of gut Enterobacteriaceae . CMEs provide a practical and reproducible framework that complements experiments using monocultures or synthetic communities, enabling longitudinal studies of host-microbiome interactions under conditions that better approximate natural microbial complexity.},
}

@article {pmid42367897,
year = {2026},
author = {Labossiere, A and Ramsey, M},
title = {"What's SUPP" developing an in vitro model for healthy oral biofilms.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.19.733444},
pmid = {42367897},
issn = {2692-8205},
abstract = {Human supragingival plaque (SUPP) is a polymicrobial biofilm whose contents undergo dysbiotic transitions during multiple oral diseases. The study of healthy SUPP may lead to future pro or prebiotic therapies, to help prevent or revert dysbiosis during disease. However, many oral plaque models focus on the cultivation of oral pathogens and do not well cultivate commensal SUPP populations. Here, we use a 16S microbiome guided iterative approach to develop a low-cost high sample number SUPP model. Our model demonstrates several findings including a surprisingly minimal impact on salivary preparation methods on model microbiota and the ability to test microbial interactions with added oral strains to assess their fitness. This model provides a reductionist system for the study of healthy oral commensals in a complex polymicrobial framework in the absence of host immune responses.},
}

@article {pmid42368200,
year = {2026},
author = {Chong, AEY and Sasmita, AO and Koh, RY and Ling, APK},
title = {Neuroprotective effects of ursodeoxycholic acid in Parkinson's disease and Alzheimer's disease.},
journal = {Neuroprotection (Chichester, England)},
volume = {4},
number = {2},
pages = {111-130},
pmid = {42368200},
issn = {2770-730X},
abstract = {Neurodegenerative diseases (NDDs) including Parkinson's disease (PD) and Alzheimer's disease (AD), are progressive disorders characterised by shared pathological features, including mitochondrial dysfunction, oxidative stress, apoptosis, neuroinflammation, neurotoxic protein buildup, and impaired protein clearance. Current treatments can only relieve disease symptoms but cannot delay the disease progression. Ursodeoxycholic acid (UDCA), a hydrophilic bile acid traditionally used in hepatology, has recently gained attention for its neuroprotective properties. This review critically evaluates UDCA's mechanisms of action, including the restoration of mitochondrial function, inhibition of apoptosis, reduction of oxidative stress and neuroinflammation, and enhancement of autophagy in both PD and AD models. In vitro and in vivo studies demonstrate UDCA's ability to preserve neuronal integrity, improve motor and cognitive outcomes, and reduce toxic protein aggregates. Although early-phase clinical trials, such as the UDCA for Parkinson's (UP) study in PD, show promising mitochondrial benefits and safety, clinical evidence in AD remains limited. Future directions emphasise the need for large-scale trials, personalised medicine, improved central nervous system (CNS) delivery strategies, or dietary interventions to modulate UDCA production from the gut microbiome. While not a first-line treatment, UDCA represents a compelling mitochondrial stabiliser with disease-modifying potential in NDDs.},
}

@article {pmid42368406,
year = {2026},
author = {Takahashi, T and Goel, A},
title = {The Gut Microbiome and Colorectal Cancer: From Association to Causation.},
journal = {Cancer biome and targeted therapy},
volume = {1},
number = {2},
pages = {1-8},
pmid = {42368406},
issn = {3070-9989},
abstract = {This mini-review discusses the emerging role of the gut microbiome as an active driver of colorectal cancer initiation, progression, and therapeutic response. Key mechanisms include microbiome-induced genomic instability, modulation of host immune responses, and epigenetic reprogramming mediated by tumor-associated bacteria such as Fusobacterium nucleatum. Emerging evidence suggests that specific microbial signatures are not only associated with disease but can functionally shape tumor behavior, influence treatment sensitivity, and serve as clinically actionable biomarkers. These insights highlight the potential of integrating microbiome profiling into precision oncology and underscore the need for mechanistic and translational studies to harness host-microbe interactions for improved cancer prevention and therapy.},
}

@article {pmid42368511,
year = {2026},
author = {Hwang, JH and Choi, YK},
title = {Herbal and Natural Product Interventions to Modulate Gut Microbiota in Acid Suppression-Associated Dysbiosis: a systematic review protocol.},
journal = {Journal of pharmacopuncture},
volume = {29},
number = {2},
pages = {149-154},
pmid = {42368511},
issn = {2093-6966},
abstract = {OBJECTIVES: Proton pump inhibitors are widely used to manage acid-related gastrointestinal disorders; however, prolonged use has been associated with gut dysbiosis, including reduced microbial diversity and the proliferation of opportunistic pathogens. Herbal medicines and natural products, characterized by multitarget effects, have been proposed as potential strategies for modulating the gut microbiota and restoring microbial homeostasis. This systematic review aims to evaluate the effects of these interventions on the gut microbiota in patients receiving acid suppression therapy.

METHODS: This protocol is registered in the PROSPERO international prospective register of systematic reviews (CRD420261346672) and will be conducted in accordance with the PRISMA-P guidelines. A comprehensive literature search will be performed in PubMed, Scopus, Web of Science, CENTRAL, and CNKI from database inception to March 2026. Randomized controlled trials and nonrandomized controlled clinical studies evaluating herbal or natural product interventions in adult patients receiving acid suppression therapy will be included. Two independent reviewers will perform study screening, data extraction, and risk-of-bias assessment using the RoB 2 and ROBINS-I tools. The overall certainty of the evidence will be evaluated using the GRADE approach.

RESULTS: Findings will be synthesized narratively, with a focus on taxonomic shifts (from the phylum to genus level) and diversity indices (alpha and beta diversity). Where sufficient data are available, a quantitative meta-analysis will be conducted using a random-effects model. Subgroup analyses will explore differences according to herbal intervention type (e.g., single extracts vs. multiherb formulations) and microbiome assessment methods.

CONCLUSION: This review will provide a structured overview of the microbiota-modulating effects of herbal and natural product interventions during acid suppression therapy. By bridging traditional medicine and modern microbiome science, the findings may help inform integrative therapeutic strategies and guide the design of future high-quality clinical trials.},
}

@article {pmid42368826,
year = {2026},
author = {Martínez-Noriega, M and Jean-Louis, P and Philippon, M and Sanchez-Flores, A and Gonzalez-Rizzo, S},
title = {Revealing the bacterial diversity and variation of white filamentous microbial mats in marine mangroves of Guadeloupe Island in relation to human activities.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag034},
pmid = {42368826},
issn = {2633-6685},
abstract = {White filamentous microbial mats are complex benthic communities, typically structured by sulfur-oxidizing bacteria from the Beggiatoaceae family, yet their diversity and ecological responses in mangrove ecosystems remain poorly characterized. Here, we provide a high-resolution analysis of bacterial communities associated with white microbial mats in marine mangrove sediments of Guadeloupe using 16S rRNA metabarcoding. Bacterial community composition was compared across sites with different levels of anthropogenic impact (protected, natural, and urban). While overall diversity remained stable, richness differed significantly between conditions, and beta diversity analyses revealed clear compositional structuring along the disturbance gradient. A conserved core microbiome was identified across all sites, whereas rare taxa were detected exclusively in urban sites, including Ferrimicrobium, Thermonospora, Alcanivorax, and Serratia, which has been previously associated with human-induced environmental changes. In contrast, Prosthecochloris and Chlorobaculum were highly abundant in protected sites, whereas Sulfurovum and Sulfurimonas dominated urban environments. The relative abundance of Beggiatoaceae also varied across sites, suggesting sensitivity to anthropogenic disturbance. Despite these compositional shifts, measured physicochemical parameters did not significantly correlate with the community structure, suggesting that microbial mat organization is influenced by fine-scale or unmeasured environmental gradients. Together, these findings indicate that white microbial mats respond to anthropogenic disturbance primarily through taxonomic restructuring rather than loss of diversity, highlighting their potential as sensitive indicators of environmental change in mangrove ecosystems.},
}

@article {pmid42368952,
year = {2026},
author = {Zhang, K and Wang, B and Ji, Y and Jiang, H},
title = {Nutritional status and cancer survival among rural Chinese women: biological mechanisms, health disparities, and translational opportunities.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1887699},
pmid = {42368952},
issn = {2296-2565},
mesh = {Humans ; Female ; China/epidemiology ; *Nutritional Status ; *Health Status Disparities ; *Neoplasms/mortality/epidemiology ; *Rural Population/statistics & numerical data ; East Asian People ; },
abstract = {Cancer remains a major cause of premature mortality among women worldwide, and its burden is particularly pronounced in rural China, where delayed diagnosis, uneven access to oncology services, and nutritional vulnerability may jointly affect survival. This narrative review synthesizes mechanistic, clinical, and population-level evidence on the relationship between nutritional status and cancer survival among rural Chinese women, with a focus on breast, cervical, gastric, and colorectal cancers. It first outlines the epidemiological profile of major female cancers in rural China and summarizes persistent rural-urban disparities in cancer incidence, stage at diagnosis, treatment access, and survival. It then examines nutrition-related challenges in rural settings, including dietary transition, micronutrient insufficiency, metabolic vulnerability, food insecurity, limited dietary diversity, and the increasing availability of energy-dense ultra-processed foods. The biological pathways linking nutritional status to cancer progression, treatment tolerance, and survivorship are discussed across four interconnected domains: insulin-IGF-1 and AMPK-mTOR signaling, adiposity-related inflammation and tumor microenvironment remodeling, gut microbiome-diet-metabolite interactions affecting estrogen metabolism, and micronutrient-dependent epigenetic regulation. Available clinical and epidemiological evidence on dietary patterns, nutritional biomarkers, and cancer prognosis in Chinese women is reviewed, with attention to methodological limitations and the shortage of rural-specific longitudinal data. The review further considers how food insecurity, low nutrition literacy, weak integration of oncology and nutrition services, and structural inequities in rural health systems may amplify survival disparities. Finally, translational opportunities are discussed, including community-based nutritional screening, integration of nutrition assessment into county-level oncology care, digital health tools, and scalable dietary counseling models adapted to rural contexts. Overall, this review highlights the need for prospective cohort studies with repeated nutritional biomarker assessments, mechanistic validation in rural populations, and equity-oriented policy strategies to improve cancer survivorship among rural Chinese women.},
}

Humans
Female
China/epidemiology
*Nutritional Status
*Health Status Disparities
*Neoplasms/mortality/epidemiology
*Rural Population/statistics & numerical data
East Asian People

@article {pmid42368984,
year = {2026},
author = {Basbouss-Serhal, I and Fayad, F},
title = {Familial Mediterranean Fever and the Gut Microbiota: A Dual Perspective Review of Current Evidence.},
journal = {Mediterranean journal of rheumatology},
volume = {37},
number = {2},
pages = {302-308},
pmid = {42368984},
issn = {2529-198X},
abstract = {Familial Mediterranean Fever is a well-known autoinflammatory disease resulting from mutations in the MEFV gene. A recent development has linked FMF pathogenesis and mode of expression to the gut micro-biota. There may be a change in the gut microbiota profile of FMF patients, characterised by low diversity and a depletion of beneficial bacteria. Dysbiosis tends to be linked to increased gut permeability, systemic inflammation, and low response to colchicine treatment. Probiotics and prebiotics, in this case, may help restore the previous idyllic state of the microbial balance, along with a reduction in inflammatory markers, thereby demonstrating therapeutic merit. Notably, however, it did argue in some instances that changes in the microbiota were secondary to the genetic and inflammatory nature of FMF itself. It is still important to carry out longitudinal studies of naïve patients that will integrate metagenomics with immune profiling to ascertain whether microbial changes arise from causes, contributions, or coincidence in the pathogenesis of FMF.},
}

@article {pmid42369014,
year = {2026},
author = {Ryan, N and Leahy Warren, P and O'Mahony, SM and Mulcahy, H and Philpott, LF},
title = {Reasons why Mothers Choose Human Milk as Their Method of Infant Nutrition: A Mixed Methods Systematic Review Protocol.},
journal = {Campbell systematic reviews},
volume = {22},
number = {2},
pages = {18911803261462950},
pmid = {42369014},
issn = {1891-1803},
abstract = {BACKGROUND: Human milk is a complex, dynamic, living biological fluid uniquely tailored to meet the nutritional needs of the human species. In addition to this it also has a protective role in health by providing beneficial microbes and prebiotic oligosaccharides that aid in developing the neonatal gut microbiome, and by containing immune molecules that help regulate long-term inflammatory responses. Despite growing evidence of human milk's composition and benefits, breastfeeding rates remain low in many countries. Some studies suggest that understanding the health benefits and composition of human milk may increase a mother's motivation to breastfeed or provide human milk. However, first it is necessary to summarize and synthesize the available data on maternal reasons for providing human milk in any form to their infants, to examine the evidence in this area.

METHODS: A mixed method systematic review will be conducted including qualitative, quantitative, and primary mixed-methods studies that explore the reasons why mothers choose breastmilk as their method of infant nutrition. The PICo framework will inform the search strategy including five databases CINAHL Complete (EBSCOhost), Medline (PubMed), Web of Science and Scopus (Elsevier) from inception to date of searching. Following screening the quality of the studies will be assessed using the standardized JBI critical appraisal tools, selected based on each study's methodology. Data extraction will follow the JBI mixed methods data extraction form, and will involve data transformation, synthesis, and integration. This systematic review will adopt a convergent integrated approach in line with JBI guidelines.

PROTOCOL REGISTRATION: Registered with Prospero (CRD42024586984).},
}

@article {pmid42369048,
year = {2026},
author = {Celada-Guerrero, JA and Rubio-Gordón, L and Jiménez-Perez, Y and López-Lora, L and López-González, A and Delbuono, S and Huertas, A and Martínez-Urbistondo, D and Ordovás, JM and de la O, V and Daimiel, L},
title = {Time-restricted eating versus calorie restriction for improving biomarkers of age in adults with overweight or obesity and incipient fatty liver disease: protocol for the ENSATI randomized controlled parallel groups trial.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1849550},
pmid = {42369048},
issn = {1664-2392},
mesh = {Humans ; *Caloric Restriction/methods ; Intermittent Fasting ; *Biomarkers/analysis/metabolism ; *Obesity/diet therapy/metabolism/complications ; *Overweight/diet therapy/metabolism/complications ; Middle Aged ; *Aging ; Male ; Female ; Randomized Controlled Trials as Topic ; Aged ; },
abstract = {INTRODUCTION: The increasing global lifespan has shifted the primary objective of geroscience from merely extending lifespan to maximizing health span. Biological aging is a gradual, time-dependent process marked by progressive cellular deterioration that culminates in increased vulnerability, frailty, morbidity, and mortality. Understanding the mechanisms that accelerate or decelerate this deterioration is crucial for developing effective interventions. Diet is recognized as the leading modifiable behavioral risk factor influencing the global burden of noncommunicable diseases and mortality. Therefore, nutritional interventions constitute a highly practical and scalable strategy for promoting healthy aging.

METHODS: The ENSATI trial is a randomized, open-label, controlled study with three parallel arms: active dietary counseling control, 25% calorie restriction, and time-restricted eating (14-hour fasting/10-hour eating window) over six months, followed by six months of post-intervention monitoring. A total of 177 adults aged 50-70 years with overweight/obesity and incipient fatty liver disease will be enrolled.

ANALYSES: Primary outcomes include changes in body composition (dual X ray densitometry), hepatic fat (elastography) and metabolism (indirect calorimetry). Secondary outcomes encompass glucose regulation (continuous glucose monitoring), gut microbiome profiles, molecular biomarkers of aging (epigenetics, autophagy, immunosenescence), alongside psychological, cognitive, sleep, and dietary assessments using validated tools. Analyses will follow an intention-to-treat approach, with per-protocol sensitivity analyses and sex-stratified models. Mixed-effects models adjusted for potential confounders will assess intervention effects.

DISCUSSION: Current TRE and caloric restriction studies are limited by short durations, small samples, and poor control of energy intake, often lacking molecular biomarkers of aging. ENSATI overcomes these gaps through a 12-month, adequately powered, randomized, multi-arm design with rigorous dietary monitoring and comprehensive molecular and physiological profiling, enabling a more rigorous exploration of the relative contributions of caloric intake versus chronobiological effects on obesity and aging.

ETHICS AND DISSEMINATION: This study was approved by IMDEA Ethics Committee (IMF PI-057). All participants will provide written informed consent. The findings will be disseminated in peer-reviewed scientific journals and at scientific conferences.},
}

Humans
*Caloric Restriction/methods
Intermittent Fasting
*Biomarkers/analysis/metabolism
*Obesity/diet therapy/metabolism/complications
*Overweight/diet therapy/metabolism/complications
Middle Aged
*Aging
Male
Female
Randomized Controlled Trials as Topic
Aged

@article {pmid42369077,
year = {2025},
author = {Liu, C and Han, H and Qi, Y and Ling, W},
title = {A Knowledge-Guided Large Language Model Framework for Microbiome-Based Disease Diagnosis.},
journal = {Proceedings. IEEE International Conference on Bioinformatics and Biomedicine},
volume = {2025},
number = {},
pages = {7012-7019},
pmid = {42369077},
issn = {2156-1125},
abstract = {Gut microbiome-based disease diagnosis holds significant promise but remains challenging due to the high data dimensionality, typically small sample sizes, and the necessity of incorporating biological knowledge. Due to these challenges, traditional machine learning approaches often tend to overfit the data and fail to capture true biological relationships, resulting in inaccurate diagnoses. To fill in the gap, we propose a two-phase, knowledge-guided large language model (LLM) framework for disease diagnosis that integrates biomedical expertise with in-context learning. In Phase 1, an LLM is employed to identify disease-associated taxa from hundreds of microbial families and to infer their biological relationships with the disease outcome. This process reduces the feature space dimensionality through biologically-informed feature selection and acquires essential domain knowledge. In Phase 2, we employ few-shot prompting to guide the LLM in disease outcome classification based on the domain knowledge acquired in Phase 1. Thanks to the universal applicability of LLM and our two-phase approach, this is a generic framework that can be applied to a wide range of microbiome-based disease diagnostic tasks. We demonstrate the superiority of our framework using inflammatory bowel disease (IBD) as a representative case study, where our approach achieves an accuracy of 73.91%, significantly outperforming an optimized XGBoost classifier. Overall, our knowledge-guided framework provides a powerful and generalizable strategy for leveraging LLMs in microbiome-based disease diagnosis, and opens a new avenue for disease diagnosis in the era of LLM.},
}

@article {pmid42369219,
year = {2026},
author = {Clemente-Suárez, VJ and Beltrán-Velasco, AI and Ramos-Campo, DJ and Rubio-Zarapuz, A and Tornero-Aguilera, JF and Martín-Rodríguez, A and Yáñez-Sepúlveda, R and López-Gil, JF},
title = {Link between physical activity, nutrition, and antimicrobial pharmacokinetics and therapeutic efficacy: Implications for resistance management.},
journal = {SAGE open medicine},
volume = {14},
number = {},
pages = {20503121261462838},
pmid = {42369219},
issn = {2050-3121},
abstract = {Antimicrobial resistance (AMR) is a critical global health challenge, as it reduces the effectiveness of current therapies and demands novel integrative approaches. This narrative, integrative review analyzes how physical activity and nutrition interact with the pharmacological design of antimicrobial agents, influencing their absorption, metabolism, distribution, efficacy, and resistance development, drawing on studies published between 2015 and 2025 across microbiology, pharmacology, nutrition, and exercise physiology. Available evidence indicates that physical activity enhances immune competence, modifies pharmacokinetics, and promotes microbiome diversity, whereas nutrition influences bioavailability, micronutrient support, and nutrient-drug interactions. Conditions such as obesity, malnutrition, and metabolic disorders can critically alter drug disposition and therapeutic outcomes. Nutraceuticals and functional foods may act synergistically with antimicrobials, although antagonistic effects can impair their absorption or potency, and lifestyle-driven modulation of the microbiota and host metabolism appears to play an important role in resistance pathways. Emerging strategies, including prodrugs, nanocarriers, and personalized dosing algorithms, have the potential to optimize therapy according to lifestyle and metabolic profiles. Overall, incorporating lifestyle determinants into antimicrobial research and stewardship may improve therapeutic efficacy, reduce resistance, support precision medicine, and position diet and physical activity as key modulators of infection management.},
}

@article {pmid42369406,
year = {2025},
author = {Chougule, PR and Sinha, SN},
title = {Next-generation non-animal models for inflammatory bowel disease: In vitro and in silico approaches for mechanistic understanding.},
journal = {NAM journal},
volume = {1},
number = {},
pages = {100051},
pmid = {42369406},
issn = {3050-6204},
abstract = {Inflammatory bowel disease (IBD), encompassing ulcerative colitis and Crohn's disease, is a chronic and relapsing inflammatory condition of the gastrointestinal tract resulting from a complex interplay of oxidative stress, immune dysregulation, microbial imbalance, and epithelial dysfunction. While animal models have primarily contributed to our understanding of IBD pathogenesis, their limited translational relevance and ethical concerns have led to the accelerated adoption of New Approach Methodologies (NAMs). This review highlights the increasing importance of in vitro platforms, including intestinal epithelial cell lines, 3D organoids, and microfluidic gut-on-chip models, which offer physiologically relevant and ethically sustainable solutions. In silico strategies, such as molecular docking, network pharmacology, toxicogenomics, artificial intelligence, and machine learning, enhance these models by enabling predictive simulations of drug interactions and molecular targets. Emerging mechanisms, such as barrier modulation and multi-targeted inflammatory regulation, are being explored using NAMs. Despite significant progress, challenges remain in standardization, integrating the immune and microbiome systems, and achieving regulatory acceptance. The combination of NAMs, multi-omics, and real-world data represents a promising avenue for mechanistic research, therapeutic screening, and precision medicine in IBD.},
}

@article {pmid42369550,
year = {2026},
author = {Tang, C and Li, H and Shi, X and Ge, H and Kou, Y and Yang, S and Jia, R and Zhao, X},
title = {Crop rotation patterns affect the growth, soil properties, and rhizosphere microbiome of cut chrysanthemums.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1763144},
pmid = {42369550},
issn = {1664-302X},
abstract = {BACKGROUND: Continuous cropping obstacles in cut chrysanthemum, which are characterized by soil nutrient imbalance, reduced enzyme activities, and disrupted rhizosphere microbial communities, restrict the development of its industry. This study investigated the regulatory effects of crop rotation on soil properties and microbial communities, and compared the mitigation efficiency of different rotation patterns.

RESULTS: At 60 days of growth, cut chrysanthemums under crop rotation systems exhibited significant increases in stem diameter, as well as fresh and dry weights of both aboveground and underground biomass, compared to continuous cropping. Rotation significantly increased soil total nitrogen, hydrolyzable nitrogen, and available phosphorus, with cabbage rotation exhibiting the most prominent phosphorus accumulation effect. The activities of soil catalase, alkaline phosphatase, and sucrase were higher in rotation groups, whereas the activity of urease decreased with successive planting cycles. Bacterial richness increased with planting cycles, while fungal diversity declined. Notably, rotation reduced the relative abundance of pathogenic Fusarium by 17.1-28.1%. Multivariate analyses indicated that soil nitrogen and phosphorus were closely correlated with bacterial community structure, while phosphorus was the most influential factor on fungal communities. Critically, the two crop rotation systems exhibited distinct mechanisms: maize primarily exerts regulatory effects on soil microbial community structure and enzyme activities, while cabbage focuses on optimizing soil nutrient element status.

CONCLUSION: Crop rotation with maize or cabbage alleviates continuous cropping obstacles by improving soil nutrient status, enhancing enzyme activities, and optimizing rhizosphere microbial communities. Maize rotation excels in regulating soil enzyme activities and bacterial communities, whereas cabbage rotation is more effective in promoting plant biomass during the vegetative growth stage, accumulating soil phosphorus, and inhibiting pathogenic fungi. This study provides a theoretical basis for sustainable cut chrysanthemum production via rotation management strategies designed to enhance soil microbial and physicochemical properties.},
}

@article {pmid42369552,
year = {2026},
author = {, },
title = {Correction: Crop rotation patterns affect the growth, soil properties, and rhizosphere microbiome of cut chrysanthemums.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1900191},
doi = {10.3389/fmicb.2026.1900191},
pmid = {42369552},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2026.1763144.].},
}

@article {pmid42369717,
year = {2026},
author = {Huang, J and Gong, T and Zhou, X and Zheng, X},
title = {[The Role of Salivary Microbiota in Oral and Systemic Disease Development and Diagnosis].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {57},
number = {3},
pages = {870-879},
pmid = {42369717},
issn = {1672-173X},
mesh = {Humans ; *Microbiota ; *Saliva/microbiology ; Dysbiosis ; *Mouth Diseases/microbiology/diagnosis ; Autoimmune Diseases/microbiology/diagnosis ; Periodontal Diseases/microbiology ; Cardiovascular Diseases/microbiology/diagnosis ; Dental Caries/microbiology ; },
abstract = {The salivary microbiome plays a crucial role in both oral health and systemic diseases, offering significant insights into disease development and early diagnosis. Under normal conditions, a balanced relationship exists between the microbiota and the host; however, when this balance is disrupted, it can lead to the onset of oral diseases such as dental caries, periodontal disease, and oral cancer. Changes in the salivary microbiome provide valuable information for the early diagnosis of oral diseases. Moreover, microbial dysbiosis in the oral cavity may promote the translocation of pathogenic microorganisms via the gastrointestinal tract, lungs, or bacteremia, leading to ectopic colonization outside the oral cavity and contributing to the onset and progression of systemic diseases such as colorectal cancer, cardiovascular diseases, and autoimmune disorders. Therefore, this review summarizes the role of the salivary microbiome in disease development and diagnosis, based on recent advancements in research on salivary microbiota, offering new perspectives for the early prevention and clinical management of systemic diseases.},
}

Humans
*Microbiota
*Saliva/microbiology
Dysbiosis
*Mouth Diseases/microbiology/diagnosis
Autoimmune Diseases/microbiology/diagnosis
Periodontal Diseases/microbiology
Cardiovascular Diseases/microbiology/diagnosis
Dental Caries/microbiology

@article {pmid42369718,
year = {2026},
author = {Chen, Z and Zhang, X},
title = {[The Oral Microbiome: Maintenance of Homeostasis, Disease Associations, and Mechanisms of Pathogenesis].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {57},
number = {3},
pages = {861-869},
pmid = {42369718},
issn = {1672-173X},
mesh = {Humans ; *Microbiota/physiology ; *Homeostasis ; *Dental Caries/microbiology ; *Mouth/microbiology ; Periodontitis/microbiology ; Dysbiosis ; Biofilms ; Dental Plaque/microbiology ; },
abstract = {The oral microbiome is a complex and highly structured ecosystem composed of diverse microorganisms, including bacteria, fungi, viruses, and other microbes, which establish an intimate symbiotic relationship with the host. Its composition across distinct ecological niches, such as teeth and mucosa, is modulated by multiple factors, including age, genetics, and lifestyle. A stable microbial community acts as an essential barrier for sustaining oral and systemic health. This review systematically examines the structure and function of the oral microbiome under healthy and diseased conditions, with an emphasis on the formation mechanisms of plaque biofilms and their pivotal roles in the initiation and progression of dental caries and periodontitis. Dental caries is predominantly driven by acidogenic and aciduric bacteria, such as Streptococcus mutans and Lactobacillus spp., accompanied by microenvironmental acidification and enamel demineralization. Periodontitis is closely associated with the enrichment of pathogenic microorganisms, including the "red complex" in subgingival plaque, and host immune dysregulation. Furthermore, ecological dysbiosis of the oral microbiome, particularly the abnormal proliferation of pathogens such as Fusobacterium nucleatum and Porphyromonas gingivalis, not only contributes to the development and progression of oral squamous cell carcinoma but also closely correlates with numerous systemic disorders, including cardiovascular diseases, diabetes mellitus, rheumatoid arthritis, and pancreatic cancer, via mechanisms such as inflammatory induction, immunosuppression, and microbial translocation. Systematic elucidation of the ecological characteristics and pathogenic mechanisms of the oral microbiome will provide a critical theoretical foundation for maintaining oral microecological homeostasis and for preventing and treating oral and systemic comorbidities.},
}

Humans
*Microbiota/physiology
*Homeostasis
*Dental Caries/microbiology
*Mouth/microbiology
Periodontitis/microbiology
Dysbiosis
Biofilms
Dental Plaque/microbiology

@article {pmid42370310,
year = {2026},
author = {Ramírez-Durán, N and Manzanares-Leal, GL},
title = {Signatures of the maternal-infant oral microbiome in contexts of imprisonment and social vulnerability.},
journal = {Frontiers in dental medicine},
volume = {7},
number = {},
pages = {1805944},
pmid = {42370310},
issn = {2673-4915},
abstract = {INTRODUCTION: The oral microbiome is a dynamic ecosystem that develops in early life through physiological processes and environmental exposures and plays a key role in oral and systemic health. In socially vulnerable settings, such as prisons, altered living conditions may shape the establishment of the pediatric oral microbiome. This study aimed to characterize the oral microbiome signatures in mothers, children, and pregnant women living in prisons, and to explore microbial variation in relation to confinement-related living conditions.

METHODS: A cross-sectional study was conducted that included the entire maternal-child population (n = 43 samples) residing in five prisons and social reintegration centers in the State of Mexico. Saliva and oral biofilm samples were collected from mothers (n = 19), children (n = 19), and pregnant women (n = 5). The taxonomic composition was evaluated by sequencing the 16S rRNA gene. Analyses of alpha diversity (Shannon index), beta diversity (weighted UniFrac), and differential abundance (DESeq2) were performed.

RESULTS: A shared core microbiome, dominated by Streptococcus and Veillonella, was identified in all groups. However, significant differences in microbial diversity were observed according to prison (p = 0.03) and population group (p = 0.01). Children exhibited the lowest diversity and a pronounced dominance of Streptococcus (58%), consistent with microbiome profiles in the early stages of life but consistent with early-life microbiome profiles. Mothers showed a greater abundance of opportunistic environmental taxa, including Pseudomonas (13.2%) and Raoultella (5.2%). Pregnant women showed the greatest diversity and a distinctive signature characterized by enrichment of Actinomyces and Leptotrichia. Beta diversity analyses revealed partial overlap between mothers and children, suggesting shared microbial patterns potentially related to common living conditions.

CONCLUSION: These findings provide an exploratory characterization of the oral microbiome in mothers, children, and pregnant women living in prison settings. The lower diversity observed in children, along with the presence of opportunistic environmental taxa, underscores the importance of accounting for confinement-related living conditions in oral health research and prevention strategies for historically marginalized populations. Future comparative and longitudinal studies are needed to clarify the relationship between prison-specific conditions and variation in the oral microbiome.},
}

@article {pmid42370348,
year = {2026},
author = {Dotis, J},
title = {Nutritional bioactives for preventing recurrent urinary tract infections in children: microbiome-mediated mechanisms and clinical implications.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1855301},
pmid = {42370348},
issn = {2296-861X},
abstract = {Recurrent urinary tract infections in children represent a common clinical challenge associated with repeated antibiotic exposure and rising antimicrobial resistance. These limitations have intensified interest in non-antibiotic preventive strategies, particularly nutritional bioactives capable of modulating host-microbe interactions. This review provides a clinically oriented synthesis of current evidence on dietary and nutraceutical interventions for the prevention of recurrent pediatric urinary tract infections. Particular attention is given to the limited availability of high-quality pediatric-specific evidence and the heterogeneity of current clinical data. It focuses on cranberry-derived type A proanthocyanidins, probiotics, selected micronutrients and D-mannose. Key mechanistic pathways are also highlighted, including inhibition of uropathogen adhesion, microbiome-mediated biotransformation of bioactives into anti-inflammatory metabolites, and modulation of host immune and epithelial responses within the gut-bladder axis. Available evidence suggests that cranberry products standardized to deliver approximately 36 mg/day of type A proanthocyanidins may reduce recurrence risk, whereas probiotics and vitamins A, C, and D may provide adjunctive benefits through microbiome modulation and enhancement of innate immune responses. However, substantial heterogeneity in study design, variability in formulations and dosing, and the limited availability of high-quality pediatric randomized trials remain important limitations. Building on current evidence, we propose a pragmatic multimodal framework for non-antibiotic prevention in children that integrates nutritional strategies with clinical risk stratification and individualized care, with particular attention to bioavailability, dose standardization and pediatric-specific factors such as age-related microbiome maturation. Future research should prioritize biomarker-driven endpoints, microbiome-informed stratification and adequately powered pediatric studies to define responders and optimize personalized prevention strategies.},
}

@article {pmid42370368,
year = {2026},
author = {Aziz, T and Owona, EP and Okoa, NTA and Sandrine, MNY and Rahman, IU and Sarwar, A and Zhao, L and Yang, Z and Alharbi, M and Alasmari, AF},
title = {Evaluating the anti-gut dysbiotic potential of bioactive primary metabolites derivatives from Lactaplantibacillus plantarum 12-3. An integrated ADMET, network pharmacology, molecular docking and normal mode analysis approaches.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1844467},
pmid = {42370368},
issn = {2296-861X},
abstract = {INTRODUCTION: Intestinal dysbiosis is a disorder of the gut microbiome, characterized by a loss of equilibrium between the microorganisms found in the gastrointestinal tract and their hosts. It leads to metabolic changes in both the gut and in the body's inflammatory response, and adversely affects the epithelial cells that line the intestines. This article aimed to study the mechanisms whereby three metabolites, produced from Lactiplantibacillus plantarum, including 2,4-decadienal, (Z)-ethyl heptadec-9-enoate, and octadecanoic acid, may alter protein activity associated with diseases of the gut.

METHODS: Using a variety of in-silico methods, including ADMET modeling and prediction, docking of two target proteins, Fatty Acid-Binding Protein 4 (FABP4) and B-Raf Proto-Oncogene, Serine/Threonine Kinase (BRAF), and molecular normal mode analysis and network pharmacology, we investigated the potential interaction of these compounds. Dynamics simulation was performed using GROMACS (2019.2) and GROMOS96 (43a1) force fields.

RESULTS AND DISCUSSION: ADMET indicates good oral absorption, moderate ability to dissolve in your intestinal tract (lipophilicity), and low toxicity when consumed. Additionally, molecular docking techniques indicated that metabolite-protein binding is stable via primarily hydrophobic bonds, hydrogen bonds, and all have similar binding energies in the range of -5.1 to -6.2 kcal/mol. Normal mode analysis and dynamic simulation confirmed that the metabolite-protein complexes were stable. Network pharmacology studies suggest that the use of L. plantarum-derived metabolites as BRAF and FABP4 regulators of dysbiosis in the gut may result in therapeutic targets to restore homeostasis in the epithelial lining of the intestines and reduce inflammation.

CONCLUSION: This work demonstrates the protective potential against intestinal dysbiosis of primary metabolites of L. plantarum. However, future experiments are essential to verify the predictions made from the in silico studies and optimize various types of metabolite-based treatments.},
}

@article {pmid42370369,
year = {2026},
author = {Zhang, Y and Wang, H and Deng, T},
title = {Integrative AI driven microbiome analysis for optimizing sports nutrition and enhancing athletic performance through personalized dietary interventions.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1754203},
pmid = {42370369},
issn = {2296-861X},
abstract = {INTRODUCTION: The relationship between microbiome composition, athletic performance, and personalized nutrition offers significant potential for optimizing sports nutrition and enhancing athletic outcomes through tailored dietary strategies.

METHODS: This study presents a novel framework, Integrative Microbiome Athletic Performance Optimization Network (IMAPON), designed to address this challenge by integrating microbiome data, athletic performance metrics, and demographic and physiological information to generate precise dietary recommendations. IMAPON consists of three core modules: the Microbiome Feature Extraction Module (MFEM), the Athletic Performance Prediction Module (APPM), and the Personalized Dietary Recommendation Module (PDRM). Two innovative strategies, the Adaptive Feature Integration Strategy (AFIS) and the Performance Driven Optimization Strategy (PDOS), are incorporated to improve system efficacy. AFIS facilitates dynamic integration of features from heterogeneous data sources, while PDOS aligns dietary interventions with specific athletic performance objectives. The framework employs advanced computational techniques, including feature extraction, representation learning, and optimization, formalized through mathematical models to capture latent interactions between microbiome composition, physiological factors, and performance metrics.

RESULTS AND DISCUSSION: Experimental results demonstrate the effectiveness of IMAPON in generating actionable dietary recommendations, highlighting its potential to transform sports nutrition by enabling precise, data driven interventions tailored to individual athletes. This approach represents a significant advancement in leveraging artificial intelligence for personalized nutrition and athletic performance enhancement.},
}

@article {pmid42370482,
year = {2026},
author = {Kar, B},
title = {Occurrence of Antimicrobial Resistance in Kocuria rhizophila Bacteria Isolated From Salmo munzuricus (Teleostei: Salmonidae) Samples in Natural Resources.},
journal = {MicrobiologyOpen},
volume = {15},
number = {4},
pages = {e70354},
pmid = {42370482},
issn = {2045-8827},
mesh = {Animals ; *Micrococcaceae/drug effects/isolation & purification/genetics/classification ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Drug Resistance, Bacterial ; DNA, Bacterial/genetics/chemistry ; Microbial Sensitivity Tests ; Sequence Analysis, DNA ; DNA, Ribosomal/genetics/chemistry ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {Global warming and environmental pollution trigger the emergence of antimicrobial-resistant (AMR) opportunistic pathogens in the aquatic microflora. This study aimed to determine the characterization and AMR profile of the opportunistic pathogen Kocuria rhizophila isolated from the tissues of Salmo munzuricus (Munzur trout), an endemic species. Samples collected from the Munzur River were identified using morphological and molecular (16S rDNA) methods; bacterial isolates were characterized by MALDI-TOF and sequencing. The resistance status against 11 different antibiotics was analyzed with the Kirby-Bauer method. The findings revealed that the isolates (with 99.51% accuracy as K. rhizophila) showed full resistance to Penicillin G (p < 0.01) and were moderately sensitive to gentamicin and tetracycline. High sensitivity to amoxicillin and ampicillin was detected. These findings demonstrate that even in natural environments, the fish microbiome in wild endemic populations can be susceptible to the development of AMR in response to environmental changes. Therefore, determining the resistance of opportunistic pathogens in wild fish species such as Salmo munzuricus to different classes of antibiotics and studying their spread is extremely important for natural ecosystems.},
}

Animals
*Micrococcaceae/drug effects/isolation & purification/genetics/classification
*Anti-Bacterial Agents/pharmacology
RNA, Ribosomal, 16S/genetics
*Drug Resistance, Bacterial
DNA, Bacterial/genetics/chemistry
Microbial Sensitivity Tests
Sequence Analysis, DNA
DNA, Ribosomal/genetics/chemistry
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

@article {pmid42370523,
year = {2026},
author = {Fouad, AF},
title = {Can Artificial Intelligence Be Utilised to Develop Point-of-Care Endodontic Microbiological Technologies?.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.70212},
pmid = {42370523},
issn = {1365-2591},
abstract = {BACKGROUND: Primary or persistent endodontic disease is caused by microbial biofilms that irritate the pulp and periapical tissues. Extensive microbiological analyses of these biofilms and their constituent pathogens have revealed their diversity and complexity. However, these studies have not resulted in many direct clinical chairside diagnostic, prognostic, or therapeutic technologies or paradigms. The overwhelming volume of endodontic antimicrobial strategies represents generic approaches that aim to reduce microbial loads to facilitate healing.

OBJECTIVES: This narrative review explores the potential applications of artificial intelligence (AI) in endodontic microbiology, highlighting current challenges in endodontic treatment, advances in microbiology and potential future applications of AI in endodontic microbiology and treatment strategies.

RESULTS AND CONCLUSION: AI continues to revolutionize various fields of medicine, including microbiology. The discipline of microbiology has already exploited AI to develop various diagnostic and biomarker technologies, as well as to facilitate and expedite common tasks. Several of these advances could be used to benefit research and clinical practice in endodontics.},
}

@article {pmid42370690,
year = {2026},
author = {Dietz, M and Subramanian, S and Staley, C},
title = {The gut microbiome and colorectal cancer.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0033225},
doi = {10.1128/cmr.00332-25},
pmid = {42370690},
issn = {1098-6618},
abstract = {SUMMARYColorectal cancer (CRC) is a significant global health concern that is growing in prevalence, especially in younger populations. The gut microbiome is an increasingly recognized factor in the development and progression of numerous diseases, including CRC. This review explores the current research on the causal relationship between the microbiome and CRC, including the strengths and limitations of the current models for studying this complex interaction. We then delve into key microbial metabolites and their effects on host signaling pathways in the context of CRC and highlight specific bacterial species with direct links to CRC development and progression. Existing microbiota-targeted therapies such as pre- and pro-biotics and fecal microbiota transplantation are described, as well as innovative microbiome-focused strategies that are currently in development, like quorum quenching. Finally, we address the major challenges in the field, such as conflicting research findings and the need for a systems-level, multi-omic approach to describe the intertwined and bidirectional host-microbe interactions.},
}

@article {pmid42370706,
year = {2026},
author = {Schiml, VC and Stalder, K and Várnai, A and Bergaust, LL and Bakken, LR and Arntzen, MØ},
title = {Microbial consortia mediating lignocellulose turnover and denitrification in eutrophic lake sediment enrichments.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0057726},
doi = {10.1128/msystems.00577-26},
pmid = {42370706},
issn = {2379-5077},
abstract = {Lignocellulose is a major component of plant biomass and is recalcitrant, with efficient degradation typically requiring oxygen-dependent oxidative and carbohydrate-active enzymes (CAZymes). Anaerobic turnover is slower but can be supported by microbes capable of nitrate respiration, including denitrifiers and dissimilatory nitrate reduction to ammonium (DNRA) bacteria, which may use nitrate or nitric oxide as alternative oxidants. Anoxic layers beneath the oxic zones of eutrophic lake sediments, where nitrate penetrates from surface waters, provide a natural habitat for such organisms. To investigate these processes, we established nitrate-amended enrichments from organic-rich sediments of 10 eutrophic lakes and applied gas kinetics alongside metagenomics and metaproteomics to characterize the microbial communities. We identified a set of core microbial metagenome-assembled genomes (MAGs) present in all enrichments, dominated by Pseudomonadota, Bacteroidota, Verrucomicrobiota, and Actinomycetota, which played key roles in denitrification and fermentation. Lignocellulose degradation, however, was largely carried out by species outside the core microbiome-that is, different key degraders between lakes, suggesting lake-specific specialization. Among these, we observed potential respiratory DNRA pathways and a broad repertoire of CAZymes targeting various lignocellulose subfractions. Interestingly, many MAGs also encoded nitric oxide dismutases (NODs), enzymes postulated to convert NO to molecular oxygen and dinitrogen gas. Together, these findings advance our understanding of anaerobic biomass degradation and nitrogen cycling in eutrophic freshwater sediments, while highlighting the unexplored functional diversity of NOD-containing bacteria as an intriguing open question for future research.IMPORTANCELignocellulose, the main structural component of plant biomass, represents a vast reservoir of organic carbon in natural environments. Although lignocellulose breakdown is commonly associated with oxygen-rich conditions, it also occurs in oxygen-depleted habitats such as lake sediments, where the responsible microbes and processes are poorly understood. This study reveals how diverse microbial communities can degrade lignocellulose while respiring nitrate, linking carbon turnover to nitrogen cycling in anoxic environments. By identifying shared and lake-specific microbial strategies, as well as a widespread but poorly characterized class of enzymes associated with nitric oxide metabolism, our work advances our understanding of anaerobic biomass degradation. These insights have implications for ecosystem functioning in nutrient-rich waters and for the development of sustainable, oxygen-free biotechnological processes.},
}

@article {pmid42370731,
year = {2026},
author = {Bresette, N and Ericsson, AC and Woods, C and Lin, A-L},
title = {MeLSI: Metric Learning for Statistical Inference in microbiome community composition analysis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0040726},
doi = {10.1128/msystems.00407-26},
pmid = {42370731},
issn = {2379-5077},
abstract = {Microbiome beta diversity analysis relies on distance-based methods, including permutational multivariate analysis of variance (PERMANOVA) combined with fixed ecological distance metrics (Bray-Curtis, Euclidean, Jaccard, and UniFrac), which treat all microbial taxa uniformly, regardless of their biological relevance to community differences. This "one-size-fits-all" approach may miss subtle but biologically meaningful patterns in complex microbiome data. We present Metric Learning for Statistical Inference (MeLSI), a novel machine learning framework that learns data-adaptive distance metrics optimized for detecting community composition differences in multivariate microbiome analyses. MeLSI employs an ensemble of weak learners using bootstrap sampling, feature subsampling, and gradient-based optimization to learn optimal feature weights, combined with rigorous permutation testing for statistical inference. The learned metrics can be used with PERMANOVA for hypothesis testing and with principal coordinates analysis for ordination visualization. Comprehensive validation on synthetic benchmarks and real data sets shows that MeLSI maintains proper type I error control while delivering competitive or superior statistical power for detecting subtle community shifts and, crucially, supplies interpretable feature-weight profiles that clarify which taxa drive group separation. On the DietSwap data set, MeLSI was the only method to achieve significance at α = 0.05, demonstrating that adaptive weighting can detect diet-induced community shifts that fixed metrics miss. Across all data sets, the learned feature weights identified biologically relevant taxa while providing actionable insight that no fixed distance metric can supply. MeLSI therefore offers a statistically rigorous tool that augments beta diversity analysis with transparent, data-driven interpretability.IMPORTANCEUnderstanding which microbes differ between groups of interest could reveal therapeutic targets and diagnostic biomarkers. However, current analysis methods treat all microbes equally (similar to using the same ruler to measure everything, regardless of what matters most). This means subtle but biologically important differences may go undetected, especially when only a few key species drive disease states while hundreds of "bystander" species add noise. Metric Learning for Statistical Inference (MeLSI) solves this by learning which microbes matter most for each specific comparison. In comparing male and female gut microbiomes, MeLSI identified specific bacterial families driving the differences, providing actionable biological insights that standard methods miss. This capability is particularly crucial for detecting early disease biomarkers, where differences are subtle and masked by biological variability. By telling researchers not just whether groups differ, but which specific microbes drive those differences, MeLSI accelerates the path from microbiome data to testable biological hypotheses and clinical applications.},
}

@article {pmid42370747,
year = {2026},
author = {Plominsky, AM and Oliver, A and Henriquez-Castillo, C and Podell, S and Minich, JJ and Augyte, S and Lowell-Hawkins, J and Sims, NA and Allen, EE},
title = {Detoxifying and depolymerizing microorganisms reveal intertwined guild collaborations in the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens.},
journal = {mBio},
volume = {},
number = {},
pages = {e0338225},
doi = {10.1128/mbio.03382-25},
pmid = {42370747},
issn = {2150-7511},
abstract = {The biotransformation of macroalgal biomass represents a major catabolic challenge due to its structurally diverse polysaccharides and inhibitory polyphenols. Unlike terrestrial lignocellulosic substrates, macroalgal polysaccharides contain multiple monomer types, branching patterns, and sulfation states. Additionally, toxic macroalgal polyphenols have been shown to inhibit both microbial growth and their catalytic enzymes. While herbivorous fishes have evolved specialized gut microbiota to process these substrates, the enzymatic pathways remain poorly characterized, with few experimentally validated polysaccharide utilization loci or biochemically defined marine sulfatases, and limited understanding of polyphenol degradation. Here, we developed in vitro microcosms, based on the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens, to temporally resolve the activity of the microbial guilds involved in macroalgal polysaccharide and polyphenol transformation. First, parallel cDNA/DNA amplicon sequencing was employed to distinguish the natural active fraction from transient gut microbiome taxa that became inactive/dead after their ingestion. Four medium combinations were able to propagate between 96% and 99% of the active hindgut microbial families, reproducing the cooperative degradation dynamics observed in vivo. Metagenomic and metatranscriptomic profiling of these four optimized in vitro microcosms served as models to assess the stepwise functional successions occurring in the natural gut microbiome. Early Gammaproteobacteria expressed enzymes linked to polyphenol detoxification and alginate degradation, followed by Bacillota, Bacteroidota, and Verrucomicrobiota guilds targeting more recalcitrant sulfated polysaccharides and polyphenols. Together, these results identified temporal and taxonomic coordination as key features of macroalgal biomass deconstruction, providing an experimentally tractable model for discovering novel carbohydrate-active enzymes and elucidating poorly understood pathways of marine polyphenol degradation.IMPORTANCESeaweed represents a source of sustainable biomass for various applications, but scalable industrial methods struggle to break down seaweed biomass into intermediate products due to the complexity of its constituents. Fish of the genus Kyphosus feed on different seaweed types by leveraging gastrointestinal bacteria to neutralize inhibitory polyphenols and convert their polysaccharides into simple sugars. This study identifies microbial groups that are transcriptionally active in natural fish hindgut microbiomes and how to propagate these active microbial communities in vitro. This enabled assessing how distinct microbial guilds act in succession to transform complex polysaccharides and polyphenols. Notably, this is the first study to assess the biotransformation capacities of macroalgal polyphenols by complex in vitro hindgut microbiomes of a generalist herbivorous fish. These findings advance our ecological understanding of cooperative degradation in marine gut symbioses and establish a tractable platform for discovering new enzymes and pathways with potential applications in algal biomass utilization.},
}

@article {pmid42370841,
year = {2026},
author = {Dang, J and Lee, Y and Wills, MV and Brown, JM and Madsen, K and Mocanu, V},
title = {The Gut Microbiome in Surgical Oncology: Mechanisms, Perioperative Outcomes, and Therapeutic Opportunities.},
journal = {The British journal of surgery},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjs/znag082},
pmid = {42370841},
issn = {1365-2168},
abstract = {INTRODUCTION: The gut microbiome is a fundamental determinant of gastrointestinal physiology. It is essential in maintaining host homeostasis while also implicated in cancer pathogenesis and alteration in physiological response to surgical stress. This narrative review evaluates the microbiome's mechanistic role in surgical oncology, assessing it as a biomarker for risk stratification and an emerging therapeutic target.

METHOD: The current literature was synthesized to examine microbial impacts on tumourigenesis and perioperative surgical outcomes across the lower and upper gastrointestinal tracts (including the gut-lung axis), the hepatopancreatobiliary system, and extra-abdominal malignancies (breast cancer and melanoma).

RESULTS: Dysbiotic microbial signatures, termed the oncobiome, actively drive tumour progression and immune evasion. Perioperative interventions induce acute microbial shifts linked to serious complications such as anastomotic leaks and pneumonia. Clinically, targeted modulation yields significant benefits as demonstrated by: perioperative synbiotics reducing infectious complications by 45% in colorectal surgery and 64% in major liver surgery. Furthermore, preoperative oral care reduces post-esophagectomy pneumonia by up to 50%, while Helicobacter pylori eradication halves metachronous gastric cancer risk. However, a detrimental "antibiotic paradox" exists in melanoma, where pre-treatment antibiotic exposure severely impairs immune checkpoint inhibitor efficacy. Conversely, faecal microbiota transplantation can reverse this immunotherapy resistance, achieving up to 80% response rates in trials.

CONCLUSION: The microbiome is a critical, modifiable determinant of both short-term surgical recovery and long-term oncologic survival. Future surgical oncology practice will need to integrate precision surgical microbiome-mediated biotherapeutics to optimise outcomes in multidisciplinary cancer care.},
}

@article {pmid42370943,
year = {2026},
author = {Yang, W and Tan, TM},
title = {Post-bariatric hypoglycaemia: from altered gut physiology to targeted therapies.},
journal = {Endocrine connections},
volume = {},
number = {},
pages = {},
doi = {10.1530/EC-25-0850},
pmid = {42370943},
issn = {2049-3614},
abstract = {Post-bariatric hypoglycaemia (PBH) is an increasingly recognised complication of bariatric and metabolic surgery, that can markedly impair quality of life and jeopardise the long-term benefits of surgery. This review summarises the current evidence on the epidemiology, pathophysiology and management of PBH, with a particular focus on mechanism-based treatment strategies. We first point out the limitations of existing epidemiological data and then outline a practical diagnostic framework. We next review the evolving understanding of PBH as a heterogeneous, pathophysiology driven syndrome arising from rapid nutrient delivery, exaggerated incretin responses, excessive insulin secretion, impaired glucagon secretion and emerging contributors such as post-prandial serotonin hypersecretion, bile acid signalling and microbiome change. On this basis, we review therapeutic options by mechanistic target, covering dietary and lifestyle interventions, acarbose, SGLT inhibition, somatostatin analogues, GLP-1 receptor antagonists, diazoxide, glucagon-based approaches and experimental serotonin receptor antagonism, and briefly discuss agents with limited supportive evidence. Finally, we explore key knowledge gaps and future directions, including the need for long-term prospective data, precision medicine approaches, rational combination therapy and greater integration of continuous glucose monitoring and digital decision support. Mechanism-based, multidisciplinary care from bariatric physicians, dietitians and surgeons, offers the best prospect of managing PBH, preserving quality of life and safeguarding the metabolic benefits of bariatric surgery.},
}

@article {pmid42371145,
year = {2026},
author = {Dang, K and Yang, Y and Wang, X and Cui, T and Zhou, Y and Liu, J and Xiao, J},
title = {Development and validation of a predictive model for calcium oxalate kidney stone recurrence integrating gut microbiome and clinical features.},
journal = {World journal of urology},
volume = {44},
number = {1},
pages = {},
pmid = {42371145},
issn = {1433-8726},
support = {20240930//Beijing Key Clinical Specialty Project/ ; 20240930//Beijing Key Clinical Specialty Project/ ; 20240930//Beijing Key Clinical Specialty Project/ ; 20240930//Beijing Key Clinical Specialty Project/ ; 20240930//Beijing Key Clinical Specialty Project/ ; 20240930//Beijing Key Clinical Specialty Project/ ; 20240930//Beijing Key Clinical Specialty Project/ ; 20250829//National Clinical Key Specialty Project Foundation/ ; 20250829//National Clinical Key Specialty Project Foundation/ ; 20250829//National Clinical Key Specialty Project Foundation/ ; 20250829//National Clinical Key Specialty Project Foundation/ ; 20250829//National Clinical Key Specialty Project Foundation/ ; 20250829//National Clinical Key Specialty Project Foundation/ ; 20250829//National Clinical Key Specialty Project Foundation/ ; BJPSTP-2024-30//Beijing Physician Scientist Training Project/ ; 82000717//National Natural Science Foundation of China/ ; QML20190106//Beijing Hospitals Authority Youth Programme/ ; No. 2024-1-4072//Capital Health Research and Development Program/ ; },
mesh = {Humans ; Recurrence ; *Calcium Oxalate/analysis ; *Kidney Calculi/chemistry ; *Nomograms ; Female ; Prospective Studies ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Risk Factors ; Adult ; },
abstract = {OBJECTIVE: To characterize the gut microbiome and clinical profiles of patients with recurrent calcium oxalate kidney stones, identify risk factors for recurrence, and develop an integrated predictive model.

METHODS: The development and validation of the prediction model followed the reporting standards outlined in the TRIPOD checklist. In this prospective study, patients with a first calcium oxalate stone episode were enrolled and followed for two years. Gut microbiota were profiled using 16 S rDNA sequencing. Independent risk factors were identified by logistic regression, and a nomogram was constructed and validated with receiver operating characteristic curves, calibration plots, and decision curve analysis.

RESULTS: Among 268 patients, 75 (27.99%) developed recurrence. The recurrent group showed significantly lower gut microbial alpha diversity. LEfSe analysis revealed enrichment of Proteobacteria, Enterococcaceae, Limosilactobacillus, and Escherichia-Shigella, with reduced Firmicutes. Family history of stones (OR = 10.684), elevated serum creatinine (OR = 1.025), and increased Escherichia-Shigella relative abundance (OR = 1.063) were independent risk factors. The nomogram achieved an AUC of 0.978 in the training cohort and 0.943 in the validation cohort, with excellent calibration and net clinical benefit.

CONCLUSION: Recurrent calcium oxalate stone patients exhibit gut dysbiosis characterized by reduced diversity and Escherichia-Shigella enrichment. Family history, serum creatinine, and Escherichia-Shigella abundance independently predict recurrence. The nomogram integrating these factors provides a reliable tool for recurrence risk assessment.},
}

Humans
Recurrence
*Calcium Oxalate/analysis
*Kidney Calculi/chemistry
*Nomograms
Female
Prospective Studies
*Gastrointestinal Microbiome
Male
Middle Aged
Risk Factors
Adult

@article {pmid42371248,
year = {2026},
author = {Tlaskalová-Hogenová, H and Hrnčíř, T and Štěpánková, R and Trebichavský, I and Hudcovic, T and Šplíchal, I and Šplíchalová, A and Šinkora, M and Funda, D and Sánchez, D and Kverka, M and Jirásková Zákostelská, Z and Kostovčíková, K and Coufal, Š and Procházková, P and Roubalová, R and Vannucci, L and Miler, I},
title = {Gnotobiology: from 19th-century global foundations to 21st-century omics - six decades of Czech contribution to microbiome research.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {42371248},
issn = {1874-9356},
support = {22-12533S, 22-21356S, 23-05645S, 25-16094S, 26-21469S//Czech Science Foundation (GAČR)/ ; LUAUS23014//Ministry of Education, Youth and Sports of the Czech Republic/ ; CZ.02.01.01/00/22_008/0004597//European Union - Next Generation EU (Operational Programme Johannes Amos Comenius)/ ; LX22NPO5102//European Union - Next Generation EU (National Institute for Cancer Research, Programme EXCELES)/ ; RVO: 61388971//Institute of Microbiology of the Czech Academy of Sciences/ ; NU21-04-00443, NU22-09-00493, NU22J-05-00056, NU23-01-00288, NU23-04-00381, NU23-05-00133, NW24-06-00509, NW24-07-00042, NW25-04-00079//Czech Health Research Council (AZV ČR)/ ; },
abstract = {Gnotobiology, from the Greek gnotos (meaning 'known') and bios (meaning 'life'), is a research discipline that uses organisms with a defined microbiological status to study the interaction between hosts and microbes. This review traces six decades of Czech gnotobiology, beginning with the launch of a dedicated gnotobiology programme at Nový Hrádek in 1962 by Jaroslav Šterzl, whose visionary aims anticipated by decades the current recognition of the microbiota as a central determinant of immune and broader physiological function. The site - originally established in 1953 as the Biological Station - was thereby transformed into one of only four gnotobiological laboratories worldwide at that time and the first in Central and Eastern Europe. The facility pioneered the rearing of germ-free piglets, rats, rabbits, and mice, establishing the experimental foundation for the laboratory's work on immune ontogeny, mucosal immunity and tolerance, and microbiota-host interactions in immune development and regulation. This review discusses the key discoveries made using these models. Among them, work at the Institute of Microbiology (Prague and Nový Hrádek) demonstrated that germ-free animals have underdeveloped lymphoid tissue and impaired adaptive immunity. The review also describes the subsequent development of gnotobiotic models of human metabolic, immune-mediated, neoplastic, and neuropsychiatric diseases. The completion of the Human Genome Project in 2001 and the emergence of microbial metagenomics in the early 2000s sparked renewed interest in host-microbe interactions and led to a rediscovery of gnotobiotic approaches as essential tools for establishing causation in microbiome research. We examine how integrating these approaches with high-throughput sequencing, metabolomics, and other omics technologies has shifted the focus from cataloguing the microbiome to mechanistically dissecting host-microbe interactions. Finally, we outline future directions, including humanized gnotobiotic models, microbiota-based therapeutics, and the convergence of gnotobiology with personalized medicine and synthetic biology.},
}

@article {pmid42371249,
year = {2026},
author = {Liu, Y and Liu, C and Yin, X and Yuan, X},
title = {The integrative role of the microbiome in systemic immuno-inflammatory aberrations.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {42371249},
issn = {1874-9356},
support = {YWJKJJHKYJJB2025032601//Medical Science Research Fund Project of Beijing Medical and Health Public Welfare Foundation/ ; },
abstract = {The human immune system maintains a delicate balance between protective immunity and self-tolerance. Disruption of this equilibrium leads to immune-mediated diseases (IMDs), a heterogeneous group of disorders including autoimmune, allergy, and autoinflammatory conditions [examples include familial Mediterranean fever (FMF) and cryopyrin-associated periodic syndromes (CAPS)]. Traditionally viewed as organ-specific pathologies, IMDs are now recognized as systemic disorders driven by chronic, self-sustaining low-grade inflammation. The microbiome, a key regulator of immune development and barrier function, acts as a central driver of this systemic inflammatory circuit. Dysbiosis impairs epithelial integrity, promotes microbial translocation, and triggers aberrant activation of pattern-recognition receptors, inflammasomes, and inflammatory signaling pathways. It skews cytokine networks toward pro-inflammatory phenotypes and disrupts the differentiation and function of critical immune cell populations, establishing a vicious cycle that propagates systemic inflammation and multi-organ comorbidities via gut-skin, gut-joint, and gut-lung axes. This review summarizes the roles of microbiome dysbiosis in IMD pathogenesis, highlights related biomarkers, and evaluates emerging therapeutic strategies targeting the host-microbiota axis. We advocate a systems immunology paradigm that integrates the microbiome as a core therapeutic target to restore immune homeostasis, achieve durable remission, and reduce the systemic comorbidity burden in patients with IMDs.},
}

@article {pmid42371546,
year = {2026},
author = {Yu, Q and Ding, H and Chen, Y and Gao, X},
title = {The multifaceted role of bile acids in breast cancer: pathogenesis, therapeutic potential, and drug delivery.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21195},
pmid = {42371546},
issn = {2167-8359},
mesh = {Humans ; *Breast Neoplasms/drug therapy/metabolism/pathology ; *Bile Acids and Salts/metabolism ; Female ; Drug Delivery Systems ; Animals ; Antineoplastic Agents/administration & dosage ; },
abstract = {BACKGROUND: Bile acids (BAs), once often considered tumor-promoting, are now recognized for their complex roles in breast cancer. Their effects are influenced by the gut microbiota and may vary across cancer subtypes and exposure contexts.

OBJECTIVES: This systematic review aims to summarize the current evidence on the clinical relevance, molecular mechanisms, and therapeutic applications of BAs in breast cancer.

METHODS: We performed a systematic literature search of four international (PubMed, Web of Science, Embase, Cochrane Library) and two Chinese (China National Knowledge Infrastructure, Wanfang) databases, along with clinical trial registries, from inception to February 8, 2026. Study selection adhered to PRISMA guidelines, and we focused on original studies investigating the role of BAs in breast cancer pathogenesis, therapy, or drug development.

RESULTS: Evidence mapping across clinical profiling, receptor biology, direct BA interventions, and translational applications indicates that human BA measurements do not converge on a stable systemic "BA signature". Our qualitative heterogeneity assessment indicates that the apparent contradictions are largely driven by differences in exposure compartment, comparator definition, analytical platform and BA speciation/coverage, and variable control of clinical confounders and subtype/stage or treatment background. When these sources of heterogeneity are considered, more coherent patterns emerge: receptor studies support context-dependent outputs across tumor subtypes and microenvironmental states, while direct BA interventions report both anti-tumor and pro-tumor phenotypes that depend strongly on BA species/form and concentration, with many in vitro experiments using pharmacologic or supraphysiologic exposures. In translational research, BAs have been explored as active derivatives targeting defined pathways and as enabling components in drug delivery systems. In the latter setting, BAs mainly serve as biocompatible scaffolds to improve delivery of established chemotherapeutics in preclinical models.

CONCLUSION: The BA system represents a promising but challenging therapeutic target for breast cancer. However, its clinical translation requires carefully designed strategies to overcome major hurdles. The inherent lack of tissue specificity poses risks for systemic toxicity. Future efforts must focus on developing tumor-targeted approaches, understanding the gut-microbiome-liver-breast axis, and performing subtype-stratified (especially estrogen receptor status-stratified) research to establish robust patient stratification biomarkers and safely realize the potential of BA-based therapies.},
}

Humans
*Breast Neoplasms/drug therapy/metabolism/pathology
*Bile Acids and Salts/metabolism
Female
Drug Delivery Systems
Animals
Antineoplastic Agents/administration & dosage

@article {pmid42371558,
year = {2026},
author = {Zhong, S and Guo, F and Chen, Q and Zhang, S},
title = {Microbiota-oriented strategies to mitigate parenteral nutrition-related complications in intestinal failure: A narrative review.},
journal = {Intestinal Failure (New York, N.Y.)},
volume = {10},
number = {},
pages = {100355},
pmid = {42371558},
issn = {2950-4562},
abstract = {BACKGROUND: Parenteral nutrition (PN) is essential for patients with intestinal failure (IF) but is associated with complications such as dysbiosis, small intestinal bacterial overgrowth, catheter-related infections, and intestinal failure-associated liver disease (IFALD). Growing evidence indicates that gut microbiota alterations contribute to the pathogenesis of these complications, supporting microbiota-oriented interventions as potential adjunctive therapies.

METHODS: Data sources: A structured literature search was conducted in PubMed, Web of Science, and Scopus from inception to December 2025.Study eligibility criteria: Clinical trials, observational studies, mechanistic studies, and relevant reviews evaluating gut microbiota features or microbiome-targeted interventions in IF or PN-dependent populations were included.Participants: Pediatric and adult patients with intestinal failure or short bowel syndrome, as well as relevant animal models.Interventions: Microbiota-oriented strategies, including probiotics, prebiotics, synbiotics, antibiotics, and fecal microbiota transplantation (FMT).Statistical analysis: Due to substantial heterogeneity in study design, interventions, and outcomes, meta-analysis was not performed; findings were synthesized qualitatively.

RESULTS: PN dependence was consistently associated with reduced microbial diversity, enrichment of Proteobacteria and Lactobacillaceae, and depletion of obligate anaerobes and short-chain fatty acid-producing taxa. Microbiota-oriented interventions demonstrated biological plausibility and microbiome modulation in selected studies; however, clinical benefits were variable and generally modest. Safety concerns, limited microbial engraftment, small sample sizes, and patient heterogeneity limited generalizability.

CONCLUSION: Gut microbiota dysbiosis plays a contributory role in PN-related complications of IF. Microbiota-oriented interventions are promising but remain unproven, underscoring the need for well-designed, stratified clinical studies to define efficacy, safety, and responsive patient subgroups.},
}

@article {pmid42371650,
year = {2026},
author = {Ahn, J and Halloran, Z and Beggs, DB and Wu, F and Duan, Y and Hwang, H and Zhu, Z and Flores, V and Albergamo, V and Kwak, S and Kim, S and Mei, S and Đoàn, LN and Yi, SS and Li, H and Hayes, RB},
title = {The Food and Microbiome Longitudinal Investigation (FAMiLI) Study: an Asian American (AsA) Enriched Multi-ethnic Environmental Cohort.},
journal = {Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology},
volume = {},
number = {},
pages = {},
doi = {10.1158/1055-9965.EPI-26-0178},
pmid = {42371650},
issn = {1538-7755},
abstract = {BACKGROUND: Over 90% of Asian American (AsA) adults are first- or second-generation immigrants, undergoing substantial environmental and sociocultural transitions; yet most environmental epidemiology cohorts have included few AsA participants.

METHODS: The Food and Microbiome Longitudinal Investigation (FAMiLI) is an environmental health cohort enriched with AsA adults (predominantly Korean and Chinese American) and designed to capture environmental exposures, dietary acculturation, and sociocultural factors across immigration generations. Its biobank-including buccal and stool specimens-supports research on the oral and gut microbiomes, human genomics, and other multi-omics.

RESULTS: Since its launch in 2018, FAMiLI has completed baseline recruitment and biospecimen collection for 13,183 adults aged 40-75 years. The cohort is now expanding to include an additional 3,000 Asian American adults, bringing the total to approximately 16,000 participants, with an expected distribution of ~50% Asian American and ~50% from other racial/ethnic groups. This expansion provides an opportunity to examine AsA environmental health experiences within the broader U.S.

CONCLUSIONS: FAMiLI is a unique national resource to address priority questions in environmental health, including microbiome and exposome science, individual susceptibility, and large-scale data analytics.

IMPACT: The cohort supports investigation of critical windows of environmental change across the immigration experience, racial and ethnic disparities, and drivers of emerging health outcomes, including cancer, cardiovascular disease, diabetes and other outcomes. This cohort offers essential data to inform prevention strategies and shape public health policy to improve health outcomes in AsA communities.},
}

@article {pmid42238434,
year = {2026},
author = {Basson, AR and Katz, J and Nguyen, V and Singh, D and Menghini, P and Gomez-Nguyen, A and Sieg, J and Bell, M and Thamma, K and Ponzani, G and Osme, A and Rodriguez-Palacios, A and Cominelli, F},
title = {A Randomized Controlled Trial Comparing Soy-Pea Protein to Animal Protein in Adults with Crohn's Disease.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.20.26353678},
pmid = {42238434},
abstract = {BACKGROUND AND AIMS: Diet plays a critical role in managing Crohn's disease (CD) inflammation. We assessed whether dietary replacement of animal protein (AnimalP) by soy-pea protein (SoyP) decreases the pro-inflammatory potential of gut microbiota and intestinal inflammation in CD patients.

DESIGN: In an open-label, randomized controlled feeding trial at University Hospitals Cleveland Medical Center, CD participants and healthy controls were randomized (1:1) to a soy-pea or animal protein diet for 7-days. Primary outcomes were the absolute difference (Δd7-d0) in; Crohn's Disease Activity Index (CDAI) score and fecal myeloperoxidase (MPO). Secondary outcomes included fecal calprotectin (FC) and high-sensitivity C-reactive protein (hsCRP). Murine fecal transplantation experiments were performed to determine the inflammatory potential of diet-altered gut microbiota.

RESULTS: The study randomized 66 participants, of whom 60 were included in the final analysis (n=31 CD, n=29 HC). After 7 days, CD participants assigned to the SoyP diet were more likely than those assigned to the AnimalP diet to demonstrate reductions in fecal MPO (RR=2.30, 95% CI: 1.04-4.85, P=0.032) and HBI (RR=4.68, 95% CI: 1.22-17.98, P=0.009). The association between SoyP and reduced fecal MPO remained significant after Bonferroni adjustment (FWER-adjusted P=0.006). A similar directional trend was observed for CDAI (RR=1.52, 95% CI: 0.89-2.58, P=0.135), although this did not reach statistical significance. No participants experienced worsening of CDAI. The exploratory post hoc rank-based CDAI-MPO composite score was lower in the CD-SoyP versus CD-AnimalP group (median [IQR]: 5 [4-6] vs 8 [7-9]; P=0.012). Stratified analyses demonstrated significant reductions in fecal MPO among CD participants with lower baseline disease activity (CDAI <150; P<0.0001), but not among those with higher disease activity (P=0.799).

CONCLUSION: Short-term addition of plant-based soy-pea protein within a controlled diet was associated with reductions in objective inflammatory markers in CD, with evidence of greater effects among participants with lower baseline disease activity. ClinicalTrials.gov, Number NCT04065048.},
}

@article {pmid42358320,
year = {2026},
author = {Banchi, P and Mila, H and Selma-Royo, M and Tal, S and Péron, F and Gaillard, V},
title = {Correction: The perinatal microbiota in dogs and cats: a narrative review from human research to veterinary practice.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1866749},
doi = {10.3389/fvets.2026.1866749},
pmid = {42358320},
issn = {2297-1769},
abstract = {[This corrects the article DOI: 10.3389/fvets.2026.1817504.].},
}

@article {pmid42358325,
year = {2026},
author = {de Souza, RBMDS and Fernandes, EL and Santos, LNA and da Silva Lima, L and Silva, HL and de Oliveira, SG and Félix, AP},
title = {Effects of a single-cell protein source from Paecilomyces variotii on diet digestibility and palatability and intestinal functionality of adult dogs.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1787800},
pmid = {42358325},
issn = {2297-1769},
abstract = {INTRODUCTION: This study aimed to evaluate the effects of a single-cell protein (SCP) source from Paecilomyces variotii on the apparent total tract digestibility (ATTD) of macronutrients and energy, diet palatability, fecal fermentative metabolites, and microbiota in dogs.

MATERIALS AND METHODS: Five extruded diets containing 0, 4, 8, 12, and 16% of SCP were manufactured. To isolate the metabolizable energy (ME) and the ATTD of the SCP, an additional test diet was manufactured containing 80% of the 0% diet and 20% of SCP. In Experiment I, 15 adult Beagle dogs were distributed in a randomized block design with 5 diets (0 to 16% SCP) and two periods of 21 days each, totaling 6 repetitions/treatment. In Experiment II, for the palatability test, 16 adult dogs were used, comparing the diets: 0 vs. 4% SCP; 0% vs. 8% SCP; and 4% vs. 16% SCP. In Experiment III, the SCP digestibility was estimated by the substitution method with 12 adult Beagle dogs.

RESULTS: The SCP presented ATTD of dry matter (DM) = 64.3%; ATTD of crude protein = 83.9%; ATTD of acid-hydrolyzed ether extract = 78.3%; and ME of 3843.3 kcal/kg. The ATTD of DM, organic matter, gross energy and the ME of the diets decreased linearly as the dietary inclusion of SCP increased (0 to 16% SCP; p < 0.05). There was a quadratic effect in fecal concentrations of propionate, butyrate, and total short-chain fatty acids, and a linear increase in isobutyrate and total branched-chain fatty acids, with the dietary inclusion of SCP (p < 0.05). Animals fed the 8% SCP diet presented an increase in alpha-diversity indexes (p < 0.05). Dogs fed the 4% SCP diet presented higher fecal abundance of Lactobacillus and Limosilactobacillus, when compared to the 0% group (p < 0.05). Besides, a higher fecal abundance of Lactobacillus and Butyricicoccus and lower abundance of Enterococcus, and Enterocloster was observed in dogs fed the 8% SCP diet compared to the 0% group (p < 0.05).

CONCLUSION: These results demonstrate that the dietary inclusion of 4 and 8% SCP promotes less impact on diet digestibility and may beneficially modulate the fecal microbiome and its metabolites in dogs, without affecting diet palatability.},
}

@article {pmid42358347,
year = {2026},
author = {Fang, X and Wang, M and Yalikun, K and Luo, X and Jiang, X and Nasser, MI and Liu, C and Pu, L},
title = {Relationship between oral microbiota and chronic kidney disease: facts and perspectives.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2687208},
pmid = {42358347},
issn = {2000-2297},
abstract = {BACKGROUND: The human microbiome comprises the microorganisms inhabiting the body, with the oral cavity representing the second most densely colonized site after the colon. Periodontal disease-associated oral bacteria are more common in patients with kidney disorders than in the general population. Oral dysbiosis disrupts host-microbiota homeostasis and promotes destructive periodontal inflammation, which has been linked to chronic kidney disease (CKD). However, current interventional evidence, including randomized controlled trials, remains limited by small sample sizes, short follow-up, heterogeneous periodontal interventions, inconsistent renal endpoints, limited blinding, and inadequate adjustment for confounders such as smoking, glycemic control, and medication use. Thus, causality between oral microbiota modulation and CKD progression remains unproven.

METHODS: This review synthesizes current evidence on the mechanisms by which oral microbiota influence various forms of nephropathy, with a particular focus on the impact of periodontitis (PD) on the progression of renal disease.This review summarizes evidence on mechanisms by which oral microbiota and periodontitis may contribute to nephropathy and renal disease progression.

RESULTS: Oral dysbiosis may affect CKD through systemic inflammation, endothelial dysfunction, and oxidative stress. It may also promote abnormal IgA1 glycosylation in IgA nephropathy and contribute to immune dysregulation and persistent inflammation in glomerulonephritis.

CONCLUSION: Periodontitis-associated oral dysbiosis may contribute to renal disease pathogenesis and progression. Clarifying these mechanisms could support preventive and therapeutic strategies for patients with nephropathy.},
}

@article {pmid42358426,
year = {2026},
author = {Mishra, AK and Tiwari, S},
title = {Topic: boron toxicity in semi-arid crops: the overlooked metalloid in abiotic stress.},
journal = {Physiology and molecular biology of plants : an international journal of functional plant biology},
volume = {32},
number = {6},
pages = {1325-1349},
pmid = {42358426},
issn = {0971-5894},
abstract = {Boron (B) is an essential micronutrient, yet its excess induces phytotoxicity, especially in semi-arid and alkaline soils, severely constraining crop productivity. This review delineates the physiological, biochemical, and molecular responses of plants to B toxicity, highlighting oxidative stress, membrane disruption, metabolic imbalance, and photosynthetic impairment as primary consequences. Multi-omics studies, including transcriptomics, proteomics, and metabolomics, have identified key components of B tolerance, such as BOR and NIP transporters, antioxidant enzymes, and stress-inducible proteins. Proteomic investigations reveal tissue-specific responses, with the upregulation of detoxification proteins, SA-dependent defence proteins, and transcriptional regulators like RING1B, which is also implicated in stem cell maintenance. Emerging evidence underscores the role of epigenetic modifications, DNA methylation, and histone acetylation in modulating B-responsive gene expression. However, the absence of high-resolution spatial mapping of B toxicity zones and limited access to high-throughput phenotyping platforms hinder progress in breeding resilient genotypes. Additionally, the interplay between B toxicity and climate change remains underexplored, despite its likely influence on B solubility and plant uptake. Advancements in nanotechnology and microbiome engineering present novel strategies for mitigation, including nano-sensors for real-time B detection, nano-formulations for controlled delivery, and beneficial microbes for enhancing plant tolerance. Integrating these tools with precision breeding and systems biology offers a sustainable framework to counteract B toxicity. This review advocates for a transdisciplinary approach combining spatial analytics, molecular insights, and ecological resilience to manage B toxicity and ensure long-term agricultural sustainability.},
}

@article {pmid42358480,
year = {2026},
author = {Flores, GD and Damon, ZF and Ford, M and Gancz, NN and Savoca, PW and Esfand, SM and Chu, KA and Querdasi, FR and McCann, CF and Westman, JG and Labus, JS and Clewett, D and Parr, AC and Hsiao, EY and Jacobs, J and Silvers, J and Callaghan, BL},
title = {A protocol for the Teen Bugs study: An integrative, multi-omics approach to understanding the role of the gut microbiome and mesocorticolimbic system in adolescent mental health following early adverse caregiving.},
journal = {Brain, behavior, & immunity - health},
volume = {55},
number = {},
pages = {101275},
pmid = {42358480},
issn = {2666-3546},
abstract = {Caregiving-related early adversities (crEAs) are potent risk factors for the development of internalizing psychopathology (e.g., depression, anxiety). Alterations to the dopaminergic mesocorticolimbic system, which supports the construction of reward-related experiences, are commonly observed following crEA exposure and are thought to mediate this risk. Indeed, many internalizing disorders are characterized by disruptions in how reward-related information is represented and used to guide affective and motivational states. Critically, the effects of crEA on mesocorticolimbic functioning may be shaped by input from peripheral systems, such as the gut microbiome, though such bottom-up signaling has been markedly understudied in humans. The Teen Bugs study was thus developed to identify gut microbiome-dependent metabolic pathways linking crEA exposure to mesocorticolimbic functioning and internalizing symptoms in adolescents, a group that experiences a disproportionate incidence of psychopathology relative to other age groups and is underrepresented in the gut microbiome literature. Adolescents aged 12-15 years, with and without histories of crEA exposure, will be followed across three timepoints over five years. At each timepoint, participants will complete a semi-structured clinical interview, a reward-guided decision-making task, and self-report questionnaires assessing mental health, previous caregiving experiences, reward-related behaviors, as well as developmental and lifestyle factors. Participants will also undergo multimodal neuroimaging that leverages MRI-based proxy markers of dopaminergic neurobiology and provide stool and blood samples for metagenomic and metabolomic profiling, respectively. This integrative design has the potential to clarify developmentally salient mechanisms that may serve as novel therapeutic targets for youth most at risk of, or already experiencing, internalizing psychopathology.},
}

@article {pmid42358596,
year = {2026},
author = {Kent, J and Chao, J and Liao, W and Singla, S},
title = {Exploring the Gut Microbiome's Association in Psoriasis and Psoriatic Arthritis: A Scoping Review.},
journal = {Journal of psoriasis and psoriatic arthritis},
volume = {},
number = {},
pages = {24755303261464171},
pmid = {42358596},
issn = {2475-5311},
abstract = {INTRODUCTION: Psoriasis (PsO) and psoriatic arthritis (PsA) are chronic inflammatory conditions treated with primarily immune-modulating medication. However, interest is growing in gut microbiome therapies. Studies have reported altered gut microbiota in PsO/PsA and explored probiotics and fecal microbiota transplantation (FMT) as potential therapies. This review synthesizes global studies on the microbiome's associations in PsO/PsA.

METHODS: We conducted a scoping literature review to understand the association between gut microbiota in PsO and PsA patients. Pubmed was used to identify 4,126 published manuscripts between 2015-2025. Thirty studies were included, encompassing 749,275 participants, with balanced gender representation and ages ranging from 18 to 76 years. These studies included 21 case-control studies, 1 case-series, 2 genome-wide analyses, 5 clinical trials, and 1 retrospective review.

RESULTS: Eighteen studies reported significant gut microbiome differences in PsO/PsA vs healthy controls. Variation in the Firmicutes/Bacteroides (F/B) ratio was of interest, with one study suggesting a low F/B ratio and five studies suggesting an elevated F/B ratio in PsO. A higher F/B ratio was linked to increased acetate production. Acetate and propionate, key short-chain fatty acids (SCFAs), were associated with modulation of the IL-23/Th17 axis in psoriasis and activation of keratinocytes. The role of therapeutics targeting the gut microbiome was explored. Ustekinumab and tofacitinib altered gut microbiome composition. Probiotic and FMT interventions showed mixed outcomes. Six of eight probiotic studies reported increased SCFA producing species and/or reduced inflammatory markers. FMT improved immune markers in mice but had no significant benefit in human trials.

CONCLUSION: Alterations in the microbiome linked to inflammation and immune response, suggest the microbiome as a potential therapeutic target for PsO/PsA.},
}

@article {pmid42358748,
year = {2026},
author = {Shah, SAUR and Tang, B and He, D and Ahmad, M and Nabi, G and Wang, C and Fan, F and Zheng, J and Wang, K and Hao, Y},
title = {Sex and social group altered the gut microbiome and fecal metabolome in the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis).},
journal = {Current zoology},
volume = {72},
number = {3},
pages = {395-408},
pmid = {42358748},
issn = {1674-5507},
abstract = {Factors like sex, diet changes, hormone levels, and stressors disrupt animals' symbiotic bacterial communities. Maintaining healthy bacterial communities is particularly challenging for social species, as group membership, social relationships, microbial transfer, and social stressors influence their microbiotas. This study investigated the influence of sex and social dynamics on the gut microbiome and associated metabolites in the captive Yangtze finless porpoise (YFP), employing 16S rRNA gene sequencing and ultra-high-performance liquid chromatography with tandem mass spectrometry-based metabolomic analyses. The present study reveals that sex and social grouping, that is, male-male (MM), female-female (FF), and male-female (MF) groups, significantly influence the alpha and beta diversity in the captive YFP. The phylum Firmicutes were increased considerably in the FF social group, while Proteobacteria, Cyanobacteria, and Fusobacteriota were significantly increased in the MM group, while Desulfobacterota were risen considerably in the MF group. The genera Macrococcus, Clostridium_sensu_stricto_13, and Cetobacterium were considerably raised in the MM group, Paeniclostridium and Turicibacter were substantially raised in the FF group, while the genus Peptostreptococcaceae were substantially raised in the MF group. The current research also presented significant metabolite variations in the sex and social groups which significantly altered the metabolic pathways such as bile secretion, glycerophospholipid metabolism, protein digestion and absorption, citrate cycle, and carbohydrate digestion in the captive YFPs. Additionally, the research identified a significant correlation between the gut microbiome and fecal metabolome across different sex and social groups. In conclusion, this research highlights the connection between changes in fecal microbiota and host metabolism in captive YFP. It shows how sex and social group dynamics affect both metabolic and bacterial variations, offering valuable insights for improving health and social welfare management in captive YFPs.},
}

@article {pmid42358754,
year = {2026},
author = {Liu, C and Wu, Z and Li, D and He, J and Li, G and Wei, F},
title = {Disentangling host identity and storage time effects on gut microbiota composition in captive migratory birds using absolute and relative quantification.},
journal = {Current zoology},
volume = {72},
number = {3},
pages = {441-450},
pmid = {42358754},
issn = {1674-5507},
abstract = {Understanding how gut microbiota support migratory birds is essential; yet, fecal sample freshness is often a challenge, particularly for rare species that cannot be captured directly. Here, we collected fecal samples from multiple captive migratory bird species at Nanchang Zoo and grouped them by post-defecation time (0, 1, 2, and 4 h). Using both relative and absolute quantification, we assessed the effects of host identity, short-term storage, and their interaction on gut microbiota composition. Species identity and quantification method significantly shaped microbiota profiles. Absolute quantification revealed Firmicutes (763,405.73 copies/μL) and Proteobacteria (340,231.03 copies/μL) as dominant in Grey-crowned Cranes, whereas relative quantification indicated Firmicutes (96.74%) predominated in Swan Geese and Proteobacteria (30.30%) in Black-necked Cranes. Red-crowned Cranes showed higher species richness than Black Swans and Swan Geese, with a significantly greater Shannon index than the latter. PCoA demonstrated clear interspecific differences, especially between crane and waterfowl lineages. Storage time had no significant effects on alpha and beta diversity across 6 species, except for reduced richness in Swan Geese at 2 and 4 h. While overall community structure was stable, a few conditionally rare taxa displayed time-sensitive shifts shortly after defecation. Our findings highlight that both host identity and quantification approach are critical determinants of avian gut microbiota profiles and emphasize that fecal sample freshness mainly affects rare taxa. This study provides methodological insights for optimizing fecal sampling protocols in field-based microbiome research on migratory birds.},
}

@article {pmid42358885,
year = {2026},
author = {Benites-Goñi, H and Cabrera, D and Mauricio-Vilchez, C and Munive-Degregori, A and Espinoza-Carhuancho, F and Mayta-Tovalino, F},
title = {A Scientometric Exploration of Helicobacter Pylori in Cancer Gastric: Impact, Trends, and Collaboration Dynamics.},
journal = {International journal of preventive medicine},
volume = {17},
number = {},
pages = {17},
pmid = {42358885},
issn = {2008-7802},
abstract = {BACKGROUND: Helicobacter pylori (Hp) has been widely linked to various gastric pathologies, including gastric cancer (GC). Understanding how scientific production in this area has been structured, developed, and impacted is key to guiding future research and clinical strategies. To scientometrically explore the oncological literature related to Hp and GC, evaluating its volume, impact, collaboration, and thematic evolution between 2019 and 2025.

METHODS: A descriptive scientometric study with an exploratory approach was conducted. The search was performed in Scopus on June 7, 2025, using the strategy with Boolean operators and broad terms related to Hp and GC. Documents published between January 2019 and June 2025 were selected. The analysis was performed using SciVal, Bibliometrix (R), and VOSviewer, exploring performance indicators, collaborative networks, and thematic evolution. The report was guided by the Reporting and Measurement of Items for Bibliometric or Scientometric Studies in Health Sciences (RAMIBS) guideline.

RESULTS: A total of 4573 documents discussed were obtained from 1445 sources. The number of documents obtained each year declined on average (-8.74%), with an average of 14.09 citations per document (high collaboration rate at 20%), with high impact authors (P. Malfertheiner, h-index 99, countries such as China, Japan, and United States), and the leading journals of Helicobacter and Gastroenterology for productivity and impact in the field. The amount of output was highly concentrated based upon Bradford's Law (46 core journals identified) and there was a strong bibliographic core (in co-citation), whilst thematic evolution showed that the focus of scholarship has evolved from virulence factors focused to integrative approaches around antimicrobial resistance, microbiome, and artificial intelligence.

CONCLUSIONS: The field of research on Hp and GC is an established and collaborative domain currently undergoing a methodological change. The study presents the roadmap that provides guidance for future scientific production and making editorial and clinical decisions.},
}

@article {pmid42358948,
year = {2026},
author = {Fu, J and Shan, J and Xu, H and Zhu, Z and Yang, P and Wang, Q and Han, J and Cao, G},
title = {Altered GABA and secondary bile acids in Guillain-Barré syndrome: association with gut dysbiosis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1849216},
pmid = {42358948},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/microbiology/metabolism ; *Guillain-Barre Syndrome/microbiology/metabolism/blood ; *Gastrointestinal Microbiome ; Female ; *Bile Acids and Salts/metabolism/blood ; Male ; *gamma-Aminobutyric Acid/metabolism/blood ; Adult ; Middle Aged ; Metabolomics/methods ; Metabolome ; Metagenomics ; Feces/microbiology ; Aged ; },
abstract = {OBJECTIVE: Guillain-Barré syndrome (GBS) is a rare, immune-mediated inflammatory disease of the complex peripheral nervous system that often follows acute infections, and may also be associated with long-term 'silent infections'. Long-term "silent infections" can alter the gut microbiota, which in turn may contribute to immune-mediated inflammatory diseases. Emerging evidence suggests that gut dysbiosis and altered serum metabolites are associated with GBS, but the causative link between GBS and gut microbiota remains unclear. Therefore, this study aimed to evaluate the association between gut microbiota structure and serum metabolic profile in GBS.

METHODS: Untargeted metabolomics profiling of serum and metagenomics sequencing of stool samples were performed to capture the global metabolic and microbial differences between GBS subjects and healthy controls. Multivariate statistical analyses, including PLS-DA, were applied to identify distinct clustering patterns and differential abundances of metabolites and gut microbiota. Pearson's correlation analysis was used to estimate the correlations between abundance of gut microbiota and serum metabolic profile. Seven different media were used to isolate the potential pathogens from GBS stool samples.

RESULTS: The metabolome data revealed that gamma-aminobutyric acid (GABA) metabolism and secondary cholic acid metabolism were perturbed in GBS. Specifically, GABA was increased significantly (approximately 14.3-fold), while multiple secondary cholic acids (methyl deoxycholate, glycodeoxycholic acid, glycolithocholic acid, taurolithocholic acid, and coprocholic acid) were decreased significantly in GBS subjects. Regarding the gut microbiota identified via metagenomic sequencing of stool samples, Ligilactobacillus salivarius, Enterocloster bolteae, and the opportunistic pathogenic Klebsiella pneumonia were notably more abundant in GBS subjects, while Bacteroides sp., Roseburia hominis and Paraprevotella xylaniphila were decreased significantly. In addition, pathogens such as K. pneumoniae were also isolated from GBS subjects. Further analysis of the metagenomic data revealed enrichment of prokaryotic genes involved in the GABA biosynthesis pathway, while genes associated with secondary cholic acid metabolism pathways were decreased in gut microbiome in GBS subjects. On this basis, correlation analysis revealed that changes in GABA were associated with altered levels of gut microbes including Enterococcus species, Ligilactobacillus salivarius and Enterocloster bolteae, whereas changes in secondary cholic acids were positively correlated with altered levels of Bacteroides species and Roseburia species.

CONCLUSION: GABA metabolism and secondary cholic acid metabolism were significantly disturbed in GBS subjects, potentially resulting from the dysbiosis of the gut microbiota. K. pneumonia and other no gut microbes were significantly enriched and isolated in GBS and may contribute to the inflammatory response in this immune-mediated inflammatory disease. These findings also suggest that GABA may be a promising biomarker for the diagnosis of GBS and that modulation of gut microbiota might impact the clinical course of GBS.},
}

Humans
*Dysbiosis/microbiology/metabolism
*Guillain-Barre Syndrome/microbiology/metabolism/blood
*Gastrointestinal Microbiome
Female
*Bile Acids and Salts/metabolism/blood
Male
*gamma-Aminobutyric Acid/metabolism/blood
Adult
Middle Aged
Metabolomics/methods
Metabolome
Metagenomics
Feces/microbiology
Aged

@article {pmid42359004,
year = {2026},
author = {Bai, Z and Lin, X and Wang, B and Li, Z and Qu, X and Hou, Y},
title = {Periodontitis as a potential amplifier of diabetes-related genitourinary complications: evidence gradients and mechanistic insights into the inflammation-microvascular injury axis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1843576},
pmid = {42359004},
issn = {2235-2988},
mesh = {Humans ; *Periodontitis/complications ; *Inflammation ; *Diabetes Complications ; Diabetic Nephropathies ; Male ; *Diabetes Mellitus, Type 2/complications ; Urinary Tract Infections/etiology ; Erectile Dysfunction/etiology ; Oxidative Stress ; },
abstract = {Periodontitis is increasingly recognized as a chronic systemic inflammatory burden that may be associated with greater vulnerability to selected diabetes-related genitourinary complications through overlapping inflammatory and microvascular pathways. This review integrates current epidemiological, mechanistic, and clinical evidence and proposes a conceptual "oral-metabolic-genitourinary axis" to describe potential links between periodontal inflammation and diabetic kidney disease (DKD), diabetes-related erectile dysfunction (ED), and recurrent urinary tract infections (UTIs). Available evidence is strongest for renal endpoints: observational studies and recent cohort data suggest associations between periodontitis and albuminuria, renal function decline, or dialysis risk in patients with type 2 diabetes. In contrast, evidence for ED and recurrent UTIs remains limited, with much of the support derived from mechanistic inference and indirect clinical observations. The proposed biologically plausible pathways include amplification of chronic low-grade systemic inflammation, endothelial and microvascular dysfunction, oxidative stress, advanced glycation end products-receptor for advanced glycation end products (AGE-RAGE) signaling, and microbiome interactions involving the oral-gut-genitourinary axis. These proposed associations and pathways may be modified or intensified by poor glycemic control, obesity, smoking, vitamin D deficiency, and gut dysbiosis. Clinically, periodontal therapy has been associated with improved glycemic control and may improve selected inflammatory or renal-related surrogate indicators, suggesting that oral health management could be considered a supportive component of multidisciplinary diabetes care. Overall, periodontitis is best viewed at present as a plausible amplifying factor rather than a confirmed independent cause of these outcomes, and this hypothesis requires confirmation in large prospective cohorts, randomized trials, and multi-omics studies.},
}

Humans
*Periodontitis/complications
*Inflammation
*Diabetes Complications
Diabetic Nephropathies
Male
*Diabetes Mellitus, Type 2/complications
Urinary Tract Infections/etiology
Erectile Dysfunction/etiology
Oxidative Stress

@article {pmid42359007,
year = {2026},
author = {Lu, J and Bi, S and Gao, Y and Zhang, Y and Zhang, T and Sun, M and He, M and Chen, X and Yang, B},
title = {Evaluation of electroacupuncture acupoint selection's potential in the treatment of inflammatory bowel disease: an investigation using a mouse gut microbiome and metabolomics model.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1830455},
pmid = {42359007},
issn = {2235-2988},
mesh = {Animals ; *Electroacupuncture/methods ; *Inflammatory Bowel Diseases/therapy/chemically induced/pathology ; *Acupuncture Points ; Disease Models, Animal ; Mice ; Metabolomics ; *Gastrointestinal Microbiome ; Cytokines/metabolism ; Dextran Sulfate ; Colon/pathology ; Male ; Interleukin-1beta/metabolism ; Body Weight ; Interleukin-6/metabolism ; },
abstract = {Electroacupuncture (EA) serves as an effective complementary therapy in the treatment of inflammatory bowel disease (IBD) within traditional Chinese medicine, with the therapeutic efficacy significantly influenced by the selection of specific acupoints. However, the regulatory mechanisms by which certain acupoints exhibit therapeutic benefits in IBD remain poorly understood. The research project intends to explore the mechanisms of action and regulatory variations in the treatment of IBD by the points Dachangshu (BL25), Tianshu (ST25), and Shangjuxu (ST37). This study used a sodium dextran sulfate-induced IBD mouse model to assess the therapeutic efficacy of three acupoints by evaluating body weight, colon morphology, inflammatory cytokines, gut microbiota, and metabolites. The results indicate that electroacupuncture of these three acupoints did not significantly alter IL-1β levels, but all three acupoints reduced IL-6 levels, with the most significant reduction observed at the Dachangshu acupoint. Furthermore, electroacupuncture treatment improved the structural characteristics of intestinal tissue and slowed the rate of weight loss. In IBD mice, electroacupuncture of three acupoints was associated with significant alterations in the intestinal microbiota and metabolic pathways. The majority of the metabolic pathways involved by these three acupoints are related to lipid, amino acid, and energy metabolism. Additionally, different acupuncture stimulation points also exhibited their own unique metabolic characteristics. These findings provide preliminary correlative evidence for the clinical application of acupuncture point selection in the treatment of IBD.},
}

Animals
*Electroacupuncture/methods
*Inflammatory Bowel Diseases/therapy/chemically induced/pathology
*Acupuncture Points
Disease Models, Animal
Mice
Metabolomics
*Gastrointestinal Microbiome
Cytokines/metabolism
Dextran Sulfate
Colon/pathology
Male
Interleukin-1beta/metabolism
Body Weight
Interleukin-6/metabolism

@article {pmid42359371,
year = {2026},
author = {Zhang, K and Paul, KC and Jacobs, JP and Lin, Y and Kwon, D and Nianogo, R and Bronstein, JM and Keener, AM and Yu, Y and Folle, AD and Jones, DP and Ritz, B},
title = {Integration of the serum metabolome and gut microbiome underscores the importance of altered lipid metabolism and potential immune modulation in Parkinson's Disease.},
journal = {Brain disorders (Amsterdam, Netherlands)},
volume = {21},
number = {},
pages = {},
pmid = {42359371},
issn = {2666-4593},
abstract = {INTRODUCTION: Single-omics studies have deepened our understanding of disease-related molecular processes, though integrated approaches are needed to uncover cross-system interactions. We previously reported changes in the serum metabolome and gut microbiome in Parkinson's disease (PD). To build on these findings, we conducted a multi-omics integration analysis to examine the interplay between the gut microbiome and human metabolism in PD.

METHODS: In a community-based study of 113 PD patients from rural California, microbiome profiles were obtained via 16S rRNA gene sequencing of fecal samples. Serum metabolomic profiles were generated using untargeted high-resolution LC-MS. Residual matrices of metabolomics data were extracted after adjusting for age, sex, racial minority status, and study wave. We identified PD-associated bacterial genera and summarized their abundance using principal component analysis. Using this summary score as the dependent variable, we performed partial least squares (PLS) regression to identify serum metabolites associated with the PD-related gut microbiome. Pathway enrichment analysis was then conducted on selected metabolite features from the PLS model.

RESULTS: We identified 266 metabolite features and annotated 29 metabolic compounds associated with PD-related microbes (p < 0.1). Enrichment analysis revealed perturbed pathways in lipid metabolism, including fatty acid activation and metabolism, linoleate metabolism, and glycerophospholipid metabolism, as well as carbohydrate metabolism such as hexose phosphorylation and starch/sucrose metabolism.

CONCLUSION: Our multi-omics integration analysis revealed that PD-associated gut microbiota are involved in host lipid metabolism, immune-related pathways, and potentially vitamin B-mediated regulation of kynurenine pathway metabolism, providing insights into potential microbiome-metabolome interactions in PD pathophysiology.},
}

@article {pmid42359619,
year = {2026},
author = {Chen, Z and Li, G and Tang, X and Liu, X},
title = {Cardiovascular Adverse Events Associated with Immune Checkpoint Inhibitors from the Perspective of Gut Microecology: Potential Roles and Research Advances of the Gut Microbiota.},
journal = {Journal of cardiovascular pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1097/FJC.0000000000001842},
pmid = {42359619},
issn = {1533-4023},
abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized cancer immunotherapy by significantly improving the prognosis of patients with various malignancies. Despite their clinical benefits, ICIs are increasingly recognized for inducing cardiovascular adverse events (CVAEs), including severe toxicities such as myocarditis, which pose substantial challenges in oncology practice. Emerging evidence highlights the gut microbiota as a critical regulator of host immunity, potentially influencing the development and progression of ICI-associated cardiovascular toxicities. This review comprehensively examines the current understanding of the interplay between gut microbiota and ICI-associated CVAEs. We systematically analyze the incidence, pathophysiological mechanisms, diagnostic criteria, and prognosis of major cardiovascular toxicities linked to ICIs. Furthermore, we explore the immunomodulatory functions of the gut microbiome that may underlie these adverse events, emphasizing microbiota-mediated systemic immune dysregulation and cardiovascular-specific toxicity pathways. We also discuss future research directions and the clinical implications of integrating gut microbiota modulation into the management of ICI-associated cardiovascular complications. By synthesizing multidisciplinary insights, this review aims to provide a theoretical foundation and research framework to advance both basic and clinical studies in this emerging field.},
}

@article {pmid42359789,
year = {2026},
author = {Lakey, BD and Wozniak, KJ and Britton, RA and Tabor, JJ},
title = {Mucin-derived sugars act as metabolic brakes controlling growth initiation in Akkermansia muciniphila.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2691334},
pmid = {42359789},
issn = {1949-0984},
mesh = {*Mucins/metabolism/chemistry ; Animals ; Humans ; *Akkermansia/growth & development/metabolism ; Mice ; Gastrointestinal Microbiome ; Polysaccharides/metabolism ; *Dietary Sugars/metabolism ; Colon/microbiology ; Citric Acid Cycle ; *Verrucomicrobia/growth & development/metabolism ; },
abstract = {Akkermansia muciniphila is a key member of the gut microbiota and plays important roles in host metabolism and health. In the colon, A. muciniphila extracts nutrients from oligosaccharide-rich mucin glycans that comprise the mucosa. However, this environment is complex and shaped by dietary inputs, microbiome metabolism, and mucin glycan composition varying across hosts, gastrointestinal regions, and physiological states. How strains of A. muciniphila integrate these nutrient signals into growth initiation and niche colonization remains unclear. Here, we compare physiological responses of a human- and mouse-derived strain of A. muciniphila, finding that dietary sugars differentially affect these isolates, suggesting host-associated tuning of metabolic capacity. In contrast, several mucin-derived sugars impose a conserved, concentration-dependent delay in growth initiation, implicating the lag phase as a critical metabolic checkpoint for growth. Genetic suppressor analysis identified sugar kinases and a component of the tricarboxylic acid cycle as genetically encoded control points linking glycan sugar exposure to the energy balance required for growth. These findings demonstrate that mucin-derived sugars function as both nutrients and metabolic stressors, regulating growth initiation. We propose that A. muciniphila employs metabolic "brakes" to coordinate growth with mucin composition, putatively linking host glycan landscapes to microbial physiology and ecological fitness within the mucus layer.},
}

*Mucins/metabolism/chemistry
Animals
Humans
*Akkermansia/growth & development/metabolism
Mice
Gastrointestinal Microbiome
Polysaccharides/metabolism
*Dietary Sugars/metabolism
Colon/microbiology
Citric Acid Cycle
*Verrucomicrobia/growth & development/metabolism

@article {pmid42359815,
year = {2026},
author = {Delgado Ocaña, S and Herrera, G and Guzmán, D and Self, DW and Cuesta, S},
title = {Gut Proteobacteria glycine metabolism regulates neuroplasticity, motivation, and reinstatement of cocaine self-administration in mice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2693397},
pmid = {42359815},
issn = {1949-0984},
mesh = {Animals ; Mice ; *Glycine/metabolism ; *Cocaine/administration & dosage/adverse effects ; Male ; Self Administration ; *Motivation ; Mice, Inbred C57BL ; *Proteobacteria/metabolism ; *Neuronal Plasticity ; *Gastrointestinal Microbiome ; Humans ; *Cocaine-Related Disorders/metabolism/microbiology ; Nucleus Accumbens/metabolism ; Escherichia coli/metabolism/genetics ; },
abstract = {Addiction is a chronic and relapsing disorder that affects millions of people worldwide; nonetheless, currently available FDA-approved treatments are limited in number and effectiveness. In past years, the gut-brain axis has emerged as a key modulatory factor associated with different psychiatric disorders, including addiction. Working in mice, we have shown that cocaine exposure alters the composition of the gut microbiome, increasing the abundance of Proteobacteria. This microbial shift, in turn, leads to a depletion in host glycine levels, altering cocaine-induced transcriptional changes in the Nucleus Accumbens (NAc) and facilitating the development of behavioral sensitization and conditioned place preference. Among the behavioral models to study psychostimulant use disorders, cocaine self-administration (SA) remains the most translational. Therefore, here we investigated whether Proteobacteria-induced glycine depletion can affect cocaine SA in mice. Using the human Escherichia coli HS and the glycine-uptake-deficient mutant E. coli HS ΔCycA, we build upon our previous findings and demonstrate that the ability of gut Proteobacteria to use glycine during cocaine SA shapes the trajectory and long-term neurobehavioral plasticity induced by the drug. Furthermore, we show that this bacterial-induced glycine depletion impacts the NAc proteome, altering its vulnerability to undergo molecular adaptations across different stages of the SA paradigm. Altogether, our findings show that the gut microbiome, and particularly the Proteobacteria phylum, is a crucial factor influencing short and long-term adaptation underlying motivation and cocaine-seeking behaviors.},
}

Animals
Mice
*Glycine/metabolism
*Cocaine/administration & dosage/adverse effects
Male
Self Administration
*Motivation
Mice, Inbred C57BL
*Proteobacteria/metabolism
*Neuronal Plasticity
*Gastrointestinal Microbiome
Humans
*Cocaine-Related Disorders/metabolism/microbiology
Nucleus Accumbens/metabolism
Escherichia coli/metabolism/genetics

@article {pmid42359986,
year = {2026},
author = {Wang, X and Meng, H and Yuan, B and Liu, D and Dong, Y and Zhang, F and Cao, H and Li, D and Yang, J and Sun, J and Wang, Y and Chen, B and Yan, J},
title = {Short-Chain Fatty Acids as Potential Mediators of NSAIDs' Effects on Arthritis Pain Relief.},
journal = {Pain research & management},
volume = {2026},
number = {1},
pages = {e9190926},
pmid = {42359986},
issn = {1918-1523},
support = {BJ2023052//The Grants of Top Talent Support Program for Young and Middle-Aged People of Wuxi Committee of Health/ ; 82370809//National Natural Science Foundation of China/ ; 32101033//National Natural Science Foundation of China/ ; BK20210060//Natural Science Foundation of Jiangsu Province/ ; K2023004//The Key Research Project of Health Commission of Jiangsu Province/ ; CXTD2021003//Key Discipline Construction Program of Wuxi Commission of Health/ ; K20253003//Wuxi Science and Technology Bureau, "Taihu Light" Science and Technology Research Program/ ; },
mesh = {Animals ; *Fatty Acids, Volatile/metabolism ; *Anti-Inflammatory Agents, Non-Steroidal/therapeutic use/pharmacology ; Male ; Rats ; Diclofenac/pharmacology/therapeutic use ; Rats, Sprague-Dawley ; Gastrointestinal Microbiome/drug effects ; Celecoxib/pharmacology/therapeutic use ; Tramadol/pharmacology/therapeutic use ; Disease Models, Animal ; *Osteoarthritis/drug therapy ; *Pain/drug therapy/etiology ; },
abstract = {BACKGROUND: Nonsteroidal anti-inflammatory drugs (NSAIDs) are the preeminent choice for treating osteoarthritis (OA) and have demonstrated the ability to regulate the gut microbiome. This study aims to explore the possibility that pharmacologically modified microbiome plays a role in improvement of arthritis.

METHOD: Rats with the right knee joint subjected to anterior cruciate ligament transection (ACLT) surgery were randomly allocated to eight groups. Four weeks after the procedure, the rats were given an intervention with saline (NS), celecoxib (CE), diclofenac (DF), and tramadol (TM). The rats were executed after 6 weeks of intervention, serum was used to evaluate the levels of inflammation and pain-related factors (IL-1β, IL-6, TNF-α, LPS, CGRP, and NGF), rat joints were used to assess local inflammation in the joints (MyD88) and the effect of the drug on the cartilage (Micro CT, Safranin O-Fast Green stain), Von Frey fibrous filaments were used to assess the sensation of pain in rats, and the differences in feces for the gut microbiome and short-chain fatty acids (SCFAs) were compared by 16S rRNA sequencing and gas chromatographic analyses.

RESULT: Rats treated with CE, DF, and TM experienced significant relief from joint pain, but the analgesic effect of CE and DF was significantly weakened after the combined application of antibiotics, while the effect of TM on pain remained after the application of antibiotics. The expression of MyD88 in the articular cartilage was somewhat reduced by CE and DF. Additionally, the gas analysis showed a significant increase in the SCFA content in the feces of the drug-intervention group.

CONCLUSION: NSAID-induced changes in gut microbiota structure and the subsequent increase in SCFA production may contribute to their pain-alleviating effects in rats. Although to a lesser extent, NSAIDs can also slightly reduce localized inflammation in the joints.},
}

Animals
*Fatty Acids, Volatile/metabolism
*Anti-Inflammatory Agents, Non-Steroidal/therapeutic use/pharmacology
Male
Rats
Diclofenac/pharmacology/therapeutic use
Rats, Sprague-Dawley
Gastrointestinal Microbiome/drug effects
Celecoxib/pharmacology/therapeutic use
Tramadol/pharmacology/therapeutic use
Disease Models, Animal
*Osteoarthritis/drug therapy
*Pain/drug therapy/etiology

@article {pmid42359989,
year = {2026},
author = {Oprea, OG and Balmus, IM and Ilie, T and Plavan, G and Nicoara, MN and Gorgan, L and Trifan, A and Stoica, B and Tamba, BI and Ciobica, A and Ciorpac, M},
title = {Natural products modulate social behavior and gut microbiota in a valproic acid-induced zebrafish model of autism spectrum disorder.},
journal = {Biomolecules & biomedicine},
volume = {},
number = {},
pages = {},
doi = {10.17305/bb.2026.14302},
pmid = {42359989},
issn = {2831-090X},
abstract = {Natural products rich in honey- and plant-derived bioactive compounds are increasingly investigated as modulators of the gut-brain-microbiome axis, a pathway implicated in autism spectrum disorder (ASD)-related behavioral and gastrointestinal alterations. This study evaluated whether two novel formulations, a honey-based product (API) and a plant extract-based product (MOD), modulate exploratory, anxiety-like, and social behavior and intestinal microbiota composition in an adult valproic acid (VPA)-induced zebrafish model of ASD. Adult wild-type zebrafish were assigned to control, VPA (300 μM), API (500 mg/L), MOD (500 mg/L), VPA+API, and VPA+MOD groups. Behavioral outcomes were assessed using the novel tank test and a T-maze social behavior test, while intestinal microbiota was profiled by 16S rRNA gene sequencing using an Oxford Nanopore platform. VPA exposure induced mild locomotor and anxiety-like behavioral alterations, whereas API and MOD further modified exploratory and social behavioral readouts in both healthy and VPA-treated zebrafish. Both formulations increased the time spent near the social stimulus; however, this finding should be interpreted cautiously because treatment-associated hypolocomotion and altered exploratory activity may influence T-maze performance. Microbiota profiling revealed a Pseudomonadota-dominated community across all groups, with descriptive treatment-associated shifts in secondary phyla and diversity patterns, particularly in combined VPA+API and VPA+MOD groups. However, no significant differences in alpha diversity, beta diversity, or genus-level abundance remained after multiple-testing correction. These findings suggest that API and MOD may modulate behavioral outcomes in adult zebrafish exposed to VPA, while their effects on gut microbiota remain exploratory and require validation in larger, adequately powered studies.},
}

@article {pmid42359998,
year = {2026},
author = {Boon, D and O'Rourke, B and Carmody, M and Woods, DF and Gloe, A and Platero-Rochart, D and Sánchez-Murcia, PA and McGlacken, GP and Reen, FJ},
title = {Coumarins Disrupt Cell-Cell Communication and Virulence in Priority Pathogens: Targeting the PQS Signalling System in Pseudomonas aeruginosa.},
journal = {Microbial biotechnology},
volume = {19},
number = {7},
pages = {e70404},
pmid = {42359998},
issn = {1751-7915},
support = {12/RC/2275_2/SFI_/Science Foundation Ireland/Ireland ; SFI/12/IP/1315/SFI_/Science Foundation Ireland/Ireland ; 21/FFP-A/8784/SFI_/Science Foundation Ireland/Ireland ; SFI 15/RI/3221/SFI_/Science Foundation Ireland/Ireland ; 21/RI/9705/SFI_/Science Foundation Ireland/Ireland ; ILP-POR-2019-004/HRBI_/Health Research Board/Ireland ; GOIPG/2021/692//Irish Research Council for Science, Engineering and Technology/ ; //Medizinische Universität Graz/ ; },
mesh = {*Pseudomonas aeruginosa/drug effects/pathogenicity/physiology/metabolism/genetics ; *Quorum Sensing/drug effects ; *Coumarins/pharmacology/metabolism ; Virulence/drug effects ; *Signal Transduction/drug effects ; Biofilms/drug effects/growth & development ; *Quinolones/metabolism ; Pyocyanine/metabolism ; *Cell Communication/drug effects ; Umbelliferones/pharmacology/metabolism ; },
abstract = {Cell-to-cell communication in microbial systems is known for its vital role in cellular signalling and gene expression. A specific form termed Quorum Sensing (QS) has received considerable attention since its discovery in the marine symbiont Aliivibrio fischeri. QS-controlled microbial functions are associated with bacterial virulence, pathogenicity, host-microbe interactions, and biofilm development. Interference in these signalling systems can modulate microbial virulence and pathogenicity, and microbial infection caused by drug-resistant pathogens. Plant-derived phytochemicals are considered a promising candidate, with coumarins emerging as significant plant-derived signalling molecules shaping microbiome dynamics and pathogen behaviours from a broad spectrum of ecosystems. Here we explored the role of natural and synthetic coumarin compounds in the control of signalling and virulence traits in Pseudomonas aeruginosa and other priority bacterial pathogens, including the fungal opportunist Aspergillus fumigatus. We uncovered an important 'hydroxylation-bias' favouring coumarin, umbelliferone (7-OH), and 6-hydroxy-coumarin (6-OH) in the specific competitive inhibition of the Pseudomonas Quinolone Signal (PQS), associated with reduced activity of a PqsR translational fusion and suppression of pyocyanin production. Conversely, while esculetin (6,7-OH) was most effective at Acyl Homoserine Lactone (AHL) QS biosensor inhibition, it did not affect PQS production. Anti-biofilm activity of coumarins against P. aeruginosa was independent of initial attachment but linked to changes in exopolysaccharide production. As the very real threat posed by antimicrobial resistance persists, these data support a role for phytochemicals such as coumarins in delivering an ecological solution to dysbiosis in the host-microbe interaction.},
}

*Pseudomonas aeruginosa/drug effects/pathogenicity/physiology/metabolism/genetics
*Quorum Sensing/drug effects
*Coumarins/pharmacology/metabolism
Virulence/drug effects
*Signal Transduction/drug effects
Biofilms/drug effects/growth & development
*Quinolones/metabolism
Pyocyanine/metabolism
*Cell Communication/drug effects
Umbelliferones/pharmacology/metabolism

@article {pmid42360048,
year = {2026},
author = {Mauri, M and Unger, K and Gershenzon, J and Allen, RJ and Agler, MT},
title = {Bacterial degradation of a plant toxin and nutrient competition with commensals trade off to constrain pathogen growth.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0006426},
doi = {10.1128/msystems.00064-26},
pmid = {42360048},
issn = {2379-5077},
abstract = {Healthy plant leaves potentially host both commensal bacteria and opportunistic pathogens, which, under some circumstances, may cause disease. The interactions between commensals and opportunistic pathogens are generally poorly understood, but such understanding is crucial for developing effective biocontrol strategies. In Arabidopsis thaliana, isothiocyanates (ITCs) are defense metabolites that suppress most bacteria; commensals are especially affected as they do not express ITC resistance genes. The ITC hydrolase SaxA detoxifies ITCs, making it an important virulence factor for bacterial and fungal pathogens. To investigate pathogen-commensal interactions based on SaxA-mediated ITC degradation, we used five ITC-sensitive bacterial commensals and the opportunistic pathogen Pseudomonas viridiflava 3D9 (PS). All strains were isolated from healthy A. thaliana leaves. PS degrades 4-methylsulfinylbutyl-ITC (4MSOB-ITC) with SaxA. We examined commensal growth in the presence of 4MSOB-ITC, both in monoculture and in coculture with PS or a saxA-deficient mutant (PSKO). We used the growth data to develop a generalizable consumer-resource mathematical model incorporating ITC toxicity, ITC degradation, and nutrient use. We predicted and confirmed experimentally that the extent to which SaxA benefits the pathogen depends on its effects on commensals. In some contexts, commensal rescue and the resultant nutrient competition limit pathogen growth. In addition, we tested in silico how commensal ITC susceptibility, pathogen ITC degradation rates, and growth parameters affect the trade-off between SaxA-mediated virulence (strong pathogen growth) and commensal rescue (commensal growth). Our findings suggest that the effects of microbial traits-traditionally viewed as either virulence or plant-beneficial factors-are constrained in the microbiome context. This underscores the need to reconsider how such traits are classified in the context of plant-microbiome interactions.IMPORTANCEHealthy plant leaves host a variety of bacteria; these can be beneficial, but some (opportunistic pathogens) can also be harmful under certain conditions. To design effective biocontrol strategies to sustainably protect plants, it is important to understand how opportunistic pathogens thrive as part of a healthy leaf microbiome. Plant defense metabolites, such as isothiocyanates (ITCs), which kill commensal leaf bacteria, and bacterial ITC resistance mechanisms, such as the ITC hydrolase SaxA, which are often expressed in pathogens and degrade ITCs, may play key roles in the plant microbiome composition. In this study, we explore how SaxA-mediated ITC degradation by a pathogen also benefits diverse ITC-sensitive commensals and how this, in turn, could shape microbiome stability and plant health. Using mathematical modeling based on growth data from Pseudomonas viridiflava with diverse commensals, we find that interaction dynamics can be explained by ITC detoxification and nutrient competition. We predict and experimentally confirm that conditions exist under which SaxA favors commensal growth so strongly that the pathogen is outcompeted for resources, thus not benefiting from its own virulence factor. Our findings suggest that the effects of microbial traits, including virulence factors, are context-dependent, especially when functioning as a public good in a community context like SaxA. Moreover, we propose that this concept, which has been known from antibiotic-degrading microbes, may be worth considering as well when studying plant-pathogen interactions under natural conditions where the commensal microbiome might play an important role in plant disease outcomes.},
}

@article {pmid42360058,
year = {2026},
author = {Puhachova, M and Klair, HK and Hariharan, B and Imtiaz, I and Zambrano Valenzuela, JJ and Alradi, EHA and Gbobbo, E and Zahoor, F and Shah, H and Kale, V and Narasimhan, N and Jamaleddin Ahmad, FA},
title = {Extending the Eisenbarth Model: Stage 0 as a Provisional Framework for Early Risk Stratification and Prevention in Type 1 Diabetes.},
journal = {Journal of diabetes research},
volume = {2026},
number = {1},
pages = {e9970365},
pmid = {42360058},
issn = {2314-6753},
mesh = {Humans ; *Diabetes Mellitus, Type 1/prevention & control/immunology/diagnosis/genetics ; Autoantibodies/immunology/blood ; Disease Progression ; Animals ; Risk Assessment ; Autoimmunity ; Risk Factors ; Biomarkers ; Genetic Predisposition to Disease ; Early Diagnosis ; },
abstract = {BACKGROUND: Type 1 diabetes (T1D) is an autoimmune disease characterized primarily by T cell-mediated pancreatic β-cell destruction, with islet autoantibodies serving as important biomarkers of autoimmune activity and risk progression. Early detection of immune imbalances before seroconversion may help identify individuals at increased risk before established autoimmunity develops. In this review, the proposed "Stage 0" construct is framed as a hypothesis-driven, preautoimmune research construct rather than an established clinical stage.

OBJECTIVE: This narrative review evaluates the proposed Stage 0 construct as a hypothesis-driven, preautoimmune conceptual framework for T1D, summarizes genetic, environmental, metabolic, and immunological factors that may precede islet autoantibody seroconversion, and outlines research priorities for risk stratification and prevention.

METHODS: This review searched PubMed and Google Scholar using MeSH and free-text terms to identify studies on early T1D pathogenesis, genetics, immunity, omics, metabolism, biomarkers, screening, and prevention. English-language human studies, mechanistic studies, reviews, and selected animal studies were included when relevant to early T1D biology. The SANRA framework was used to assess methodological quality.

KEY CONTENT AND FINDINGS: This review discusses Stage 0 as a proposed preautoimmune phase and evaluates factors that may affect T1D progression, including early signs of inflammation, metabolic changes, gut dysbiosis, and β-cell stress. Polygenic and HLA-based risk scores may improve disease prediction, but their performance differs across ancestries and requires population-specific validation. The evidence remains strongest for genetic risk and islet autoantibody status, whereas many preautoantibody biomarkers remain exploratory and require replication. Prevention strategies are reviewed across immune-modulating, antigen-specific, metabolic, microbiome-oriented, and screening-linked pathways.

CONCLUSION: Existing evidence supports additional research into preautoimmune biological alterations prior to the emergence of autoantibodies; however, Stage 0 should not be recognized as a clinical stage at this time. Standard biomarkers, ancestry-inclusive risk models, and prospective validation are essential before Stage 0 screening is considered for routine practice. Future research should determine whether this provisional framework can be translated into ethical, evidence-based screening and prevention pathways.},
}

Humans
*Diabetes Mellitus, Type 1/prevention & control/immunology/diagnosis/genetics
Autoantibodies/immunology/blood
Disease Progression
Animals
Risk Assessment
Autoimmunity
Risk Factors
Biomarkers
Genetic Predisposition to Disease
Early Diagnosis

@article {pmid42360164,
year = {2026},
author = {Sahu, BK and Panda, SK and Mallick, U and Panda, SH and Sahu, MC},
title = {The role of probiotics in restoring and maintaining vaginal microbiome health: a review.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0001126},
doi = {10.1128/iai.00011-26},
pmid = {42360164},
issn = {1098-5522},
abstract = {The vaginal microbiome is an important aspect of female reproductive health. The dominant microbial species of this ecosystem, Lactobacillus, offers protection from vaginal infections by maintaining lower pH levels and reducing potential pathogen colonization. Dysbiosis, or imbalance of the vaginal microbial ecosystem, has been associated with both common infections, such as bacterial vaginosis (BV), vulvovaginal candidiasis (VVC), and urinary tract infections (UTIs), and obstetric complications, including gestational diabetes, preterm labor, and obstetric anemia. This review provides an overview of the composition and function of the vaginal microbiota, emphasizing the role of Lactobacillus and other beneficial microbes and their mechanisms of action, including lactic acid and hydrogen peroxide production, competitive adherence, and immune modulation. Evidence from clinical trials supports the efficacy of these strains in reducing recurrence of BV, VVC, and UTIs. Additionally, emerging research shows promise for probiotic use in managing reproductive conditions such as gestational diabetes mellitus, preterm labor, and obstetric anemia. The review also discusses safety considerations, particularly in immunocompromised individuals, and the expanding interest in non-Lactobacillus genera like Bifidobacterium and Bacillus. Targeted probiotic interventions have great potential for restoring and maintaining a healthy vaginal microbiome, preventing recurrent infections, and helping improve reproductive outcomes. However, in order to incorporate these approaches in clinical practice, probiotic strains, delivery method, and dosage all need standardization.},
}

@article {pmid42360210,
year = {2026},
author = {Sayfitdinkhazhaev, ZF and Zhukova, NG and Israilova, GM and Zhukova, IA and Masenko, AY and Gaponova, OV},
title = {[Parkinson's disease associated with a mutation in the glucocerebrosidase gene].},
journal = {Zhurnal nevrologii i psikhiatrii imeni S.S. Korsakova},
volume = {126},
number = {6},
pages = {17-22},
doi = {10.17116/jnevro202612606117},
pmid = {42360210},
issn = {1997-7298},
mesh = {Humans ; *Glucosylceramidase/genetics ; *Parkinson Disease/genetics ; *Mutation ; alpha-Synuclein/metabolism ; },
abstract = {Parkinson's disease (PD) is one of the most socially significant neurodegenerative disorders due to its high prevalence and progressive nature. The key link in PD pathogenesis is the accumulation of the pathological alpha-synuclein. However, neuroinflammation, oxidative stress, mitochondrial dysfunction, and dysregulation of the brain-gut-microbiome axis also contribute significantly to the development of the disease. The etiology of PD remains controversial. This review of modern medical literature, covering domestic and foreign papers, summarizes recent studies on GBA1 gene mutations in PD patients. It showed that the prevalence of GBA1 gene mutations varies by geographical location. In addition, mutations in the GBA1 gene potentiate alpha-synuclein accumulation, lysosomal and mitochondrial dysfunction, and affect neuroinflammation in PD. The mechanisms of action of modern targeted therapies for PD associated with GBA1 gene mutations are described.},
}

Humans
*Glucosylceramidase/genetics
*Parkinson Disease/genetics
*Mutation
alpha-Synuclein/metabolism

@article {pmid42360315,
year = {2026},
author = {Paila, B and Asok, S and Suresh, AK},
title = {Physicochemical stability and protein corona profiling on the interaction of iron oxide nanoparticles with human tears.},
journal = {Journal of materials chemistry. B},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5tb02620b},
pmid = {42360315},
issn = {2050-7518},
abstract = {The integration of nanotechnology into ophthalmology represents a promising frontier for the development of precision diagnostics and therapeutics aimed at enhancing ocular health. While the systemic interactions of iron oxide nanoparticles (IONPs) with blood plasma have been extensively studied, their biomolecular interactions within the ocular environment, particularly human tears, remain largely unexplored. In this study, we comprehensively investigate the physicochemical behaviour and proteomic corona interactions of IONPs upon exposure to human tear extracts. Dynamic light scattering (DLS) revealed a modest increase in hydrodynamic diameter from ∼115 ± 3.3 nm to ∼139 ± 0.7 nm, accompanied by a reduction in the zeta potential (ZP) from ∼-36 ± 1.7 mV to ∼-29 ± 1 mV, likely due to protein adsorption. Proteomic profiling via liquid chromatography-mass spectrometry (LC-MS/MS) identified that 25 tear proteins got adsorbed onto the IONPs when compared to tear alone samples with 91 proteins, revealing the association of Lysozyme C, Lactotransferrin, Mammaglobin B, Lipocalin-1, keratins, immunoglobulins, opiorphin propeptide, Keratin II, Protein S100 and mesothelin proteins implicated in bacteriolysis, iron transport, transcriptional regulation, immune response, the cytoskeleton, tissue integrity, nucleotide binding, inflammation regulation, skin tissue formation, endogenous inhibition, microbiome homeostasis and signal transduction. These findings provide protein dynamics of the ocular nano-bio interface, emphasizing the influence of tear protein composition on IONPs. Our results highlight how tear protein corona formation defines the physicochemical stability of IONPs within the human tear environment and provide a basic understanding of these alterations, which may influence IONP-based ocular therapeutic systems.},
}

@article {pmid42360481,
year = {2026},
author = {Bhandari, R and Wills, Z and Harris, J and Salie, M and Ankrah, NYD and Wong, AC and Eastman, K and Ringbauer, J and Striegler, RK and Kang, DS},
title = {Rare Taxa and Stochastic Drift Drive the Microbiome Assembly of the Invasive Pest Drosophila suzukii, While Host Filtering Structures the Grape Sour Rot Community.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02819-x},
pmid = {42360481},
issn = {1432-184X},
abstract = {Understanding the processes that shape microbial community structure is a central challenge in ecology. The relative importance of deterministic and stochastic processes in driving the microbiome assembly and composition remains poorly understood across diverse animal and plant hosts. Here, we characterized the bacterial (16 S rRNA) and fungal (ITS rRNA) communities in invasive pest spotted wing Drosophila (SWD, Drosophila suzukii) and sour-rot-affected grapes from seven California vineyards using high-throughput sequencing. We found that while the bacterial microbiome of male and female SWD was compositionally similar, these communities were entirely distinct from those on sour rot-affected grapes, indicating strong host-specific filtering. SWD also harbored substantially higher microbial density and greater diversity compared to grapes. Ecological modeling revealed a fundamental divergence in assembly mechanisms: SWD communities were predominantly shaped by stochastic processes, with a neutral model explaining 40% of the variation. In contrast, sour-rot-affected grape communities were structured by a combination of stochastic and deterministic factors. Importantly, taxa that deviated from neutral predictions, thereby indicating selection, were primarily classified as rare or intermediate in abundance. This suggests that low-abundance taxa may act as keystone drivers of dysbiosis during rot development. These results highlight the differing assembly rules governing a vector-host system: the mobile vector acts as a stochastic reservoir, promoting pathogen dispersal, while the sessile host imposes strict environmental filtering. This underscores the critical role of rare taxa in shaping community structure and ecosystem stability in SWD and its host grapes.},
}

@article {pmid42360674,
year = {2026},
author = {Olenik, M and Güderer, İ and Wang, Y and Alvi, T and Pandey, P and Dönertaş, HM},
title = {Design and analysis strategies for robust microbiome ageing research.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.70397},
pmid = {42360674},
issn = {1873-3468},
support = {P2021-00-007//Carl-Zeiss-Stiftung/ ; },
abstract = {The gut microbiome changes systematically with age and associates with age-related morbidity and mortality, establishing it as a candidate biomarker and intervention target for ageing. Realising this potential requires methodological rigour, as distinguishing genuine biological signals from methodological artefacts remains challenging given variable findings across cohorts. This review provides an integrated framework for human microbiome-ageing research, organised around five methodological challenges that will collectively strengthen causal inference. We examine how age-associated factors can correlate with chronological age and may confound the microbiome-age associations, while selection biases shape old-age cohorts towards healthier profiles. We address within-host temporal dynamics and between-individual heterogeneity that require appropriate sampling to distinguish age-related signatures from transient states, and validation strategies that separate ageing from batch effects in predictive models. Mendelian randomisation provides causal leverage when triangulated with longitudinal and interventional evidence. Throughout, we examine how design choices determine the limits of analytical inference. The review concludes with a practical checklist, equipping researchers to strengthen reproducibility, improve generalisability and advance microbiome-based metrics towards validated indicators of biological ageing.},
}

@article {pmid42360706,
year = {2026},
author = {Glynn, VM and Lawrence, EC and Cleves, PA and Barrett, RDH},
title = {Symbiont identity impacts prokaryotic microbiome dynamics during heat stress in a model system for corals.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icag086},
pmid = {42360706},
issn = {1557-7023},
abstract = {The coral microbiome is highly complex, and interactions between microbiome members have been proposed as an important component of coral thermotolerance. However, establishing causal links among specific microbiome members remains difficult in corals because these communities are diverse and difficult to manipulate experimentally. We used Aiptasia, an emerging coral model system, to test how algal symbiont identity influences the structure and dynamics of the prokaryotic microbiome during heat stress. We generated clonal Aiptasia lines hosting two well-defined strains of photosynthetic algae in the family Symbiodiniaceae. We exposed these animals to an acute thermal stress assay while tracking prokaryotic dynamics with 16S sequencing. Among heat-stressed animals, algal strain was the strongest driver of prokaryotic community composition. We also identified line-associated indicator taxa that may be linked to differences in bleaching resistance. Finally, the more thermally sensitive host-algal association showed greater inter-sample dissimilarity in prokaryotic community structure under heat stress, suggesting that sustained microbiome variability may characterize more stress-sensitive cnidarian holobionts. These results suggest algal symbionts may shape bleaching responses not only through effects on host physiology, but also through their influence on prokaryotic microbiome dynamics.},
}

@article {pmid42361106,
year = {2026},
author = {Pal, NK and Kibria, MK and Noor, T and Ahmed, MF and Islam, MS and Ahmed, MF and Latif, MA and Ali, M and Noman, MA and Kundu, D and Sharma, O and Mollah, MNH},
title = {In-silico identification of bacterial key-genes directly or indirectly associated with the development and progression of colorectal cancer for exploring anti-bacterial agents.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0343565},
pmid = {42361106},
issn = {1932-6203},
mesh = {*Colorectal Neoplasms/microbiology/drug therapy/genetics/pathology ; *Anti-Bacterial Agents/pharmacology ; Humans ; RNA, Ribosomal, 16S/genetics ; Computer Simulation ; *Gastrointestinal Microbiome/genetics/drug effects ; Disease Progression ; *Genes, Bacterial ; *Bacteria/genetics/drug effects ; },
abstract = {Colorectal cancer (CRC), which includes malignancies of the colon and rectum, constitutes a major global health challenge. Though there are several drugs that targets CRC-related genes/proteins, but their performance is not yet reach to the satisfactory level. Moreover, their effectiveness gradually decreases over time with long-term use, a phenomenon known as drug resistance. Therefore, it is required to explore new alternative candidate drugs against CRC. Several studies recommended CRC-related dysregulated host-genes guided candidate drugs. However, microbiome guided drug discovery particularly targeting bacterial key genes (bKGs) within CRC-associated gut microbiota remains very limited. This study aims to identify bKGs as antibacterial targets within CRC-associated bacterial taxa for exploring anti-bacterial agents. At first, we analysed a 16S rRNA-seq profile dataset that contained 24 CRC and 50 healthy samples, where beta diversity analysis results showed significant differences in bacterial compositions between CRC and HC groups. Differential abundance analysis with threshold values at |log2FC| > 1.0 and adjusted p-value < 0.05 identified 42 significantly altered bacterial taxa of which Bacteroides fragilis, Bacteroides ovatus, Bacteroides uniformis, and Flavonifractor plautii were prioritized based on effect size and published literature reporting their association with CRC. Further, an integrative subtractive genomics and protein-protein interaction (PPI) network analyses was used to identify top-ranked 10 essential bKGs (ribD, ribBA, murA, alr, hisI, hisE, hisD, hisG, hisH, and hisB) from these four CRC-associated bacterial taxa as putative antibacterial targets. Finally, three candidate drug molecules (Sulfasalazine, Aminoglutethimide, and Tipiracil) were recommended as the preliminary bKGs-guided candidate anti-bacterial agents for CRC through molecular docking and ADME/T analyses. Further experimental and clinical validation is required to establish these compounds as the effective drugs targeting the bKGs for CRC. Thus, these findings may provide insights for developing innovative anti-bacterial treatment approach relevant to CRC.},
}

*Colorectal Neoplasms/microbiology/drug therapy/genetics/pathology
*Anti-Bacterial Agents/pharmacology
Humans
RNA, Ribosomal, 16S/genetics
Computer Simulation
*Gastrointestinal Microbiome/genetics/drug effects
Disease Progression
*Genes, Bacterial
*Bacteria/genetics/drug effects

@article {pmid42361405,
year = {2026},
author = {Sun, Z and Wang, T and Lasky-Su, JA and Litonjua, AA and Weiss, ST and Chavarro, JE and Liu, YY},
title = {Intrapartum caesarean delivery and childhood BMI trajectories in relation to the infant gut microbiome in the VDAART prospective birth cohort.},
journal = {EBioMedicine},
volume = {129},
number = {},
pages = {106347},
doi = {10.1016/j.ebiom.2026.106347},
pmid = {42361405},
issn = {2352-3964},
abstract = {BACKGROUND: The rising global health crisis of childhood overweight and obesity is potentially influenced by caesarean delivery (CD), but it remains a subject of ongoing debate. The gut microbiome, which is affected by delivery mode and can impact body weight, might play a role in this issue. However, the complex relationship between them remains poorly understood.

METHODS: We analysed data from a randomised, double-blind, placebo-controlled trial VDAART cohort, including BMI percentiles from 683 children aged 2-8 years and 1672 stool samples collected between 3 months and 5 years (all data in this study were collected between May 2010 and February 2018). To evaluate how CD relates to BMI trajectories, we conducted permutation testing and discussed the effect of confounding factors. We then used PERMANOVA, random forest classification, and Generalised Microbe Phenotype Triangulation (GMPT) to explore the role of the gut microbiota in mediating this relationship.

FINDINGS: Compared with vaginal delivery, intrapartum CD (iCD) rather than antepartum CD (aCD) was associated with a higher BMI percentile trajectory (Δ = 31.8%; 95% CI, 16.25%-47.55%; P = 0.001, Permutation test), and this was observed only among female children. Moreover, delivery mode was significantly associated with early-life gut microbiota, with effects also limited to females (F = 2.15 and 2.47 at months 3-6 and at age 1; P = 0.035 and 0.007, PERMANOVA). Random Forest models using early microbiota data can predict later overweight/obesity, performing best among iCD-born females (AUROC = 0.88; 95% CI, 0.83-0.94 for age 2), indicating an optimal intervention window before age one. Finally, GMPT identified 24 early-life taxa potentially mediating iCD-related overweight/obesity risk (11 preventive; 13 permissive), including Bacteroides ovatus, Bifidobacterium bifidum, Clostridium leptum, Eggerthella lenta, etc. INTERPRETATION: Our results indicate that CD types and children's sex are key factors in this interaction, offering a possible explanation for the ongoing debate about whether CD is linked to childhood overweight/obesity, and providing valuable insights for future intervention strategies.

FUNDING: This work was supported by the National Institutes of Health.},
}

@article {pmid42361802,
year = {2026},
author = {Fink, T and Rybniker, J and Bollenbach, T},
title = {Predicting antimicrobial resistance for precision medicine.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.05.031},
pmid = {42361802},
issn = {1934-6069},
abstract = {Antibiotics are among medicine's greatest successes, but resistance evolution threatens their continued efficacy. Decades of research have deepened our understanding of the mechanisms and evolutionary dynamics of antimicrobial resistance. More recently, advances in machine learning (ML) and artificial intelligence (AI) show promise in predicting antimicrobial resistance in pathogens based on rapid whole-genome sequencing and other accessible data. In this perspective, we highlight advances in understanding the mechanisms and spread of antimicrobial resistance. We discuss how this knowledge, coupled with ML- and AI-based approaches, can inform the prediction of resistance and a precision-medicine strategy that targets pathogenic bacteria specifically, thereby limiting resistance evolution and collateral damage to the microbiome. These accurate predictions of bacterial vulnerabilities will enable the adaptation of classical antimicrobial treatments with adjuvants, as well as the use of novel, narrow-spectrum therapeutics. Implementing these strategies, while also identifying key challenges, will help bring this strategy into clinical practice.},
}

@article {pmid42362124,
year = {2026},
author = {Chen, R and Zhan, Z and Zhang, S and Tang, S and Qin, H and Deng, Z and Gao, J},
title = {Duality of Bacteroides cross-feeding networks in health and disease.},
journal = {Pharmacological research},
volume = {230},
number = {},
pages = {108327},
doi = {10.1016/j.phrs.2026.108327},
pmid = {42362124},
issn = {1096-1186},
abstract = {Bacteroides species occupy central positions in gut microbial cross-feeding networks as dominant degraders of dietary and host-derived glycans. By releasing diffusible metabolites, Bacteroides can support beneficial commensals and host homeostasis, yet the same interactions may be co-opted under dysbiotic conditions to promote opportunistic expansion, disease progression, or therapeutic resistance. These divergent outcomes arise from context-dependent network structures, strain-level heterogeneity, and spatial organization rather than intrinsic microbial traits. Despite growing mechanistic insight, clinical translation remains limited by poor reproducibility, insufficient strain-level resolution, overreliance on association studies, and single-species frameworks that neglect network behavior. Here, we synthesize recent advances in the molecular architecture of Bacteroides-mediated cross-feeding, including polysaccharide utilization loci (PULs), spatially deployed surface enzymes, and outer membrane vesicles (OMVs), as well as their ecological dynamics and functional consequences, and critically evaluate why these interactions fail to yield predictable clinical outcomes. We propose a shift toward network-based microbiome therapeutics, highlighting predictive metabolic modeling, cross-feeding-guided consortium design, improved spatiotemporal resolution, and targeted modulation of host-microbe interfaces as key future directions. The principal novelty of this review lies in reframing Bacteroides cross-feeding networks, rather than individual species, as the fundamental unit of microbiome therapeutics, and in tracing this network logic from molecular mechanisms through ecological dynamics to a concrete, experimentally addressable translational roadmap. Embracing cross-feeding networks as therapeutic units may enable more reproducible, mechanism-driven, and personalized microbiome interventions.},
}

@article {pmid42362173,
year = {2026},
author = {Pan, T and Yang, H and Yang, C and Zhao, Y},
title = {Non-antibiotic drug-induced microbiotoxicity as a pharmacological variable.},
journal = {Chemico-biological interactions},
volume = {},
number = {},
pages = {112220},
doi = {10.1016/j.cbi.2026.112220},
pmid = {42362173},
issn = {1872-7786},
abstract = {Traditional pharmacology typically explains individual differences in efficacy and toxicity through the host's genetic background, drug-metabolizing enzymes, transporter activity, dietary exposure, and comorbidities; however, these factors alone are insufficient to fully account for the clinically prevalent phenomena of "same drug, different efficacy" and "same drug, different toxicity." Recent studies have shown that the gut microbiota not only directly participates in drug biotransformation but also continuously influences drug exposure, therapeutic efficacy, and susceptibility to adverse reactions through the reshaping of metabolite profiles, alterations in barrier function, regulation of mucosal immunity, and the restructuring of the host's absorption, distribution, metabolism, and excretion systems. Based on this, this article begins at the conceptual level of pharmacomicrobiomics and microbiotoxicity to systematically review the primary mechanisms by which non-antibiotic drugs induce gut microbiota disruption. It integrates representative evidence from metabolic, neuropsychiatric, gastrointestinal, anticancer, and immunomodulatory drugs, and further discusses their clinical significance in therapeutic stratification, toxicity prediction, infection risk assessment, and the design of microbiome interventions. Current evidence suggests that microbiotoxicity induced by non-antibiotic drugs is not merely a concomitant phenomenon but should be incorporated as a critical variable within the pharmacological explanatory framework. Future drug evaluations should not be limited to the host target organs and traditional pharmacokinetic processes but should also fully consider their impact on the host microbiome to advance more predictive and intervention-oriented precision medicine.},
}

@article {pmid42362546,
year = {2026},
author = {Vemuganti, V and Kang, JW and Zhang, Q and McGregor, ER and Hilser, JR and Aquino-Martinez, R and Harding, S and Harpt, JL and Beck, KR and Bussan, H and Kuehn, JF and Deming, Y and Studer, R and Johnson, SC and Asthana, S and Zetterberg, H and Blennow, K and Engelman, CD and Allayee, H and Anderson, RM and Ulland, TK and Bäckhed, F and Bendlin, BB and Rey, FE},
title = {Gut bacterial metabolite imidazole propionate potentiates Alzheimer's disease pathology.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-74744-z},
pmid = {42362546},
issn = {2041-1723},
abstract = {The gut microbiome modulates metabolic and neurovascular processes implicated in Alzheimer's disease and related dementias (ADRD), but the underlying mechanisms remain unclear. Here, we identify the bacterial metabolite imidazole propionate (ImP) as a modifier of ADRD pathology. In a cohort of 1196 cognitively unimpaired adults, higher plasma ImP levels were associated with lower preclinical cognitive scores and biomarkers of ADRD, both cross-sectionally and longitudinally. Fecal metagenomic analysis linked putative ImP producers to ADRD phenotypes. Genome-wide integrative analysis revealed a locus on chromosome 12 associated with both plasma ImP levels and AD risk in humans, supporting a host genetic contribution to ImP regulation and a causal role of this metabolite in AD. In mice, chronic ImP administration exacerbated AD-like pathology. ImP impaired brain endothelial barrier and promoted tau hyperphosphorylation in primary neurons, an effect blocked by glycogen synthase kinase-3β inhibition. Together, this study links ImP to hallmarks of neurodegeneration and suggests that targeting ImP may represent a potential strategy to modify ADRD risk.},
}

@article {pmid42362550,
year = {2026},
author = {Falshaw, N and Ducarmon, QR and King, A and Grundler, F and Mesnage, R},
title = {Remodelling of the gut virome after long-term fasting.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42362550},
issn = {2055-5008},
mesh = {*Fasting ; *Virome ; *Gastrointestinal Microbiome ; Bacteriophages/genetics/classification/isolation & purification ; Humans ; Metagenomics/methods ; Bacteria/virology/classification ; Feces/virology/microbiology ; Bacteroides/virology ; Faecalibacterium/virology ; },
abstract = {Long-term fasting is a promising strategy to restore metabolic health. Emerging evidence suggests that the gut microbiome may mediate some of fasting benefits, but the role of its viral component remains poorly understood. Using shotgun metagenomic data from a single-arm, monocentric fasting intervention, this study profiled the gut virome (n = 89 individuals, n = 241 samples) before and after 9.8 days of fasting (~ 250 kcal/day) as well as one and three months afterwards. Fasting induced a transient loss of viral diversity and a shift toward increased representation of virulent phages. External dataset validation identified 49 phages showing reproducible directional changes during fasting. Many were linked to bacterial hosts, showing concordant shifts, including depletion of Faecalibacterium-associated phages and enrichment of Bacteroides-associated phages. Cross-domain network analyses revealed denser viral-bacterial networks at the end of fast, with enriched connections to butyrate producers, suggesting phages may participate in the fasting-induced restructuring of microbial networks involving health-associated taxa. Collectively, these findings indicate that fasting remodels the gut virome cross-domain associations through reproducible, functionally relevant phage-host interactions, with reorganisation persisting for up to three months and occurring in parallel with improvements in cardiometabolic markers.},
}

*Fasting
*Virome
*Gastrointestinal Microbiome
Bacteriophages/genetics/classification/isolation & purification
Humans
Metagenomics/methods
Bacteria/virology/classification
Feces/virology/microbiology
Bacteroides/virology
Faecalibacterium/virology

@article {pmid42362661,
year = {2026},
author = {Ichikawa, S and Shimura, A and Kikuchi, A and Sanda, R and Sasayama, K and Nonoue, K and Tamura, H and Kano, T and Shimada, Y},
title = {Gut microbiome composition and predicted functions relate to growth and behavior in a Japanese preschool cohort.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-59018-4},
pmid = {42362661},
issn = {2045-2322},
abstract = {Early childhood is a period of rapid brain maturation and gut microbiome assembly, when emerging behavioral difficulties can shape later mental health and learning trajectories. Microbiota-gut-brain communication has been implicated in neurodevelopment through microbial metabolites and immune signaling. However, most pediatric evidence comes from high-risk or clinically referred cohorts, and gut microbiome-related correlates of typical behavioral variation in community-based preschool children remain poorly defined. In a cross-sectional sample of typically developing Japanese preschool children, we observed exploratory nominal associations between behavioral variation within normative ranges and gut microbiome composition and predicted functions. Internalizing domains showed candidate links with taxa and predicted pathways related to inflammatory potential and nucleotide biosynthesis, whereas somatic complaints and withdrawn behavior showed nominal associations with lower predicted respiratory and fermentative activity. Sleep-related difficulties showed multiple representative nominal pathway-level associations, including pathways related to methyl-donor and heme biosynthesis, while externalizing domains showed candidate links with predicted cell-envelope and carbohydrate-remodeling pathways. In contrast, age, height, and weight tracked expected maturation-related microbiome features, indicating that behavioral associations were not simple proxies of growth. Together, these findings provide an exploratory profile of microbiome-behavior correlations in a low-risk Japanese preschool cohort and highlight pathway-level candidates that may interface with neurodevelopment.},
}

@article {pmid42362797,
year = {2026},
author = {Mizuno, K and Chretien, B and Nishida, K and Ito, T and Kawashima, H and Ando, Y},
title = {Vonoprazan is associated with a phenotype-specific increase in cholangitis reporting in immune checkpoint inhibitor-treated patients: a VigiBase pharmacovigilance study.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {42362797},
issn = {1435-5922},
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) can cause immune-related adverse events (irAEs), including cholangitis, a rare but clinically severe hepatobiliary phenotype. Whether potassium-competitive acid blockers (PCABs) such as vonoprazan are associated with hepatobiliary adverse-event reporting among ICI-treated patients remains unclear.

METHODS: We performed a READUS-PV-compliant case-noncase disproportionality analysis using VigiBase, the WHO global individual case safety report database (inception through December 1, 2025; MedDRA v27.1). Adjusted reporting odds ratios (aRORs) were estimated for composite liver injury and a custom cholangitis-related endpoint for vonoprazan, proton pump inhibitors (PPIs), and histamine-2 receptor antagonists (H2RAs). The primary analysis was restricted to ICI-exposed reports and adjusted for age, sex, region, hepatotoxic co-medications, and ICI class. Sensitivity analyses addressed treatment intensity, microbiome-modifying co-medications, regional restriction, endpoint definition, sparse-data bias, and ICI subgroup. Six additional irAE categories were analyzed as comparator outcomes.

RESULTS: Among 295,671 ICI-exposed reports, 1098 co-reported vonoprazan and 1186 reports met the cholangitis-related endpoint. Cholangitis was reported in 35 of 1098 vonoprazan-exposed reports (3.19%) versus 0.39% of ICI reports without vonoprazan. Vonoprazan was associated with increased cholangitis reporting (aROR 2.79; 95% CI 1.93-4.02; P < 0.001; E-value 5.02), whereas PPIs and H2RAs showed no significant association. The association persisted across sensitivity analyses, including Western Pacific restriction, microbiome- and treatment-intensity adjustment, and PD-1/PD-L1 monotherapy. Comparator irAE associations were modest and heterogeneous.

CONCLUSIONS: Vonoprazan was associated with a phenotype-specific increase in cholangitis reporting among ICI-treated patients, a pattern absent with PPIs or H2RAs and unmatched across comparator irAEs. Prospective clinical validation is warranted.},
}

@article {pmid42362941,
year = {2026},
author = {Tan, W},
title = {Microbiome and cancer immunotherapy: a bibliometric analysis.},
journal = {Journal of the Egyptian National Cancer Institute},
volume = {38},
number = {1},
pages = {},
pmid = {42362941},
issn = {2589-0409},
mesh = {Humans ; Bibliometrics ; *Immunotherapy/methods ; *Neoplasms/therapy/immunology/microbiology ; *Microbiota/immunology ; },
abstract = {OBJECTIVE: To systematically analyze the global research landscape, collaboration patterns, knowledge flow pathways, and frontier trends in the synergistic effects between the microbiome and cancer immunotherapy.

METHODS: A systematic bibliometric analysis of publications on the synergistic effects between the microbiome and cancer immunotherapy (2010-2026) was performed using the Web of Science Core Collection. After deduplication, 3,058 publications were analyzed with CiteSpace 6.3.1 (co-citation, keyword burst, timeline), VOSviewer 1.6.19 (co-authorship, co-occurrence networks), and bibliometrix R package 4.4.1 (dual-map overlay, knowledge flow).

RESULTS: Annual publications grew at an average rate of 23.0%, reaching 715 in 2025. China and the United States contributed 60.1% of global output, with MD Anderson Cancer Center, Shanghai Jiao Tong University, and Paris-Saclay University serving as core collaboration hubs. Three major academic lineages (fundamental mechanisms, clinical translation, tumor-specific research) and three knowledge flow pathways (mathematical modeling → molecular genetics; clinical medicine → molecular biology; ecology → molecular biology) were identified, shaping distinct research paradigms. Hotspots evolved from "gut microbiota-ICIs" toward "oral microbiota," "engineered bacteria," and "precision prediction."

CONCLUSION: The field has transitioned from mechanistic exploration to precision intervention, with multidisciplinary integration and clinical translation as future priorities. The identified knowledge flow pathways and academic lineages provide a framework for understanding the intellectual structure of this rapidly evolving domain.},
}

Humans
Bibliometrics
*Immunotherapy/methods
*Neoplasms/therapy/immunology/microbiology
*Microbiota/immunology

@article {pmid42363045,
year = {2026},
author = {Li, X and Wang, G and Huang, W and Xiao, R and Wang, J and Ke, L and Wu, C and Chen, L and Wang, B},
title = {Geographic patterns and soil-to-bark microbial transmission shape microbiome assembly in tea trees.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09111-7},
pmid = {42363045},
issn = {1471-2229},
support = {NO. 32060697//National Natural Science Foundation of China/ ; NO. 202401BD070001-009//Yunnan Fundamental Research Projects/ ; },
abstract = {BACKGROUND: Understanding the ecological links in the microbiome of Camellia sinensis is vital for exploring beneficial interactions between microorganisms and economically important woody plants.

RESULT: This study investigates the characteristics of microbial communities, source-sink dynamics, driving factors, and functional differentiation of tea tree bark and bulk soil in the primary tea-producing regions of Yunnan, China (City of Pu'er, Lincang, and Xishuangbanna). Using amplicon sequencing, FEAST source tracking, and functional prediction, we analyzed microbial community differences and ecological roles. Findings revealed that bulk soil may served as the microbial reservoir for bark, sharing all bark bacteria and 68.09% of bark fungi in Pu'er, with minimal reverse flow. Soil harbored higher alpha diversity dominated by Chloroflexi, Acidobacteriota, and Sordariomycetes, while bark selectively enriched Gammaproteobacteria, Cyanobacteriia, and Lecanoromycetes. Plant type mainly influenced bark bacterial communities (R²=76.49%, P < 0.001), whereas geographic location significantly impacted soil bacterial composition (R²=45.72%, P < 0.001) and fungi in both bark (R²=63.06%, P < 0.001) and soil (R²=78.84%, P < 0.01). Total nitrogen (TN) and organic matter (OM) in bulk soil emerged as the predominant factors influencing community variation both for niches of soil and bark. Functional differentiation was observed, with soil microbiomes primarily engaged in chemoheterotrophy and nutrient cycling, while bark microbiomes were more involved in carbon fixation and stress resistance. LEfSe analysis identified 30 bacterial and 64 fungal biomarkers (LDA ≥ 4, P < 0.05), including Xanthobacteraceae in soil and Pleosporaceae in bark.

CONCLUSIONS: This study highlights soil's crucial role as a microbial reservoir and the impact of niche-specific factors, providing a framework to understand how microbial diversity is maintained and regulated along the Soil-Bark Continuum in tea plants.},
}

@article {pmid42363135,
year = {2026},
author = {Öz, ÖF and Seval, MM and Doğan, Ö and Varli, B and Çetinkaya, ŞE and Dökmeci, F},
title = {Elevated urinary succinate in women with symptom-defined overactive bladder without clinically recognized cardiometabolic disease: a cross-sectional study.},
journal = {BMC women's health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12905-026-04596-8},
pmid = {42363135},
issn = {1472-6874},
abstract = {BACKGROUND: Overactive bladder (OAB) is a symptom-defined syndrome, and its metabolic correlates remain incompletely understood. This study investigated whether urinary tricarboxylic acid cycle metabolites differ between women with symptom-defined probable OAB and controls without clinically recognized cardiometabolic disease.

METHODS: In this cross-sectional clinic-based study, women aged 18 years and older attending a gynecology outpatient clinic were enrolled. Participants with self-reported cardiometabolic disease or related medication use were excluded. Probable OAB was defined by an Overactive Bladder Awareness Tool Version 8 score of 8 or higher. Midstream urine samples were analyzed for succinate and malate by gas chromatography-mass spectrometry and normalized to urinary creatinine. Group comparisons, Spearman correlations, multivariable log-linear regression, sensitivity analyses, and exploratory receiver operating characteristic analyses were performed.

RESULTS: A total of 186 women were included, comprising 81 with OAB and 105 controls. Women with OAB were older, had slightly higher body mass index, higher parity, and were more frequently postmenopausal. Urinary succinate and malate levels were higher in the OAB group. After adjustment for age, body mass index, parity, and menopausal status, OAB remained associated with higher urinary succinate (adjusted geometric mean ratio, 1.69; 95% CI, 1.34-2.12) and malate (1.25; 95% CI, 1.02-1.52). Succinate showed modest exploratory discrimination (AUC, 0.678), whereas malate showed limited discrimination (AUC, 0.560).

CONCLUSIONS: Urinary succinate was higher in women with symptom-defined probable OAB even after adjustment for major demographic covariates, while the association with malate was weaker. These findings are hypothesis-generating and require confirmation in adequately powered, prospectively phenotyped cohorts with standardized metabolic, dietary, and urinary microbiome assessment.},
}

@article {pmid42363297,
year = {2026},
author = {Wang, Y and Liu, M and Dogra, SK and Vidal, K and Godin, JP and Darwish, N and Wei, X and Reymond, L and Li, Q and Dong, J and Vyllioti, AT and Bettler, J and Kennedy, E and Wang, K and Zhai, Q and O'Regan, J and Samuel, TM and Cai, W},
title = {Effects of an infant formula containing a whey protein concentrate on feeding tolerance and markers of intestinal immune defense in Chinese infants.},
journal = {BMC nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40795-026-01395-0},
pmid = {42363297},
issn = {2055-0928},
abstract = {BACKGROUND: Human milk (HM) bioactive components can have immune modulatory functions, impact the gut microbiome, and may result in functional benefits when added to infant formula (IF). In this single-arm, prospective, intervention study, we tested the effectiveness of an IF with a whey protein concentrate co-enriched in α-lactalbumin, milk fat globule membrane (MFGM), and Sn-2 palmitate resulting in protein and lipid profiles observed in HM. The outcomes tested were feeding tolerance, Bifidobacteria abundance, and intestinal and immune health of Chinese infants.

METHODS: Predominantly formula-fed (FF) and breastfed (BF) infants were enrolled between 3 and 28 days and assigned to the FF (N = 60) or BF (N = 60) group, per their feeding practice, for 6 weeks. The primary endpoint was Infant Gastrointestinal Symptom Questionnaire (IGSQ) index score assessed using a validated IGSQ-13 questionnaire after 6 weeks of intervention; non-inferiority of FF vs BF was tested. Secondary endpoints included fecal Bifidobacteria abundance assessed using shotgun metagenomics sequencing; fecal short chain fatty acids (SCFAs) analyzed by ultra-performance liquid chromatography-tandem mass spectrometry; fecal markers of immune response, inflammation, intestinal barrier integrity (secretory immunoglobulin A sIgA), cytokines, calprotectin, α1 antitrypsin, lipocalin-2) assessed using enzyme-linked immunosorbent assay; stool consistency assessed using gastrointestinal (GI) diary; anthropometric assessments; quality of life; physician reported adverse events; and use of medications.

RESULTS: Good GI tolerance was observed in both groups at V2 (mean ± SD IGSQ score FF: 19.9 ± 7.4; BF: 16.8 ± 4.2); difference of means 1.35 [95% CI: -1.312, 4.012]). After 6 weeks, Bifidobacterium genus relative abundance was not significantly different between the groups. Total SCFAs were significantly higher (p < 0.05) in the FF versus BF group, driven by increased levels of valeric and propanoic acids (p < 0.05 for both). The IGSQ domain scores, stool consistency, fecal markers of immunity, inflammation, and intestinal barrier integrity (except lipocalin-2 which was significantly higher in BF vs FF), anthropometric Z-scores, common illnesses, antibiotic use, and adverse events were not significantly different between groups at week 6.

CONCLUSIONS: Our results support the effectiveness of this tested infant formula in supporting good GI tolerance, growth, specific intestinal and immune health markers, and Bifidobacteria abundance similar to that of the BF group.

TRIAL REGISTRATION: NCT04880083 (2021-05-06).},
}